[med-svn] [khmer] 01/05: Revert "Merge tag 'upstream/2.0-rc1'"
Michael Crusoe
misterc-guest at moszumanska.debian.org
Thu Jul 9 00:12:59 UTC 2015
This is an automated email from the git hooks/post-receive script.
misterc-guest pushed a commit to branch master
in repository khmer.
commit b80fa2e5cffb9cb5b6e91bb3c8802539572a433c
Author: Michael R. Crusoe <michael.crusoe at gmail.com>
Date: Wed Jul 8 16:40:07 2015 -0700
Revert "Merge tag 'upstream/2.0-rc1'"
This reverts commit de9a33473ab505130cd6fc828246b8ba63f03ea3, reversing
changes made to b04fcb4dcaada444d2027eb86352e5fe18183690.
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third-party/zlib/infback.c | 640 -
third-party/zlib/inffast.c | 340 -
third-party/zlib/inffast.h | 11 -
third-party/zlib/inffixed.h | 94 -
third-party/zlib/inflate.c | 1512 -
third-party/zlib/inflate.h | 122 -
third-party/zlib/inftrees.c | 306 -
third-party/zlib/inftrees.h | 62 -
third-party/zlib/make_vms.com | 867 -
third-party/zlib/msdos/Makefile.bor | 115 -
third-party/zlib/msdos/Makefile.dj2 | 104 -
third-party/zlib/msdos/Makefile.emx | 69 -
third-party/zlib/msdos/Makefile.msc | 112 -
third-party/zlib/msdos/Makefile.tc | 100 -
third-party/zlib/nintendods/README | 5 -
third-party/zlib/old/Makefile.emx | 69 -
third-party/zlib/old/Makefile.riscos | 151 -
third-party/zlib/old/README | 3 -
third-party/zlib/old/descrip.mms | 48 -
third-party/zlib/old/os2/Makefile.os2 | 136 -
third-party/zlib/old/os2/zlib.def | 51 -
third-party/zlib/old/visual-basic.txt | 160 -
third-party/zlib/qnx/package.qpg | 141 -
third-party/zlib/test/example.c | 601 -
third-party/zlib/test/infcover.c | 671 -
third-party/zlib/test/minigzip.c | 651 -
third-party/zlib/treebuild.xml | 116 -
third-party/zlib/trees.c | 1226 -
third-party/zlib/trees.h | 128 -
third-party/zlib/uncompr.c | 59 -
third-party/zlib/watcom/watcom_f.mak | 43 -
third-party/zlib/watcom/watcom_l.mak | 43 -
third-party/zlib/win32/DLL_FAQ.txt | 397 -
third-party/zlib/win32/Makefile.bor | 110 -
third-party/zlib/win32/Makefile.gcc | 182 -
third-party/zlib/win32/Makefile.msc | 163 -
third-party/zlib/win32/README-WIN32.txt | 103 -
third-party/zlib/win32/VisualC.txt | 3 -
third-party/zlib/win32/zlib.def | 86 -
third-party/zlib/win32/zlib1.rc | 40 -
third-party/zlib/zconf.h.cmakein | 513 -
third-party/zlib/zconf.h.in | 511 -
third-party/zlib/zlib.3 | 151 -
third-party/zlib/zlib.3.pdf | Bin 8734 -> 0 bytes
third-party/zlib/zlib.h | 1768 -
third-party/zlib/zlib.map | 83 -
third-party/zlib/zlib.pc.cmakein | 13 -
third-party/zlib/zlib.pc.in | 13 -
third-party/zlib/zlib2ansi | 152 -
third-party/zlib/zutil.c | 324 -
third-party/zlib/zutil.h | 253 -
versioneer.py | 1 -
482 files changed, 5580 insertions(+), 197873 deletions(-)
diff --git a/.gitignore b/.gitignore
index c0abc60..543df72 100644
--- a/.gitignore
+++ b/.gitignore
@@ -17,12 +17,9 @@ doc/_build
/.project
/.pydevproject
/.Rhistory
-.idea
coverage.xml
coverage-gcovr.xml
coverage-debug
-htmlcov/
-diff-cover.html
khmer-cov.tgz
cppcheck-result.xml
MANIFEST
diff --git a/CITATION b/CITATION
index 3b4b3c6..41679ee 100644
--- a/CITATION
+++ b/CITATION
@@ -153,7 +153,7 @@ implement the probabilistic k-mer counting described in:
digital normalization of reads in the context of high khmer false positive
rates. khmer is implemented in C++ wrapped in a Python interface, offers a
tested and robust API, and is freely available under the BSD license at
- github.com/dib-lab/khmer.</p>",
+ github.com/ged-lab/khmer.</p>",
number = "7",
doi = "10.1371/journal.pone.0101271"
}
diff --git a/ChangeLog b/ChangeLog
index 2aeb3db..ec2c779 100644
--- a/ChangeLog
+++ b/ChangeLog
@@ -1,351 +1,7 @@
-2015-06-30 Jacob Fenton <bocajnotnef at gmail.com>
+2015-05-13 Scott Sievert <sieve121 at umn.edu>
- * tests/{test_script_arguments,test_functions}.py: changed tests to use
- stderr redirection to prevent leaks
- * tests/test_normalize_by_median.py: changed to not duplicate a test
- * tests/test_script_arguments.py: changed tests to use stderr redirection
-
-2015-06-30 Titus Brown <titus at idyll.org>
-
- * tests/test_normalize_by_median.py: disabled running
- test_normalize_by_median_report_fp during normal test running.
-
-2015-06-30 Titus Brown <titus at idyll.org>
-
- * khmer/khmer_args.py: removed incorrect warning for default max_tablesize
- when -M is used.
- * tests/test_scripts.py: added test for correct max_tablesize behavior.
-
-2015-06-30 Titus Brown <titus at idyll.org>
-
- * setup.cfg: changed 'stop=TRUE' to 'stop=FALSE', so that tests do not
- stop running at first failure.
-
-2015-06-30 Kevin Murray <spam at kdmurray.id.au>
-
- * scripts/{extract-paired-reads,split-paired-reads}.py: Fix creation of
- default output files even when output files were provided on CLI.
-
-2015-06-29 Sherine Awad <drmahmoud at ucdavis.edu>
-
- * khmer/utils.py: Fix bug in naming in interleave-reads.py
- * tests/test_scripts.py: Add a test function for the new behavior
- * tests/test-data/*.fq: Add 3 test files needed for the testing
-
-2015-06-28 Jacob Fenton <bocajnotnef at gmail.com>
-
- * tests/test_sandbox_scripts.py: made error more informative and not crashy
- * sandbox/{estimate_optimal_hash,optimal_args_hashbits}.py: minor cleanups
-
-2015-06-28 Qingpeng Zhang <qingpeng at msu.edu>
-
- * sandbox/{estimate_optimal_hash,optimal_args_hashbits}.py: added sandbox
- methods for estimating memory usage based on desired fp rate, etc.
-
-2015-06-27 Kevin Murray <spam at kdmurray.id.au>
-
- * doc/dev/binary-file-formats.rst: Fix issue in ksize documentation for
- Countgraph
-
-2015-06-27 Kevin Murray <spam at kdmurray.id.au>
-
- * README.rst: Fix link to virtualenv installation instructions.
-
-2015-06-19 Titus Brown <titus at idyll.org>
-
- * khmer/__init__.py: split CountingHash into _CountingHash (CPython) and
- CountingHash to mimic Hashbits behavior; pass IOError through
- extract_countinghash_info and extract_hashbits_info so that
- file-does-not-exist errors are correctly reported; fixed FP rate reporting;
- changed to using get_n_primes_near_x to build hashtable sizes; removed
- get_n_primes_above_x, new_hashbits, and new_counting_hash functions.
- * khmer/_khmer.cc: changed tp_flags for KCountingHash so that it could
- be a base class.
- * khmer/khmer_args.py: removed environment variable override for hash size
- defaults; added -M/--max_memory_usage, and functions create_nodegraph()
- and create_countgraph(). Also renamed --min-tablesize to --max-tablesize.
- * khmer/kfile.py: fixed check_space_for_hashtable to depend on args obj.
- * oxli/build_graph.py, scripts/{annotate-partitions.py,count-overlap.py,
- do-partition.py,filter-stoptags.py,
- merge-partitions.py}, sandbox/{assembly-diff.py,assembly-diff-2.py,
- bloom-count-intersection.py,bloom-count.py,build-sparse-graph.py,
- collect-reads.py,saturate-by-median.py, graph-size.py,print-stoptags.py,
- print-tagset.py,stoptags-by-position.py, subset-report.py,
- sweep-out-reads-with-contigs.py,sweep-reads2.py,sweep-reads3.py}: changed
- hashtype over to 'nodegraph' and 'countgraph' in call to report_on_config;
- replaced counting hash/hashbits creation with new khmer_args create*
- functions, and/or new_counting_hash/new_hashbits with CountingHash/Hashbits.
- * doc/scripts.rst: updated hashtable size help text.
- * doc/whats-new-2.0.rst: updated with description of -M/--max-memory-usage.
- * tests/test*.py: switched from new_counting_hash to CountingHash, and
- new_hashbits to Hashbits; adjusts tests for new behavior of hashtable
- size calculation.
- * tests/test_hashbits_obj.py: merged into test_hashbits.py and removed file.
- * tests/test_script_arguments.py: updated for new check_space_for_hashtable
- behavior; added tests for create_countgraph and create_nodegraph.
- * tests/test_counting_single.py: fixed countgraph size & palindrome testing
- beahavior in test_complete_no_collision.
-
-2015-06-19 Titus Brown <titus at idyll.org>
-
- * Makefile: temporarily disable 'huge' tests on Linux.
-
-2015-06-17 Titus Brown <titus at idyll.org>
-
- * scripts/normalize-by-median.py: changed DEFAULT_DESIRED_COVERAGE to 20,
- and corrected options help.
- * tests/{test_scripts.py,test_normalize_by_median.py}: moved
- normalize-by-median.py tests into a their own file.
- * tests/test-data/{dn-test-all-paired-all-keep.fa,dn-test-none-paired.fa,
- dn-test-some-paired-all-keep.fa}: added test data files for specific
- pairing/saturation behavior.
-
-2015-06-16 Kevin Murray <spam at kdmurray.id.au>
-
- * doc/dev/binary-file-formats.rst: Add documentation of khmer's binary file
- formats.
- * doc/dev/index.rst: Add above docs to developer documentation index.
-
-2015-06-14 Michael R. Crusoe <crusoe at ucdavis.edu>
-
- * khmer/__init__.py,lib/{counting,hashbits,hashtable,subset,labelhash}.cc,
- lib/khmer.hh: add signature to beginning of all binary file types
- * tests/test-data/{normC20k20.ct,badversion-k32.tagset,
- goodversion-k32.tagset}: update to new format by prepending "OXLI" to the
- data stream
- * tests/test_{counting_hash,functions,scripts,hashbits,hashbits_obj,
- labelhash}.py: tests should fail, not error (add try, except + assert
- blocks). Adapted other tests to cope with the new file formats
- * lib/magic: new, teaches the unix `file` command about khmer file types
- * doc/index.rst,doc/whats-new-2.0.rst: document these changes
-
-2015-06-14 Titus Brown <titus at idyll.org>
-
- * scripts/extract-paired-reads.py: added --output_dir, --paired-output,
- and --single-output arguments to change output file details; script
- now accepts stdin, and will output to stdout upon request.
- * scripts/split-paired-reads.py: changed script to output to stdout upon
- request; added '-' as stdin input.
- * tests/test_scripts.py: added tests for new extract-paired-reads.py
- behavior.
-
-2015-06-14 Titus Brown <titus at idyll.org>
-
- * tests/test_counting_hash.py: fixed duplicated test
- 'get_kmer_counts_too_short' by changing to 'get_kmer_hashes_too_short'.
-
-2015-06-14 Jacob Fenton <bocajnotnef at gmail.com>
-
- * scripts/abundance-dist.py: added weird bigcount circumstance detection
- * tests/test_scripts.py: added test for the above
-
-2015-06-14 Kevin Murray <spam at kdmurray.id.au>
-
- * lib/counting.cc: Fix infinite loop in gzipped CountingHash I/O
- * tests/test_counting_hash.py: Add test of large CountingHash I/O
- * setup.cfg: Skip tests with the 'huge' label by default
-
-2015-06-13 Michael R. Crusoe <crusoe at ucdavis.edu>
-
- * Makefile, build-jenkins.sh: unify sphinx dependencies
- * scripts/readstats.py: fix typo
-
-2015-06-13 Titus Brown <titus at idyll.org>
-
- * doc/dev/getting-started.rst: update instructions for creating a new
- branch name to preferred practice (fix/brief_issue_description, instead
- of fix/issuenum).
-
-2015-06-13 Michael R. Crusoe <crusoe at ucdavis.edu>
-
- * doc/dev/release.rst: remove false positive from version check
- * tests/test_{counting_hash,scripts}.py: remove scriptpath no-op method
-
-2015-06-12 Luiz Irber <khmer at luizirber.org>
-
- * setup.py: revert changes to zlib compilation.
- * setup.cfg: nose should stop on first error by default.
- * Makefile, tests/test_threaded_sequence_processor.py,
- scripts/{do-partition,partition-graph}.py, khmer/thread_utils.py: Remove
- dependency on future package.
-
-2015-06-12 Michael R. Crusoe <crusoe at ucdavis.edu>
-
- * setup.py: update screed version to 0.9
-
-2015-06-12 Luiz Irber <khmer at luizirber.org>
-
- * *.py: refactor for Python 3 compatibility. Clear separation of Unicode
- and Byte strings, use __future__ imports for compatibility (print function,
- absolute imports, unicode_literals), fix tests to consider changes to random
- number generator between Python versions.
- * khmer/_khmer.cc: rename file, methods return Unicode strings instead of
- Bytestrings.
-
-2015-06-12 Luiz Irber <khmer at luizirber.org>
-
- * khmer/{khmermodule.cc},tests/test_hashbits.py: Add Unicode support to
- hashbits.get method.
- * tests/test_hll.py: Avoid using translate for revcomp calculation.
-
-2015-06-12 Sarah Guermond <sarah.guermond at gmail.com>
-
- * scripts/trim-low-abund.py: changed _screed_record_dict to Record
-
-2015-06-11 Sherine Awad <drmahmoud at ucdavis.edu>
-
- * Change split-paired-reads.py to accept input from stdin.
- * Add test function to test new behavior of split-paired.
-
-2015-06-10 Camille Scott <camille.scott.w at gmail.com>
-
- * lib/hashtable.cc: Tweaked median_at_least to reduce number of
- conditional checks.
-
-2015-06-10 Titus Brown <titus at idyll.org>
-
- * scripts/find-knots.py: fixed invocation of check_space to take correct
- arguments.
- * tests/test_scripts.py: added simple test of find-knots.py execution.
-
-2015-06-09 Jacob Fenton <bocajnotnef at gmail.com>
-
- * scripts/normalize-by-median.py: implemented broken_paired_reader
- * tests/test_scripts.py: modified tests to properly use new args
- * khmer/utils.py: added force-paired option to broken_paired_reader (@ctb)
-
-2015-06-09 Luiz Irber <khmer at luizirber.org>
-
- * khmer/_khmermodule.cc, lib/hashtable.{cc,hh}: astyle fixes.
-
-2015-06-09 Titus Brown <titus at idyll.org>
-
- * khmer/_khmermodule.cc: fixed nasty Hashtable.get() bug.
- * lib/hashtable.{cc,hh}: add Hashtable::get_kmers(), get_kmer_hashes(),
- and get_kmer_counts().
- * khmer/_khmermodule.cc: add CPython functions for get_kmers(),
- get_kmer_hashes(), and get_kmer_counts(); reorganize hashtable_methods.
- * tests/test_counting_hash.py: add tests for get_kmers(), get_kmer_hashes(),
- and get_kmer_counts(), as well as for nasty Hashtable.get() bug.
-
-2015-06-08 Camille Scott <camille.scott.w at gmail.com>
-
- * lib/hashtable.{cc,hh}: Add filter_on_median method to check
- if median k-mer count is above a cutoff
- * khmer/_khmermodule.cc: Expose filter_on_median to python-land
- * scripts/normalize-by-median.py: Switch to new filter_on_median
- * tests/test_counting_hash.py: Tests for new method
-
-2015-06-08 Luiz Irber <khmer at luizirber.org>
-
- * tests/test_hll.py: test return values from consume_{string,fasta}.
-
-2015-06-06 Titus Brown <titus at idyll.org>
-
- * khmer/_khmermodule.cc: added hllcounter_merge.
- * tests/test_hll.py: added merge tests.
- * lib/hllcounter.cc: changed HLLCounter::consume_string to uppercase input.
- * sandbox/unique-kmers.py: added --stream-out option; updated to print out
- k-mers per file as well as k-mer size used.
-
-2015-06-04 Titus Brown <titus at idyll.org>
-
- * khmer/_khmermodule.cc: added error handling to load_partitionmap.
- * lib/subset.cc: modified partitionmap format to detect truncated files;
- changed untestable sanity checks to assertions.
- * tests/{test_counting_hash,test_hashbits,test_subset_graph}.py: added
- tests to try loading all possible truncations of binary save files.
-
-2015-06-04 Titus Brown <titus at idyll.org>
-
- * khmer/_khmermodule.cc,lib/hashbits.{cc,hh}: add Hashbits::update_from()
- and Hashbits.update().
- * tests/test_hashbits.py: associated tests.
-
-2015-06-01 Jacob Fenton <bocajnotnef at gmail.com>
-
- * scripts/normalize-by-median.py: major refactoring to use context
- managers and classes; fixed -R
- * tests/test_scripts.py: added test for normalize's -R arg
-
-2015-06-01 Tamer Mansour <drtamermansour at gmail.com>
-
- * scripts/normalize-by-median.py: changed to count kmers from both PE reads
- when either one of them is below the coverage cutoff
- * tests/test_scripts.py: Added test for new behaviour
-
-2015-05-26 Titus Brown <titus at idyll.org>
-
- * khmer/_khmermodule.cc: refactor CPython layer so that KHashtable
- is at base of CountingHash and Hashbits.
- * lib/hashbits.hh: add n_entries() function from Hashtable::n_entries.
- * lib/hashtable.hh: add several virtual functions to Hashtable that exist in
- CountingHash and Hashbits.
-
-2015-05-26 Titus Brown <titus at idyll.org>
-
- * khmer/{__init__.py,_khmermodule.cc},lib/labelhash.{cc,hh},
- lib/{hashtable,khmer}.hh: changed LabelHash to be a "friend" of Hashtable,
- rather than a subclass; allowed initialization with either a CountingHash
- or a Hashbits; added 'graph' attribute to the Python object to store a
- reference to host object.
- * lib/labelhash.{cc,hh}: changed TagPtr maps to Tag maps to fix disastrous
- bug.
- * lib/labelhash.{cc,hh}: added save/load_tags_and_labels functions for
- saving and loading labels.
- * tests/test_labelhash.py: removed unnecessary tests; added tests for save
- and load.
- * sandbox/sweep-reads.py: updated with LabelHash changes.
-
-2015-05-26 Kevin Murray <spam at kdmurray.id.au>
-
- * lib/Makefile: Remove old libkhmer.so versions during make clean
-
-2015-05-25 Kevin Murray <spam at kdmurray.id.au>
-
- * Makefile: Fix issue with 'lib' target not building by using FORCE
-
-2015-05-20 Jacob Fenton <bocajnotnef at gmail.com>
-
- * oxli/{__init__,khmer_api,common}.py,scripts/build-graph.py,
- tests/test_scripts.py: added oxli module, oxlified load_graph script, tests
- * scripts/load-graph.py: replaced with oxlified version
- * setup.py: added oxli module and entry point
-
-2015-05-20 Kevin Murray <spam at kdmurray.id.au>
-
- * .gitignore: Add htmlcov/ and diff-cover.html to gitignore
- * Makefile: Use rm -f to remove files to quash error messages on
- non-existant files
-
-2015-05-18 Sherine Awad <sherine.awad at gmail.com>
-
- * tests/test_scripts.py: Test loading of compressed counting table
- with bigcounts,and test abundance with bigcounts
-
-2015-05-18 Michael R. Crusoe <mcrusoe at msu.edu>
-
- * all files: references to github.com/ged-lab changed to
- github.com/dib-lab. All GitHub URLs normalized to use HTTPS
- * README.rst: broken landscape.io badge removed
- * doc/user/known-issues.rst: removed two known issues fixed in v1.4 release
-
-2015-05-18 Titus Brown <titus at idyll.org>
-
- * sandbox/{assembly-diff-2.py,sandbox/collect-reads.py},
- scripts/{count-median.py,filter-abund-single.py,filter-abund.py}: changed
- sequence-reading behavior to replace 'N' with 'A', to be consistent with
- rest of code base.
- * scripts/{filter-abund.py,filter-abund-single.py}: changed behavior of
- scripts to keep sequences with 'N's in them, and count them as 'A's.
- * tests/test_scripts.py: added tests for new
- filter-abund/filter-abund-single behavior.
- * tests/test-data/test-filter-abund-Ns.fq: new test file for new tests.
-
-2015-05-13 Scott Sievert <sieve121 at umn.edu>
-
- * tests/*,scripts/*,lib/*,sandbox/*,khmer/*: changed "doc/LICENSE.txt" to
- "LICENSE" in copyright header.
+ * changed "doc/LICENSE.txt" to "LICENSE" in tests/*, scripts/*, lib/*,
+ sandbox/*, khmer/*
2015-05-13 Michael R. Crusoe <mcrusoe at msu.edu>
@@ -1153,8 +809,8 @@
New FAST[AQ] parser (from the SeqAn project). Fixes known issue and a
newly found read dropping issue
- https://github.com/dib-lab/khmer/issues/249
- https://github.com/dib-lab/khmer/pull/641
+ https://github.com/ged-lab/khmer/issues/249
+ https://github.com/ged-lab/khmer/pull/641
Supports reading from non-seekable plain and gziped FAST[AQ] files (a.k.a
pipe or streaming support)
diff --git a/Doxyfile.in b/Doxyfile.in
index c9293f4..d76ba0b 100644
--- a/Doxyfile.in
+++ b/Doxyfile.in
@@ -32,7 +32,7 @@ DOXYFILE_ENCODING = UTF-8
# title of most generated pages and in a few other places.
# The default value is: My Project.
-PROJECT_NAME = khmer
+PROJECT_NAME = Khmer
# The PROJECT_NUMBER tag can be used to enter a project or revision number. This
# could be handy for archiving the generated documentation or if some version
diff --git a/Makefile b/Makefile
index 616efdc..4e1d371 100644
--- a/Makefile
+++ b/Makefile
@@ -7,8 +7,8 @@
CPPSOURCES=$(wildcard lib/*.cc lib/*.hh khmer/_khmermodule.cc)
PYSOURCES=$(wildcard khmer/*.py scripts/*.py)
SOURCES=$(PYSOURCES) $(CPPSOURCES) setup.py
-DEVPKGS=pep8==1.5.7 diff_cover autopep8 pylint coverage gcovr nose pep257 \
- screed
+DEVPKGS=sphinxcontrib-autoprogram pep8==1.5.7 diff_cover \
+autopep8 pylint coverage gcovr nose screed pep257
GCOVRURL=git+https://github.com/nschum/gcovr.git@never-executed-branches
VERSION=$(shell git describe --tags --dirty | sed s/v//)
@@ -20,9 +20,9 @@ CPPCHECK=ls lib/*.cc khmer/_khmermodule.cc | grep -v test | cppcheck -DNDEBUG \
UNAME := $(shell uname)
ifeq ($(UNAME),Linux)
- TESTATTR='!known_failing,!jenkins,!huge'
+ TESTATTR='!known_failing,!jenkins'
else
- TESTATTR='!known_failing,!jenkins,!huge'
+ TESTATTR='!known_failing,!jenkins,!linux'
endif
## all : default task; compile C++ code, build shared object library
@@ -36,8 +36,7 @@ help: Makefile
install-dep: install-dependencies
install-dependencies:
- pip install --upgrade $(DEVPKGS)
- pip install --upgrade --requirement doc/requirements.txt
+ pip2 install --upgrade $(DEVPKGS) || pip install --upgrade $(DEVPKGS)
## sharedobj : build khmer shared object file
sharedobj: khmer/_khmermodule.so
@@ -64,12 +63,11 @@ dist/khmer-$(VERSION).tar.gz: $(SOURCES)
clean: FORCE
cd lib && ${MAKE} clean || true
cd tests && rm -rf khmertest_* || true
- rm -f khmer/_khmermodule.so
- rm -f khmer/*.pyc lib/*.pyc
+ rm -f khmer/_khmermodule.so || true
+ rm khmer/*.pyc lib/*.pyc || true
./setup.py clean --all || true
- rm -f coverage-debug
- rm -Rf .coverage
- rm -f diff-cover.html
+ rm coverage-debug || true
+ rm -Rf .coverage || true
debug: FORCE
export CFLAGS="-pg -fprofile-arcs"; python setup.py build_ext --debug \
@@ -103,10 +101,10 @@ cppcheck: $(CPPSOURCES)
## pep8 : check Python code style
pep8: $(PYSOURCES) $(wildcard tests/*.py)
pep8 --exclude=_version.py --show-source --show-pep8 setup.py khmer/ \
- scripts/ tests/ oxli/ || true
+ scripts/ tests/ || true
pep8_report.txt: $(PYSOURCES) $(wildcard tests/*.py)
- pep8 --exclude=_version.py setup.py khmer/ scripts/ tests/ oxli/ \
+ pep8 --exclude=_version.py setup.py khmer/ scripts/ tests/ \
> pep8_report.txt || true
diff_pep8_report: pep8_report.txt
@@ -131,7 +129,7 @@ astyle: $(CPPSOURCES)
## autopep8 : fix most Python code indentation and formatting
autopep8: $(PYSOURCES) $(wildcard tests/*.py)
autopep8 --recursive --in-place --exclude _version.py --ignore E309 \
- setup.py khmer/*.py scripts/*.py tests/*.py oxli/*.py
+ setup.py khmer/*.py scripts/*.py tests/*.py
# A command to automatically run astyle and autopep8 on appropriate files
## format : check/fix all code indentation and formatting (runs astyle and autopep8)
@@ -142,12 +140,12 @@ format: astyle autopep8
pylint: $(PYSOURCES) $(wildcard tests/*.py)
pylint --msg-template="{path}:{line}: [{msg_id}({symbol}), {obj}] {msg}" \
setup.py khmer/[!_]*.py khmer/__init__.py scripts/*.py tests \
- oxli/*.py || true
+ || true
pylint_report.txt: ${PYSOURCES} $(wildcard tests/*.py)
pylint --msg-template="{path}:{line}: [{msg_id}({symbol}), {obj}] {msg}" \
setup.py khmer/[!_]*.py khmer/__init__.py scripts/*.py tests \
- sandbox/*.py oxli/*.py > pylint_report.txt || true
+ sandbox/*.py > pylint_report.txt || true
diff_pylint_report: pylint_report.txt
diff-quality --violations=pylint pylint_report.txt
@@ -156,7 +154,7 @@ diff_pylint_report: pylint_report.txt
# python module we can't tell nosetests to look for them (via an import
# statement). So we run nose inside of coverage.
.coverage: $(PYSOURCES) $(wildcard tests/*.py) khmer/_khmermodule.so
- coverage run --branch --source=scripts,khmer,oxli --omit=khmer/_version.py \
+ coverage run --branch --source=scripts,khmer --omit=khmer/_version.py \
-m nose --with-xunit --attr=\!known_failing --processes=0
coverage.xml: .coverage
@@ -194,7 +192,7 @@ doc/doxygen/html/index.html: ${CPPSOURCES} ${PYSOURCES}
Doxyfile
doxygen
-lib: FORCE
+lib:
cd lib && \
$(MAKE)
diff --git a/README.rst b/README.rst
index 130cb9b..97bd1c4 100644
--- a/README.rst
+++ b/README.rst
@@ -6,24 +6,27 @@ Welcome to khmer: k-mer counting, filtering and graph traversal FTW!
.. image:: https://readthedocs.org/projects/khmer/badge
:target: https://readthedocs.org/projects/khmer/
:alt: Documentation Status
-.. image:: https://badge.fury.io/py/khmer.svg
+.. image:: https://badge.fury.io/py/khmer.png
:target: http://badge.fury.io/py/khmer
:alt: PyPI Package
-.. image:: https://pypip.in/d/khmer/badge.svg
+.. image:: https://pypip.in/d/khmer/badge.png
:target: https://crate.io/packages/khmer
:alt: Downloads Counter
-.. image:: https://pypip.in/license/khmer/badge.svg
+.. image:: https://pypip.in/license/khmer/badge.png
:target: https://pypi.python.org/pypi/khmer/
:alt: License
.. image:: http://ci.ged.msu.edu/job/khmer-master/badge/icon
:target: http://ci.ged.msu.edu/job/khmer-master/
+.. image:: https://landscape.io/github/ged-lab/khmer/master/landscape.png
+ :target: https://landscape.io/github/ged-lab/khmer/master
+ :alt: Python Code Health
.. image:: https://scan.coverity.com/projects/621/badge.svg
:target: https://scan.coverity.com/projects/621
:alt: Coverity Scan Build Status
The official repository is at
-https://github.com/dib-lab/khmer
+https://github.com/ged-lab/khmer
and you can read the docs online here:
@@ -37,7 +40,7 @@ them, please visit the following URLs:
- Announcements: http://lists.idyll.org/listinfo/khmer-announce
-We chat at https://gitter.im/dib-lab/khmer and the maintainers can be
+We chat at https://gitter.im/ged-lab/khmer and the maintainers can be
contacted at khmer-project at idyll.org.
For getting help with please see this guide: http://khmer.readthedocs.org/user/getting-help.html
@@ -63,7 +66,7 @@ version.
For more details see `doc/install.txt <https://khmer.readthedocs.org/en/latest/user/install.html>`_
The use of a virtualenv is recommended, see
-https://virtualenv.readthedocs.org/en/latest/installation.html
+https://virtualenv.pypa.io/en/latest/virtualenv.html#installation
khmer is under the BSD license; see doc/LICENSE.txt. Distribution,
modification and redistribution, incorporation into other software, and
diff --git a/doc/conf.py b/doc/conf.py
index e400ab2..99017b4 100644
--- a/doc/conf.py
+++ b/doc/conf.py
@@ -193,7 +193,7 @@ htmlhelp_basename = 'khmerdoc'
html_context = {
"google_analytics_id" : 'UA-51731094-1',
"disqus_shortname" : 'khmer-docs',
-# "github_base_account" : 'dib-lab',
+# "github_base_account" : 'ged-lab',
"github_project" : 'khmer',
}
diff --git a/doc/dev/binary-file-formats.rst b/doc/dev/binary-file-formats.rst
deleted file mode 100644
index 8359af3..0000000
--- a/doc/dev/binary-file-formats.rst
+++ /dev/null
@@ -1,115 +0,0 @@
-khmer/Oxli Binary File Formats
-==============================
-
-- C++ macro definitions are given in parenthesis.
-- C++ types are given in square brackets.
-- ``Len`` is the field's size, in bytes, and ``Off`` is the field's zero-based
- byte offset in the file/section.
-
-khmer v1.4 and previous
-~~~~~~~~~~~~~~~~~~~~~~~
-
-CountingHash
-------------
-
-The header is in the format below, in file offset order. There is no magic
-string.
-
-================== =========== ==============================================
-Field Length Value
-================== =========== ==============================================
-Version 1 ``0x04`` (``SAVED_FORMAT_VERSION``)
-File Type 1 ``0x01`` (``SAVED_COUNTING_HT``)
-Use Bigcount 1 ``1`` if bigcounts is used, else ``0``
-K-size 1 k-mer length, ``1 <= k <= 32``
-Number of Tables 1 Number of Count-min Sketch tables
-================== =========== ==============================================
-
-
-khmer v2.0 formats
-~~~~~~~~~~~~~~~~~~
-
-
-Magic string
-------------
-
-All formats shall have the "magic string" ``OXLI`` as their first bytes, after
-any external compression/encoding (e.g. gzip encapsulation) is removed. Note
-that this makes them incompatible with older versions of khmer.
-
-Countgraph
-----------
-
-(a.k.a ``CountingHash``, a Count-min Sketch)
-
-:Preferred extension: '.ct' (count table)
-
-The header is in the format below, again in the order of file offset.
-
-================== ===== ===== ==============================================
-Field Len Off Value
-================== ===== ===== ==============================================
-Magic string 4 0 ``OXLI`` (``SAVED_SIGNATURE``)
-Version 1 4 ``0x04`` (``SAVED_FORMAT_VERSION``)
-File Type 1 5 ``0x01`` (``SAVED_COUNTING_HT``)
-Use Bigcount 1 6 ``0x01`` if bigcounts is used, else ``0x00``
-K-size 4 7 k-mer length, ``ht._ksize``. [``uint32_t``]
-Number of Tables 1 11 Number of Count-min Sketch tables,
- ``ht._n_tables``. [``uint8_t``]
-================== ===== ===== ==============================================
-
-Then follows the Countgraph's tables. For each table:
-
-================== ===== ===== ==============================================
-Field Len Off Value
-================== ===== ===== ==============================================
-Table size 8 0 Length of this table, ``ht._tablesizes[i]``.
- [``uint64_t``]
-Bins N 8 This table's bins, length given by previous
- field. [``uint8_t``]
-================== ===== ===== ==============================================
-
-Then follows a single value, the [``uint64_t``] number of ``kmer: count``
-pairs. Then follows the Bigcount map, if this number is greater than zero. For
-each kmer:
-
-================== ===== ===== ==============================================
-Field Len Off Value
-================== ===== ===== ==============================================
-Kmer 8 0 Kmer's hash [``HashIntoType/uint64_t``].
-Count 2 8 Kmer's count [``uint16_t``].
-================== ===== ===== ==============================================
-
-
-Nodegraph
----------
-
-(a.k.a ``HashBits``, a Bloom Filter)
-
-:Preferred extension: '.pt' (presence table)
-
-The header is in the format below, again in the order of file offset. Value
-macro definitions are given in parenthesis
-
-================== ===== ===== ==============================================
-Field Len Off Value
-================== ===== ===== ==============================================
-Magic string 4 0 ``OXLI`` (``SAVED_SIGNATURE``)
-Version 1 4 ``0x04`` (``SAVED_FORMAT_VERSION``)
-File Type 1 5 ``0x02`` (``SAVED_HASHBITS``)
-K-size 4 6 k-mer length, ``ht._ksize``. [``unsigned int``]
-Number of Tables 1 10 Number of Nodegraph tables. ``ht._n_tables``.
- [``uint8_t``]
-================== ===== ===== ==============================================
-
-Then follows the Nodegraph's tables. For each table:
-
-================== ======= ===== ==============================================
-Field Len Off Value
-================== ======= ===== ==============================================
-Table size 8 0 Length of table, **in bits** (``uint64_t``).
-Bins N/8+1 8 This table's bytes, length given by previous
- field, divided by 8, plus 1 (``uint8_t``).
-================== ======= ===== ==============================================
-
-.. todo:: Document ``Tags``, ``Stoptags``, ``Subset``, ``Labelset``
diff --git a/doc/dev/development.rst b/doc/dev/development.rst
index 414f914..d9dac70 100644
--- a/doc/dev/development.rst
+++ b/doc/dev/development.rst
@@ -23,11 +23,11 @@ git and GitHub strategies
Still in the works, but read `this
<http://scottchacon.com/2011/08/31/github-flow.html>`__.
-Make a branch on dib-lab (preferred so others can contribute) or fork the
+Make a branch on ged-lab (preferred so others can contribute) or fork the
repository and make a branch there.
Each piece or fix you are working on should have its own branch; make a pull-
-request to dib-lab/master to aid in code review, testing, and feedback.
+request to ged-lab/master to aid in code review, testing, and feedback.
If you want your code integrated then it needs to be mergable
@@ -38,7 +38,7 @@ Example pull request update using the command line:
#. Checkout the source branch of the pull request
``git checkout my-pull-request``
#. Pull in the destination of the pull request and resolve any conflicts
- ``git pull git at github.com:dib-lab/khmer.git master``
+ ``git pull git at github.com:ged-lab/khmer.git master``
#. Push your update to the source of the pull request ``git push``
#. Jenkins will automatically attempt to build and test your pull requests.
diff --git a/doc/dev/for-khmer-developers.rst b/doc/dev/for-khmer-developers.rst
index bbf6368..b62d05e 100644
--- a/doc/dev/for-khmer-developers.rst
+++ b/doc/dev/for-khmer-developers.rst
@@ -1,11 +1,11 @@
A guide for khmer committers
============================
-This document is for people with commit rights to github.com/dib-lab/khmer.
+This document is for people with commit rights to github.com/ged-lab/khmer.
----
-If you have commit privileges to the dib-lab/khmer repository, here are a
+If you have commit privileges to the ged-lab/khmer repository, here are a
few useful tips.
First, never merge something unless it's been through a review! This
diff --git a/doc/dev/getting-started.rst b/doc/dev/getting-started.rst
index a07c743..87e3ed1 100644
--- a/doc/dev/getting-started.rst
+++ b/doc/dev/getting-started.rst
@@ -1,4 +1,4 @@
-.. This file is part of khmer, https://github.com/dib-lab/khmer/, and is
+.. This file is part of khmer, http://github.com/ged-lab/khmer/, and is
Copyright (C) Michigan State University, 2009-2015. It is licensed under
the three-clause BSD license; see doc/LICENSE.txt.
Contact: khmer-project at idyll.org
@@ -61,7 +61,7 @@ One-time Preparation
(We use GitHub to manage khmer contributions.)
-#. Fork `github.com/dib-lab/khmer <https://github.com/dib-lab/khmer>`__.
+#. Fork `github.com/ged-lab/khmer <http://github.com/ged-lab/khmer>`__.
Visit that page, and then click on the 'fork' button (upper right).
@@ -79,10 +79,10 @@ One-time Preparation
(This makes a local copy of khmer on your development machine.)
-#. Add a git reference to the khmer dib-lab repository::
+#. Add a git reference to the khmer ged-lab repository::
cd khmer
- git remote add dib https://github.com/dib-lab/khmer.git
+ git remote add ged https://github.com/ged-lab/khmer.git
cd ../
(This makes it easy for you to pull down the latest changes in the
@@ -171,7 +171,7 @@ Building khmer and running the tests
make
If this fails, we apologize -- please `go create a new issue
- <https://github.com/dib-lab/khmer/issues?direction=desc&sort=created&state=open>`__,
+ <https://github.com/ged-lab/khmer/issues?direction=desc&sort=created&state=open>`__,
paste in the failure message, and we'll try to help you work through it!
(This takes the C++ source code and compiles it into something that Python
@@ -199,8 +199,8 @@ Claiming an issue and starting to develop
#. Find an open issue and claim it.
Go to `the list of open khmer issues
- <https://github.com/dib-lab/khmer/issues?direction=desc&sort=created&state=open>`__
- and find one you like; we suggest starting with `the low-hanging fruit issues <https://github.com/dib-lab/khmer/issues?direction=desc&labels=low-hanging-fruit&page=1&sort=created&state=open>`__).
+ <https://github.com/ged-lab/khmer/issues?direction=desc&sort=created&state=open>`__
+ and find one you like; we suggest starting with `the low-hanging fruit issues <https://github.com/ged-lab/khmer/issues?direction=desc&labels=low-hanging-fruit&page=1&sort=created&state=open>`__).
Once you've found an issue you like, make sure that no one has been
assigned to it (see "assignee", bottom right near "notifications").
@@ -213,18 +213,17 @@ Claiming an issue and starting to develop
from the main khmer master branch::
git checkout master
- git pull dib master
+ git pull ged master
(This pulls in all of the latest changes from whatever we've been
- doing on dib-lab.)
+ doing on ged-lab.)
#. Create a new branch and link it to your fork on GitHub::
- git checkout -b fix/brief_issue_description
- git push -u origin fix/brief_issue_description
+ git checkout -b fix/issue_number
+ git push -u origin fix/issue_number
- where you replace "brief_issue_description" with 2-3 words, separated
- by underscores, describing the issue.
+ where you replace "issue_number" with the number of the issue.
(This is the set of changes you're going to ask to be merged into khmer.)
@@ -236,10 +235,10 @@ Claiming an issue and starting to develop
#. Periodically update your branch from the main khmer master branch::
- git pull dib master
+ git pull ged master
(This pulls in all of the latest changes from whatever we've been
- doing on dib-lab - important especially during periods of fast change
+ doing on ged-lab - important especially during periods of fast change
or for long-running pull requests.
#. Run the tests and/or build the docs *before* pushing to GitHub::
diff --git a/doc/dev/hackathon.rst b/doc/dev/hackathon.rst
index a74a0f9..4b49aab 100644
--- a/doc/dev/hackathon.rst
+++ b/doc/dev/hackathon.rst
@@ -7,7 +7,7 @@ blog post <http://ivory.idyll.org/blog/2014-khmer-hackathon.html>`__).
----
Please track `khmer issue #446
-<https://github.com/dib-lab/khmer/issues/446>`__ for up-to-the-minute
+<https://github.com/ged-lab/khmer/issues/446>`__ for up-to-the-minute
information. You can subscribe to this issue (lower right on issue page)
to get automatic e-mail updates.
@@ -21,7 +21,7 @@ khmer is a piece of scientific software that does cool stuff in biology.
can read more about khmer `here <http://figshare.com/articles/The_khmer_software_package_enabling_efficient_sequence_analysis/979190>`__ if you like.)
The important bit about khmer is that we develop it openly,
-at https://github.com/dib-lab/khmer; we use reasonably OK software development
+at http://github.com/ged-lab/khmer; we use reasonably OK software development
practices; and we're interested in spreading the gospel, so to speak.
So! For this Hackathon, we're providing a "mentored software
@@ -37,9 +37,9 @@ To get started, go to :doc:`getting-started`!
You can contact us directly at khmer-project at idyll.org, but if you're
experience trouble of any kind, please feel to `create an issue
-<https://github.com/dib-lab/khmer/issues?direction=desc&sort=created&state=open>`__
+<https://github.com/ged-lab/khmer/issues?direction=desc&sort=created&state=open>`__
where we can help you out. Also keep an eye on `issue #446
-<https://github.com/dib-lab/khmer/issues/446>`__ where we're updating
+<https://github.com/ged-lab/khmer/issues/446>`__ where we're updating
Hackathon information more generally.
Problems, questions, and solutions
@@ -54,7 +54,7 @@ Problems, questions, and solutions
#. There's a bug in this documentation! But I can fix it...
Oh noes! Fixes are welcome -- these docs are in branch
- 'docs/hackathon' on https://github.com/dib-lab/khmer/, so please
+ 'docs/hackathon' on http://github.com/ged-lab/khmer/, so please
send PRs there. Or if you haven't worked through the process yet,
please `add an issue
- <https://github.com/dib-lab/khmer/issues?direction=desc&sort=created&state=open>`__ and we'll be on it.
+ <https://github.com/ged-lab/khmer/issues?direction=desc&sort=created&state=open>`__ and we'll be on it.
diff --git a/doc/dev/index.rst b/doc/dev/index.rst
index cead1c3..d5b2b15 100644
--- a/doc/dev/index.rst
+++ b/doc/dev/index.rst
@@ -26,4 +26,3 @@ Contents:
details
development
crazy-ideas
- binary-file-formats
diff --git a/doc/dev/release.rst b/doc/dev/release.rst
index cb3da63..8e6ed67 100644
--- a/doc/dev/release.rst
+++ b/doc/dev/release.rst
@@ -16,7 +16,7 @@ release makers, following this checklist by MRC.
#. The below should be done in a clean checkout::
cd `mktemp -d`
- git clone git at github.com:dib-lab/khmer.git
+ git clone git at github.com:ged-lab/khmer.git
cd khmer
#. (Optional) Check for updates to versioneer::
@@ -65,7 +65,7 @@ release makers, following this checklist by MRC.
the letter 'v'::
git tag v${new_version}-${rc}
- git push --tags git at github.com:dib-lab/khmer.git
+ git push --tags git at github.com:ged-lab/khmer.git
#. Test the release candidate. Bonus: repeat on Mac OS X::
@@ -78,11 +78,11 @@ release makers, following this checklist by MRC.
cd testenv1
source bin/activate
- git clone --depth 1 --branch v${new_version}-${rc} https://github.com/dib-lab/khmer.git
+ git clone --depth 1 --branch v${new_version}-${rc} https://github.com/ged-lab/khmer.git
cd khmer
make install-dependencies
make test
- normalize-by-median.py --version 2>&1 | grep khmer\ ${new_version}-${rc} && \
+ normalize-by-median.py --version 2>&1 | grep ${new_version}-${rc} && \
echo 1st manual version check passed
pip uninstall -y khmer; pip uninstall -y khmer; make install
mkdir ../not-khmer # if there is a subdir named 'khmer' nosetest will execute tests
@@ -92,10 +92,10 @@ release makers, following this checklist by MRC.
# Secondly we test via pip
- cd ../../testenv2
+ cd ../testenv2
source bin/activate
pip install -U setuptools==3.4.1
- pip install -e git+https://github.com/dib-lab/khmer.git@v${new_version}-${rc}#egg=khmer
+ pip install -e git+https://github.com/ged-lab/khmer.git@v${new_version}-${rc}#egg=khmer
cd src/khmer
make install-dependencies
make dist
@@ -103,7 +103,7 @@ release makers, following this checklist by MRC.
cp dist/khmer*tar.gz ../../../testenv3/
pip uninstall -y khmer; pip uninstall -y khmer; make install
cd ../.. # no subdir named khmer here, safe for nosetesting installed khmer module
- normalize-by-median.py --version 2>&1 | grep khmer\ ${new_version}-${rc} && \
+ normalize-by-median.py --version 2>&1 | grep ${new_version}-${rc} && \
echo 2nd manual version check passed
nosetests khmer --attr '!known_failing'
@@ -141,7 +141,7 @@ release makers, following this checklist by MRC.
pip install screed nose
pip install -i https://testpypi.python.org/pypi --pre --no-clean khmer
nosetests khmer --attr '!known_failing'
- normalize-by-median.py --version 2>&1 | grep khmer\ ${new_version}-${rc} && \
+ normalize-by-median.py --version 2>&1 | grep ${new_version}-${rc} && \
echo 3rd manual version check passed
cd build/khmer
make test
@@ -166,8 +166,8 @@ so:
#. Delete the release candidate tag and push the tag updates to GitHub.::
git tag -d v${new_version}-${rc}
- git push git at github.com:dib-lab/khmer.git
- git push --tags git at github.com:dib-lab/khmer.git
+ git push git at github.com:ged-lab/khmer.git
+ git push --tags git at github.com:ged-lab/khmer.git
#. Add the release on GitHub, using the tag you just pushed. Name
it 'version X.Y.Z', and copy and paste in the release notes.
diff --git a/doc/dev/scripts-and-sandbox.rst b/doc/dev/scripts-and-sandbox.rst
index 3b149cc..b8a11af 100644
--- a/doc/dev/scripts-and-sandbox.rst
+++ b/doc/dev/scripts-and-sandbox.rst
@@ -66,7 +66,7 @@ Copyright message
Our current Copyright message is::
#
- # This file is part of khmer, https://github.com/dib-lab/khmer/, and is
+ # This file is part of khmer, http://github.com/ged-lab/khmer/, and is
# Copyright (C) Michigan State University, 2009-2015. It is licensed under
# the three-clause BSD license; see doc/LICENSE.txt.
# Contact: khmer-project at idyll.org
diff --git a/doc/index.rst b/doc/index.rst
index 47fcf72..8135f1f 100644
--- a/doc/index.rst
+++ b/doc/index.rst
@@ -12,8 +12,8 @@ khmer -- k-mer counting & filtering FTW
Rajaram Srinivasan, Qingpeng Zhang, and C. Titus Brown
:Contact: khmer-project at idyll.org
-:GitHub: https://github.com/dib-lab/khmer
-:Chat: https://gitter.im/dib-lab/khmer
+:GitHub: https://github.com/ged-lab/khmer
+:Chat: https://gitter.im/ged-lab/khmer
:License: BSD
@@ -52,7 +52,6 @@ Contents:
introduction
contributors
citations
- whats-new-2.0
release-notes/index
user/index
dev/index
diff --git a/doc/release-notes/release-1.0.1.md b/doc/release-notes/release-1.0.1.md
index e2121bc..5668731 100644
--- a/doc/release-notes/release-1.0.1.md
+++ b/doc/release-notes/release-1.0.1.md
@@ -29,25 +29,25 @@ All of these are pre-existing.
Some users have reported that normalize-by-median.py will utilize more
memory than it was configured for. This is being investigated in
-https://github.com/dib-lab/khmer/issues/266
+https://github.com/ged-lab/khmer/issues/266
Some FASTQ files confuse our parser when running with more than one thread.
For example, while using load-into-counting.py. If you experience this then
add "--threads=1" to your command line. This issue is being tracked in
-https://github.com/dib-lab/khmer/issues/249
+https://github.com/ged-lab/khmer/issues/249
If your k-mer table (hashfile) gets truncated, perhaps from a full filesystem, then our
-tools currently will get stuck. This is being tracked in https://github.com/dib-lab/khmer/issues/247 and https://github.com/dib-lab/khmer/issues/246
+tools currently will get stuck. This is being tracked in https://github.com/ged-lab/khmer/issues/247 and https://github.com/ged-lab/khmer/issues/246
Paired-end reads from Casava 1.8 currently require renaming for use in
normalize-by-median and abund-filter when used in paired mode. The
-integration of a fix for this is being tracked in https://github.com/dib-lab/khmer/issues/23
+integration of a fix for this is being tracked in https://github.com/ged-lab/khmer/issues/23
annotate-partitions.py only outputs FASTA even if given a FASTQ file. This
-issue is being tracked in https://github.com/dib-lab/khmer/issues/46
+issue is being tracked in https://github.com/ged-lab/khmer/issues/46
A user reported that abundance-dist-single.py fails with small files and many
-threads. This issue is being tracked in https://github.com/dib-lab/khmer/issues/75
+threads. This issue is being tracked in https://github.com/ged-lab/khmer/issues/75
## Contributors
diff --git a/doc/release-notes/release-1.0.1.rst b/doc/release-notes/release-1.0.1.rst
index d491759..8b57b76 100644
--- a/doc/release-notes/release-1.0.1.rst
+++ b/doc/release-notes/release-1.0.1.rst
@@ -40,30 +40,30 @@ All of these are pre-existing.
Some users have reported that normalize-by-median.py will utilize more
memory than it was configured for. This is being investigated in
-https://github.com/dib-lab/khmer/issues/266
+https://github.com/ged-lab/khmer/issues/266
Some FASTQ files confuse our parser when running with more than one
thread. For example, while using load-into-counting.py. If you
experience this then add "--threads=1" to your command line. This issue
-is being tracked in https://github.com/dib-lab/khmer/issues/249
+is being tracked in https://github.com/ged-lab/khmer/issues/249
If your k-mer table (hashfile) gets truncated, perhaps from a full
filesystem, then our tools currently will get stuck. This is being
-tracked in https://github.com/dib-lab/khmer/issues/247 and
-https://github.com/dib-lab/khmer/issues/246
+tracked in https://github.com/ged-lab/khmer/issues/247 and
+https://github.com/ged-lab/khmer/issues/246
Paired-end reads from Casava 1.8 currently require renaming for use in
normalize-by-median and abund-filter when used in paired mode. The
integration of a fix for this is being tracked in
-https://github.com/dib-lab/khmer/issues/23
+https://github.com/ged-lab/khmer/issues/23
annotate-partitions.py only outputs FASTA even if given a FASTQ file.
This issue is being tracked in
-https://github.com/dib-lab/khmer/issues/46
+https://github.com/ged-lab/khmer/issues/46
A user reported that abundance-dist-single.py fails with small files and
many threads. This issue is being tracked in
-https://github.com/dib-lab/khmer/issues/75
+https://github.com/ged-lab/khmer/issues/75
Contributors
------------
diff --git a/doc/release-notes/release-1.0.md b/doc/release-notes/release-1.0.md
index 598a2c5..99ce8ab 100644
--- a/doc/release-notes/release-1.0.md
+++ b/doc/release-notes/release-1.0.md
@@ -61,25 +61,25 @@ All of these are pre-existing.
Some users have reported that normalize-by-median.py will utilize more
memory than it was configured for. This is being investigated in
-https://github.com/dib-lab/khmer/issues/266
+https://github.com/ged-lab/khmer/issues/266
Some FASTQ files confuse our parser when running with more than one thread.
For example, while using load-into-counting.py. If you experience this then
add "--threads=1" to your command line. This issue is being tracked in
-https://github.com/dib-lab/khmer/issues/249
+https://github.com/ged-lab/khmer/issues/249
If your k-mer table (hashfile) gets truncated, perhaps from a full filesystem, then our
-tools currently will get stuck. This is being tracked in https://github.com/dib-lab/khmer/issues/247 and https://github.com/dib-lab/khmer/issues/96 and https://github.com/dib-lab/khmer/issues/246
+tools currently will get stuck. This is being tracked in https://github.com/ged-lab/khmer/issues/247 and https://github.com/ged-lab/khmer/issues/96 and https://github.com/ged-lab/khmer/issues/246
Paired-end reads from Casava 1.8 currently require renaming for use in
normalize-by-median and abund-filter when used in paired mode. The
-integration of a fix for this is being tracked in https://github.com/dib-lab/khmer/issues/23
+integration of a fix for this is being tracked in https://github.com/ged-lab/khmer/issues/23
annotate-partitions.py only outputs FASTA even if given a FASTQ file. This
-issue is being tracked in https://github.com/dib-lab/khmer/issues/46
+issue is being tracked in https://github.com/ged-lab/khmer/issues/46
A user reported that abundance-dist-single.py fails with small files and many
-threads. This issue is being tracked in https://github.com/dib-lab/khmer/issues/75
+threads. This issue is being tracked in https://github.com/ged-lab/khmer/issues/75
## Contributors
diff --git a/doc/release-notes/release-1.0.rst b/doc/release-notes/release-1.0.rst
index 7b7b3ab..94dc769 100644
--- a/doc/release-notes/release-1.0.rst
+++ b/doc/release-notes/release-1.0.rst
@@ -76,31 +76,31 @@ All of these are pre-existing.
Some users have reported that normalize-by-median.py will utilize more
memory than it was configured for. This is being investigated in
-https://github.com/dib-lab/khmer/issues/266
+https://github.com/ged-lab/khmer/issues/266
Some FASTQ files confuse our parser when running with more than one
thread. For example, while using load-into-counting.py. If you
experience this then add "--threads=1" to your command line. This issue
-is being tracked in https://github.com/dib-lab/khmer/issues/249
+is being tracked in https://github.com/ged-lab/khmer/issues/249
If your k-mer table (hashfile) gets truncated, perhaps from a full
filesystem, then our tools currently will get stuck. This is being
-tracked in https://github.com/dib-lab/khmer/issues/247 and
-https://github.com/dib-lab/khmer/issues/96 and
-https://github.com/dib-lab/khmer/issues/246
+tracked in https://github.com/ged-lab/khmer/issues/247 and
+https://github.com/ged-lab/khmer/issues/96 and
+https://github.com/ged-lab/khmer/issues/246
Paired-end reads from Casava 1.8 currently require renaming for use in
normalize-by-median and abund-filter when used in paired mode. The
integration of a fix for this is being tracked in
-https://github.com/dib-lab/khmer/issues/23
+https://github.com/ged-lab/khmer/issues/23
annotate-partitions.py only outputs FASTA even if given a FASTQ file.
This issue is being tracked in
-https://github.com/dib-lab/khmer/issues/46
+https://github.com/ged-lab/khmer/issues/46
A user reported that abundance-dist-single.py fails with small files and
many threads. This issue is being tracked in
-https://github.com/dib-lab/khmer/issues/75
+https://github.com/ged-lab/khmer/issues/75
Contributors
------------
diff --git a/doc/release-notes/release-1.1.md b/doc/release-notes/release-1.1.md
index cd01bcb..0629f04 100644
--- a/doc/release-notes/release-1.1.md
+++ b/doc/release-notes/release-1.1.md
@@ -4,7 +4,7 @@ This is v1.1, a minor version release; this version adds several new scripts.
Docs at: https://khmer.readthedocs.org/en/v1.1/
-Release notes w/links: https://github.com/dib-lab/khmer/releases/tag/v1.1
+Release notes w/links: https://github.com/ged-lab/khmer/releases/tag/v1.1
## New items of note:
@@ -32,27 +32,27 @@ All of these are pre-existing.
Some users have reported that normalize-by-median.py will utilize more
memory than it was configured for. This is being investigated in
-https://github.com/dib-lab/khmer/issues/266
+https://github.com/ged-lab/khmer/issues/266
Some FASTQ files confuse our parser when running with more than one thread.
For example, while using load-into-counting.py. If you experience this then
add "--threads=1" to your command line. This issue is being tracked in
-https://github.com/dib-lab/khmer/issues/249
+https://github.com/ged-lab/khmer/issues/249
If your k-mer table is truncated on write, an error may not be reported; this
-is being tracked in https://github.com/dib-lab/khmer/issues/443.
+is being tracked in https://github.com/ged-lab/khmer/issues/443.
However, khmer will now (correctly) fail when trying to read a truncated file
(See #333).
Paired-end reads from Casava 1.8 currently require renaming for use in
normalize-by-median and abund-filter when used in paired mode. The
-integration of a fix for this is being tracked in https://github.com/dib-lab/khmer/issues/23
+integration of a fix for this is being tracked in https://github.com/ged-lab/khmer/issues/23
Some scripts only output FASTA even if given a FASTQ file. This issue
-is being tracked in https://github.com/dib-lab/khmer/issues/46
+is being tracked in https://github.com/ged-lab/khmer/issues/46
A user reported that abundance-dist-single.py fails with small files and many
-threads. This issue is being tracked in https://github.com/dib-lab/khmer/issues/75
+threads. This issue is being tracked in https://github.com/ged-lab/khmer/issues/75
## Contributors
diff --git a/doc/release-notes/release-1.1.rst b/doc/release-notes/release-1.1.rst
index d08da5c..edcd85b 100644
--- a/doc/release-notes/release-1.1.rst
+++ b/doc/release-notes/release-1.1.rst
@@ -7,7 +7,7 @@ scripts.
Docs at: https://khmer.readthedocs.org/en/v1.1/
Release notes w/links:
-https://github.com/dib-lab/khmer/releases/tag/v1.1
+https://github.com/ged-lab/khmer/releases/tag/v1.1
New items of note:
------------------
@@ -46,29 +46,29 @@ All of these are pre-existing.
Some users have reported that normalize-by-median.py will utilize more
memory than it was configured for. This is being investigated in
-https://github.com/dib-lab/khmer/issues/266
+https://github.com/ged-lab/khmer/issues/266
Some FASTQ files confuse our parser when running with more than one
thread. For example, while using load-into-counting.py. If you
experience this then add "--threads=1" to your command line. This issue
-is being tracked in https://github.com/dib-lab/khmer/issues/249
+is being tracked in https://github.com/ged-lab/khmer/issues/249
If your k-mer table is truncated on write, an error may not be reported;
-this is being tracked in https://github.com/dib-lab/khmer/issues/443.
+this is being tracked in https://github.com/ged-lab/khmer/issues/443.
However, khmer will now (correctly) fail when trying to read a truncated
file (See #333).
Paired-end reads from Casava 1.8 currently require renaming for use in
normalize-by-median and abund-filter when used in paired mode. The
integration of a fix for this is being tracked in
-https://github.com/dib-lab/khmer/issues/23
+https://github.com/ged-lab/khmer/issues/23
Some scripts only output FASTA even if given a FASTQ file. This issue is
-being tracked in https://github.com/dib-lab/khmer/issues/46
+being tracked in https://github.com/ged-lab/khmer/issues/46
A user reported that abundance-dist-single.py fails with small files and
many threads. This issue is being tracked in
-https://github.com/dib-lab/khmer/issues/75
+https://github.com/ged-lab/khmer/issues/75
Contributors
------------
diff --git a/doc/release-notes/release-1.2.md b/doc/release-notes/release-1.2.md
index 22a6dac..9f7bd4a 100644
--- a/doc/release-notes/release-1.2.md
+++ b/doc/release-notes/release-1.2.md
@@ -61,33 +61,33 @@ Multithreaded reading will drop reads. This major issue has been present for
several khmer releases and was only found via a much larger test case that we
had been previously using. Credit to @camillescott. Workaround: disable
threading. The next release will fix this and the other FAST[AQ] parsing
-issues. https://github.com/dib-lab/khmer/issues/681
+issues. https://github.com/ged-lab/khmer/issues/681
Some users have reported that normalize-by-median.py will utilize more
memory than it was configured for. This is being investigated in
-https://github.com/dib-lab/khmer/issues/266
+https://github.com/ged-lab/khmer/issues/266
Some FASTQ files confuse our parser when running with more than one thread.
For example, while using load-into-counting.py. If you experience this then
add "--threads=1" to your command line. This issue is being tracked in
-https://github.com/dib-lab/khmer/issues/249
+https://github.com/ged-lab/khmer/issues/249
If your k-mer table is truncated on write, an error may not be reported; this
-is being tracked in https://github.com/dib-lab/khmer/issues/443.
+is being tracked in https://github.com/ged-lab/khmer/issues/443.
However, khmer will now (correctly) fail when trying to read a truncated file
(See #333).
Paired-end reads from Casava 1.8 currently require renaming for use in
normalize-by-median and abund-filter when used in paired mode. The
integration of a fix for this is being tracked in
-https://github.com/dib-lab/khmer/issues/23
+https://github.com/ged-lab/khmer/issues/23
Some scripts only output FASTA even if given a FASTQ file. This issue
-is being tracked in https://github.com/dib-lab/khmer/issues/46
+is being tracked in https://github.com/ged-lab/khmer/issues/46
A user reported that abundance-dist-single.py fails with small files and many
threads. This issue is being tracked in
-https://github.com/dib-lab/khmer/issues/75
+https://github.com/ged-lab/khmer/issues/75
## Contributors
diff --git a/doc/release-notes/release-1.2.rst b/doc/release-notes/release-1.2.rst
index 9a2ee66..9e851ec 100644
--- a/doc/release-notes/release-1.2.rst
+++ b/doc/release-notes/release-1.2.rst
@@ -65,33 +65,33 @@ for several khmer releases and was only found via a much larger test
case that we had been previously using. Credit to @camillescott.
Workaround: disable threading. The next release will fix this and the
other FAST[AQ] parsing issues.
-https://github.com/dib-lab/khmer/issues/681
+https://github.com/ged-lab/khmer/issues/681
Some users have reported that normalize-by-median.py will utilize more
memory than it was configured for. This is being investigated in
-https://github.com/dib-lab/khmer/issues/266
+https://github.com/ged-lab/khmer/issues/266
Some FASTQ files confuse our parser when running with more than one
thread. For example, while using load-into-counting.py. If you
experience this then add "--threads=1" to your command line. This issue
-is being tracked in https://github.com/dib-lab/khmer/issues/249
+is being tracked in https://github.com/ged-lab/khmer/issues/249
If your k-mer table is truncated on write, an error may not be reported;
-this is being tracked in https://github.com/dib-lab/khmer/issues/443.
+this is being tracked in https://github.com/ged-lab/khmer/issues/443.
However, khmer will now (correctly) fail when trying to read a truncated
file (See #333).
Paired-end reads from Casava 1.8 currently require renaming for use in
normalize-by-median and abund-filter when used in paired mode. The
integration of a fix for this is being tracked in
-https://github.com/dib-lab/khmer/issues/23
+https://github.com/ged-lab/khmer/issues/23
Some scripts only output FASTA even if given a FASTQ file. This issue is
-being tracked in https://github.com/dib-lab/khmer/issues/46
+being tracked in https://github.com/ged-lab/khmer/issues/46
A user reported that abundance-dist-single.py fails with small files and
many threads. This issue is being tracked in
-https://github.com/dib-lab/khmer/issues/75
+https://github.com/ged-lab/khmer/issues/75
Contributors
------------
diff --git a/doc/release-notes/release-1.3.md b/doc/release-notes/release-1.3.md
index 9d21c0d..95edb2c 100644
--- a/doc/release-notes/release-1.3.md
+++ b/doc/release-notes/release-1.3.md
@@ -41,7 +41,7 @@ Some users have reported that normalize-by-median.py will utilize more memory
than it was configured for. This is being investigated in #266
If your k-mer table is truncated on write, an error may not be reported; this
-is being tracked in https://github.com/dib-lab/khmer/issues/443. However, khmer
+is being tracked in https://github.com/ged-lab/khmer/issues/443. However, khmer
will now (correctly) fail when trying to read a truncated file (See #333).
Paired-end reads from Casava 1.8 currently require renaming for use in
diff --git a/doc/release-notes/release-1.3.rst b/doc/release-notes/release-1.3.rst
index 5b0b317..68347f3 100644
--- a/doc/release-notes/release-1.3.rst
+++ b/doc/release-notes/release-1.3.rst
@@ -42,7 +42,7 @@ Some users have reported that normalize-by-median.py will utilize more
memory than it was configured for. This is being investigated in #266
If your k-mer table is truncated on write, an error may not be reported;
-this is being tracked in https://github.com/dib-lab/khmer/issues/443.
+this is being tracked in https://github.com/ged-lab/khmer/issues/443.
However, khmer will now (correctly) fail when trying to read a truncated
file (See #333).
diff --git a/doc/release-notes/release-1.4.md b/doc/release-notes/release-1.4.md
index 793172e..7329f96 100644
--- a/doc/release-notes/release-1.4.md
+++ b/doc/release-notes/release-1.4.md
@@ -217,10 +217,10 @@ All of these are pre-existing.
Some users have reported that normalize-by-median.py will utilize more memory
than it was configured for. This is being investigated in
-https://github.com/dib-lab/khmer/issues/266
+https://github.com/ged-lab/khmer/issues/266
Some scripts only output FASTA even if given a FASTQ file. This issue is being
-tracked in https://github.com/dib-lab/khmer/issues/46
+tracked in https://github.com/ged-lab/khmer/issues/46
## Contributors
diff --git a/doc/release-notes/release-1.4.rst b/doc/release-notes/release-1.4.rst
index c257299..667f7d3 100644
--- a/doc/release-notes/release-1.4.rst
+++ b/doc/release-notes/release-1.4.rst
@@ -233,10 +233,10 @@ All of these are pre-existing.
Some users have reported that normalize-by-median.py will utilize more
memory than it was configured for. This is being investigated in
-https://github.com/dib-lab/khmer/issues/266
+https://github.com/ged-lab/khmer/issues/266
Some scripts only output FASTA even if given a FASTQ file. This issue is
-being tracked in https://github.com/dib-lab/khmer/issues/46
+being tracked in https://github.com/ged-lab/khmer/issues/46
Contributors
------------
diff --git a/doc/roadmap.rst b/doc/roadmap.rst
index cc25cfd..d0011ef 100644
--- a/doc/roadmap.rst
+++ b/doc/roadmap.rst
@@ -12,7 +12,7 @@ fundamental changes need to happen. This document outlines our plan to do so
while minimizing the impact of these changes on our existing users.
The discussion that lead to this document can be read at
-https://github.com/dib-lab/khmer/issues/389
+https://github.com/ged-lab/khmer/issues/389
Remainder of v1.x series
========================
diff --git a/doc/run-corn-50m.sh b/doc/run-corn-50m.sh
index 8ce5a0b..4755644 100644
--- a/doc/run-corn-50m.sh
+++ b/doc/run-corn-50m.sh
@@ -1,7 +1,7 @@
#! /bin/bash
#
-# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
-# Copyright (C) Michigan State University, 2009-2015. It is licensed under
+# This file is part of khmer, http://github.com/ged-lab/khmer/, and is
+# Copyright (C) Michigan State University, 2009-2013. It is licensed under
# the three-clause BSD license; see doc/LICENSE.txt.
# Contact: khmer-project at idyll.org
#
diff --git a/doc/user/choosing-table-sizes.rst b/doc/user/choosing-table-sizes.rst
index caba889..bbc112d 100644
--- a/doc/user/choosing-table-sizes.rst
+++ b/doc/user/choosing-table-sizes.rst
@@ -1,55 +1,53 @@
.. vim: set filetype=rst
-==========================
-Setting khmer memory usage
-==========================
+==============================
+Choosing table sizes for khmer
+==============================
If you look at the documentation for the scripts (:doc:`scripts`) you'll
-see a :option:`-M` parameter that sets the maximum memory usage for
-any script that uses k-mer counting tables or k-mer graphs. What is this?
-
-khmer uses a special data structure that lets it store counting tables
-and k-mer graphs in very low memory; the trick is that you must fix
-the amount of memory khmer can use before running it. (See `Pell et
-al., 2012 <http://www.ncbi.nlm.nih.gov/pubmed/22847406>`__ and `Zhang
-et al., 2014 <http://www.ncbi.nlm.nih.gov/pubmed/25062443>`__ for the
-details.) This is what the :option:`-M` parameter does.
-
-If you set it too low, khmer will warn you to set it higher at the end.
-See below for some good choices for various kinds of data.
-
-**Note for khmer 1.x users:** as of khmer 2.0, the :option:`-M`
-parameter sets the :option:`-N`/:option:`--n_tables` and
-:option:`-x`/:option:`--max_tablesize` parameters automatically.
-You can still set these parameters directly if you wish.
+see two mysterious parameters -- :option:`-N` and :option:`-x`, or, more
+verbosely, :option:`-n_tables` and :option:`--tablesize`. What are these, and
+how do you specify them?
The really short version
========================
There is no way (except for experience, rules of thumb, and intuition) to
-know what this parameter should be up front. So, use the maximum
-available memory::
+know what these parameters should be up front. So, make the product of
+these two parameters be the size of your available memory::
- -M 16e9
+ -N 4 -x 4e9
-for a machine with 16 GB of free memory, for example.
+for a machine with 16 GB of free memory, for example. Also see
+the rules of thumb, below.
The short version
=================
-This parameter specifies the maximum memory usage of the primary data
+These parameters specify the maximum memory usage of the primary data
structure in khmer, which is basically N big hash tables of size x.
The **product** of the number of hash tables and the size of the hash
-tables specifies the total amount of memory used, which is what the
-:option:`-M` parameter sets.
+tables specifies the total amount of memory used.
-These tables are used to track k-mers. If they are too small, khmer
-will fail in various ways (and will complain), but there is no harm
+This table is used to track k-mers. If it is too small, khmer
+will fail in various ways (and should complain), but there is no harm
in making it too large. So, **the absolute safest thing to do is to
specify as much memory as is available**. Most scripts will inform
you of the total memory usage, and (at the end) will complain if it's
too small.
+For normalize-by-median, khmer uses one byte per hash entry, so: if
+you had 16 GB of available RAM, you should specify something like ``-N
+4 -x 4e9``, which multiplies out to about 16 GB.
+
+For the graph partitioning stuff, khmer uses only 1 bit per k-mer, so
+you can multiple your available memory by 8: for 16 GB of RAM, you could
+use ::
+
+ -N 4 -x 32e9
+
+which multiplies out to 128 Gbits of RAM, or 16 Gbytes.
+
Life is a bit more complicated than this, however, because some scripts --
load-into-counting and load-graph -- keep ancillary information that will
consume memory beyond this table data structure. So if you run out of
@@ -126,24 +124,26 @@ an error-code.
Rules of thumb
--------------
+Just use -N 4, always, and vary the -x parameter.
+
For digital normalization, we recommend:
- - ``-M 8e9`` for any amount of sequencing for a single microbial genome,
+ - ``-x 2e9`` for any amount of sequencing for a single microbial genome,
MDA-amplified or single colony.
- - ``-M 16e9`` for up to a billion mRNAseq reads from any organism. Past that,
+ - ``-x 4e9`` for up to a billion mRNAseq reads from any organism. Past that,
increase it.
- - ``-M 32e9`` for most eukaryotic genome samples.
+ - ``-x 8e9`` for most eukaryotic genome samples.
- - ``-M 32e9`` will also handle most "simple" metagenomic samples (HMP on down)
+ - ``-x 8e9`` will also handle most "simple" metagenomic samples (HMP on down)
- For metagenomic samples that are more complex, such as soil or marine,
- start as high as possible. For example, we are using ``-M 256e9`` for
+ start as high as possible. For example, we are using ``-x 64e9`` for
~300 Gbp of soil reads.
For partitioning of complex metagenome samples, we recommend starting
as high as you can -- something like half your system memory. So if
-you have 256 GB of RAM, use ``-M 128e9`` which will use 128 GB of RAM
-for the basic graph storage, leaving other memory for the ancillary
-data structures.
+you have 256 GB of RAM, use ``-N 4 -x 256e9`` which will use 4 x 256 /
+8 = 128 GB of RAM for the basic graph storage, leaving other memory
+for the ancillary data structures.
diff --git a/doc/user/examples.rst b/doc/user/examples.rst
index d7443ea..e692ede 100644
--- a/doc/user/examples.rst
+++ b/doc/user/examples.rst
@@ -18,9 +18,9 @@ as the effect of digital normalization and partitioning on the k-mer
abundance distribution.
See `the script for running everything
-<https://github.com/dib-lab/khmer/blob/master/examples/stamps/do.sh>`__
+<https://github.com/ged-lab/khmer/blob/master/examples/stamps/do.sh>`__
and `the IPython Notebook
-<http://nbviewer.ipython.org/urls/raw.github.com/dib-lab/khmer/master/examples/stamps%2520k-mer%2520distributions.ipynb>`__.
+<http://nbviewer.ipython.org/urls/raw.github.com/ged-lab/khmer/master/examples/stamps%2520k-mer%2520distributions.ipynb>`__.
For an overall discussion and some slides to explain what's going on,
visit `the Web site for a 2013 HMP metagenome assembly webinar that
diff --git a/doc/user/getting-help.rst b/doc/user/getting-help.rst
index e84ff67..007b02a 100644
--- a/doc/user/getting-help.rst
+++ b/doc/user/getting-help.rst
@@ -51,4 +51,4 @@ GitHub
------
You are also welcome to report an issue you are having using GitHub::
-https://github.com/dib-lab/khmer/issues/new
+https://github.com/ged-lab/khmer/issues/new
diff --git a/doc/user/guide.rst b/doc/user/guide.rst
index 8f3714c..54458b5 100644
--- a/doc/user/guide.rst
+++ b/doc/user/guide.rst
@@ -29,7 +29,7 @@ khmer is a general `framework for low-memory k-mer counting, filtering,
and advanced trickery <http://khmer.readthedocs.org/en/latest/>`__.
The latest source is always available `here
-<https://github.com/dib-lab/khmer>`__.
+<https://github.com/ged-lab/khmer>`__.
khmer is really focused on short read data, and, more specifically,
Illumina, because that's where we have a too-much-data problem.
diff --git a/doc/user/known-issues.rst b/doc/user/known-issues.rst
index b6ab542..842adbd 100644
--- a/doc/user/known-issues.rst
+++ b/doc/user/known-issues.rst
@@ -5,7 +5,17 @@ Known Issues
Some users have reported that normalize-by-median.py will utilize more
memory than it was configured for. This is being investigated in
-https://github.com/dib-lab/khmer/issues/266
+https://github.com/ged-lab/khmer/issues/266
+
+If your k-mer table is truncated on write, an error may not be reported; this
+is being tracked in https://github.com/ged-lab/khmer/issues/443.
+However, khmer will now (correctly) fail when trying to read a truncated file
+(See #333).
+
+Paired-end reads from Casava 1.8 currently require renaming for use in
+normalize-by-median and abund-filter when used in paired mode. The
+integration of a fix for this is being tracked in
+https://github.com/ged-lab/khmer/issues/23
Some scripts only output FASTA even if given a FASTQ file. This issue
-is being tracked in https://github.com/dib-lab/khmer/issues/46
+is being tracked in https://github.com/ged-lab/khmer/issues/46
diff --git a/doc/user/scripts.rst b/doc/user/scripts.rst
index 3bc0cbb..157af7b 100644
--- a/doc/user/scripts.rst
+++ b/doc/user/scripts.rst
@@ -10,10 +10,14 @@ distribution. Below is our documentation for these scripts. Note
that all scripts can be given :option:`-h` which will print out
a list of arguments taken by that script.
-Scripts that use k-mer counting tables or k-mer graphs take an
-:option:`-M` parameter, which sets the maximum memory usage in bytes.
-This should generally be set as high as possible; see
-:doc:`choosing-table-sizes` for more information.
+Many scripts take :option:`-x` and :option:`-N` parameters, which drive khmer's
+memory usage. These parameters depend on details of your data set; for more information
+on how to choose them, see :doc:`choosing-table-sizes`.
+
+You can also override the default values of :option:`--ksize`/:option:`-k`,
+:option:`--n_tables`/:option:`-N`, and :option:`--min-tablesize`/:option:`-x` with
+the environment variables `KHMER_KSIZE`, `KHMER_N_TABLES`, and
+`KHMER_MIN_TABLESIZE` respectively.
1. :ref:`scripts-counting`
2. :ref:`scripts-partitioning`
diff --git a/doc/whats-new-2.0.rst b/doc/whats-new-2.0.rst
deleted file mode 100644
index 2a7f0c7..0000000
--- a/doc/whats-new-2.0.rst
+++ /dev/null
@@ -1,29 +0,0 @@
-.. vim: set filetype=rst
-
-What's New In khmer 2.0?
-########################
-
-Incompatible changes
-====================
-
-New parameter for tablesize/number of table parameters.
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
-There is now a :option:`-M`/:option:`--max-memory-usage` parameter
-that sets the number of tables (:option:`-N`/:option:`--num_tables`)
-and tablesize (:option:`-x`/:option:`--max-tablesize`) parameters
-automatically to match the desired memory usage.
-
-(:option:`--min-tablesize` was also renamed to
-:option:`--max-tablesize` to reflect this more desirable behavior.)
-
-Binary file formats have changed!
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
-All binary khmer formats (presence tables, counting tables, tag sets,
-stop tags, and partition subsets) have changed. Files are now
-pre-pended with the string ``OXLI`` to indicate that they are from
-this project.
-
-Files of the above types made in previous versions of khmer are not compatible
-with v2.0; the reverse is also true.
diff --git a/examples/stamps/do.sh b/examples/stamps/do.sh
index 8a170c7..4777142 100755
--- a/examples/stamps/do.sh
+++ b/examples/stamps/do.sh
@@ -1,7 +1,7 @@
#!/bin/bash
#
-# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
-# Copyright (C) Michigan State University, 2009-2015. It is licensed under
+# This file is part of khmer, http://github.com/ged-lab/khmer/, and is
+# Copyright (C) Michigan State University, 2009-2013. It is licensed under
# the three-clause BSD license; see LICENSE.
# Contact: khmer-project at idyll.org
#
diff --git a/jenkins-build.sh b/jenkins-build.sh
index 94f7d78..96007e9 100755
--- a/jenkins-build.sh
+++ b/jenkins-build.sh
@@ -56,7 +56,7 @@ then
#hg clone http://bitbucket.org/mcrusoe/sphinx-contrib
#hg clone http://athyra.ged.msu.edu/~mcrusoe/sphinx-contrib
#pip install --upgrade sphinx-contrib/autoprogram/
- #pip install -r doc/requirements.txt # now covered by make install-dep
+ pip install -r doc/requirements.txt
make doc
fi
make pylint 2>&1 > pylint.out
diff --git a/khmer/__init__.py b/khmer/__init__.py
index 032ca7b..b48d763 100644
--- a/khmer/__init__.py
+++ b/khmer/__init__.py
@@ -1,14 +1,12 @@
#
-# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
+# This file is part of khmer, http://github.com/ged-lab/khmer/, and is
# Copyright (C) Michigan State University, 2010-2015. It is licensed under
# the three-clause BSD license; see doc/LICENSE.txt.
# Contact: khmer-project at idyll.org
#
"""This is khmer; please see http://khmer.readthedocs.org/."""
-from __future__ import print_function
-
-from khmer._khmer import CountingHash as _CountingHash
+from khmer._khmer import CountingHash
from khmer._khmer import LabelHash as _LabelHash
from khmer._khmer import Hashbits as _Hashbits
from khmer._khmer import HLLCounter as _HLLCounter
@@ -45,6 +43,36 @@ __version__ = get_versions()['version']
del get_versions
+def new_hashbits(k, starting_size, n_tables=2):
+ """Return a new hashbits object. Deprecated.
+
+ This factory method is deprecated in favor of creating a Hashbits object
+ directly via 'new Hashbits(...)'.
+
+ Keyword argument:
+ k -- kmer size to use
+ starting_size -- lower bound on hashsize to use
+ n_tables -- number of hash tables to use (default = 2)
+ """
+ primes = get_n_primes_above_x(n_tables, starting_size)
+
+ return _Hashbits(k, primes)
+
+
+def new_counting_hash(k, starting_size, n_tables=2):
+ """Return a new countinghash object.
+
+ Keyword arguments:
+ k -- kmer size to use
+ starting_size -- lower bound on hashsize to use
+ n_tables -- number of hash tables to use (default = 2)
+ n_threads -- number of simultaneous threads to execute (default = 1)
+ """
+ primes = get_n_primes_above_x(n_tables, starting_size)
+
+ return CountingHash(k, primes)
+
+
def load_hashbits(filename):
"""Load a hashbits object from the given filename and return it.
@@ -63,7 +91,7 @@ def load_counting_hash(filename):
Keyword argument:
filename -- the name of the counting_hash file
"""
- hashtable = _CountingHash(1, [1])
+ hashtable = CountingHash(1, [1])
hashtable.load(filename)
return hashtable
@@ -81,7 +109,6 @@ def extract_hashbits_info(filename):
ksize = None
n_tables = None
table_size = None
- signature = None
version = None
ht_type = None
@@ -91,15 +118,11 @@ def extract_hashbits_info(filename):
try:
with open(filename, 'rb') as hashbits:
- signature, = unpack('4s', hashbits.read(4))
version, = unpack('B', hashbits.read(1))
ht_type, = unpack('B', hashbits.read(1))
ksize, = unpack('I', hashbits.read(uint_size))
n_tables, = unpack('B', hashbits.read(uchar_size))
table_size, = unpack('Q', hashbits.read(ulonglong_size))
- if signature != b"OXLI":
- raise ValueError("Node graph '{}' is missing file type "
- "signature".format(filename) + str(signature))
except:
raise ValueError("Presence table '{}' is corrupt ".format(filename))
@@ -118,7 +141,6 @@ def extract_countinghash_info(filename):
ksize = None
n_tables = None
table_size = None
- signature = None
version = None
ht_type = None
use_bigcount = None
@@ -128,16 +150,12 @@ def extract_countinghash_info(filename):
try:
with open(filename, 'rb') as countinghash:
- signature, = unpack('4s', countinghash.read(4))
version, = unpack('B', countinghash.read(1))
ht_type, = unpack('B', countinghash.read(1))
use_bigcount, = unpack('B', countinghash.read(1))
ksize, = unpack('I', countinghash.read(uint_size))
n_tables, = unpack('B', countinghash.read(1))
table_size, = unpack('Q', countinghash.read(ulonglong_size))
- if signature != b'OXLI':
- raise ValueError("Counting table '{}' is missing file type "
- "signature. ".format(filename) + str(signature))
except:
raise ValueError("Counting table '{}' is corrupt ".format(filename))
@@ -161,20 +179,12 @@ def calc_expected_collisions(hashtable, force=False, max_false_pos=.2):
fp_all = fp_one ** n_ht
if fp_all > max_false_pos:
- print("**", file=sys.stderr)
- print("** ERROR: the graph structure is too small for ",
- file=sys.stderr)
- print("** this data set. Increase data structure size",
- file=sys.stderr)
- print("** with --max_memory_usage/-M.", file=sys.stderr)
- print("**", file=sys.stderr)
- print("** Do not use these results!!", file=sys.stderr)
- print("**", file=sys.stderr)
- print("** (estimated false positive rate of %.3f;" % fp_all,
- file=sys.stderr)
- print("max allowable %.3f" % max_false_pos, file=sys.stderr)
- print("**", file=sys.stderr)
-
+ print >>sys.stderr, "**"
+ print >>sys.stderr, "** ERROR: the graph structure is too small for "
+ print >>sys.stderr, "this data set. Increase k-mer presence table "
+ print >>sys.stderr, "size/num of tables."
+ print >>sys.stderr, "** Do not use these results!!"
+ print >>sys.stderr, "**"
if not force:
sys.exit(1)
@@ -205,9 +215,6 @@ def get_n_primes_near_x(number, target):
number -- the number of primes to find
target -- the number to step backwards from
"""
- if target == 1 and number == 1:
- return [1]
-
primes = []
i = target - 1
if i % 2 == 0:
@@ -216,11 +223,27 @@ def get_n_primes_near_x(number, target):
if is_prime(i):
primes.append(i)
i -= 2
+ return primes
+
- if len(primes) != number:
- raise Exception("unable to find %d prime numbers < %d" % (number,
- target))
+def get_n_primes_above_x(number, target):
+ """Forward-find primes smaller than target.
+
+ Step forwards until a number of primes (other than 2) have been
+ found that are smaller than the target and return them.
+ Keyword arguments:
+ number -- the number of primes to find
+ target -- the number to step forwards from
+ """
+ primes = []
+ i = target + 1
+ if i % 2 == 0:
+ i += 1
+ while len(primes) != number and i > 0:
+ if is_prime(i):
+ primes.append(i)
+ i += 2
return primes
@@ -230,38 +253,19 @@ def get_n_primes_near_x(number, target):
# Additional functionality can be added to these classes as appropriate.
-class CountingHash(_CountingHash):
-
- def __new__(cls, k, starting_size, n_tables):
- primes = get_n_primes_near_x(n_tables, starting_size)
- c = _CountingHash.__new__(cls, k, primes)
- c.primes = primes
- return c
-
-
class LabelHash(_LabelHash):
def __new__(cls, k, starting_size, n_tables):
- hb = Hashbits(k, starting_size, n_tables)
- c = _LabelHash.__new__(cls, hb)
- c.graph = hb
- return c
-
-
-class CountingLabelHash(_LabelHash):
-
- def __new__(cls, k, starting_size, n_tables):
- primes = get_n_primes_near_x(n_tables, starting_size)
- hb = _CountingHash(k, primes)
- c = _LabelHash.__new__(cls, hb)
- c.graph = hb
+ primes = get_n_primes_above_x(n_tables, starting_size)
+ c = _LabelHash.__new__(cls, k, primes)
+ c.primes = primes
return c
class Hashbits(_Hashbits):
def __new__(cls, k, starting_size, n_tables):
- primes = get_n_primes_near_x(n_tables, starting_size)
+ primes = get_n_primes_above_x(n_tables, starting_size)
c = _Hashbits.__new__(cls, k, primes)
c.primes = primes
return c
diff --git a/khmer/_khmer.cc b/khmer/_khmermodule.cc
similarity index 72%
rename from khmer/_khmer.cc
rename to khmer/_khmermodule.cc
index d58e832..8a90c77 100644
--- a/khmer/_khmer.cc
+++ b/khmer/_khmermodule.cc
@@ -1,5 +1,5 @@
//
-// This file is part of khmer, https://github.com/dib-lab/khmer/, and is
+// This file is part of khmer, http://github.com/ged-lab/khmer/, and is
// Copyright (C) Michigan State University, 2009-2015. It is licensed under
// the three-clause BSD license; see doc/LICENSE.txt.
// Contact: khmer-project at idyll.org
@@ -34,7 +34,6 @@ using namespace read_parsers;
#if (PY_MAJOR_VERSION >= 3)
#define PyInt_Check(arg) PyLong_Check(arg)
#define PyInt_AsLong(arg) PyLong_AsLong(arg)
-#define PyInt_FromLong(arg) PyLong_FromLong(arg)
#endif
//
@@ -44,27 +43,6 @@ using namespace read_parsers;
#include "bytesobject.h"
-//
-// Python 2/3 compatibility: Module initialization
-// http://python3porting.com/cextensions.html#module-initialization
-//
-
-#if PY_MAJOR_VERSION >= 3
- #define MOD_ERROR_VAL NULL
- #define MOD_SUCCESS_VAL(val) val
- #define MOD_INIT(name) PyMODINIT_FUNC PyInit_##name(void)
- #define MOD_DEF(ob, name, doc, methods) \
- static struct PyModuleDef moduledef = { \
- PyModuleDef_HEAD_INIT, name, doc, -1, methods, }; \
- ob = PyModule_Create(&moduledef);
-#else
- #define MOD_ERROR_VAL
- #define MOD_SUCCESS_VAL(val)
- #define MOD_INIT(name) void init##name(void)
- #define MOD_DEF(ob, name, doc, methods) \
- ob = Py_InitModule3(name, methods, doc);
-#endif
-
using namespace khmer;
//
@@ -72,7 +50,7 @@ using namespace khmer;
//
extern "C" {
- MOD_INIT(_khmer);
+ void init_khmer();
}
// Configure module logging.
@@ -126,6 +104,14 @@ public:
};
};
+class _khmer_signal : public _khmer_exception
+{
+public:
+ _khmer_signal(std::string message) : _khmer_exception(message) { };
+};
+
+typedef pre_partition_info _pre_partition_info;
+
/***********************************************************************/
//
@@ -159,7 +145,7 @@ static
PyObject *
Read_get_name(khmer_Read_Object * obj, void * closure )
{
- return PyUnicode_FromString(obj->read->name.c_str()) ;
+ return PyBytes_FromString(obj->read->name.c_str()) ;
}
@@ -167,7 +153,7 @@ static
PyObject *
Read_get_sequence(khmer_Read_Object * obj, void * closure)
{
- return PyUnicode_FromString(obj->read->sequence.c_str()) ;
+ return PyBytes_FromString(obj->read->sequence.c_str()) ;
}
@@ -175,7 +161,7 @@ static
PyObject *
Read_get_quality(khmer_Read_Object * obj, void * closure)
{
- return PyUnicode_FromString(obj->read->quality.c_str()) ;
+ return PyBytes_FromString(obj->read->quality.c_str()) ;
}
@@ -183,7 +169,7 @@ static
PyObject *
Read_get_annotations(khmer_Read_Object * obj, void * closure)
{
- return PyUnicode_FromString(obj->read->annotations.c_str()) ;
+ return PyBytes_FromString(obj->read->annotations.c_str()) ;
}
@@ -349,7 +335,7 @@ _ReadParser_iternext( PyObject * self )
exc = e.what();
} catch (InvalidRead &e) {
exc = e.what();
- }
+ }
}
Py_END_ALLOW_THREADS
@@ -630,57 +616,40 @@ _PyObject_to_khmer_ReadParser( PyObject * py_object )
return ((python:: khmer_ReadParser_Object *)py_object)->parser;
}
-typedef struct {
- PyObject_HEAD
- pre_partition_info * PrePartitionInfo;
-} khmer_PrePartitionInfo_Object;
-static
-void
-khmer_PrePartitionInfo_dealloc(khmer_PrePartitionInfo_Object * obj)
-{
- delete obj->PrePartitionInfo;
- obj->PrePartitionInfo = NULL;
- Py_TYPE(obj)->tp_free((PyObject*)obj);
-}
+/***********************************************************************/
-static PyTypeObject khmer_PrePartitionInfo_Type = {
- PyVarObject_HEAD_INIT(NULL, 0) /* init & ob_size */
- "_khmer.PrePartitionInfo", /* tp_name */
- sizeof(khmer_PrePartitionInfo_Object),/* tp_basicsize */
- 0, /* tp_itemsize */
- (destructor)khmer_PrePartitionInfo_dealloc, /* tp_dealloc */
- 0, /* tp_print */
- 0, /* tp_getattr */
- 0, /* tp_setattr */
- 0, /* tp_compare */
- 0, /* tp_repr */
- 0, /* tp_as_number */
- 0, /* tp_as_sequence */
- 0, /* tp_as_mapping */
- 0, /* tp_hash */
- 0, /* tp_call */
- 0, /* tp_str */
- 0, /* tp_getattro */
- 0, /* tp_setattro */
- 0, /* tp_as_buffer */
- Py_TPFLAGS_DEFAULT, /* tp_flags */
- "Stores a k-kmer and a set of tagged seen k-mers.", /* tp_doc */
-};
+//
+// KCountingHash object
+//
+void free_pre_partition_info(void * p)
+{
+ _pre_partition_info * ppi = (_pre_partition_info *) p;
+ delete ppi;
+}
-/***********************************************************************/
+void free_subset_partition_info(void * p)
+{
+ SubsetPartition * subset_p = (SubsetPartition *) p;
+ delete subset_p;
+}
typedef struct {
PyObject_HEAD
- Hashtable * hashtable;
-} khmer_KHashtable_Object;
+ CountingHash * counting;
+} khmer_KCountingHash_Object;
typedef struct {
PyObject_HEAD
SubsetPartition * subset;
} khmer_KSubsetPartition_Object;
+typedef struct {
+ PyObject_HEAD
+ Hashbits * hashbits;
+} khmer_KHashbits_Object;
+
static void khmer_subset_dealloc(khmer_KSubsetPartition_Object * obj);
static PyTypeObject khmer_KSubsetPartition_Type = {
@@ -708,78 +677,81 @@ static PyTypeObject khmer_KSubsetPartition_Type = {
};
typedef struct {
- khmer_KHashtable_Object khashtable;
- Hashbits * hashbits;
-} khmer_KHashbits_Object;
+ PyObject_HEAD
+ ReadAligner * aligner;
+} khmer_ReadAligner_Object;
-static void khmer_hashbits_dealloc(khmer_KHashbits_Object * obj);
-static PyObject* khmer_hashbits_new(PyTypeObject * type, PyObject * args,
- PyObject * kwds);
+static void khmer_counting_dealloc(khmer_KCountingHash_Object * obj);
-static PyTypeObject khmer_KHashbits_Type
-CPYCHECKER_TYPE_OBJECT_FOR_TYPEDEF("khmer_KHashbits_Object")
-= {
- PyVarObject_HEAD_INIT(NULL, 0) /* init & ob_size */
- "_khmer.Hashbits", /* tp_name */
- sizeof(khmer_KHashbits_Object), /* tp_basicsize */
- 0, /* tp_itemsize */
- (destructor)khmer_hashbits_dealloc, /*tp_dealloc*/
- 0, /*tp_print*/
- 0, /*tp_getattr*/
- 0, /*tp_setattr*/
- 0, /*tp_compare*/
- 0, /*tp_repr*/
- 0, /*tp_as_number*/
- 0, /*tp_as_sequence*/
- 0, /*tp_as_mapping*/
- 0, /*tp_hash */
- 0, /*tp_call*/
- 0, /*tp_str*/
- 0, /*tp_getattro*/
- 0, /*tp_setattro*/
- 0, /*tp_as_buffer*/
- Py_TPFLAGS_DEFAULT | Py_TPFLAGS_BASETYPE, /*tp_flags*/
- "hashbits object", /* tp_doc */
- 0, /* tp_traverse */
- 0, /* tp_clear */
- 0, /* tp_richcompare */
- 0, /* tp_weaklistoffset */
- 0, /* tp_iter */
- 0, /* tp_iternext */
- 0, /* tp_methods */
- 0, /* tp_members */
- 0, /* tp_getset */
- 0, /* tp_base */
- 0, /* tp_dict */
- 0, /* tp_descr_get */
- 0, /* tp_descr_set */
- 0, /* tp_dictoffset */
- 0, /* tp_init */
- 0, /* tp_alloc */
- khmer_hashbits_new, /* tp_new */
-};
+static
+PyObject *
+hash_abundance_distribution(khmer_KCountingHash_Object * me, PyObject * args);
+
+static
+PyObject *
+hash_abundance_distribution_with_reads_parser(khmer_KCountingHash_Object * me,
+ PyObject * args);
+
+static
+PyObject *
+hash_get_raw_tables(khmer_KCountingHash_Object * self, PyObject * args)
+{
+ CountingHash * counting = self->counting;
+
+ khmer::Byte ** table_ptrs = counting->get_raw_tables();
+ std::vector<HashIntoType> sizes = counting->get_tablesizes();
+
+ PyObject * raw_tables = PyList_New(sizes.size());
+ for (unsigned int i=0; i<sizes.size(); ++i) {
+ PyObject * buf = PyBuffer_FromMemory(table_ptrs[i], sizes[i]);
+ if(!PyBuffer_Check(buf)) {
+ return NULL;
+ }
+ PyList_SET_ITEM(raw_tables, i, buf);
+ }
+
+ return raw_tables;
+}
+
+static
+PyObject *
+hash_set_use_bigcount(khmer_KCountingHash_Object * me, PyObject * args)
+{
+ CountingHash * counting = me->counting;
+
+ PyObject * x;
+ if (!PyArg_ParseTuple(args, "O", &x)) {
+ return NULL;
+ }
+ int setme = PyObject_IsTrue(x);
+ if (setme < 0) {
+ return NULL;
+ }
+ counting->set_use_bigcount((bool)setme);
+ Py_RETURN_NONE;
+}
static
PyObject *
-hashtable_get_ksize(khmer_KHashtable_Object * me, PyObject * args)
+hash_get_use_bigcount(khmer_KCountingHash_Object * me, PyObject * args)
{
- Hashtable * hashtable = me->hashtable;
+ CountingHash * counting = me->counting;
if (!PyArg_ParseTuple(args, "")) {
return NULL;
}
- unsigned int k = hashtable->ksize();
+ bool val = counting->get_use_bigcount();
- return PyLong_FromLong(k);
+ return PyBool_FromLong((int)val);
}
static
PyObject *
-hashtable_n_occupied(khmer_KHashtable_Object * me, PyObject * args)
+hash_n_occupied(khmer_KCountingHash_Object * me, PyObject * args)
{
- Hashtable * hashtable = me->hashtable;
+ CountingHash * counting = me->counting;
HashIntoType start = 0, stop = 0;
@@ -787,40 +759,40 @@ hashtable_n_occupied(khmer_KHashtable_Object * me, PyObject * args)
return NULL;
}
- HashIntoType n = hashtable->n_occupied(start, stop);
+ HashIntoType n = counting->n_occupied(start, stop);
return PyLong_FromUnsignedLongLong(n);
}
static
PyObject *
-hashtable_n_unique_kmers(khmer_KHashtable_Object * me, PyObject * args)
+hash_n_unique_kmers(khmer_KCountingHash_Object * me, PyObject * args)
{
- Hashtable * hashtable = me->hashtable;
+ CountingHash * counting = me->counting;
- HashIntoType n = hashtable->n_unique_kmers();
+ HashIntoType n = counting->n_unique_kmers();
return PyLong_FromUnsignedLongLong(n);
}
static
PyObject *
-hashtable_n_entries(khmer_KHashtable_Object * me, PyObject * args)
+hash_n_entries(khmer_KCountingHash_Object * me, PyObject * args)
{
- Hashtable * hashtable = me->hashtable;
+ CountingHash * counting = me->counting;
if (!PyArg_ParseTuple(args, "")) {
return NULL;
}
- return PyLong_FromUnsignedLongLong(hashtable->n_entries());
+ return PyLong_FromUnsignedLongLong(counting->n_entries());
}
static
PyObject *
-hashtable_count(khmer_KHashtable_Object * me, PyObject * args)
+hash_count(khmer_KCountingHash_Object * me, PyObject * args)
{
- Hashtable * hashtable = me->hashtable;
+ CountingHash * counting = me->counting;
const char * kmer;
@@ -828,22 +800,41 @@ hashtable_count(khmer_KHashtable_Object * me, PyObject * args)
return NULL;
}
- if (strlen(kmer) != hashtable->ksize()) {
+ if (strlen(kmer) != counting->ksize()) {
PyErr_SetString(PyExc_ValueError,
"k-mer length must be the same as the hashtable k-size");
return NULL;
}
- hashtable->count(kmer);
+ counting->count(kmer);
return PyLong_FromLong(1);
}
static
PyObject *
-hashtable_consume_fasta(khmer_KHashtable_Object * me, PyObject * args)
+hash_output_fasta_kmer_pos_freq(khmer_KCountingHash_Object * me,
+ PyObject * args)
+{
+ CountingHash * counting = me->counting;
+
+ const char * infile;
+ const char * outfile;
+
+ if (!PyArg_ParseTuple(args, "ss", &infile, &outfile)) {
+ return NULL;
+ }
+
+ counting->output_fasta_kmer_pos_freq(infile, outfile);
+
+ return PyLong_FromLong(0);
+}
+
+static
+PyObject *
+hash_consume_fasta(khmer_KCountingHash_Object * me, PyObject * args)
{
- Hashtable * hashtable = me->hashtable;
+ CountingHash * counting = me->counting;
const char * filename;
@@ -855,7 +846,10 @@ hashtable_consume_fasta(khmer_KHashtable_Object * me, PyObject * args)
unsigned long long n_consumed = 0;
unsigned int total_reads = 0;
try {
- hashtable->consume_fasta(filename, total_reads, n_consumed);
+ counting->consume_fasta(filename, total_reads, n_consumed);
+ } catch (_khmer_signal &e) {
+ PyErr_SetString(PyExc_IOError, e.get_message().c_str());
+ return NULL;
} catch (khmer_file_exception &e) {
PyErr_SetString(PyExc_IOError, e.what());
return NULL;
@@ -866,10 +860,10 @@ hashtable_consume_fasta(khmer_KHashtable_Object * me, PyObject * args)
static
PyObject *
-hashtable_consume_fasta_with_reads_parser(khmer_KHashtable_Object * me,
- PyObject * args)
+hash_consume_fasta_with_reads_parser(khmer_KCountingHash_Object * me,
+ PyObject * args)
{
- Hashtable * hashtable = me->hashtable;
+ CountingHash * counting = me->counting;
PyObject * rparser_obj = NULL;
@@ -880,21 +874,32 @@ hashtable_consume_fasta_with_reads_parser(khmer_KHashtable_Object * me,
read_parsers:: IParser * rparser =
_PyObject_to_khmer_ReadParser( rparser_obj );
+ char const * exc = "";
// call the C++ function, and trap signals => Python
unsigned long long n_consumed = 0;
unsigned int total_reads = 0;
+ bool exc_raised = false;
Py_BEGIN_ALLOW_THREADS
- hashtable->consume_fasta(rparser, total_reads, n_consumed);
+ try {
+ counting->consume_fasta(rparser, total_reads, n_consumed);
+ } catch (_khmer_signal &e) {
+ exc = e.get_message().c_str();
+ exc_raised = true;
+ }
Py_END_ALLOW_THREADS
+ if (exc_raised) {
+ PyErr_SetString(PyExc_IOError, exc);
+ return NULL;
+ }
return Py_BuildValue("IK", total_reads, n_consumed);
}
static
PyObject *
-hashtable_consume(khmer_KHashtable_Object * me, PyObject * args)
+hash_consume(khmer_KCountingHash_Object * me, PyObject * args)
{
- Hashtable * hashtable = me->hashtable;
+ CountingHash * counting = me->counting;
const char * long_str;
@@ -902,375 +907,337 @@ hashtable_consume(khmer_KHashtable_Object * me, PyObject * args)
return NULL;
}
- if (strlen(long_str) < hashtable->ksize()) {
+ if (strlen(long_str) < counting->ksize()) {
PyErr_SetString(PyExc_ValueError,
"string length must >= the hashtable k-mer size");
return NULL;
}
unsigned int n_consumed;
- n_consumed = hashtable->consume_string(long_str);
+ n_consumed = counting->consume_string(long_str);
return PyLong_FromLong(n_consumed);
}
static
PyObject *
-hashtable_get(khmer_KHashtable_Object * me, PyObject * args)
+hash_get_min_count(khmer_KCountingHash_Object * me, PyObject * args)
{
- Hashtable * hashtable = me->hashtable;
+ CountingHash * counting = me->counting;
- PyObject * arg;
+ const char * long_str;
- if (!PyArg_ParseTuple(args, "O", &arg)) {
+ if (!PyArg_ParseTuple(args, "s", &long_str)) {
return NULL;
}
- unsigned long count = 0;
-
- if (PyInt_Check(arg) || PyLong_Check(arg)) {
- long pos = PyInt_AsLong(arg);
- count = hashtable->get_count((unsigned int) pos);
- } else if (PyUnicode_Check(arg)) {
- std::string s = PyBytes_AsString(PyUnicode_AsEncodedString(
- arg, "utf-8", "strict"));
- if (strlen(s.c_str()) != hashtable->ksize()) {
- PyErr_SetString(PyExc_ValueError,
- "k-mer size must equal the presence table k-mer size");
- return NULL;
- }
- count = hashtable->get_count(s.c_str());
- } else if (PyBytes_Check(arg)) {
- std::string s = PyBytes_AsString(arg);
-
- if (strlen(s.c_str()) != hashtable->ksize()) {
- PyErr_SetString(PyExc_ValueError,
- "k-mer size must equal the counting table k-mer size");
- return NULL;
- }
-
- count = hashtable->get_count(s.c_str());
- } else {
+ if (strlen(long_str) < counting->ksize()) {
PyErr_SetString(PyExc_ValueError,
- "please pass either a hash value or a string");
+ "string length must >= the hashtable k-mer size");
return NULL;
}
- return PyLong_FromLong(count);
+ BoundedCounterType c = counting->get_min_count(long_str);
+ unsigned int N = c;
+
+ return PyLong_FromLong(N);
}
static
PyObject *
-hashtable_load(khmer_KHashtable_Object * me, PyObject * args)
+hash_get_max_count(khmer_KCountingHash_Object * me, PyObject * args)
{
- Hashtable * hashtable = me->hashtable;
+ CountingHash * counting = me->counting;
- const char * filename = NULL;
+ const char * long_str;
- if (!PyArg_ParseTuple(args, "s", &filename)) {
+ if (!PyArg_ParseTuple(args, "s", &long_str)) {
return NULL;
}
- try {
- hashtable->load(filename);
- } catch (khmer_file_exception &e) {
- PyErr_SetString(PyExc_IOError, e.what());
+ if (strlen(long_str) < counting->ksize()) {
+ PyErr_SetString(PyExc_ValueError,
+ "string length must >= the hashtable k-mer size");
return NULL;
}
- Py_RETURN_NONE;
+ BoundedCounterType c = counting->get_max_count(long_str);
+ unsigned int N = c;
+
+ return PyLong_FromLong(N);
}
static
PyObject *
-hashtable_save(khmer_KHashtable_Object * me, PyObject * args)
+hash_get_median_count(khmer_KCountingHash_Object * me, PyObject * args)
{
- Hashtable * hashtable = me->hashtable;
+ CountingHash * counting = me->counting;
- const char * filename = NULL;
+ const char * long_str;
- if (!PyArg_ParseTuple(args, "s", &filename)) {
+ if (!PyArg_ParseTuple(args, "s", &long_str)) {
return NULL;
}
- try {
- hashtable->save(filename);
- } catch (khmer_file_exception &e) {
- PyErr_SetString(PyExc_IOError, e.what());
+ if (strlen(long_str) < counting->ksize()) {
+ PyErr_SetString(PyExc_ValueError,
+ "string length must >= the hashtable k-mer size");
return NULL;
}
- Py_RETURN_NONE;
+ BoundedCounterType med = 0;
+ float average = 0, stddev = 0;
+
+ counting->get_median_count(long_str, med, average, stddev);
+
+ return Py_BuildValue("iff", med, average, stddev);
}
static
PyObject *
-hashtable_get_hashsizes(khmer_KHashtable_Object * me, PyObject * args)
+hash_get_kadian_count(khmer_KCountingHash_Object * me, PyObject * args)
{
- Hashtable * hashtable = me->hashtable;
+ CountingHash * counting = me->counting;
+ const char * long_str;
+ unsigned int nk = 1;
- if (!PyArg_ParseTuple(args, "")) {
+ if (!PyArg_ParseTuple(args, "s|I", &long_str, &nk)) {
return NULL;
}
- std::vector<HashIntoType> ts = hashtable->get_tablesizes();
-
- PyObject * x = PyList_New(ts.size());
- for (size_t i = 0; i < ts.size(); i++) {
- PyList_SET_ITEM(x, i, PyLong_FromUnsignedLongLong(ts[i]));
+ if (strlen(long_str) < counting->ksize()) {
+ PyErr_SetString(PyExc_ValueError,
+ "string length must >= the hashtable k-mer size");
+ return NULL;
}
- return x;
-}
+ BoundedCounterType kad = 0;
-static
-PyObject *
-hashtable_consume_and_tag(khmer_KHashtable_Object * me, PyObject * args)
-{
- Hashtable * hashtable = me->hashtable;
-
- const char * seq;
-
- if (!PyArg_ParseTuple(args, "s", &seq)) {
- return NULL;
- }
-
- // call the C++ function, and trap signals => Python
-
- unsigned long long n_consumed = 0;
-
- // @CTB needs to normalize
- hashtable->consume_sequence_and_tag(seq, n_consumed);
+ counting->get_kadian_count(long_str, kad, nk);
- return Py_BuildValue("K", n_consumed);
+ return Py_BuildValue("i", kad);
}
static
PyObject *
-hashtable_get_tags_and_positions(khmer_KHashtable_Object * me, PyObject * args)
+hash_get(khmer_KCountingHash_Object * me, PyObject * args)
{
- Hashtable * hashtable = me->hashtable;
+ CountingHash * counting = me->counting;
- const char * seq;
+ PyObject * arg;
- if (!PyArg_ParseTuple(args, "s", &seq)) {
+ if (!PyArg_ParseTuple(args, "O", &arg)) {
return NULL;
}
- // call the C++ function, and trap signals => Python
-
- std::vector<unsigned int> posns;
- std::vector<HashIntoType> tags;
+ unsigned long count = 0;
- unsigned int pos = 1;
- KMerIterator kmers(seq, hashtable->ksize());
+ if (PyInt_Check(arg)) {
+ long pos = PyInt_AsLong(arg);
+ count = counting->get_count((unsigned int) pos);
+ } else if (PyBytes_Check(arg)) {
+ std::string s = PyBytes_AsString(arg);
- while (!kmers.done()) {
- HashIntoType kmer = kmers.next();
- if (set_contains(hashtable->all_tags, kmer)) {
- posns.push_back(pos);
- tags.push_back(kmer);
+ if (strlen(s.c_str()) != counting->ksize()) {
+ PyErr_SetString(PyExc_ValueError,
+ "k-mer size must equal the counting table k-mer size");
+ return NULL;
}
- pos++;
- }
- PyObject * posns_list = PyList_New(posns.size());
- for (size_t i = 0; i < posns.size(); i++) {
- PyObject * tup = Py_BuildValue("IK", posns[i], tags[i]);
- PyList_SET_ITEM(posns_list, i, tup);
+ count = counting->get_count(s.c_str());
}
- return posns_list;
+ return PyLong_FromLong(count);
}
static
PyObject *
-hashtable_find_all_tags_list(khmer_KHashtable_Object * me, PyObject * args)
+count_trim_on_abundance(khmer_KCountingHash_Object * me, PyObject * args)
{
- Hashtable * hashtable = me->hashtable;
-
- const char * kmer_s = NULL;
+ CountingHash * counting = me->counting;
- if (!PyArg_ParseTuple(args, "s", &kmer_s)) {
- return NULL;
- }
+ const char * seq = NULL;
+ unsigned int min_count_i = 0;
- if (strlen(kmer_s) != hashtable->ksize()) {
- PyErr_SetString(PyExc_ValueError,
- "k-mer length must equal the counting table k-mer size");
+ if (!PyArg_ParseTuple(args, "sI", &seq, &min_count_i)) {
return NULL;
}
- SeenSet tags;
-
+ unsigned long trim_at;
Py_BEGIN_ALLOW_THREADS
- HashIntoType kmer_f, kmer_r;
- _hash(kmer_s, hashtable->ksize(), kmer_f, kmer_r);
+ BoundedCounterType min_count = min_count_i;
- hashtable->partition->find_all_tags(kmer_f, kmer_r, tags,
- hashtable->all_tags);
+ trim_at = counting->trim_on_abundance(seq, min_count);
- Py_END_ALLOW_THREADS
+ Py_END_ALLOW_THREADS;
- PyObject * x = PyList_New(tags.size());
- if (x == NULL) {
+ PyObject * trim_seq = PyBytes_FromStringAndSize(seq, trim_at);
+ if (trim_seq == NULL) {
return NULL;
}
- SeenSet::iterator si;
- unsigned long long i = 0;
- for (si = tags.begin(); si != tags.end(); ++si) {
- // type K for python unsigned long long
- PyList_SET_ITEM(x, i, Py_BuildValue("K", *si));
- i++;
- }
+ PyObject * ret = Py_BuildValue("Ok", trim_seq, trim_at);
+ Py_DECREF(trim_seq);
- return x;
+ return ret;
}
static
PyObject *
-hashtable_consume_fasta_and_tag(khmer_KHashtable_Object * me, PyObject * args)
+count_trim_below_abundance(khmer_KCountingHash_Object * me, PyObject * args)
{
- Hashtable * hashtable = me->hashtable;
+ CountingHash * counting = me->counting;
- const char * filename;
+ const char * seq = NULL;
+ BoundedCounterType max_count_i = 0;
- if (!PyArg_ParseTuple(args, "s", &filename)) {
+ if (!PyArg_ParseTuple(args, "sH", &seq, &max_count_i)) {
return NULL;
}
- // call the C++ function, and trap signals => Python
+ unsigned long trim_at;
+ Py_BEGIN_ALLOW_THREADS
- unsigned long long n_consumed;
- unsigned int total_reads;
+ BoundedCounterType max_count = max_count_i;
+
+ trim_at = counting->trim_below_abundance(seq, max_count);
- hashtable->consume_fasta_and_tag(filename, total_reads, n_consumed);
+ Py_END_ALLOW_THREADS;
- return Py_BuildValue("IK", total_reads, n_consumed);
+ PyObject * trim_seq = PyBytes_FromStringAndSize(seq, trim_at);
+ if (trim_seq == NULL) {
+ return NULL;
+ }
+ PyObject * ret = Py_BuildValue("Ok", trim_seq, trim_at);
+ Py_DECREF(trim_seq);
+
+ return ret;
}
static
PyObject *
-hashtable_get_median_count(khmer_KHashtable_Object * me, PyObject * args)
+count_find_spectral_error_positions(khmer_KCountingHash_Object * me,
+ PyObject * args)
{
- Hashtable * hashtable = me->hashtable;
+ khmer::CountingHash * counting = me->counting;
- const char * long_str;
+ char * seq = NULL;
+ khmer::BoundedCounterType max_count = 0; // unsigned short int
- if (!PyArg_ParseTuple(args, "s", &long_str)) {
+ if (!PyArg_ParseTuple(args, "sH", &seq, &max_count)) {
return NULL;
}
- if (strlen(long_str) < hashtable->ksize()) {
- PyErr_SetString(PyExc_ValueError,
- "string length must >= the hashtable k-mer size");
+ std::vector<unsigned int> posns;
+
+ try {
+ posns = counting->find_spectral_error_positions(seq, max_count);
+ } catch (khmer_exception &e) {
+ PyErr_SetString(PyExc_ValueError, e.what());
return NULL;
}
- BoundedCounterType med = 0;
- float average = 0, stddev = 0;
+ Py_ssize_t posns_size = posns.size();
- hashtable->get_median_count(long_str, med, average, stddev);
+ PyObject * x = PyList_New(posns_size);
+ if (x == NULL) {
+ return NULL;
+ }
+ for (Py_ssize_t i = 0; i < posns_size; i++) {
+ PyList_SET_ITEM(x, i, PyLong_FromLong(posns[i]));
+ }
- return Py_BuildValue("iff", med, average, stddev);
+ return x;
}
static
PyObject *
-hashtable_median_at_least(khmer_KHashtable_Object * me, PyObject * args)
+hash_fasta_count_kmers_by_position(khmer_KCountingHash_Object * me,
+ PyObject * args)
{
- Hashtable * hashtable = me->hashtable;
+ CountingHash * counting = me->counting;
- const char * long_str;
- unsigned int cutoff;
+ const char * inputfile;
+ unsigned int max_read_len = 0;
+ long max_read_len_long;
+ int limit_by_count_int;
- if (!PyArg_ParseTuple(args, "sI", &long_str, &cutoff)) {
+ if (!PyArg_ParseTuple(args, "sli", &inputfile, &max_read_len_long,
+ &limit_by_count_int)) {
return NULL;
}
-
- if (strlen(long_str) < hashtable->ksize()) {
- PyErr_SetString(PyExc_ValueError,
- "string length must >= the hashtable k-mer size");
+ if (max_read_len_long < 0 || max_read_len_long >= pow(2, 32)) {
+ PyErr_SetString(
+ PyExc_ValueError,
+ "The 2nd argument must be positive and less than 2^32");
return NULL;
}
-
- if (hashtable->median_at_least(long_str, cutoff)) {
- Py_RETURN_TRUE;
+ if (limit_by_count_int < 0 || limit_by_count_int >= pow(2, 16)) {
+ PyErr_SetString(
+ PyExc_ValueError,
+ "The 3rd argument must be positive and less than 2^16");
+ return NULL;
}
- Py_RETURN_FALSE;
-
-}
+ max_read_len = (unsigned int) max_read_len_long;
-static
-PyObject *
-hashtable_n_tags(khmer_KHashtable_Object * me, PyObject * args)
-{
- Hashtable * hashtable = me->hashtable;
+ unsigned long long * counts;
+ counts = counting->fasta_count_kmers_by_position(inputfile, max_read_len,
+ (unsigned short) limit_by_count_int);
- if (!PyArg_ParseTuple(args, "")) {
+ PyObject * x = PyList_New(max_read_len);
+ if (x == NULL) {
+ delete[] counts;
return NULL;
}
- return PyLong_FromSize_t(hashtable->n_tags());
-}
-
-static
-PyObject *
-hashtable_print_stop_tags(khmer_KHashtable_Object * me, PyObject * args)
-{
- Hashtable * hashtable = me->hashtable;
-
- const char * filename = NULL;
-
- if (!PyArg_ParseTuple(args, "s", &filename)) {
- return NULL;
+ for (unsigned int i = 0; i < max_read_len; i++) {
+ int ret = PyList_SetItem(x, i, PyLong_FromUnsignedLongLong(counts[i]));
+ if (ret < 0) {
+ delete[] counts;
+ return NULL;
+ }
}
- hashtable->print_stop_tags(filename);
+ delete[] counts;
- Py_RETURN_NONE;
+ return x;
}
static
PyObject *
-hashtable_print_tagset(khmer_KHashtable_Object * me, PyObject * args)
+hash_fasta_dump_kmers_by_abundance(khmer_KCountingHash_Object * me,
+ PyObject * args)
{
- Hashtable * hashtable = me->hashtable;
+ CountingHash * counting = me->counting;
- const char * filename = NULL;
+ const char * inputfile;
+ int limit_by = 0;
- if (!PyArg_ParseTuple(args, "s", &filename)) {
+ if (!PyArg_ParseTuple(args, "si", &inputfile, &limit_by)) {
return NULL;
}
- hashtable->print_tagset(filename);
+ counting->fasta_dump_kmers_by_abundance(inputfile,
+ limit_by);
Py_RETURN_NONE;
}
static
PyObject *
-hashtable_load_stop_tags(khmer_KHashtable_Object * me, PyObject * args)
+hash_load(khmer_KCountingHash_Object * me, PyObject * args)
{
- Hashtable * hashtable = me->hashtable;
+ CountingHash * counting = me->counting;
const char * filename = NULL;
- PyObject * clear_tags_o = NULL;
- if (!PyArg_ParseTuple(args, "s|O", &filename, &clear_tags_o)) {
+ if (!PyArg_ParseTuple(args, "s", &filename)) {
return NULL;
}
- bool clear_tags = true;
- if (clear_tags_o && !PyObject_IsTrue(clear_tags_o)) {
- clear_tags = false;
- }
-
-
try {
- hashtable->load_stop_tags(filename, clear_tags);
+ counting->load(filename);
} catch (khmer_file_exception &e) {
PyErr_SetString(PyExc_IOError, e.what());
return NULL;
@@ -1279,12 +1246,11 @@ hashtable_load_stop_tags(khmer_KHashtable_Object * me, PyObject * args)
Py_RETURN_NONE;
}
-
static
PyObject *
-hashtable_save_stop_tags(khmer_KHashtable_Object * me, PyObject * args)
+hash_save(khmer_KCountingHash_Object * me, PyObject * args)
{
- Hashtable * hashtable = me->hashtable;
+ CountingHash * counting = me->counting;
const char * filename = NULL;
@@ -1293,7 +1259,7 @@ hashtable_save_stop_tags(khmer_KHashtable_Object * me, PyObject * args)
}
try {
- hashtable->save_stop_tags(filename);
+ counting->save(filename);
} catch (khmer_file_exception &e) {
PyErr_SetString(PyExc_IOError, e.what());
return NULL;
@@ -1302,291 +1268,161 @@ hashtable_save_stop_tags(khmer_KHashtable_Object * me, PyObject * args)
Py_RETURN_NONE;
}
-static PyObject * hashtable_traverse_from_tags(khmer_KHashtable_Object * me,
- PyObject * args);
-
-static PyObject * hashtable_repartition_largest_partition(
- khmer_KHashtable_Object * me,
- PyObject * args);
-
static
PyObject *
-hashtable_calc_connected_graph_size(khmer_KHashtable_Object * me,
- PyObject * args)
+hash_get_ksize(khmer_KCountingHash_Object * me, PyObject * args)
{
- Hashtable * hashtable = me->hashtable;
+ CountingHash * counting = me->counting;
- const char * _kmer;
- unsigned int max_size = 0;
- PyObject * break_on_circum_o = NULL;
- if (!PyArg_ParseTuple(args, "s|IO", &_kmer, &max_size, &break_on_circum_o)) {
+ if (!PyArg_ParseTuple(args, "")) {
return NULL;
}
- bool break_on_circum = false;
- if (break_on_circum_o && PyObject_IsTrue(break_on_circum_o)) {
- break_on_circum = true;
- }
-
- unsigned long long size = 0;
-
- Py_BEGIN_ALLOW_THREADS
- SeenSet keeper;
- hashtable->calc_connected_graph_size(_kmer, size, keeper, max_size,
- break_on_circum);
- Py_END_ALLOW_THREADS
+ unsigned int k = counting->ksize();
- return PyLong_FromUnsignedLongLong(size);
+ return PyLong_FromLong(k);
}
static
PyObject *
-hashtable_kmer_degree(khmer_KHashtable_Object * me, PyObject * args)
+hash_get_hashsizes(khmer_KCountingHash_Object * me, PyObject * args)
{
- Hashtable * hashtable = me->hashtable;
+ CountingHash * counting = me->counting;
- const char * kmer_s = NULL;
- if (!PyArg_ParseTuple(args, "s", &kmer_s)) {
+ if (!PyArg_ParseTuple(args, "")) {
return NULL;
}
- return PyLong_FromLong(hashtable->kmer_degree(kmer_s));
+ std::vector<HashIntoType> ts = counting->get_tablesizes();
+
+ PyObject * x = PyList_New(ts.size());
+ for (size_t i = 0; i < ts.size(); i++) {
+ PyList_SET_ITEM(x, i, PyLong_FromUnsignedLongLong(ts[i]));
+ }
+
+ return x;
}
static
PyObject *
-hashtable_trim_on_stoptags(khmer_KHashtable_Object * me, PyObject * args)
+hash_collect_high_abundance_kmers(khmer_KCountingHash_Object * me,
+ PyObject * args);
+
+static
+PyObject *
+hash_consume_and_tag(khmer_KCountingHash_Object * me, PyObject * args)
{
- Hashtable * hashtable = me->hashtable;
+ CountingHash * counting = me->counting;
- const char * seq = NULL;
+ const char * seq;
if (!PyArg_ParseTuple(args, "s", &seq)) {
return NULL;
}
- size_t trim_at;
- Py_BEGIN_ALLOW_THREADS
-
- trim_at = hashtable->trim_on_stoptags(seq);
-
- Py_END_ALLOW_THREADS;
+ // call the C++ function, and trap signals => Python
- PyObject * trim_seq = PyUnicode_FromStringAndSize(seq, trim_at);
- if (trim_seq == NULL) {
+ unsigned long long n_consumed = 0;
+ try {
+ // @CTB needs to normalize
+ counting->consume_sequence_and_tag(seq, n_consumed);
+ } catch (_khmer_signal &e) {
+ PyErr_SetString(PyExc_ValueError, e.get_message().c_str());
return NULL;
}
- PyObject * ret = Py_BuildValue("Ok", trim_seq, (unsigned long) trim_at);
- Py_DECREF(trim_seq);
- return ret;
+ return Py_BuildValue("K", n_consumed);
}
static
PyObject *
-hashtable_identify_stoptags_by_position(khmer_KHashtable_Object * me,
- PyObject * args)
+hash_get_tags_and_positions(khmer_KCountingHash_Object * me, PyObject * args)
{
- Hashtable * hashtable = me->hashtable;
+ CountingHash * counting = me->counting;
- const char * seq = NULL;
+ const char * seq;
if (!PyArg_ParseTuple(args, "s", &seq)) {
return NULL;
}
- std::vector<unsigned int> posns;
- Py_BEGIN_ALLOW_THREADS
-
- hashtable->identify_stop_tags_by_position(seq, posns);
-
- Py_END_ALLOW_THREADS;
-
- PyObject * x = PyList_New(posns.size());
-
- for (unsigned int i = 0; i < posns.size(); i++) {
- PyList_SET_ITEM(x, i, Py_BuildValue("I", posns[i]));
- }
-
- return x;
-}
-
-static
-PyObject *
-hashtable_do_subset_partition(khmer_KHashtable_Object * me, PyObject * args)
-{
- Hashtable * hashtable = me->hashtable;
-
- HashIntoType start_kmer = 0, end_kmer = 0;
- PyObject * break_on_stop_tags_o = NULL;
- PyObject * stop_big_traversals_o = NULL;
-
- if (!PyArg_ParseTuple(args, "|KKOO", &start_kmer, &end_kmer,
- &break_on_stop_tags_o,
- &stop_big_traversals_o)) {
- return NULL;
- }
-
- bool break_on_stop_tags = false;
- if (break_on_stop_tags_o && PyObject_IsTrue(break_on_stop_tags_o)) {
- break_on_stop_tags = true;
- }
- bool stop_big_traversals = false;
- if (stop_big_traversals_o && PyObject_IsTrue(stop_big_traversals_o)) {
- stop_big_traversals = true;
- }
-
- SubsetPartition * subset_p = NULL;
- try {
- Py_BEGIN_ALLOW_THREADS
- subset_p = new SubsetPartition(hashtable);
- subset_p->do_partition(start_kmer, end_kmer, break_on_stop_tags,
- stop_big_traversals);
- Py_END_ALLOW_THREADS
- } catch (std::bad_alloc &e) {
- return PyErr_NoMemory();
- }
-
- khmer_KSubsetPartition_Object * subset_obj = (khmer_KSubsetPartition_Object *)\
- PyObject_New(khmer_KSubsetPartition_Object, &khmer_KSubsetPartition_Type);
- subset_obj->subset = subset_p;
+ // call the C++ function, and trap signals => Python
- return (PyObject *)subset_obj;
-}
+ std::vector<unsigned int> posns;
+ std::vector<HashIntoType> tags;
-static
-PyObject *
-hashtable_join_partitions_by_path(khmer_KHashtable_Object * me, PyObject * args)
-{
- Hashtable * hashtable = me->hashtable;
+ unsigned int pos = 1;
+ KMerIterator kmers(seq, counting->ksize());
- const char * sequence = NULL;
- if (!PyArg_ParseTuple(args, "s", &sequence)) {
- return NULL;
+ while (!kmers.done()) {
+ HashIntoType kmer = kmers.next();
+ if (set_contains(counting->all_tags, kmer)) {
+ posns.push_back(pos);
+ tags.push_back(kmer);
+ }
+ pos++;
}
- hashtable->partition->join_partitions_by_path(sequence);
-
- Py_RETURN_NONE;
-}
-
-static
-PyObject *
-hashtable_merge_subset(khmer_KHashtable_Object * me, PyObject * args)
-{
- Hashtable * hashtable = me->hashtable;
-
- khmer_KSubsetPartition_Object * subset_obj;
- if (!PyArg_ParseTuple(args, "O!", &khmer_KSubsetPartition_Type, &subset_obj)) {
- return NULL;
+ PyObject * posns_list = PyList_New(posns.size());
+ for (size_t i = 0; i < posns.size(); i++) {
+ PyObject * tup = Py_BuildValue("IK", posns[i], tags[i]);
+ PyList_SET_ITEM(posns_list, i, tup);
}
- SubsetPartition * subset_p;
- subset_p = subset_obj->subset;
-
- hashtable->partition->merge(subset_p);
- Py_RETURN_NONE;
+ return posns_list;
}
static
PyObject *
-hashtable_merge_from_disk(khmer_KHashtable_Object * me, PyObject * args)
+hash_find_all_tags_list(khmer_KCountingHash_Object * me, PyObject * args)
{
- Hashtable * hashtable = me->hashtable;
+ CountingHash * counting = me->counting;
- const char * filename = NULL;
- if (!PyArg_ParseTuple(args, "s", &filename)) {
- return NULL;
- }
+ const char * kmer_s = NULL;
- try {
- hashtable->partition->merge_from_disk(filename);
- } catch (khmer_file_exception &e) {
- PyErr_SetString(PyExc_IOError, e.what());
+ if (!PyArg_ParseTuple(args, "s", &kmer_s)) {
return NULL;
}
- Py_RETURN_NONE;
-}
-
-static
-PyObject *
-hashtable_consume_fasta_and_tag_with_reads_parser(khmer_KHashtable_Object * me,
- PyObject * args)
-{
- Hashtable * hashtable = me->hashtable;
-
- python::khmer_ReadParser_Object * rparser_obj = NULL;
-
- if (!PyArg_ParseTuple( args, "O!", &python::khmer_ReadParser_Type,
- &rparser_obj)) {
+ if (strlen(kmer_s) != counting->ksize()) {
+ PyErr_SetString(PyExc_ValueError,
+ "k-mer length must equal the counting table k-mer size");
return NULL;
}
- read_parsers:: IParser * rparser = rparser_obj-> parser;
+ SeenSet tags;
- // call the C++ function, and trap signals => Python
- unsigned long long n_consumed = 0;
- unsigned int total_reads = 0;
- char const * exc = NULL;
Py_BEGIN_ALLOW_THREADS
- try {
- hashtable->consume_fasta_and_tag(
- rparser, total_reads, n_consumed
- );
- } catch (khmer::read_parsers::NoMoreReadsAvailable &e) {
- exc = e.what();
- }
- Py_END_ALLOW_THREADS
- if (exc != NULL) {
- PyErr_SetString(PyExc_IOError, exc);
- return NULL;
- }
-
- return Py_BuildValue("IK", total_reads, n_consumed);
-}
-
-static PyObject * hashtable_consume_fasta_and_traverse(
- khmer_KHashtable_Object * me,
- PyObject * args);
+ HashIntoType kmer_f, kmer_r;
+ _hash(kmer_s, counting->ksize(), kmer_f, kmer_r);
-static
-PyObject *
-hashtable_consume_fasta_and_tag_with_stoptags(khmer_KHashtable_Object * me,
- PyObject * args)
-{
- Hashtable * hashtable = me->hashtable;
+ counting->partition->find_all_tags(kmer_f, kmer_r, tags,
+ counting->all_tags);
- const char * filename;
+ Py_END_ALLOW_THREADS
- if (!PyArg_ParseTuple(args, "s", &filename)) {
+ PyObject * x = PyList_New(tags.size());
+ if (x == NULL) {
return NULL;
}
-
- // call the C++ function, and trap signals => Python
-
- unsigned long long n_consumed;
- unsigned int total_reads;
-
- try {
- hashtable->consume_fasta_and_tag_with_stoptags(filename,
- total_reads, n_consumed);
- } catch (khmer_file_exception &e) {
- PyErr_SetString(PyExc_IOError, e.what());
- return NULL;
+ SeenSet::iterator si;
+ unsigned long long i = 0;
+ for (si = tags.begin(); si != tags.end(); ++si) {
+ // type K for python unsigned long long
+ PyList_SET_ITEM(x, i, Py_BuildValue("K", *si));
+ i++;
}
- return Py_BuildValue("IK", total_reads, n_consumed);
+ return x;
}
static
PyObject *
-hashtable_consume_partitioned_fasta(khmer_KHashtable_Object * me,
- PyObject * args)
+hash_consume_fasta_and_tag(khmer_KCountingHash_Object * me, PyObject * args)
{
- Hashtable * hashtable = me->hashtable;
+ CountingHash * counting = me->counting;
const char * filename;
@@ -1600,9 +1436,9 @@ hashtable_consume_partitioned_fasta(khmer_KHashtable_Object * me,
unsigned int total_reads;
try {
- hashtable->consume_partitioned_fasta(filename, total_reads, n_consumed);
- } catch (khmer_file_exception &e) {
- PyErr_SetString(PyExc_IOError, e.what());
+ counting->consume_fasta_and_tag(filename, total_reads, n_consumed);
+ } catch (_khmer_signal &e) {
+ PyErr_SetString(PyExc_IOError, e.get_message().c_str());
return NULL;
}
@@ -1611,245 +1447,887 @@ hashtable_consume_partitioned_fasta(khmer_KHashtable_Object * me,
static
PyObject *
-hashtable_find_all_tags(khmer_KHashtable_Object * me, PyObject * args)
+hash_do_subset_partition_with_abundance(khmer_KCountingHash_Object * me,
+ PyObject * args)
{
- Hashtable * hashtable = me->hashtable;
+ CountingHash * counting = me->counting;
- const char * kmer_s = NULL;
+ HashIntoType start_kmer = 0, end_kmer = 0;
+ PyObject * break_on_stop_tags_o = NULL;
+ PyObject * stop_big_traversals_o = NULL;
+ BoundedCounterType min_count, max_count;
- if (!PyArg_ParseTuple(args, "s", &kmer_s)) {
+ if (!PyArg_ParseTuple(args, "HH|KKOO",
+ &min_count, &max_count,
+ &start_kmer, &end_kmer,
+ &break_on_stop_tags_o,
+ &stop_big_traversals_o)) {
return NULL;
}
- if (strlen(kmer_s) != hashtable->ksize()) {
- PyErr_SetString( PyExc_ValueError,
- "k-mer size must equal the k-mer size of the presence table");
- return NULL;
+ bool break_on_stop_tags = false;
+ if (break_on_stop_tags_o && PyObject_IsTrue(break_on_stop_tags_o)) {
+ break_on_stop_tags = true;
+ }
+ bool stop_big_traversals = false;
+ if (stop_big_traversals_o && PyObject_IsTrue(stop_big_traversals_o)) {
+ stop_big_traversals = true;
}
- pre_partition_info * ppi = NULL;
-
- Py_BEGIN_ALLOW_THREADS
-
- HashIntoType kmer, kmer_f, kmer_r;
- kmer = _hash(kmer_s, hashtable->ksize(), kmer_f, kmer_r);
-
+ SubsetPartition * subset_p = NULL;
try {
- ppi = new pre_partition_info(kmer);
+ Py_BEGIN_ALLOW_THREADS
+ subset_p = new SubsetPartition(counting);
+ subset_p->do_partition_with_abundance(start_kmer, end_kmer,
+ min_count, max_count,
+ break_on_stop_tags,
+ stop_big_traversals);
+ Py_END_ALLOW_THREADS
+ } catch (_khmer_signal &e) {
+ return NULL;
} catch (std::bad_alloc &e) {
return PyErr_NoMemory();
}
- hashtable->partition->find_all_tags(kmer_f, kmer_r, ppi->tagged_kmers,
- hashtable->all_tags);
- hashtable->add_kmer_to_tags(kmer);
-
- Py_END_ALLOW_THREADS
-
- khmer_PrePartitionInfo_Object * ppi_obj = (khmer_PrePartitionInfo_Object *) \
- PyObject_New(khmer_PrePartitionInfo_Object, &khmer_PrePartitionInfo_Type);
- ppi_obj->PrePartitionInfo = ppi;
-
- return (PyObject*)ppi_obj;
-}
-
-static
-PyObject *
-hashtable_assign_partition_id(khmer_KHashtable_Object * me, PyObject * args)
-{
- Hashtable * hashtable = me->hashtable;
+ khmer_KSubsetPartition_Object * subset_obj = (khmer_KSubsetPartition_Object *)\
+ PyObject_New(khmer_KSubsetPartition_Object, &khmer_KSubsetPartition_Type);
- khmer_PrePartitionInfo_Object * ppi_obj;
- if (!PyArg_ParseTuple(args, "O!", &khmer_PrePartitionInfo_Type, &ppi_obj)) {
+ if (subset_obj == NULL) {
+ delete subset_p;
return NULL;
}
- pre_partition_info * ppi;
- ppi = ppi_obj->PrePartitionInfo;
-
- PartitionID p;
- p = hashtable->partition->assign_partition_id(ppi->kmer,
- ppi->tagged_kmers);
+ subset_obj->subset = subset_p;
- return PyLong_FromLong(p);
+ return (PyObject *) subset_obj;
}
-static
-PyObject *
-hashtable_add_tag(khmer_KHashtable_Object * me, PyObject * args)
-{
- Hashtable * hashtable = me->hashtable;
-
- const char * kmer_s = NULL;
- if (!PyArg_ParseTuple(args, "s", &kmer_s)) {
- return NULL;
- }
-
- HashIntoType kmer = _hash(kmer_s, hashtable->ksize());
- hashtable->add_tag(kmer);
+static PyMethodDef khmer_counting_methods[] = {
+ {
+ "ksize",
+ (PyCFunction)hash_get_ksize,
+ METH_VARARGS,
+ ""
+ },
+ { "hashsizes", (PyCFunction)hash_get_hashsizes, METH_VARARGS, "" },
+ { "set_use_bigcount", (PyCFunction)hash_set_use_bigcount, METH_VARARGS, "" },
+ { "get_use_bigcount", (PyCFunction)hash_get_use_bigcount, METH_VARARGS, "" },
+ { "n_unique_kmers", (PyCFunction)hash_n_unique_kmers, METH_VARARGS, "Count the number of unique kmers" },
+ { "n_occupied", (PyCFunction)hash_n_occupied, METH_VARARGS, "Count the number of occupied bins" },
+ { "n_entries", (PyCFunction)hash_n_entries, METH_VARARGS, "" },
+ { "count", (PyCFunction)hash_count, METH_VARARGS, "Count the given kmer" },
+ { "consume", (PyCFunction)hash_consume, METH_VARARGS, "Count all k-mers in the given string" },
+ { "consume_fasta", (PyCFunction)hash_consume_fasta, METH_VARARGS, "Count all k-mers in a given file" },
+ {
+ "consume_fasta_with_reads_parser", (PyCFunction)hash_consume_fasta_with_reads_parser,
+ METH_VARARGS, "Count all k-mers using a given reads parser"
+ },
+ { "output_fasta_kmer_pos_freq", (PyCFunction)hash_output_fasta_kmer_pos_freq, METH_VARARGS, "" },
+ { "get", (PyCFunction)hash_get, METH_VARARGS, "Get the count for the given k-mer" },
+ {
+ "get_raw_tables", (PyCFunction)hash_get_raw_tables,
+ METH_VARARGS, "Get a list of the raw tables as memoryview objects"
+ },
+ { "get_min_count", (PyCFunction)hash_get_min_count, METH_VARARGS, "Get the smallest count of all the k-mers in the string" },
+ { "get_max_count", (PyCFunction)hash_get_max_count, METH_VARARGS, "Get the largest count of all the k-mers in the string" },
+ { "get_median_count", (PyCFunction)hash_get_median_count, METH_VARARGS, "Get the median, average, and stddev of the k-mer counts in the string" },
+ { "get_kadian_count", (PyCFunction)hash_get_kadian_count, METH_VARARGS, "Get the kadian (abundance of k-th rank-ordered k-mer) of the k-mer counts in the string" },
+ { "trim_on_abundance", (PyCFunction)count_trim_on_abundance, METH_VARARGS, "Trim on >= abundance" },
+ { "trim_below_abundance", (PyCFunction)count_trim_below_abundance, METH_VARARGS, "Trim on >= abundance" },
+ { "find_spectral_error_positions", (PyCFunction)count_find_spectral_error_positions, METH_VARARGS, "Identify positions of low-abundance k-mers" },
+ { "abundance_distribution", (PyCFunction)hash_abundance_distribution, METH_VARARGS, "" },
+ { "abundance_distribution_with_reads_parser", (PyCFunction)hash_abundance_distribution_with_reads_parser, METH_VARARGS, "" },
+ { "fasta_count_kmers_by_position", (PyCFunction)hash_fasta_count_kmers_by_position, METH_VARARGS, "" },
+ { "fasta_dump_kmers_by_abundance", (PyCFunction)hash_fasta_dump_kmers_by_abundance, METH_VARARGS, "" },
+ { "load", (PyCFunction)hash_load, METH_VARARGS, "" },
+ { "save", (PyCFunction)hash_save, METH_VARARGS, "" },
+ {
+ "collect_high_abundance_kmers", (PyCFunction)hash_collect_high_abundance_kmers,
+ METH_VARARGS, ""
+ },
+ { "consume_and_tag", (PyCFunction)hash_consume_and_tag, METH_VARARGS, "Consume a sequence and tag it" },
+ { "get_tags_and_positions", (PyCFunction)hash_get_tags_and_positions, METH_VARARGS, "Retrieve tags and their positions in a sequence." },
+ { "find_all_tags_list", (PyCFunction)hash_find_all_tags_list, METH_VARARGS, "Find all tags within range of the given k-mer, return as list" },
+ { "consume_fasta_and_tag", (PyCFunction)hash_consume_fasta_and_tag, METH_VARARGS, "Count all k-mers in a given file" },
+ { "do_subset_partition_with_abundance", (PyCFunction)hash_do_subset_partition_with_abundance, METH_VARARGS, "" },
+ {NULL, NULL, 0, NULL} /* sentinel */
+};
+
+static PyObject* _new_counting_hash(PyTypeObject * type, PyObject * args,
+ PyObject * kwds);
+
+static PyTypeObject khmer_KCountingHash_Type
+CPYCHECKER_TYPE_OBJECT_FOR_TYPEDEF("khmer_KCountingHash_Object")
+= {
+ PyVarObject_HEAD_INIT(NULL, 0) /* init & ob_size */
+ "_khmer.KCountingHash", /*tp_name*/
+ sizeof(khmer_KCountingHash_Object), /*tp_basicsize*/
+ 0, /*tp_itemsize*/
+ (destructor)khmer_counting_dealloc, /*tp_dealloc*/
+ 0, /*tp_print*/
+ 0, /*tp_getattr*/
+ 0, /*tp_setattr*/
+ 0, /*tp_compare*/
+ 0, /*tp_repr*/
+ 0, /*tp_as_number*/
+ 0, /*tp_as_sequence*/
+ 0, /*tp_as_mapping*/
+ 0, /*tp_hash */
+ 0, /*tp_call*/
+ 0, /*tp_str*/
+ 0, /*tp_getattro*/
+ 0, /*tp_setattro*/
+ 0, /*tp_as_buffer*/
+ Py_TPFLAGS_DEFAULT, /*tp_flags*/
+ "counting hash object", /* tp_doc */
+ 0, /* tp_traverse */
+ 0, /* tp_clear */
+ 0, /* tp_richcompare */
+ 0, /* tp_weaklistoffset */
+ 0, /* tp_iter */
+ 0, /* tp_iternext */
+ khmer_counting_methods, /* tp_methods */
+ 0, /* tp_members */
+ 0, /* tp_getset */
+ 0, /* tp_base */
+ 0, /* tp_dict */
+ 0, /* tp_descr_get */
+ 0, /* tp_descr_set */
+ 0, /* tp_dictoffset */
+ 0, /* tp_init */
+ 0, /* tp_alloc */
+ _new_counting_hash, /* tp_new */
+};
+
+#define is_counting_obj(v) (Py_TYPE(v) == &khmer_KCountingHash_Type)
+
+//
+// new_hashtable
+//
+
+static PyObject* new_hashtable(PyObject * self, PyObject * args)
+{
+ unsigned int k = 0;
+ unsigned long long size = 0;
+
+ if (!PyArg_ParseTuple(args, "IK", &k, &size)) {
+ return NULL;
+ }
+
+ khmer_KCountingHash_Object * kcounting_obj = (khmer_KCountingHash_Object *) \
+ PyObject_New(khmer_KCountingHash_Object, &khmer_KCountingHash_Type);
+
+ if (kcounting_obj == NULL) {
+ return NULL;
+ }
+
+ try {
+ kcounting_obj->counting = new CountingHash(k, size);
+ } catch (std::bad_alloc &e) {
+ return PyErr_NoMemory();
+ }
+
+ return (PyObject *) kcounting_obj;
+}
+
+//
+// new_counting_hash
+//
+
+static PyObject* _new_counting_hash(PyTypeObject * type, PyObject * args,
+ PyObject * kwds)
+{
+ khmer_KCountingHash_Object * self;
+
+ self = (khmer_KCountingHash_Object *)type->tp_alloc(type, 0);
+
+ if (self != NULL) {
+ WordLength k = 0;
+ PyListObject * sizes_list_o = NULL;
+
+ if (!PyArg_ParseTuple(args, "bO!", &k, &PyList_Type, &sizes_list_o)) {
+ Py_DECREF(self);
+ return NULL;
+ }
+
+ std::vector<HashIntoType> sizes;
+ Py_ssize_t sizes_list_o_length = PyList_GET_SIZE(sizes_list_o);
+ if (sizes_list_o_length == -1) {
+ Py_DECREF(self);
+ PyErr_SetString(PyExc_ValueError, "error with hashtable primes!");
+ return NULL;
+ }
+ for (Py_ssize_t i = 0; i < sizes_list_o_length; i++) {
+ PyObject * size_o = PyList_GET_ITEM(sizes_list_o, i);
+ if (PyLong_Check(size_o)) {
+ sizes.push_back((HashIntoType) PyLong_AsUnsignedLongLong(size_o));
+ } else if (PyInt_Check(size_o)) {
+ sizes.push_back((HashIntoType) PyInt_AsLong(size_o));
+ } else if (PyFloat_Check(size_o)) {
+ sizes.push_back((HashIntoType) PyFloat_AS_DOUBLE(size_o));
+ } else {
+ Py_DECREF(self);
+ PyErr_SetString(PyExc_TypeError,
+ "2nd argument must be a list of ints, longs, or floats");
+ return NULL;
+ }
+ }
+
+ try {
+ self->counting = new CountingHash(k, sizes);
+ } catch (std::bad_alloc &e) {
+ return PyErr_NoMemory();
+ }
+ }
+
+ return (PyObject *) self;
+}
+
+//
+// hashbits stuff
+//
+
+static void khmer_hashbits_dealloc(khmer_KHashbits_Object * obj);
+static PyObject* khmer_hashbits_new(PyTypeObject * type, PyObject * args,
+ PyObject * kwds);
+static int khmer_hashbits_init(khmer_KHashbits_Object * self, PyObject * args,
+ PyObject * kwds);
+
+static PyTypeObject khmer_KHashbits_Type
+CPYCHECKER_TYPE_OBJECT_FOR_TYPEDEF("khmer_KHashbits_Object")
+= {
+ PyVarObject_HEAD_INIT(NULL, 0) /* init & ob_size */
+ "_khmer.Hashbits", /* tp_name */
+ sizeof(khmer_KHashbits_Object), /* tp_basicsize */
+ 0, /* tp_itemsize */
+ (destructor)khmer_hashbits_dealloc, /*tp_dealloc*/
+ 0, /*tp_print*/
+ 0, /*tp_getattr*/
+ 0, /*tp_setattr*/
+ 0, /*tp_compare*/
+ 0, /*tp_repr*/
+ 0, /*tp_as_number*/
+ 0, /*tp_as_sequence*/
+ 0, /*tp_as_mapping*/
+ 0, /*tp_hash */
+ 0, /*tp_call*/
+ 0, /*tp_str*/
+ 0, /*tp_getattro*/
+ 0, /*tp_setattro*/
+ 0, /*tp_as_buffer*/
+ Py_TPFLAGS_DEFAULT | Py_TPFLAGS_BASETYPE, /*tp_flags*/
+ "hashbits object", /* tp_doc */
+ 0, /* tp_traverse */
+ 0, /* tp_clear */
+ 0, /* tp_richcompare */
+ 0, /* tp_weaklistoffset */
+ 0, /* tp_iter */
+ 0, /* tp_iternext */
+ 0, /* tp_methods */
+ 0, /* tp_members */
+ 0, /* tp_getset */
+ 0, /* tp_base */
+ 0, /* tp_dict */
+ 0, /* tp_descr_get */
+ 0, /* tp_descr_set */
+ 0, /* tp_dictoffset */
+ (initproc)khmer_hashbits_init, /* tp_init */
+ 0, /* tp_alloc */
+ khmer_hashbits_new, /* tp_new */
+};
+
+static
+PyObject *
+hash_abundance_distribution_with_reads_parser(khmer_KCountingHash_Object * me,
+ PyObject * args)
+{
+ CountingHash * counting = me->counting;
+
+ khmer :: python :: khmer_ReadParser_Object * rparser_obj = NULL;
+ khmer_KHashbits_Object *tracking_obj = NULL;
+
+ if (!PyArg_ParseTuple(args, "O!O!", &python::khmer_ReadParser_Type,
+ &rparser_obj, &khmer_KHashbits_Type, &tracking_obj)) {
+ return NULL;
+ }
+
+ read_parsers:: IParser * rparser = rparser_obj->parser;
+ Hashbits * hashbits = tracking_obj->hashbits;
+
+ HashIntoType * dist = NULL;
+
+ Py_BEGIN_ALLOW_THREADS
+ dist = counting->abundance_distribution(rparser, hashbits);
+ Py_END_ALLOW_THREADS
+
+ PyObject * x = PyList_New(MAX_BIGCOUNT + 1);
+ if (x == NULL) {
+ delete[] dist;
+ return NULL;
+ }
+ for (int i = 0; i < MAX_BIGCOUNT + 1; i++) {
+ PyList_SET_ITEM(x, i, PyLong_FromUnsignedLongLong(dist[i]));
+ }
+
+ delete[] dist;
+ return x;
+}
+
+static
+PyObject *
+hash_abundance_distribution(khmer_KCountingHash_Object * me, PyObject * args)
+{
+ CountingHash * counting = me->counting;
+
+ const char * filename = NULL;
+ khmer_KHashbits_Object * tracking_obj = NULL;
+ if (!PyArg_ParseTuple(args, "sO!", &filename, &khmer_KHashbits_Type,
+ &tracking_obj)) {
+ return NULL;
+ }
+
+ Hashbits * hashbits = tracking_obj->hashbits;
+ HashIntoType * dist;
+
+ char const * result = "";
+ bool exception = false;
+ Py_BEGIN_ALLOW_THREADS
+ try {
+ dist = counting->abundance_distribution(filename, hashbits);
+ } catch (khmer_file_exception &e) {
+ exception = true;
+ result = e.what();
+ }
+ Py_END_ALLOW_THREADS
+
+ if (exception) {
+ PyErr_SetString(PyExc_IOError, result);
+ return NULL;
+ }
+
+ PyObject * x = PyList_New(MAX_BIGCOUNT + 1);
+ if (x == NULL) {
+ delete[] dist;
+ return NULL;
+ }
+ for (int i = 0; i < MAX_BIGCOUNT + 1; i++) {
+ PyList_SET_ITEM(x, i, PyLong_FromUnsignedLongLong(dist[i]));
+ }
+
+ delete[] dist;
+
+ return x;
+}
+
+static
+PyObject *
+hashbits_n_unique_kmers(khmer_KHashbits_Object * me, PyObject * args)
+{
+ Hashbits * hashbits = me->hashbits;
+
+ HashIntoType n = hashbits->n_unique_kmers();
+
+ return PyLong_FromUnsignedLongLong(n);
+}
+
+
+static
+PyObject *
+hashbits_count_overlap(khmer_KHashbits_Object * me, PyObject * args)
+{
+ Hashbits * hashbits = me->hashbits;
+ khmer_KHashbits_Object * ht2_argu;
+ const char * filename;
+ Hashbits * ht2;
+
+ if (!PyArg_ParseTuple(args, "sO!", &filename, &khmer_KHashbits_Type,
+ &ht2_argu)) {
+ return NULL;
+ }
+
+ ht2 = ht2_argu->hashbits;
+
+// call the C++ function, and trap signals => Python
+
+ unsigned long long n_consumed;
+ unsigned int total_reads;
+ HashIntoType curve[2][100];
+
+ try {
+ hashbits->consume_fasta_overlap(filename, curve, *ht2, total_reads, n_consumed);
+ } catch (_khmer_signal &e) {
+ PyErr_SetString(PyExc_IOError, e.get_message().c_str());
+ return NULL;
+ } catch (InvalidStreamHandle &e) {
+ PyErr_SetString(PyExc_IOError, e.what());
+ return NULL;
+ }
+
+ HashIntoType n = hashbits->n_unique_kmers();
+ HashIntoType n_overlap = hashbits->n_overlap_kmers();
+
+ PyObject * x = PyList_New(200);
+
+ for (unsigned int i = 0; i < 100; i++) {
+ PyList_SetItem(x, i, Py_BuildValue("K", curve[0][i]));
+ }
+ for (unsigned int i = 0; i < 100; i++) {
+ PyList_SetItem(x, i + 100, Py_BuildValue("K", curve[1][i]));
+ }
+ return Py_BuildValue("KKO", n, n_overlap, x);
+}
+
+static
+PyObject *
+hashbits_n_occupied(khmer_KHashbits_Object * me, PyObject * args)
+{
+ Hashbits * hashbits = me->hashbits;
+
+ HashIntoType start = 0, stop = 0;
+
+ if (!PyArg_ParseTuple(args, "|KK", &start, &stop)) {
+ return NULL;
+ }
+
+ HashIntoType n = hashbits->n_occupied(start, stop);
+
+ return PyLong_FromUnsignedLongLong(n);
+}
+
+static
+PyObject *
+hashbits_n_tags(khmer_KHashbits_Object * me, PyObject * args)
+{
+ Hashbits * hashbits = me->hashbits;
+
+ if (!PyArg_ParseTuple(args, "")) {
+ return NULL;
+ }
+
+ return PyLong_FromSize_t(hashbits->n_tags());
+}
+
+static
+PyObject *
+hashbits_count(khmer_KHashbits_Object * me, PyObject * args)
+{
+ Hashbits * hashbits = me->hashbits;
+
+ const char * kmer;
+
+ if (!PyArg_ParseTuple(args, "s", &kmer)) {
+ return NULL;
+ }
+
+ if (strlen(kmer) != hashbits->ksize()) {
+ PyErr_SetString(PyExc_ValueError,
+ "k-mer length must equal the presence table k-mer size");
+ return NULL;
+ }
+
+ hashbits->count(kmer);
+
+ return PyLong_FromLong(1);
+}
+
+static
+PyObject *
+hashbits_consume(khmer_KHashbits_Object * me, PyObject * args)
+{
+ Hashbits * hashbits = me->hashbits;
+
+ const char * long_str;
+
+ if (!PyArg_ParseTuple(args, "s", &long_str)) {
+ return NULL;
+ }
+
+ if (strlen(long_str) < hashbits->ksize()) {
+ PyErr_SetString(PyExc_ValueError,
+ "string length must >= the hashbits k-mer size");
+ return NULL;
+ }
+
+ unsigned int n_consumed;
+ n_consumed = hashbits->consume_string(long_str);
+
+ return PyLong_FromLong(n_consumed);
+}
+
+static
+PyObject *
+hashbits_print_stop_tags(khmer_KHashbits_Object * me, PyObject * args)
+{
+ Hashbits * hashbits = me->hashbits;
+
+ const char * filename = NULL;
+
+ if (!PyArg_ParseTuple(args, "s", &filename)) {
+ return NULL;
+ }
+
+ hashbits->print_stop_tags(filename);
+
+ Py_RETURN_NONE;
+}
+
+static
+PyObject *
+hashbits_print_tagset(khmer_KHashbits_Object * me, PyObject * args)
+{
+ Hashbits * hashbits = me->hashbits;
+
+ const char * filename = NULL;
+
+ if (!PyArg_ParseTuple(args, "s", &filename)) {
+ return NULL;
+ }
+
+ hashbits->print_tagset(filename);
+
+ Py_RETURN_NONE;
+}
+
+static
+PyObject *
+hashbits_load_stop_tags(khmer_KHashbits_Object * me, PyObject * args)
+{
+ Hashbits * hashbits = me->hashbits;
+
+ const char * filename = NULL;
+ PyObject * clear_tags_o = NULL;
+
+ if (!PyArg_ParseTuple(args, "s|O", &filename, &clear_tags_o)) {
+ return NULL;
+ }
+
+ bool clear_tags = true;
+ if (clear_tags_o && !PyObject_IsTrue(clear_tags_o)) {
+ clear_tags = false;
+ }
+
+
+ try {
+ hashbits->load_stop_tags(filename, clear_tags);
+ } catch (khmer_file_exception &e) {
+ PyErr_SetString(PyExc_IOError, e.what());
+ return NULL;
+ }
+
+ Py_RETURN_NONE;
+}
- Py_RETURN_NONE;
-}
static
PyObject *
-hashtable_add_stop_tag(khmer_KHashtable_Object * me, PyObject * args)
+hashbits_save_stop_tags(khmer_KHashbits_Object * me, PyObject * args)
{
- Hashtable * hashtable = me->hashtable;
+ Hashbits * hashbits = me->hashbits;
- const char * kmer_s = NULL;
- if (!PyArg_ParseTuple(args, "s", &kmer_s)) {
+ const char * filename = NULL;
+
+ if (!PyArg_ParseTuple(args, "s", &filename)) {
return NULL;
}
- HashIntoType kmer = _hash(kmer_s, hashtable->ksize());
- hashtable->add_stop_tag(kmer);
+ try {
+ hashbits->save_stop_tags(filename);
+ } catch (khmer_file_exception &e) {
+ PyErr_SetString(PyExc_IOError, e.what());
+ return NULL;
+ }
Py_RETURN_NONE;
}
static
PyObject *
-hashtable_get_stop_tags(khmer_KHashtable_Object * me, PyObject * args)
+hashbits_traverse_from_tags(khmer_KHashbits_Object * me, PyObject * args)
{
- Hashtable * hashtable = me->hashtable;
+ Hashbits * hashbits = me->hashbits;
- if (!PyArg_ParseTuple(args, "")) {
+ khmer_KCountingHash_Object * counting_o = NULL;
+ unsigned int distance, threshold, frequency;
+
+ if (!PyArg_ParseTuple(args, "O!III", &khmer_KCountingHash_Type, &counting_o,
+ &distance, &threshold, &frequency)) {
return NULL;
}
- WordLength k = hashtable->ksize();
- SeenSet::const_iterator si;
+ hashbits->traverse_from_tags(distance, threshold, frequency,
+ * counting_o->counting);
- PyObject * x = PyList_New(hashtable->stop_tags.size());
- unsigned long long i = 0;
- for (si = hashtable->stop_tags.begin(); si != hashtable->stop_tags.end();
- si++) {
- std::string s = _revhash(*si, k);
- PyList_SET_ITEM(x, i, Py_BuildValue("s", s.c_str()));
- i++;
+ Py_RETURN_NONE;
+}
+
+static
+PyObject *
+hashbits_repartition_largest_partition(khmer_KHashbits_Object * me,
+ PyObject * args)
+{
+ Hashbits * hashbits = me->hashbits;
+
+ khmer_KCountingHash_Object * counting_o = NULL;
+ PyObject * subset_o = NULL;
+ unsigned int distance, threshold, frequency;
+
+ if (!PyArg_ParseTuple(args, "OO!III", &subset_o, &khmer_KCountingHash_Type,
+ &counting_o, &distance, &threshold, &frequency)) {
+ return NULL;
}
- return x;
+ SubsetPartition * subset_p;
+ if (subset_o != Py_None) {
+ subset_p = (SubsetPartition *) PyCObject_AsVoidPtr(subset_o);
+ } else {
+ subset_p = hashbits->partition;
+ }
+
+ CountingHash * counting = counting_o->counting;
+
+ unsigned long next_largest;
+ try {
+ next_largest = subset_p->repartition_largest_partition(distance,
+ threshold, frequency, *counting);
+ } catch (khmer_exception &e) {
+ PyErr_SetString(PyExc_RuntimeError, e.what());
+ return NULL;
+ }
+
+ return PyLong_FromLong(next_largest);
}
static
PyObject *
-hashtable_get_tagset(khmer_KHashtable_Object * me, PyObject * args)
+hashbits_get(khmer_KHashbits_Object * me, PyObject * args)
{
- Hashtable * hashtable = me->hashtable;
+ Hashbits * hashbits = me->hashbits;
- if (!PyArg_ParseTuple(args, "")) {
+ PyObject * arg;
+
+ if (!PyArg_ParseTuple(args, "O", &arg)) {
return NULL;
}
- WordLength k = hashtable->ksize();
- SeenSet::const_iterator si;
+ unsigned long count = 0;
- PyObject * x = PyList_New(hashtable->all_tags.size());
- unsigned long long i = 0;
- for (si = hashtable->all_tags.begin(); si != hashtable->all_tags.end(); si++) {
- std::string s = _revhash(*si, k);
- PyList_SET_ITEM(x, i, Py_BuildValue("s", s.c_str()));
- i++;
+ if (PyInt_Check(arg)) {
+ long pos = PyInt_AsLong(arg);
+ count = hashbits->get_count((unsigned int) pos);
+ } else if (PyBytes_Check(arg)) {
+ std::string s = PyBytes_AsString(arg);
+
+ if (strlen(s.c_str()) < hashbits->ksize()) {
+ PyErr_SetString(PyExc_ValueError,
+ "string length must equal the presence table k-mer size");
+ return NULL;
+ }
+
+ count = hashbits->get_count(s.c_str());
+ } else {
+ PyErr_SetString(PyExc_ValueError, "must pass in an int or string");
+ return NULL;
}
- return x;
+ return PyLong_FromLong(count);
}
static
PyObject *
-hashtable_output_partitions(khmer_KHashtable_Object * me, PyObject * args)
+hashbits_calc_connected_graph_size(khmer_KHashbits_Object * me, PyObject * args)
{
- Hashtable * hashtable = me->hashtable;
+ Hashbits * hashbits = me->hashbits;
- const char * filename = NULL;
- const char * output = NULL;
- PyObject * output_unassigned_o = NULL;
+ const char * _kmer;
+ unsigned int max_size = 0;
+ PyObject * break_on_circum_o = NULL;
+ if (!PyArg_ParseTuple(args, "s|IO", &_kmer, &max_size, &break_on_circum_o)) {
+ return NULL;
+ }
- if (!PyArg_ParseTuple(args, "ss|O", &filename, &output,
- &output_unassigned_o)) {
+ bool break_on_circum = false;
+ if (break_on_circum_o && PyObject_IsTrue(break_on_circum_o)) {
+ break_on_circum = true;
+ }
+
+ unsigned long long size = 0;
+
+ Py_BEGIN_ALLOW_THREADS
+ SeenSet keeper;
+ hashbits->calc_connected_graph_size(_kmer, size, keeper, max_size,
+ break_on_circum);
+ Py_END_ALLOW_THREADS
+
+ return PyLong_FromUnsignedLongLong(size);
+}
+
+static
+PyObject *
+hashbits_kmer_degree(khmer_KHashbits_Object * me, PyObject * args)
+{
+ Hashbits * hashbits = me->hashbits;
+
+ const char * kmer_s = NULL;
+
+ if (!PyArg_ParseTuple(args, "s", &kmer_s)) {
return NULL;
}
- bool output_unassigned = false;
- if (output_unassigned_o != NULL && PyObject_IsTrue(output_unassigned_o)) {
- output_unassigned = true;
+ return PyLong_FromLong(hashbits->kmer_degree(kmer_s));
+}
+
+static
+PyObject *
+hashbits_trim_on_stoptags(khmer_KHashbits_Object * me, PyObject * args)
+{
+ Hashbits * hashbits = me->hashbits;
+
+ const char * seq = NULL;
+
+ if (!PyArg_ParseTuple(args, "s", &seq)) {
+ return NULL;
}
- size_t n_partitions = 0;
+ size_t trim_at;
+ Py_BEGIN_ALLOW_THREADS
- try {
- SubsetPartition * subset_p = hashtable->partition;
- n_partitions = subset_p->output_partitioned_file(filename,
- output,
- output_unassigned);
- } catch (khmer_file_exception &e) {
- PyErr_SetString(PyExc_IOError, e.what());
+ trim_at = hashbits->trim_on_stoptags(seq);
+
+ Py_END_ALLOW_THREADS;
+
+ PyObject * trim_seq = PyBytes_FromStringAndSize(seq, trim_at);
+ if (trim_seq == NULL) {
return NULL;
}
+ PyObject * ret = Py_BuildValue("Ok", trim_seq, (unsigned long) trim_at);
+ Py_DECREF(trim_seq);
- return PyLong_FromLong(n_partitions);
+ return ret;
}
static
PyObject *
-hashtable_find_unpart(khmer_KHashtable_Object * me, PyObject * args)
+hashbits_identify_stoptags_by_position(khmer_KHashbits_Object * me,
+ PyObject * args)
{
- Hashtable * hashtable = me->hashtable;
+ Hashbits * hashbits = me->hashbits;
- const char * filename = NULL;
- PyObject * traverse_o = NULL;
+ const char * seq = NULL;
+
+ if (!PyArg_ParseTuple(args, "s", &seq)) {
+ return NULL;
+ }
+
+ std::vector<unsigned int> posns;
+ Py_BEGIN_ALLOW_THREADS
+
+ hashbits->identify_stop_tags_by_position(seq, posns);
+
+ Py_END_ALLOW_THREADS;
+
+ PyObject * x = PyList_New(posns.size());
+
+ for (unsigned int i = 0; i < posns.size(); i++) {
+ PyList_SET_ITEM(x, i, Py_BuildValue("I", posns[i]));
+ }
+
+ return x;
+}
+
+static
+PyObject *
+hashbits_do_subset_partition(khmer_KHashbits_Object * me, PyObject * args)
+{
+ Hashbits * hashbits = me->hashbits;
+
+ HashIntoType start_kmer = 0, end_kmer = 0;
+ PyObject * break_on_stop_tags_o = NULL;
PyObject * stop_big_traversals_o = NULL;
- if (!PyArg_ParseTuple(args, "sOO", &filename, &traverse_o,
+ if (!PyArg_ParseTuple(args, "|KKOO", &start_kmer, &end_kmer,
+ &break_on_stop_tags_o,
&stop_big_traversals_o)) {
return NULL;
}
- bool traverse = PyObject_IsTrue(traverse_o);
- bool stop_big_traversals = PyObject_IsTrue(stop_big_traversals_o);
- unsigned int n_singletons = 0;
+ bool break_on_stop_tags = false;
+ if (break_on_stop_tags_o && PyObject_IsTrue(break_on_stop_tags_o)) {
+ break_on_stop_tags = true;
+ }
+ bool stop_big_traversals = false;
+ if (stop_big_traversals_o && PyObject_IsTrue(stop_big_traversals_o)) {
+ stop_big_traversals = true;
+ }
- SubsetPartition * subset_p = hashtable->partition;
- n_singletons = subset_p->find_unpart(filename, traverse,
- stop_big_traversals);
+ SubsetPartition * subset_p = NULL;
+ try {
+ Py_BEGIN_ALLOW_THREADS
+ subset_p = new SubsetPartition(hashbits);
+ subset_p->do_partition(start_kmer, end_kmer, break_on_stop_tags,
+ stop_big_traversals);
+ Py_END_ALLOW_THREADS
+ } catch (_khmer_signal &e) {
+ return NULL;
+ } catch (std::bad_alloc &e) {
+ return PyErr_NoMemory();
+ }
- return PyLong_FromLong(n_singletons);
+ return PyCObject_FromVoidPtr(subset_p, free_subset_partition_info);
}
static
PyObject *
-hashtable_filter_if_present(khmer_KHashtable_Object * me, PyObject * args)
+hashbits_join_partitions_by_path(khmer_KHashbits_Object * me, PyObject * args)
{
- Hashtable * hashtable = me->hashtable;
+ Hashbits * hashbits = me->hashbits;
- const char * filename = NULL;
- const char * output = NULL;
+ const char * sequence = NULL;
+ if (!PyArg_ParseTuple(args, "s", &sequence)) {
+ return NULL;
+ }
- if (!PyArg_ParseTuple(args, "ss", &filename, &output)) {
+ hashbits->partition->join_partitions_by_path(sequence);
+
+ Py_RETURN_NONE;
+}
+
+static
+PyObject *
+hashbits_merge_subset(khmer_KHashbits_Object * me, PyObject * args)
+{
+ Hashbits * hashbits = me->hashbits;
+
+ PyObject * subset_obj;
+ if (!PyArg_ParseTuple(args, "O", &subset_obj)) {
+ return NULL;
+ }
+
+ if (!PyCObject_Check(subset_obj)) {
+ PyErr_SetString( PyExc_ValueError, "invalid subset");
return NULL;
}
- hashtable->filter_if_present(filename, output);
+ SubsetPartition * subset_p;
+ subset_p = (SubsetPartition *) PyCObject_AsVoidPtr(subset_obj);
+
+ hashbits->partition->merge(subset_p);
Py_RETURN_NONE;
}
static
PyObject *
-hashtable_save_partitionmap(khmer_KHashtable_Object * me, PyObject * args)
+hashbits_merge_from_disk(khmer_KHashbits_Object * me, PyObject * args)
{
- Hashtable * hashtable = me->hashtable;
+ Hashbits * hashbits = me->hashbits;
const char * filename = NULL;
-
if (!PyArg_ParseTuple(args, "s", &filename)) {
return NULL;
}
try {
- hashtable->partition->save_partitionmap(filename);
+ hashbits->partition->merge_from_disk(filename);
} catch (khmer_file_exception &e) {
PyErr_SetString(PyExc_IOError, e.what());
return NULL;
@@ -1860,1449 +2338,1109 @@ hashtable_save_partitionmap(khmer_KHashtable_Object * me, PyObject * args)
static
PyObject *
-hashtable_load_partitionmap(khmer_KHashtable_Object * me, PyObject * args)
+hashbits_consume_fasta(khmer_KHashbits_Object * me, PyObject * args)
{
- Hashtable * hashtable = me->hashtable;
+ Hashbits * hashbits = me->hashbits;
- const char * filename = NULL;
+ const char * filename;
if (!PyArg_ParseTuple(args, "s", &filename)) {
return NULL;
}
+// call the C++ function, and trap signals => Python
+
+ unsigned long long n_consumed = 0;
+ unsigned int total_reads = 0;
+
try {
- hashtable->partition->load_partitionmap(filename);
+ hashbits->consume_fasta(filename, total_reads, n_consumed);
+ } catch (_khmer_signal &e) {
+ PyErr_SetString(PyExc_IOError, e.get_message().c_str());
+ return NULL;
} catch (khmer_file_exception &e) {
PyErr_SetString(PyExc_IOError, e.what());
return NULL;
}
- Py_RETURN_NONE;
+ return Py_BuildValue("IK", total_reads, n_consumed);
}
static
PyObject *
-hashtable__validate_partitionmap(khmer_KHashtable_Object * me, PyObject * args)
+hashbits_consume_fasta_with_reads_parser(khmer_KHashbits_Object * me,
+ PyObject * args)
{
- Hashtable * hashtable = me->hashtable;
+ Hashbits * hashbits = me->hashbits;
+
+ PyObject * rparser_obj = NULL;
+
+ if (!PyArg_ParseTuple(
+ args, "O", &rparser_obj)) {
+ return NULL;
+ }
+
+ read_parsers:: IParser * rparser =
+ _PyObject_to_khmer_ReadParser( rparser_obj );
+
+// call the C++ function, and trap signals => Python
+ unsigned long long n_consumed = 0;
+ unsigned int total_reads = 0;
+ char const * exc = NULL;
+ Py_BEGIN_ALLOW_THREADS
+ try {
+ hashbits->consume_fasta(rparser, total_reads, n_consumed);
+ } catch (_khmer_signal &e) {
+ exc = e.get_message().c_str();
+ }
- if (!PyArg_ParseTuple(args, "")) {
+ Py_END_ALLOW_THREADS
+ if (exc != NULL) {
+ PyErr_SetString(PyExc_IOError, exc);
return NULL;
}
- hashtable->partition->_validate_pmap();
-
- Py_RETURN_NONE;
+ return Py_BuildValue("IK", total_reads, n_consumed);
}
static
PyObject *
-hashtable_count_partitions(khmer_KHashtable_Object * me, PyObject * args)
+hashbits_consume_fasta_and_traverse(khmer_KHashbits_Object * me,
+ PyObject * args)
{
- Hashtable * hashtable = me->hashtable;
+ Hashbits * hashbits = me->hashbits;
- if (!PyArg_ParseTuple(args, "")) {
+ const char * filename;
+ unsigned int radius, big_threshold, transfer_threshold;
+ khmer_KCountingHash_Object * counting_o = NULL;
+
+ if (!PyArg_ParseTuple(args, "sIIIO!", &filename,
+ &radius, &big_threshold, &transfer_threshold,
+ &khmer_KCountingHash_Type, &counting_o)) {
return NULL;
}
- size_t n_partitions = 0, n_unassigned = 0;
- hashtable->partition->count_partitions(n_partitions, n_unassigned);
-
- return Py_BuildValue("nn", (Py_ssize_t) n_partitions,
- (Py_ssize_t) n_unassigned);
-}
+ CountingHash * counting = counting_o->counting;
-static
-PyObject *
-hashtable_subset_count_partitions(khmer_KHashtable_Object * me, PyObject * args)
-{
- khmer_KSubsetPartition_Object * subset_obj = NULL;
+ hashbits->consume_fasta_and_traverse(filename, radius, big_threshold,
+ transfer_threshold, *counting);
- if (!PyArg_ParseTuple(args, "O!", &khmer_KSubsetPartition_Type, &subset_obj)) {
- return NULL;
- }
- size_t n_partitions = 0, n_unassigned = 0;
- subset_obj->subset->count_partitions(n_partitions, n_unassigned);
+ Py_RETURN_NONE;
+}
- return Py_BuildValue("nn", (Py_ssize_t) n_partitions,
- (Py_ssize_t) n_unassigned);
+void sig(unsigned int total_reads, unsigned int n_consumed)
+{
+ std::cout << total_reads << " " << n_consumed << std::endl;
}
static
PyObject *
-hashtable_subset_partition_size_distribution(khmer_KHashtable_Object * me,
- PyObject * args)
+hashbits_consume_fasta_and_tag(khmer_KHashbits_Object * me, PyObject * args)
{
- khmer_KSubsetPartition_Object * subset_obj = NULL;
- if (!PyArg_ParseTuple(args, "O!", &khmer_KSubsetPartition_Type, &subset_obj)) {
- return NULL;
- }
-
- SubsetPartition * subset_p;
- subset_p = subset_obj->subset;
-
- PartitionCountDistribution d;
+ Hashbits * hashbits = me->hashbits;
- unsigned int n_unassigned = 0;
- subset_p->partition_size_distribution(d, n_unassigned);
+ const char * filename;
- PyObject * x = PyList_New(d.size());
- if (x == NULL) {
+ if (!PyArg_ParseTuple(args, "s", &filename)) {
return NULL;
}
- PartitionCountDistribution::iterator di;
- unsigned int i;
- for (i = 0, di = d.begin(); di != d.end(); di++, i++) {
- PyObject * value = Py_BuildValue("KK", di->first, di->second);
- if (value == NULL) {
- Py_DECREF(x);
- return NULL;
- }
- PyList_SET_ITEM(x, i, value);
- }
- if (!(i == d.size())) {
- throw khmer_exception();
- }
+ // call the C++ function, and trap signals => Python
- PyObject * returnValue = Py_BuildValue("NI", x, n_unassigned);
- if (returnValue == NULL) {
- Py_DECREF(x);
+ unsigned long long n_consumed;
+ unsigned int total_reads;
+
+ try {
+ hashbits->consume_fasta_and_tag(filename, total_reads, n_consumed);
+ } catch (_khmer_signal &e) {
+ PyErr_SetString(PyExc_IOError, e.get_message().c_str());
+ return NULL;
+ } catch (khmer_file_exception &e) {
+ PyErr_SetString(PyExc_IOError, e.what());
return NULL;
}
- return returnValue;
+
+ return Py_BuildValue("IK", total_reads, n_consumed);
}
static
PyObject *
-hashtable_load_tagset(khmer_KHashtable_Object * me, PyObject * args)
+hashbits_consume_fasta_and_tag_with_reads_parser(khmer_KHashbits_Object * me,
+ PyObject * args)
{
- Hashtable * hashtable = me->hashtable;
+ Hashbits * hashbits = me->hashbits;
- const char * filename = NULL;
- PyObject * clear_tags_o = NULL;
+ python::khmer_ReadParser_Object * rparser_obj = NULL;
- if (!PyArg_ParseTuple(args, "s|O", &filename, &clear_tags_o)) {
+ if (!PyArg_ParseTuple( args, "O!", &python::khmer_ReadParser_Type,
+ &rparser_obj)) {
return NULL;
}
- bool clear_tags = true;
- if (clear_tags_o && !PyObject_IsTrue(clear_tags_o)) {
- clear_tags = false;
- }
+ read_parsers:: IParser * rparser = rparser_obj-> parser;
+ // call the C++ function, and trap signals => Python
+ unsigned long long n_consumed = 0;
+ unsigned int total_reads = 0;
+ char const * exc = NULL;
+ Py_BEGIN_ALLOW_THREADS
try {
- hashtable->load_tagset(filename, clear_tags);
- } catch (khmer_file_exception &e) {
- PyErr_SetString(PyExc_IOError, e.what());
+ hashbits->consume_fasta_and_tag(
+ rparser, total_reads, n_consumed
+ );
+ } catch (_khmer_signal &e) {
+ exc = e.get_message().c_str();
+ } catch (khmer::read_parsers::NoMoreReadsAvailable &e) {
+ exc = e.what();
+ }
+ Py_END_ALLOW_THREADS
+ if (exc != NULL) {
+ PyErr_SetString(PyExc_IOError, exc);
return NULL;
}
- Py_RETURN_NONE;
+ return Py_BuildValue("IK", total_reads, n_consumed);
}
static
PyObject *
-hashtable_save_tagset(khmer_KHashtable_Object * me, PyObject * args)
+hashbits_consume_fasta_and_tag_with_stoptags(khmer_KHashbits_Object * me,
+ PyObject * args)
{
- Hashtable * hashtable = me->hashtable;
+ Hashbits * hashbits = me->hashbits;
- const char * filename = NULL;
+ const char * filename;
if (!PyArg_ParseTuple(args, "s", &filename)) {
return NULL;
}
+ // call the C++ function, and trap signals => Python
+
+ unsigned long long n_consumed;
+ unsigned int total_reads;
+
try {
- hashtable->save_tagset(filename);
+ hashbits->consume_fasta_and_tag_with_stoptags(filename,
+ total_reads, n_consumed);
+ } catch (_khmer_signal &e) {
+ PyErr_SetString(PyExc_IOError, e.get_message().c_str());
+ return NULL;
} catch (khmer_file_exception &e) {
PyErr_SetString(PyExc_IOError, e.what());
return NULL;
}
- Py_RETURN_NONE;
+ return Py_BuildValue("IK", total_reads, n_consumed);
}
static
PyObject *
-hashtable_save_subset_partitionmap(khmer_KHashtable_Object * me,
- PyObject * args)
+hashbits_consume_partitioned_fasta(khmer_KHashbits_Object * me, PyObject * args)
{
- const char * filename = NULL;
- khmer_KSubsetPartition_Object * subset_obj = NULL;
+ Hashbits * hashbits = me->hashbits;
+
+ const char * filename;
- if (!PyArg_ParseTuple(args, "O!s", &khmer_KSubsetPartition_Type, &subset_obj, &filename)) {
+ if (!PyArg_ParseTuple(args, "s", &filename)) {
return NULL;
}
- SubsetPartition * subset_p;
- subset_p = subset_obj->subset;
+ // call the C++ function, and trap signals => Python
- Py_BEGIN_ALLOW_THREADS
+ unsigned long long n_consumed;
+ unsigned int total_reads;
try {
- subset_p->save_partitionmap(filename);
+ hashbits->consume_partitioned_fasta(filename, total_reads, n_consumed);
+ } catch (_khmer_signal &e) {
+ PyErr_SetString(PyExc_IOError, e.get_message().c_str());
+ return NULL;
} catch (khmer_file_exception &e) {
PyErr_SetString(PyExc_IOError, e.what());
return NULL;
}
- Py_END_ALLOW_THREADS
-
- Py_RETURN_NONE;
+ return Py_BuildValue("IK", total_reads, n_consumed);
}
static
PyObject *
-hashtable_load_subset_partitionmap(khmer_KHashtable_Object * me,
- PyObject * args)
+hashbits_find_all_tags(khmer_KHashbits_Object * me, PyObject * args)
{
- Hashtable * hashtable = me->hashtable;
+ Hashbits * hashbits = me->hashbits;
- const char * filename = NULL;
+ const char * kmer_s = NULL;
- if (!PyArg_ParseTuple(args, "s", &filename)) {
+ if (!PyArg_ParseTuple(args, "s", &kmer_s)) {
return NULL;
}
- SubsetPartition * subset_p;
- try {
- subset_p = new SubsetPartition(hashtable);
- } catch (std::bad_alloc &e) {
- return PyErr_NoMemory();
+ if (strlen(kmer_s) != hashbits->ksize()) {
+ PyErr_SetString( PyExc_ValueError,
+ "k-mer size must equal the k-mer size of the presence table");
+ return NULL;
}
- bool fail = false;
- std::string err;
+ _pre_partition_info * ppi = NULL;
Py_BEGIN_ALLOW_THREADS
+ HashIntoType kmer, kmer_f, kmer_r;
+ kmer = _hash(kmer_s, hashbits->ksize(), kmer_f, kmer_r);
+
try {
- subset_p->load_partitionmap(filename);
- } catch (khmer_file_exception &e) {
- fail = true;
- err = e.what();
+ ppi = new _pre_partition_info(kmer);
+ } catch (std::bad_alloc &e) {
+ return PyErr_NoMemory();
}
+ hashbits->partition->find_all_tags(kmer_f, kmer_r, ppi->tagged_kmers,
+ hashbits->all_tags);
+ hashbits->add_kmer_to_tags(kmer);
Py_END_ALLOW_THREADS
- if (fail) {
- PyErr_SetString(PyExc_IOError, err.c_str());
- delete subset_p;
- return NULL;
- } else {
- khmer_KSubsetPartition_Object * subset_obj = (khmer_KSubsetPartition_Object *)\
- PyObject_New(khmer_KSubsetPartition_Object, &khmer_KSubsetPartition_Type);
- subset_obj->subset = subset_p;
- return (PyObject*) subset_obj;
- }
+ return PyCObject_FromVoidPtr(ppi, free_pre_partition_info);
}
static
PyObject *
-hashtable__set_tag_density(khmer_KHashtable_Object * me, PyObject * args)
+hashbits_assign_partition_id(khmer_KHashbits_Object * me, PyObject * args)
{
- Hashtable * hashtable = me->hashtable;
+ Hashbits * hashbits = me->hashbits;
- unsigned int d;
- if (!PyArg_ParseTuple(args, "I", &d)) {
+ PyObject * ppi_obj;
+ if (!PyArg_ParseTuple(args, "O", &ppi_obj)) {
return NULL;
}
- hashtable->_set_tag_density(d);
-
- Py_RETURN_NONE;
-}
-
-static
-PyObject *
-hashtable__get_tag_density(khmer_KHashtable_Object * me, PyObject * args)
-{
- Hashtable * hashtable = me->hashtable;
-
- if (!PyArg_ParseTuple(args, "")) {
+ if (!PyCObject_Check(ppi_obj)) {
+ PyErr_SetString( PyExc_ValueError, "invalid pre_partition_info");
return NULL;
}
- unsigned int d = hashtable->_get_tag_density();
+ _pre_partition_info * ppi;
+ ppi = (_pre_partition_info *) PyCObject_AsVoidPtr(ppi_obj);
- return PyLong_FromLong(d);
+ PartitionID p;
+ p = hashbits->partition->assign_partition_id(ppi->kmer,
+ ppi->tagged_kmers);
+
+ return PyLong_FromLong(p);
}
static
PyObject *
-hashtable__validate_subset_partitionmap(khmer_KHashtable_Object * me,
- PyObject * args)
+hashbits_add_tag(khmer_KHashbits_Object * me, PyObject * args)
{
- khmer_KSubsetPartition_Object * subset_obj = NULL;
+ Hashbits * hashbits = me->hashbits;
- if (!PyArg_ParseTuple(args, "O!", &khmer_KSubsetPartition_Type, &subset_obj)) {
+ const char * kmer_s = NULL;
+ if (!PyArg_ParseTuple(args, "s", &kmer_s)) {
return NULL;
}
- subset_obj->subset->_validate_pmap();
+ HashIntoType kmer = _hash(kmer_s, hashbits->ksize());
+ hashbits->add_tag(kmer);
Py_RETURN_NONE;
}
static
PyObject *
-hashtable_set_partition_id(khmer_KHashtable_Object * me, PyObject * args)
+hashbits_add_stop_tag(khmer_KHashbits_Object * me, PyObject * args)
{
- Hashtable * hashtable = me->hashtable;
-
- const char * kmer = NULL;
- PartitionID p = 0;
+ Hashbits * hashbits = me->hashbits;
- if (!PyArg_ParseTuple(args, "sI", &kmer, &p)) {
+ const char * kmer_s = NULL;
+ if (!PyArg_ParseTuple(args, "s", &kmer_s)) {
return NULL;
}
- hashtable->partition->set_partition_id(kmer, p);
+ HashIntoType kmer = _hash(kmer_s, hashbits->ksize());
+ hashbits->add_stop_tag(kmer);
Py_RETURN_NONE;
}
static
PyObject *
-hashtable_join_partitions(khmer_KHashtable_Object * me, PyObject * args)
+hashbits_get_stop_tags(khmer_KHashbits_Object * me, PyObject * args)
{
- Hashtable * hashtable = me->hashtable;
-
- PartitionID p1 = 0, p2 = 0;
+ Hashbits * hashbits = me->hashbits;
- if (!PyArg_ParseTuple(args, "II", &p1, &p2)) {
+ if (!PyArg_ParseTuple(args, "")) {
return NULL;
}
- p1 = hashtable->partition->join_partitions(p1, p2);
-
- return PyLong_FromLong(p1);
-}
-
-static
-PyObject *
-hashtable_get_partition_id(khmer_KHashtable_Object * me, PyObject * args)
-{
- Hashtable * hashtable = me->hashtable;
-
- const char * kmer = NULL;
+ WordLength k = hashbits->ksize();
+ SeenSet::const_iterator si;
- if (!PyArg_ParseTuple(args, "s", &kmer)) {
- return NULL;
+ PyObject * x = PyList_New(hashbits->stop_tags.size());
+ unsigned long long i = 0;
+ for (si = hashbits->stop_tags.begin(); si != hashbits->stop_tags.end(); si++) {
+ std::string s = _revhash(*si, k);
+ PyList_SET_ITEM(x, i, Py_BuildValue("s", s.c_str()));
+ i++;
}
- PartitionID partition_id;
- partition_id = hashtable->partition->get_partition_id(kmer);
-
- return PyLong_FromLong(partition_id);
+ return x;
}
static
PyObject *
-hashtable_is_single_partition(khmer_KHashtable_Object * me, PyObject * args)
+hashbits_get_tagset(khmer_KHashbits_Object * me, PyObject * args)
{
- Hashtable * hashtable = me->hashtable;
-
- const char * seq = NULL;
+ Hashbits * hashbits = me->hashbits;
- if (!PyArg_ParseTuple(args, "s", &seq)) {
+ if (!PyArg_ParseTuple(args, "")) {
return NULL;
}
- bool v = hashtable->partition->is_single_partition(seq);
+ WordLength k = hashbits->ksize();
+ SeenSet::const_iterator si;
- PyObject * val;
- if (v) {
- val = Py_True;
- } else {
- val = Py_False;
+ PyObject * x = PyList_New(hashbits->all_tags.size());
+ unsigned long long i = 0;
+ for (si = hashbits->all_tags.begin(); si != hashbits->all_tags.end(); si++) {
+ std::string s = _revhash(*si, k);
+ PyList_SET_ITEM(x, i, Py_BuildValue("s", s.c_str()));
+ i++;
}
- Py_INCREF(val);
- return val;
+ return x;
}
static
PyObject *
-hashtable_divide_tags_into_subsets(khmer_KHashtable_Object * me,
- PyObject * args)
+hashbits_output_partitions(khmer_KHashbits_Object * me, PyObject * args)
{
- Hashtable * hashtable = me->hashtable;
+ Hashbits * hashbits = me->hashbits;
- unsigned int subset_size = 0;
+ const char * filename = NULL;
+ const char * output = NULL;
+ PyObject * output_unassigned_o = NULL;
- if (!PyArg_ParseTuple(args, "I", &subset_size)) {
+ if (!PyArg_ParseTuple(args, "ss|O", &filename, &output,
+ &output_unassigned_o)) {
return NULL;
}
- SeenSet divvy;
- hashtable->divide_tags_into_subsets(subset_size, divvy);
+ bool output_unassigned = false;
+ if (output_unassigned_o != NULL && PyObject_IsTrue(output_unassigned_o)) {
+ output_unassigned = true;
+ }
- PyObject * x = PyList_New(divvy.size());
- unsigned int i = 0;
- for (SeenSet::const_iterator si = divvy.begin(); si != divvy.end();
- si++, i++) {
- PyList_SET_ITEM(x, i, PyLong_FromUnsignedLongLong(*si));
+ size_t n_partitions = 0;
+
+ try {
+ SubsetPartition * subset_p = hashbits->partition;
+ n_partitions = subset_p->output_partitioned_file(filename,
+ output,
+ output_unassigned);
+ } catch (_khmer_signal &e) {
+ PyErr_SetString(PyExc_IOError, e.get_message().c_str());
+ return NULL;
+ } catch (khmer_file_exception &e) {
+ PyErr_SetString(PyExc_IOError, e.what());
+ return NULL;
}
- return x;
+ return PyLong_FromLong(n_partitions);
}
static
PyObject *
-hashtable_count_kmers_within_radius(khmer_KHashtable_Object * me,
- PyObject * args)
+hashbits_find_unpart(khmer_KHashbits_Object * me, PyObject * args)
{
- Hashtable * hashtable = me->hashtable;
+ Hashbits * hashbits = me->hashbits;
- const char * kmer = NULL;
- unsigned int radius = 0;
- unsigned int max_count = 0;
+ const char * filename = NULL;
+ PyObject * traverse_o = NULL;
+ PyObject * stop_big_traversals_o = NULL;
- if (!PyArg_ParseTuple(args, "sI|I", &kmer, &radius, &max_count)) {
+ if (!PyArg_ParseTuple(args, "sOO", &filename, &traverse_o,
+ &stop_big_traversals_o)) {
return NULL;
}
- unsigned int n;
-
- Py_BEGIN_ALLOW_THREADS
+ bool traverse = PyObject_IsTrue(traverse_o);
+ bool stop_big_traversals = PyObject_IsTrue(stop_big_traversals_o);
+ unsigned int n_singletons = 0;
- HashIntoType kmer_f, kmer_r;
- _hash(kmer, hashtable->ksize(), kmer_f, kmer_r);
- n = hashtable->count_kmers_within_radius(kmer_f, kmer_r, radius,
- max_count);
+ try {
+ SubsetPartition * subset_p = hashbits->partition;
+ n_singletons = subset_p->find_unpart(filename, traverse,
+ stop_big_traversals);
+ } catch (_khmer_signal &e) {
+ return NULL;
+ }
- Py_END_ALLOW_THREADS
+ return PyLong_FromLong(n_singletons);
- return PyLong_FromUnsignedLong(n);
+ // Py_INCREF(Py_None);
+ // return Py_None;
}
static
PyObject *
-hashtable_extract_unique_paths(khmer_KHashtable_Object * me, PyObject * args)
+hashbits_filter_if_present(khmer_KHashbits_Object * me, PyObject * args)
{
- Hashtable * hashtable = me->hashtable;
-
- const char * sequence = NULL;
- unsigned int min_length = 0;
- float min_unique_f = 0;
- if (!PyArg_ParseTuple(args, "sIf", &sequence, &min_length, &min_unique_f)) {
- return NULL;
- }
+ Hashbits * hashbits = me->hashbits;
- std::vector<std::string> results;
- hashtable->extract_unique_paths(sequence, min_length, min_unique_f, results);
+ const char * filename = NULL;
+ const char * output = NULL;
- PyObject * x = PyList_New(results.size());
- if (x == NULL) {
+ if (!PyArg_ParseTuple(args, "ss", &filename, &output)) {
return NULL;
}
- for (unsigned int i = 0; i < results.size(); i++) {
- PyList_SET_ITEM(x, i, PyUnicode_FromString(results[i].c_str()));
+ try {
+ hashbits->filter_if_present(filename, output);
+ } catch (_khmer_signal &e) {
+ return NULL;
}
- return x;
+ Py_RETURN_NONE;
}
-
static
PyObject *
-hashtable_get_kmers(khmer_KHashtable_Object * me, PyObject * args)
+hashbits_save_partitionmap(khmer_KHashbits_Object * me, PyObject * args)
{
- Hashtable * hashtable = me->hashtable;
- const char * sequence;
+ Hashbits * hashbits = me->hashbits;
- if (!PyArg_ParseTuple(args, "s", &sequence)) {
+ const char * filename = NULL;
+
+ if (!PyArg_ParseTuple(args, "s", &filename)) {
return NULL;
}
- std::vector<std::string> kmers;
-
- hashtable->get_kmers(sequence, kmers);
-
- PyObject * x = PyList_New(kmers.size());
- for (unsigned int i = 0; i < kmers.size(); i++) {
- PyObject * obj = PyUnicode_FromString(kmers[i].c_str());
- PyList_SET_ITEM(x, i, obj);
+ try {
+ hashbits->partition->save_partitionmap(filename);
+ } catch (khmer_file_exception &e) {
+ PyErr_SetString(PyExc_IOError, e.what());
+ return NULL;
}
- return x;
+ Py_RETURN_NONE;
}
static
PyObject *
-hashtable_get_kmer_counts(khmer_KHashtable_Object * me, PyObject * args)
+hashbits_load_partitionmap(khmer_KHashbits_Object * me, PyObject * args)
{
- Hashtable * hashtable = me->hashtable;
- const char * sequence;
+ Hashbits * hashbits = me->hashbits;
- if (!PyArg_ParseTuple(args, "s", &sequence)) {
+ const char * filename = NULL;
+
+ if (!PyArg_ParseTuple(args, "s", &filename)) {
return NULL;
}
- std::vector<BoundedCounterType> counts;
- hashtable->get_kmer_counts(sequence, counts);
+ hashbits->partition->load_partitionmap(filename);
- PyObject * x = PyList_New(counts.size());
- for (unsigned int i = 0; i <counts.size(); i++) {
- PyObject * obj = PyInt_FromLong(counts[i]);
- PyList_SET_ITEM(x, i, obj);
- }
-
- return x;
+ Py_RETURN_NONE;
}
-
static
PyObject *
-hashtable_get_kmer_hashes(khmer_KHashtable_Object * me, PyObject * args)
+hashbits__validate_partitionmap(khmer_KHashbits_Object * me, PyObject * args)
{
- Hashtable * hashtable = me->hashtable;
- const char * sequence;
+ Hashbits * hashbits = me->hashbits;
- if (!PyArg_ParseTuple(args, "s", &sequence)) {
+ if (!PyArg_ParseTuple(args, "")) {
return NULL;
}
- std::vector<HashIntoType> hashes;
- hashtable->get_kmer_hashes(sequence, hashes);
+ hashbits->partition->_validate_pmap();
- PyObject * x = PyList_New(hashes.size());
- for (unsigned int i = 0; i < hashes.size(); i++) {
- PyObject * obj = PyLong_FromUnsignedLongLong(hashes[i]);
- PyList_SET_ITEM(x, i, obj);
- }
-
- return x;
+ Py_RETURN_NONE;
}
-
-static PyMethodDef khmer_hashtable_methods[] = {
- //
- // Basic methods
- //
-
- {
- "ksize",
- (PyCFunction)hashtable_get_ksize, METH_VARARGS,
- "Returns the k-mer size of this graph."
- },
- { "hashsizes", (PyCFunction)hashtable_get_hashsizes, METH_VARARGS, "" },
- {
- "n_unique_kmers",
- (PyCFunction)hashtable_n_unique_kmers, METH_VARARGS,
- "Count the number of unique kmers in this graph."
- },
- {
- "n_occupied", (PyCFunction)hashtable_n_occupied, METH_VARARGS,
- "Count the number of occupied bins."
- },
- { "n_entries", (PyCFunction)hashtable_n_entries, METH_VARARGS, "" },
- {
- "count",
- (PyCFunction)hashtable_count, METH_VARARGS,
- "Increment the count of this k-mer."
- },
- {
- "consume",
- (PyCFunction)hashtable_consume, METH_VARARGS,
- "Increment the counts of all of the k-mers in the string."
- },
- {
- "consume_fasta",
- (PyCFunction)hashtable_consume_fasta, METH_VARARGS,
- "Incrment the counts of all the k-mers in the sequences in the "
- "given file"
- },
- {
- "consume_fasta_with_reads_parser",
- (PyCFunction)hashtable_consume_fasta_with_reads_parser, METH_VARARGS,
- "Count all k-mers retrieved with this reads parser object."
- },
- {
- "get",
- (PyCFunction)hashtable_get, METH_VARARGS,
- "Retrieve the count for the given k-mer."
- },
- {
- "load",
- (PyCFunction)hashtable_load, METH_VARARGS,
- "Load the graph from the specified file."
- },
- {
- "save",
- (PyCFunction)hashtable_save, METH_VARARGS,
- "Save the graph to the specified file."
- },
- {
- "get_median_count",
- (PyCFunction)hashtable_get_median_count, METH_VARARGS,
- "Get the median, average, and stddev of the k-mer counts "
- " in the string"
- },
- {
- "get_kmers",
- (PyCFunction)hashtable_get_kmers, METH_VARARGS,
- "Generate an ordered list of all substrings of length k in the string."
- },
- {
- "get_kmer_hashes",
- (PyCFunction)hashtable_get_kmer_hashes, METH_VARARGS,
- "Retrieve an ordered list of all hashes of all k-mers in the string."
- },
- {
- "get_kmer_counts",
- (PyCFunction)hashtable_get_kmer_counts, METH_VARARGS,
- "Retrieve an ordered list of the counts of all k-mers in the string."
- },
-
- //
- // graph/traversal functionality
- //
-
- {
- "calc_connected_graph_size",
- (PyCFunction)hashtable_calc_connected_graph_size, METH_VARARGS, ""
- },
- {
- "kmer_degree",
- (PyCFunction)hashtable_kmer_degree, METH_VARARGS,
- "Calculate the number of immediate neighbors this k-mer has in "
- "the graph."
- },
- {
- "count_kmers_within_radius",
- (PyCFunction)hashtable_count_kmers_within_radius, METH_VARARGS,
- "Calculate the number of neighbors with given radius in the graph."
- },
-
- //
- // tagging / sparse graph functionality
- //
-
- { "consume_and_tag", (PyCFunction)hashtable_consume_and_tag, METH_VARARGS, "Consume a sequence and tag it" },
- { "get_tags_and_positions", (PyCFunction)hashtable_get_tags_and_positions, METH_VARARGS, "Retrieve tags and their positions in a sequence." },
- { "find_all_tags_list", (PyCFunction)hashtable_find_all_tags_list, METH_VARARGS, "Find all tags within range of the given k-mer, return as list" },
- { "consume_fasta_and_tag", (PyCFunction)hashtable_consume_fasta_and_tag, METH_VARARGS, "Count all k-mers in a given file" },
- { "get_median_count", (PyCFunction)hashtable_get_median_count, METH_VARARGS, "Get the median, average, and stddev of the k-mer counts in the string" },
- { "median_at_least", (PyCFunction)hashtable_median_at_least, METH_VARARGS, "Return true if the median is at least the given cutoff" },
- { "extract_unique_paths", (PyCFunction)hashtable_extract_unique_paths, METH_VARARGS, "" },
- { "print_tagset", (PyCFunction)hashtable_print_tagset, METH_VARARGS, "" },
- { "add_tag", (PyCFunction)hashtable_add_tag, METH_VARARGS, "" },
- { "get_tagset", (PyCFunction)hashtable_get_tagset, METH_VARARGS, "" },
- { "load_tagset", (PyCFunction)hashtable_load_tagset, METH_VARARGS, "" },
- { "save_tagset", (PyCFunction)hashtable_save_tagset, METH_VARARGS, "" },
- { "n_tags", (PyCFunction)hashtable_n_tags, METH_VARARGS, "" },
- { "divide_tags_into_subsets", (PyCFunction)hashtable_divide_tags_into_subsets, METH_VARARGS, "" },
- { "_get_tag_density", (PyCFunction)hashtable__get_tag_density, METH_VARARGS, "" },
- { "_set_tag_density", (PyCFunction)hashtable__set_tag_density, METH_VARARGS, "" },
-
- // partitioning
- { "do_subset_partition", (PyCFunction)hashtable_do_subset_partition, METH_VARARGS, "" },
- { "find_all_tags", (PyCFunction)hashtable_find_all_tags, METH_VARARGS, "" },
- { "assign_partition_id", (PyCFunction)hashtable_assign_partition_id, METH_VARARGS, "" },
- { "output_partitions", (PyCFunction)hashtable_output_partitions, METH_VARARGS, "" },
- { "find_unpart", (PyCFunction)hashtable_find_unpart, METH_VARARGS, "" },
- { "load_partitionmap", (PyCFunction)hashtable_load_partitionmap, METH_VARARGS, "" },
- { "save_partitionmap", (PyCFunction)hashtable_save_partitionmap, METH_VARARGS, "" },
- { "_validate_partitionmap", (PyCFunction)hashtable__validate_partitionmap, METH_VARARGS, "" },
- { "consume_fasta_and_traverse", (PyCFunction)hashtable_consume_fasta_and_traverse, METH_VARARGS, "" },
- {
- "consume_fasta_and_tag_with_reads_parser", (PyCFunction)hashtable_consume_fasta_and_tag_with_reads_parser,
- METH_VARARGS, "Count all k-mers using a given reads parser"
- },
- { "consume_partitioned_fasta", (PyCFunction)hashtable_consume_partitioned_fasta, METH_VARARGS, "Count all k-mers in a given file" },
- { "join_partitions_by_path", (PyCFunction)hashtable_join_partitions_by_path, METH_VARARGS, "" },
- { "merge_subset", (PyCFunction)hashtable_merge_subset, METH_VARARGS, "" },
- { "merge_subset_from_disk", (PyCFunction)hashtable_merge_from_disk, METH_VARARGS, "" },
- { "count_partitions", (PyCFunction)hashtable_count_partitions, METH_VARARGS, "" },
- { "subset_count_partitions", (PyCFunction)hashtable_subset_count_partitions, METH_VARARGS, "" },
- { "subset_partition_size_distribution", (PyCFunction)hashtable_subset_partition_size_distribution, METH_VARARGS, "" },
- { "save_subset_partitionmap", (PyCFunction)hashtable_save_subset_partitionmap, METH_VARARGS },
- { "load_subset_partitionmap", (PyCFunction)hashtable_load_subset_partitionmap, METH_VARARGS },
- { "_validate_subset_partitionmap", (PyCFunction)hashtable__validate_subset_partitionmap, METH_VARARGS, "" },
- { "set_partition_id", (PyCFunction)hashtable_set_partition_id, METH_VARARGS, "" },
- { "join_partitions", (PyCFunction)hashtable_join_partitions, METH_VARARGS, "" },
- { "get_partition_id", (PyCFunction)hashtable_get_partition_id, METH_VARARGS, "" },
- { "is_single_partition", (PyCFunction)hashtable_is_single_partition, METH_VARARGS, "" },
- { "traverse_from_tags", (PyCFunction)hashtable_traverse_from_tags, METH_VARARGS, "" },
- { "repartition_largest_partition", (PyCFunction)hashtable_repartition_largest_partition, METH_VARARGS, "" },
-
- // stop tags
- { "load_stop_tags", (PyCFunction)hashtable_load_stop_tags, METH_VARARGS, "" },
- { "save_stop_tags", (PyCFunction)hashtable_save_stop_tags, METH_VARARGS, "" },
- { "print_stop_tags", (PyCFunction)hashtable_print_stop_tags, METH_VARARGS, "" },
- { "trim_on_stoptags", (PyCFunction)hashtable_trim_on_stoptags, METH_VARARGS, "" },
- { "identify_stoptags_by_position", (PyCFunction)hashtable_identify_stoptags_by_position, METH_VARARGS, "" },
- { "filter_if_present", (PyCFunction)hashtable_filter_if_present, METH_VARARGS, "" },
- { "add_stop_tag", (PyCFunction)hashtable_add_stop_tag, METH_VARARGS, "" },
- { "get_stop_tags", (PyCFunction)hashtable_get_stop_tags, METH_VARARGS, "" },
- { "consume_fasta_and_tag_with_stoptags", (PyCFunction)hashtable_consume_fasta_and_tag_with_stoptags, METH_VARARGS, "Count all k-mers in a given file" },
-
- {NULL, NULL, 0, NULL} /* sentinel */
-};
-
-static PyTypeObject khmer_KHashtable_Type
-CPYCHECKER_TYPE_OBJECT_FOR_TYPEDEF("khmer_KHashtable_Object")
-= {
- PyVarObject_HEAD_INIT(NULL, 0) /* init & ob_size */
- "_khmer.KHashtable ", /*tp_name*/
- sizeof(khmer_KHashtable_Object) , /*tp_basicsize*/
- 0, /*tp_itemsize*/
- 0, /*tp_dealloc*/
- 0, /*tp_print*/
- 0, /*tp_getattr*/
- 0, /*tp_setattr*/
- 0, /*tp_compare*/
- 0, /*tp_repr*/
- 0, /*tp_as_number*/
- 0, /*tp_as_sequence*/
- 0, /*tp_as_mapping*/
- 0, /*tp_hash */
- 0, /*tp_call*/
- 0, /*tp_str*/
- 0, /*tp_getattro*/
- 0, /*tp_setattro*/
- 0, /*tp_as_buffer*/
- Py_TPFLAGS_DEFAULT, /*tp_flags*/
- "base hashtable object", /* tp_doc */
- 0, /* tp_traverse */
- 0, /* tp_clear */
- 0, /* tp_richcompare */
- 0, /* tp_weaklistoffset */
- 0, /* tp_iter */
- 0, /* tp_iternext */
- khmer_hashtable_methods, /* tp_methods */
- 0, /* tp_members */
- 0, /* tp_getset */
- 0, /* tp_base */
- 0, /* tp_dict */
- 0, /* tp_descr_get */
- 0, /* tp_descr_set */
- 0, /* tp_dictoffset */
- 0, /* tp_init */
- 0, /* tp_alloc */
- 0, /* tp_new */
-};
-
-#define is_hashtable_obj(v) (Py_TYPE(v) == &khmer_KHashtable_Type)
-
-//
-// _new_hashtable
-//
-
-//
-// KCountingHash object
-//
-
-typedef struct {
- khmer_KHashtable_Object khashtable;
- CountingHash * counting;
-} khmer_KCountingHash_Object;
-
-typedef struct {
- PyObject_HEAD
- ReadAligner * aligner;
-} khmer_ReadAligner_Object;
-
-static void khmer_counting_dealloc(khmer_KCountingHash_Object * obj);
-
static
PyObject *
-count_trim_on_abundance(khmer_KCountingHash_Object * me, PyObject * args)
+hashbits_count_partitions(khmer_KHashbits_Object * me, PyObject * args)
{
- CountingHash * counting = me->counting;
-
- const char * seq = NULL;
- unsigned int min_count_i = 0;
+ Hashbits * hashbits = me->hashbits;
- if (!PyArg_ParseTuple(args, "sI", &seq, &min_count_i)) {
+ if (!PyArg_ParseTuple(args, "")) {
return NULL;
}
- unsigned long trim_at;
- Py_BEGIN_ALLOW_THREADS
-
- BoundedCounterType min_count = min_count_i;
+ size_t n_partitions = 0, n_unassigned = 0;
+ hashbits->partition->count_partitions(n_partitions, n_unassigned);
- trim_at = counting->trim_on_abundance(seq, min_count);
+ return Py_BuildValue("nn", (Py_ssize_t) n_partitions,
+ (Py_ssize_t) n_unassigned);
+}
- Py_END_ALLOW_THREADS;
+static
+PyObject *
+hashbits_subset_count_partitions(khmer_KHashbits_Object * me, PyObject * args)
+{
+ PyObject * subset_obj = NULL;
- PyObject * trim_seq = PyUnicode_FromStringAndSize(seq, trim_at);
- if (trim_seq == NULL) {
+ if (!PyArg_ParseTuple(args, "O", &subset_obj)) {
return NULL;
}
- PyObject * ret = Py_BuildValue("Ok", trim_seq, trim_at);
- Py_DECREF(trim_seq);
- return ret;
+ SubsetPartition * subset_p;
+ subset_p = (SubsetPartition *) PyCObject_AsVoidPtr(subset_obj);
+
+ size_t n_partitions = 0, n_unassigned = 0;
+ subset_p->count_partitions(n_partitions, n_unassigned);
+
+ return Py_BuildValue("nn", (Py_ssize_t) n_partitions,
+ (Py_ssize_t) n_unassigned);
}
static
PyObject *
-count_trim_below_abundance(khmer_KCountingHash_Object * me, PyObject * args)
+hashbits_subset_partition_size_distribution(khmer_KHashbits_Object * me,
+ PyObject * args)
{
- CountingHash * counting = me->counting;
-
- const char * seq = NULL;
- BoundedCounterType max_count_i = 0;
-
- if (!PyArg_ParseTuple(args, "sH", &seq, &max_count_i)) {
+ PyObject * subset_obj = NULL;
+ if (!PyArg_ParseTuple(args, "O", &subset_obj)) {
return NULL;
}
- unsigned long trim_at;
- Py_BEGIN_ALLOW_THREADS
+ SubsetPartition * subset_p;
+ subset_p = (SubsetPartition *) PyCObject_AsVoidPtr(subset_obj);
- BoundedCounterType max_count = max_count_i;
+ PartitionCountDistribution d;
- trim_at = counting->trim_below_abundance(seq, max_count);
+ unsigned int n_unassigned = 0;
+ subset_p->partition_size_distribution(d, n_unassigned);
- Py_END_ALLOW_THREADS;
+ PyObject * x = PyList_New(d.size());
+ if (x == NULL) {
+ return NULL;
+ }
+ PartitionCountDistribution::iterator di;
- PyObject * trim_seq = PyUnicode_FromStringAndSize(seq, trim_at);
- if (trim_seq == NULL) {
+ unsigned int i;
+ for (i = 0, di = d.begin(); di != d.end(); di++, i++) {
+ PyObject * value = Py_BuildValue("KK", di->first, di->second);
+ if (value == NULL) {
+ Py_DECREF(x);
+ return NULL;
+ }
+ PyList_SET_ITEM(x, i, value);
+ }
+ if (!(i == d.size())) {
+ throw khmer_exception();
+ }
+
+ PyObject * returnValue = Py_BuildValue("NI", x, n_unassigned);
+ if (returnValue == NULL) {
+ Py_DECREF(x);
return NULL;
}
- PyObject * ret = Py_BuildValue("Ok", trim_seq, trim_at);
- Py_DECREF(trim_seq);
-
- return ret;
+ return returnValue;
}
static
PyObject *
-count_find_spectral_error_positions(khmer_KCountingHash_Object * me,
- PyObject * args)
+hashbits_load(khmer_KHashbits_Object * me, PyObject * args)
{
- khmer::CountingHash * counting = me->counting;
+ Hashbits * hashbits = me->hashbits;
- char * seq = NULL;
- khmer::BoundedCounterType max_count = 0; // unsigned short int
+ const char * filename = NULL;
- if (!PyArg_ParseTuple(args, "sH", &seq, &max_count)) {
+ if (!PyArg_ParseTuple(args, "s", &filename)) {
return NULL;
}
- std::vector<unsigned int> posns;
-
try {
- posns = counting->find_spectral_error_positions(seq, max_count);
- } catch (khmer_exception &e) {
- PyErr_SetString(PyExc_ValueError, e.what());
- return NULL;
- }
-
- Py_ssize_t posns_size = posns.size();
-
- PyObject * x = PyList_New(posns_size);
- if (x == NULL) {
+ hashbits->load(filename);
+ } catch (khmer_file_exception &e) {
+ PyErr_SetString(PyExc_IOError, e.what());
return NULL;
}
- for (Py_ssize_t i = 0; i < posns_size; i++) {
- PyList_SET_ITEM(x, i, PyLong_FromLong(posns[i]));
- }
- return x;
+ Py_RETURN_NONE;
}
static
PyObject *
-count_fasta_dump_kmers_by_abundance(khmer_KCountingHash_Object * me,
- PyObject * args)
+hashbits_save(khmer_KHashbits_Object * me, PyObject * args)
{
- CountingHash * counting = me->counting;
+ Hashbits * hashbits = me->hashbits;
- const char * inputfile;
- int limit_by = 0;
+ const char * filename = NULL;
- if (!PyArg_ParseTuple(args, "si", &inputfile, &limit_by)) {
+ if (!PyArg_ParseTuple(args, "s", &filename)) {
return NULL;
}
- counting->fasta_dump_kmers_by_abundance(inputfile,
- limit_by);
+ try {
+ hashbits->save(filename);
+ } catch (khmer_file_exception &e) {
+ PyErr_SetString(PyExc_IOError, e.what());
+ return NULL;
+ }
Py_RETURN_NONE;
}
static
PyObject *
-count_get_kadian_count(khmer_KCountingHash_Object * me, PyObject * args)
+hashbits_load_tagset(khmer_KHashbits_Object * me, PyObject * args)
{
- CountingHash * counting = me->counting;
+ Hashbits * hashbits = me->hashbits;
- const char * long_str;
- unsigned int nk = 1;
+ const char * filename = NULL;
+ PyObject * clear_tags_o = NULL;
- if (!PyArg_ParseTuple(args, "s|I", &long_str, &nk)) {
+ if (!PyArg_ParseTuple(args, "s|O", &filename, &clear_tags_o)) {
return NULL;
}
- if (strlen(long_str) < counting->ksize()) {
- PyErr_SetString(PyExc_ValueError,
- "string length must >= the hashtable k-mer size");
- return NULL;
+ bool clear_tags = true;
+ if (clear_tags_o && !PyObject_IsTrue(clear_tags_o)) {
+ clear_tags = false;
}
- BoundedCounterType kad = 0;
-
- counting->get_kadian_count(long_str, kad, nk);
+ try {
+ hashbits->load_tagset(filename, clear_tags);
+ } catch (khmer_file_exception &e) {
+ PyErr_SetString(PyExc_IOError, e.what());
+ return NULL;
+ }
- return Py_BuildValue("i", kad);
+ Py_RETURN_NONE;
}
static
PyObject *
-count_get_raw_tables(khmer_KCountingHash_Object * self, PyObject * args)
+hashbits_save_tagset(khmer_KHashbits_Object * me, PyObject * args)
{
- CountingHash * counting = self->counting;
+ Hashbits * hashbits = me->hashbits;
- khmer::Byte ** table_ptrs = counting->get_raw_tables();
- std::vector<HashIntoType> sizes = counting->get_tablesizes();
+ const char * filename = NULL;
- PyObject * raw_tables = PyList_New(sizes.size());
- for (unsigned int i=0; i<sizes.size(); ++i) {
- Py_buffer buffer;
- int res = PyBuffer_FillInfo(&buffer, NULL, table_ptrs[i], sizes[i], 0, PyBUF_FULL_RO);
- if (res == -1) {
- return NULL;
- }
- PyObject * buf = PyMemoryView_FromBuffer(&buffer);
- if(!PyMemoryView_Check(buf)) {
- return NULL;
- }
- PyList_SET_ITEM(raw_tables, i, buf);
+ if (!PyArg_ParseTuple(args, "s", &filename)) {
+ return NULL;
}
- return raw_tables;
+ try {
+ hashbits->save_tagset(filename);
+ } catch (khmer_file_exception &e) {
+ PyErr_SetString(PyExc_IOError, e.what());
+ return NULL;
+ }
+
+ Py_RETURN_NONE;
}
static
PyObject *
-count_set_use_bigcount(khmer_KCountingHash_Object * me, PyObject * args)
+hashbits_save_subset_partitionmap(khmer_KHashbits_Object * me, PyObject * args)
{
- CountingHash * counting = me->counting;
+ const char * filename = NULL;
+ PyObject * subset_obj = NULL;
- PyObject * x;
- if (!PyArg_ParseTuple(args, "O", &x)) {
- return NULL;
- }
- int setme = PyObject_IsTrue(x);
- if (setme < 0) {
+ if (!PyArg_ParseTuple(args, "Os", &subset_obj, &filename)) {
return NULL;
}
- counting->set_use_bigcount((bool)setme);
- Py_RETURN_NONE;
-}
+ SubsetPartition * subset_p;
+ subset_p = (SubsetPartition *) PyCObject_AsVoidPtr(subset_obj);
-static
-PyObject *
-count_get_use_bigcount(khmer_KCountingHash_Object * me, PyObject * args)
-{
- CountingHash * counting = me->counting;
+ Py_BEGIN_ALLOW_THREADS
- if (!PyArg_ParseTuple(args, "")) {
+ try {
+ subset_p->save_partitionmap(filename);
+ } catch (khmer_file_exception &e) {
+ PyErr_SetString(PyExc_IOError, e.what());
return NULL;
}
- bool val = counting->get_use_bigcount();
+ Py_END_ALLOW_THREADS
- return PyBool_FromLong((int)val);
+ Py_RETURN_NONE;
}
static
PyObject *
-count_get_min_count(khmer_KCountingHash_Object * me, PyObject * args)
+hashbits_load_subset_partitionmap(khmer_KHashbits_Object * me, PyObject * args)
{
- CountingHash * counting = me->counting;
+ Hashbits * hashbits = me->hashbits;
- const char * long_str;
+ const char * filename = NULL;
- if (!PyArg_ParseTuple(args, "s", &long_str)) {
+ if (!PyArg_ParseTuple(args, "s", &filename)) {
return NULL;
}
- if (strlen(long_str) < counting->ksize()) {
- PyErr_SetString(PyExc_ValueError,
- "string length must >= the hashtable k-mer size");
- return NULL;
+ SubsetPartition * subset_p;
+ try {
+ subset_p = new SubsetPartition(hashbits);
+ } catch (std::bad_alloc &e) {
+ return PyErr_NoMemory();
}
- BoundedCounterType c = counting->get_min_count(long_str);
- unsigned int N = c;
-
- return PyLong_FromLong(N);
-}
-
-static
-PyObject *
-count_get_max_count(khmer_KCountingHash_Object * me, PyObject * args)
-{
- CountingHash * counting = me->counting;
+ bool fail = false;
+ std::string err;
- const char * long_str;
+ Py_BEGIN_ALLOW_THREADS
- if (!PyArg_ParseTuple(args, "s", &long_str)) {
- return NULL;
+ try {
+ subset_p->load_partitionmap(filename);
+ } catch (khmer_file_exception &e) {
+ fail = true;
+ err = e.what();
}
- if (strlen(long_str) < counting->ksize()) {
- PyErr_SetString(PyExc_ValueError,
- "string length must >= the hashtable k-mer size");
+ Py_END_ALLOW_THREADS
+
+ if (fail) {
+ PyErr_SetString(PyExc_IOError, err.c_str());
+ delete subset_p;
return NULL;
+ } else {
+ return PyCObject_FromVoidPtr(subset_p, free_subset_partition_info);
}
-
- BoundedCounterType c = counting->get_max_count(long_str);
- unsigned int N = c;
-
- return PyLong_FromLong(N);
}
static
PyObject *
-count_output_fasta_kmer_pos_freq(khmer_KCountingHash_Object * me,
- PyObject * args)
+hashbits__set_tag_density(khmer_KHashbits_Object * me, PyObject * args)
{
- CountingHash * counting = me->counting;
-
- const char * infile;
- const char * outfile;
+ Hashbits * hashbits = me->hashbits;
- if (!PyArg_ParseTuple(args, "ss", &infile, &outfile)) {
+ unsigned int d;
+ if (!PyArg_ParseTuple(args, "I", &d)) {
return NULL;
}
- counting->output_fasta_kmer_pos_freq(infile, outfile);
+ hashbits->_set_tag_density(d);
- return PyLong_FromLong(0);
+ Py_RETURN_NONE;
}
static
PyObject *
-count_fasta_count_kmers_by_position(khmer_KCountingHash_Object * me,
- PyObject * args)
+hashbits__get_tag_density(khmer_KHashbits_Object * me, PyObject * args)
{
- CountingHash * counting = me->counting;
-
- const char * inputfile;
- unsigned int max_read_len = 0;
- long max_read_len_long;
- int limit_by_count_int;
-
- if (!PyArg_ParseTuple(args, "sli", &inputfile, &max_read_len_long,
- &limit_by_count_int)) {
- return NULL;
- }
- if (max_read_len_long < 0 || max_read_len_long >= pow(2, 32)) {
- PyErr_SetString(
- PyExc_ValueError,
- "The 2nd argument must be positive and less than 2^32");
- return NULL;
- }
- if (limit_by_count_int < 0 || limit_by_count_int >= pow(2, 16)) {
- PyErr_SetString(
- PyExc_ValueError,
- "The 3rd argument must be positive and less than 2^16");
- return NULL;
- }
- max_read_len = (unsigned int) max_read_len_long;
-
- unsigned long long * counts;
- counts = counting->fasta_count_kmers_by_position(inputfile, max_read_len,
- (unsigned short) limit_by_count_int);
+ Hashbits * hashbits = me->hashbits;
- PyObject * x = PyList_New(max_read_len);
- if (x == NULL) {
- delete[] counts;
+ if (!PyArg_ParseTuple(args, "")) {
return NULL;
}
- for (unsigned int i = 0; i < max_read_len; i++) {
- int ret = PyList_SetItem(x, i, PyLong_FromUnsignedLongLong(counts[i]));
- if (ret < 0) {
- delete[] counts;
- return NULL;
- }
- }
-
- delete[] counts;
+ unsigned int d = hashbits->_get_tag_density();
- return x;
+ return PyLong_FromLong(d);
}
static
PyObject *
-count_abundance_distribution_with_reads_parser(khmer_KCountingHash_Object * me,
- PyObject * args)
+hashbits__validate_subset_partitionmap(khmer_KHashbits_Object * me,
+ PyObject * args)
{
- CountingHash * counting = me->counting;
+ PyObject * subset_obj = NULL;
- khmer :: python :: khmer_ReadParser_Object * rparser_obj = NULL;
- khmer_KHashbits_Object *tracking_obj = NULL;
-
- if (!PyArg_ParseTuple(args, "O!O!", &python::khmer_ReadParser_Type,
- &rparser_obj, &khmer_KHashbits_Type, &tracking_obj)) {
+ if (!PyArg_ParseTuple(args, "O", &subset_obj)) {
return NULL;
}
- read_parsers:: IParser * rparser = rparser_obj->parser;
- Hashbits * hashbits = tracking_obj->hashbits;
+ SubsetPartition * subset_p;
+ subset_p = (SubsetPartition *) PyCObject_AsVoidPtr(subset_obj);
+ subset_p->_validate_pmap();
- HashIntoType * dist = NULL;
+ Py_RETURN_NONE;
+}
- Py_BEGIN_ALLOW_THREADS
- dist = counting->abundance_distribution(rparser, hashbits);
- Py_END_ALLOW_THREADS
+static
+PyObject *
+hashbits_set_partition_id(khmer_KHashbits_Object * me, PyObject * args)
+{
+ Hashbits * hashbits = me->hashbits;
- PyObject * x = PyList_New(MAX_BIGCOUNT + 1);
- if (x == NULL) {
- delete[] dist;
+ const char * kmer = NULL;
+ PartitionID p = 0;
+
+ if (!PyArg_ParseTuple(args, "sI", &kmer, &p)) {
return NULL;
}
- for (int i = 0; i < MAX_BIGCOUNT + 1; i++) {
- PyList_SET_ITEM(x, i, PyLong_FromUnsignedLongLong(dist[i]));
- }
- delete[] dist;
- return x;
+ hashbits->partition->set_partition_id(kmer, p);
+
+ Py_RETURN_NONE;
}
static
PyObject *
-count_abundance_distribution(khmer_KCountingHash_Object * me, PyObject * args)
+hashbits_join_partitions(khmer_KHashbits_Object * me, PyObject * args)
{
- CountingHash * counting = me->counting;
+ Hashbits * hashbits = me->hashbits;
- const char * filename = NULL;
- khmer_KHashbits_Object * tracking_obj = NULL;
- if (!PyArg_ParseTuple(args, "sO!", &filename, &khmer_KHashbits_Type,
- &tracking_obj)) {
+ PartitionID p1 = 0, p2 = 0;
+
+ if (!PyArg_ParseTuple(args, "II", &p1, &p2)) {
return NULL;
}
- Hashbits * hashbits = tracking_obj->hashbits;
- HashIntoType * dist;
+ p1 = hashbits->partition->join_partitions(p1, p2);
- char const * result = "";
- bool exception = false;
- Py_BEGIN_ALLOW_THREADS
- try {
- dist = counting->abundance_distribution(filename, hashbits);
- } catch (khmer_file_exception &e) {
- exception = true;
- result = e.what();
- }
- Py_END_ALLOW_THREADS
+ return PyLong_FromLong(p1);
+}
- if (exception) {
- PyErr_SetString(PyExc_IOError, result);
- return NULL;
- }
+static
+PyObject *
+hashbits_get_partition_id(khmer_KHashbits_Object * me, PyObject * args)
+{
+ Hashbits * hashbits = me->hashbits;
- PyObject * x = PyList_New(MAX_BIGCOUNT + 1);
- if (x == NULL) {
- delete[] dist;
+ const char * kmer = NULL;
+
+ if (!PyArg_ParseTuple(args, "s", &kmer)) {
return NULL;
}
- for (int i = 0; i < MAX_BIGCOUNT + 1; i++) {
- PyList_SET_ITEM(x, i, PyLong_FromUnsignedLongLong(dist[i]));
- }
- delete[] dist;
+ PartitionID partition_id;
+ partition_id = hashbits->partition->get_partition_id(kmer);
- return x;
+ return PyLong_FromLong(partition_id);
}
static
PyObject *
-count_do_subset_partition_with_abundance(khmer_KCountingHash_Object * me,
- PyObject * args)
+hashbits_is_single_partition(khmer_KHashbits_Object * me, PyObject * args)
{
- CountingHash * counting = me->counting;
+ Hashbits * hashbits = me->hashbits;
- HashIntoType start_kmer = 0, end_kmer = 0;
- PyObject * break_on_stop_tags_o = NULL;
- PyObject * stop_big_traversals_o = NULL;
- BoundedCounterType min_count, max_count;
+ const char * seq = NULL;
- if (!PyArg_ParseTuple(args, "HH|KKOO",
- &min_count, &max_count,
- &start_kmer, &end_kmer,
- &break_on_stop_tags_o,
- &stop_big_traversals_o)) {
+ if (!PyArg_ParseTuple(args, "s", &seq)) {
return NULL;
}
- bool break_on_stop_tags = false;
- if (break_on_stop_tags_o && PyObject_IsTrue(break_on_stop_tags_o)) {
- break_on_stop_tags = true;
- }
- bool stop_big_traversals = false;
- if (stop_big_traversals_o && PyObject_IsTrue(stop_big_traversals_o)) {
- stop_big_traversals = true;
- }
+ bool v = hashbits->partition->is_single_partition(seq);
- SubsetPartition * subset_p = NULL;
- try {
- Py_BEGIN_ALLOW_THREADS
- subset_p = new SubsetPartition(counting);
- subset_p->do_partition_with_abundance(start_kmer, end_kmer,
- min_count, max_count,
- break_on_stop_tags,
- stop_big_traversals);
- Py_END_ALLOW_THREADS
- } catch (std::bad_alloc &e) {
- return PyErr_NoMemory();
+ PyObject * val;
+ if (v) {
+ val = Py_True;
+ } else {
+ val = Py_False;
}
+ Py_INCREF(val);
- khmer_KSubsetPartition_Object * subset_obj = (khmer_KSubsetPartition_Object *)\
- PyObject_New(khmer_KSubsetPartition_Object, &khmer_KSubsetPartition_Type);
+ return val;
+}
- if (subset_obj == NULL) {
- delete subset_p;
+static
+PyObject *
+hashbits_divide_tags_into_subsets(khmer_KHashbits_Object * me, PyObject * args)
+{
+ Hashbits * hashbits = me->hashbits;
+
+ unsigned int subset_size = 0;
+
+ if (!PyArg_ParseTuple(args, "I", &subset_size)) {
return NULL;
}
- subset_obj->subset = subset_p;
+ SeenSet divvy;
+ hashbits->divide_tags_into_subsets(subset_size, divvy);
- return (PyObject *) subset_obj;
+ PyObject * x = PyList_New(divvy.size());
+ unsigned int i = 0;
+ for (SeenSet::const_iterator si = divvy.begin(); si != divvy.end();
+ si++, i++) {
+ PyList_SET_ITEM(x, i, PyLong_FromUnsignedLongLong(*si));
+ }
+
+ return x;
}
-static PyMethodDef khmer_counting_methods[] = {
- { "set_use_bigcount", (PyCFunction)count_set_use_bigcount, METH_VARARGS, "" },
- { "get_use_bigcount", (PyCFunction)count_get_use_bigcount, METH_VARARGS, "" },
- { "output_fasta_kmer_pos_freq", (PyCFunction)count_output_fasta_kmer_pos_freq, METH_VARARGS, "" },
- { "get_min_count", (PyCFunction)count_get_min_count, METH_VARARGS, "Get the smallest count of all the k-mers in the string" },
- { "get_max_count", (PyCFunction)count_get_max_count, METH_VARARGS, "Get the largest count of all the k-mers in the string" },
- { "get_kadian_count", (PyCFunction)count_get_kadian_count, METH_VARARGS, "Get the kadian (abundance of k-th rank-ordered k-mer) of the k-mer counts in the string" },
- { "trim_on_abundance", (PyCFunction)count_trim_on_abundance, METH_VARARGS, "Trim on >= abundance" },
- { "trim_below_abundance", (PyCFunction)count_trim_below_abundance, METH_VARARGS, "Trim on >= abundance" },
- { "find_spectral_error_positions", (PyCFunction)count_find_spectral_error_positions, METH_VARARGS, "Identify positions of low-abundance k-mers" },
- { "abundance_distribution", (PyCFunction)count_abundance_distribution, METH_VARARGS, "" },
- { "abundance_distribution_with_reads_parser", (PyCFunction)count_abundance_distribution_with_reads_parser, METH_VARARGS, "" },
- { "fasta_count_kmers_by_position", (PyCFunction)count_fasta_count_kmers_by_position, METH_VARARGS, "" },
- { "fasta_dump_kmers_by_abundance", (PyCFunction)count_fasta_dump_kmers_by_abundance, METH_VARARGS, "" },
- {
- "get_raw_tables", (PyCFunction)count_get_raw_tables,
- METH_VARARGS, "Get a list of the raw tables as memoryview objects"
- },
- { "do_subset_partition_with_abundance", (PyCFunction)count_do_subset_partition_with_abundance, METH_VARARGS, "" },
- {NULL, NULL, 0, NULL} /* sentinel */
-};
+static
+PyObject *
+hashbits_count_kmers_within_radius(khmer_KHashbits_Object * me, PyObject * args)
+{
+ Hashbits * hashbits = me->hashbits;
-static PyObject* _new_counting_hash(PyTypeObject * type, PyObject * args,
- PyObject * kwds);
+ const char * kmer = NULL;
+ unsigned int radius = 0;
+ unsigned int max_count = 0;
-static PyTypeObject khmer_KCountingHash_Type
-CPYCHECKER_TYPE_OBJECT_FOR_TYPEDEF("khmer_KCountingHash_Object")
-= {
- PyVarObject_HEAD_INIT(NULL, 0) /* init & ob_size */
- "_khmer.CountingHash", /*tp_name*/
- sizeof(khmer_KCountingHash_Object), /*tp_basicsize*/
- 0, /*tp_itemsize*/
- (destructor)khmer_counting_dealloc, /*tp_dealloc*/
- 0, /*tp_print*/
- 0, /*tp_getattr*/
- 0, /*tp_setattr*/
- 0, /*tp_compare*/
- 0, /*tp_repr*/
- 0, /*tp_as_number*/
- 0, /*tp_as_sequence*/
- 0, /*tp_as_mapping*/
- 0, /*tp_hash */
- 0, /*tp_call*/
- 0, /*tp_str*/
- 0, /*tp_getattro*/
- 0, /*tp_setattro*/
- 0, /*tp_as_buffer*/
- Py_TPFLAGS_DEFAULT | Py_TPFLAGS_BASETYPE, /*tp_flags*/
- "counting hash object", /* tp_doc */
- 0, /* tp_traverse */
- 0, /* tp_clear */
- 0, /* tp_richcompare */
- 0, /* tp_weaklistoffset */
- 0, /* tp_iter */
- 0, /* tp_iternext */
- khmer_counting_methods, /* tp_methods */
- 0, /* tp_members */
- 0, /* tp_getset */
- 0, /* tp_base */
- 0, /* tp_dict */
- 0, /* tp_descr_get */
- 0, /* tp_descr_set */
- 0, /* tp_dictoffset */
- 0, /* tp_init */
- 0, /* tp_alloc */
- _new_counting_hash, /* tp_new */
-};
+ if (!PyArg_ParseTuple(args, "sI|I", &kmer, &radius, &max_count)) {
+ return NULL;
+ }
-#define is_counting_obj(v) (Py_TYPE(v) == &khmer_KCountingHash_Type)
+ unsigned int n;
-//
-// new_hashtable
-//
+ Py_BEGIN_ALLOW_THREADS
-static PyObject* new_hashtable(PyObject * self, PyObject * args)
-{
- unsigned int k = 0;
- unsigned long long size = 0;
+ HashIntoType kmer_f, kmer_r;
+ _hash(kmer, hashbits->ksize(), kmer_f, kmer_r);
+ n = hashbits->count_kmers_within_radius(kmer_f, kmer_r, radius,
+ max_count);
- if (!PyArg_ParseTuple(args, "IK", &k, &size)) {
- return NULL;
- }
+ Py_END_ALLOW_THREADS
- khmer_KCountingHash_Object * kcounting_obj = (khmer_KCountingHash_Object *) \
- PyObject_New(khmer_KCountingHash_Object, &khmer_KCountingHash_Type);
+ return PyLong_FromUnsignedLong(n);
+}
- if (kcounting_obj == NULL) {
+static
+PyObject *
+hashbits_get_ksize(khmer_KHashbits_Object * me, PyObject * args)
+{
+ Hashbits * hashbits = me->hashbits;
+
+ if (!PyArg_ParseTuple(args, "")) {
return NULL;
}
- try {
- kcounting_obj->counting = new CountingHash(k, size);
- } catch (std::bad_alloc &e) {
- return PyErr_NoMemory();
- }
- kcounting_obj->khashtable.hashtable = kcounting_obj->counting;
+ unsigned int k = hashbits->ksize();
- return (PyObject *) kcounting_obj;
+ return PyLong_FromLong(k);
}
-//
-// _new_counting_hash
-//
-static PyObject* _new_counting_hash(PyTypeObject * type, PyObject * args,
- PyObject * kwds)
+static
+PyObject *
+hashbits_get_hashsizes(khmer_KHashbits_Object * me, PyObject * args)
{
- khmer_KCountingHash_Object * self;
-
- self = (khmer_KCountingHash_Object *)type->tp_alloc(type, 0);
-
- if (self != NULL) {
- WordLength k = 0;
- PyListObject * sizes_list_o = NULL;
+ Hashbits * hashbits = me->hashbits;
- if (!PyArg_ParseTuple(args, "bO!", &k, &PyList_Type, &sizes_list_o)) {
- Py_DECREF(self);
- return NULL;
- }
+ if (!PyArg_ParseTuple(args, "")) {
+ return NULL;
+ }
- std::vector<HashIntoType> sizes;
- Py_ssize_t sizes_list_o_length = PyList_GET_SIZE(sizes_list_o);
- if (sizes_list_o_length == -1) {
- Py_DECREF(self);
- PyErr_SetString(PyExc_ValueError, "error with hashtable primes!");
- return NULL;
- }
- for (Py_ssize_t i = 0; i < sizes_list_o_length; i++) {
- PyObject * size_o = PyList_GET_ITEM(sizes_list_o, i);
- if (PyLong_Check(size_o)) {
- sizes.push_back((HashIntoType) PyLong_AsUnsignedLongLong(size_o));
- } else if (PyInt_Check(size_o)) {
- sizes.push_back((HashIntoType) PyInt_AsLong(size_o));
- } else if (PyFloat_Check(size_o)) {
- sizes.push_back((HashIntoType) PyFloat_AS_DOUBLE(size_o));
- } else {
- Py_DECREF(self);
- PyErr_SetString(PyExc_TypeError,
- "2nd argument must be a list of ints, longs, or floats");
- return NULL;
- }
- }
+ std::vector<HashIntoType> ts = hashbits->get_tablesizes();
- try {
- self->counting = new CountingHash(k, sizes);
- } catch (std::bad_alloc &e) {
- Py_DECREF(self);
- return PyErr_NoMemory();
- }
- self->khashtable.hashtable = (Hashtable *) self->counting;
+ PyObject * x = PyList_New(ts.size());
+ for (size_t i = 0; i < ts.size(); i++) {
+ PyList_SET_ITEM(x, i, PyLong_FromUnsignedLongLong(ts[i]));
}
- return (PyObject *) self;
+ return x;
}
static
PyObject *
-hashbits_count_overlap(khmer_KHashbits_Object * me, PyObject * args)
+hashbits_extract_unique_paths(khmer_KHashbits_Object * me, PyObject * args)
{
Hashbits * hashbits = me->hashbits;
- khmer_KHashbits_Object * ht2_argu;
- const char * filename;
- Hashbits * ht2;
- if (!PyArg_ParseTuple(args, "sO!", &filename, &khmer_KHashbits_Type,
- &ht2_argu)) {
+ const char * sequence = NULL;
+ unsigned int min_length = 0;
+ float min_unique_f = 0;
+ if (!PyArg_ParseTuple(args, "sIf", &sequence, &min_length, &min_unique_f)) {
return NULL;
}
- ht2 = ht2_argu->hashbits;
-
-// call the C++ function, and trap signals => Python
-
- unsigned long long n_consumed;
- unsigned int total_reads;
- HashIntoType curve[2][100];
+ std::vector<std::string> results;
+ hashbits->extract_unique_paths(sequence, min_length, min_unique_f, results);
- try {
- hashbits->consume_fasta_overlap(filename, curve, *ht2, total_reads, n_consumed);
- } catch (InvalidStreamHandle &e) {
- PyErr_SetString(PyExc_IOError, e.what());
+ PyObject * x = PyList_New(results.size());
+ if (x == NULL) {
return NULL;
}
- HashIntoType n = hashbits->n_unique_kmers();
- HashIntoType n_overlap = hashbits->n_overlap_kmers();
-
- PyObject * x = PyList_New(200);
-
- for (unsigned int i = 0; i < 100; i++) {
- PyList_SetItem(x, i, Py_BuildValue("K", curve[0][i]));
- }
- for (unsigned int i = 0; i < 100; i++) {
- PyList_SetItem(x, i + 100, Py_BuildValue("K", curve[1][i]));
+ for (unsigned int i = 0; i < results.size(); i++) {
+ PyList_SET_ITEM(x, i, PyBytes_FromString(results[i].c_str()));
}
- return Py_BuildValue("KKO", n, n_overlap, x);
+
+ return x;
}
static
PyObject *
-hashbits_update(khmer_KHashbits_Object * me, PyObject * args)
+hashbits_get_median_count(khmer_KHashbits_Object * me, PyObject * args)
{
Hashbits * hashbits = me->hashbits;
- Hashbits * other;
- khmer_KHashbits_Object * other_o;
- if (!PyArg_ParseTuple(args, "O!", &khmer_KHashbits_Type, &other_o)) {
+ const char * long_str;
+
+ if (!PyArg_ParseTuple(args, "s", &long_str)) {
return NULL;
}
- other = other_o->hashbits;
-
- try {
- hashbits->update_from(*other);
- } catch (khmer_exception &e) {
- PyErr_SetString(PyExc_ValueError, e.what());
+ if (strlen(long_str) < hashbits->ksize()) {
+ PyErr_SetString(PyExc_ValueError,
+ "string length must >= the hashtable k-mer size");
return NULL;
}
- Py_RETURN_NONE;
+ BoundedCounterType med = 0;
+ float average = 0, stddev = 0;
+
+ hashbits->get_median_count(long_str, med, average, stddev);
+
+ return Py_BuildValue("iff", med, average, stddev);
}
static PyMethodDef khmer_hashbits_methods[] = {
+ { "extract_unique_paths", (PyCFunction)hashbits_extract_unique_paths, METH_VARARGS, "" },
+ { "ksize", (PyCFunction)hashbits_get_ksize, METH_VARARGS, "" },
+ { "hashsizes", (PyCFunction)hashbits_get_hashsizes, METH_VARARGS, "" },
+ { "n_occupied", (PyCFunction)hashbits_n_occupied, METH_VARARGS, "Count the number of occupied bins" },
+ { "n_unique_kmers", (PyCFunction)hashbits_n_unique_kmers, METH_VARARGS, "Count the number of unique kmers" },
+ { "count", (PyCFunction)hashbits_count, METH_VARARGS, "Count the given kmer" },
{ "count_overlap", (PyCFunction)hashbits_count_overlap, METH_VARARGS, "Count overlap kmers in two datasets" },
+ { "consume", (PyCFunction)hashbits_consume, METH_VARARGS, "Count all k-mers in the given string" },
+ { "load_stop_tags", (PyCFunction)hashbits_load_stop_tags, METH_VARARGS, "" },
+ { "save_stop_tags", (PyCFunction)hashbits_save_stop_tags, METH_VARARGS, "" },
+ { "print_stop_tags", (PyCFunction)hashbits_print_stop_tags, METH_VARARGS, "" },
+ { "print_tagset", (PyCFunction)hashbits_print_tagset, METH_VARARGS, "" },
+ { "get", (PyCFunction)hashbits_get, METH_VARARGS, "Get the count for the given k-mer" },
+ { "calc_connected_graph_size", (PyCFunction)hashbits_calc_connected_graph_size, METH_VARARGS, "" },
+ { "kmer_degree", (PyCFunction)hashbits_kmer_degree, METH_VARARGS, "" },
+ { "trim_on_stoptags", (PyCFunction)hashbits_trim_on_stoptags, METH_VARARGS, "" },
+ { "identify_stoptags_by_position", (PyCFunction)hashbits_identify_stoptags_by_position, METH_VARARGS, "" },
+ { "do_subset_partition", (PyCFunction)hashbits_do_subset_partition, METH_VARARGS, "" },
+ { "find_all_tags", (PyCFunction)hashbits_find_all_tags, METH_VARARGS, "" },
+ { "assign_partition_id", (PyCFunction)hashbits_assign_partition_id, METH_VARARGS, "" },
+ { "output_partitions", (PyCFunction)hashbits_output_partitions, METH_VARARGS, "" },
+ { "find_unpart", (PyCFunction)hashbits_find_unpart, METH_VARARGS, "" },
+ { "filter_if_present", (PyCFunction)hashbits_filter_if_present, METH_VARARGS, "" },
+ { "add_tag", (PyCFunction)hashbits_add_tag, METH_VARARGS, "" },
+ { "add_stop_tag", (PyCFunction)hashbits_add_stop_tag, METH_VARARGS, "" },
+ { "get_stop_tags", (PyCFunction)hashbits_get_stop_tags, METH_VARARGS, "" },
+ { "get_tagset", (PyCFunction)hashbits_get_tagset, METH_VARARGS, "" },
+ { "load", (PyCFunction)hashbits_load, METH_VARARGS, "" },
+ { "save", (PyCFunction)hashbits_save, METH_VARARGS, "" },
+ { "load_tagset", (PyCFunction)hashbits_load_tagset, METH_VARARGS, "" },
+ { "save_tagset", (PyCFunction)hashbits_save_tagset, METH_VARARGS, "" },
+ { "n_tags", (PyCFunction)hashbits_n_tags, METH_VARARGS, "" },
+ { "divide_tags_into_subsets", (PyCFunction)hashbits_divide_tags_into_subsets, METH_VARARGS, "" },
+ { "load_partitionmap", (PyCFunction)hashbits_load_partitionmap, METH_VARARGS, "" },
+ { "save_partitionmap", (PyCFunction)hashbits_save_partitionmap, METH_VARARGS, "" },
+ { "_validate_partitionmap", (PyCFunction)hashbits__validate_partitionmap, METH_VARARGS, "" },
+ { "_get_tag_density", (PyCFunction)hashbits__get_tag_density, METH_VARARGS, "" },
+ { "_set_tag_density", (PyCFunction)hashbits__set_tag_density, METH_VARARGS, "" },
+ { "consume_fasta", (PyCFunction)hashbits_consume_fasta, METH_VARARGS, "Count all k-mers in a given file" },
+ { "consume_fasta_with_reads_parser", (PyCFunction)hashbits_consume_fasta_with_reads_parser, METH_VARARGS, "Count all k-mers in a given file" },
+ { "consume_fasta_and_tag", (PyCFunction)hashbits_consume_fasta_and_tag, METH_VARARGS, "Count all k-mers in a given file" },
{
- "update",
- (PyCFunction) hashbits_update, METH_VARARGS,
- "a set update: update this nodegraph with all the entries from the other"
+ "consume_fasta_and_tag_with_reads_parser", (PyCFunction)hashbits_consume_fasta_and_tag_with_reads_parser,
+ METH_VARARGS, "Count all k-mers using a given reads parser"
},
+ { "consume_fasta_and_traverse", (PyCFunction)hashbits_consume_fasta_and_traverse, METH_VARARGS, "" },
+ { "consume_fasta_and_tag_with_stoptags", (PyCFunction)hashbits_consume_fasta_and_tag_with_stoptags, METH_VARARGS, "Count all k-mers in a given file" },
+ { "consume_partitioned_fasta", (PyCFunction)hashbits_consume_partitioned_fasta, METH_VARARGS, "Count all k-mers in a given file" },
+ { "join_partitions_by_path", (PyCFunction)hashbits_join_partitions_by_path, METH_VARARGS, "" },
+ { "merge_subset", (PyCFunction)hashbits_merge_subset, METH_VARARGS, "" },
+ { "merge_subset_from_disk", (PyCFunction)hashbits_merge_from_disk, METH_VARARGS, "" },
+ { "count_partitions", (PyCFunction)hashbits_count_partitions, METH_VARARGS, "" },
+ { "subset_count_partitions", (PyCFunction)hashbits_subset_count_partitions, METH_VARARGS, "" },
+ { "subset_partition_size_distribution", (PyCFunction)hashbits_subset_partition_size_distribution, METH_VARARGS, "" },
+ { "save_subset_partitionmap", (PyCFunction)hashbits_save_subset_partitionmap, METH_VARARGS },
+ { "load_subset_partitionmap", (PyCFunction)hashbits_load_subset_partitionmap, METH_VARARGS },
+ { "_validate_subset_partitionmap", (PyCFunction)hashbits__validate_subset_partitionmap, METH_VARARGS, "" },
+ { "set_partition_id", (PyCFunction)hashbits_set_partition_id, METH_VARARGS, "" },
+ { "join_partitions", (PyCFunction)hashbits_join_partitions, METH_VARARGS, "" },
+ { "get_partition_id", (PyCFunction)hashbits_get_partition_id, METH_VARARGS, "" },
+ { "is_single_partition", (PyCFunction)hashbits_is_single_partition, METH_VARARGS, "" },
+ { "count_kmers_within_radius", (PyCFunction)hashbits_count_kmers_within_radius, METH_VARARGS, "" },
+ { "traverse_from_tags", (PyCFunction)hashbits_traverse_from_tags, METH_VARARGS, "" },
+ { "repartition_largest_partition", (PyCFunction)hashbits_repartition_largest_partition, METH_VARARGS, "" },
+ { "get_median_count", (PyCFunction)hashbits_get_median_count, METH_VARARGS, "Get the median, average, and stddev of the k-mer counts in the string" },
{NULL, NULL, 0, NULL} /* sentinel */
};
@@ -3346,14 +3484,19 @@ static PyObject* khmer_hashbits_new(PyTypeObject * type, PyObject * args,
try {
self->hashbits = new Hashbits(k, sizes);
} catch (std::bad_alloc &e) {
- Py_DECREF(self);
return PyErr_NoMemory();
}
- self->khashtable.hashtable = self->hashbits;
}
return (PyObject *) self;
}
+// there are no attributes that we need at this time, so we'll just return 0
+static int khmer_hashbits_init(khmer_KHashbits_Object * self, PyObject * args,
+ PyObject * kwds)
+{
+ return 0;
+}
+
#define is_hashbits_obj(v) (Py_TYPE(v) == &khmer_KHashbits_Type)
////////////////////////////////////////////////////////////////////////////
@@ -3581,10 +3724,13 @@ static PyMethodDef khmer_subset_methods[] = {
// LabelHash addition
typedef struct {
- PyObject_HEAD
+ //PyObject_HEAD
+ khmer_KHashbits_Object khashbits;
LabelHash * labelhash;
} khmer_KLabelHash_Object;
+static int khmer_labelhash_init(khmer_KLabelHash_Object * self, PyObject *args,
+ PyObject *kwds);
static PyObject * khmer_labelhash_new(PyTypeObject * type, PyObject *args,
PyObject *kwds);
@@ -3602,6 +3748,9 @@ static void khmer_labelhash_dealloc(khmer_KLabelHash_Object * obj)
Py_TYPE(obj)->tp_free((PyObject*)obj);
}
+// a little weird; we don't actually want to call Hashbits' new method. Rather, we
+// define our own new method, and redirect the base's hashbits object to point to our
+// labelhash object
static PyObject * khmer_labelhash_new(PyTypeObject *type, PyObject *args,
PyObject *kwds)
{
@@ -3609,38 +3758,59 @@ static PyObject * khmer_labelhash_new(PyTypeObject *type, PyObject *args,
self = (khmer_KLabelHash_Object*)type->tp_alloc(type, 0);
if (self != NULL) {
- PyObject * hashtable_o;
- khmer::Hashtable * hashtable = NULL;
+ WordLength k = 0;
+ PyListObject * sizes_list_o = NULL;
- if (!PyArg_ParseTuple(args, "O", &hashtable_o)) {
+ if (!PyArg_ParseTuple(args, "bO!", &k, &PyList_Type, &sizes_list_o)) {
Py_DECREF(self);
return NULL;
}
- if (PyObject_TypeCheck(hashtable_o, &khmer_KHashbits_Type)) {
- khmer_KHashbits_Object * kho = (khmer_KHashbits_Object *) hashtable_o;
- hashtable = kho->hashbits;
- } else if (PyObject_TypeCheck(hashtable_o, &khmer_KCountingHash_Type)) {
- khmer_KCountingHash_Object * cho = (khmer_KCountingHash_Object *) hashtable_o;
- hashtable = cho->counting;
- } else {
- PyErr_SetString(PyExc_ValueError,
- "graph object must be a NodeGraph or CountGraph");
- Py_DECREF(self);
- return NULL;
+ std::vector<HashIntoType> sizes;
+ Py_ssize_t sizes_list_o_length = PyList_GET_SIZE(sizes_list_o);
+ for (Py_ssize_t i = 0; i < sizes_list_o_length; i++) {
+ PyObject * size_o = PyList_GET_ITEM(sizes_list_o, i);
+ if (PyLong_Check(size_o)) {
+ sizes.push_back((HashIntoType) PyLong_AsUnsignedLongLong(size_o));
+ } else if (PyInt_Check(size_o)) {
+ sizes.push_back((HashIntoType) PyInt_AsLong(size_o));
+ } else if (PyFloat_Check(size_o)) {
+ sizes.push_back((HashIntoType) PyFloat_AS_DOUBLE(size_o));
+ } else {
+ Py_DECREF(self);
+ PyErr_SetString(PyExc_TypeError,
+ "2nd argument must be a list of ints, longs, or floats");
+ return NULL;
+ }
}
+
+ // We want the hashbits pointer in the base class to point to our labelhash,
+ // so that the KHashbits methods are called on the correct object (a LabelHash)
try {
- self->labelhash = new LabelHash(hashtable);
+ self->labelhash = new LabelHash(k, sizes);
} catch (std::bad_alloc &e) {
Py_DECREF(self);
return PyErr_NoMemory();
}
+ self->khashbits.hashbits = (Hashbits *)self->labelhash;
}
return (PyObject *) self;
}
+static int khmer_labelhash_init(khmer_KLabelHash_Object * self, PyObject *args,
+ PyObject *kwds)
+{
+ if (khmer_KHashbits_Type.tp_init((PyObject *)self, args, kwds) < 0) {
+ return -1;
+ }
+ //std::cout << "testing my pointer ref to hashbits: " << self->khashbits.hashbits->n_tags() << std::endl;
+ //std::cout << "hashbits: " << self->khashbits.hashbits << std::endl;
+ //std::cout << "labelhash: " << self->labelhash << std::endl;
+ return 0;
+}
+
static
PyObject *
labelhash_get_label_dict(khmer_KLabelHash_Object * me, PyObject * args)
@@ -3688,6 +3858,8 @@ labelhash_consume_fasta_and_tag_with_labels(khmer_KLabelHash_Object * me,
try {
hb->consume_fasta_and_tag_with_labels(filename, total_reads,
n_consumed);
+ } catch (_khmer_signal &e) {
+ exc = e.get_message().c_str();
} catch (khmer_file_exception &e) {
exc = e.what();
}
@@ -3722,6 +3894,10 @@ labelhash_consume_partitioned_fasta_and_tag_with_labels(
try {
labelhash->consume_partitioned_fasta_and_tag_with_labels(filename,
total_reads, n_consumed);
+ } catch (_khmer_signal &e) {
+ PyErr_SetString(PyExc_IOError,
+ "error parsing in consume_partitioned_fasta_and_tag_with_labels");
+ return NULL;
} catch (khmer_file_exception &e) {
PyErr_SetString(PyExc_IOError, e.what());
return NULL;
@@ -3742,7 +3918,12 @@ labelhash_consume_sequence_and_tag_with_labels(khmer_KLabelHash_Object * me,
}
unsigned long long n_consumed = 0;
Label * the_label = hb->check_and_allocate_label(c);
- hb->consume_sequence_and_tag_with_labels(seq, n_consumed, *the_label);
+
+ try {
+ hb->consume_sequence_and_tag_with_labels(seq, n_consumed, *the_label);
+ } catch (_khmer_signal &e) {
+ return NULL;
+ }
return Py_BuildValue("K", n_consumed);
}
@@ -3764,7 +3945,7 @@ labelhash_sweep_label_neighborhood(khmer_KLabelHash_Object * me,
return NULL;
}
- unsigned int range = (2 * hb->graph->_get_tag_density()) + 1;
+ unsigned int range = (2 * hb->_get_tag_density()) + 1;
if (r >= 0) {
range = r;
}
@@ -3778,7 +3959,7 @@ labelhash_sweep_label_neighborhood(khmer_KLabelHash_Object * me,
stop_big_traversals = true;
}
- if (strlen(seq) < hb->graph->ksize()) {
+ if (strlen(seq) < hb->ksize()) {
PyErr_SetString(PyExc_ValueError,
"string length must >= the hashtable k-mer size");
return NULL;
@@ -3787,14 +3968,23 @@ labelhash_sweep_label_neighborhood(khmer_KLabelHash_Object * me,
//std::pair<TagLabelPtrPair::iterator, TagLabelPtrPair::iterator> ret;
LabelPtrSet found_labels;
+ bool exc_raised = false;
//unsigned int num_traversed = 0;
//Py_BEGIN_ALLOW_THREADS
- hb->sweep_label_neighborhood(seq, found_labels, range, break_on_stop_tags,
+ try {
+ hb->sweep_label_neighborhood(seq, found_labels, range, break_on_stop_tags,
stop_big_traversals);
+ } catch (_khmer_signal &e) {
+ exc_raised = true;
+ }
//Py_END_ALLOW_THREADS
//printf("...%u kmers traversed\n", num_traversed);
+ if (exc_raised) {
+ return NULL;
+ }
+
PyObject * x = PyList_New(found_labels.size());
LabelPtrSet::const_iterator si;
unsigned long long i = 0;
@@ -3827,7 +4017,7 @@ labelhash_sweep_tag_neighborhood(khmer_KLabelHash_Object * me, PyObject * args)
return NULL;
}
- unsigned int range = (2 * labelhash->graph->_get_tag_density()) + 1;
+ unsigned int range = (2 * labelhash->_get_tag_density()) + 1;
if (r >= 0) {
range = r;
}
@@ -3841,7 +4031,7 @@ labelhash_sweep_tag_neighborhood(khmer_KLabelHash_Object * me, PyObject * args)
stop_big_traversals = true;
}
- if (strlen(seq) < labelhash->graph->ksize()) {
+ if (strlen(seq) < labelhash->ksize()) {
PyErr_SetString(PyExc_ValueError,
"string length must >= the hashtable k-mer size");
return NULL;
@@ -3851,10 +4041,8 @@ labelhash_sweep_tag_neighborhood(khmer_KLabelHash_Object * me, PyObject * args)
//Py_BEGIN_ALLOW_THREADS
- labelhash->graph->partition->sweep_for_tags(seq, tagged_kmers,
- labelhash->graph->all_tags,
- range, break_on_stop_tags,
- stop_big_traversals);
+ labelhash->partition->sweep_for_tags(seq, tagged_kmers,
+ labelhash->all_tags, range, break_on_stop_tags, stop_big_traversals);
//Py_END_ALLOW_THREADS
@@ -3915,48 +4103,6 @@ labelhash_n_labels(khmer_KLabelHash_Object * me, PyObject * args)
return PyLong_FromSize_t(labelhash->n_labels());
}
-static
-PyObject *
-labelhash_save_labels_and_tags(khmer_KLabelHash_Object * me, PyObject * args)
-{
- const char * filename = NULL;
- LabelHash * labelhash = me->labelhash;
-
- if (!PyArg_ParseTuple(args, "s", &filename)) {
- return NULL;
- }
-
- try {
- labelhash->save_labels_and_tags(filename);
- } catch (khmer_file_exception &e) {
- PyErr_SetString(PyExc_IOError, e.what());
- return NULL;
- }
-
- Py_RETURN_NONE;
-}
-
-static
-PyObject *
-labelhash_load_labels_and_tags(khmer_KLabelHash_Object * me, PyObject * args)
-{
- const char * filename = NULL;
- LabelHash * labelhash = me->labelhash;
-
- if (!PyArg_ParseTuple(args, "s", &filename)) {
- return NULL;
- }
-
- try {
- labelhash->load_labels_and_tags(filename);
- } catch (khmer_file_exception &e) {
- PyErr_SetString(PyExc_IOError, e.what());
- return NULL;
- }
-
- Py_RETURN_NONE;
-}
-
static PyMethodDef khmer_labelhash_methods[] = {
{ "consume_fasta_and_tag_with_labels", (PyCFunction)labelhash_consume_fasta_and_tag_with_labels, METH_VARARGS, "" },
{ "sweep_label_neighborhood", (PyCFunction)labelhash_sweep_label_neighborhood, METH_VARARGS, "" },
@@ -3966,8 +4112,7 @@ static PyMethodDef khmer_labelhash_methods[] = {
{"consume_sequence_and_tag_with_labels", (PyCFunction)labelhash_consume_sequence_and_tag_with_labels, METH_VARARGS, "" },
{"n_labels", (PyCFunction)labelhash_n_labels, METH_VARARGS, ""},
{"get_label_dict", (PyCFunction)labelhash_get_label_dict, METH_VARARGS, "" },
- { "save_labels_and_tags", (PyCFunction)labelhash_save_labels_and_tags, METH_VARARGS, "" },
- { "load_labels_and_tags", (PyCFunction)labelhash_load_labels_and_tags, METH_VARARGS, "" }, {NULL, NULL, 0, NULL} /* sentinel */
+ {NULL, NULL, 0, NULL} /* sentinel */
};
static PyTypeObject khmer_KLabelHash_Type = {
@@ -4006,67 +4151,11 @@ static PyTypeObject khmer_KLabelHash_Type = {
0, /* tp_descr_get */
0, /* tp_descr_set */
0, /* tp_dictoffset */
- 0, /* tp_init */
+ (initproc)khmer_labelhash_init, /* tp_init */
0, /* tp_alloc */
khmer_labelhash_new, /* tp_new */
};
-static
-PyObject *
-hashtable_traverse_from_tags(khmer_KHashtable_Object * me, PyObject * args)
-{
- Hashtable * hashtable = me->hashtable;
-
- khmer_KCountingHash_Object * counting_o = NULL;
- unsigned int distance, threshold, frequency;
-
- if (!PyArg_ParseTuple(args, "O!III", &khmer_KCountingHash_Type, &counting_o,
- &distance, &threshold, &frequency)) {
- return NULL;
- }
-
- hashtable->traverse_from_tags(distance, threshold, frequency,
- * counting_o->counting);
-
- Py_RETURN_NONE;
-}
-
-static
-PyObject *
-hashtable_repartition_largest_partition(khmer_KHashtable_Object * me,
- PyObject * args)
-{
- Hashtable * hashtable = me->hashtable;
- khmer_KCountingHash_Object * counting_o = NULL;
- PyObject * subset_o = NULL;
- SubsetPartition * subset_p;
- unsigned int distance, threshold, frequency;
-
- if (!PyArg_ParseTuple(args, "OO!III", &subset_o, &khmer_KCountingHash_Type,
- &counting_o, &distance, &threshold, &frequency)) {
- return NULL;
- }
-
- if (subset_o != Py_None) {
- subset_p = ((khmer_KSubsetPartition_Object *) subset_o)->subset;
- } else {
- subset_p = hashtable->partition;
- }
-
- CountingHash * counting = counting_o->counting;
-
- unsigned long next_largest;
- try {
- next_largest = subset_p->repartition_largest_partition(distance,
- threshold, frequency, *counting);
- } catch (khmer_exception &e) {
- PyErr_SetString(PyExc_RuntimeError, e.what());
- return NULL;
- }
-
- return PyLong_FromLong(next_largest);
-}
-
static PyObject * readaligner_align(khmer_ReadAligner_Object * me,
PyObject * args)
{
@@ -4178,30 +4267,41 @@ static PyTypeObject khmer_ReadAlignerType = {
khmer_ReadAligner_new, /* tp_new */
};
-static
-PyObject *
-hashtable_consume_fasta_and_traverse(khmer_KHashtable_Object * me,
- PyObject * args)
+static PyObject * hash_collect_high_abundance_kmers(khmer_KCountingHash_Object *
+ me , PyObject * args)
{
- Hashtable * hashtable = me->hashtable;
+ CountingHash * counting = me->counting;
- const char * filename;
- unsigned int radius, big_threshold, transfer_threshold;
- khmer_KCountingHash_Object * counting_o = NULL;
+ const char * filename = NULL;
+ unsigned int lower_count, upper_count;
- if (!PyArg_ParseTuple(args, "sIIIO!", &filename,
- &radius, &big_threshold, &transfer_threshold,
- &khmer_KCountingHash_Type, &counting_o)) {
+ if (!PyArg_ParseTuple(args, "sII", &filename, &lower_count, &upper_count)) {
return NULL;
}
- CountingHash * counting = counting_o->counting;
+ SeenSet found_kmers;
+ counting->collect_high_abundance_kmers(filename, lower_count, upper_count,
+ found_kmers);
- hashtable->consume_fasta_and_traverse(filename, radius, big_threshold,
- transfer_threshold, *counting);
+ // create a new hashbits object...
+ std::vector<HashIntoType> sizes;
+ sizes.push_back(1);
+ khmer_KHashbits_Object * khashbits_obj = (khmer_KHashbits_Object *) \
+ PyObject_New(khmer_KHashbits_Object, &khmer_KHashbits_Type);
+ if (khashbits_obj == NULL) {
+ return NULL;
+ }
- Py_RETURN_NONE;
+ // ...and set the collected kmers as the stoptags.
+ try {
+ khashbits_obj->hashbits = new Hashbits(counting->ksize(), sizes);
+ } catch (std::bad_alloc &e) {
+ return PyErr_NoMemory();
+ }
+ khashbits_obj->hashbits->stop_tags.swap(found_kmers);
+
+ return (PyObject *) khashbits_obj;
}
//
@@ -4355,6 +4455,9 @@ static PyObject * hllcounter_consume_fasta(khmer_KHLLCounter_Object * me,
unsigned int total_reads = 0;
try {
me->hllcounter->consume_fasta(filename, total_reads, n_consumed);
+ } catch (_khmer_signal &e) {
+ PyErr_SetString(PyExc_IOError, e.get_message().c_str());
+ return NULL;
} catch (khmer_file_exception &e) {
PyErr_SetString(PyExc_IOError, e.what());
return NULL;
@@ -4363,9 +4466,6 @@ static PyObject * hllcounter_consume_fasta(khmer_KHLLCounter_Object * me,
return Py_BuildValue("IK", total_reads, n_consumed);
}
-static PyObject * hllcounter_merge(khmer_KHLLCounter_Object * me,
- PyObject * args);
-
static
PyObject *
hllcounter_get_erate(khmer_KHLLCounter_Object * me)
@@ -4490,11 +4590,6 @@ static PyMethodDef khmer_hllcounter_methods[] = {
"Read sequences from file, break into k-mers, "
"and add each k-mer to the counter."
},
- {
- "merge", (PyCFunction)hllcounter_merge,
- METH_VARARGS,
- "Merge other counter into this one."
- },
{NULL} /* Sentinel */
};
@@ -4573,24 +4668,6 @@ static PyTypeObject khmer_KHLLCounter_Type = {
#define is_hllcounter_obj(v) (Py_TYPE(v) == &khmer_KHLLCounter_Type)
-static PyObject * hllcounter_merge(khmer_KHLLCounter_Object * me,
- PyObject * args)
-{
- khmer_KHLLCounter_Object * other;
-
- if (!PyArg_ParseTuple(args, "O!", &khmer_KHLLCounter_Type, &other)) {
- return NULL;
- }
-
- try {
- me->hllcounter->merge(*(other->hllcounter));
- } catch (khmer_exception &e) {
- PyErr_SetString(PyExc_ValueError, e.what());
- return NULL;
- }
-
- Py_RETURN_NONE;
-}
//////////////////////////////
// standalone functions
@@ -4657,7 +4734,7 @@ static PyObject * reverse_hash(PyObject * self, PyObject * args)
return NULL;
}
- return PyUnicode_FromString(_revhash(val, ksize).c_str());
+ return PyBytes_FromString(_revhash(val, ksize).c_str());
}
static PyObject * murmur3_forward_hash(PyObject * self, PyObject * args)
@@ -4694,7 +4771,7 @@ get_version_cpp( PyObject * self, PyObject * args )
#define xstr(s) str(s)
#define str(s) #s
std::string dVersion = xstr(VERSION);
- return PyUnicode_FromString(dVersion.c_str());
+ return PyBytes_FromString(dVersion.c_str());
}
@@ -4752,106 +4829,89 @@ static PyMethodDef KhmerMethods[] = {
{ NULL, NULL, 0, NULL } // sentinel
};
-MOD_INIT(_khmer)
+PyMODINIT_FUNC
+init_khmer(void)
{
using namespace python;
- if (PyType_Ready(&khmer_KHashtable_Type) < 0) {
- return MOD_ERROR_VAL;
- }
-
- khmer_KCountingHash_Type.tp_base = &khmer_KHashtable_Type;
if (PyType_Ready(&khmer_KCountingHash_Type) < 0) {
- return MOD_ERROR_VAL;
- }
-
- if (PyType_Ready(&khmer_PrePartitionInfo_Type) < 0) {
- return MOD_ERROR_VAL;
+ return;
}
khmer_KSubsetPartition_Type.tp_methods = khmer_subset_methods;
if (PyType_Ready(&khmer_KSubsetPartition_Type) < 0) {
- return MOD_ERROR_VAL;
+ return;
}
- khmer_KHashbits_Type.tp_base = &khmer_KHashtable_Type;
khmer_KHashbits_Type.tp_methods = khmer_hashbits_methods;
if (PyType_Ready(&khmer_KHashbits_Type) < 0) {
- return MOD_ERROR_VAL;
+ return;
}
+ // add LabelHash
khmer_KLabelHash_Type.tp_base = &khmer_KHashbits_Type;
- khmer_KLabelHash_Type.tp_methods = khmer_labelhash_methods;
- khmer_KLabelHash_Type.tp_new = khmer_labelhash_new;
if (PyType_Ready(&khmer_KLabelHash_Type) < 0) {
- return MOD_ERROR_VAL;
+ return;
+ }
+
+ if (PyType_Ready(&khmer_ReadAlignerType) < 0) {
+ return;
}
if (PyType_Ready(&khmer_KHLLCounter_Type) < 0) {
- return MOD_ERROR_VAL;
+ return;
}
if (PyType_Ready(&khmer_ReadAlignerType) < 0) {
- return MOD_ERROR_VAL;
+ return;
}
_init_ReadParser_Type_constants();
if (PyType_Ready( &khmer_ReadParser_Type ) < 0) {
- return MOD_ERROR_VAL;
+ return;
}
if (PyType_Ready(&khmer_Read_Type ) < 0) {
- return MOD_ERROR_VAL;
+ return;
}
if (PyType_Ready(&khmer_ReadPairIterator_Type ) < 0) {
- return MOD_ERROR_VAL;
+ return;
}
PyObject * m;
-
- MOD_DEF(m, "_khmer", "interface for the khmer module low-level extensions",
- KhmerMethods);
-
+ m = Py_InitModule3( "_khmer", KhmerMethods,
+ "interface for the khmer module low-level extensions" );
if (m == NULL) {
- return MOD_ERROR_VAL;
+ return;
}
Py_INCREF(&khmer_ReadParser_Type);
if (PyModule_AddObject( m, "ReadParser",
(PyObject *)&khmer_ReadParser_Type ) < 0) {
- return MOD_ERROR_VAL;
+ return;
}
Py_INCREF(&khmer_KCountingHash_Type);
if (PyModule_AddObject( m, "CountingHash",
(PyObject *)&khmer_KCountingHash_Type ) < 0) {
- return MOD_ERROR_VAL;
+ return;
}
Py_INCREF(&khmer_KHashbits_Type);
if (PyModule_AddObject(m, "Hashbits", (PyObject *)&khmer_KHashbits_Type) < 0) {
- return MOD_ERROR_VAL;
+ return;
}
Py_INCREF(&khmer_KLabelHash_Type);
if (PyModule_AddObject(m, "LabelHash",
(PyObject *)&khmer_KLabelHash_Type) < 0) {
- return MOD_ERROR_VAL;
+ return;
}
Py_INCREF(&khmer_KHLLCounter_Type);
- if (PyModule_AddObject(m, "HLLCounter",
- (PyObject *)&khmer_KHLLCounter_Type) < 0) {
- return MOD_ERROR_VAL;
- }
-
+ PyModule_AddObject(m, "HLLCounter", (PyObject *)&khmer_KHLLCounter_Type);
Py_INCREF(&khmer_ReadAlignerType);
- if (PyModule_AddObject(m, "ReadAligner",
- (PyObject *)&khmer_ReadAlignerType) < 0) {
- return MOD_ERROR_VAL;
- }
-
- return MOD_SUCCESS_VAL(m);
+ PyModule_AddObject(m, "ReadAligner", (PyObject *)&khmer_ReadAlignerType);
}
// vim: set ft=cpp sts=4 sw=4 tw=79:
diff --git a/khmer/_version.py b/khmer/_version.py
index 5f61635..acac511 100644
--- a/khmer/_version.py
+++ b/khmer/_version.py
@@ -1,4 +1,3 @@
-from __future__ import print_function
# This file helps to compute a version number in source trees obtained from
# git-archive tarball (such as those provided by githubs download-from-tag
@@ -16,8 +15,8 @@ import subprocess
import sys
# these strings will be replaced by git during git-archive
-git_refnames = " (tag: v2.0-rc1)"
-git_full = "bbd38a6d3d0960f71c65dd46ecda3b61584a8b4c"
+git_refnames = " (tag: v1.4)"
+git_full = "ffb8865d28ccf584e5de3362f9150a6b020eaa11"
# these strings are filled in when 'setup.py versioneer' creates _version.py
tag_prefix = "v"
@@ -115,7 +114,7 @@ def git_versions_from_keywords(keywords, tag_prefix, verbose=False):
# "stabilization", as well as "HEAD" and "master".
tags = set([r for r in refs if re.search(r'\d', r)])
if verbose:
- print("discarding '%s', no digits" % ",".join(refs - tags))
+ print("discarding '%s', no digits" % ",".join(refs-tags))
if verbose:
print("likely tags: %s" % ",".join(sorted(tags)))
for ref in sorted(tags):
@@ -145,13 +144,13 @@ def git_parse_vcs_describe(git_describe, tag_prefix, verbose=False):
# now we have TAG-NUM-gHEX or HEX
if "-" not in git_describe: # just HEX
- return "0+untagged.g" + git_describe + dirty_suffix, dirty
+ return "0+untagged.g"+git_describe+dirty_suffix, dirty
# just TAG-NUM-gHEX
mo = re.search(r'^(.+)-(\d+)-g([0-9a-f]+)$', git_describe)
if not mo:
# unparseable. Maybe git-describe is misbehaving?
- return "0+unparseable" + dirty_suffix, dirty
+ return "0+unparseable"+dirty_suffix, dirty
# tag
full_tag = mo.group(1)
diff --git a/khmer/kfile.py b/khmer/kfile.py
index 9a01f59..a5ff6b4 100644
--- a/khmer/kfile.py
+++ b/khmer/kfile.py
@@ -1,5 +1,5 @@
#
-# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
+# This file is part of khmer, http://github.com/ged-lab/khmer/, and is
# Copyright (C) Michigan State University, 2014-2015. It is licensed under
# the three-clause BSD license; see LICENSE.
# Contact: khmer-project at idyll.org
@@ -7,13 +7,10 @@
"""File handling/checking utilities for command-line scripts."""
-from __future__ import print_function, unicode_literals
-
import os
import sys
import errno
from stat import S_ISBLK, S_ISFIFO
-from khmer import khmer_args
def check_input_files(file_path, force):
@@ -25,16 +22,16 @@ def check_input_files(file_path, force):
"""
mode = None
- if file_path == '-':
+ if file_path is '-':
return
try:
mode = os.stat(file_path).st_mode
except OSError:
- print("ERROR: Input file %s does not exist" %
- file_path, file=sys.stderr)
+ print >>sys.stderr, "ERROR: Input file %s does not exist" % \
+ file_path
if not force:
- print("Exiting", file=sys.stderr)
+ print >>sys.stderr, "Exiting"
sys.exit(1)
else:
return
@@ -44,14 +41,14 @@ def check_input_files(file_path, force):
return
if not os.path.exists(file_path):
- print("ERROR: Input file %s does not exist; exiting" %
- file_path, file=sys.stderr)
+ print >>sys.stderr, "ERROR: Input file %s does not exist; exiting" % \
+ file_path
if not force:
sys.exit(1)
else:
if os.stat(file_path).st_size == 0:
- print("ERROR: Input file %s is empty; exiting." %
- file_path, file=sys.stderr)
+ print >>sys.stderr, "ERROR: Input file %s is empty; exiting." % \
+ file_path
if not force:
sys.exit(1)
@@ -62,11 +59,11 @@ def check_file_writable(file_path):
file_obj = open(file_path, "a")
except IOError as error:
if error.errno == errno.EACCES:
- print("ERROR: File %s does not have write "
- % file_path + "permission; exiting", file=sys.stderr)
+ print >>sys.stderr, "ERROR: File %s does not have write " \
+ % file_path + "permission; exiting"
sys.exit(1)
else:
- print("ERROR: " + error.strerror, file=sys.stderr)
+ print >>sys.stderr, "ERROR: " + error.strerror
else:
file_obj.close()
return
@@ -100,23 +97,20 @@ def check_space(in_files, force, _testhook_free_space=None):
size_diff = total_size - free_space
if size_diff > 0:
- print("ERROR: Not enough free space on disk "
- "for output files;\n"
- " Need at least %.1f GB more."
- % (float(size_diff) / 1e9), file=sys.stderr)
- print(" Estimated output size: %.1f GB"
- % (float(total_size) / 1e9,), file=sys.stderr)
- print(" Free space: %.1f GB"
- % (float(free_space) / 1e9,), file=sys.stderr)
+ print >>sys.stderr, "ERROR: Not enough free space on disk " \
+ "for output files;\n" \
+ " Need at least %.1f GB more." \
+ % (float(size_diff) / 1e9)
+ print >>sys.stderr, " Estimated output size: %.1f GB" \
+ % (float(total_size) / 1e9,)
+ print >>sys.stderr, " Free space: %.1f GB" \
+ % (float(free_space) / 1e9,)
if not force:
sys.exit(1)
-def check_space_for_hashtable(args, hashtype, force,
- _testhook_free_space=None):
+def check_space_for_hashtable(hash_size, force, _testhook_free_space=None):
"""Check we have enough size to write a hash table."""
- hash_size = khmer_args._calculate_tablesize(args, hashtype)
-
cwd = os.getcwd()
dir_path = os.path.dirname(os.path.realpath(cwd))
target = os.statvfs(dir_path)
@@ -127,14 +121,14 @@ def check_space_for_hashtable(args, hashtype, force,
size_diff = hash_size - free_space
if size_diff > 0:
- print("ERROR: Not enough free space on disk "
- "for saved table files;"
- " Need at least %s GB more."
- % (float(size_diff) / 1e9,), file=sys.stderr)
- print(" Table size: %.1f GB"
- % (float(hash_size) / 1e9,), file=sys.stderr)
- print(" Free space: %.1f GB"
- % (float(free_space) / 1e9,), file=sys.stderr)
+ print >>sys.stderr, "ERROR: Not enough free space on disk " \
+ "for saved table files;" \
+ " Need at least %s GB more." \
+ % (float(size_diff) / 1e9,)
+ print >>sys.stderr, " Table size: %.1f GB" \
+ % (float(hash_size) / 1e9,)
+ print >>sys.stderr, " Free space: %.1f GB" \
+ % (float(free_space) / 1e9,)
if not force:
sys.exit(1)
@@ -152,8 +146,8 @@ def check_valid_file_exists(in_files):
if os.stat(in_file).st_size > 0:
return
else:
- print('WARNING: Input file %s is empty' %
- in_file, file=sys.stderr)
+ print >>sys.stderr, 'WARNING: Input file %s is empty' % \
+ in_file
else:
- print('WARNING: Input file %s not found' %
- in_file, file=sys.stderr)
+ print >>sys.stderr, 'WARNING: Input file %s not found' % \
+ in_file
diff --git a/khmer/khmer_args.py b/khmer/khmer_args.py
index a9e9358..c33d501 100644
--- a/khmer/khmer_args.py
+++ b/khmer/khmer_args.py
@@ -1,74 +1,53 @@
#
# vim: set encoding=utf-8
-# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
-# Copyright (C) Michigan State University, 2014-2015. It is licensed under
+# This file is part of khmer, http://github.com/ged-lab/khmer/, and is
+# Copyright (C) Michigan State University, 2014. It is licensed under
# the three-clause BSD license; see LICENSE.
# Contact: khmer-project at idyll.org
#
-from __future__ import unicode_literals
-
import sys
import os
import argparse
-from argparse import _VersionAction
-
-import screed
-import khmer
from khmer import extract_countinghash_info, extract_hashbits_info
from khmer import __version__
-from khmer.utils import print_error
-
+import screed
DEFAULT_K = 32
DEFAULT_N_TABLES = 4
-DEFAULT_MAX_TABLESIZE = 1e6
+DEFAULT_MIN_TABLESIZE = 1e6
DEFAULT_N_THREADS = 1
-class _VersionStdErrAction(_VersionAction):
-
- def __call__(self, parser, namespace, values, option_string=None):
- version = self.version
- if version is None:
- version = parser.version
- formatter = parser._get_formatter()
- formatter.add_text(version)
- parser._print_message(formatter.format_help(), sys.stderr)
- parser.exit()
-
-
class ComboFormatter(argparse.ArgumentDefaultsHelpFormatter,
argparse.RawDescriptionHelpFormatter):
pass
-def build_hash_args(descr=None, epilog=None, parser=None):
+def build_hash_args(descr=None, epilog=None):
"""Build an ArgumentParser with args for bloom filter based scripts."""
- if parser is None:
- parser = argparse.ArgumentParser(description=descr, epilog=epilog,
- formatter_class=ComboFormatter)
+ parser = argparse.ArgumentParser(
+ description=descr, epilog=epilog,
+ formatter_class=ComboFormatter)
- parser.add_argument('--version', action=_VersionStdErrAction,
+ env_ksize = os.environ.get('KHMER_KSIZE', DEFAULT_K)
+ env_n_tables = os.environ.get('KHMER_N_TABLES', DEFAULT_N_TABLES)
+ env_tablesize = os.environ.get('KHMER_MIN_TABLESIZE',
+ DEFAULT_MIN_TABLESIZE)
+
+ parser.add_argument('--version', action='version',
version='khmer {v}'.format(v=__version__))
parser.add_argument('-q', '--quiet', dest='quiet', default=False,
action='store_true')
- parser.add_argument('--ksize', '-k', type=int, default=DEFAULT_K,
+ parser.add_argument('--ksize', '-k', type=int, default=env_ksize,
help='k-mer size to use')
-
parser.add_argument('--n_tables', '-N', type=int,
- default=DEFAULT_N_TABLES,
+ default=env_n_tables,
help='number of k-mer counting tables to use')
-
- group = parser.add_mutually_exclusive_group()
- group.add_argument('--max-tablesize', '-x', type=float,
- default=DEFAULT_MAX_TABLESIZE,
- help='upper bound on tablesize to use; overrides ' +
- '--max-memory-usage/-M.')
- group.add_argument('-M', '--max-memory-usage', type=float,
- help='maximum amount of memory to use for data ' +
- 'structure.')
+ parser.add_argument('--min-tablesize', '-x', type=float,
+ default=env_tablesize,
+ help='lower bound on tablesize to use')
return parser
@@ -76,16 +55,15 @@ def build_hash_args(descr=None, epilog=None, parser=None):
def build_counting_args(descr=None, epilog=None):
"""Build an ArgumentParser with args for counting_hash based scripts."""
parser = build_hash_args(descr=descr, epilog=epilog)
- parser.hashtype = 'countgraph'
+ parser.hashtype = 'counting'
return parser
-def build_hashbits_args(descr=None, epilog=None, parser=None):
+def build_hashbits_args(descr=None, epilog=None):
"""Build an ArgumentParser with args for hashbits based scripts."""
-
- parser = build_hash_args(descr=descr, epilog=epilog, parser=parser)
- parser.hashtype = 'nodegraph'
+ parser = build_hash_args(descr=descr, epilog=epilog)
+ parser.hashtype = 'hashbits'
return parser
@@ -97,24 +75,31 @@ def add_loadhash_args(parser):
class LoadAction(argparse.Action):
def __call__(self, parser, namespace, values, option_string=None):
+ env_ksize = os.environ.get('KHMER_KSIZE', DEFAULT_K)
+ env_n_tables = os.environ.get('KHMER_N_TABLES', DEFAULT_N_TABLES)
+ env_tablesize = os.environ.get('KHMER_MIN_TABLESIZE',
+ DEFAULT_MIN_TABLESIZE)
+
+ from khmer.utils import print_error
+
setattr(namespace, self.dest, values)
- if getattr(namespace, 'ksize') != DEFAULT_K or \
- getattr(namespace, 'n_tables') != DEFAULT_N_TABLES or \
- getattr(namespace, 'max_tablesize') != DEFAULT_MAX_TABLESIZE:
+ if getattr(namespace, 'ksize') != env_ksize or \
+ getattr(namespace, 'n_tables') != env_n_tables or \
+ getattr(namespace, 'min_tablesize') != env_tablesize:
if values:
print_error('''
** WARNING: You are loading a saved k-mer table from
-** {hashfile}, but have set k-mer table parameters.
-** Your values for ksize, n_tables, and tablesize
-** will be ignored.'''.format(hashfile=values))
+{hashfile}, but have set k-mer table parameters.
+Your values for ksize, n_tables, and tablesize
+will be ignored.'''.format(hashfile=values))
if hasattr(parser, 'hashtype'):
info = None
- if parser.hashtype == 'nodegraph':
+ if parser.hashtype == 'hashbits':
info = extract_hashbits_info(
getattr(namespace, self.dest))
- elif parser.hashtype == 'countgraph':
+ elif parser.hashtype == 'counting':
info = extract_countinghash_info(
getattr(namespace, self.dest))
if info:
@@ -123,96 +108,52 @@ def add_loadhash_args(parser):
n = info[2]
setattr(namespace, 'ksize', K)
setattr(namespace, 'n_tables', n)
- setattr(namespace, 'max_tablesize', x)
+ setattr(namespace, 'min_tablesize', x)
parser.add_argument('-l', '--loadtable', metavar="filename", default=None,
help='load a precomputed k-mer table from disk',
action=LoadAction)
-def _calculate_tablesize(args, hashtype, multiplier=1.0):
- if hashtype not in ('countgraph', 'nodegraph'):
- raise Exception("unknown graph type: %s" % (hashtype,))
-
- if args.max_memory_usage:
- if hashtype == 'countgraph':
- tablesize = args.max_memory_usage / args.n_tables / \
- float(multiplier)
- elif hashtype == 'nodegraph':
- tablesize = 8. * args.max_memory_usage / args.n_tables / \
- float(multiplier)
- else:
- tablesize = args.max_tablesize
-
- return tablesize
-
-
-def create_nodegraph(args, ksize=None, multiplier=1.0):
- if ksize is None:
- ksize = args.ksize
- if ksize > 32:
- print_error("\n** ERROR: khmer only supports k-mer sizes <= 32.\n")
- sys.exit(1)
-
- tablesize = _calculate_tablesize(args, 'nodegraph', multiplier=multiplier)
- return khmer.Hashbits(ksize, tablesize, args.n_tables)
-
-
-def create_countgraph(args, ksize=None, multiplier=1.0):
- if ksize is None:
- ksize = args.ksize
- if ksize > 32:
- print_error("\n** ERROR: khmer only supports k-mer sizes <= 32.\n")
- sys.exit(1)
-
- tablesize = _calculate_tablesize(args, 'countgraph', multiplier=multiplier)
- return khmer.CountingHash(ksize, tablesize, args.n_tables)
-
-
-def report_on_config(args, hashtype='countgraph'):
+def report_on_config(args, hashtype='counting'):
"""Print out configuration.
Summarize the configuration produced by the command-line arguments
made available by this module.
"""
from khmer.utils import print_error
- if hashtype not in ('countgraph', 'nodegraph'):
- raise Exception("unknown graph type: %s" % (hashtype,))
if args.quiet:
return
- tablesize = _calculate_tablesize(args, hashtype)
-
print_error("\nPARAMETERS:")
print_error(" - kmer size = {0} \t\t(-k)".format(args.ksize))
print_error(" - n tables = {0} \t\t(-N)".format(args.n_tables))
print_error(
- " - max tablesize = {0:5.2g} \t(-x)".format(tablesize)
+ " - min tablesize = {0:5.2g} \t(-x)".format(args.min_tablesize)
)
print_error("")
- if hashtype == 'countgraph':
+ if hashtype == 'counting':
print_error(
"Estimated memory usage is {0:.2g} bytes "
- "(n_tables x max_tablesize)".format(
- args.n_tables * tablesize))
- elif hashtype == 'nodegraph':
+ "(n_tables x min_tablesize)".format(
+ args.n_tables * args.min_tablesize))
+ elif hashtype == 'hashbits':
print_error(
"Estimated memory usage is {0:.2g} bytes "
- "(n_tables x max_tablesize / 8)".format(args.n_tables *
- tablesize / 8)
+ "(n_tables x min_tablesize / 8)".format(args.n_tables *
+ args.min_tablesize / 8)
)
print_error("-" * 8)
- if DEFAULT_MAX_TABLESIZE == tablesize and \
- not getattr(args, 'loadtable', None):
- print_error('''\
-
-** WARNING: tablesize is default!
-** You probably want to increase this with -M/--max-memory-usage!
-** Please read the docs!
-''')
+ if DEFAULT_MIN_TABLESIZE == args.min_tablesize and \
+ not hasattr(args, 'loadtable'):
+ print_error(
+ "** WARNING: tablesize is default! "
+ "You absodefly want to increase this!\n** "
+ "Please read the docs!\n"
+ )
def add_threading_args(parser):
@@ -255,13 +196,7 @@ def info(scriptname, algorithm_list=None):
for alg in algorithm_list:
sys.stderr.write("|| * ")
- algstr = _algorithms[alg].encode(
- 'utf-8', 'surrogateescape').decode('utf-8', 'replace')
- try:
- sys.stderr.write(algstr)
- except UnicodeEncodeError:
- sys.stderr.write(
- algstr.encode(sys.getfilesystemencoding(), 'replace'))
+ sys.stderr.write(_algorithms[alg])
sys.stderr.write("\n")
sys.stderr.write("||\n|| Please see http://khmer.readthedocs.org/en/"
diff --git a/khmer/thread_utils.py b/khmer/thread_utils.py
index 41c3914..a604fe2 100644
--- a/khmer/thread_utils.py
+++ b/khmer/thread_utils.py
@@ -1,25 +1,16 @@
#
-# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
-# Copyright (C) Michigan State University, 2009-2015. It is licensed under
+# This file is part of khmer, http://github.com/ged-lab/khmer/, and is
+# Copyright (C) Michigan State University, 2009-2013. It is licensed under
# the three-clause BSD license; see LICENSE.
# Contact: khmer-project at idyll.org
#
-
"""Utilities for dealing with multithreaded processing of short reads."""
-from __future__ import print_function, unicode_literals
-
import threading
+import Queue
import sys
import screed
from khmer import utils
-
-# stdlib queue module was renamed on Python 3
-try:
- import queue
-except ImportError:
- import Queue as queue
-
DEFAULT_WORKER_THREADS = 8
DEFAULT_GROUPSIZE = 100
@@ -29,7 +20,7 @@ def verbose_loader(filename):
screed_iter = screed.open(filename, parse_description=False)
for n, record in enumerate(screed_iter):
if n % 100000 == 0:
- print('... filtering', n, file=sys.stderr)
+ print >>sys.stderr, '... filtering', n
yield record
verbose_fasta_iter = verbose_loader
@@ -58,8 +49,8 @@ class ThreadedSequenceProcessor(object):
self.n_workers = n_workers
self.group_size = group_size
- self.inqueue = queue.Queue(self.QUEUESIZE)
- self.outqueue = queue.Queue(self.QUEUESIZE)
+ self.inqueue = Queue.Queue(self.QUEUESIZE)
+ self.outqueue = Queue.Queue(self.QUEUESIZE)
self.worker_count = 0
self.worker_count_lock = threading.Lock()
@@ -74,7 +65,7 @@ class ThreadedSequenceProcessor(object):
def start(self, inputiter, outfp):
if self.verbose:
- print('starting threads', file=sys.stderr)
+ print >>sys.stderr, 'starting threads'
try:
for _ in range(self.n_workers):
@@ -83,18 +74,18 @@ class ThreadedSequenceProcessor(object):
t.start()
if self.verbose:
- print('starting writer', file=sys.stderr)
+ print >>sys.stderr, 'starting writer'
w = threading.Thread(target=self.do_write, args=(outfp,))
w.start()
if self.verbose:
- print('loading...', file=sys.stderr)
+ print >>sys.stderr, 'loading...'
self.push_sequences(inputiter)
if self.verbose:
- print('done loading in sequences', file=sys.stderr)
+ print >>sys.stderr, 'done loading in sequences'
self.done = True
w.join()
@@ -138,7 +129,7 @@ class ThreadedSequenceProcessor(object):
while not self.done or not inq.empty():
try:
g = inq.get(True, 1)
- except queue.Empty:
+ except Queue.Empty:
continue
bp_processed = 0
@@ -166,16 +157,17 @@ class ThreadedSequenceProcessor(object):
self.bp_written += bp_written
if self.verbose and self.n_processed % 500000 == 0:
- print("processed %d / wrote %d / removed %d" %
- (self.n_processed, self.n_written,
- self.n_processed - self.n_written), file=sys.stderr)
- print("processed %d bp / wrote %d bp / removed %d bp" %
- (self.bp_processed, self.bp_written,
- self.bp_processed - self.bp_written),
- file=sys.stderr)
+ print >>sys.stderr, \
+ "processed %d / wrote %d / removed %d" % \
+ (self.n_processed, self.n_written,
+ self.n_processed - self.n_written)
+ print >>sys.stderr, \
+ "processed %d bp / wrote %d bp / removed %d bp" % \
+ (self.bp_processed, self.bp_written,
+ self.bp_processed - self.bp_written)
discarded = self.bp_processed - self.bp_written
f = float(discarded) / float(self.bp_processed) * 100
- print("discarded %.1f%%" % f, file=sys.stderr)
+ print >>sys.stderr, "discarded %.1f%%" % f
# end of thread; exit, decrement worker count.
with self.worker_count_lock:
@@ -186,7 +178,7 @@ class ThreadedSequenceProcessor(object):
while self.worker_count > 0 or not outq.empty():
try:
g = outq.get(True, 1)
- except queue.Empty:
+ except Queue.Empty:
continue
for name, seq, quality in g.seqlist:
@@ -196,14 +188,16 @@ class ThreadedSequenceProcessor(object):
outfp.write('>%s\n%s\n' % (name, seq,))
if self.verbose:
- print("DONE writing.\nprocessed %d / wrote %d / removed %d" %
- (self.n_processed, self.n_written,
- self.n_processed - self.n_written), file=sys.stderr)
- print("processed %d bp / wrote %d bp / removed %d bp" %
- (self.bp_processed, self.bp_written,
- self.bp_processed - self.bp_written), file=sys.stderr)
+ print >>sys.stderr, \
+ "DONE writing.\nprocessed %d / wrote %d / removed %d" % \
+ (self.n_processed, self.n_written,
+ self.n_processed - self.n_written)
+ print >>sys.stderr, \
+ "processed %d bp / wrote %d bp / removed %d bp" % \
+ (self.bp_processed, self.bp_written,
+ self.bp_processed - self.bp_written)
discarded = self.bp_processed - self.bp_written
f = float(discarded) / float(self.bp_processed) * 100
- print("discarded %.1f%%" % f, file=sys.stderr)
+ print >>sys.stderr, "discarded %.1f%%" % f
# vim: set ft=python ts=4 sts=4 sw=4 et tw=79:
diff --git a/khmer/utils.py b/khmer/utils.py
index 0e1d5e1..1495fa2 100644
--- a/khmer/utils.py
+++ b/khmer/utils.py
@@ -1,6 +1,5 @@
-from __future__ import print_function, unicode_literals
#
-# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
+# This file is part of khmer, http://github.com/ged-lab/khmer/, and is
# Copyright (C) Michigan State University, 2009-2015. It is licensed under
# the three-clause BSD license; see LICENSE.
# Contact: khmer-project at idyll.org
@@ -13,7 +12,7 @@ def print_error(msg):
"""Print the given message to 'stderr'."""
import sys
- print(msg, file=sys.stderr)
+ print >>sys.stderr, msg
def _split_left_right(name):
@@ -55,10 +54,6 @@ def check_is_pair(record1, record2):
elif lhs1 == lhs2 and rhs1.startswith('1:') and rhs2.startswith('2:'):
return True
- # handle @name seq/1
- elif lhs1 == lhs2 and rhs1.endswith('/1') and rhs2.endswith('/2'):
- return True
-
return False
@@ -75,9 +70,6 @@ def check_is_left(name):
elif rhs.startswith('1:'): # handle '@name 1:rst'
return True
- elif rhs.endswith('/1'): # handles '@name seq/1'
- return True
-
return False
@@ -94,14 +86,10 @@ def check_is_right(name):
elif rhs.startswith('2:'): # handle '@name 2:rst'
return True
- elif rhs.endswith('/2'): # handles '@name seq/2'
- return True
-
return False
-def broken_paired_reader(screed_iter, min_length=None,
- force_single=False, require_paired=False):
+def broken_paired_reader(screed_iter, min_length=None, force_single=False):
"""Read pairs from a stream.
A generator that yields singletons and pairs from a stream of FASTA/FASTQ
@@ -129,9 +117,6 @@ def broken_paired_reader(screed_iter, min_length=None,
prev_record = None
n = 0
- if force_single and require_paired:
- raise ValueError("force_single and require_paired cannot both be set!")
-
# handle the majority of the stream.
for record in screed_iter:
# ignore short reads
@@ -145,9 +130,6 @@ def broken_paired_reader(screed_iter, min_length=None,
n += 2
record = None
else: # orphan.
- if require_paired:
- raise ValueError("Unpaired reads when require_paired"
- " is set!")
yield n, False, prev_record, None
n += 1
@@ -156,27 +138,21 @@ def broken_paired_reader(screed_iter, min_length=None,
# handle the last record, if it exists (i.e. last two records not a pair)
if prev_record:
- if require_paired:
- raise ValueError("Unpaired reads when require_paired is set!")
yield n, False, prev_record, None
def write_record(record, fileobj):
"""Write sequence record to 'fileobj' in FASTA/FASTQ format."""
if hasattr(record, 'quality'):
- recstr = '@{name}\n{sequence}\n+\n{quality}\n'.format(
- name=record.name,
- sequence=record.sequence,
- quality=record.quality)
+ fileobj.write(
+ '@{name}\n{seq}\n'
+ '+\n{qual}\n'.format(name=record.name,
+ seq=record.sequence,
+ qual=record.quality))
else:
- recstr = '>{name}\n{sequence}\n'.format(
- name=record.name,
- sequence=record.sequence)
-
- try:
- fileobj.write(bytes(recstr, 'utf-8'))
- except TypeError:
- fileobj.write(recstr)
+ fileobj.write(
+ '>{name}\n{seq}\n'.format(name=record.name,
+ seq=record.sequence))
def write_record_pair(read1, read2, fileobj):
diff --git a/lib/.check_openmp.cc b/lib/.check_openmp.cc
index 52dfdd5..d4375ca 100644
--- a/lib/.check_openmp.cc
+++ b/lib/.check_openmp.cc
@@ -1,5 +1,5 @@
//
-// This file is part of khmer, https://github.com/dib-lab/khmer/, and is
+// This file is part of khmer, http://github.com/ged-lab/khmer/, and is
// Copyright (C) Michigan State University, 2015. It is licensed under
// the three-clause BSD license; see doc/LICENSE.txt.
// Contact: khmer-project at idyll.org
diff --git a/lib/Makefile b/lib/Makefile
index f3518ea..c100a0f 100644
--- a/lib/Makefile
+++ b/lib/Makefile
@@ -214,7 +214,7 @@ TEST_PROGS = test-Colors test-read-aligner test-compile
all: $(LIBKHMERSO) libkhmer.a khmer.pc
clean:
- rm -f *.o *.a *.so* khmer.pc $(TEST_PROGS)
+ rm -f *.o *.a *.so khmer.pc $(LIBKHMERSO) $(TEST_PROGS)
(cd $(ZLIB_DIR) && make distclean)
(cd $(BZIP2_DIR) && make -f Makefile-libbz2_so clean)
diff --git a/lib/counting.cc b/lib/counting.cc
index 27b23ad..b201bdc 100644
--- a/lib/counting.cc
+++ b/lib/counting.cc
@@ -1,5 +1,5 @@
//
-// This file is part of khmer, https://github.com/dib-lab/khmer/, and is
+// This file is part of khmer, http://github.com/ged-lab/khmer/, and is
// Copyright (C) Michigan State University, 2009-2015. It is licensed under
// the three-clause BSD license; see LICENSE.
// Contact: khmer-project at idyll.org
@@ -511,19 +511,11 @@ CountingHashFileReader::CountingHashFileReader(
unsigned int save_ksize = 0;
unsigned char save_n_tables = 0;
unsigned long long save_tablesize = 0;
- char signature [4];
unsigned char version = 0, ht_type = 0, use_bigcount = 0;
- infile.read(signature, 4);
infile.read((char *) &version, 1);
infile.read((char *) &ht_type, 1);
- if (!(std::string(signature, 4) == SAVED_SIGNATURE)) {
- std::ostringstream err;
- err << "Does not start with signature for a khmer " <<
- "file: " << signature << " Should be: " <<
- SAVED_SIGNATURE;
- throw khmer_file_exception(err.str());
- } else if (!(version == SAVED_FORMAT_VERSION)) {
+ if (!(version == SAVED_FORMAT_VERSION)) {
std::ostringstream err;
err << "Incorrect file format version " << (int) version
<< " while reading k-mer count file from " << infilename
@@ -620,23 +612,16 @@ CountingHashGzFileReader::CountingHashGzFileReader(
unsigned int save_ksize = 0;
unsigned char save_n_tables = 0;
unsigned long long save_tablesize = 0;
- char signature [4];
unsigned char version, ht_type, use_bigcount;
- int read_s = gzread(infile, signature, 4);
int read_v = gzread(infile, (char *) &version, 1);
int read_t = gzread(infile, (char *) &ht_type, 1);
- if (read_s <= 0 || read_v <= 0 || read_t <= 0) {
+
+ if (read_v <= 0 || read_t <= 0) {
std::string err = "K-mer count file read error: " + infilename + " "
+ strerror(errno);
gzclose(infile);
throw khmer_file_exception(err);
- } else if (!(std::string(signature, 4) == SAVED_SIGNATURE)) {
- std::ostringstream err;
- err << "Does not start with signature for a khmer " <<
- "file: " << signature << " Should be: " <<
- SAVED_SIGNATURE;
- throw khmer_file_exception(err.str());
} else if (!(version == SAVED_FORMAT_VERSION)
|| !(ht_type == SAVED_COUNTING_HT)) {
if (!(version == SAVED_FORMAT_VERSION)) {
@@ -700,15 +685,8 @@ CountingHashGzFileReader::CountingHashGzFileReader(
HashIntoType loaded = 0;
while (loaded != tablesize) {
- unsigned long long to_read_ll = tablesize - loaded;
- unsigned int to_read_int;
- // Zlib can only read chunks of at most INT_MAX bytes.
- if (to_read_ll > INT_MAX) {
- to_read_int = INT_MAX;
- } else {
- to_read_int = to_read_ll;
- }
- read_b = gzread(infile, (char *) ht._counts[i], to_read_int);
+ read_b = gzread(infile, (char *) ht._counts[i],
+ (unsigned) (tablesize - loaded));
if (read_b <= 0) {
std::string gzerr = gzerror(infile, &read_b);
@@ -783,7 +761,6 @@ CountingHashFileWriter::CountingHashFileWriter(
ofstream outfile(outfilename.c_str(), ios::binary);
- outfile.write(SAVED_SIGNATURE, 4);
unsigned char version = SAVED_FORMAT_VERSION;
outfile.write((const char *) &version, 1);
@@ -846,7 +823,6 @@ CountingHashGzFileWriter::CountingHashGzFileWriter(
}
}
- gzwrite(outfile, SAVED_SIGNATURE, 4);
unsigned char version = SAVED_FORMAT_VERSION;
gzwrite(outfile, (const char *) &version, 1);
@@ -869,38 +845,8 @@ CountingHashGzFileWriter::CountingHashGzFileWriter(
sizeof(save_tablesize));
unsigned long long written = 0;
while (written != save_tablesize) {
- unsigned long long to_write_ll = save_tablesize - written;
- unsigned int to_write_int;
- int gz_result;
- // Zlib can only write chunks of at most INT_MAX bytes.
- if (to_write_ll > INT_MAX) {
- to_write_int = INT_MAX;
- } else {
- to_write_int = to_write_ll;
- }
- gz_result = gzwrite(outfile, (const char *) ht._counts[i],
- to_write_int);
- // Zlib returns 0 on error
- if (gz_result == 0) {
- int errcode = 0;
- const char *err_msg;
- std::ostringstream msg;
-
- msg << "gzwrite failed while writing counting hash: ";
- // Get zlib error
- err_msg = gzerror(outfile, &errcode);
- if (errcode != Z_ERRNO) {
- // Zlib error, not stdlib
- msg << err_msg;
- gzclearerr(outfile);
- } else {
- // stdlib error
- msg << strerror(errno);
- }
- gzclose(outfile);
- throw khmer_file_exception(msg.str().c_str());
- }
- written += gz_result;
+ written += gzwrite(outfile, (const char *) ht._counts[i],
+ (int) (save_tablesize - written));
}
}
diff --git a/lib/counting.hh b/lib/counting.hh
index 4849870..31d0f0f 100644
--- a/lib/counting.hh
+++ b/lib/counting.hh
@@ -1,5 +1,5 @@
//
-// This file is part of khmer, https://github.com/dib-lab/khmer/, and is
+// This file is part of khmer, http://github.com/ged-lab/khmer/, and is
// Copyright (C) Michigan State University, 2009-2015. It is licensed under
// the three-clause BSD license; see LICENSE.
// Contact: khmer-project at idyll.org
diff --git a/lib/get_version.py b/lib/get_version.py
index 5d7fa66..6ad89b8 100644
--- a/lib/get_version.py
+++ b/lib/get_version.py
@@ -1,4 +1,3 @@
-from __future__ import print_function
import sys
sys.path.insert(0, '../')
import versioneer
@@ -8,4 +7,4 @@ versioneer.versionfile_build = '../khmer/_version.py'
versioneer.tag_prefix = 'v' # tags are like v1.2.0
versioneer.parentdir_prefix = '..'
-print(versioneer.get_version())
+print versioneer.get_version()
diff --git a/lib/graphtest.cc b/lib/graphtest.cc
index c4ad3f7..438971c 100644
--- a/lib/graphtest.cc
+++ b/lib/graphtest.cc
@@ -1,6 +1,6 @@
//
-// This file is part of khmer, https://github.com/dib-lab/khmer/, and is
-// Copyright (C) Michigan State University, 2009-2015. It is licensed under
+// This file is part of khmer, http://github.com/ged-lab/khmer/, and is
+// Copyright (C) Michigan State University, 2009-2013. It is licensed under
// the three-clause BSD license; see LICENSE.
// Contact: khmer-project at idyll.org
//
diff --git a/lib/hashbits.cc b/lib/hashbits.cc
index 8119305..270f6d1 100644
--- a/lib/hashbits.cc
+++ b/lib/hashbits.cc
@@ -1,6 +1,6 @@
//
-// This file is part of khmer, https://github.com/dib-lab/khmer/, and is
-// Copyright (C) Michigan State University, 2009-2015. It is licensed under
+// This file is part of khmer, http://github.com/ged-lab/khmer/, and is
+// Copyright (C) Michigan State University, 2009-2013. It is licensed under
// the three-clause BSD license; see LICENSE.
// Contact: khmer-project at idyll.org
//
@@ -29,7 +29,6 @@ void Hashbits::save(std::string outfilename)
ofstream outfile(outfilename.c_str(), ios::binary);
- outfile.write(SAVED_SIGNATURE, 4);
unsigned char version = SAVED_FORMAT_VERSION;
outfile.write((const char *) &version, 1);
@@ -91,19 +90,11 @@ void Hashbits::load(std::string infilename)
unsigned int save_ksize = 0;
unsigned char save_n_tables = 0;
unsigned long long save_tablesize = 0;
- char signature[4];
unsigned char version, ht_type;
- infile.read(signature, 4);
infile.read((char *) &version, 1);
infile.read((char *) &ht_type, 1);
- if (!(std::string(signature, 4) == SAVED_SIGNATURE)) {
- std::ostringstream err;
- err << "Does not start with signature for a khmer " <<
- "file: " << signature << " Should be: " <<
- SAVED_SIGNATURE;
- throw khmer_file_exception(err.str());
- } else if (!(version == SAVED_FORMAT_VERSION)) {
+ if (!(version == SAVED_FORMAT_VERSION)) {
std::ostringstream err;
err << "Incorrect file format version " << (int) version
<< " while reading k-mer graph from " << infilename
@@ -262,24 +253,4 @@ unsigned int Hashbits::consume_string_overlap(const std::string &s,
return n_consumed;
}
-void Hashbits::update_from(const Hashbits &other)
-{
- if (_ksize != other._ksize) {
- throw khmer_exception("both nodegraphs must have same k size");
- }
- if (_tablesizes != other._tablesizes) {
- throw khmer_exception("both nodegraphs must have same table sizes");
- }
- for (unsigned int table_num = 0; table_num < _n_tables; table_num++) {
- Byte * me = _counts[table_num];
- Byte * ot = other._counts[table_num];
- HashIntoType tablesize = _tablesizes[table_num];
- HashIntoType tablebytes = tablesize / 8 + 1;
-
- for (HashIntoType index = 0; index < tablebytes; index++) {
- me[index] |= ot[index]; // bitwise or
- }
- }
-}
-
// vim: set sts=2 sw=2:
diff --git a/lib/hashbits.hh b/lib/hashbits.hh
index 3139650..894c526 100644
--- a/lib/hashbits.hh
+++ b/lib/hashbits.hh
@@ -1,6 +1,6 @@
//
-// This file is part of khmer, https://github.com/dib-lab/khmer/, and is
-// Copyright (C) Michigan State University, 2009-2015. It is licensed under
+// This file is part of khmer, http://github.com/ged-lab/khmer/, and is
+// Copyright (C) Michigan State University, 2009-2013. It is licensed under
// the three-clause BSD license; see LICENSE.
// Contact: khmer-project at idyll.org
//
@@ -246,13 +246,6 @@ public:
}
return 1;
}
- // accessors to get table info
- const HashIntoType n_entries() const
- {
- return _tablesizes[0];
- }
-
- void update_from(const Hashbits &other);
};
};
diff --git a/lib/hashtable.cc b/lib/hashtable.cc
index cf4c2cb..726484e 100644
--- a/lib/hashtable.cc
+++ b/lib/hashtable.cc
@@ -1,6 +1,6 @@
//
-// This file is part of khmer, https://github.com/dib-lab/khmer/, and is
-// Copyright (C) Michigan State University, 2009-2015. It is licensed under
+// This file is part of khmer, http://github.com/ged-lab/khmer/, and is
+// Copyright (C) Michigan State University, 2009-2013. It is licensed under
// the three-clause BSD license; see LICENSE.
// Contact: khmer-project at idyll.org
//
@@ -193,10 +193,24 @@ void Hashtable::get_median_count(const std::string &s,
float &stddev)
{
std::vector<BoundedCounterType> counts;
- this->get_kmer_counts(s, counts);
+ KMerIterator kmers(s.c_str(), _ksize);
+
+ while(!kmers.done()) {
+ HashIntoType kmer = kmers.next();
+ BoundedCounterType count = this->get_count(kmer);
+ counts.push_back(count);
+ }
if (!counts.size()) {
- throw khmer_exception("no k-mer counts for this string; too short?");
+ throw khmer_exception();
+ }
+
+ if (!counts.size()) {
+ median = 0;
+ average = 0;
+ stddev = 0;
+
+ return;
}
average = 0;
@@ -218,42 +232,6 @@ void Hashtable::get_median_count(const std::string &s,
median = counts[counts.size() / 2]; // rounds down
}
-//
-// Optimized filter function for normalize-by-median
-//
-bool Hashtable::median_at_least(const std::string &s,
- unsigned int cutoff)
-{
- KMerIterator kmers(s.c_str(), _ksize);
- unsigned int min_req = 0.5 + float(s.size() - _ksize + 1) / 2;
- unsigned int num_cutoff_kmers = 0;
-
- // first loop:
- // accumulate at least min_req worth of counts before checking to see
- // if we have enough high-abundance k-mers to indicate success.
- for (unsigned int i = 0; i < min_req; ++i) {
- HashIntoType kmer = kmers.next();
- if (this->get_count(kmer) >= cutoff) {
- ++num_cutoff_kmers;
- }
- }
-
- // second loop: now check to see if we pass the threshold for each k-mer.
- if (num_cutoff_kmers >= min_req) {
- return true;
- }
- while(!kmers.done()) {
- HashIntoType kmer = kmers.next();
- if (this->get_count(kmer) >= cutoff) {
- ++num_cutoff_kmers;
- if (num_cutoff_kmers >= min_req) {
- return true;
- }
- }
- }
- return false;
-}
-
void Hashtable::save_tagset(std::string outfilename)
{
ofstream outfile(outfilename.c_str(), ios::binary);
@@ -262,7 +240,6 @@ void Hashtable::save_tagset(std::string outfilename)
HashIntoType * buf = new HashIntoType[tagset_size];
- outfile.write(SAVED_SIGNATURE, 4);
unsigned char version = SAVED_FORMAT_VERSION;
outfile.write((const char *) &version, 1);
@@ -314,23 +291,15 @@ void Hashtable::load_tagset(std::string infilename, bool clear_tags)
}
unsigned char version, ht_type;
- char signature[4];
unsigned int save_ksize = 0;
size_t tagset_size = 0;
HashIntoType * buf = NULL;
try {
- infile.read(signature, 4);
infile.read((char *) &version, 1);
infile.read((char *) &ht_type, 1);
- if (!(std::string(signature, 4) == SAVED_SIGNATURE)) {
- std::ostringstream err;
- err << "Incorrect file signature " << signature
- << " while reading tagset from " << infilename
- << "; should be " << SAVED_SIGNATURE;
- throw khmer_file_exception(err.str());
- } else if (!(version == SAVED_FORMAT_VERSION)) {
+ if (!(version == SAVED_FORMAT_VERSION)) {
std::ostringstream err;
err << "Incorrect file format version " << (int) version
<< " while reading tagset from " << infilename
@@ -1296,22 +1265,14 @@ void Hashtable::load_stop_tags(std::string infilename, bool clear_tags)
}
unsigned char version, ht_type;
- char signature[4];
unsigned int save_ksize = 0;
size_t tagset_size = 0;
try {
- infile.read(signature, 4);
infile.read((char *) &version, 1);
infile.read((char *) &ht_type, 1);
- if (!(std::string(signature, 4) == SAVED_SIGNATURE)) {
- std::ostringstream err;
- err << "Incorrect file signature " << signature
- << " while reading stoptags from " << infilename
- << "; should be " << SAVED_SIGNATURE;
- throw khmer_file_exception(err.str());
- } else if (!(version == SAVED_FORMAT_VERSION)) {
+ if (!(version == SAVED_FORMAT_VERSION)) {
std::ostringstream err;
err << "Incorrect file format version " << (int) version
<< " while reading stoptags from " << infilename
@@ -1354,7 +1315,6 @@ void Hashtable::save_stop_tags(std::string outfilename)
HashIntoType * buf = new HashIntoType[tagset_size];
- outfile.write(SAVED_SIGNATURE, 4);
unsigned char version = SAVED_FORMAT_VERSION;
outfile.write((const char *) &version, 1);
@@ -1542,43 +1502,4 @@ void Hashtable::extract_unique_paths(std::string seq,
}
}
}
-
-
-void Hashtable::get_kmers(const std::string &s,
- std::vector<std::string> &kmers_vec) const
-{
- if (s.length() < _ksize) {
- return;
- }
- for (unsigned int i = 0; i < s.length() - _ksize + 1; i++) {
- std::string sub = s.substr(i, i + _ksize);
- kmers_vec.push_back(sub);
- }
-}
-
-
-void Hashtable::get_kmer_hashes(const std::string &s,
- std::vector<HashIntoType> &kmers_vec) const
-{
- KMerIterator kmers(s.c_str(), _ksize);
-
- while(!kmers.done()) {
- HashIntoType kmer = kmers.next();
- kmers_vec.push_back(kmer);
- }
-}
-
-
-void Hashtable::get_kmer_counts(const std::string &s,
- std::vector<BoundedCounterType> &counts) const
-{
- KMerIterator kmers(s.c_str(), _ksize);
-
- while(!kmers.done()) {
- HashIntoType kmer = kmers.next();
- BoundedCounterType c = this->get_count(kmer);
- counts.push_back(c);
- }
-}
-
// vim: set sts=2 sw=2:
diff --git a/lib/hashtable.hh b/lib/hashtable.hh
index d18be70..dd0f521 100644
--- a/lib/hashtable.hh
+++ b/lib/hashtable.hh
@@ -1,6 +1,6 @@
//
-// This file is part of khmer, https://github.com/dib-lab/khmer/, and is
-// Copyright (C) Michigan State University, 2009-2015. It is licensed under
+// This file is part of khmer, http://github.com/ged-lab/khmer/, and is
+// Copyright (C) Michigan State University, 2009-2013. It is licensed under
// the three-clause BSD license; see LICENSE.
// Contact: khmer-project at idyll.org
//
@@ -174,7 +174,6 @@ public:
class Hashtable // Base class implementation of a Bloom ht.
{
friend class SubsetPartition;
- friend class LabelHash;
protected:
unsigned int _tag_density;
@@ -292,9 +291,6 @@ public:
unsigned long long &n_consumed
);
- bool median_at_least(const std::string &s,
- unsigned int cutoff);
-
void get_median_count(const std::string &s,
BoundedCounterType &median,
float &average,
@@ -392,12 +388,6 @@ public:
virtual BoundedCounterType test_and_set_bits(const char * kmer) = 0;
virtual BoundedCounterType test_and_set_bits(HashIntoType khash) = 0;
- virtual std::vector<HashIntoType> get_tablesizes() const = 0;
- virtual const size_t n_tables() const = 0;
- virtual const HashIntoType n_occupied(HashIntoType start=0,
- HashIntoType stop=0) const = 0;
- virtual const HashIntoType n_entries() const = 0;
-
void filter_if_present(const std::string &infilename,
const std::string &outputfilename);
@@ -465,18 +455,6 @@ public:
return kmer_degree(kmer_f, kmer_r);
}
-
- // return all k-mer substrings, on the forward strand.
- void get_kmers(const std::string &s, std::vector<std::string> &kmers)
- const;
-
- // return hash values for all k-mer substrings
- void get_kmer_hashes(const std::string &s,
- std::vector<HashIntoType> &kmers) const;
-
- // return counts of all k-mers in this string.
- void get_kmer_counts(const std::string &s,
- std::vector<BoundedCounterType> &counts) const;
};
};
diff --git a/lib/hllcounter.cc b/lib/hllcounter.cc
index 91ac9f7..299e70e 100644
--- a/lib/hllcounter.cc
+++ b/lib/hllcounter.cc
@@ -1,5 +1,5 @@
//
-// This file is part of khmer, https://github.com/dib-lab/khmer/, and is
+// This file is part of khmer, http://github.com/ged-lab/khmer/, and is
// Copyright (C) Michigan State University, 2014-2015. It is licensed under
// the three-clause BSD license; see LICENSE.
// Contact: khmer-project at idyll.org
@@ -16,7 +16,6 @@
#include "khmer.hh"
#include "kmer_hash.hh"
#include "read_parsers.hh"
-#include "khmer_exception.hh"
#ifdef _OPENMP
#include <omp.h>
@@ -322,15 +321,10 @@ void HLLCounter::add(const std::string &value)
this->M[j] = std::max(this->M[j], get_rho(x >> this->p, 64 - this->p));
}
-unsigned int HLLCounter::consume_string(const std::string &inp)
+unsigned int HLLCounter::consume_string(const std::string &s)
{
unsigned int n_consumed = 0;
std::string kmer = "";
- std::string s = inp;
-
- for (unsigned int i = 0; i < s.length(); i++) {
- s[i] &= 0xdf; // toupper - knock out the "lowercase bit"
- }
for(std::string::const_iterator it = s.begin(); it != s.end(); ++it) {
kmer.push_back(*it);
@@ -461,9 +455,6 @@ bool HLLCounter::check_and_normalize_read(std::string &read) const
void HLLCounter::merge(HLLCounter &other)
{
- if (this->p != other.p || this->_ksize != other._ksize) {
- throw khmer_exception("HLLCounters to be merged must be created with same parameters");
- }
for(unsigned int i=0; i < this->M.size(); ++i) {
this->M[i] = std::max(other.M[i], this->M[i]);
}
diff --git a/lib/hllcounter.hh b/lib/hllcounter.hh
index f03cff0..f314107 100644
--- a/lib/hllcounter.hh
+++ b/lib/hllcounter.hh
@@ -1,5 +1,5 @@
//
-// This file is part of khmer, https://github.com/dib-lab/khmer/, and is
+// This file is part of khmer, http://github.com/ged-lab/khmer/, and is
// Copyright (C) Michigan State University, 2014-2015. It is licensed under
// the three-clause BSD license; see LICENSE.
// Contact: khmer-project at idyll.org
diff --git a/lib/ht-diff.cc b/lib/ht-diff.cc
index e6b9bed..85f342d 100644
--- a/lib/ht-diff.cc
+++ b/lib/ht-diff.cc
@@ -1,6 +1,6 @@
//
-// This file is part of khmer, https://github.com/dib-lab/khmer/, and is
-// Copyright (C) Michigan State University, 2009-2015. It is licensed under
+// This file is part of khmer, http://github.com/ged-lab/khmer/, and is
+// Copyright (C) Michigan State University, 2009-2013. It is licensed under
// the three-clause BSD license; see LICENSE.
// Contact: khmer-project at idyll.org
//
diff --git a/lib/khmer.hh b/lib/khmer.hh
index 60928c4..661b144 100644
--- a/lib/khmer.hh
+++ b/lib/khmer.hh
@@ -1,6 +1,6 @@
//
-// This file is part of khmer, https://github.com/dib-lab/khmer/, and is
-// Copyright (C) Michigan State University, 2009-2015. It is licensed under
+// This file is part of khmer, http://github.com/ged-lab/khmer/, and is
+// Copyright (C) Michigan State University, 2009-2013. It is licensed under
// the three-clause BSD license; see LICENSE.
// Contact: khmer-project at idyll.org
//
@@ -53,14 +53,12 @@ private:\
# define CIRCUM_RADIUS 2 // @CTB remove
# define CIRCUM_MAX_VOL 200 // @CTB remove
-# define SAVED_SIGNATURE "OXLI"
# define SAVED_FORMAT_VERSION 4
# define SAVED_COUNTING_HT 1
# define SAVED_HASHBITS 2
# define SAVED_TAGS 3
# define SAVED_STOPTAGS 4
# define SAVED_SUBSET 5
-# define SAVED_LABELSET 6
# define VERBOSE_REPARTITION 0
@@ -106,11 +104,11 @@ PartitionCountDistribution;
// types used in @camillescott's sparse labeling extension
typedef unsigned long long int Label;
typedef std::multimap<HashIntoType, Label*> TagLabelPtrMap;
-typedef std::multimap<Label, HashIntoType> LabelTagMap;
+typedef std::multimap<Label, HashIntoType*> LabelTagPtrMap;
typedef std::pair<HashIntoType, Label*> TagLabelPtrPair;
-typedef std::pair<Label, HashIntoType> LabelTagPair;
+typedef std::pair<Label, HashIntoType*> LabelTagPtrPair;
typedef std::set<Label*> LabelPtrSet;
-typedef std::set<HashIntoType> TagSet;
+typedef std::set<HashIntoType*> TagPtrSet;
typedef std::map<Label, Label*> LabelPtrMap;
template <typename T>
diff --git a/lib/khmer_exception.hh b/lib/khmer_exception.hh
index 95553df..e278335 100644
--- a/lib/khmer_exception.hh
+++ b/lib/khmer_exception.hh
@@ -1,6 +1,6 @@
//
-// This file is part of khmer, https://github.com/dib-lab/khmer/, and is
-// Copyright (C) Michigan State University, 2009-2015. It is licensed under
+// This file is part of khmer, http://github.com/ged-lab/khmer/, and is
+// Copyright (C) Michigan State University, 2009-2013. It is licensed under
// the three-clause BSD license; see LICENSE.
// Contact: khmer-project at idyll.org
//
diff --git a/lib/kmer_hash.cc b/lib/kmer_hash.cc
index 61c3741..deacbf1 100644
--- a/lib/kmer_hash.cc
+++ b/lib/kmer_hash.cc
@@ -1,5 +1,5 @@
//
-// This file is part of khmer, https://github.com/dib-lab/khmer/, and is
+// This file is part of khmer, http://github.com/ged-lab/khmer/, and is
// Copyright (C) Michigan State University, 2009-2015. It is licensed under
// the three-clause BSD license; see LICENSE.
// Contact: khmer-project at idyll.org
diff --git a/lib/kmer_hash.hh b/lib/kmer_hash.hh
index 33ea909..f9033a3 100644
--- a/lib/kmer_hash.hh
+++ b/lib/kmer_hash.hh
@@ -1,5 +1,5 @@
//
-// This file is part of khmer, https://github.com/dib-lab/khmer/, and is
+// This file is part of khmer, http://github.com/ged-lab/khmer/, and is
// Copyright (C) Michigan State University, 2009-2015. It is licensed under
// the three-clause BSD license; see LICENSE.
// Contact: khmer-project at idyll.org
diff --git a/lib/labelhash.cc b/lib/labelhash.cc
index b6366f5..1ba2414 100644
--- a/lib/labelhash.cc
+++ b/lib/labelhash.cc
@@ -1,21 +1,15 @@
//
-// This file is part of khmer, https://github.com/dib-lab/khmer/, and is
-// Copyright (C) Michigan State University, 2009-2015. It is licensed under
+// This file is part of khmer, http://github.com/ged-lab/khmer/, and is
+// Copyright (C) Michigan State University, 2009-2013. It is licensed under
// the three-clause BSD license; see LICENSE.
// Contact: khmer-project at idyll.org
//
#include "labelhash.hh"
-#include <sstream>
-#include <errno.h>
-
-#define IO_BUF_SIZE 250*1000*1000
-
#define LABEL_DBG 0
#define printdbg(m) if(LABEL_DBG) std::cout << #m << std::endl;
-using namespace std;
using namespace khmer;
using namespace khmer:: read_parsers;
@@ -67,7 +61,7 @@ LabelHash::consume_fasta_and_tag_with_labels(
while (!parser->is_complete( )) {
read = parser->get_next_read( );
- if (graph->check_and_normalize_read( read.sequence )) {
+ if (check_and_normalize_read( read.sequence )) {
// TODO: make threadsafe!
unsigned long long this_n_consumed = 0;
the_label = check_and_allocate_label(_tag_label);
@@ -89,10 +83,9 @@ LabelHash::consume_fasta_and_tag_with_labels(
#if (0)
// run callback, if specified
if (total_reads_TL % CALLBACK_PERIOD == 0 && callback) {
- std::cout << "n tags: " << graph->all_tags.size() << "\n";
+ std::cout << "n tags: " << all_tags.size() << "\n";
try {
- callback("consume_fasta_and_tag_with_labels", callback_data,
- total_reads_TL,
+ callback("consume_fasta_and_tag_with_labels", callback_data, total_reads_TL,
n_consumed);
} catch (...) {
delete parser;
@@ -133,9 +126,8 @@ void LabelHash::consume_partitioned_fasta_and_tag_with_labels(
read = parser->get_next_read();
seq = read.sequence;
- if (graph->check_and_normalize_read(seq)) {
- // First, figure out what the partition is (if non-zero), and
- // save that.
+ if (check_and_normalize_read(seq)) {
+ // First, figure out what the partition is (if non-zero), and save that.
printdbg(parsing partition id)
p = _parse_partition_id(read.name);
printdbg(checking label and allocating if necessary) {
@@ -176,7 +168,7 @@ void LabelHash::link_tag_and_label(HashIntoType& kmer, Label& kmer_label)
{
printdbg(linking tag and label)
tag_labels.insert(TagLabelPtrPair(kmer, &kmer_label));
- label_tag_ptrs.insert(LabelTagPair(kmer_label, kmer));
+ label_tag_ptrs.insert(LabelTagPtrPair(kmer_label, &kmer));
printdbg(done linking tag and label)
}
@@ -190,17 +182,17 @@ void LabelHash::consume_sequence_and_tag_with_labels(const std::string& seq,
bool kmer_tagged;
- KMerIterator kmers(seq.c_str(), graph->_ksize);
+ KMerIterator kmers(seq.c_str(), _ksize);
HashIntoType kmer;
- unsigned int since = graph->_tag_density / 2 + 1;
+ unsigned int since = _tag_density / 2 + 1;
printdbg(entering while loop)
while(!kmers.done()) {
kmer = kmers.next();
bool is_new_kmer;
- if ((is_new_kmer = graph->test_and_set_bits( kmer ))) {
+ if ((is_new_kmer = test_and_set_bits( kmer ))) {
++n_consumed;
printdbg(test_and_set_bits)
}
@@ -211,7 +203,7 @@ void LabelHash::consume_sequence_and_tag_with_labels(const std::string& seq,
} else {
printdbg(entering tag spin lock)
//ACQUIRE_ALL_TAGS_SPIN_LOCK
- kmer_tagged = set_contains(graph->all_tags, kmer);
+ kmer_tagged = set_contains(all_tags, kmer);
//RELEASE_ALL_TAGS_SPIN_LOCK
printdbg(released tag spin lock)
if (kmer_tagged) {
@@ -236,7 +228,7 @@ void LabelHash::consume_sequence_and_tag_with_labels(const std::string& seq,
}
}
#else
- if (!is_new_kmer && set_contains(graph->all_tags, kmer)) {
+ if (!is_new_kmer && set_contains(all_tags, kmer)) {
since = 1;
if (found_tags) {
found_tags->insert(kmer);
@@ -246,12 +238,11 @@ void LabelHash::consume_sequence_and_tag_with_labels(const std::string& seq,
}
#endif
//
- if (since >= graph->_tag_density) {
- printdbg(exceeded tag density: drop a tag and label --
- getting tag lock)
+ if (since >= _tag_density) {
+ printdbg(exceeded tag density: drop a tag and label -- getting tag lock)
//ACQUIRE_ALL_TAGS_SPIN_LOCK
printdbg(in tag spin lock)
- graph->all_tags.insert(kmer);
+ all_tags.insert(kmer);
//RELEASE_ALL_TAGS_SPIN_LOCK
printdbg(released tag spin lock)
@@ -269,9 +260,9 @@ void LabelHash::consume_sequence_and_tag_with_labels(const std::string& seq,
printdbg(moving to next iter)
} // iteration over kmers
printdbg(finished iteration: dropping last tag)
- if (since >= graph->_tag_density/2 - 1) {
+ if (since >= _tag_density/2 - 1) {
//ACQUIRE_ALL_TAGS_SPIN_LOCK
- graph->all_tags.insert(kmer); // insert the last k-mer, too.
+ all_tags.insert(kmer); // insert the last k-mer, too.
//RELEASE_ALL_TAGS_SPIN_LOCK
// Label code: TODO: MAKE THREADSAFE!
@@ -293,13 +284,12 @@ unsigned int LabelHash::sweep_label_neighborhood(const std::string& seq,
SeenSet tagged_kmers;
unsigned int num_traversed;
- num_traversed = graph->partition->sweep_for_tags(seq, tagged_kmers,
- graph->all_tags,
+ num_traversed = partition->sweep_for_tags(seq, tagged_kmers, all_tags,
range, break_on_stoptags, stop_big_traversals);
traverse_labels_and_resolve(tagged_kmers, found_labels);
//printf("range=%u ", range);
if (range == 0) {
- if (!(num_traversed == seq.length()-graph->ksize()+1)) {
+ if (!(num_traversed == seq.length()-ksize()+1)) {
throw khmer_exception();
}
}
@@ -315,6 +305,14 @@ LabelPtrSet LabelHash::get_tag_labels(const HashIntoType& tag)
return labels;
}
+TagPtrSet LabelHash::get_label_tags(const Label& label)
+{
+ TagPtrSet tags;
+ //unsigned int num_tags;
+ _get_tags_from_label(label, label_tag_ptrs, tags);
+ return tags;
+}
+
void LabelHash::traverse_labels_and_resolve(const SeenSet& tagged_kmers,
LabelPtrSet& found_labels)
{
@@ -338,195 +336,3 @@ LabelHash::~LabelHash()
delete itr->second;
}
}
-
-
-// Save a partition map to disk.
-
-void LabelHash::save_labels_and_tags(std::string filename)
-{
- ofstream outfile(filename.c_str(), ios::binary);
-
- outfile.write(SAVED_SIGNATURE, 4);
- unsigned char version = SAVED_FORMAT_VERSION;
- outfile.write((const char *) &version, 1);
-
- unsigned char ht_type = SAVED_LABELSET;
- outfile.write((const char *) &ht_type, 1);
-
- unsigned int save_ksize = graph->ksize();
- outfile.write((const char *) &save_ksize, sizeof(save_ksize));
-
- unsigned long n_labeltags = tag_labels.size();
- outfile.write((const char *) &n_labeltags, sizeof(n_labeltags));
-
- ///
-
- char * buf = NULL;
- buf = new char[IO_BUF_SIZE];
- unsigned int n_bytes = 0;
-
- // For each tag in the partition map, save the tag and the associated
- // partition ID.
-
- TagLabelPtrMap::const_iterator pi = tag_labels.begin();
- for (; pi != tag_labels.end(); ++pi) {
- HashIntoType *k_p = (HashIntoType *) (buf + n_bytes);
- *k_p = pi->first;
- n_bytes += sizeof(HashIntoType);
-
- Label * l_p = (Label *) (buf + n_bytes);
- *l_p = *(pi->second);
- n_bytes += sizeof(Label);
-
- // flush to disk
- if (n_bytes >= IO_BUF_SIZE - sizeof(HashIntoType) - sizeof(Label)) {
- outfile.write(buf, n_bytes);
- n_bytes = 0;
- }
- }
- // save remainder.
- if (n_bytes) {
- outfile.write(buf, n_bytes);
- }
-
- if (outfile.fail()) {
- delete[] buf;
- throw khmer_file_exception(strerror(errno));
- }
- outfile.close();
-
- delete[] buf;
-}
-
-void LabelHash::load_labels_and_tags(std::string filename)
-{
- ifstream infile;
-
- // configure ifstream to raise exceptions for everything.
- infile.exceptions(std::ifstream::failbit | std::ifstream::badbit);
-
- try {
- infile.open(filename.c_str(), ios::binary);
- } catch (std::ifstream::failure &e) {
- std::string err;
- if (!infile.is_open()) {
- err = "Cannot open labels/tags file: " + filename;
- } else {
- err = "Unknown error in opening file: " + filename;
- }
- throw khmer_file_exception(err);
- }
-
- unsigned long n_labeltags = 1;
- try {
- unsigned int save_ksize = 0;
- char signature[4];
- unsigned char version = 0, ht_type = 0;
-
- infile.read(signature, 4);
- infile.read((char *) &version, 1);
- infile.read((char *) &ht_type, 1);
- if (!(std::string(signature, 4) == SAVED_SIGNATURE)) {
- std::ostringstream err;
- err << "Incorrect file signature " << signature
- << " while reading labels/tags from " << filename
- << " Should be: " << SAVED_SIGNATURE;
- throw khmer_file_exception(err.str());
- } else if (!(version == SAVED_FORMAT_VERSION)) {
- std::ostringstream err;
- err << "Incorrect file format version " << (int) version
- << " while reading labels/tags from " << filename;
- throw khmer_file_exception(err.str());
- } else if (!(ht_type == SAVED_LABELSET)) {
- std::ostringstream err;
- err << "Incorrect file format type " << (int) ht_type
- << " while reading labels/tags from " << filename;
- throw khmer_file_exception(err.str());
- }
-
- infile.read((char *) &save_ksize, sizeof(save_ksize));
- if (!(save_ksize == graph->ksize())) {
- std::ostringstream err;
- err << "Incorrect k-mer size " << save_ksize
- << " while reading labels/tags from " << filename;
- throw khmer_file_exception(err.str());
- }
-
- infile.read((char *) &n_labeltags, sizeof(n_labeltags));
- } catch (std::ifstream::failure &e) {
- std::string err;
- err = "Unknown error reading header info from: " + filename;
- throw khmer_file_exception(err);
- }
-
- char * buf = new char[IO_BUF_SIZE];
-
- unsigned long loaded = 0;
- long remainder;
-
-
- HashIntoType * kmer_p = NULL;
- Label * labelp = NULL;
-
- remainder = 0;
- unsigned int iteration = 0;
- while (!infile.eof()) {
- unsigned int i;
-
- try {
- infile.read(buf + remainder, IO_BUF_SIZE - remainder);
- } catch (std::ifstream::failure &e) {
-
- // We may get an exception here if we fail to read all the
- // expected bytes due to EOF -- only pass it up if we read
- // _nothing_. Note that the while loop exits on EOF.
-
- if (infile.gcount() == 0) {
- delete[] buf;
-
- std::string err;
- err = "Unknown error reading data from: " + filename;
- throw khmer_file_exception(err);
- }
- }
-
- long n_bytes = infile.gcount() + remainder;
- remainder = n_bytes % (sizeof(Label) + sizeof(HashIntoType));
- n_bytes -= remainder;
-
- iteration++;
-
- for (i = 0; i < n_bytes;) {
- kmer_p = (HashIntoType *) (buf + i);
- i += sizeof(HashIntoType);
-
- labelp = (Label *) (buf + i);
- i += sizeof(Label);
-
- Label * labelp2;
-
- graph->all_tags.insert(*kmer_p);
- labelp2 = check_and_allocate_label(*labelp);
- link_tag_and_label(*kmer_p, *labelp2);
-
- loaded++;
- }
- if (!(i == n_bytes)) {
- delete[] buf;
- throw khmer_file_exception("unknown error reading labels and tags");
- }
- memcpy(buf, buf + n_bytes, remainder);
- }
-
- if (remainder != 0) {
- delete[] buf;
- throw khmer_file_exception("unknown error reading labels and tags");
- }
-
- if (loaded != n_labeltags) {
- delete[] buf;
- throw khmer_file_exception("error loading labels: too few loaded");
- }
-
- delete[] buf;
-}
diff --git a/lib/labelhash.hh b/lib/labelhash.hh
index d2f754f..3f06631 100644
--- a/lib/labelhash.hh
+++ b/lib/labelhash.hh
@@ -1,6 +1,6 @@
//
-// This file is part of khmer, https://github.com/dib-lab/khmer/, and is
-// Copyright (C) Michigan State University, 2009-2015. It is licensed under
+// This file is part of khmer, http://github.com/ged-lab/khmer/, and is
+// Copyright (C) Michigan State University, 2009-2013. It is licensed under
// the three-clause BSD license; see LICENSE.
// Contact: khmer-project at idyll.org
//
@@ -18,7 +18,7 @@
namespace khmer
{
-class LabelHash
+class LabelHash : public khmer::Hashbits
{
protected:
// Does the given tag already have the given label?
@@ -37,14 +37,14 @@ protected:
}
// Does the given label already have a tag associated with it?
- bool _cmap_contains_tag(const LabelTagMap& cmap,
+ bool _cmap_contains_tag(const LabelTagPtrMap& cmap,
Label& the_label,
HashIntoType& kmer)
{
- std::pair<LabelTagMap::const_iterator, LabelTagMap::const_iterator> ret;
+ std::pair<LabelTagPtrMap::const_iterator, LabelTagPtrMap::const_iterator> ret;
ret = cmap.equal_range(the_label);
- for (LabelTagMap::const_iterator it=ret.first; it!=ret.second; ++it) {
- if(it->second == kmer) {
+ for (LabelTagPtrMap::const_iterator it=ret.first; it!=ret.second; ++it) {
+ if(*(it->second) == kmer) {
return true;
}
}
@@ -66,13 +66,13 @@ protected:
}
unsigned int _get_tags_from_label(const Label& label,
- const LabelTagMap& cmap,
- TagSet& labeled_tags)
+ const LabelTagPtrMap& cmap,
+ TagPtrSet& labeled_tags)
{
unsigned int num_tags = 0;
- std::pair<LabelTagMap::const_iterator, LabelTagMap::const_iterator> ret;
+ std::pair<LabelTagPtrMap::const_iterator, LabelTagPtrMap::const_iterator> ret;
ret = cmap.equal_range(label);
- for (LabelTagMap::const_iterator it=ret.first; it!=ret.second; ++it) {
+ for (LabelTagPtrMap::const_iterator it=ret.first; it!=ret.second; ++it) {
labeled_tags.insert(it->second);
++num_tags;
}
@@ -82,18 +82,19 @@ protected:
uint32_t _tag_labels_spin_lock;
public:
- khmer::Hashtable * graph;
- explicit LabelHash(Hashtable * ht) : graph(ht)
+ LabelHash( WordLength ksize, std::vector<HashIntoType>& tablesizes)
+ : khmer::Hashbits(ksize, tablesizes)
{
_tag_labels_spin_lock = 0;
+ _all_tags_spin_lock = 0;
}
~LabelHash();
TagLabelPtrMap tag_labels;
- LabelTagMap label_tag_ptrs;
+ LabelTagPtrMap label_tag_ptrs;
LabelPtrMap label_ptrs;
size_t n_labels() const
@@ -139,6 +140,7 @@ public:
SeenSet * new_tags = 0);
LabelPtrSet get_tag_labels(const HashIntoType& tag);
+ TagPtrSet get_label_tags(const Label& label);
void link_tag_and_label(HashIntoType& kmer, Label& label);
@@ -151,9 +153,6 @@ public:
void traverse_labels_and_resolve(const SeenSet& tagged_kmers,
LabelPtrSet& found_labels);
- void save_labels_and_tags(std::string);
- void load_labels_and_tags(std::string);
-
};
};
diff --git a/lib/magic b/lib/magic
deleted file mode 100644
index 1ab0707..0000000
--- a/lib/magic
+++ /dev/null
@@ -1,11 +0,0 @@
-# Magic descriptions of khmer file types for file(1) command.
-# Format is described in magic(5).
-
-0 string OXLI Binary from the khmer project,
->4 byte x file format version %u,
->5 byte 1 k-mer count table
->5 byte 2 k-mer presence table
->5 byte 3 k-mer tagset
->5 byte 4 k-mer partition stoptags
->5 byte 5 k-mer partition subset
->5 byte 6 labels/tags for implicit k-mer De Bruijn graph
diff --git a/lib/perf_metrics.cc b/lib/perf_metrics.cc
index a0c348a..374be0f 100644
--- a/lib/perf_metrics.cc
+++ b/lib/perf_metrics.cc
@@ -1,6 +1,6 @@
//
-// This file is part of khmer, https://github.com/dib-lab/khmer/, and is
-// Copyright (C) Michigan State University, 2009-2015. It is licensed under
+// This file is part of khmer, http://github.com/ged-lab/khmer/, and is
+// Copyright (C) Michigan State University, 2009-2013. It is licensed under
// the three-clause BSD license; see LICENSE.
// Contact: khmer-project at idyll.org
//
diff --git a/lib/perf_metrics.hh b/lib/perf_metrics.hh
index 63a0e49..b45c052 100644
--- a/lib/perf_metrics.hh
+++ b/lib/perf_metrics.hh
@@ -1,6 +1,6 @@
//
-// This file is part of khmer, https://github.com/dib-lab/khmer/, and is
-// Copyright (C) Michigan State University, 2009-2015. It is licensed under
+// This file is part of khmer, http://github.com/ged-lab/khmer/, and is
+// Copyright (C) Michigan State University, 2009-2013. It is licensed under
// the three-clause BSD license; see LICENSE.
// Contact: khmer-project at idyll.org
//
diff --git a/lib/primes.hh b/lib/primes.hh
index ba806e4..938f4fa 100644
--- a/lib/primes.hh
+++ b/lib/primes.hh
@@ -1,6 +1,6 @@
//
-// This file is part of khmer, https://github.com/dib-lab/khmer/, and is
-// Copyright (C) Michigan State University, 2009-2015. It is licensed under
+// This file is part of khmer, http://github.com/ged-lab/khmer/, and is
+// Copyright (C) Michigan State University, 2009-2013. It is licensed under
// the three-clause BSD license; see LICENSE.
// Contact: khmer-project at idyll.org
//
diff --git a/lib/read_aligner.cc b/lib/read_aligner.cc
index 569cc52..9bf4343 100644
--- a/lib/read_aligner.cc
+++ b/lib/read_aligner.cc
@@ -1,6 +1,6 @@
//
-// This file is part of khmer, https://github.com/dib-lab/khmer/, and is
-// Copyright (C) Michigan State University, 2009-2015. It is licensed under
+// This file is part of khmer, http://github.com/ged-lab/khmer/, and is
+// Copyright (C) Michigan State University, 2009-2013. It is licensed under
// the three-clause BSD license; see LICENSE. Contact: ctb at msu.edu
//
#include "read_aligner.hh"
diff --git a/lib/read_aligner.hh b/lib/read_aligner.hh
index 20b1654..3d7e7a5 100644
--- a/lib/read_aligner.hh
+++ b/lib/read_aligner.hh
@@ -1,6 +1,6 @@
//
-// This file is part of khmer, https://github.com/dib-lab/khmer/, and is
-// Copyright (C) Michigan State University, 2009-2015. It is licensed under
+// This file is part of khmer, http://github.com/ged-lab/khmer/, and is
+// Copyright (C) Michigan State University, 2009-2013. It is licensed under
// the three-clause BSD license; see LICENSE. Contact: ctb at msu.edu
//
diff --git a/lib/read_parsers.cc b/lib/read_parsers.cc
index 1e8506c..6bb4b35 100644
--- a/lib/read_parsers.cc
+++ b/lib/read_parsers.cc
@@ -1,6 +1,6 @@
//
-// This file is part of khmer, https://github.com/dib-lab/khmer/, and is
-// Copyright (C) Michigan State University, 2009-2015. It is licensed under
+// This file is part of khmer, http://github.com/ged-lab/khmer/, and is
+// Copyright (C) Michigan State University, 2009-2013. It is licensed under
// the three-clause BSD license; see LICENSE.
// Contact: khmer-project at idyll.org
//
diff --git a/lib/read_parsers.hh b/lib/read_parsers.hh
index b8ceadf..d030a0b 100644
--- a/lib/read_parsers.hh
+++ b/lib/read_parsers.hh
@@ -1,6 +1,6 @@
//
-// This file is part of khmer, https://github.com/dib-lab/khmer/, and is
-// Copyright (C) Michigan State University, 2009-2015. It is licensed under
+// This file is part of khmer, http://github.com/ged-lab/khmer/, and is
+// Copyright (C) Michigan State University, 2009-2013. It is licensed under
// the three-clause BSD license; see LICENSE.
// Contact: khmer-project at idyll.org
//
diff --git a/lib/subset.cc b/lib/subset.cc
index c62ed39..339a2c9 100644
--- a/lib/subset.cc
+++ b/lib/subset.cc
@@ -1,6 +1,6 @@
//
-// This file is part of khmer, https://github.com/dib-lab/khmer/, and is
-// Copyright (C) Michigan State University, 2009-2015. It is licensed under
+// This file is part of khmer, http://github.com/ged-lab/khmer/, and is
+// Copyright (C) Michigan State University, 2009-2014. It is licensed under
// the three-clause BSD license; see LICENSE.
// Contact: khmer-project at idyll.org
//
@@ -11,7 +11,6 @@
#include <sstream>
#include <errno.h>
-#include <assert.h>
#define IO_BUF_SIZE 250*1000*1000
#define BIG_TRAVERSALS_ARE 200
@@ -1256,7 +1255,6 @@ void SubsetPartition::_merge_other(
void SubsetPartition::merge_from_disk(string other_filename)
{
ifstream infile;
- unsigned long long expected_pmap_size;
// configure ifstream to raise exceptions for everything.
infile.exceptions(std::ifstream::failbit | std::ifstream::badbit);
@@ -1275,19 +1273,11 @@ void SubsetPartition::merge_from_disk(string other_filename)
try {
unsigned int save_ksize = 0;
- char signature[4];
unsigned char version, ht_type;
- infile.read(signature, 4);
infile.read((char *) &version, 1);
infile.read((char *) &ht_type, 1);
- if (!(std::string(signature, 4) == SAVED_SIGNATURE)) {
- std::ostringstream err;
- err << "Incorrect file signature " << signature
- << " while reading subset pmap from " << other_filename
- << " Should be: " << SAVED_SIGNATURE;
- throw khmer_file_exception(err.str());
- } else if (!(version == SAVED_FORMAT_VERSION)) {
+ if (!(version == SAVED_FORMAT_VERSION)) {
std::ostringstream err;
err << "Incorrect file format version " << (int) version
<< " while reading subset pmap from " << other_filename;
@@ -1306,8 +1296,6 @@ void SubsetPartition::merge_from_disk(string other_filename)
<< " while reading subset pmap from " << other_filename;
throw khmer_file_exception(err.str());
}
-
- infile.read((char *) &expected_pmap_size, sizeof(expected_pmap_size));
} catch (std::ifstream::failure &e) {
std::string err;
err = "Unknown error reading header info from: " + other_filename;
@@ -1344,7 +1332,6 @@ void SubsetPartition::merge_from_disk(string other_filename)
// _nothing_. Note that the while loop exits on EOF.
if (infile.gcount() == 0) {
- delete[] buf;
std::string err;
err = "Unknown error reading data from: " + other_filename;
throw khmer_file_exception(err);
@@ -1363,21 +1350,21 @@ void SubsetPartition::merge_from_disk(string other_filename)
diskp = (PartitionID *) (buf + i);
i += sizeof(PartitionID);
- assert((*diskp != 0)); // sanity check!
+ if (!(*diskp != 0)) { // sanity check.
+ throw khmer_exception();
+ }
_merge_other(*kmer_p, *diskp, diskp_to_pp);
loaded++;
}
- assert(i == n_bytes);
+ if (!(i == n_bytes)) {
+ throw khmer_exception();
+ }
memcpy(buf, buf + n_bytes, remainder);
}
- delete[] buf;
- if (loaded != expected_pmap_size) {
- throw khmer_file_exception("error loading partitionmap - "
- "invalid # of items");
- }
+ delete[] buf;
}
// Save a partition map to disk.
@@ -1387,7 +1374,6 @@ void SubsetPartition::save_partitionmap(string pmap_filename)
ofstream outfile(pmap_filename.c_str(), ios::binary);
unsigned char version = SAVED_FORMAT_VERSION;
- outfile.write(SAVED_SIGNATURE, 4);
outfile.write((const char *) &version, 1);
unsigned char ht_type = SAVED_SUBSET;
@@ -1396,9 +1382,6 @@ void SubsetPartition::save_partitionmap(string pmap_filename)
unsigned int save_ksize = _ht->ksize();
outfile.write((const char *) &save_ksize, sizeof(save_ksize));
- unsigned long long pmap_size = partition_map.size();
- outfile.write((const char *) &pmap_size, sizeof(pmap_size));
-
///
char * buf = NULL;
diff --git a/lib/subset.hh b/lib/subset.hh
index a7d053e..b1c06df 100644
--- a/lib/subset.hh
+++ b/lib/subset.hh
@@ -1,6 +1,6 @@
//
-// This file is part of khmer, https://github.com/dib-lab/khmer/, and is
-// Copyright (C) Michigan State University, 2009-2015. It is licensed under
+// This file is part of khmer, http://github.com/ged-lab/khmer/, and is
+// Copyright (C) Michigan State University, 2009-2014. It is licensed under
// the three-clause BSD license; see LICENSE.
// Contact: khmer-project at idyll.org
//
diff --git a/lib/test-Colors.cc b/lib/test-Colors.cc
index 92e14d4..7e70309 100644
--- a/lib/test-Colors.cc
+++ b/lib/test-Colors.cc
@@ -1,6 +1,6 @@
//
-// This file is part of khmer, https://github.com/dib-lab/khmer/, and is
-// Copyright (C) Michigan State University, 2013-2015. It is licensed under
+// This file is part of khmer, http://github.com/ged-lab/khmer/, and is
+// Copyright (C) Michigan State University, 2013. It is licensed under
// the three-clause BSD license; see LICENSE.
// Contact: khmer-project at idyll.org
//
diff --git a/lib/test-HashTables.cc b/lib/test-HashTables.cc
index baa0fd2..dccf1ef 100644
--- a/lib/test-HashTables.cc
+++ b/lib/test-HashTables.cc
@@ -1,6 +1,6 @@
//
-// This file is part of khmer, https://github.com/dib-lab/khmer/, and is
-// Copyright (C) Michigan State University, 2009-2015. It is licensed under
+// This file is part of khmer, http://github.com/ged-lab/khmer/, and is
+// Copyright (C) Michigan State University, 2009-2013. It is licensed under
// the three-clause BSD license; see LICENSE.
// Contact: khmer-project at idyll.org
//
diff --git a/lib/test-Parser.cc b/lib/test-Parser.cc
index 1424cef..5d068cd 100644
--- a/lib/test-Parser.cc
+++ b/lib/test-Parser.cc
@@ -1,6 +1,6 @@
//
-// This file is part of khmer, https://github.com/dib-lab/khmer/, and is
-// Copyright (C) Michigan State University, 2009-2015. It is licensed under
+// This file is part of khmer, http://github.com/ged-lab/khmer/, and is
+// Copyright (C) Michigan State University, 2009-2013. It is licensed under
// the three-clause BSD license; see LICENSE.
// Contact: khmer-project at idyll.org
//
diff --git a/lib/test-compile.cc b/lib/test-compile.cc
index f0c4bb0..cedfe4c 100644
--- a/lib/test-compile.cc
+++ b/lib/test-compile.cc
@@ -1,5 +1,5 @@
//
-// This file is part of khmer, https://github.com/dib-lab/khmer/, and is
+// This file is part of khmer, http://github.com/ged-lab/khmer/, and is
// Copyright (C) Michigan State University, 2015. It is licensed under
// the three-clause BSD license; see LICENSE.
// Contact: khmer-project at idyll.org
diff --git a/lib/trace_logger.cc b/lib/trace_logger.cc
index 9600d99..06dd34a 100644
--- a/lib/trace_logger.cc
+++ b/lib/trace_logger.cc
@@ -1,6 +1,6 @@
//
-// This file is part of khmer, https://github.com/dib-lab/khmer/, and is
-// Copyright (C) Michigan State University, 2009-2015. It is licensed under
+// This file is part of khmer, http://github.com/ged-lab/khmer/, and is
+// Copyright (C) Michigan State University, 2009-2013. It is licensed under
// the three-clause BSD license; see LICENSE.
// Contact: khmer-project at idyll.org
//
diff --git a/lib/trace_logger.hh b/lib/trace_logger.hh
index 9c24161..54d57e1 100644
--- a/lib/trace_logger.hh
+++ b/lib/trace_logger.hh
@@ -1,6 +1,6 @@
//
-// This file is part of khmer, https://github.com/dib-lab/khmer/, and is
-// Copyright (C) Michigan State University, 2009-2015. It is licensed under
+// This file is part of khmer, http://github.com/ged-lab/khmer/, and is
+// Copyright (C) Michigan State University, 2009-2013. It is licensed under
// the three-clause BSD license; see LICENSE.
// Contact: khmer-project at idyll.org
//
diff --git a/oxli/__init__.py b/oxli/__init__.py
deleted file mode 100755
index 742c4fc..0000000
--- a/oxli/__init__.py
+++ /dev/null
@@ -1,55 +0,0 @@
-#!/usr/bin/env python
-#
-# This file is a part of khmer, http://github.com/ged-lab/khmer/, and is
-# Copyright (C) Michigan State University, 2015. It is licensed under the
-# three-clause BSD license; see doc/LICENSE.txt.
-# Contact: khmer-project at idyll.org
-#
-
-"""
-Single entry point script for khmer
-"""
-
-import argparse
-import textwrap
-from khmer import khmer_args
-from oxli import build_graph
-
-
-def get_parser():
- """
- returns the parser object for the oxli subcommand handler
- """
-
- parser = argparse.ArgumentParser(
- description='Single entry point script for khmer',
- formatter_class=argparse.ArgumentDefaultsHelpFormatter)
-
- subparsers = parser.add_subparsers()
-
- # build-graph (formerly load-graph) parsers here
- parser_build_graph = \
- subparsers.add_parser('build-graph',
- help="Load sequences into the compressible graph"
- "format plus optional tagset",
- description="Load sequences into the "
- "compressible graph format plus optional tagset")
-
- khmer_args.build_hashbits_args("Load sequences into the compressible"
- "graph format plus optional tagset.",
- None, parser=parser_build_graph)
- build_graph.build_parser(parser_build_graph)
- parser_build_graph.set_defaults(func=build_graph.main)
-
- return parser
-
-
-def main():
- """
- main function; does the parsing and kicks off the subcommand
- """
- args = get_parser().parse_args()
- args.func(args)
-
-if __name__ == '__main__':
- main()
diff --git a/oxli/build_graph.py b/oxli/build_graph.py
deleted file mode 100644
index 43b5a33..0000000
--- a/oxli/build_graph.py
+++ /dev/null
@@ -1,103 +0,0 @@
-#! /usr/bin/env python
-#
-# This file is part of khmer, http://github.com/ged-lab/khmer/, and is
-# Copyright (C) Michigan State University, 2009-2015. It is licensed under
-# the three-clause BSD license; see doc/LICENSE.txt.
-# Contact: khmer-project at idyll.org
-#
-# pylint: disable=invalid-name,missing-docstring
-"""
-Build a graph from the given sequences, save in <ptname>.
-
-% python scripts/load-graph.py <ptname> <data1> [ <data2> <...> ]
-
-Use '-h' for parameter help.
-"""
-
-from __future__ import print_function, absolute_import, unicode_literals
-
-import sys
-
-import khmer
-from khmer import khmer_args
-from khmer.khmer_args import (report_on_config, info, add_threading_args)
-from khmer.kfile import check_input_files, check_space
-from khmer.kfile import check_space_for_hashtable
-from oxli import functions
-
-
-def build_parser(parser):
- add_threading_args(parser)
- parser.add_argument('--no-build-tagset', '-n', default=False,
- action='store_true', dest='no_build_tagset',
- help='Do NOT construct tagset while loading sequences')
- parser.add_argument('output_filename',
- metavar='output_presence_table_filename', help='output'
- ' k-mer presence table filename.')
- parser.add_argument('input_filenames', metavar='input_sequence_filename',
- nargs='+', help='input FAST[AQ] sequence filename')
- parser.add_argument('-f', '--force', default=False, action='store_true',
- help='Overwrite output file if it exists')
- return parser
-
-
-def main(args):
- info('build-graph.py', ['graph', 'SeqAn'])
-
- report_on_config(args, hashtype='nodegraph')
- base = args.output_filename
- filenames = args.input_filenames
-
- for fname in args.input_filenames:
- check_input_files(fname, args.force)
-
- check_space(args.input_filenames, args.force)
- check_space_for_hashtable(args, 'nodegraph', args.force)
-
- print('Saving k-mer presence table to %s' % base, file=sys.stderr)
- print('Loading kmers from sequences in %s' %
- repr(filenames), file=sys.stderr)
- if args.no_build_tagset:
- print('We WILL NOT build the tagset.', file=sys.stderr)
- else:
- print('We WILL build the tagset (for partitioning/traversal).',
- file=sys.stderr)
-
- print('making nodegraph', file=sys.stderr)
- htable = khmer_args.create_nodegraph(args)
-
- functions.build_graph(filenames, htable, args.threads,
- not args.no_build_tagset)
-
- print('Total number of unique k-mers: {0}'.format(htable.n_unique_kmers()),
- file=sys.stderr)
-
- print('saving k-mer presence table in', base + '.pt', file=sys.stderr)
- htable.save(base + '.pt')
-
- if not args.no_build_tagset:
- print('saving tagset in', base + '.tagset', file=sys.stderr)
- htable.save_tagset(base + '.tagset')
-
- info_fp = open(base + '.info', 'w')
- info_fp.write('%d unique k-mers' % htable.n_unique_kmers())
-
- fp_rate = \
- khmer.calc_expected_collisions(htable, args.force, max_false_pos=.15)
- # 0.18 is ACTUAL MAX. Do not change.
-
- print('false positive rate estimated to be %1.3f' % fp_rate,
- file=sys.stderr)
- print('\nfalse positive rate estimated to be %1.3f' % fp_rate,
- file=info_fp)
-
- print('wrote to', base + '.info and', base + '.pt', file=sys.stderr)
- if not args.no_build_tagset:
- print('and ' + base + '.tagset', file=sys.stderr)
-
- sys.exit(0)
-
-if __name__ == '__main__':
- main(None)
-
-# vim: set ft=python ts=4 sts=4 sw=4 et tw=79:
diff --git a/oxli/functions.py b/oxli/functions.py
deleted file mode 100644
index e429efd..0000000
--- a/oxli/functions.py
+++ /dev/null
@@ -1,103 +0,0 @@
-#
-# This file is part of khmer, http://github.com/ged-lab/khmer/, and is
-# Copyright (C) Michigan State University, 2009-2015. It is licensed under
-# the three-clause BSD license; see doc/LICENSE.txt.
-# Contact: khmer-project at idyll.org
-#
-
-
-from collections import namedtuple
-import threading
-import math
-import khmer.utils
-
-
-def estimate_optimal_with_N_and_M(N, M):
- """
- Utility function for estimating optimal counting table args where N is the
- number of unique kmer and M is the allotted amount of memory
- """
- Z = math.log(2)*(M/float(N))
- intZ = int(Z)
- if intZ == 0:
- intZ = 1
- H = int(M/intZ)
- M = H*intZ
- f2 = (1-math.exp(-N/float(H)))**intZ
- res = namedtuple("result", ["num_htables", "htable_size", "mem_use",
- "fp_rate"])
- return res(intZ, H, M, f2)
-
-
-def estimate_optimal_with_N_and_f(N, f):
- """
- Utility function for estimating optimal memory where N is the number of
- unique kmers and f is the desired false positive rate
- """
- Z = math.log(f, 0.5)
- intZ = int(Z)
- if intZ == 0:
- intZ = 1
-
- H1 = int(-N/(math.log(1-f**(1/float(intZ)))))
- M1 = H1 * intZ
- f1 = (1-math.exp(-N/float(H1)))**intZ
-
- res = namedtuple("result", ["num_htables", "htable_size", "mem_use",
- "fp_rate"])
- return res(intZ, H1, M1, f1)
-
-
-def optimal_args_output_gen(unique_kmers, fp_rate):
- """
- Assembles output string for optimal arg sandbox scripts
- """
- to_print = []
-
- to_print.append('') # blank line
- to_print.append('number of unique k-mers: \t{0}'.format(unique_kmers))
- to_print.append('false positive rate: \t{:>.3f}'.format(fp_rate))
- to_print.append('') # blank line
- to_print.append('If you have expected false positive rate to achieve:')
- to_print.append('expected_fp\tnumber_hashtable(Z)\tsize_hashtable(H)\t'
- 'expected_memory_usage')
-
- for fp_rate in range(1, 10):
- Z, H, M, f = estimate_optimal_with_N_and_f(unique_kmers, fp_rate/10.0)
- to_print.append('{:11.3f}\t{:19}\t{:17e}\t{:21e}'.format(f, Z, H, M))
-
- mem_list = [1, 5, 10, 20, 50, 100, 200, 300, 400, 500, 1000, 2000, 5000]
-
- to_print.append('') # blank line
- to_print.append('If you have expected memory to use:')
- to_print.append('expected_memory_usage\tnumber_hashtable(Z)\t'
- 'size_hashtable(H)\texpected_fp')
-
- for mem in mem_list:
- Z, H, M, f = estimate_optimal_with_N_and_M(unique_kmers,
- mem*1000000000)
- to_print.append('{:21e}\t{:19}\t{:17e}\t{:11.3f}'.format(M, Z, H, f))
- return "\n".join(to_print)
-
-
-def build_graph(ifilenames, graph, num_threads=1, tags=False):
- """
- Algorithm to construct a counting graph from a set of input files
- """
-
- if tags:
- eat = graph.consume_fasta_and_tag_with_reads_parser
- else:
- eat = graph.consume_fasta_with_reads_parser
-
- for _, ifile in enumerate(ifilenames):
- rparser = khmer.ReadParser(ifile)
- threads = []
-
- for _ in range(num_threads):
- cur_thread = threading.Thread(target=eat, args=(rparser,))
- threads.append(cur_thread)
- cur_thread.start()
-
- for thread in threads:
- thread.join()
diff --git a/sandbox/README.rst b/sandbox/README.rst
index 48af420..f50b1a7 100644
--- a/sandbox/README.rst
+++ b/sandbox/README.rst
@@ -18,10 +18,10 @@ Awaiting promotion to sandbox:
Scripts with recipes:
-* calc-median-distribution.py - plot coverage distribution; see `khmer-recipes #1 <https://github.com/dib-lab/khmer-recipes/tree/master/001-extract-reads-by-coverage>`__
-* collect-reads.py - subsample reads until a particular average coverage; see `khmer-recipes #2 <https://github.com/dib-lab/khmer-recipes/tree/master/002-collect-subset-of-high-coverage>`__
-* saturate-by-median.py - calculate collector's curve on shotgun sequencing; see `khmer-recipes #4 <https://github.com/dib-lab/khmer-recipes/tree/master/004-estimate-sequencing-saturation>`__
-* slice-reads-by-coverage.py - extract reads based on coverage; see `khmer-recipes #1 <https://github.com/dib-lab/khmer-recipes/tree/master/001-extract-reads-by-coverage>`__
+* calc-median-distribution.py - plot coverage distribution; see `khmer-recipes #1 <https://github.com/ged-lab/khmer-recipes/tree/master/001-extract-reads-by-coverage>`__
+* collect-reads.py - subsample reads until a particular average coverage; see `khmer-recipes #2 <https://github.com/ged-lab/khmer-recipes/tree/master/002-collect-subset-of-high-coverage>`__
+* saturate-by-median.py - calculate collector's curve on shotgun sequencing; see `khmer-recipes #4 <https://github.com/ged-lab/khmer-recipes/tree/master/004-estimate-sequencing-saturation>`__
+* slice-reads-by-coverage.py - extract reads based on coverage; see `khmer-recipes #1 <https://github.com/ged-lab/khmer-recipes/tree/master/001-extract-reads-by-coverage>`__
To keep, document, and build recipes for:
@@ -70,117 +70,117 @@ Good ideas to rewrite using newer tools/approaches:
Present in commit d295bc847 but removed thereafter:
-* `combine-pe.py <https://github.com/dib-lab/khmer/blob/d295bc8477022e8c34649f131a2abe333a891d3d/sandbox/combine-pe.py>`__ - combine partitions based on shared PE reads.
-* `compare-partitions.py <https://github.com/dib-lab/khmer/blob/d295bc8477022e8c34649f131a2abe333a891d3d/sandbox/compare-partitions.py>`__ - compare read membership in partitions.
-* `count-within-radius.py <https://github.com/dib-lab/khmer/blob/d295bc8477022e8c34649f131a2abe333a891d3d/sandbox/count-within-radius.py>`__ - calculating graph density by position with seq
-* `degree-by-position.py <https://github.com/dib-lab/khmer/blob/d295bc8477022e8c34649f131a2abe333a891d3d/sandbox/degree-by-position.py>`__ - calculating graph degree by position in seq
-* `dn-identify-errors.py <https://github.com/dib-lab/khmer/blob/d295bc8477022e8c34649f131a2abe333a891d3d/sandbox/dn-identify-errors.py>`__ - prototype script to identify errors in reads based on diginorm principles
-* `ec.py <https://github.com/dib-lab/khmer/blob/d295bc8477022e8c34649f131a2abe333a891d3d/sandbox/ec.py>`__ - new error correction foo
-* `error-correct-pass2.py <https://github.com/dib-lab/khmer/blob/d295bc8477022e8c34649f131a2abe333a891d3d/sandbox/error-correct-pass2.py>`__ - new error correction foo
-* `find-unpart.py <https://github.com/dib-lab/khmer/blob/d295bc8477022e8c34649f131a2abe333a891d3d/sandbox/find-unpart.py>`__ - something to do with finding unpartitioned sequences
-* `normalize-by-align.py <https://github.com/dib-lab/khmer/blob/d295bc8477022e8c34649f131a2abe333a891d3d/sandbox/normalize-by-align.py>`__ - new error correction foo
-* `read_aligner.py <https://github.com/dib-lab/khmer/blob/d295bc8477022e8c34649f131a2abe333a891d3d/sandbox/read_aligner.py>`__ - new error correction foo
-* `shuffle-fasta.py <https://github.com/dib-lab/khmer/blob/d295bc8477022e8c34649f131a2abe333a891d3d/sandbox/shuffle-fasta.py>`__ - FASTA file shuffler for small FASTA files
-* `to-casava-1.8-fastq.py <https://github.com/dib-lab/khmer/blob/d295bc8477022e8c34649f131a2abe333a891d3d/sandbox/to-casava-1.8-fastq.py>`__ - convert reads to different Casava format
-* `uniqify-sequences.py <https://github.com/dib-lab/khmer/blob/d295bc8477022e8c34649f131a2abe333a891d3d/sandbox/uniqify-sequences.py>`__ - print out paths that are unique in the graph
-* `write-interleave.py <https://github.com/dib-lab/khmer/blob/d295bc8477022e8c34649f131a2abe333a891d3d/sandbox/write-interleave.py>`__ - is this used by any protocol etc?
+* `combine-pe.py <https://github.com/ged-lab/khmer/blob/d295bc8477022e8c34649f131a2abe333a891d3d/sandbox/combine-pe.py>`__ - combine partitions based on shared PE reads.
+* `compare-partitions.py <https://github.com/ged-lab/khmer/blob/d295bc8477022e8c34649f131a2abe333a891d3d/sandbox/compare-partitions.py>`__ - compare read membership in partitions.
+* `count-within-radius.py <https://github.com/ged-lab/khmer/blob/d295bc8477022e8c34649f131a2abe333a891d3d/sandbox/count-within-radius.py>`__ - calculating graph density by position with seq
+* `degree-by-position.py <https://github.com/ged-lab/khmer/blob/d295bc8477022e8c34649f131a2abe333a891d3d/sandbox/degree-by-position.py>`__ - calculating graph degree by position in seq
+* `dn-identify-errors.py <https://github.com/ged-lab/khmer/blob/d295bc8477022e8c34649f131a2abe333a891d3d/sandbox/dn-identify-errors.py>`__ - prototype script to identify errors in reads based on diginorm principles
+* `ec.py <https://github.com/ged-lab/khmer/blob/d295bc8477022e8c34649f131a2abe333a891d3d/sandbox/ec.py>`__ - new error correction foo
+* `error-correct-pass2.py <https://github.com/ged-lab/khmer/blob/d295bc8477022e8c34649f131a2abe333a891d3d/sandbox/error-correct-pass2.py>`__ - new error correction foo
+* `find-unpart.py <https://github.com/ged-lab/khmer/blob/d295bc8477022e8c34649f131a2abe333a891d3d/sandbox/find-unpart.py>`__ - something to do with finding unpartitioned sequences
+* `normalize-by-align.py <https://github.com/ged-lab/khmer/blob/d295bc8477022e8c34649f131a2abe333a891d3d/sandbox/normalize-by-align.py>`__ - new error correction foo
+* `read_aligner.py <https://github.com/ged-lab/khmer/blob/d295bc8477022e8c34649f131a2abe333a891d3d/sandbox/read_aligner.py>`__ - new error correction foo
+* `shuffle-fasta.py <https://github.com/ged-lab/khmer/blob/d295bc8477022e8c34649f131a2abe333a891d3d/sandbox/shuffle-fasta.py>`__ - FASTA file shuffler for small FASTA files
+* `to-casava-1.8-fastq.py <https://github.com/ged-lab/khmer/blob/d295bc8477022e8c34649f131a2abe333a891d3d/sandbox/to-casava-1.8-fastq.py>`__ - convert reads to different Casava format
+* `uniqify-sequences.py <https://github.com/ged-lab/khmer/blob/d295bc8477022e8c34649f131a2abe333a891d3d/sandbox/uniqify-sequences.py>`__ - print out paths that are unique in the graph
+* `write-interleave.py <https://github.com/ged-lab/khmer/blob/d295bc8477022e8c34649f131a2abe333a891d3d/sandbox/write-interleave.py>`__ - is this used by any protocol etc?
Present in commit 691b0b3ae but removed thereafter:
-* `annotate-with-median-count.py <https://github.com/dib-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/annotate-with-median-count.py>`__ - replaced by count-median.py
-* `assemble-individual-partitions.py <https://github.com/dib-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/assemble-individual-partitions.py>`__ - better done with parallel
-* `assemstats.py <https://github.com/dib-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/assemstats.py>`__ - statistics gathering; see assemstats3.
-* `assemstats2.py <https://github.com/dib-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/assemstats2.py>`__ - statistics gathering; see assemstats3.
-* `abund-ablate-reads.py <https://github.com/dib-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/abund-ablate-reads.py>`__ - trim reads of high abundance k-mers.
-* `bench-graphsize-orig.py <https://github.com/dib-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/bench-graphsize-orig.py>`__ - benchmarking script for graphsize elimination
-* `bench-graphsize-th.py <https://github.com/dib-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/bench-graphsize-th.py>`__ - benchmarking script for graphsize elimination
-* `bin-reads-by-abundance.py <https://github.com/dib-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/bin-reads-by-abundance.py>`__ - see slice-reads-by-coverage.py
-* `bowtie-parser.py <https://github.com/dib-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/bowtie-parser.py>`__ - parse bowtie map file
-* `calc-degree.py <https://github.com/dib-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/calc-degree.py>`__ - various k-mer statistics
-* `calc-kmer-partition-counts.py <https://github.com/dib-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/calc-kmer-partition-counts.py>`__ - various k-mer statistics
-* `calc-kmer-read-abunds.py <https://github.com/dib-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/calc-kmer-read-abunds.py>`__ - various k-mer statistics
-* `calc-kmer-read-stats.py <https://github.com/dib-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/calc-kmer-read-stats.py>`__ - various k-mer statistics
-* `calc-kmer-to-partition-ratio.py <https://github.com/dib-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/calc-kmer-to-partition-ratio.py>`__ - various k-mer statistics
-* `calc-sequence-entropy.py <https://github.com/dib-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/calc-sequence-entropy.py>`__ - calculate per-sequence entropy
-* `choose-largest-assembly.py <https://github.com/dib-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/choose-largest-assembly.py>`__ - see calc-best-assembly.py
-* `consume-and-traverse.py <https://github.com/dib-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/consume-and-traverse.py>`__ - replaced by load-graph.py
-* `contig-coverage.py <https://github.com/dib-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/contig-coverage.py>`__ - calculate coverage of contigs by k-mers
-* `count-circum-by-position.py <https://github.com/dib-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/count-circum-by-position.py>`__ - k-mer graph statistics by position within read
-* `count-density-by-position.py <https://github.com/dib-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/count-density-by-position.py>`__ - k-mer graph stats by position within read
-* `count-distance-to-volume.py <https://github.com/dib-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/count-distance-to-volume.py>`__ - k-mer stats from graph
-* `count-median-abund-by-partition.py <https://github.com/dib-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/count-median-abund-by-partition.py>`__ - count median k-mer abundance by partition;
-* `count-shared-kmers-btw-assemblies.py <https://github.com/dib-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/count-shared-kmers-btw-assemblies.py>`__ - count shared k-mers between assemblies;
-* `ctb-iterative-bench-2-old.py <https://github.com/dib-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/ctb-iterative-bench-2-old.py>`__ - old benchmarking code
-* `ctb-iterative-bench.py <https://github.com/dib-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/ctb-iterative-bench.py>`__ - old benchmarking code
-* `discard-high-abund.py <https://github.com/dib-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/discard-high-abund.py>`__ - discard reads by coverage; see slice-reads-by-coverage.py
-* `discard-pre-high-abund.py <https://github.com/dib-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/discard-pre-high-abund.py>`__ - discard reads by coverage; see slice-reads-by-coverage.py
-* `do-intertable-part.py <https://github.com/dib-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/do-intertable-part.py>`__ - unused partitioning method
-* `do-partition-2.py <https://github.com/dib-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/do-partition-2.py>`__ - replaced by scripts/do-partition.py
-* `do-partition-stop.py <https://github.com/dib-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/do-partition-stop.py>`__ - replaced by scripts/do-partition.py
-* `do-partition.py <https://github.com/dib-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/do-partition.py>`__ - moved to scripts/
-* `do-subset-merge.py <https://github.com/dib-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/do-subset-merge.py>`__ - replaced by scripts/merge-partitions.py
-* `do-th-subset-calc.py <https://github.com/dib-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/do-th-subset-calc.py>`__ - unused benchmarking scripts
-* `do-th-subset-load.py <https://github.com/dib-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/do-th-subset-load.py>`__ - unused benchmarking scripts
-* `do-th-subset-save.py <https://github.com/dib-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/do-th-subset-save.py>`__ - unused benchmarking scripts
-* `extract-surrender.py <https://github.com/dib-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/extract-surrender.py>`__ - no longer used partitioning feature
-* `extract-with-median-count.py <https://github.com/dib-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/extract-with-median-count.py>`__ - see slice-reads-by-coverage.py
-* `fasta-to-fastq.py <https://github.com/dib-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/fasta-to-fastq.py>`__ - just a bad idea
-* `filter-above-median.py <https://github.com/dib-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/filter-above-median.py>`__ - replaced by filter-below-abund.py
-* `filter-abund-output-by-length.py <https://github.com/dib-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/filter-abund-output-by-length.py>`__ - replaced by filter-abund/filter-below-abund
-* `filter-area.py <https://github.com/dib-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/filter-area.py>`__ - trim highly connected k-mers
-* `filter-degree.py <https://github.com/dib-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/filter-degree.py>`__ - trim highly connected k-mers
-* `filter-density-explosion.py <https://github.com/dib-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/filter-density-explosion.py>`__ - trim highly connected k-mers
-* `filter-if-present.py <https://github.com/dib-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/filter-if-present.py>`__ - replaced by filter-abund and others
-* `filter-max255.py <https://github.com/dib-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/filter-max255.py>`__ - remove reads w/high-abundance k-mers.
-* `filter-min2-multi.py <https://github.com/dib-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/filter-min2-multi.py>`__ - remove reads w/low-abundance k-mers
-* `filter-sodd.py <https://github.com/dib-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/filter-sodd.py>`__ - no longer used partitioning feature
-* `filter-subsets-by-partsize.py <https://github.com/dib-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/filter-subsets-by-partsize.py>`__ - deprecated way to filter out partitions by size
-* `get-occupancy.py <https://github.com/dib-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/get-occupancy.py>`__ - utility script no longer needed
-* `get-occupancy2.py <https://github.com/dib-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/get-occupancy2.py>`__ - utility script no longer needed
-* `graph-partition-separate.py <https://github.com/dib-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/graph-partition-separate.py>`__ - deprecated graph partitioning stuff
-* `graph-size-circum-trim.py <https://github.com/dib-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/graph-size-circum-trim.py>`__ - experimental mods to graph-size.py
-* `graph-size-degree-trim.py <https://github.com/dib-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/graph-size-degree-trim.py>`__ - experimental mods to graph-size.py
-* `graph-size-py.py <https://github.com/dib-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/graph-size-py.py>`__ - experimental mods to graph-size.py
-* `join_pe.py <https://github.com/dib-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/join_pe.py>`__ - silly attempts to deal with PE interleaving?
-* `keep-stoptags.py <https://github.com/dib-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/keep-stoptags.py>`__ - trim at stoptags
-* `label-pairs.py <https://github.com/dib-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/label-pairs.py>`__ - deprecated PE fixing script
-* `length-dist.py <https://github.com/dib-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/length-dist.py>`__ - deprecated length distribution calc script
-* `load-ht-and-tags.py <https://github.com/dib-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/load-ht-and-tags.py>`__ - load and examine hashtable & tags
-* `multi-abyss.py <https://github.com/dib-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/multi-abyss.py>`__ - better done with parallel
-* `make-coverage-by-position-for-node.py <https://github.com/dib-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/make-coverage-by-position-for-node.py>`__ - deprecated coverage calculation
-* `make-coverage-histogram.py <https://github.com/dib-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/make-coverage-histogram.py>`__ - build coverage histograms
-* `make-random.py <https://github.com/dib-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/make-random.py>`__ - make random DNA; see dbg-graph-null project.
-* `make-read-stats.py <https://github.com/dib-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/make-read-stats.py>`__ - see readstats.py
-* `multi-stats.py <https://github.com/dib-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/multi-stats.py>`__ - see readstats.py
-* `multi-velvet.py <https://github.com/dib-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/multi-velvet.py>`__ - better done with parallel
-* `normalize-by-min.py <https://github.com/dib-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/normalize-by-min.py>`__ - normalize by min k-mer abundance in seq; just a bad idea
-* `occupy.py <https://github.com/dib-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/occupy.py>`__ - no longer needed utility script
-* `parse-bowtie-pe.py <https://github.com/dib-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/parse-bowtie-pe.py>`__ - no longer needed utility script
-* `parse-stats.py <https://github.com/dib-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/parse-stats.py>`__ - partition stats
-* `partition-by-contig.py <https://github.com/dib-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/partition-by-contig.py>`__ - various approaches to partitioning
-* `partition-by-contig2.py <https://github.com/dib-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/partition-by-contig2.py>`__ - various approaches to partitioning
-* `partition-size-dist-running.py <https://github.com/dib-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/partition-size-dist-running.py>`__ - various approaches to partitioning
-* `partition-size-dist.py <https://github.com/dib-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/partition-size-dist.py>`__ - various approaches to partitioning
-* `path-compare-to-vectors.py <https://github.com/dib-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/path-compare-to-vectors.py>`__ - ??
-* `print-exact-abund-kmer.py <https://github.com/dib-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/print-exact-abund-kmer.py>`__ - ??
-* `print-high-density-kmers.py <https://github.com/dib-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/print-high-density-kmers.py>`__ - display high abundance k-mers
-* `quality-trim-pe.py <https://github.com/dib-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/quality-trim-pe.py>`__ - no longer needed utility script
-* `quality-trim.py <https://github.com/dib-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/quality-trim.py>`__ - no longer needed utility script
-* `reformat.py <https://github.com/dib-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/reformat.py>`__ - FASTA sequence description line reformatter for partitioned files
-* `remove-N.py <https://github.com/dib-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/remove-N.py>`__ - eliminate sequences that have Ns in them
-* `softmask-high-abund.py <https://github.com/dib-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/softmask-high-abund.py>`__ - softmask high abundance sequences (convert ACGT to acgt)
-* `split-fasta-on-circum.py <https://github.com/dib-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/split-fasta-on-circum.py>`__ - various ways of breaking sequences on graph properties
-* `split-fasta-on-circum2.py <https://github.com/dib-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/split-fasta-on-circum2.py>`__ - various ways of breaking sequences on graph properties
-* `split-fasta-on-circum3.py <https://github.com/dib-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/split-fasta-on-circum3.py>`__ - various ways of breaking sequences on graph properties
-* `split-fasta-on-circum4.py <https://github.com/dib-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/split-fasta-on-circum4.py>`__ - various ways of breaking sequences on graph properties
-* `split-fasta-on-degree-th.py <https://github.com/dib-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/split-fasta-on-degree-th.py>`__ - various ways of breaking sequences on graph properties
-* `split-fasta-on-degree.py <https://github.com/dib-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/split-fasta-on-degree.py>`__ - various ways of breaking sequences on graph properties
-* `split-fasta-on-density.py <https://github.com/dib-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/split-fasta-on-density.py>`__ - various ways of breaking sequences on graph properties
-* `split-N.py <https://github.com/dib-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/split-N.py>`__ - truncate sequences on N
-* `split-reads-on-median-diff.py <https://github.com/dib-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/split-reads-on-median-diff.py>`__ - various ways of breaking sequences on graph properties
-* `summarize.py <https://github.com/dib-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/summarize.py>`__ - sequence stats calculator
-* `sweep_perf.py <https://github.com/dib-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/sweep_perf.py>`__ - benchmarking tool
-* `test_scripts.py <https://github.com/dib-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/test_scripts.py>`__ - old test file
-* `traverse-contigs.py <https://github.com/dib-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/traverse-contigs.py>`__ - deprecated graph traversal stuff
-* `traverse-from-reads.py <https://github.com/dib-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/traverse-from-reads.py>`__ - deprecated graph traversal stuff
-* `validate-partitioning.py <https://github.com/dib-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/validate-partitioning.py>`__ - unneeded test
+* `annotate-with-median-count.py <https://github.com/ged-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/annotate-with-median-count.py>`__ - replaced by count-median.py
+* `assemble-individual-partitions.py <https://github.com/ged-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/assemble-individual-partitions.py>`__ - better done with parallel
+* `assemstats.py <https://github.com/ged-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/assemstats.py>`__ - statistics gathering; see assemstats3.
+* `assemstats2.py <https://github.com/ged-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/assemstats2.py>`__ - statistics gathering; see assemstats3.
+* `abund-ablate-reads.py <https://github.com/ged-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/abund-ablate-reads.py>`__ - trim reads of high abundance k-mers.
+* `bench-graphsize-orig.py <https://github.com/ged-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/bench-graphsize-orig.py>`__ - benchmarking script for graphsize elimination
+* `bench-graphsize-th.py <https://github.com/ged-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/bench-graphsize-th.py>`__ - benchmarking script for graphsize elimination
+* `bin-reads-by-abundance.py <https://github.com/ged-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/bin-reads-by-abundance.py>`__ - see slice-reads-by-coverage.py
+* `bowtie-parser.py <https://github.com/ged-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/bowtie-parser.py>`__ - parse bowtie map file
+* `calc-degree.py <https://github.com/ged-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/calc-degree.py>`__ - various k-mer statistics
+* `calc-kmer-partition-counts.py <https://github.com/ged-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/calc-kmer-partition-counts.py>`__ - various k-mer statistics
+* `calc-kmer-read-abunds.py <https://github.com/ged-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/calc-kmer-read-abunds.py>`__ - various k-mer statistics
+* `calc-kmer-read-stats.py <https://github.com/ged-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/calc-kmer-read-stats.py>`__ - various k-mer statistics
+* `calc-kmer-to-partition-ratio.py <https://github.com/ged-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/calc-kmer-to-partition-ratio.py>`__ - various k-mer statistics
+* `calc-sequence-entropy.py <https://github.com/ged-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/calc-sequence-entropy.py>`__ - calculate per-sequence entropy
+* `choose-largest-assembly.py <https://github.com/ged-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/choose-largest-assembly.py>`__ - see calc-best-assembly.py
+* `consume-and-traverse.py <https://github.com/ged-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/consume-and-traverse.py>`__ - replaced by load-graph.py
+* `contig-coverage.py <https://github.com/ged-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/contig-coverage.py>`__ - calculate coverage of contigs by k-mers
+* `count-circum-by-position.py <https://github.com/ged-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/count-circum-by-position.py>`__ - k-mer graph statistics by position within read
+* `count-density-by-position.py <https://github.com/ged-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/count-density-by-position.py>`__ - k-mer graph stats by position within read
+* `count-distance-to-volume.py <https://github.com/ged-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/count-distance-to-volume.py>`__ - k-mer stats from graph
+* `count-median-abund-by-partition.py <https://github.com/ged-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/count-median-abund-by-partition.py>`__ - count median k-mer abundance by partition;
+* `count-shared-kmers-btw-assemblies.py <https://github.com/ged-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/count-shared-kmers-btw-assemblies.py>`__ - count shared k-mers between assemblies;
+* `ctb-iterative-bench-2-old.py <https://github.com/ged-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/ctb-iterative-bench-2-old.py>`__ - old benchmarking code
+* `ctb-iterative-bench.py <https://github.com/ged-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/ctb-iterative-bench.py>`__ - old benchmarking code
+* `discard-high-abund.py <https://github.com/ged-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/discard-high-abund.py>`__ - discard reads by coverage; see slice-reads-by-coverage.py
+* `discard-pre-high-abund.py <https://github.com/ged-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/discard-pre-high-abund.py>`__ - discard reads by coverage; see slice-reads-by-coverage.py
+* `do-intertable-part.py <https://github.com/ged-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/do-intertable-part.py>`__ - unused partitioning method
+* `do-partition-2.py <https://github.com/ged-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/do-partition-2.py>`__ - replaced by scripts/do-partition.py
+* `do-partition-stop.py <https://github.com/ged-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/do-partition-stop.py>`__ - replaced by scripts/do-partition.py
+* `do-partition.py <https://github.com/ged-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/do-partition.py>`__ - moved to scripts/
+* `do-subset-merge.py <https://github.com/ged-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/do-subset-merge.py>`__ - replaced by scripts/merge-partitions.py
+* `do-th-subset-calc.py <https://github.com/ged-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/do-th-subset-calc.py>`__ - unused benchmarking scripts
+* `do-th-subset-load.py <https://github.com/ged-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/do-th-subset-load.py>`__ - unused benchmarking scripts
+* `do-th-subset-save.py <https://github.com/ged-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/do-th-subset-save.py>`__ - unused benchmarking scripts
+* `extract-surrender.py <https://github.com/ged-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/extract-surrender.py>`__ - no longer used partitioning feature
+* `extract-with-median-count.py <https://github.com/ged-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/extract-with-median-count.py>`__ - see slice-reads-by-coverage.py
+* `fasta-to-fastq.py <https://github.com/ged-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/fasta-to-fastq.py>`__ - just a bad idea
+* `filter-above-median.py <https://github.com/ged-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/filter-above-median.py>`__ - replaced by filter-below-abund.py
+* `filter-abund-output-by-length.py <https://github.com/ged-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/filter-abund-output-by-length.py>`__ - replaced by filter-abund/filter-below-abund
+* `filter-area.py <https://github.com/ged-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/filter-area.py>`__ - trim highly connected k-mers
+* `filter-degree.py <https://github.com/ged-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/filter-degree.py>`__ - trim highly connected k-mers
+* `filter-density-explosion.py <https://github.com/ged-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/filter-density-explosion.py>`__ - trim highly connected k-mers
+* `filter-if-present.py <https://github.com/ged-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/filter-if-present.py>`__ - replaced by filter-abund and others
+* `filter-max255.py <https://github.com/ged-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/filter-max255.py>`__ - remove reads w/high-abundance k-mers.
+* `filter-min2-multi.py <https://github.com/ged-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/filter-min2-multi.py>`__ - remove reads w/low-abundance k-mers
+* `filter-sodd.py <https://github.com/ged-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/filter-sodd.py>`__ - no longer used partitioning feature
+* `filter-subsets-by-partsize.py <https://github.com/ged-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/filter-subsets-by-partsize.py>`__ - deprecated way to filter out partitions by size
+* `get-occupancy.py <https://github.com/ged-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/get-occupancy.py>`__ - utility script no longer needed
+* `get-occupancy2.py <https://github.com/ged-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/get-occupancy2.py>`__ - utility script no longer needed
+* `graph-partition-separate.py <https://github.com/ged-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/graph-partition-separate.py>`__ - deprecated graph partitioning stuff
+* `graph-size-circum-trim.py <https://github.com/ged-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/graph-size-circum-trim.py>`__ - experimental mods to graph-size.py
+* `graph-size-degree-trim.py <https://github.com/ged-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/graph-size-degree-trim.py>`__ - experimental mods to graph-size.py
+* `graph-size-py.py <https://github.com/ged-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/graph-size-py.py>`__ - experimental mods to graph-size.py
+* `join_pe.py <https://github.com/ged-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/join_pe.py>`__ - silly attempts to deal with PE interleaving?
+* `keep-stoptags.py <https://github.com/ged-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/keep-stoptags.py>`__ - trim at stoptags
+* `label-pairs.py <https://github.com/ged-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/label-pairs.py>`__ - deprecated PE fixing script
+* `length-dist.py <https://github.com/ged-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/length-dist.py>`__ - deprecated length distribution calc script
+* `load-ht-and-tags.py <https://github.com/ged-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/load-ht-and-tags.py>`__ - load and examine hashtable & tags
+* `multi-abyss.py <https://github.com/ged-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/multi-abyss.py>`__ - better done with parallel
+* `make-coverage-by-position-for-node.py <https://github.com/ged-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/make-coverage-by-position-for-node.py>`__ - deprecated coverage calculation
+* `make-coverage-histogram.py <https://github.com/ged-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/make-coverage-histogram.py>`__ - build coverage histograms
+* `make-random.py <https://github.com/ged-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/make-random.py>`__ - make random DNA; see dbg-graph-null project.
+* `make-read-stats.py <https://github.com/ged-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/make-read-stats.py>`__ - see readstats.py
+* `multi-stats.py <https://github.com/ged-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/multi-stats.py>`__ - see readstats.py
+* `multi-velvet.py <https://github.com/ged-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/multi-velvet.py>`__ - better done with parallel
+* `normalize-by-min.py <https://github.com/ged-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/normalize-by-min.py>`__ - normalize by min k-mer abundance in seq; just a bad idea
+* `occupy.py <https://github.com/ged-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/occupy.py>`__ - no longer needed utility script
+* `parse-bowtie-pe.py <https://github.com/ged-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/parse-bowtie-pe.py>`__ - no longer needed utility script
+* `parse-stats.py <https://github.com/ged-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/parse-stats.py>`__ - partition stats
+* `partition-by-contig.py <https://github.com/ged-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/partition-by-contig.py>`__ - various approaches to partitioning
+* `partition-by-contig2.py <https://github.com/ged-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/partition-by-contig2.py>`__ - various approaches to partitioning
+* `partition-size-dist-running.py <https://github.com/ged-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/partition-size-dist-running.py>`__ - various approaches to partitioning
+* `partition-size-dist.py <https://github.com/ged-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/partition-size-dist.py>`__ - various approaches to partitioning
+* `path-compare-to-vectors.py <https://github.com/ged-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/path-compare-to-vectors.py>`__ - ??
+* `print-exact-abund-kmer.py <https://github.com/ged-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/print-exact-abund-kmer.py>`__ - ??
+* `print-high-density-kmers.py <https://github.com/ged-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/print-high-density-kmers.py>`__ - display high abundance k-mers
+* `quality-trim-pe.py <https://github.com/ged-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/quality-trim-pe.py>`__ - no longer needed utility script
+* `quality-trim.py <https://github.com/ged-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/quality-trim.py>`__ - no longer needed utility script
+* `reformat.py <https://github.com/ged-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/reformat.py>`__ - FASTA sequence description line reformatter for partitioned files
+* `remove-N.py <https://github.com/ged-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/remove-N.py>`__ - eliminate sequences that have Ns in them
+* `softmask-high-abund.py <https://github.com/ged-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/softmask-high-abund.py>`__ - softmask high abundance sequences (convert ACGT to acgt)
+* `split-fasta-on-circum.py <https://github.com/ged-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/split-fasta-on-circum.py>`__ - various ways of breaking sequences on graph properties
+* `split-fasta-on-circum2.py <https://github.com/ged-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/split-fasta-on-circum2.py>`__ - various ways of breaking sequences on graph properties
+* `split-fasta-on-circum3.py <https://github.com/ged-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/split-fasta-on-circum3.py>`__ - various ways of breaking sequences on graph properties
+* `split-fasta-on-circum4.py <https://github.com/ged-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/split-fasta-on-circum4.py>`__ - various ways of breaking sequences on graph properties
+* `split-fasta-on-degree-th.py <https://github.com/ged-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/split-fasta-on-degree-th.py>`__ - various ways of breaking sequences on graph properties
+* `split-fasta-on-degree.py <https://github.com/ged-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/split-fasta-on-degree.py>`__ - various ways of breaking sequences on graph properties
+* `split-fasta-on-density.py <https://github.com/ged-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/split-fasta-on-density.py>`__ - various ways of breaking sequences on graph properties
+* `split-N.py <https://github.com/ged-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/split-N.py>`__ - truncate sequences on N
+* `split-reads-on-median-diff.py <https://github.com/ged-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/split-reads-on-median-diff.py>`__ - various ways of breaking sequences on graph properties
+* `summarize.py <https://github.com/ged-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/summarize.py>`__ - sequence stats calculator
+* `sweep_perf.py <https://github.com/ged-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/sweep_perf.py>`__ - benchmarking tool
+* `test_scripts.py <https://github.com/ged-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/test_scripts.py>`__ - old test file
+* `traverse-contigs.py <https://github.com/ged-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/traverse-contigs.py>`__ - deprecated graph traversal stuff
+* `traverse-from-reads.py <https://github.com/ged-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/traverse-from-reads.py>`__ - deprecated graph traversal stuff
+* `validate-partitioning.py <https://github.com/ged-lab/khmer/tree/691b0b3aefe83e9e8f5f2b80f5f9516664a4654a/sandbox/validate-partitioning.py>`__ - unneeded test
diff --git a/sandbox/abundance-hist-by-position.py b/sandbox/abundance-hist-by-position.py
index 5a2125f..4ba6c3b 100755
--- a/sandbox/abundance-hist-by-position.py
+++ b/sandbox/abundance-hist-by-position.py
@@ -1,12 +1,10 @@
-#! /usr/bin/env python
+#! /usr/bin/env python2
#
-# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
-# Copyright (C) Michigan State University, 2009-2015. It is licensed under
+# This file is part of khmer, http://github.com/ged-lab/khmer/, and is
+# Copyright (C) Michigan State University, 2009-2013. It is licensed under
# the three-clause BSD license; see LICENSE.
# Contact: khmer-project at idyll.org
#
-from __future__ import division
-from __future__ import print_function
import sys
def main():
@@ -16,11 +14,11 @@ def main():
freqfile = sys.argv[1]
- print('opening .freq file:', freqfile, file=sys.stderr)
+ print >>sys.stderr, 'opening .freq file:', freqfile
fd = open(freqfile)
for n, line in enumerate(fd):
if n % 100000 == 0:
- print('...', n, file=sys.stderr)
+ print >>sys.stderr, '...', n
tok = line.split()
@@ -28,7 +26,7 @@ def main():
countSum[i] += int(tok[i])
countN[i] += 1
- print('summarizing.', file=sys.stderr)
+ print >>sys.stderr, 'summarizing.'
y = [0.0] * len(countSum)
for i in range(len(countSum)):
@@ -36,7 +34,7 @@ def main():
y[i] = float(countSum[i]) / float(countN[i])
for n, i in enumerate(y):
- print(n, i)
+ print n, i
if __name__ == '__main__':
main()
diff --git a/sandbox/assembly-diff-2.py b/sandbox/assembly-diff-2.py
index 1d39969..c81bea7 100755
--- a/sandbox/assembly-diff-2.py
+++ b/sandbox/assembly-diff-2.py
@@ -1,11 +1,10 @@
-#! /usr/bin/env python
+#! /usr/bin/env python2
#
-# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
-# Copyright (C) Michigan State University, 2009-2015. It is licensed under
+# This file is part of khmer, http://github.com/ged-lab/khmer/, and is
+# Copyright (C) Michigan State University, 2009-2013. It is licensed under
# the three-clause BSD license; see LICENSE.
# Contact: khmer-project at idyll.org
#
-from __future__ import print_function
import sys
import khmer
import screed
@@ -24,24 +23,24 @@ def main():
filename2 = sys.argv[2]
uniq2 = open(os.path.basename(sys.argv[2]) + '.uniq', 'w')
- kh = khmer.Hashbits(K, HASHTABLE_SIZE, N_HT)
+ kh = khmer.new_hashbits(K, HASHTABLE_SIZE, N_HT)
for n, record in enumerate(screed.open(filename1)):
if n % 10000 == 0:
- print('...', filename1, n)
- seq = record.sequence.upper().replace('N', 'A')
+ print '...', filename1, n
+ seq = record.sequence.upper().replace('N', 'G')
kh.consume(seq)
path_n = 0
for n, record in enumerate(screed.open(filename2)):
if n % 10000 == 0:
- print('...', filename2, n)
- seq = record.sequence.upper().replace('N', 'A')
+ print '...', filename2, n
+ seq = record.sequence.upper().replace('N', 'G')
paths = kh.extract_unique_paths(seq, UNIQUE_LEN, UNIQUE_F)
kh.consume(seq)
for path in paths:
path_n += 1
- print('>%s from:%s\n%s' % (path_n, record.name, path), file=uniq2)
+ print >>uniq2, '>%s from:%s\n%s' % (path_n, record.name, path)
if __name__ == '__main__':
diff --git a/sandbox/assembly-diff.py b/sandbox/assembly-diff.py
index e3fdee0..189187c 100755
--- a/sandbox/assembly-diff.py
+++ b/sandbox/assembly-diff.py
@@ -1,12 +1,10 @@
-#! /usr/bin/env python
+#! /usr/bin/env python2
#
-# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
-# Copyright (C) Michigan State University, 2009-2015. It is licensed under
+# This file is part of khmer, http://github.com/ged-lab/khmer/, and is
+# Copyright (C) Michigan State University, 2009-2013. It is licensed under
# the three-clause BSD license; see LICENSE.
# Contact: khmer-project at idyll.org
#
-from __future__ import division
-from __future__ import print_function
import sys
import khmer
import screed
@@ -26,9 +24,9 @@ def main():
uniq2 = open(os.path.basename(sys.argv[2]) + '.uniq', 'w')
paths = sys.argv[3]
- kh1 = khmer.Hashbits(K, HASHTABLE_SIZE, N_HT)
+ kh1 = khmer.new_hashbits(K, HASHTABLE_SIZE, N_HT)
kh1.consume_fasta(filename1)
- kh2 = khmer.Hashbits(K, HASHTABLE_SIZE, N_HT)
+ kh2 = khmer.new_hashbits(K, HASHTABLE_SIZE, N_HT)
kh2.consume_fasta(filename2)
for record in screed.open(paths):
@@ -61,9 +59,9 @@ def main():
present2 = False
if present1 and not present2:
- print('>%s\n%s' % (record.name, record.sequence), file=uniq1)
+ print >>uniq1, '>%s\n%s' % (record.name, record.sequence)
elif present2 and not present1:
- print('>%s\n%s' % (record.name, record.sequence), file=uniq2)
+ print >>uniq2, '>%s\n%s' % (record.name, record.sequence)
if __name__ == '__main__':
diff --git a/sandbox/assemstats3.py b/sandbox/assemstats3.py
index 3b7ae42..a085128 100755
--- a/sandbox/assemstats3.py
+++ b/sandbox/assemstats3.py
@@ -1,7 +1,7 @@
-#! /usr/bin/env python
+#! /usr/bin/env python2
#
-# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
-# Copyright (C) Michigan State University, 2009-2015. It is licensed under
+# This file is part of khmer, http://github.com/ged-lab/khmer/, and is
+# Copyright (C) Michigan State University, 2009-2013. It is licensed under
# the three-clause BSD license; see LICENSE.
# Contact: khmer-project at idyll.org
#
@@ -21,8 +21,6 @@ Once completed, you should be able to run this script as is.
Author: Jason Pell (pelljaso at cse.msu.edu)
'''
-from __future__ import division
-from __future__ import print_function
import screed
import sys
@@ -91,23 +89,23 @@ def main():
totalSum = 0
if len(sys.argv) < 3:
- print("Usage: python assemstats.py <min contig length> [ FASTA files ]")
+ print "Usage: python assemstats.py <min contig length> [ FASTA files ]"
return
try:
minLen = int(sys.argv[1])
except ValueError:
- print("Minimum contig length must be an integer.")
+ print "Minimum contig length must be an integer."
return
- print('** cutoff:', minLen)
- print("N\tsum\tmax\tfilename")
+ print '** cutoff:', minLen
+ print "N\tsum\tmax\tfilename"
for filename in sys.argv[2:]:
if not os.path.exists(filename):
- print("WARNING: file %s does not exist." % filename, file=sys.stderr)
+ print >>sys.stderr, "WARNING: file %s does not exist." % filename
continue
-
+
lens = getLens(filename)
trimmedLens = trimLens(lens, minLen)
@@ -123,12 +121,12 @@ def main():
totalN += statTrimmedN
totalSum += statSum
- print("%d\t%d\t%d\t%s" % (statTrimmedN, statSum, statMax, filename))
+ print "%d\t%d\t%d\t%s" % (statTrimmedN, statSum, statMax, filename)
if len(sys.argv) > 3 and totalN:
- print('--')
- print('TOTAL: %g in %d contigs (mean size %d)' % (
- totalSum, totalN, totalSum / totalN + .5))
+ print '--'
+ print 'TOTAL: %g in %d contigs (mean size %d)' % (
+ totalSum, totalN, totalSum / float(totalN) + .5)
main()
diff --git a/sandbox/bloom-count-intersection.py b/sandbox/bloom-count-intersection.py
index 71405d4..d6dbc36 100755
--- a/sandbox/bloom-count-intersection.py
+++ b/sandbox/bloom-count-intersection.py
@@ -1,8 +1,7 @@
-from __future__ import print_function
-#! /usr/bin/env python
+#! /usr/bin/env python2
#
-# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
-# Copyright (C) Michigan State University, 2009-2015. It is licensed under
+# This file is part of khmer, http://github.com/ged-lab/khmer/, and is
+# Copyright (C) Michigan State University, 2009-2013. It is licensed under
# the three-clause BSD license; see LICENSE.
# Contact: khmer-project at idyll.org
#
@@ -20,7 +19,7 @@ def main():
HT_SIZE = int(sys.argv[3]) # size of hashtable
N_HT = int(sys.argv[4]) # number of hashtables
- ht = khmer.Hashbits(K, HT_SIZE, N_HT)
+ ht = khmer.new_hashbits(K, HT_SIZE, N_HT)
n_unique = 0
for n, record in enumerate(fasta_iter(open(filename))):
@@ -31,12 +30,12 @@ def main():
if (not ht.get(kmer)):
n_unique += 1
ht.count(kmer)
- print(filename, 'has been consumed.')
- print('# of unique kmers:', n_unique)
- print('# of occupied bin:', ht.n_occupied())
+ print filename, 'has been consumed.'
+ print '# of unique kmers:', n_unique
+ print '# of occupied bin:', ht.n_occupied()
filename2 = sys.argv[5]
- ht2 = khmer.Hashbits(K, HT_SIZE, N_HT)
+ ht2 = khmer.new_hashbits(K, HT_SIZE, N_HT)
n_unique = 0
n_overlap = 0
for n, record in enumerate(fasta_iter(open(filename2))):
@@ -50,11 +49,11 @@ def main():
n_overlap += 1
ht2.count(kmer)
- print(filename2, 'has been consumed.')
- print('# of unique kmers:', n_unique)
- print('# of occupied bin:', ht2.n_occupied())
+ print filename2, 'has been consumed.'
+ print '# of unique kmers:', n_unique
+ print '# of occupied bin:', ht2.n_occupied()
- print(n_overlap, 'unique kmers appears in both ', filename, ' and ', filename2)
+ print n_overlap, 'unique kmers appears in both ', filename, ' and ', filename2
if __name__ == '__main__':
diff --git a/sandbox/bloom-count.py b/sandbox/bloom-count.py
index fc833cc..19a3c80 100755
--- a/sandbox/bloom-count.py
+++ b/sandbox/bloom-count.py
@@ -1,8 +1,7 @@
-from __future__ import print_function
-#! /usr/bin/env python
+#! /usr/bin/env python2
#
-# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
-# Copyright (C) Michigan State University, 2009-2015. It is licensed under
+# This file is part of khmer, http://github.com/ged-lab/khmer/, and is
+# Copyright (C) Michigan State University, 2009-2013. It is licensed under
# the three-clause BSD license; see LICENSE.
# Contact: khmer-project at idyll.org
#
@@ -20,7 +19,7 @@ def main():
HT_SIZE = int(sys.argv[3]) # size of hashtable
N_HT = int(sys.argv[4]) # number of hashtables
- ht = khmer.Hashbits(K, HT_SIZE, N_HT)
+ ht = khmer.new_hashbits(K, HT_SIZE, N_HT)
n_unique = 0
for n, record in enumerate(fasta_iter(open(filename))):
@@ -32,9 +31,9 @@ def main():
n_unique += 1
ht.count(kmer)
- print(n_unique)
- print(ht.n_occupied())
- print(ht.n_unique_kmers())
+ print n_unique
+ print ht.n_occupied()
+ print ht.n_unique_kmers()
if __name__ == '__main__':
diff --git a/sandbox/build-sparse-graph.py b/sandbox/build-sparse-graph.py
index 6686d73..4941603 100755
--- a/sandbox/build-sparse-graph.py
+++ b/sandbox/build-sparse-graph.py
@@ -1,8 +1,7 @@
-from __future__ import print_function
-#! /usr/bin/env python
+#! /usr/bin/env python2
#
-# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
-# Copyright (C) Michigan State University, 2013-2015. It is licensed under
+# This file is part of khmer, http://github.com/ged-lab/khmer/, and is
+# Copyright (C) Michigan State University, 2013. It is licensed under
# the three-clause BSD license; see LICENSE.
# Contact: khmer-project at idyll.org
#
@@ -20,7 +19,7 @@ def main():
K = int(sys.argv[1])
x = float(sys.argv[2])
- ht = khmer.Hashbits(K, x, 4)
+ ht = khmer.new_hashbits(K, x, 4)
sparse_graph = gt.Graph()
hashes = sparse_graph.new_vertex_property("long long")
@@ -28,13 +27,13 @@ def main():
for n, record in enumerate(screed.open(input_fasta)):
if n % 1000 == 0:
- print('...loaded and tagged {} sequences'.format(n), file=sys.stderr)
+ print >>sys.stderr, '...loaded and tagged {} sequences'.format(n)
name = record.name
sequence = record.sequence
ht.consume_sequence_and_tag_with_labels(sequence, n)
tags = ht.sweep_tag_neighborhood(sequence, 0)
- for i in range(len(tags) - 1):
+ for i in xrange(len(tags) - 1):
src = tags[i]
dst = tags[i + 1]
@@ -59,7 +58,7 @@ def main():
if new:
e = sparse_graph.add_edge(srcv, dstv)
- print('Sparse graph has {} nodes, {} edges'.format(sparse_graph.num_vertices(), sparse_graph.num_edges()))
+ print 'Sparse graph has {} nodes, {} edges'.format(sparse_graph.num_vertices(), sparse_graph.num_edges())
comp = gt.label_largest_component(sparse_graph, directed=False)
#pos = gt.radial_tree_layout(sparse_graph, sparse_graph.vertex(0))
gt.graph_draw(sparse_graph, output_size=(
diff --git a/sandbox/calc-best-assembly.py b/sandbox/calc-best-assembly.py
index 931a24d..9582e44 100755
--- a/sandbox/calc-best-assembly.py
+++ b/sandbox/calc-best-assembly.py
@@ -1,10 +1,9 @@
-#! /usr/bin/env python
+#! /usr/bin/env python2
#
-# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
+# This file is part of khmer, http://github.com/ged-lab/khmer/, and is
# Copyright (C) Michigan State University, 2009-2015. It is licensed under
# the three-clause BSD license; see LICENSE. Contact: ctb at msu.edu
#
-from __future__ import print_function
import screed
import argparse
import sys
@@ -35,31 +34,31 @@ def main():
try:
total = calculate_bp_above_cutoff(filename, args.cutoff)
except IOError:
- print("** WARNING: %s does not exist, skipping" %\
- filename, file=sys.stderr)
+ print >>sys.stderr, "** WARNING: %s does not exist, skipping" %\
+ filename
continue
stats.append((total, filename))
if not args.quiet:
- print("assembly %s has %d bp > %d" % (filename,
+ print >>sys.stderr, "assembly %s has %d bp > %d" % (filename,
total,
- args.cutoff), file=sys.stderr)
+ args.cutoff)
stats.sort(reverse=True)
best_total, winner_file = stats[0]
- print('----', file=sys.stderr)
- print("assembly %s wins: %d total bp > %d" % (winner_file,
+ print >>sys.stderr, '----'
+ print >>sys.stderr, "assembly %s wins: %d total bp > %d" % (winner_file,
best_total,
- args.cutoff), file=sys.stderr)
+ args.cutoff)
if args.output_file:
for record in screed.open(winner_file, parse_description=False):
- print('>%s\n%s' % (record.name,
- record.sequence), file=args.output_file)
+ print >>args.output_file, '>%s\n%s' % (record.name,
+ record.sequence)
- print(winner_file)
+ print winner_file
if __name__ == '__main__':
main()
diff --git a/sandbox/calc-error-profile.py b/sandbox/calc-error-profile.py
index 2cceb30..f2ffddf 100755
--- a/sandbox/calc-error-profile.py
+++ b/sandbox/calc-error-profile.py
@@ -1,6 +1,6 @@
-#! /usr/bin/env python
+#! /usr/bin/env python2
#
-# This script is part of khmer, https://github.com/dib-lab/khmer/, and is
+# This script is part of khmer, http://github.com/ged-lab/khmer/, and is
# Copyright (C) Michigan State University, 2009-2015. It is licensed under
# the three-clause BSD license; see LICENSE. Contact: ctb at msu.edu
#
@@ -12,8 +12,6 @@ reads. The output is placed in <infile>.errhist in the cwd by default.
Reads FASTQ and FASTA input.
"""
-from __future__ import division
-from __future__ import print_function
import sys
import argparse
@@ -67,7 +65,7 @@ def main():
# build a small counting hash w/default parameters. In general there
# should be no need to change these parameters.
- ht = khmer.CountingHash(K, HASHSIZE, N_HT)
+ ht = khmer.new_counting_hash(K, HASHSIZE, N_HT)
# initialize list to contain counts of errors by position
positions = [0] * MAX_SEQ_LEN
@@ -82,13 +80,13 @@ def main():
# look for errors.
total = 0
for filename in args.filenames:
- print('opening', filename, file=sys.stderr)
+ print >>sys.stderr, 'opening', filename
for n, record in enumerate(screed.open(filename)):
total += 1
if total % CHECK_EXIT == 0:
- print('...', total, n_consumed, n_checked, file=sys.stderr)
+ print >>sys.stderr, '...', total, n_consumed, n_checked
# two exit conditions: first, have we hit our max reads limit?
if total >= MAX_READS:
@@ -113,8 +111,8 @@ def main():
lengths.append(len(seq))
if args.errors_per_read:
- print(record.name, \
- ",".join(map(str, posns)), file=args.errors_per_read)
+ print >>args.errors_per_read, record.name, \
+ ",".join(map(str, posns))
# track the positions => errors
for p in posns:
@@ -133,24 +131,24 @@ def main():
# write!
output_file.write('position error_count error_fraction\n')
for n, i in enumerate(positions[:max_length]):
- print(n, i, float(i) / float(length_count[n]), file=output_file)
+ print >>output_file, n, i, float(i) / float(length_count[n])
output_file.close()
- print('', file=sys.stderr)
- print('total sequences:', total, file=sys.stderr)
- print('n consumed:', n_consumed, file=sys.stderr)
- print('n checked:', n_checked, file=sys.stderr)
- print('bp consumed:', bp_consumed, bp_consumed / float(C), file=sys.stderr)
- print('error rate: %.2f%%' % \
- (100.0 * sum(positions) / float(sum(lengths))), file=sys.stderr)
+ print >>sys.stderr, ''
+ print >>sys.stderr, 'total sequences:', total
+ print >>sys.stderr, 'n consumed:', n_consumed
+ print >>sys.stderr, 'n checked:', n_checked
+ print >>sys.stderr, 'bp consumed:', bp_consumed, bp_consumed / float(C)
+ print >>sys.stderr, 'error rate: %.2f%%' % \
+ (100.0 * sum(positions) / float(sum(lengths)))
- print('Error histogram is in %s' % output_filename, file=sys.stderr)
+ print >>sys.stderr, 'Error histogram is in %s' % output_filename
if not exit_condition(n_consumed, n_checked):
- print("", file=sys.stderr)
- print("** WARNING: not enough reads to get a good result", file=sys.stderr)
- print("** Is this high diversity sample / small subset?", file=sys.stderr)
+ print >>sys.stderr, ""
+ print >>sys.stderr, "** WARNING: not enough reads to get a good result"
+ print >>sys.stderr, "** Is this high diversity sample / small subset?"
sys.exit(-1)
diff --git a/sandbox/calc-median-distribution.py b/sandbox/calc-median-distribution.py
index a67a99c..c6ef1d0 100755
--- a/sandbox/calc-median-distribution.py
+++ b/sandbox/calc-median-distribution.py
@@ -1,12 +1,10 @@
-#! /usr/bin/env python
+#! /usr/bin/env python2
#
-# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
-# Copyright (C) Michigan State University, 2009-2015. It is licensed under
+# This file is part of khmer, http://github.com/ged-lab/khmer/, and is
+# Copyright (C) Michigan State University, 2009-2013. It is licensed under
# the three-clause BSD license; see LICENSE.
# Contact: khmer-project at idyll.org
#
-from __future__ import division
-from __future__ import print_function
import sys
import khmer
import argparse
@@ -29,7 +27,7 @@ def main():
outfp = open(histout, 'w')
- print('hashtable from', hashfile)
+ print 'hashtable from', hashfile
ht = khmer.load_counting_hash(hashfile)
hist = {}
@@ -39,7 +37,7 @@ def main():
for n, record in enumerate(screed.open(seqfile)):
if n > 0 and n % 100000 == 0:
- print('...', n)
+ print '...', n
seq = record.sequence.replace('N', 'A')
diff --git a/sandbox/collect-reads.py b/sandbox/collect-reads.py
index f02c0ea..ca16608 100755
--- a/sandbox/collect-reads.py
+++ b/sandbox/collect-reads.py
@@ -1,6 +1,6 @@
-#! /usr/bin/env python
+#! /usr/bin/env python2
#
-# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
+# This file is part of khmer, http://github.com/ged-lab/khmer/, and is
# Copyright (C) Michigan State University, 2014-2015. It is licensed under
# the three-clause BSD license; see LICENSE.
# Contact: khmer-project at idyll.org
@@ -14,13 +14,10 @@ Place reads into -o output_file.
Use '-h' for parameter help.
"""
-from __future__ import division
-from __future__ import print_function
import sys
import textwrap
import khmer
-from khmer import khmer_args
from khmer.khmer_args import build_counting_args, report_on_config, info
from khmer.kfile import check_input_files, check_space
from khmer.kfile import check_space_for_hashtable
@@ -77,15 +74,15 @@ def main():
check_input_files(name, False)
check_space(args.input_sequence_filename, False)
- check_space_for_hashtable(args, 'countgraph', False)
+ check_space_for_hashtable(args.n_tables * args.min_tablesize, False)
- print('Saving k-mer counting table to %s' % base)
- print('Loading sequences from %s' % repr(filenames))
+ print 'Saving k-mer counting table to %s' % base
+ print 'Loading sequences from %s' % repr(filenames)
if args.output:
- print('Outputting sequences to', args.output)
+ print 'Outputting sequences to', args.output
- print('making countgraph', file=sys.stderr)
- htable = khmer_args.create_countgraph(args)
+ print 'making k-mer counting table'
+ htable = khmer.new_counting_hash(args.ksize, args.min_tablesize)
htable.set_use_bigcount(args.bigcount)
total_coverage = 0.
@@ -95,7 +92,7 @@ def main():
for record in screed.open(filename):
seq = record.sequence.upper()
if 'N' in seq:
- seq = seq.replace('N', 'A')
+ seq = seq.replace('N', 'G')
try:
med, _, _ = htable.get_median_count(seq)
@@ -106,8 +103,8 @@ def main():
n += 1
if total_coverage / float(n) > args.coverage:
- print('reached target average coverage:', \
- total_coverage / float(n))
+ print 'reached target average coverage:', \
+ total_coverage / float(n)
break
htable.consume(seq)
@@ -115,30 +112,29 @@ def main():
args.output.write(output_single(record))
if n % 100000 == 0:
- print('...', index, filename, n, total_coverage / float(n))
+ print '...', index, filename, n, total_coverage / float(n)
if total_coverage / float(n) > args.coverage:
break
- print('Collected %d reads' % (n,))
+ print 'Collected %d reads' % (n,)
if args.report_total_kmers:
- print('Total number of k-mers: {0}'.format(
- htable.n_occupied()), file=sys.stderr)
+ print >> sys.stderr, 'Total number of k-mers: {0}'.format(
+ htable.n_occupied())
- print('saving', base)
+ print 'saving', base
htable.save(base)
info_fp = open(base + '.info', 'w')
info_fp.write('through end: %s\n' % filenames[-1])
# Change 0.2 only if you really grok it. HINT: You don't.
- fp_rate = khmer.calc_expected_collisions(htable, False,
- max_false_pos=.2)
- print('fp rate estimated to be %1.3f' % fp_rate)
- print('fp rate estimated to be %1.3f' % fp_rate, file=info_fp)
+ fp_rate = khmer.calc_expected_collisions(htable, args.force, max_false_pos=.2)
+ print 'fp rate estimated to be %1.3f' % fp_rate
+ print >> info_fp, 'fp rate estimated to be %1.3f' % fp_rate
- print('DONE.')
+ print 'DONE.'
if __name__ == '__main__':
main()
diff --git a/sandbox/collect-variants.py b/sandbox/collect-variants.py
index db368f0..3a3669b 100755
--- a/sandbox/collect-variants.py
+++ b/sandbox/collect-variants.py
@@ -1,7 +1,7 @@
-#! /usr/bin/env python
+#! /usr/bin/env python2
#
-# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
-# Copyright (C) Michigan State University, 2013-2015. It is licensed under
+# This file is part of khmer, http://github.com/ged-lab/khmer/, and is
+# Copyright (C) Michigan State University, 2013-2014. It is licensed under
# the three-clause BSD license; see LICENSE.
# Contact: khmer-project at idyll.org
#
@@ -12,7 +12,6 @@ Use '-h' for parameter help.
TODO: add to sandbox README
"""
-from __future__ import print_function
import sys
import screed
@@ -42,16 +41,16 @@ def main():
args = parser.parse_args()
if not args.quiet:
- print('\nPARAMETERS:', file=sys.stderr)
- print(' - kmer size = %d \t\t(-k)' % args.ksize, file=sys.stderr)
- print(' - n hashes = %d \t\t(-N)' % args.n_tables, file=sys.stderr)
- print(' - min hashsize = %-5.2g \t(-x)' % \
- args.min_tablesize, file=sys.stderr)
- print('', file=sys.stderr)
- print('Estimated memory usage is %.2g bytes ' \
+ print >>sys.stderr, '\nPARAMETERS:'
+ print >>sys.stderr, ' - kmer size = %d \t\t(-k)' % args.ksize
+ print >>sys.stderr, ' - n hashes = %d \t\t(-N)' % args.n_tables
+ print >>sys.stderr, ' - min hashsize = %-5.2g \t(-x)' % \
+ args.min_tablesize
+ print >>sys.stderr, ''
+ print >>sys.stderr, 'Estimated memory usage is %.2g bytes ' \
'(n_hashes x min_hashsize)' % \
- (args.n_tables * args.min_tablesize), file=sys.stderr)
- print('-' * 8, file=sys.stderr)
+ (args.n_tables * args.min_tablesize)
+ print >>sys.stderr, '-' * 8
K = args.ksize
HT_SIZE = args.min_tablesize
@@ -60,11 +59,11 @@ def main():
filenames = args.input_filenames
if args.loadhash:
- print('loading hashtable from', args.loadhash)
+ print 'loading hashtable from', args.loadhash
ht = khmer.load_counting_hash(args.loadhash)
else:
- print('making hashtable')
- ht = khmer.CountingHash(K, HT_SIZE, N_HT)
+ print 'making hashtable'
+ ht = khmer.new_counting_hash(K, HT_SIZE, N_HT)
aligner = khmer.ReadAligner(ht, args.trusted_cutoff, args.bits_theta)
@@ -81,9 +80,9 @@ def main():
for n, record in enumerate(screed.open(input_filename)):
if n > 0 and n % 10000 == 0:
- print('... kept', total - discarded, 'of', total, ', or', \
- int(100. - discarded / float(total) * 100.), '%')
- print('... in file', input_filename)
+ print '... kept', total - discarded, 'of', total, ', or', \
+ int(100. - discarded / float(total) * 100.), '%'
+ print '... in file', input_filename
total += 1
@@ -134,19 +133,19 @@ def main():
discarded += 1
if total:
- print('DONE with', input_filename, \
+ print 'DONE with', input_filename, \
'; kept', total - discarded, 'of', total, 'or', \
- int(100. - discarded / float(total) * 100.), '%')
- print('output in', output_name)
+ int(100. - discarded / float(total) * 100.), '%'
+ print 'output in', output_name
if args.savehash:
- print('Saving hashfile through', input_filename)
- print('...saving to', args.savehash)
+ print 'Saving hashfile through', input_filename
+ print '...saving to', args.savehash
ht.save(args.savehash)
# Change 0.2 only if you really grok it. HINT: You don't.
fp_rate = khmer.calc_expected_collisions(ht, args.force, max_false_pos=.2)
- print('fp rate estimated to be %1.3f' % fp_rate)
+ print 'fp rate estimated to be %1.3f' % fp_rate
if __name__ == '__main__':
diff --git a/sandbox/correct-errors.py b/sandbox/correct-errors.py
index 71c6890..83b6ec6 100755
--- a/sandbox/correct-errors.py
+++ b/sandbox/correct-errors.py
@@ -1,7 +1,7 @@
-#! /usr/bin/env python
+#! /usr/bin/env python2
#
-# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
-# Copyright (C) Michigan State University, 2009-2015. It is licensed under
+# This file is part of khmer, http://github.com/ged-lab/khmer/, and is
+# Copyright (C) Michigan State University, 2009-2014. It is licensed under
# the three-clause BSD license; see LICENSE.
# Contact: khmer-project at idyll.org
#
@@ -18,7 +18,6 @@ TODO: move output_single elsewhere
TODO: add to sandbox/README
TODO: change name to correct-reads?
"""
-from __future__ import print_function
import sys
import screed
import os
@@ -91,13 +90,13 @@ def main():
NORMALIZE_LIMIT = args.normalize_to
- print('making hashtable')
- ht = khmer.CountingHash(K, HT_SIZE, N_HT)
+ print 'making hashtable'
+ ht = khmer.new_counting_hash(K, HT_SIZE, N_HT)
aligner = khmer.ReadAligner(ht, args.trusted_cov, args.bits_theta)
tempdir = tempfile.mkdtemp('khmer', 'tmp', args.tempdir)
- print('created temporary directory %s; use -T to change location' % tempdir)
+ print 'created temporary directory %s; use -T to change location' % tempdir
###
@@ -121,8 +120,8 @@ def main():
total_reads += 1
if n % 10000 == 0:
- print('...', n, filename, n_aligned, n_corrected, save_pass2, \
- total_reads)
+ print '...', n, filename, n_aligned, n_corrected, save_pass2, \
+ total_reads
seq = read.sequence.replace('N', 'A')
# build the alignment...
@@ -166,18 +165,18 @@ def main():
pass2fp.close()
corrfp.close()
- print('%s: kept aside %d of %d from first pass, in %s' % \
- (filename, save_pass2, n, filename))
- print('aligned %d of %d reads so far' % (n_aligned, total_reads))
- print('changed %d of %d reads so far' % (n_corrected, total_reads))
+ print '%s: kept aside %d of %d from first pass, in %s' % \
+ (filename, save_pass2, n, filename)
+ print 'aligned %d of %d reads so far' % (n_aligned, total_reads)
+ print 'changed %d of %d reads so far' % (n_corrected, total_reads)
for orig_filename, pass2filename, corrfilename in pass2list:
- print('second pass: looking at sequences kept aside in %s' % \
- pass2filename)
+ print 'second pass: looking at sequences kept aside in %s' % \
+ pass2filename
for n, read in enumerate(screed.open(pass2filename)):
if n % 10000 == 0:
- print('... x 2', n, pass2filename, n_aligned, n_corrected, \
- total_reads)
+ print '... x 2', n, pass2filename, n_aligned, n_corrected, \
+ total_reads
corrfp = open(corrfilename, 'a')
@@ -206,14 +205,14 @@ def main():
corrfp.write(output_single(read, corrected))
- print('removing %s' % pass2filename)
+ print 'removing %s' % pass2filename
os.unlink(pass2filename)
- print('removing temp directory & contents (%s)' % tempdir)
+ print 'removing temp directory & contents (%s)' % tempdir
shutil.rmtree(tempdir)
- print('Aligned %d of %d total' % (n_aligned, total_reads))
- print('Changed %d of %d total' % (n_corrected, total_reads))
+ print 'Aligned %d of %d total' % (n_aligned, total_reads)
+ print 'Changed %d of %d total' % (n_corrected, total_reads)
if __name__ == '__main__':
main()
diff --git a/sandbox/estimate_optimal_hash.py b/sandbox/estimate_optimal_hash.py
deleted file mode 100755
index 63e4932..0000000
--- a/sandbox/estimate_optimal_hash.py
+++ /dev/null
@@ -1,109 +0,0 @@
-#! /usr/bin/env python2
-#
-# This file is part of khmer, http://github.com/ged-lab/khmer/, and is
-# Copyright (C) Michigan State University, 2009-2015. It is licensed under
-# the three-clause BSD license; see doc/LICENSE.txt.
-# Contact: khmer-project at idyll.org
-#
-# pylint: disable=missing-docstring,invalid-name
-"""
-Estimate optimal choice of hash table parameters
-
-First scenario: we know the number of k-mers N and the size of memory
-available to use M. We want to know the optimal number of hash table Z
-to get the lowest false positive rate.
-
-For this scenario, use only "-M" and "number of kmers".
-% sandbox/estimate_optimal_hash.py <number_of_kmers> -M <size_of_memory>
-
-Second scenario: we know the number of k-mers N and the desired maximum
-false positive rate f. We want to know the minimum memory usage required
-to achieve f.
-
-For this scenario, use only "-f" and "number of kmers".
-% sandbox/estimate_optimal_hash.py <number_of_kmers> -f <desired_fpr>
-
-Use '-h' for parameter help.
-
-"""
-from __future__ import print_function
-import argparse
-import khmer, oxli
-from khmer.khmer_args import info
-from oxli.functions import estimate_optimal_with_N_and_M
-from oxli.functions import estimate_optimal_with_N_and_f
-import textwrap
-import sys
-
-def get_parser():
- epilog = """
-
- First scenario: we know the number of k-mers N and the size of memory
- available to use M. We want to know the optimal number of hash table Z
- to get the lowest false positive rate.
-
- For this scenario, use only "-M" and "number of kmers".
- % sandbox/estimate_optimal_hash.py <number_of_kmers> -M <size_of_memory>
-
- Second scenario: we know the number of k-mers N and the desired maximum
- false positive rate f. We want to know the minimum memory usage required
- to achieve f.
-
- For this scenario, use only "-f" and "number of kmers".
- % sandbox/estimate_optimal_hash.py <number_of_kmers> -f <desired_fpr>
-
- """
- parser = argparse.ArgumentParser(
- description='Estimate optimal choice of hash table parameters',
- formatter_class=argparse.RawDescriptionHelpFormatter,
- epilog=textwrap.dedent(epilog))
-
- parser.add_argument('-N', help='number of estimated distinct k-mers',
- type = int)
- group = parser.add_mutually_exclusive_group()
- group.add_argument('-M', help='size of memory available to use',
- type = int)
- group.add_argument('-f', help='desired maximum false posotive rate',
- type = float)
- parser.add_argument('--version', action='version', version='%(prog)s '
- + khmer.__version__)
- return parser
-
-
-def main():
- info('estimate_optimal_hash.py', ['counting'])
- args = get_parser().parse_args()
- N = args.N
- if args.M:
- M = args.M
- result = estimate_optimal_with_N_and_M(N,M)
- print("number of estimated distinct k-mers: ", N, file=sys.stderr)
- print("size of memory available to use: ", M, file=sys.stderr)
- print("optimal number of hash tables: ", result.num_htables,
- file=sys.stderr)
- print("optimal size of hash tables: ", result.htable_size,
- file=sys.stderr)
- print("estimated false positive rate: ", result.fp_rate,
- file=sys.stderr)
- print("estimated usage of memory: ", result.mem_use,
- file=sys.stderr)
-
- elif args.f:
- f = args.f
- result = estimate_optimal_with_N_and_f(N,f)
- print("number of estimated distinct k-mers: ", N, file=sys.stderr)
- print("desired maximum false positive rate: ", f, file=sys.stderr)
- print("optimal number of hash tables: ", result.num_htables,
- file=sys.stderr)
- print("optimal size of hash tables: ", result.htable_size,
- file=sys.stderr)
- print("estimated false positive rate: ", result.fp_rate,
- file=sys.stderr)
- print("estimated usage of memory: ", result.mem_use,
- file=sys.stderr)
-
- else:
- get_parser().error('No action requested, add -M (size of memory available to use) or -f (desired maximum false posotive rate)')
-
-if __name__ == '__main__':
- main()
diff --git a/sandbox/extract-single-partition.py b/sandbox/extract-single-partition.py
index ccc0f28..0e890da 100755
--- a/sandbox/extract-single-partition.py
+++ b/sandbox/extract-single-partition.py
@@ -1,11 +1,10 @@
-#! /usr/bin/env python
+#! /usr/bin/env python2
#
-# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
-# Copyright (C) Michigan State University, 2009-2015. It is licensed under
+# This file is part of khmer, http://github.com/ged-lab/khmer/, and is
+# Copyright (C) Michigan State University, 2009-2013. It is licensed under
# the three-clause BSD license; see LICENSE.
# Contact: khmer-project at idyll.org
#
-from __future__ import print_function
import sys
from screed.fasta import fasta_iter
@@ -22,7 +21,7 @@ def main():
count = 0
for n, name, pid, seq in read_partition_file(open(sys.argv[1])):
if pid == select_pid:
- print('>%s\t%d\n%s' % (name, pid, seq))
+ print '>%s\t%d\n%s' % (name, pid, seq)
count += 1
if n % 10000 == 0:
diff --git a/sandbox/fasta-to-abundance-hist.py b/sandbox/fasta-to-abundance-hist.py
index b4776cf..d101f16 100755
--- a/sandbox/fasta-to-abundance-hist.py
+++ b/sandbox/fasta-to-abundance-hist.py
@@ -1,11 +1,10 @@
-#! /usr/bin/env python
+#! /usr/bin/env python2
#
-# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
-# Copyright (C) Michigan State University, 2009-2015. It is licensed under
+# This file is part of khmer, http://github.com/ged-lab/khmer/, and is
+# Copyright (C) Michigan State University, 2009-2013. It is licensed under
# the three-clause BSD license; see LICENSE.
# Contact: khmer-project at idyll.org
#
-from __future__ import print_function
import sys
import khmer
@@ -17,11 +16,13 @@ def main():
n_consumed = len(files) * [0]
n_seq_kept = len(files) * [0]
- print('loading ht')
- ht = khmer.load_counting_hash(sys.argv[1])
+ print 'loading ht'
+ ht = khmer.new_counting_hash(1, 1, 1)
+
+ ht.load(sys.argv[1])
for i, infile in enumerate(files):
- print('outputting', infile + '.freq')
+ print 'outputting', infile + '.freq'
ht.output_fasta_kmer_pos_freq(infile, infile + ".freq")
diff --git a/sandbox/filter-below-abund.py b/sandbox/filter-below-abund.py
index e46ddee..9b4ef76 100755
--- a/sandbox/filter-below-abund.py
+++ b/sandbox/filter-below-abund.py
@@ -1,11 +1,10 @@
-#! /usr/bin/env python
+#! /usr/bin/env python2
#
-# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
-# Copyright (C) Michigan State University, 2009-2015. It is licensed under
+# This file is part of khmer, http://github.com/ged-lab/khmer/, and is
+# Copyright (C) Michigan State University, 2009-2013. It is licensed under
# the three-clause BSD license; see LICENSE.
# Contact: khmer-project at idyll.org
#
-from __future__ import print_function
import sys
import os
import khmer
@@ -23,17 +22,17 @@ def main():
counting_ht = sys.argv[1]
infiles = sys.argv[2:]
- print('file with ht: %s' % counting_ht)
- print('-- settings:')
- print('N THREADS', WORKER_THREADS)
- print('--')
+ print 'file with ht: %s' % counting_ht
+ print '-- settings:'
+ print 'N THREADS', WORKER_THREADS
+ print '--'
- print('making hashtable')
+ print 'making hashtable'
ht = khmer.load_counting_hash(counting_ht)
K = ht.ksize()
for infile in infiles:
- print('filtering', infile)
+ print 'filtering', infile
outfile = os.path.basename(infile) + '.below'
outfp = open(outfile, 'w')
diff --git a/sandbox/filter-median-and-pct.py b/sandbox/filter-median-and-pct.py
index 698aff5..ed9e251 100755
--- a/sandbox/filter-median-and-pct.py
+++ b/sandbox/filter-median-and-pct.py
@@ -1,7 +1,7 @@
-#! /usr/bin/env python
+#! /usr/bin/env python2
#
-# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
-# Copyright (C) Michigan State University, 2009-2015. It is licensed under
+# This file is part of khmer, http://github.com/ged-lab/khmer/, and is
+# Copyright (C) Michigan State University, 2009-2013. It is licensed under
# the three-clause BSD license; see LICENSE.
# Contact: khmer-project at idyll.org
#
@@ -13,7 +13,6 @@ hash table. Output sequences will be placed in 'infile.medpctfilt'.
Use '-h' for parameter help.
"""
-from __future__ import print_function
import sys
import screed.fasta
import os
@@ -38,15 +37,15 @@ def main():
counting_ht = args.input_table
infiles = args.input_filenames
- print('file with ht: %s' % counting_ht)
+ print 'file with ht: %s' % counting_ht
- print('loading hashtable')
+ print 'loading hashtable'
ht = khmer.load_counting_hash(counting_ht)
K = ht.ksize()
xxxfp = None
- print("K:", K)
+ print "K:", K
# the filtering function.
def process_fn(record):
@@ -65,20 +64,20 @@ def main():
# the filtering loop
for infile in infiles:
- print('filtering', infile)
+ print 'filtering', infile
xxxfp = open(os.path.basename(infile) + '.medpctfilt.stats', 'w')
outfile = os.path.basename(infile) + '.medpctfilt'
outfp = open(outfile, 'w')
for n, record in enumerate(screed.open(infile)):
if n % 100000 == 0:
- print('...', n)
+ print '...', n
name, seq = process_fn(record)
if name and seq:
- print('>%s\n%s' % (name, seq), file=outfp)
+ print >>outfp, '>%s\n%s' % (name, seq)
- print('output in', outfile)
+ print 'output in', outfile
if __name__ == '__main__':
main()
diff --git a/sandbox/filter-median.py b/sandbox/filter-median.py
index a417c3d..c1a126f 100755
--- a/sandbox/filter-median.py
+++ b/sandbox/filter-median.py
@@ -1,7 +1,7 @@
-#! /usr/bin/env python
+#! /usr/bin/env python2
#
-# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
-# Copyright (C) Michigan State University, 2009-2015. It is licensed under
+# This file is part of khmer, http://github.com/ged-lab/khmer/, and is
+# Copyright (C) Michigan State University, 2009-2013. It is licensed under
# the three-clause BSD license; see LICENSE.
# Contact: khmer-project at idyll.org
#
@@ -13,7 +13,6 @@ hash table. Output sequences will be placed in 'infile.medfilt'.
Use '-h' for parameter help.
"""
-from __future__ import print_function
import sys
import screed.fasta
import os
@@ -38,13 +37,13 @@ def main():
counting_ht = args.input_table
infiles = args.input_filenames
- print('file with ht: %s' % counting_ht)
+ print 'file with ht: %s' % counting_ht
- print('loading hashtable')
+ print 'loading hashtable'
ht = khmer.load_counting_hash(counting_ht)
K = ht.ksize()
- print("K:", K)
+ print "K:", K
# the filtering function.
def process_fn(record):
@@ -60,14 +59,14 @@ def main():
# the filtering loop
for infile in infiles:
- print('filtering', infile)
+ print 'filtering', infile
outfile = os.path.basename(infile) + '.medfilt'
outfp = open(outfile, 'w')
tsp = ThreadedSequenceProcessor(process_fn)
tsp.start(verbose_loader(infile), outfp)
- print('output in', outfile)
+ print 'output in', outfile
if __name__ == '__main__':
main()
diff --git a/sandbox/find-high-abund-kmers.py b/sandbox/find-high-abund-kmers.py
index db43686..687ab41 100755
--- a/sandbox/find-high-abund-kmers.py
+++ b/sandbox/find-high-abund-kmers.py
@@ -1,19 +1,18 @@
-#! /usr/bin/env python
+#! /usr/bin/env python2
#
-# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
-# Copyright (C) Michigan State University, 2009-2015. It is licensed under
+# This file is part of khmer, http://github.com/ged-lab/khmer/, and is
+# Copyright (C) Michigan State University, 2009-2013. It is licensed under
# the three-clause BSD license; see LICENSE.
# Contact: khmer-project at idyll.org
#
"""
@@
"""
-from __future__ import print_function
import sys
import screed
import khmer
-from khmer.khmer_args import build_counting_args, DEFAULT_MAX_TABLESIZE
+from khmer.khmer_args import build_counting_args, DEFAULT_MIN_TABLESIZE
DEFAULT_LOWER_CUTOFF = 2000
DEFAULT_UPPER_CUTOFF = 65535
@@ -34,21 +33,21 @@ def main():
args = parser.parse_args()
if not args.quiet:
- if args.min_hashsize == DEFAULT_MAX_TABLESIZE:
- print("** WARNING: hashsize is default! " \
+ if args.min_hashsize == DEFAULT_MIN_HASHSIZE:
+ print >>sys.stderr, "** WARNING: hashsize is default! " \
"You absodefly want to increase this!\n** " \
- "Please read the docs!", file=sys.stderr)
-
- print('\nPARAMETERS:', file=sys.stderr)
- print(' - kmer size = %d \t\t(-k)' % args.ksize, file=sys.stderr)
- print(' - n hashes = %d \t\t(-N)' % args.n_hashes, file=sys.stderr)
- print(' - min hashsize = %-5.2g \t(-x)' % \
- args.min_hashsize, file=sys.stderr)
- print('', file=sys.stderr)
- print('Estimated memory usage is %.2g bytes " \
+ "Please read the docs!"
+
+ print >>sys.stderr, '\nPARAMETERS:'
+ print >>sys.stderr, ' - kmer size = %d \t\t(-k)' % args.ksize
+ print >>sys.stderr, ' - n hashes = %d \t\t(-N)' % args.n_hashes
+ print >>sys.stderr, ' - min hashsize = %-5.2g \t(-x)' % \
+ args.min_hashsize
+ print >>sys.stderr, ''
+ print >>sys.stderr, 'Estimated memory usage is %.2g bytes " \
"(n_hashes x min_hashsize)' % (
- args.n_hashes * args.min_hashsize), file=sys.stderr)
- print('-' * 8, file=sys.stderr)
+ args.n_hashes * args.min_hashsize)
+ print >>sys.stderr, '-' * 8
K = args.ksize
HT_SIZE = args.min_hashsize
@@ -57,23 +56,23 @@ def main():
output = args.output_filename
input = args.input_filename
- print('lower cutoff:', args.lower_cutoff)
- print('upper cutoff:', args.upper_cutoff)
- print('Saving stoptags to %s' % output)
- print('Loading sequences in %s' % input)
+ print 'lower cutoff:', args.lower_cutoff
+ print 'upper cutoff:', args.upper_cutoff
+ print 'Saving stoptags to %s' % output
+ print 'Loading sequences in %s' % input
###
- print('making hashtable')
- ht = khmer.CountingHash(K, HT_SIZE, N_HT)
+ print 'making hashtable'
+ ht = khmer.new_counting_hash(K, HT_SIZE, N_HT)
ht.set_use_bigcount(True)
- print('consuming input', input)
+ print 'consuming input', input
hb = ht.collect_high_abundance_kmers(input,
args.lower_cutoff,
args.upper_cutoff)
- print('saving stoptags', output)
+ print 'saving stoptags', output
hb.save_stop_tags(output)
if __name__ == '__main__':
diff --git a/sandbox/graph-size.py b/sandbox/graph-size.py
index 41cdf07..00891b5 100755
--- a/sandbox/graph-size.py
+++ b/sandbox/graph-size.py
@@ -1,11 +1,10 @@
-#! /usr/bin/env python
+#! /usr/bin/env python2
#
-# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
-# Copyright (C) Michigan State University, 2009-2015. It is licensed under
+# This file is part of khmer, http://github.com/ged-lab/khmer/, and is
+# Copyright (C) Michigan State University, 2009-2013. It is licensed under
# the three-clause BSD license; see LICENSE.
# Contact: khmer-project at idyll.org
#
-from __future__ import print_function
import khmer
import sys
import screed
@@ -31,19 +30,19 @@ def main():
if len(sys.argv) == 3:
outfile = sys.argv[2]
- print('input file to graphsize filter: %s' % infile)
- print('filtering to output:', outfile)
- print('-- settings:')
- print('K', K)
- print('HASHTABLE SIZE %g' % HASHTABLE_SIZE)
- print('N HASHTABLES %d' % N_HT)
- print('THRESHOLD', THRESHOLD)
- print('N THREADS', WORKER_THREADS)
- print('--')
+ print 'input file to graphsize filter: %s' % infile
+ print 'filtering to output:', outfile
+ print '-- settings:'
+ print 'K', K
+ print 'HASHTABLE SIZE %g' % HASHTABLE_SIZE
+ print 'N HASHTABLES %d' % N_HT
+ print 'THRESHOLD', THRESHOLD
+ print 'N THREADS', WORKER_THREADS
+ print '--'
- print('creating ht')
- ht = khmer.Hashbits(K, HASHTABLE_SIZE, N_HT)
- print('eating fa', infile)
+ print 'creating ht'
+ ht = khmer.new_hashbits(K, HASHTABLE_SIZE, N_HT)
+ print 'eating fa', infile
total_reads, n_consumed = ht.consume_fasta(infile)
outfp = open(outfile, 'w')
diff --git a/sandbox/hi-lo-abundance-by-position.py b/sandbox/hi-lo-abundance-by-position.py
index 5c9e353..eca923f 100755
--- a/sandbox/hi-lo-abundance-by-position.py
+++ b/sandbox/hi-lo-abundance-by-position.py
@@ -1,11 +1,10 @@
-#! /usr/bin/env python
+#! /usr/bin/env python2
#
-# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
-# Copyright (C) Michigan State University, 2009-2015. It is licensed under
+# This file is part of khmer, http://github.com/ged-lab/khmer/, and is
+# Copyright (C) Michigan State University, 2009-2013. It is licensed under
# the three-clause BSD license; see LICENSE.
# Contact: khmer-project at idyll.org
#
-from __future__ import print_function
import sys
import os
import khmer
@@ -21,16 +20,16 @@ def main():
filename = sys.argv[2]
outfile = os.path.basename(filename)
- print('loading kh file', hashfile)
+ print 'loading kh file', hashfile
ht = khmer.load_counting_hash(hashfile)
x = ht.fasta_count_kmers_by_position(filename, 100, 1)
write_dist(x, open(outfile + '.pos.abund=1', 'w'))
- print('wrote', outfile + '.pos.abund=1')
+ print 'wrote', outfile + '.pos.abund=1'
y = ht.fasta_count_kmers_by_position(filename, 100, 255)
write_dist(y, open(outfile + '.pos.abund=255', 'w'))
- print('wrote', outfile + '.pos.abund=255')
+ print 'wrote', outfile + '.pos.abund=255'
if __name__ == '__main__':
diff --git a/sandbox/make-coverage.py b/sandbox/make-coverage.py
index fb4ce39..4828539 100755
--- a/sandbox/make-coverage.py
+++ b/sandbox/make-coverage.py
@@ -1,13 +1,10 @@
-#! /usr/bin/env python
+#! /usr/bin/env python2
#
-# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
+# This file is part of khmer, http://github.com/ged-lab/khmer/, and is
# Copyright (C) Michigan State University, 2009-2015. It is licensed under
# the three-clause BSD license; see LICENSE.txt.
# Contact: khmer-project at idyll.org
#
-
-from __future__ import print_function
-
import screed
import sys
@@ -19,13 +16,13 @@ def main():
lengths = {}
for n, record in enumerate(screed.open(dbfile)):
if n % 100000 == 0:
- print('...', n)
+ print '...', n
lengths[record.name] = len(record.sequence)
sums = {}
for n, line in enumerate(open(mapfile)):
if n % 100000 == 0:
- print('... 2x', n)
+ print '... 2x', n
x = line.split('\t')
name = x[2]
readlen = len(x[4])
@@ -41,12 +38,10 @@ def main():
outfp = open(dbfile + '.cov', 'w')
for n, record in enumerate(screed.open(dbfile)):
if n % 100000 == 0:
- print('...', n)
+ print '...', n
- print(">%s[cov=%d]\n%s" % (record.name,
- rpkms.get(record.name, 0),
- record.sequence),
- file=outfp)
+ print >>outfp, ">%s[cov=%d]\n%s" % (
+ record.name, rpkms.get(record.name, 0), record.sequence)
if __name__ == '__main__':
main()
diff --git a/sandbox/multi-rename.py b/sandbox/multi-rename.py
index f9c3a3d..4c03f08 100755
--- a/sandbox/multi-rename.py
+++ b/sandbox/multi-rename.py
@@ -1,11 +1,10 @@
-#! /usr/bin/env python
+#! /usr/bin/env python2
#
-# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
-# Copyright (C) Michigan State University, 2009-2015. It is licensed under
+# This file is part of khmer, http://github.com/ged-lab/khmer/, and is
+# Copyright (C) Michigan State University, 2009-2013. It is licensed under
# the three-clause BSD license; see LICENSE.
# Contact: khmer-project at idyll.org
#
-from __future__ import print_function
import screed
import sys
@@ -19,7 +18,7 @@ def main():
for record in screed.open(filename):
if len(record.sequence) >= CUTOFF:
n += 1
- print('>%s.%s %s\n%s' % (prefix, n, record.name, record.sequence))
+ print '>%s.%s %s\n%s' % (prefix, n, record.name, record.sequence)
if __name__ == '__main__':
diff --git a/sandbox/normalize-by-median-pct.py b/sandbox/normalize-by-median-pct.py
index f7dad25..b23d6d8 100755
--- a/sandbox/normalize-by-median-pct.py
+++ b/sandbox/normalize-by-median-pct.py
@@ -1,7 +1,7 @@
-#! /usr/bin/env python
+#! /usr/bin/env python2
#
-# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
-# Copyright (C) Michigan State University, 2009-2015. It is licensed under
+# This file is part of khmer, http://github.com/ged-lab/khmer/, and is
+# Copyright (C) Michigan State University, 2009-2013. It is licensed under
# the three-clause BSD license; see LICENSE.
# Contact: khmer-project at idyll.org
#
@@ -13,15 +13,13 @@ DESIRED_COVERAGE. Output sequences will be placed in 'infile.keep'.
Use '-h' for parameter help.
"""
-from __future__ import division
-from __future__ import print_function
import sys
import screed
import os
import khmer
-
-from khmer.khmer_args import build_counting_args, DEFAULT_MAX_TABLESIZE
+from itertools import izip
+from khmer.khmer_args import build_counting_args, DEFAULT_MIN_TABLESIZE
import argparse
DEFAULT_DESIRED_COVERAGE = 5
@@ -32,7 +30,7 @@ DEFAULT_DESIRED_COVERAGE = 5
def batchwise(t, size):
it = iter(t)
- return zip(*[it] * size)
+ return izip(*[it] * size)
# Returns true if the pair of records are properly pairs
@@ -58,18 +56,18 @@ def main():
args = parser.parse_args()
if not args.quiet:
- if args.min_hashsize == DEFAULT_MAX_HASHSIZE and not args.loadhash:
- print("** WARNING: hashsize is default! You absodefly want to increase this!\n** Please read the docs!", file=sys.stderr)
-
- print('\nPARAMETERS:', file=sys.stderr)
- print(' - kmer size = %d \t\t(-k)' % args.ksize, file=sys.stderr)
- print(' - n hashes = %d \t\t(-N)' % args.n_hashes, file=sys.stderr)
- print(' - min hashsize = %-5.2g \t(-x)' % args.min_hashsize, file=sys.stderr)
- print(' - paired = %s \t\t(-p)' % args.paired, file=sys.stderr)
- print('', file=sys.stderr)
- print('Estimated memory usage is %.2g bytes (n_hashes x min_hashsize)' % (
- args.n_hashes * args.min_hashsize), file=sys.stderr)
- print('-' * 8, file=sys.stderr)
+ if args.min_hashsize == DEFAULT_MIN_HASHSIZE and not args.loadhash:
+ print>>sys.stderr, "** WARNING: hashsize is default! You absodefly want to increase this!\n** Please read the docs!"
+
+ print>>sys.stderr, '\nPARAMETERS:'
+ print>>sys.stderr, ' - kmer size = %d \t\t(-k)' % args.ksize
+ print>>sys.stderr, ' - n hashes = %d \t\t(-N)' % args.n_hashes
+ print>>sys.stderr, ' - min hashsize = %-5.2g \t(-x)' % args.min_hashsize
+ print>>sys.stderr, ' - paired = %s \t\t(-p)' % args.paired
+ print>>sys.stderr, ''
+ print>>sys.stderr, 'Estimated memory usage is %.2g bytes (n_hashes x min_hashsize)' % (
+ args.n_hashes * args.min_hashsize)
+ print>>sys.stderr, '-' * 8
K = args.ksize
HT_SIZE = args.min_hashsize
@@ -84,11 +82,11 @@ def main():
batch_size = 2
if args.loadhash:
- print('loading hashtable from', args.loadhash)
+ print 'loading hashtable from', args.loadhash
ht = khmer.load_counting_hash(args.loadhash)
else:
- print('making hashtable')
- ht = khmer.CountingHash(K, HT_SIZE, N_HT)
+ print 'making hashtable'
+ ht = khmer.new_counting_hash(K, HT_SIZE, N_HT)
total = 0
discarded = 0
@@ -100,13 +98,13 @@ def main():
n = -1
for n, batch in enumerate(batchwise(screed.open(input_filename), batch_size)):
if n > 0 and n % 100000 == 0:
- print('... kept', total - discarded, 'of', total, ', or', \
- int(100. - discarded / float(total) * 100.), '%')
- print('... in file', input_filename)
+ print '... kept', total - discarded, 'of', total, ', or', \
+ int(100. - discarded / float(total) * 100.), '%'
+ print '... in file', input_filename
if report_fp:
- print(total, total - discarded, \
- 1. - (discarded / float(total)), file=report_fp)
+ print>>report_fp, total, total - discarded, \
+ 1. - (discarded / float(total))
report_fp.flush()
total += batch_size
@@ -114,8 +112,8 @@ def main():
# If in paired mode, check that the reads are properly interleaved
if args.paired:
if not validpair(batch[0], batch[1]):
- print('Error: Improperly interleaved pairs %s %s' % (
- batch[0].name, batch[1].name), file=sys.stderr)
+ print >>sys.stderr, 'Error: Improperly interleaved pairs %s %s' % (
+ batch[0].name, batch[1].name)
sys.exit(-1)
# Emit the batch of reads if any read passes the filter
@@ -152,27 +150,27 @@ def main():
discarded += batch_size
if -1 < n:
- print('DONE with', input_filename, '; kept', total - discarded, 'of',\
- total, 'or', int(100. - discarded / float(total) * 100.), '%')
- print('output in', output_name)
+ print 'DONE with', input_filename, '; kept', total - discarded, 'of',\
+ total, 'or', int(100. - discarded / float(total) * 100.), '%'
+ print 'output in', output_name
else:
- print('SKIPPED empty file', input_filename)
+ print 'SKIPPED empty file', input_filename
if args.savehash:
- print('Saving hashfile through', input_filename)
- print('...saving to', args.savehash)
+ print 'Saving hashfile through', input_filename
+ print '...saving to', args.savehash
ht.save(args.savehash)
# Change 0.2 only if you really grok it. HINT: You don't.
fp_rate = khmer.calc_expected_collisions(ht)
- print('fp rate estimated to be %1.3f' % fp_rate)
+ print 'fp rate estimated to be %1.3f' % fp_rate
if fp_rate > 0.20:
- print("**", file=sys.stderr)
- print("** ERROR: the counting hash is too small for", file=sys.stderr)
- print("** this data set. Increase hashsize/num ht.", file=sys.stderr)
- print("**", file=sys.stderr)
- print("** Do not use these results!!", file=sys.stderr)
+ print >>sys.stderr, "**"
+ print >>sys.stderr, "** ERROR: the counting hash is too small for"
+ print >>sys.stderr, "** this data set. Increase hashsize/num ht."
+ print >>sys.stderr, "**"
+ print >>sys.stderr, "** Do not use these results!!"
sys.exit(-1)
if __name__ == '__main__':
diff --git a/sandbox/optimal_args_hashbits.py b/sandbox/optimal_args_hashbits.py
deleted file mode 100644
index 1fba596..0000000
--- a/sandbox/optimal_args_hashbits.py
+++ /dev/null
@@ -1,97 +0,0 @@
-#! /usr/bin/env python2
-#
-# This file is part of khmer, http://github.com/ged-lab/khmer/, and is
-# Copyright (C) Michigan State University, 2009-2015. It is licensed under
-# the three-clause BSD license; see doc/LICENSE.txt.
-# Contact: khmer-project at idyll.org
-#
-# pylint: disable=invalid-name,missing-docstring
-"""
-Estimate optimal arguments using hashbits counting.
-
-% python sandbox/optimal_args_hashbits.py <data1> [ <data2> <...> ]
-
-Use '-h' for parameter help.
-"""
-from __future__ import print_function
-
-import sys
-import math
-import threading
-
-import khmer
-from khmer.khmer_args import build_hashbits_args
-from khmer.khmer_args import (report_on_config, info, add_threading_args)
-from khmer.kfile import check_input_files, check_space
-from khmer.kfile import check_space
-from oxli.functions import optimal_args_output_gen as output_gen
-
-
-def get_parser():
- parser = build_hashbits_args(descr="Load sequences into the compressible "
- "graph format plus optional tagset.")
- add_threading_args(parser)
- parser.add_argument('input_filenames', metavar='input_sequence_filename',
- nargs='+', help='input FAST[AQ] sequence filename')
- return parser
-
-
-def main():
- info('optimal_args_hashbits.py', ['graph', 'SeqAn'])
- args = get_parser().parse_args()
- report_on_config(args, hashtype='hashbits')
-
-
- filenames = args.input_filenames
- base = filenames[0]
- for _ in args.input_filenames:
- check_input_files(_, False)
-
- check_space(args.input_filenames, False)
-
- print('Counting kmers from sequences in %s' % repr(filenames),
- file=sys.stderr)
-
- htable = khmer.new_hashbits(args.ksize, args.min_tablesize, args.n_tables)
- target_method = htable.consume_fasta_with_reads_parser
-
- for _, filename in enumerate(filenames):
- rparser = khmer.ReadParser(filename)
- threads = []
- print('consuming input', filename, file=sys.stderr)
- for num in xrange(args.threads):
- cur_thread = threading.Thread(
- target=target_method, args=(rparser,))
- threads.append(cur_thread)
- cur_thread.start()
-
- for thread in threads:
- thread.join()
- unique_kmers = htable.n_unique_kmers()
- print('Total number of unique k-mers: {0}'.format(unique_kmers),
- file=sys.stderr)
-
- info_optimal = open(base + '.optimal_args', 'w')
-
- fp_rate = khmer.calc_expected_collisions(htable)
- print('fp rate estimated to be %1.3f' % fp_rate, file=sys.stderr)
-
- if fp_rate > 0.15: # 0.18 is ACTUAL MAX. Do not change.
- print("**", file=sys.stderr)
- print("** ERROR: the graph structure is too small for this data set."
- "Increase table size/# tables.", file=sys.stderr)
- print("**", file=sys.stderr)
- if not False:
- sys.exit(1)
-
- to_print = output_gen(unique_kmers,fp_rate)
-
- print(to_print, file=info_optimal)
-
- print('optimal arguments were written to', base + '.optimal_args',
- file=sys.stderr)
-
-if __name__ == '__main__':
- main()
-
-# vim: set ft=python ts=4 sts=4 sw=4 et tw=79:
diff --git a/sandbox/print-stoptags.py b/sandbox/print-stoptags.py
index 1e59b44..6fc327c 100755
--- a/sandbox/print-stoptags.py
+++ b/sandbox/print-stoptags.py
@@ -1,7 +1,7 @@
-#! /usr/bin/env python
+#! /usr/bin/env python2
#
-# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
-# Copyright (C) Michigan State University, 2009-2015. It is licensed under
+# This file is part of khmer, http://github.com/ged-lab/khmer/, and is
+# Copyright (C) Michigan State University, 2009-2013. It is licensed under
# the three-clause BSD license; see LICENSE.
# Contact: khmer-project at idyll.org
#
@@ -13,7 +13,7 @@ K = 32
def main():
- ht = khmer.Hashbits(32, 1, 1)
+ ht = khmer.new_hashbits(32, 1, 1)
ht.load_stop_tags(sys.argv[1])
ht.print_stop_tags(os.path.basename(sys.argv[1]) + '.txt')
diff --git a/sandbox/print-tagset.py b/sandbox/print-tagset.py
index c861278..dbe9c77 100755
--- a/sandbox/print-tagset.py
+++ b/sandbox/print-tagset.py
@@ -1,11 +1,10 @@
-#! /usr/bin/env python
+#! /usr/bin/env python2
#
-# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
-# Copyright (C) Michigan State University, 2009-2015. It is licensed under
+# This file is part of khmer, http://github.com/ged-lab/khmer/, and is
+# Copyright (C) Michigan State University, 2009-2013. It is licensed under
# the three-clause BSD license; see LICENSE.
# Contact: khmer-project at idyll.org
#
-from __future__ import print_function
import khmer
import sys
import os
@@ -14,9 +13,9 @@ K = 32
def main():
- ht = khmer.Hashbits(32, 1, 1)
+ ht = khmer.new_hashbits(32, 1, 1)
ht.load_tagset(sys.argv[1])
- print('loaded!')
+ print 'loaded!'
ht.print_tagset(os.path.basename(sys.argv[1]) + '.txt')
diff --git a/sandbox/renumber-partitions.py b/sandbox/renumber-partitions.py
index 92d3134..7a3df7b 100755
--- a/sandbox/renumber-partitions.py
+++ b/sandbox/renumber-partitions.py
@@ -1,11 +1,10 @@
-#! /usr/bin/env python
+#! /usr/bin/env python2
#
-# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
-# Copyright (C) Michigan State University, 2009-2015. It is licensed under
+# This file is part of khmer, http://github.com/ged-lab/khmer/, and is
+# Copyright (C) Michigan State University, 2009-2013. It is licensed under
# the three-clause BSD license; see LICENSE.
# Contact: khmer-project at idyll.org
#
-from __future__ import print_function
import sys
import screed
import gzip
@@ -22,7 +21,7 @@ def main():
old_to_new = {}
for n, record in enumerate(screed.open(filename)):
if n > 0 and n % 10000 == 0:
- print('...', os.path.basename(filename), n)
+ print '...', os.path.basename(filename), n
partition = record.name.split()[-1]
name = record.name.split()[0]
@@ -34,7 +33,7 @@ def main():
outfp.write('>%s\t%d\n%s\n' % (name, new_part, record.sequence))
outfp.close()
- print('renumbered %d partitions in %s' % (len(old_to_new), filename))
+ print 'renumbered %d partitions in %s' % (len(old_to_new), filename)
if __name__ == '__main__':
diff --git a/sandbox/saturate-by-median.py b/sandbox/saturate-by-median.py
index 40aee14..8d5eba4 100755
--- a/sandbox/saturate-by-median.py
+++ b/sandbox/saturate-by-median.py
@@ -1,6 +1,6 @@
-#! /usr/bin/env python
+#! /usr/bin/env python2
#
-# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
+# This file is part of khmer, http://github.com/ged-lab/khmer/, and is
# Copyright (C) Michigan State University, 2009-2015. It is licensed under
# the three-clause BSD license; see LICENSE.
# Contact: khmer-project at idyll.org
@@ -11,17 +11,15 @@ Count saturation curve for reads with a coverage of 1, but collect
reads whether or not they have high coverage. This is better for
assessing saturation of (esp) low-coverage data sets.
"""
-from __future__ import division
-from __future__ import print_function
import sys
import screed
import os
import khmer
import textwrap
-
+from itertools import izip
from khmer.khmer_args import (build_counting_args, add_loadhash_args,
- report_on_config, info, create_countgraph)
+ report_on_config, info)
import argparse
from khmer.kfile import (check_space, check_space_for_hashtable,
check_valid_file_exists)
@@ -34,7 +32,7 @@ DEFAULT_DESIRED_COVERAGE = 1
def batchwise(coll, size):
iter_coll = iter(coll)
- return zip(*[iter_coll] * size)
+ return izip(*[iter_coll] * size)
# Returns true if the pair of records are properly pairs
@@ -63,14 +61,14 @@ def normalize_by_median(input_filename, htable, args, report_fp=None,
for index, batch in enumerate(batchwise(screed.open(
input_filename), batch_size)):
if index > 0 and index % report_frequency == 0:
- print('... kept {kept} of {total} or {perc:2}%'.format(
+ print '... kept {kept} of {total} or {perc:2}%'.format(
kept=total - discarded, total=total,
- perc=int(100. - discarded / float(total) * 100.)))
- print('... in file', input_filename)
+ perc=int(100. - discarded / float(total) * 100.))
+ print '... in file', input_filename
if report_fp:
- print(total, total - discarded, \
- 1. - (discarded / float(total)), file=report_fp)
+ print >> report_fp, total, total - discarded, \
+ 1. - (discarded / float(total))
report_fp.flush()
total += batch_size
@@ -105,8 +103,8 @@ def normalize_by_median(input_filename, htable, args, report_fp=None,
def handle_error(error, input_name):
- print('** ERROR:', error, file=sys.stderr)
- print('** Failed on {name}: '.format(name=input_name), file=sys.stderr)
+ print >> sys.stderr, '** ERROR:', error
+ print >> sys.stderr, '** Failed on {name}: '.format(name=input_name)
def get_parser():
epilog = ("""
@@ -187,18 +185,19 @@ def main(): # pylint: disable=too-many-branches,too-many-statements
check_valid_file_exists(args.input_filenames)
check_space(args.input_filenames, False)
if args.savetable:
- check_space_for_hashtable(args, 'countgraph', False)
+ check_space_for_hashtable(args.n_tables * args.min_tablesize, False)
# list to save error files along with throwing exceptions
if args.force:
corrupt_files = []
if args.loadtable:
- print('loading k-mer counting table from', args.loadtable)
+ print 'loading k-mer counting table from', args.loadtable
htable = khmer.load_counting_hash(args.loadtable)
else:
- print('making countgraph')
- htable = create_countgraph(args)
+ print 'making k-mer counting table'
+ htable = khmer.new_counting_hash(args.ksize, args.min_tablesize,
+ args.n_tables)
total = 0
discarded = 0
@@ -215,37 +214,36 @@ def main(): # pylint: disable=too-many-branches,too-many-statements
except IOError as err:
handle_error(err, input_filename)
if not args.force:
- print('** Exiting!', file=sys.stderr)
+ print >> sys.stderr, '** Exiting!'
sys.exit(1)
else:
- print('*** Skipping error file, moving on...', file=sys.stderr)
+ print >> sys.stderr, '*** Skipping error file, moving on...'
corrupt_files.append(input_filename)
else:
if total_acc == 0 and discarded_acc == 0:
- print('SKIPPED empty file', input_filename)
+ print 'SKIPPED empty file', input_filename
else:
total += total_acc
discarded += discarded_acc
- print('DONE with {inp}; kept {kept} of {total} or {perc:2}%'\
+ print 'DONE with {inp}; kept {kept} of {total} or {perc:2}%'\
.format(inp=input_filename,
kept=total - discarded, total=total,
- perc=int(100. - discarded / float(total) * 100.)))
+ perc=int(100. - discarded / float(total) * 100.))
if args.savetable:
- print('Saving k-mer counting table through', input_filename)
- print('...saving to', args.savetable)
+ print 'Saving k-mer counting table through', input_filename
+ print '...saving to', args.savetable
htable.save(args.savetable)
# re: threshold, see Zhang et al.,
# http://arxiv.org/abs/1309.2975
fp_rate = khmer.calc_expected_collisions(htable, args.force, max_false_pos=.8)
- print('fp rate estimated to be {fpr:1.3f}'.format(fpr=fp_rate))
+ print 'fp rate estimated to be {fpr:1.3f}'.format(fpr=fp_rate)
if args.force and len(corrupt_files) > 0:
- print("** WARNING: Finished with errors!", file=sys.stderr)
- print("** IOErrors occurred in the following files:", file=sys.stderr)
- print("\t", " ".join(corrupt_files), file=sys.stderr)
-
+ print >> sys.stderr, "** WARNING: Finished with errors!"
+ print >> sys.stderr, "** IOErrors occurred in the following files:"
+ print >> sys.stderr, "\t", " ".join(corrupt_files)
if __name__ == '__main__':
main()
diff --git a/sandbox/shuffle-reverse-rotary.py b/sandbox/shuffle-reverse-rotary.py
index 70d4d92..9a289bf 100755
--- a/sandbox/shuffle-reverse-rotary.py
+++ b/sandbox/shuffle-reverse-rotary.py
@@ -1,8 +1,7 @@
-from __future__ import print_function
-#! /usr/bin/env python
+#! /usr/bin/env python2
#
-# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
-# Copyright (C) Michigan State University, 2009-2015. It is licensed under
+# This file is part of khmer, http://github.com/ged-lab/khmer/, and is
+# Copyright (C) Michigan State University, 2009-2013. It is licensed under
# the three-clause BSD license; see LICENSE.
# Contact: khmer-project at idyll.org
#
@@ -31,12 +30,12 @@ def main():
for record in screed.open(filename):
total += 1
if total % 10000 == 0:
- print('...', total)
+ print '...', total
loc = total % ROTARY_SIZE
fp_d[loc].write('>%s\n%s\n' % (record.name, record.sequence))
- print('reverse-rotary shuffled %d sequences into %d files (%s.NNN)' % \
- (total, ROTARY_SIZE, prefix))
+ print 'reverse-rotary shuffled %d sequences into %d files (%s.NNN)' % \
+ (total, ROTARY_SIZE, prefix)
if __name__ == '__main__':
diff --git a/sandbox/slice-reads-by-coverage.py b/sandbox/slice-reads-by-coverage.py
index 2093aa6..6b4896b 100755
--- a/sandbox/slice-reads-by-coverage.py
+++ b/sandbox/slice-reads-by-coverage.py
@@ -1,10 +1,9 @@
-#! /usr/bin/env python
-# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
-# Copyright (C) Michigan State University, 2014-2015. It is licensed under
+#! /usr/bin/env python2
+# This file is part of khmer, http://github.com/ged-lab/khmer/, and is
+# Copyright (C) Michigan State University, 2014. It is licensed under
# the three-clause BSD license; see LICENSE.
# Contact: khmer-project at idyll.org
-from __future__ import print_function
import argparse
import screed
import sys
@@ -27,16 +26,16 @@ def main():
parser.add_argument('output_readfile')
args = parser.parse_args()
- print('min_coverage: %s' % args.min_coverage, file=sys.stderr)
- print('max_coverage: %s' % args.max_coverage, file=sys.stderr)
+ print >>sys.stderr, 'min_coverage: %s' % args.min_coverage
+ print >>sys.stderr, 'max_coverage: %s' % args.max_coverage
if not (args.min_coverage or args.max_coverage):
- print("neither min nor max coverage specified!? exiting!", file=sys.stderr)
+ print >>sys.stderr, "neither min nor max coverage specified!? exiting!"
sys.exit(1)
if args.min_coverage and args.max_coverage and \
args.max_coverage < args.min_coverage:
- print("min_coverage > max_coverage!? exiting!", file=sys.stderr)
+ print >>sys.stderr, "min_coverage > max_coverage!? exiting!"
sys.exit(1)
htable = khmer.load_counting_hash(args.input_counting_table)
@@ -47,7 +46,7 @@ def main():
n = 0
for n, record in enumerate(screed.open(args.input_readfile)):
if n % 100000 == 0:
- print('...', n, n_kept, file=sys.stderr)
+ print >>sys.stderr, '...', n, n_kept
seq = record.sequence.upper()
seq = seq.replace('N', 'A')
@@ -69,7 +68,7 @@ def main():
output_fp.write(output_single(record))
- print('consumed %d reads; kept %d' % (n, n_kept), file=sys.stderr)
+ print >>sys.stderr, 'consumed %d reads; kept %d' % (n, n_kept)
if __name__ == '__main__':
main()
diff --git a/sandbox/split-fasta.py b/sandbox/split-fasta.py
index bf395da..0339693 100755
--- a/sandbox/split-fasta.py
+++ b/sandbox/split-fasta.py
@@ -1,11 +1,10 @@
-#! /usr/bin/env python
+#! /usr/bin/env python2
#
-# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
-# Copyright (C) Michigan State University, 2009-2015. It is licensed under
+# This file is part of khmer, http://github.com/ged-lab/khmer/, and is
+# Copyright (C) Michigan State University, 2009-2013. It is licensed under
# the three-clause BSD license; see LICENSE.
# Contact: khmer-project at idyll.org
#
-from __future__ import print_function
import sys
import screed
@@ -18,12 +17,12 @@ def main():
division = -1
for n, record in enumerate(screed.open(filename)):
if n % 100000 == 0:
- print('...', n)
+ print '...', n
if n % size == 0:
division += 1
new_name = '%s.%04d.fa' % (prefix, division)
- print('opening', new_name)
+ print 'opening', new_name
fp = open(new_name, 'w')
fp.write('>%s\n%s\n' % (record['name'], record['sequence']))
diff --git a/sandbox/split-sequences-by-length.py b/sandbox/split-sequences-by-length.py
index 8e5aeb3..e83c0fe 100755
--- a/sandbox/split-sequences-by-length.py
+++ b/sandbox/split-sequences-by-length.py
@@ -1,7 +1,7 @@
-#! /usr/bin/env python
+#! /usr/bin/env python2
#
-# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
-# Copyright (C) Michigan State University, 2009-2015. It is licensed under
+# This file is part of khmer, http://github.com/ged-lab/khmer/, and is
+# Copyright (C) Michigan State University, 2009-2013. It is licensed under
# the three-clause BSD license; see LICENSE.
# Contact: khmer-project at idyll.org
#
@@ -13,7 +13,6 @@ hash table. Output sequences will be placed in 'infile.abundfilt'.
Use '-h' for parameter help.
"""
-from __future__ import print_function
import sys
import screed.fasta
import os
@@ -49,12 +48,12 @@ def main():
n = 0
for filename in filenames:
- print('opening')
+ print 'opening'
for record in screed.open(filename):
out.save(record.name, record.sequence)
n += 1
if n % 10000 == 0:
- print('...', n)
+ print '...', n
if __name__ == '__main__':
main()
diff --git a/sandbox/stoptag-abundance-hist.py b/sandbox/stoptag-abundance-hist.py
index 616a9f4..b1c3d8a 100755
--- a/sandbox/stoptag-abundance-hist.py
+++ b/sandbox/stoptag-abundance-hist.py
@@ -1,11 +1,10 @@
-#! /usr/bin/env python
+#! /usr/bin/env python2
#
-# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
-# Copyright (C) Michigan State University, 2009-2015. It is licensed under
+# This file is part of khmer, http://github.com/ged-lab/khmer/, and is
+# Copyright (C) Michigan State University, 2009-2013. It is licensed under
# the three-clause BSD license; see LICENSE.
# Contact: khmer-project at idyll.org
#
-from __future__ import print_function
import sys
import khmer
import os
@@ -34,7 +33,7 @@ def main():
d[count] = d.get(count, 0) + 1
if count > 1000:
- print(sequence, count, file=outabund)
+ print >>outabund, sequence, count
outfp = open(figure + '.countshist', 'w')
sofar = 0
@@ -42,7 +41,7 @@ def main():
for k in sorted(d.keys()):
sofar += d[k]
sofar_cumu += k * d[k]
- print(k, d[k], sofar, sofar_cumu, file=outfp)
+ print >>outfp, k, d[k], sofar, sofar_cumu
hist(counts, normed=True, cumulative=True, bins=100, range=(1, 1000))
savefig(figure)
diff --git a/sandbox/stoptags-by-position.py b/sandbox/stoptags-by-position.py
index 1b92fa6..653b441 100755
--- a/sandbox/stoptags-by-position.py
+++ b/sandbox/stoptags-by-position.py
@@ -1,8 +1,7 @@
-from __future__ import print_function
-#! /usr/bin/env python
+#! /usr/bin/env python2
#
-# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
-# Copyright (C) Michigan State University, 2009-2015. It is licensed under
+# This file is part of khmer, http://github.com/ged-lab/khmer/, and is
+# Copyright (C) Michigan State University, 2009-2013. It is licensed under
# the three-clause BSD license; see LICENSE.
# Contact: khmer-project at idyll.org
#
@@ -14,7 +13,7 @@ K = 32
def main():
- ht = khmer.Hashbits(K, 1, 1)
+ ht = khmer.new_hashbits(K, 1, 1)
x = [0] * 255
y = [0] * 255
@@ -39,7 +38,7 @@ def main():
for i, (n, m) in enumerate(zip(x, y)):
if m:
- print('%d,%d,%d' % (i, n, m))
+ print '%d,%d,%d' % (i, n, m)
if __name__ == '__main__':
diff --git a/sandbox/strip-partition.py b/sandbox/strip-partition.py
index ab972ab..5dbd82d 100755
--- a/sandbox/strip-partition.py
+++ b/sandbox/strip-partition.py
@@ -1,11 +1,10 @@
-#! /usr/bin/env python
+#! /usr/bin/env python2
#
-# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
-# Copyright (C) Michigan State University, 2009-2015. It is licensed under
+# This file is part of khmer, http://github.com/ged-lab/khmer/, and is
+# Copyright (C) Michigan State University, 2009-2013. It is licensed under
# the three-clause BSD license; see LICENSE.
# Contact: khmer-project at idyll.org
#
-from __future__ import print_function
import screed
import sys
@@ -17,7 +16,7 @@ def main():
name = name.split()[0]
- print('>%s\n%s' % (name, sequence,))
+ print '>%s\n%s' % (name, sequence,)
if __name__ == '__main__':
diff --git a/sandbox/subset-report.py b/sandbox/subset-report.py
index fe230e6..dd580d8 100755
--- a/sandbox/subset-report.py
+++ b/sandbox/subset-report.py
@@ -1,11 +1,10 @@
-#! /usr/bin/env python
+#! /usr/bin/env python2
#
-# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
-# Copyright (C) Michigan State University, 2009-2015. It is licensed under
+# This file is part of khmer, http://github.com/ged-lab/khmer/, and is
+# Copyright (C) Michigan State University, 2009-2013. It is licensed under
# the three-clause BSD license; see LICENSE.
# Contact: khmer-project at idyll.org
#
-from __future__ import print_function
import khmer
import sys
import gc
@@ -17,21 +16,21 @@ K = 32
def main():
subset_filenames = sys.argv[1:]
- ht = khmer.Hashbits(K, 1, 1)
+ ht = khmer.new_hashbits(K, 1, 1)
for filename in subset_filenames:
- print('--')
- print('partition map:', filename)
+ print '--'
+ print 'partition map:', filename
subset = ht.load_subset_partitionmap(filename)
n_part, n_orphan = ht.subset_count_partitions(subset)
- print('num partitions:', n_part)
- print('num orphans:', n_orphan)
+ print 'num partitions:', n_part
+ print 'num orphans:', n_orphan
(dist, n_unassigned) = ht.subset_partition_size_distribution(subset)
for (size, count) in dist:
- print(size, count)
- print('%d unassigned tags' % n_unassigned)
+ print size, count
+ print '%d unassigned tags' % n_unassigned
- print('--')
+ print '--'
if __name__ == '__main__':
diff --git a/sandbox/sweep-files.py b/sandbox/sweep-files.py
index 6b44ea6..74f0675 100755
--- a/sandbox/sweep-files.py
+++ b/sandbox/sweep-files.py
@@ -1,6 +1,6 @@
-#! /usr/bin/env python
+#! /usr/bin/env python2
#
-# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
+# This file is part of khmer, http://github.com/ged-lab/khmer/, and is
# Copyright (C) Michigan State University, 2009-2015. It is licensed under
# the three-clause BSD license; see LICENSE. Contact: ctb at msu.edu
#
@@ -12,7 +12,6 @@ Find all reads connected to the given contigs on a per-partition basis.
% sweep-files.py -r <range> --db <fasta/q files> \
--query <fasta/q files separate>
"""
-from __future__ import print_function
EPILOG = """
Output will be a collection of fasta/q files, each corresponding to a database
@@ -108,7 +107,7 @@ def main():
if args.ksize < MIN_KSIZE:
args.ksize = MIN_KSIZE
- report_on_config(args, hashtype='nodegraph')
+ report_on_config(args, hashtype='hashbits')
K = args.ksize
HT_SIZE = args.min_tablesize
@@ -122,7 +121,7 @@ def main():
# de Bruin graph; open a file and output queue for each file as well.
ht = khmer.LabelHash(K, HT_SIZE, N_HT)
try:
- print('consuming and labeling input sequences...', file=sys.stderr)
+ print >>sys.stderr, 'consuming and labeling input sequences...'
for i, dbfile in enumerate(args.db):
@@ -133,17 +132,18 @@ def main():
for n, record in enumerate(screed.open(dbfile)):
if n % 50000 == 0:
- print('...consumed {n} sequences...'.format(n=n), file=sys.stderr)
+ print >>sys.stderr, \
+ '...consumed {n} sequences...'.format(n=n)
ht.consume_sequence_and_tag_with_labels(record.sequence, i)
except IOError as e:
- print('!! ERROR: !!', e, file=sys.stderr)
- print('...error setting up outputs. exiting...', file=sys.stderr)
+ print >>sys.stderr, '!! ERROR: !!', e
+ print >>sys.stderr, '...error setting up outputs. exiting...'
- print('done consuming input sequence. \
+ print >>sys.stderr, 'done consuming input sequence. \
added {t} tags and {l} labels...' \
- .format(t=ht.n_tags(), l=ht.n_labels()), file=sys.stderr)
+ .format(t=ht.n_tags(), l=ht.n_labels())
n_orphaned = 0
n_labeled = 0
@@ -152,20 +152,21 @@ def main():
# Iterate through all the reads and check for the labels with which they
# intersect. Queue to the corresponding label when found.
for read_file in args.query:
- print('** sweeping {read_file} for labels...'.format(
- read_file=read_file), file=sys.stderr)
+ print >>sys.stderr, '** sweeping {read_file} for labels...'.format(
+ read_file=read_file)
try:
read_fp = screed.open(read_file)
except IOError as error:
- print('!! ERROR: !!', error, file=sys.stderr)
- print('*** Could not open {fn}, skipping...'.format(
- fn=read_file), file=sys.stderr)
+ print >>sys.stderr, '!! ERROR: !!', error
+ print >>sys.stderr, '*** Could not open {fn}, skipping...'.format(
+ fn=read_file)
else:
for n, record in enumerate(read_fp):
if n % 50000 == 0 and n > 0:
- print('\tswept {n} reads [{nc} labeled, {no} orphaned]' \
+ print >>sys.stderr, \
+ '\tswept {n} reads [{nc} labeled, {no} orphaned]' \
.format(n=n, nc=n_labeled,
- no=n_orphaned), file=sys.stderr)
+ no=n_orphaned)
seq = record.sequence
try:
labels = ht.sweep_label_neighborhood(seq, traversal_range)
@@ -183,19 +184,19 @@ def main():
else:
n_orphaned += 1
- print('** End of file {fn}...'.format(fn=read_file), file=sys.stderr)
+ print >>sys.stderr, '** End of file {fn}...'.format(fn=read_file)
read_fp.close()
# gotta output anything left in the buffers at the end!
- print('** End of run...', file=sys.stderr)
- for q in list(outputs.values()):
+ print >>sys.stderr, '** End of run...'
+ for q in outputs.values():
q.clear()
- print('swept {n_reads}...'.format(
- n_reads=n_labeled + n_orphaned), file=sys.stderr)
- print('...with {nc} labeled and {no} orphaned'.format(
- nc=n_labeled, no=n_orphaned), file=sys.stderr)
- print('...and {nmc} multilabeled'.format(nmc=n_mlabeled), file=sys.stderr)
+ print >>sys.stderr, 'swept {n_reads}...'.format(
+ n_reads=n_labeled + n_orphaned)
+ print >>sys.stderr, '...with {nc} labeled and {no} orphaned'.format(
+ nc=n_labeled, no=n_orphaned)
+ print >>sys.stderr, '...and {nmc} multilabeled'.format(nmc=n_mlabeled)
if __name__ == '__main__':
main()
diff --git a/sandbox/sweep-out-reads-with-contigs.py b/sandbox/sweep-out-reads-with-contigs.py
index f053f62..29b3e3b 100755
--- a/sandbox/sweep-out-reads-with-contigs.py
+++ b/sandbox/sweep-out-reads-with-contigs.py
@@ -1,11 +1,10 @@
-#! /usr/bin/env python
+#! /usr/bin/env python2
#
-# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
-# Copyright (C) Michigan State University, 2009-2015. It is licensed under
+# This file is part of khmer, http://github.com/ged-lab/khmer/, and is
+# Copyright (C) Michigan State University, 2009-2013. It is licensed under
# the three-clause BSD license; see LICENSE.
# Contact: khmer-project at idyll.org
#
-from __future__ import print_function
import sys
import khmer
import os.path
@@ -22,18 +21,18 @@ def main():
outfile = sys.argv[3]
# create a hashbits data structure
- ht = khmer.Hashbits(K, 1, 1)
+ ht = khmer.new_hashbits(K, 1, 1)
# tag every k-mer in the contigs
ht._set_tag_density(0)
# load contigs, connect into N partitions
- print('loading contigs from', contigfile)
+ print 'loading contigs from', contigfile
ht.consume_fasta_and_tag(contigfile)
subset = ht.do_subset_partition(0, 0)
ht.merge_subset(subset)
- print('outputting contig-partitioned reads to', outfile)
+ print 'outputting contig-partitioned reads to', outfile
ht.output_partitions(readsfile, outfile, True)
diff --git a/sandbox/sweep-reads.py b/sandbox/sweep-reads.py
index fbf2ccb..a344938 100755
--- a/sandbox/sweep-reads.py
+++ b/sandbox/sweep-reads.py
@@ -1,14 +1,11 @@
-from __future__ import print_function, unicode_literals
-#! /usr/bin/env python
+#! /usr/bin/env python2
#
-# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
+# This file is part of khmer, http://github.com/ged-lab/khmer/, and is
# Copyright (C) Michigan State University, 2009-2015. It is licensed under
# the three-clause BSD license; see LICENSE. Contact: ctb at msu.edu
#
# pylint: disable=invalid-name,missing-docstring,no-member
-from io import open
-
from khmer import utils
"""
@@ -50,7 +47,7 @@ DEFAULT_BUFFER_SIZE = 10
DEFAULT_OUT_PREF = 'reads'
DEFAULT_RANGE = -1
-MAX_HSIZE = 4e7
+MIN_HSIZE = 4e7
MIN_KSIZE = 21
@@ -106,12 +103,12 @@ class ReadBufferManager(object):
self.num_write_errors = 0
self.num_file_errors = 0
- print('''Init new ReadBuffer [
+ print >>sys.stderr, '''Init new ReadBuffer [
Max Buffers: {num_bufs}
Max Reads: {max_reads}
Buffer flush: {buf_flush}
]'''.format(num_bufs=self.max_buffers, max_reads=self.max_reads,
- buf_flush=self.buffer_flush), file=sys.stderr)
+ buf_flush=self.buffer_flush)
def flush_buffer(self, buf_id):
fn = '{prefix}_{buffer_id}.{ext}'.format(prefix=self.output_pref,
@@ -122,9 +119,9 @@ class ReadBufferManager(object):
try:
outfp = open(fpath, 'a')
except IOError as _:
- print('!! ERROR: {_} !!'.format(_=_), file=sys.stderr)
- print('*** Failed to open {fn} for \
- buffer flush'.format(fn=fpath), file=sys.stderr)
+ print >>sys.stderr, '!! ERROR: {_} !!'.format(_=_)
+ print >>sys.stderr, '*** Failed to open {fn} for \
+ buffer flush'.format(fn=fpath)
self.num_file_errors += 1
else:
outfp.write(buf.flush())
@@ -145,16 +142,16 @@ class ReadBufferManager(object):
self.cur_reads += 1
if self.cur_reads > self.max_reads:
- print('** Reached max num reads...', file=sys.stderr)
+ print >>sys.stderr, '** Reached max num reads...'
self.flush_all()
if len(self.buffers) > self.max_buffers:
# self.clean_buffers(2)
- print('** Reached max num buffers...', file=sys.stderr)
+ print >>sys.stderr, '** Reached max num buffers...'
self.flush_all()
def flush_all(self):
- print('*** Flushing all to files...', file=sys.stderr)
- buf_ids = list(self.buffers.keys())
+ print >>sys.stderr, '*** Flushing all to files...'
+ buf_ids = self.buffers.keys()
for buf_id in buf_ids:
self.flush_buffer(buf_id)
assert self.cur_reads == 0
@@ -208,15 +205,15 @@ def main():
parser = get_parser()
args = parser.parse_args()
- if args.max_tablesize < MAX_HSIZE:
- args.max_tablesize = MAX_HSIZE
+ if args.min_tablesize < MIN_HSIZE:
+ args.min_tablesize = MIN_HSIZE
if args.ksize < MIN_KSIZE:
args.ksize = MIN_KSIZE
- report_on_config(args, hashtype='nodegraph')
+ report_on_config(args, hashtype='hashbits')
K = args.ksize
- HT_SIZE = args.max_tablesize
+ HT_SIZE = args.min_tablesize
N_HT = args.n_tables
traversal_range = args.traversal_range
@@ -242,7 +239,7 @@ def main():
# figure out input file type (FA/FQ) -- based on first file
ix = iter(screed.open(args.input_files[0]))
- record = next(ix)
+ record = ix.next()
del ix
extension = 'fa'
@@ -255,19 +252,21 @@ def main():
# consume the partitioned fasta with which to label the graph
ht = khmer.LabelHash(K, HT_SIZE, N_HT)
try:
- print('consuming input sequences...', file=sys.stderr)
+ print >>sys.stderr, 'consuming input sequences...'
if args.label_by_pid:
- print('...labeling by partition id (pid)', file=sys.stderr)
+ print >>sys.stderr, '...labeling by partition id (pid)'
ht.consume_partitioned_fasta_and_tag_with_labels(input_fastp)
elif args.label_by_seq:
- print('...labeling by sequence', file=sys.stderr)
+ print >>sys.stderr, '...labeling by sequence'
for n, record in enumerate(screed.open(input_fastp)):
if n % 50000 == 0:
- print('...consumed {n} sequences...'.format(n=n), file=sys.stderr)
+ print >>sys.stderr, \
+ '...consumed {n} sequences...'.format(n=n)
ht.consume_sequence_and_tag_with_labels(record.sequence, n)
else:
- print('...labeling to create groups of size {s}'.format(
- s=args.group_size), file=sys.stderr)
+ print >>sys.stderr, \
+ '...labeling to create groups of size {s}'.format(
+ s=args.group_size)
label = -1
g = 0
try:
@@ -284,25 +283,25 @@ def main():
pref=output_pref, g=g,
ext=extension), 'wb')
if n % 50000 == 0:
- print('...consumed {n} sequences...'.format(n=n), file=sys.stderr)
+ print >>sys.stderr, \
+ '...consumed {n} sequences...'.format(n=n)
ht.consume_sequence_and_tag_with_labels(record.sequence,
label)
write_record(record, outfp)
-
+
except IOError as e:
- print('!! ERROR !!', e, file=sys.stderr)
- print('...error splitting input. exiting...', file=sys.stderr)
+ print >>sys.stderr, '!! ERROR !!', e
+ print >>sys.stderr, '...error splitting input. exiting...'
except IOError as e:
- print('!! ERROR: !!', e, file=sys.stderr)
- print('...error consuming \
- {i}. exiting...'.format(i=input_fastp), file=sys.stderr)
+ print >>sys.stderr, '!! ERROR: !!', e
+ print >>sys.stderr, '...error consuming \
+ {i}. exiting...'.format(i=input_fastp)
- print('done consuming input sequence. \
+ print >>sys.stderr, 'done consuming input sequence. \
added {t} tags and {l} \
- labels...'.format(t=ht.graph.n_tags(),
- l=ht.n_labels()))
+ labels...'.format(t=ht.n_tags(), l=ht.n_labels())
label_dict = defaultdict(int)
label_number_dist = []
@@ -314,27 +313,27 @@ def main():
total_t = time.clock()
start_t = time.clock()
for read_file in args.input_files:
- print('** sweeping {read_file} for labels...'.format(
- read_file=read_file), file=sys.stderr)
+ print >>sys.stderr, '** sweeping {read_file} for labels...'.format(
+ read_file=read_file)
file_t = 0.0
try:
read_fp = screed.open(read_file)
except IOError as error:
- print('!! ERROR: !!', error, file=sys.stderr)
- print('*** Could not open {fn}, skipping...'.format(
- fn=read_file), file=sys.stderr)
+ print >>sys.stderr, '!! ERROR: !!', error
+ print >>sys.stderr, '*** Could not open {fn}, skipping...'.format(
+ fn=read_file)
else:
for _, record in enumerate(read_fp):
if _ % 50000 == 0:
end_t = time.clock()
batch_t = end_t - start_t
file_t += batch_t
- print('\tswept {n} reads [{nc} labeled, \
+ print >>sys.stderr, '\tswept {n} reads [{nc} labeled, \
{no} orphaned] \
** {sec}s ({sect}s total)' \
.format(n=_, nc=n_labeled,
no=n_orphaned,
- sec=batch_t, sect=file_t), file=sys.stderr)
+ sec=batch_t, sect=file_t)
start_t = time.clock()
seq = record.sequence
name = record.name
@@ -361,37 +360,37 @@ def main():
n_orphaned += 1
output_buffer.queue(seq_str, 'orphaned')
label_dict['orphaned'] += 1
- print('** End of file {fn}...'.format(fn=read_file), file=sys.stderr)
+ print >>sys.stderr, '** End of file {fn}...'.format(fn=read_file)
output_buffer.flush_all()
read_fp.close()
# gotta output anything left in the buffers at the end!
- print('** End of run...', file=sys.stderr)
+ print >>sys.stderr, '** End of run...'
output_buffer.flush_all()
total_t = time.clock() - total_t
if output_buffer.num_write_errors > 0 or output_buffer.num_file_errors > 0:
- print('! WARNING: Sweep finished with errors !', file=sys.stderr)
- print('** {writee} reads not written'.format(
- writee=output_buffer.num_write_errors), file=sys.stderr)
- print('** {filee} errors opening files'.format(
- filee=output_buffer.num_file_errors), file=sys.stderr)
-
- print('swept {n_reads} for labels...'.format(
- n_reads=n_labeled + n_orphaned), file=sys.stderr)
- print('...with {nc} labeled and {no} orphaned'.format(
- nc=n_labeled, no=n_orphaned), file=sys.stderr)
- print('...and {nmc} multilabeled'.format(nmc=n_mlabeled), file=sys.stderr)
-
- print('** outputting label number distribution...', file=sys.stderr)
+ print >>sys.stderr, '! WARNING: Sweep finished with errors !'
+ print >>sys.stderr, '** {writee} reads not written'.format(
+ writee=output_buffer.num_write_errors)
+ print >>sys.stderr, '** {filee} errors opening files'.format(
+ filee=output_buffer.num_file_errors)
+
+ print >>sys.stderr, 'swept {n_reads} for labels...'.format(
+ n_reads=n_labeled + n_orphaned)
+ print >>sys.stderr, '...with {nc} labeled and {no} orphaned'.format(
+ nc=n_labeled, no=n_orphaned)
+ print >>sys.stderr, '...and {nmc} multilabeled'.format(nmc=n_mlabeled)
+
+ print >>sys.stderr, '** outputting label number distribution...'
fn = os.path.join(outdir, '{pref}.dist.txt'.format(pref=output_pref))
- with open(fn, 'w', encoding='utf-8') as outfp:
+ with open(fn, 'wb') as outfp:
for nc in label_number_dist:
outfp.write('{nc}\n'.format(nc=nc))
fn = os.path.join(outdir, '{pref}.counts.csv'.format(pref=output_pref))
- print('** outputting label read counts...', file=sys.stderr)
- with open(fn, 'w', encoding='utf-8') as outfp:
+ print >>sys.stderr, '** outputting label read counts...'
+ with open(fn, 'wb') as outfp:
for k in label_dict:
outfp.write('{l},{c}\n'.format(l=k, c=label_dict[k]))
diff --git a/sandbox/sweep-reads2.py b/sandbox/sweep-reads2.py
index 38d6e6a..4ccea30 100755
--- a/sandbox/sweep-reads2.py
+++ b/sandbox/sweep-reads2.py
@@ -1,7 +1,7 @@
-#! /usr/bin/env python
+#! /usr/bin/env python2
#
-# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
-# Copyright (C) Michigan State University, 2009-2015. It is licensed under
+# This file is part of khmer, http://github.com/ged-lab/khmer/, and is
+# Copyright (C) Michigan State University, 2009-2013. It is licensed under
# the three-clause BSD license; see LICENSE.
# Contact: khmer-project at idyll.org
#
@@ -14,13 +14,12 @@ Results end up in <search reads>.sweep2.
Use '-h' for parameter help.
"""
-from __future__ import print_function
import sys
import khmer
import os.path
import screed
-from khmer.khmer_args import (build_hashbits_args, DEFAULT_MAX_TABLESIZE)
+from khmer.khmer_args import (build_hashbits_args, DEFAULT_MIN_TABLESIZE)
def main():
@@ -31,21 +30,21 @@ def main():
args = parser.parse_args()
if not args.quiet:
- if args.min_hashsize == DEFAULT_MAX_TABLESIZE:
- print("** WARNING: hashsize is default! " \
+ if args.min_hashsize == DEFAULT_MIN_HASHSIZE:
+ print >>sys.stderr, "** WARNING: hashsize is default! " \
"You absodefly want to increase this!\n** " \
- "Please read the docs!", file=sys.stderr)
-
- print('\nPARAMETERS:', file=sys.stderr)
- print(' - kmer size = %d \t\t(-k)' % args.ksize, file=sys.stderr)
- print(' - n hashes = %d \t\t(-N)' % args.n_hashes, file=sys.stderr)
- print(' - min hashsize = %-5.2g \t(-x)' % \
- args.min_hashsize, file=sys.stderr)
- print('', file=sys.stderr)
- print('Estimated memory usage is %.2g bytes ' \
+ "Please read the docs!"
+
+ print >>sys.stderr, '\nPARAMETERS:'
+ print >>sys.stderr, ' - kmer size = %d \t\t(-k)' % args.ksize
+ print >>sys.stderr, ' - n hashes = %d \t\t(-N)' % args.n_hashes
+ print >>sys.stderr, ' - min hashsize = %-5.2g \t(-x)' % \
+ args.min_hashsize
+ print >>sys.stderr, ''
+ print >>sys.stderr, 'Estimated memory usage is %.2g bytes ' \
'(n_hashes x min_hashsize / 8)' % (
- args.n_hashes * args.min_hashsize / 8.), file=sys.stderr)
- print('-' * 8, file=sys.stderr)
+ args.n_hashes * args.min_hashsize / 8.)
+ print >>sys.stderr, '-' * 8
K = args.ksize
HT_SIZE = args.min_hashsize
@@ -58,13 +57,13 @@ def main():
outfp = open(outfile, 'w')
# create a hashbits data structure
- ht = khmer.Hashbits(K, HT_SIZE, N_HT)
+ ht = khmer.new_hashbits(K, HT_SIZE, N_HT)
# load contigs, connect into N partitions
- print('loading input reads from', inp)
+ print 'loading input reads from', inp
ht.consume_fasta(inp)
- print('starting sweep.')
+ print 'starting sweep.'
n = 0
m = 0
@@ -73,7 +72,7 @@ def main():
continue
if n % 10000 == 0:
- print('...', n, m)
+ print '...', n, m
count = ht.get_median_count(record.sequence)[0]
if count:
diff --git a/sandbox/sweep-reads3.py b/sandbox/sweep-reads3.py
index c0c5329..9e66e1f 100755
--- a/sandbox/sweep-reads3.py
+++ b/sandbox/sweep-reads3.py
@@ -1,7 +1,7 @@
-#! /usr/bin/env python
+#! /usr/bin/env python2
#
-# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
-# Copyright (C) Michigan State University, 2009-2015. It is licensed under
+# This file is part of khmer, http://github.com/ged-lab/khmer/, and is
+# Copyright (C) Michigan State University, 2009-2013. It is licensed under
# the three-clause BSD license; see LICENSE.
# Contact: khmer-project at idyll.org
#
@@ -14,13 +14,12 @@ Results end up in <search reads>.sweep3.
Use '-h' for parameter help.
"""
-from __future__ import print_function
import sys
import os.path
import screed
import khmer
-from khmer.khmer_args import (build_hashbits_args, DEFAULT_MAX_TABLESIZE)
+from khmer.khmer_args import (build_hashbits_args, DEFAULT_MIN_TABLESIZE)
def output_single(r):
@@ -38,21 +37,21 @@ def main():
args = parser.parse_args()
if not args.quiet:
- if args.min_hashsize == DEFAULT_MAX_TABLESIZE:
- print("** WARNING: hashsize is default! " \
+ if args.min_hashsize == DEFAULT_MIN_HASHSIZE:
+ print >>sys.stderr, "** WARNING: hashsize is default! " \
"You absodefly want to increase this!\n** " \
- "Please read the docs!", file=sys.stderr)
-
- print('\nPARAMETERS:', file=sys.stderr)
- print(' - kmer size = %d \t\t(-k)' % args.ksize, file=sys.stderr)
- print(' - n hashes = %d \t\t(-N)' % args.n_hashes, file=sys.stderr)
- print(' - min hashsize = %-5.2g \t(-x)' % \
- args.min_hashsize, file=sys.stderr)
- print('', file=sys.stderr)
- print('Estimated memory usage is %.2g bytes ' \
+ "Please read the docs!"
+
+ print >>sys.stderr, '\nPARAMETERS:'
+ print >>sys.stderr, ' - kmer size = %d \t\t(-k)' % args.ksize
+ print >>sys.stderr, ' - n hashes = %d \t\t(-N)' % args.n_hashes
+ print >>sys.stderr, ' - min hashsize = %-5.2g \t(-x)' % \
+ args.min_hashsize
+ print >>sys.stderr, ''
+ print >>sys.stderr, 'Estimated memory usage is %.2g bytes ' \
'(n_hashes x min_hashsize / 8)' % (
- args.n_hashes * args.min_hashsize * len(args.input_filenames) / 8.), file=sys.stderr)
- print('-' * 8, file=sys.stderr)
+ args.n_hashes * args.min_hashsize * len(args.input_filenames) / 8.)
+ print >>sys.stderr, '-' * 8
K = args.ksize
HT_SIZE = args.min_hashsize
@@ -64,7 +63,7 @@ def main():
query_list = []
for n, inp_name in enumerate(inputlist):
# create a hashbits data structure
- ht = khmer.Hashbits(K, HT_SIZE, N_HT)
+ ht = khmer.new_hashbits(K, HT_SIZE, N_HT)
outfile = os.path.basename(inp_name) + '.sweep3'
outfp = open(outfile, 'w')
@@ -74,10 +73,10 @@ def main():
ht = query_list[n][0]
# load contigs, connect into N partitions
- print('loading input reads from', inp_name)
+ print 'loading input reads from', inp_name
ht.consume_fasta(inp_name)
- print('starting sweep.')
+ print 'starting sweep.'
n = 0
m = 0
@@ -86,7 +85,7 @@ def main():
continue
if n % 10000 == 0:
- print('...', n, m)
+ print '...', n, m
for ht, outfp in query_list:
count = ht.get_median_count(record.sequence)[0]
diff --git a/sandbox/unique-kmers.py b/sandbox/unique-kmers.py
index aa78d88..6aa5b6a 100755
--- a/sandbox/unique-kmers.py
+++ b/sandbox/unique-kmers.py
@@ -1,6 +1,6 @@
-#! /usr/bin/env python
+#! /usr/bin/env python2
#
-# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
+# This file is part of khmer, http://github.com/ged-lab/khmer/, and is
# Copyright (C) Michigan State University, 2009-2015. It is licensed under
# the three-clause BSD license; see LICENSE.
# Contact: khmer-project at idyll.org
@@ -13,7 +13,6 @@ Estimate number of unique k-mers, with precision <= ERROR_RATE.
Use '-h' for parameter help.
"""
-from __future__ import print_function
import argparse
@@ -23,9 +22,8 @@ import textwrap
import khmer
from khmer.khmer_args import DEFAULT_K, info, ComboFormatter
-from oxli.functions import optimal_args_output_gen as output_gen
from khmer import __version__
-import screed
+
def get_parser():
descr = "Estimate number of unique k-mers, with precision <= ERROR_RATE."
@@ -68,9 +66,6 @@ def get_parser():
parser.add_argument('-R', '--report',
metavar='filename', type=argparse.FileType('w'))
- parser.add_argument('--stream-out', '-S', default=False,
- action='store_true')
-
parser.add_argument('input_filenames', metavar='input_sequence_filename',
help='Input FAST[AQ] sequence filename.', nargs='+')
@@ -82,39 +77,19 @@ def main():
info('unique-kmers.py', ['SeqAn', 'hll'])
args = get_parser().parse_args()
- total_hll = khmer.HLLCounter(args.error_rate, args.ksize)
+ hllcpp = khmer.HLLCounter(args.error_rate, args.ksize)
report_fp = args.report
input_filename = None
for index, input_filename in enumerate(args.input_filenames):
- hllcpp = khmer.HLLCounter(args.error_rate, args.ksize)
- for record in screed.open(input_filename):
- seq = record.sequence.upper().replace('N', 'A')
- hllcpp.consume_string(seq)
- if args.stream_out:
- write_record(record, sys.stdout)
-
- cardinality = hllcpp.estimate_cardinality()
- print('Estimated number of unique {0}-mers in {1}: {2}'.format(
- args.ksize, input_filename, cardinality),
- file=sys.stderr)
-
- if report_fp:
- print(cardinality, args.ksize, '(total)', file=report_fp)
- report_fp.flush()
- total_hll.merge(hllcpp)
-
- cardinality = total_hll.estimate_cardinality()
- print('Total estimated number of unique {0}-mers: {1}'.format(
- args.ksize, cardinality),
- file=sys.stderr)
-
- to_print = output_gen(cardinality, args.error_rate)
- print(to_print)
+ hllcpp.consume_fasta(input_filename)
+
+ cardinality = hllcpp.estimate_cardinality()
+ print >> sys.stdout, 'Estimated number of unique k-mers: {0}'.format(
+ cardinality)
if report_fp:
- print(cardinality, args.ksize, 'total', file=report_fp)
- print(to_print, file=report_fp)
+ print >> report_fp, cardinality
report_fp.flush()
if __name__ == "__main__":
diff --git a/sandbox/write-trimmomatic.py b/sandbox/write-trimmomatic.py
index 5ab61e0..49c9638 100755
--- a/sandbox/write-trimmomatic.py
+++ b/sandbox/write-trimmomatic.py
@@ -1,11 +1,10 @@
-#! /usr/bin/env python
+#! /usr/bin/env python2
#
-# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
-# Copyright (C) Michigan State University, 2009-2015. It is licensed under
+# This file is part of khmer, http://github.com/ged-lab/khmer/, and is
+# Copyright (C) Michigan State University, 2009-2013. It is licensed under
# the three-clause BSD license; see LICENSE.
# Contact: khmer-project at idyll.org
#
-from __future__ import print_function
import glob
filelist = glob.glob('*R1*.fastq.gz')
@@ -14,7 +13,7 @@ for r1 in filelist:
r2 = r1.replace('R1', 'R2')
final_pe = r1[:-9] + '.pe.fq.gz'
final_se = r1[:-9] + '.se.fq.gz'
- print("""\
+ print """\
mkdir trim
cd trim
java -jar /usr/local/bin/trimmomatic-0.30.jar PE ../%s ../%s s1_pe s1_se s2_pe s2_se ILLUMINACLIP:/usr/local/share/adapters/TruSeq3-PE.fa:2:30:10
@@ -25,4 +24,4 @@ cd ..
rm -r ./trim/
chmod u-w %s %s
-""" % (r1, r2, final_pe, final_se, final_pe, final_se))
+""" % (r1, r2, final_pe, final_se, final_pe, final_se)
diff --git a/scripts/abundance-dist-single.py b/scripts/abundance-dist-single.py
index 10d2109..f719a5a 100755
--- a/scripts/abundance-dist-single.py
+++ b/scripts/abundance-dist-single.py
@@ -1,6 +1,6 @@
-#! /usr/bin/env python
+#! /usr/bin/env python2
#
-# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
+# This file is part of khmer, http://github.com/ged-lab/khmer/, and is
# Copyright (C) Michigan State University, 2010-2015. It is licensed under
# the three-clause BSD license; see LICENSE.
# Contact: khmer-project at idyll.org
@@ -15,14 +15,12 @@ The script does not load a prebuilt k-mer counting table.
Use '-h' for parameter help.
"""
-from __future__ import print_function
import os
import sys
import csv
import khmer
import threading
import textwrap
-from khmer import khmer_args
from khmer.khmer_args import (build_counting_args, add_threading_args,
report_on_config, info)
from khmer.kfile import (check_input_files, check_space,
@@ -80,12 +78,13 @@ def main(): # pylint: disable=too-many-locals,too-many-branches
check_input_files(args.input_sequence_filename, args.force)
check_space([args.input_sequence_filename], args.force)
if args.savetable:
- check_space_for_hashtable(args, 'countgraph', args.force)
+ check_space_for_hashtable(args.n_tables * args.min_tablesize,
+ args.force)
if (not args.squash_output and
os.path.exists(args.output_histogram_filename)):
- print('ERROR: %s exists; not squashing.' %
- args.output_histogram_filename, file=sys.stderr)
+ print >> sys.stderr, 'ERROR: %s exists; not squashing.' % \
+ args.output_histogram_filename
sys.exit(1)
else:
hist_fp = open(args.output_histogram_filename, 'w')
@@ -95,24 +94,26 @@ def main(): # pylint: disable=too-many-locals,too-many-branches
hist_fp_csv.writerow(['abundance', 'count', 'cumulative',
'cumulative_fraction'])
- print('making countgraph', file=sys.stderr)
- counting_hash = khmer_args.create_countgraph(args, multiplier=1.1)
+ print >>sys.stderr, 'making k-mer counting table'
+ counting_hash = khmer.new_counting_hash(args.ksize, args.min_tablesize,
+ args.n_tables)
counting_hash.set_use_bigcount(args.bigcount)
- print('building k-mer tracking table', file=sys.stderr)
- tracking = khmer_args.create_nodegraph(args, multiplier=1.1)
+ print >> sys.stderr, 'building k-mer tracking table'
+ tracking = khmer.new_hashbits(counting_hash.ksize(), args.min_tablesize,
+ args.n_tables)
- print('kmer_size:', counting_hash.ksize(), file=sys.stderr)
- print('k-mer counting table sizes:',
- counting_hash.hashsizes(), file=sys.stderr)
- print('outputting to', args.output_histogram_filename, file=sys.stderr)
+ print >>sys.stderr, 'kmer_size:', counting_hash.ksize()
+ print >>sys.stderr, 'k-mer counting table sizes:', \
+ counting_hash.hashsizes()
+ print >>sys.stderr, 'outputting to', args.output_histogram_filename
# start loading
rparser = khmer.ReadParser(args.input_sequence_filename)
threads = []
- print('consuming input, round 1 --',
- args.input_sequence_filename, file=sys.stderr)
- for _ in range(args.threads):
+ print >>sys.stderr, 'consuming input, round 1 --', \
+ args.input_sequence_filename
+ for _ in xrange(args.threads):
thread = \
threading.Thread(
target=counting_hash.consume_fasta_with_reads_parser,
@@ -125,8 +126,8 @@ def main(): # pylint: disable=too-many-locals,too-many-branches
thread.join()
if args.report_total_kmers:
- print('Total number of unique k-mers: {0}'.format(
- counting_hash.n_unique_kmers()), file=sys.stderr)
+ print >> sys.stderr, 'Total number of unique k-mers: {0}'.format(
+ counting_hash.n_unique_kmers())
abundance_lists = []
@@ -135,13 +136,13 @@ def main(): # pylint: disable=too-many-locals,too-many-branches
read_parser, tracking)
abundance_lists.append(abundances)
- print('preparing hist from %s...' %
- args.input_sequence_filename, file=sys.stderr)
+ print >>sys.stderr, 'preparing hist from %s...' % \
+ args.input_sequence_filename
rparser = khmer.ReadParser(args.input_sequence_filename)
threads = []
- print('consuming input, round 2 --',
- args.input_sequence_filename, file=sys.stderr)
- for _ in range(args.threads):
+ print >>sys.stderr, 'consuming input, round 2 --', \
+ args.input_sequence_filename
+ for _ in xrange(args.threads):
thread = \
threading.Thread(
target=__do_abundance_dist__,
@@ -162,10 +163,10 @@ def main(): # pylint: disable=too-many-locals,too-many-branches
total = sum(abundance.values())
if 0 == total:
- print("ERROR: abundance distribution is uniformly zero; "
- "nothing to report.", file=sys.stderr)
- print(
- "\tPlease verify that the input files are valid.", file=sys.stderr)
+ print >> sys.stderr, \
+ "ERROR: abundance distribution is uniformly zero; " \
+ "nothing to report."
+ print >> sys.stderr, "\tPlease verify that the input files are valid."
sys.exit(1)
sofar = 0
@@ -179,17 +180,17 @@ def main(): # pylint: disable=too-many-locals,too-many-branches
if args.csv:
hist_fp_csv.writerow([_, i, sofar, round(frac, 3)])
else:
- print(_, i, sofar, round(frac, 3), file=hist_fp)
+ print >> hist_fp, _, i, sofar, round(frac, 3)
if sofar == total:
break
if args.savetable:
- print('Saving k-mer counting table ', args.savetable, file=sys.stderr)
- print('...saving to', args.savetable, file=sys.stderr)
+ print >>sys.stderr, 'Saving k-mer counting table ', args.savetable
+ print >>sys.stderr, '...saving to', args.savetable
counting_hash.save(args.savetable)
- print('wrote to: ' + args.output_histogram_filename, file=sys.stderr)
+ print >> sys.stderr, 'wrote to: ' + args.output_histogram_filename
if __name__ == '__main__':
main()
diff --git a/scripts/abundance-dist.py b/scripts/abundance-dist.py
index 7661ec6..966bfe8 100755
--- a/scripts/abundance-dist.py
+++ b/scripts/abundance-dist.py
@@ -1,6 +1,6 @@
-#! /usr/bin/env python
+#! /usr/bin/env python2
#
-# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
+# This file is part of khmer, http://github.com/ged-lab/khmer/, and is
# Copyright (C) Michigan State University, 2010-2015. It is licensed under
# the three-clause BSD license; see LICENSE.
# Contact: khmer-project at idyll.org
@@ -44,9 +44,6 @@ def get_parser():
parser.add_argument('-s', '--squash', dest='squash_output', default=False,
action='store_true',
help='Overwrite existing output_histogram_filename')
- parser.add_argument('-b', '--no-bigcount', dest='bigcount', default=True,
- action='store_false',
- help='Do not count k-mers past 255')
parser.add_argument('--csv', default=False, action='store_true',
help='Use the CSV format for the histogram. '
'Includes column headers.')
@@ -66,27 +63,19 @@ def main():
for infile in infiles:
check_input_files(infile, args.force)
- print('hashtable from', args.input_counting_table_filename,
- file=sys.stderr)
+ print ('hashtable from', args.input_counting_table_filename,
+ file=sys.stderr)
counting_hash = khmer.load_counting_hash(
args.input_counting_table_filename)
- if not counting_hash.get_use_bigcount() and args.bigcount:
- print("WARNING: The loaded graph has bigcount DISABLED while bigcount"
- " reporting is ENABLED--counts higher than 255 will not be "
- "reported.",
- file=sys.stderr)
-
- counting_hash.set_use_bigcount(args.bigcount)
-
kmer_size = counting_hash.ksize()
hashsizes = counting_hash.hashsizes()
tracking = khmer._Hashbits( # pylint: disable=protected-access
kmer_size, hashsizes)
- print('K:', kmer_size, file=sys.stderr)
- print('HT sizes:', hashsizes, file=sys.stderr)
- print('outputting to', args.output_histogram_filename, file=sys.stderr)
+ print ('K:', kmer_size, file=sys.stderr)
+ print ('HT sizes:', hashsizes, file=sys.stderr)
+ print ('outputting to', args.output_histogram_filename, file=sys.stderr)
if os.path.exists(args.output_histogram_filename):
if not args.squash_output:
diff --git a/scripts/annotate-partitions.py b/scripts/annotate-partitions.py
index e09f958..aed932e 100755
--- a/scripts/annotate-partitions.py
+++ b/scripts/annotate-partitions.py
@@ -1,6 +1,6 @@
-#! /usr/bin/env python
+#! /usr/bin/env python2
#
-# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
+# This file is part of khmer, http://github.com/ged-lab/khmer/, and is
# Copyright (C) Michigan State University, 2009-2015. It is licensed under
# the three-clause BSD license; see LICENSE.
# Contact: khmer-project at idyll.org
@@ -15,7 +15,6 @@ Partition-annotated sequences will be in <fileN>.part.
Use '-h' for parameter help.
"""
-from __future__ import print_function
import os
import argparse
@@ -67,7 +66,7 @@ def main():
ksize = args.ksize
filenames = args.input_filenames
- htable = khmer.Hashbits(ksize, 1, 1)
+ htable = khmer.new_hashbits(ksize, 1, 1)
partitionmap_file = args.graphbase + '.pmap.merged'
@@ -77,16 +76,16 @@ def main():
check_space(filenames, args.force)
- print('loading partition map from:', partitionmap_file, file=sys.stderr)
+ print >>sys.stderr, 'loading partition map from:', partitionmap_file
htable.load_partitionmap(partitionmap_file)
for infile in filenames:
- print('outputting partitions for', infile, file=sys.stderr)
+ print >>sys.stderr, 'outputting partitions for', infile
outfile = os.path.basename(infile) + '.part'
part_count = htable.output_partitions(infile, outfile)
- print('output %d partitions for %s' % (
- part_count, infile), file=sys.stderr)
- print('partitions are in', outfile, file=sys.stderr)
+ print >>sys.stderr, 'output %d partitions for %s' % (
+ part_count, infile)
+ print >>sys.stderr, 'partitions are in', outfile
if __name__ == '__main__':
main()
diff --git a/scripts/count-median.py b/scripts/count-median.py
index 19e6473..58b36a6 100755
--- a/scripts/count-median.py
+++ b/scripts/count-median.py
@@ -1,6 +1,6 @@
-#! /usr/bin/env python
+#! /usr/bin/env python2
#
-# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
+# This file is part of khmer, http://github.com/ged-lab/khmer/, and is
# Copyright (C) Michigan State University, 2009-2015. It is licensed under
# the three-clause BSD license; see LICENSE.
# Contact: khmer-project at idyll.org
@@ -19,9 +19,8 @@ Use '-h' for parameter help.
The output file contains sequence id, median, average, stddev, and seq length.
-NOTE: All 'N's in the input sequences are converted to 'A's.
+NOTE: All 'N's in the input sequences are converted to 'G's.
"""
-from __future__ import print_function
import screed
import argparse
import sys
@@ -50,7 +49,7 @@ def get_parser():
count-median.py counts.ct tests/test-data/test-reads.fq.gz medians.txt
- NOTE: All 'N's in the input sequences are converted to 'A's.
+ NOTE: All 'N's in the input sequences are converted to 'G's.
"""
parser = argparse.ArgumentParser(
description='Count k-mers summary stats for sequences',
@@ -86,11 +85,11 @@ def main():
check_space(infiles, args.force)
- print('loading k-mer counting table from', htfile, file=sys.stderr)
+ print >>sys.stderr, 'loading k-mer counting table from', htfile
htable = khmer.load_counting_hash(htfile)
ksize = htable.ksize()
- print('writing to', output_filename, file=sys.stderr)
+ print >>sys.stderr, 'writing to', output_filename
output = open(output_filename, 'w')
if args.csv:
@@ -106,15 +105,14 @@ def main():
parse_description=parse_description):
seq = record.sequence.upper()
if 'N' in seq:
- seq = seq.replace('N', 'A')
+ seq = seq.replace('N', 'G')
if ksize <= len(seq):
medn, ave, stdev = htable.get_median_count(seq)
- ave, stdev = [round(x, 9) for x in (ave, stdev)]
if args.csv:
output.writerow([record.name, medn, ave, stdev, len(seq)])
else:
- print(record.name, medn, ave, stdev, len(seq), file=output)
+ print >> output, record.name, medn, ave, stdev, len(seq)
if __name__ == '__main__':
main()
diff --git a/scripts/count-overlap.py b/scripts/count-overlap.py
index a8c715d..a5d7f95 100755
--- a/scripts/count-overlap.py
+++ b/scripts/count-overlap.py
@@ -1,7 +1,7 @@
-#! /usr/bin/env python
+#! /usr/bin/env python2
#
-# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
-# Copyright (C) Michigan State University, 2012-2015-2015. It is licensed under
+# This file is part of khmer, http://github.com/ged-lab/khmer/, and is
+# Copyright (C) Michigan State University, 2012-2015. It is licensed under
# the three-clause BSD license; see LICENSE.
# Contact: khmer-project at idyll.org
#
@@ -18,15 +18,17 @@ usage: count-overlap_cpp.py [-h] [-q] [--ksize KSIZE] [--n_tables N_HASHES]
Use '-h' for parameter help.
"""
-from __future__ import print_function
import sys
import csv
import khmer
import textwrap
-from khmer import khmer_args
from khmer.kfile import check_input_files, check_space
from khmer.khmer_args import (build_hashbits_args, report_on_config, info)
+DEFAULT_K = 32
+DEFAULT_N_HT = 4
+DEFAULT_HASHSIZE = 1e6
+
def get_parser():
epilog = """
@@ -55,14 +57,14 @@ def get_parser():
def main():
info('count-overlap.py', ['counting'])
args = get_parser().parse_args()
- report_on_config(args, hashtype='nodegraph')
+ report_on_config(args, hashtype='hashbits')
for infile in [args.ptfile, args.fafile]:
check_input_files(infile, args.force)
check_space([args.ptfile, args.fafile], args.force)
- print('loading k-mer presence table from', args.ptfile, file=sys.stderr)
+ print >>sys.stderr, 'loading k-mer presence table from', args.ptfile
ht1 = khmer.load_hashbits(args.ptfile)
kmer_size = ht1.ksize()
@@ -73,7 +75,7 @@ def main():
# write headers:
f_curve_obj_csv.writerow(['input_seq', 'overlap_kmer'])
- ht2 = khmer_args.create_nodegraph(args, ksize=kmer_size)
+ ht2 = khmer.new_hashbits(kmer_size, args.min_tablesize, args.n_tables)
(n_unique, n_overlap, list_curve) = ht2.count_overlap(args.fafile, ht1)
@@ -91,9 +93,9 @@ dataset2: %s
if args.csv:
f_curve_obj_csv.writerow([list_curve[100 + i], list_curve[i]])
else:
- print(list_curve[100 + i], list_curve[i], file=f_curve_obj)
+ print >> f_curve_obj, list_curve[100 + i], list_curve[i]
- print('wrote to: ' + args.report_filename, file=sys.stderr)
+ print >> sys.stderr, 'wrote to: ' + args.report_filename
if __name__ == '__main__':
main()
diff --git a/scripts/do-partition.py b/scripts/do-partition.py
index f502145..0fcf64f 100755
--- a/scripts/do-partition.py
+++ b/scripts/do-partition.py
@@ -1,6 +1,6 @@
-#! /usr/bin/env python
+#! /usr/bin/env python2
#
-# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
+# This file is part of khmer, http://github.com/ged-lab/khmer/, and is
# Copyright (C) Michigan State University, 2009-2015. It is licensed under
# the three-clause BSD license; see LICENSE.
# Contact: khmer-project at idyll.org
@@ -13,16 +13,15 @@ Do all the partition steps in one script.
Use '-h' for parameter help.
"""
-from __future__ import print_function
import khmer
import sys
import threading
+import Queue
import gc
import os.path
import os
import textwrap
-from khmer import khmer_args
from khmer.khmer_args import (build_hashbits_args, report_on_config, info,
add_threading_args)
import glob
@@ -30,12 +29,6 @@ from khmer.kfile import check_input_files, check_space
import re
import platform
-# stdlib queue module was renamed on Python 3
-try:
- import queue
-except ImportError:
- import Queue as queue
-
DEFAULT_SUBSET_SIZE = int(1e5)
DEFAULT_N_THREADS = 4
DEFAULT_K = 32
@@ -43,9 +36,9 @@ DEFAULT_K = 32
# Debugging Support
if "Linux" == platform.system():
def __debug_vm_usage(msg):
- print("===> DEBUG: " + msg, file=sys.stderr)
+ print >>sys.stderr, "===> DEBUG: " + msg
for vmstat in re.findall(r".*Vm.*", file("/proc/self/status").read()):
- print(vmstat)
+ print vmstat
else:
def __debug_vm_usage(msg): # pylint: disable=unused-argument
pass
@@ -55,23 +48,23 @@ def worker(queue, basename, stop_big_traversals):
while True:
try:
(htable, index, start, stop) = queue.get(False)
- except queue.Empty:
- print('exiting', file=sys.stderr)
+ except Queue.Empty:
+ print >>sys.stderr, 'exiting'
return
outfile = basename + '.subset.%d.pmap' % (index,)
if os.path.exists(outfile):
- print('SKIPPING', outfile, ' -- already exists', file=sys.stderr)
+ print >>sys.stderr, 'SKIPPING', outfile, ' -- already exists'
continue
- print('starting:', basename, index, file=sys.stderr)
+ print >>sys.stderr, 'starting:', basename, index
# pay attention to stoptags when partitioning; take command line
# direction on whether or not to exhaustively traverse.
subset = htable.do_subset_partition(start, stop, True,
stop_big_traversals)
- print('saving:', basename, index, file=sys.stderr)
+ print >>sys.stderr, 'saving:', basename, index
htable.save_subset_partitionmap(subset, outfile)
del subset
gc.collect()
@@ -114,46 +107,45 @@ def main(): # pylint: disable=too-many-locals,too-many-statements
info('do-partition.py', ['graph'])
args = get_parser().parse_args()
- report_on_config(args, hashtype='nodegraph')
+ report_on_config(args, hashtype='hashbits')
for infile in args.input_filenames:
check_input_files(infile, args.force)
check_space(args.input_filenames, args.force)
- print('Saving k-mer presence table to %s' %
- args.graphbase, file=sys.stderr)
- print('Loading kmers from sequences in %s' %
- repr(args.input_filenames), file=sys.stderr)
- print('--', file=sys.stderr)
- print('SUBSET SIZE', args.subset_size, file=sys.stderr)
- print('N THREADS', args.threads, file=sys.stderr)
- print('--', file=sys.stderr)
+ print >>sys.stderr, 'Saving k-mer presence table to %s' % args.graphbase
+ print >>sys.stderr, 'Loading kmers from sequences in %s' % \
+ repr(args.input_filenames)
+ print >>sys.stderr, '--'
+ print >>sys.stderr, 'SUBSET SIZE', args.subset_size
+ print >>sys.stderr, 'N THREADS', args.threads
+ print >>sys.stderr, '--'
# load-graph
- print('making nodegraph', file=sys.stderr)
- htable = khmer_args.create_nodegraph(args)
+ print >>sys.stderr, 'making k-mer presence table'
+ htable = khmer.new_hashbits(args.ksize, args.min_tablesize, args.n_tables)
for _, filename in enumerate(args.input_filenames):
- print('consuming input', filename, file=sys.stderr)
+ print >>sys.stderr, 'consuming input', filename
htable.consume_fasta_and_tag(filename)
# 0.18 is ACTUAL MAX. Do not change.
fp_rate = \
khmer.calc_expected_collisions(htable, args.force, max_false_pos=.15)
- print('fp rate estimated to be %1.3f' % fp_rate, file=sys.stderr)
+ print >>sys.stderr, 'fp rate estimated to be %1.3f' % fp_rate
# partition-graph
# do we want to exhaustively traverse the graph?
stop_big_traversals = args.no_big_traverse
if stop_big_traversals:
- print('** This script brakes for lumps: ',
- 'stop_big_traversals is true.', file=sys.stderr)
+ print >>sys.stderr, '** This script brakes for lumps: ', \
+ 'stop_big_traversals is true.'
else:
- print('** Traverse all the things:',
- ' stop_big_traversals is false.', file=sys.stderr)
+ print >>sys.stderr, '** Traverse all the things:', \
+ ' stop_big_traversals is false.'
#
# now, partition!
@@ -165,7 +157,7 @@ def main(): # pylint: disable=too-many-locals,too-many-statements
divvy.append(0)
# build a queue of tasks:
- worker_q = queue.Queue()
+ worker_q = Queue.Queue()
# break up the subsets into a list of worker tasks
for _ in range(0, n_subsets):
@@ -173,7 +165,7 @@ def main(): # pylint: disable=too-many-locals,too-many-statements
end = divvy[_ + 1]
worker_q.put((htable, _, start, end))
- print('enqueued %d subset tasks' % n_subsets, file=sys.stderr)
+ print >>sys.stderr, 'enqueued %d subset tasks' % n_subsets
open('%s.info' % args.graphbase, 'w').write('%d subsets total\n'
% (n_subsets))
@@ -181,8 +173,8 @@ def main(): # pylint: disable=too-many-locals,too-many-statements
args.threads = n_subsets
# start threads!
- print('starting %d threads' % args.threads, file=sys.stderr)
- print('---', file=sys.stderr)
+ print >>sys.stderr, 'starting %d threads' % args.threads
+ print >>sys.stderr, '---'
threads = []
for _ in range(args.threads):
@@ -194,43 +186,43 @@ def main(): # pylint: disable=too-many-locals,too-many-statements
assert threading.active_count() == args.threads + 1
- print('done starting threads', file=sys.stderr)
+ print >>sys.stderr, 'done starting threads'
# wait for threads
for _ in threads:
_.join()
- print('---', file=sys.stderr)
- print('done making subsets! see %s.subset.*.pmap' %
- (args.graphbase,), file=sys.stderr)
+ print >>sys.stderr, '---'
+ print >>sys.stderr, 'done making subsets! see %s.subset.*.pmap' % \
+ (args.graphbase,)
# merge-partitions
pmap_files = glob.glob(args.graphbase + '.subset.*.pmap')
- print('loading %d pmap files (first one: %s)' %
- (len(pmap_files), pmap_files[0]), file=sys.stderr)
+ print >>sys.stderr, 'loading %d pmap files (first one: %s)' % \
+ (len(pmap_files), pmap_files[0])
- htable = khmer.Hashbits(args.ksize, 1, 1)
+ htable = khmer.new_hashbits(args.ksize, 1, 1)
for pmap_file in pmap_files:
- print('merging', pmap_file, file=sys.stderr)
+ print >>sys.stderr, 'merging', pmap_file
htable.merge_subset_from_disk(pmap_file)
if args.remove_subsets:
- print('removing pmap files', file=sys.stderr)
+ print >>sys.stderr, 'removing pmap files'
for pmap_file in pmap_files:
os.unlink(pmap_file)
# annotate-partitions
for infile in args.input_filenames:
- print('outputting partitions for', infile, file=sys.stderr)
+ print >>sys.stderr, 'outputting partitions for', infile
outfile = os.path.basename(infile) + '.part'
part_count = htable.output_partitions(infile, outfile)
- print('output %d partitions for %s' % (
- part_count, infile), file=sys.stderr)
- print('partitions are in', outfile, file=sys.stderr)
+ print >>sys.stderr, 'output %d partitions for %s' % (
+ part_count, infile)
+ print >>sys.stderr, 'partitions are in', outfile
if __name__ == '__main__':
main()
diff --git a/scripts/extract-long-sequences.py b/scripts/extract-long-sequences.py
index 7155070..dcaf481 100755
--- a/scripts/extract-long-sequences.py
+++ b/scripts/extract-long-sequences.py
@@ -1,6 +1,6 @@
-#! /usr/bin/env python
+#! /usr/bin/env python2
#
-# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
+# This file is part of khmer, http://github.com/ged-lab/khmer/, and is
# Copyright (C) Michigan State University, 2009-2015. It is licensed under
# the three-clause BSD license; see LICENSE.
# Contact: khmer-project at idyll.org
@@ -18,7 +18,6 @@ length.
Use '-h' for parameter help.
"""
-from __future__ import print_function
import argparse
import screed
import sys
@@ -48,7 +47,7 @@ def main():
for record in screed.open(filename, parse_description=False):
if len(record['sequence']) >= args.length:
write_record(record, outfp)
- print('wrote to: ' + args.output, file=sys.stderr)
+ print >> sys.stderr, 'wrote to: ' + args.output
if __name__ == '__main__':
main()
diff --git a/scripts/extract-paired-reads.py b/scripts/extract-paired-reads.py
index ea8bebf..ef224cb 100755
--- a/scripts/extract-paired-reads.py
+++ b/scripts/extract-paired-reads.py
@@ -1,6 +1,6 @@
-#! /usr/bin/env python
+#! /usr/bin/env python2
#
-# This script is part of khmer, https://github.com/dib-lab/khmer/, and is
+# This script is part of khmer, http://github.com/ged-lab/khmer/, and is
# Copyright (C) Michigan State University, 2009-2015. It is licensed under
# the three-clause BSD license; see LICENSE.
# Contact: khmer-project at idyll.org
@@ -16,7 +16,6 @@ extract them into separate files (.pe and .se).
Reads FASTQ and FASTA input, retains format for output.
"""
-from __future__ import print_function
import screed
import sys
import os.path
@@ -31,27 +30,15 @@ from khmer.utils import broken_paired_reader, write_record, write_record_pair
def get_parser():
epilog = """
- Many read-handling programs (assemblers, mappers, etc.) require
- that you give them either perfectly interleaved files, or files
- containing only single reads. This script takes files that were
- originally interleaved but where reads may have been orphaned (via
- error filtering, application of abundance filtering, digital
- normalization in non-paired mode, or partitioning) and separates
- the interleaved reads from the orphaned reads.
-
- The default output is two files, <input file>.pe and <input
- file>.se, placed in the current directory. The .pe file contains
- interleaved and properly paired sequences, while the .se file
- contains orphan sequences.
-
- The directory into which the interleaved and orphaned reads are
- output may be specified using :option:`-o`/:option:`--output-dir`.
- This directory will be created if it does not already exist.
-
- Alternatively, you can specify the filenames directly with
- :option:`-p`/:option:`--output-paired` and
- :option:`-s`/:option:`--output-single`, which will override the
- :option:`-o`/:option:`--output-dir` option.
+ The output is two files, <input file>.pe and <input file>.se, placed in the
+ current directory. The .pe file contains interleaved and properly paired
+ sequences, while the .se file contains orphan sequences.
+
+ Many assemblers (e.g. Velvet) require that you give them either perfectly
+ interleaved files, or files containing only single reads. This script takes
+ files that were originally interleaved but where reads may have been
+ orphaned via error filtering, application of abundance filtering, digital
+ normalization in non-paired mode, or partitioning.
Example::
@@ -60,21 +47,9 @@ def get_parser():
parser = argparse.ArgumentParser(
description='Take a mixture of reads and split into pairs and '
'orphans.', epilog=textwrap.dedent(epilog))
- parser.add_argument('infile', nargs='?', default='/dev/stdin')
+ parser.add_argument('infile')
parser.add_argument('--version', action='version', version='%(prog)s ' +
khmer.__version__)
-
- parser.add_argument('-o', '--output-dir', default='', help='Output '
- 'split reads to specified directory. Creates '
- 'directory if necessary')
-
- parser.add_argument('-p', '--output-paired', metavar='output_paired',
- default=None, help='Output paired reads to this '
- 'file', type=argparse.FileType('w'))
- parser.add_argument('-s', '--output-single', metavar='output_single',
- default=None, help='Output orphaned reads to this '
- 'file', type=argparse.FileType('w'))
-
parser.add_argument('-f', '--force', default=False, action='store_true',
help='Overwrite output file if it exists')
return parser
@@ -84,50 +59,28 @@ def main():
info('extract-paired-reads.py')
args = get_parser().parse_args()
- infile = args.infile
- check_input_files(infile, args.force)
- check_space([infile], args.force)
-
- # decide where to put output files - specific directory? or just default?
- if infile == '/dev/stdin' or infile == '-':
- if not (args.output_paired and args.output_single):
- print("Accepting input from stdin; output filenames must be "
- "provided.", file=sys.stderr)
- sys.exit(1)
- elif args.output_dir:
- if not os.path.exists(args.output_dir):
- os.makedirs(args.output_dir)
- out1 = args.output_dir + '/' + os.path.basename(infile) + '.se'
- out2 = args.output_dir + '/' + os.path.basename(infile) + '.pe'
- else:
- out1 = os.path.basename(infile) + '.se'
- out2 = os.path.basename(infile) + '.pe'
-
- # OVERRIDE default output file locations with -p, -s
- if args.output_paired:
- paired_fp = args.output_paired
- out2 = paired_fp.name
- else:
- # Don't override, just open the default filename from above
- paired_fp = open(out2, 'w')
- if args.output_single:
- single_fp = args.output_single
- out1 = single_fp.name
- else:
- # Don't override, just open the default filename from above
- single_fp = open(out1, 'w')
-
- print('reading file "%s"' % infile, file=sys.stderr)
- print('outputting interleaved pairs to "%s"' % out2, file=sys.stderr)
- print('outputting orphans to "%s"' % out1, file=sys.stderr)
+ check_input_files(args.infile, args.force)
+ infiles = [args.infile]
+ check_space(infiles, args.force)
+
+ outfile = os.path.basename(args.infile)
+ if len(sys.argv) > 2:
+ outfile = sys.argv[2]
+
+ single_fp = open(outfile + '.se', 'w')
+ paired_fp = open(outfile + '.pe', 'w')
+
+ print >>sys.stderr, 'reading file "%s"' % args.infile
+ print >>sys.stderr, 'outputting interleaved pairs to "%s.pe"' % outfile
+ print >>sys.stderr, 'outputting orphans to "%s.se"' % outfile
n_pe = 0
n_se = 0
- screed_iter = screed.open(infile, parse_description=False)
+ screed_iter = screed.open(args.infile, parse_description=False)
for index, is_pair, read1, read2 in broken_paired_reader(screed_iter):
if index % 100000 == 0 and index > 0:
- print('...', index, file=sys.stderr)
+ print >>sys.stderr, '...', index
if is_pair:
write_record_pair(read1, read2, paired_fp)
@@ -142,12 +95,12 @@ def main():
if n_pe == 0:
raise Exception("no paired reads!? check file formats...")
- print('DONE; read %d sequences,'
- ' %d pairs and %d singletons' %
- (n_pe * 2 + n_se, n_pe, n_se), file=sys.stderr)
+ print >>sys.stderr, 'DONE; read %d sequences,' \
+ ' %d pairs and %d singletons' % \
+ (n_pe * 2 + n_se, n_pe, n_se)
- print('wrote to: %s and %s' % (out2, out1),
- file=sys.stderr)
+ print >> sys.stderr, 'wrote to: ' + outfile \
+ + '.se' + ' and ' + outfile + '.pe'
if __name__ == '__main__':
diff --git a/scripts/extract-partitions.py b/scripts/extract-partitions.py
index 777db38..6cbd37d 100755
--- a/scripts/extract-partitions.py
+++ b/scripts/extract-partitions.py
@@ -1,6 +1,6 @@
-#! /usr/bin/env python
+#! /usr/bin/env python2
#
-# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
+# This file is part of khmer, http://github.com/ged-lab/khmer/, and is
# Copyright (C) Michigan State University, 2009-2015. It is licensed under
# the three-clause BSD license; see LICENSE.
# Contact: khmer-project at idyll.org
@@ -18,7 +18,6 @@ Use '-h' for parameter help.
@CTB note that if threshold is != 1, those sequences will not be output
by output_unassigned...
"""
-from __future__ import print_function
import sys
import screed
@@ -95,24 +94,24 @@ def main(): # pylint: disable=too-many-locals,too-many-branches
check_space(args.part_filenames, args.force)
- print('---', file=sys.stderr)
- print('reading partitioned files:', repr(
- args.part_filenames), file=sys.stderr)
+ print >>sys.stderr, '---'
+ print >>sys.stderr, 'reading partitioned files:', repr(args.part_filenames)
if args.output_groups:
- print('outputting to files named "%s.groupN.fa"' %
- args.prefix, file=sys.stderr)
- print('min reads to keep a partition:',
- args.min_part_size, file=sys.stderr)
- print('max size of a group file:', args.max_size, file=sys.stderr)
+ print >>sys.stderr, 'outputting to files named "%s.groupN.fa"' % \
+ args.prefix
+ print >>sys.stderr, 'min reads to keep a partition:', \
+ args.min_part_size
+ print >>sys.stderr, 'max size of a group file:', args.max_size
else:
- print('NOT outputting groups! Beware!', file=sys.stderr)
+ print >>sys.stderr, 'NOT outputting groups! Beware!'
if args.output_unassigned:
- print('outputting unassigned reads to "%s.unassigned.fa"' %
- args.prefix, file=sys.stderr)
- print('partition size distribution will go to %s'
- % distfilename, file=sys.stderr)
- print('---', file=sys.stderr)
+ print >>sys.stderr, \
+ 'outputting unassigned reads to "%s.unassigned.fa"' % \
+ args.prefix
+ print >>sys.stderr, 'partition size distribution will go to %s' \
+ % distfilename
+ print >>sys.stderr, '---'
#
@@ -143,7 +142,7 @@ def main(): # pylint: disable=too-many-locals,too-many-branches
for filename in args.part_filenames:
for index, read, pid in read_partition_file(filename):
if index % 100000 == 0:
- print('...', index, file=sys.stderr)
+ print >>sys.stderr, '...', index
count[pid] = count.get(pid, 0) + 1
@@ -160,7 +159,7 @@ def main(): # pylint: disable=too-many-locals,too-many-branches
# develop histogram of partition sizes
dist = {}
- for pid, size in list(count.items()):
+ for pid, size in count.items():
dist[size] = dist.get(size, 0) + 1
# output histogram
@@ -178,7 +177,7 @@ def main(): # pylint: disable=too-many-locals,too-many-branches
sys.exit(0)
# sort groups by size
- divvy = sorted(list(count.items()), key=lambda y: y[1])
+ divvy = sorted(count.items(), key=lambda y: y[1])
divvy = [y for y in divvy if y[1] > args.min_part_size]
# divvy up into different groups, based on having max_size sequences
@@ -206,9 +205,9 @@ def main(): # pylint: disable=too-many-locals,too-many-branches
# print 'group_d', partition_id, group_n
group_n += 1
- print('%d groups' % group_n, file=sys.stderr)
+ print >>sys.stderr, '%d groups' % group_n
if group_n == 0:
- print('nothing to output; exiting!', file=sys.stderr)
+ print >>sys.stderr, 'nothing to output; exiting!'
return
# open a bunch of output files for the different groups
@@ -226,7 +225,7 @@ def main(): # pylint: disable=too-many-locals,too-many-branches
for index, read, partition_id in read_partition_file(filename):
total_seqs += 1
if index % 100000 == 0:
- print('...x2', index, file=sys.stderr)
+ print >>sys.stderr, '...x2', index
if partition_id == 0:
continue
@@ -243,19 +242,20 @@ def main(): # pylint: disable=too-many-locals,too-many-branches
write_record(read, outfp)
part_seqs += 1
- print('---', file=sys.stderr)
- print('Of %d total seqs,' % total_seqs, file=sys.stderr)
- print('extracted %d partitioned seqs into group files,' %
- part_seqs, file=sys.stderr)
- print('discarded %d sequences from small partitions (see -m),' %
- toosmall_parts, file=sys.stderr)
- print('and found %d unpartitioned sequences (see -U).' %
- n_unassigned, file=sys.stderr)
- print('', file=sys.stderr)
- print('Created %d group files named %s.groupXXXX.%s' %
- (len(group_fps),
- args.prefix,
- suffix), file=sys.stderr)
+ print >>sys.stderr, '---'
+ print >>sys.stderr, 'Of %d total seqs,' % total_seqs
+ print >>sys.stderr, 'extracted %d partitioned seqs into group files,' % \
+ part_seqs
+ print >>sys.stderr, \
+ 'discarded %d sequences from small partitions (see -m),' % \
+ toosmall_parts
+ print >>sys.stderr, 'and found %d unpartitioned sequences (see -U).' % \
+ n_unassigned
+ print >>sys.stderr, ''
+ print >>sys.stderr, 'Created %d group files named %s.groupXXXX.%s' % \
+ (len(group_fps),
+ args.prefix,
+ suffix)
if __name__ == '__main__':
main()
diff --git a/scripts/fastq-to-fasta.py b/scripts/fastq-to-fasta.py
index ef21cda..76393ea 100755
--- a/scripts/fastq-to-fasta.py
+++ b/scripts/fastq-to-fasta.py
@@ -1,7 +1,7 @@
-#! /usr/bin/env python
+#! /usr/bin/env python2
#
-# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
-# Copyright (C) Michigan State University, 2009-2015. It is licensed under
+# This file is part of khmer, http://github.com/ged-lab/khmer/, and is
+# Copyright (C) Michigan State University, 2009-2014. It is licensed under
# the three-clause BSD license; see LICENSE.
# Contact: khmer-project at idyll.org
#
@@ -14,7 +14,6 @@ Convert FASTQ files to FASTA format.
Use '-h' for parameter help.
"""
-from __future__ import print_function
import sys
import argparse
import screed
@@ -40,13 +39,13 @@ def get_parser():
def main():
args = get_parser().parse_args()
- print(('fastq from ', args.input_sequence), file=sys.stderr)
+ print >> sys.stderr, ('fastq from ', args.input_sequence)
n_count = 0
for n, record in enumerate(screed.open(args.input_sequence,
parse_description=False)):
if n % 10000 == 0:
- print('...', n, file=sys.stderr)
+ print>>sys.stderr, '...', n
sequence = record['sequence']
name = record['name']
@@ -59,15 +58,15 @@ def main():
args.output.write('>' + name + '\n')
args.output.write(sequence + '\n')
- print('\n' + 'lines from ' + args.input_sequence, file=sys.stderr)
+ print >> sys.stderr, '\n' + 'lines from ' + args.input_sequence
if not args.n_keep:
- print(str(n_count) + ' lines dropped.', file=sys.stderr)
+ print >> sys.stderr, str(n_count) + ' lines dropped.'
else:
- print('No lines dropped from file.', file=sys.stderr)
+ print >> sys.stderr, 'No lines dropped from file.'
- print('Wrote output to', args.output, file=sys.stderr)
+ print >> sys.stderr, 'Wrote output to', args.output
if __name__ == '__main__':
main()
diff --git a/scripts/filter-abund-single.py b/scripts/filter-abund-single.py
index b22a494..5300b5b 100755
--- a/scripts/filter-abund-single.py
+++ b/scripts/filter-abund-single.py
@@ -1,6 +1,6 @@
-#! /usr/bin/env python
+#! /usr/bin/env python2
#
-# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
+# This file is part of khmer, http://github.com/ged-lab/khmer/, and is
# Copyright (C) Michigan State University, 2009-2015. It is licensed under
# the three-clause BSD license; see LICENSE.
# Contact: khmer-project at idyll.org
@@ -17,14 +17,12 @@ placed in 'infile.abundfilt'.
Use '-h' for parameter help.
"""
-from __future__ import print_function
import os
import sys
import khmer
import threading
import textwrap
from khmer.thread_utils import ThreadedSequenceProcessor, verbose_loader
-from khmer import khmer_args
from khmer.khmer_args import (build_counting_args, report_on_config,
add_threading_args, info)
from khmer.kfile import (check_input_files, check_space,
@@ -71,17 +69,19 @@ def main():
check_input_files(args.datafile, args.force)
check_space([args.datafile], args.force)
if args.savetable:
- check_space_for_hashtable(args, 'countgraph', args.force)
+ check_space_for_hashtable(
+ args.n_tables * args.min_tablesize, args.force)
report_on_config(args)
- print('making countgraph', file=sys.stderr)
- htable = khmer_args.create_countgraph(args)
+ print >>sys.stderr, 'making k-mer counting table'
+ htable = khmer.new_counting_hash(args.ksize, args.min_tablesize,
+ args.n_tables)
# first, load reads into hash table
rparser = khmer.ReadParser(args.datafile)
threads = []
- print('consuming input, round 1 --', args.datafile, file=sys.stderr)
- for _ in range(args.threads):
+ print >>sys.stderr, 'consuming input, round 1 --', args.datafile
+ for _ in xrange(args.threads):
cur_thread = \
threading.Thread(
target=htable.consume_fasta_with_reads_parser,
@@ -94,45 +94,44 @@ def main():
_.join()
if args.report_total_kmers:
- print('Total number of unique k-mers: {0}'.format(
- htable.n_unique_kmers()), file=sys.stderr)
+ print >> sys.stderr, 'Total number of unique k-mers: {0}'.format(
+ htable.n_unique_kmers())
fp_rate = khmer.calc_expected_collisions(htable, args.force)
- print('fp rate estimated to be %1.3f' % fp_rate, file=sys.stderr)
+ print >>sys.stderr, 'fp rate estimated to be %1.3f' % fp_rate
# now, trim.
# the filtering function.
def process_fn(record):
- name = record.name
- seq = record.sequence
- seqN = seq.replace('N', 'A')
+ name = record['name']
+ seq = record['sequence']
+ if 'N' in seq:
+ return None, None
- _, trim_at = htable.trim_on_abundance(seqN, args.cutoff)
+ trim_seq, trim_at = htable.trim_on_abundance(seq, args.cutoff)
if trim_at >= args.ksize:
- # be sure to not to change the 'N's in the trimmed sequence -
- # so, return 'seq' and not 'seqN'.
- return name, seq[:trim_at]
+ return name, trim_seq
return None, None
# the filtering loop
- print('filtering', args.datafile, file=sys.stderr)
+ print >>sys.stderr, 'filtering', args.datafile
outfile = os.path.basename(args.datafile) + '.abundfilt'
outfp = open(outfile, 'w')
tsp = ThreadedSequenceProcessor(process_fn)
tsp.start(verbose_loader(args.datafile), outfp)
- print('output in', outfile, file=sys.stderr)
+ print >>sys.stderr, 'output in', outfile
if args.savetable:
- print('Saving k-mer counting table filename',
- args.savetable, file=sys.stderr)
- print('...saving to', args.savetable, file=sys.stderr)
+ print >>sys.stderr, 'Saving k-mer counting table filename', \
+ args.savetable
+ print >>sys.stderr, '...saving to', args.savetable
htable.save(args.savetable)
- print('wrote to: ', outfile, file=sys.stderr)
+ print >>sys.stderr, 'wrote to: ', outfile
if __name__ == '__main__':
main()
diff --git a/scripts/filter-abund.py b/scripts/filter-abund.py
index e994c60..4701c42 100755
--- a/scripts/filter-abund.py
+++ b/scripts/filter-abund.py
@@ -1,6 +1,6 @@
-#! /usr/bin/env python
+#! /usr/bin/env python2
#
-# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
+# This file is part of khmer, http://github.com/ged-lab/khmer/, and is
# Copyright (C) Michigan State University, 2009-2015. It is licensed under
# the three-clause BSD license; see LICENSE.
# Contact: khmer-project at idyll.org
@@ -16,7 +16,6 @@ hash table. Output sequences will be placed in 'infile.abundfilt'.
Use '-h' for parameter help.
"""
-from __future__ import print_function
import os
import khmer
import textwrap
@@ -81,41 +80,39 @@ def main():
check_input_files(args.input_table, args.force)
infiles = args.input_filename
- for filename in infiles:
- check_input_files(filename, args.force)
+ for _ in infiles:
+ check_input_files(_, args.force)
check_space(infiles, args.force)
- print('loading counting table:', args.input_table,
- file=sys.stderr)
+ print >>sys.stderr, 'loading hashtable'
htable = khmer.load_counting_hash(args.input_table)
ksize = htable.ksize()
- print("K:", ksize, file=sys.stderr)
+ print >>sys.stderr, "K:", ksize
# the filtering function.
def process_fn(record):
- name = record.name
- seq = record.sequence
- seqN = seq.replace('N', 'A')
+ name = record['name']
+ seq = record['sequence']
+ if 'N' in seq:
+ return None, None
if args.variable_coverage: # only trim when sequence has high enough C
- med, _, _ = htable.get_median_count(seqN)
+ med, _, _ = htable.get_median_count(seq)
if med < args.normalize_to:
return name, seq
- _, trim_at = htable.trim_on_abundance(seqN, args.cutoff)
+ trim_seq, trim_at = htable.trim_on_abundance(seq, args.cutoff)
if trim_at >= ksize:
- # be sure to not to change the 'N's in the trimmed sequence -
- # so, return 'seq' and not 'seqN'.
- return name, seq[:trim_at]
+ return name, trim_seq
return None, None
# the filtering loop
for infile in infiles:
- print('filtering', infile, file=sys.stderr)
+ print >>sys.stderr, 'filtering', infile
if args.single_output_filename != '':
outfile = args.single_output_filename
outfp = open(outfile, 'a')
@@ -126,7 +123,7 @@ def main():
tsp = ThreadedSequenceProcessor(process_fn, n_workers=args.threads)
tsp.start(verbose_loader(infile), outfp)
- print('output in', outfile, file=sys.stderr)
+ print >>sys.stderr, 'output in', outfile
if __name__ == '__main__':
main()
diff --git a/scripts/filter-stoptags.py b/scripts/filter-stoptags.py
index d7e87f2..24175ff 100755
--- a/scripts/filter-stoptags.py
+++ b/scripts/filter-stoptags.py
@@ -1,6 +1,6 @@
-#! /usr/bin/env python
+#! /usr/bin/env python2
#
-# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
+# This file is part of khmer, http://github.com/ged-lab/khmer/, and is
# Copyright (C) Michigan State University, 2009-2015. It is licensed under
# the three-clause BSD license; see LICENSE.
# Contact: khmer-project at idyll.org
@@ -16,7 +16,6 @@ will be placed in 'infile.stopfilt'.
Use '-h' for parameter help.
"""
-from __future__ import print_function
import os
import khmer
@@ -64,8 +63,8 @@ def main():
check_space(infiles, args.force)
- print('loading stop tags, with K', args.ksize, file=sys.stderr)
- htable = khmer.Hashbits(args.ksize, 1, 1)
+ print >>sys.stderr, 'loading stop tags, with K', args.ksize
+ htable = khmer.new_hashbits(args.ksize, 1, 1)
htable.load_stop_tags(stoptags)
def process_fn(record):
@@ -83,7 +82,7 @@ def main():
# the filtering loop
for infile in infiles:
- print('filtering', infile, file=sys.stderr)
+ print >>sys.stderr, 'filtering', infile
outfile = os.path.basename(infile) + '.stopfilt'
outfp = open(outfile, 'w')
@@ -91,7 +90,7 @@ def main():
tsp = ThreadedSequenceProcessor(process_fn)
tsp.start(verbose_loader(infile), outfp)
- print('output in', outfile, file=sys.stderr)
+ print >>sys.stderr, 'output in', outfile
if __name__ == '__main__':
main()
diff --git a/scripts/find-knots.py b/scripts/find-knots.py
index d224e06..bd41bfb 100755
--- a/scripts/find-knots.py
+++ b/scripts/find-knots.py
@@ -1,6 +1,6 @@
-#! /usr/bin/env python
+#! /usr/bin/env python2
#
-# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
+# This file is part of khmer, http://github.com/ged-lab/khmer/, and is
# Copyright (C) Michigan State University, 2009-2015. It is licensed under
# the three-clause BSD license; see LICENSE.
# Contact: khmer-project at idyll.org
@@ -13,7 +13,6 @@ k-mers are output into a .stoptags file, for later use in partitioning.
% python scripts/find-knots.py <base>
"""
-from __future__ import print_function
import argparse
import glob
@@ -22,9 +21,7 @@ import textwrap
import khmer
import sys
from khmer.kfile import check_input_files, check_space
-from khmer import khmer_args
-from khmer.khmer_args import (build_counting_args, info, add_loadhash_args,
- report_on_config)
+from khmer.khmer_args import info
# counting hash parameters.
DEFAULT_COUNTING_HT_SIZE = 3e6 # number of bytes
@@ -64,14 +61,21 @@ def get_parser():
process, and if you eliminate the already-processed pmap files, you can
continue where you left off.
"""
- parser = build_counting_args(
- descr="Find all highly connected k-mers.",
- epilog=textwrap.dedent(epilog))
-
+ parser = argparse.ArgumentParser(
+ description="Find all highly connected k-mers.",
+ epilog=textwrap.dedent(epilog),
+ formatter_class=argparse.ArgumentDefaultsHelpFormatter)
+
+ parser.add_argument('--n_tables', '-N', type=int,
+ default=DEFAULT_COUNTING_HT_N,
+ help='number of k-mer counting tables to use')
+ parser.add_argument('--min-tablesize', '-x', type=float,
+ default=DEFAULT_COUNTING_HT_SIZE, help='lower bound on'
+ ' the size of the k-mer counting table(s)')
parser.add_argument('graphbase', help='Basename for the input and output '
'files.')
- parser.add_argument('-f', '--force', default=False, action='store_true',
- help='Continue past warnings')
+ parser.add_argument('--version', action='version', version='%(prog)s ' +
+ khmer.__version__)
return parser
@@ -86,67 +90,65 @@ def main():
if os.path.exists(graphbase + '.stoptags'):
infiles.append(graphbase + '.stoptags')
for _ in infiles:
- check_input_files(_, args.force)
+ check_input_files(_, False)
- check_space(infiles, args.force)
+ check_space(infiles)
- print('loading k-mer presence table %s.pt' % graphbase, file=sys.stderr)
+ print >>sys.stderr, 'loading k-mer presence table %s.pt' % graphbase
htable = khmer.load_hashbits(graphbase + '.pt')
- print('loading tagset %s.tagset...' % graphbase, file=sys.stderr)
+ print >>sys.stderr, 'loading tagset %s.tagset...' % graphbase
htable.load_tagset(graphbase + '.tagset')
initial_stoptags = False # @CTB regularize with make-initial
if os.path.exists(graphbase + '.stoptags'):
- print('loading stoptags %s.stoptags' % graphbase, file=sys.stderr)
+ print >>sys.stderr, 'loading stoptags %s.stoptags' % graphbase
htable.load_stop_tags(graphbase + '.stoptags')
initial_stoptags = True
pmap_files = glob.glob(args.graphbase + '.subset.*.pmap')
- print('loading %d pmap files (first one: %s)' %
- (len(pmap_files), pmap_files[0]), file=sys.stderr)
- print('---', file=sys.stderr)
- print('output stoptags will be in',
- graphbase + '.stoptags', file=sys.stderr)
+ print >>sys.stderr, 'loading %d pmap files (first one: %s)' % \
+ (len(pmap_files), pmap_files[0])
+ print >>sys.stderr, '---'
+ print >>sys.stderr, 'output stoptags will be in', graphbase + '.stoptags'
if initial_stoptags:
- print(
- '(these output stoptags will include the already-loaded set)',
- file=sys.stderr)
- print('---', file=sys.stderr)
+ print >>sys.stderr, \
+ '(these output stoptags will include the already-loaded set)'
+ print >>sys.stderr, '---'
# create counting hash
ksize = htable.ksize()
- counting = khmer_args.create_countgraph(args, ksize=ksize)
+ counting = khmer.new_counting_hash(ksize, args.min_tablesize,
+ args.n_tables)
# load & merge
for index, subset_file in enumerate(pmap_files):
- print('<-', subset_file, file=sys.stderr)
+ print >>sys.stderr, '<-', subset_file
subset = htable.load_subset_partitionmap(subset_file)
- print('** repartitioning subset... %s' % subset_file, file=sys.stderr)
+ print >>sys.stderr, '** repartitioning subset... %s' % subset_file
htable.repartition_largest_partition(subset, counting,
EXCURSION_DISTANCE,
EXCURSION_KMER_THRESHOLD,
EXCURSION_KMER_COUNT_THRESHOLD)
- print('** merging subset... %s' % subset_file, file=sys.stderr)
+ print >>sys.stderr, '** merging subset... %s' % subset_file
htable.merge_subset(subset)
- print('** repartitioning, round 2... %s' %
- subset_file, file=sys.stderr)
+ print >>sys.stderr, '** repartitioning, round 2... %s' % subset_file
size = htable.repartition_largest_partition(
None, counting, EXCURSION_DISTANCE, EXCURSION_KMER_THRESHOLD,
EXCURSION_KMER_COUNT_THRESHOLD)
- print('** repartitioned size:', size, file=sys.stderr)
+ print >>sys.stderr, '** repartitioned size:', size
- print('saving stoptags binary', file=sys.stderr)
+ print >>sys.stderr, 'saving stoptags binary'
htable.save_stop_tags(graphbase + '.stoptags')
os.rename(subset_file, subset_file + '.processed')
- print('(%d of %d)\n' % (index, len(pmap_files)), file=sys.stderr)
+ print >>sys.stderr, '(%d of %d)\n' % (index, len(pmap_files))
- print('done!', file=sys.stderr)
+ print >>sys.stderr, 'done!'
if __name__ == '__main__':
main()
diff --git a/scripts/interleave-reads.py b/scripts/interleave-reads.py
index 94d5776..4f2696d 100755
--- a/scripts/interleave-reads.py
+++ b/scripts/interleave-reads.py
@@ -1,6 +1,6 @@
-#! /usr/bin/env python
+#! /usr/bin/env python2
#
-# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
+# This file is part of khmer, http://github.com/ged-lab/khmer/, and is
# Copyright (C) Michigan State University, 2009-2015. It is licensed under
# the three-clause BSD license; see LICENSE.
# Contact: khmer-project at idyll.org
@@ -16,13 +16,13 @@ and interleave them.
By default, output is sent to stdout; or use -o. Use '-h' for parameter help.
"""
-from __future__ import print_function
# TODO: take fa as well?
# support gzip option?
import screed
import sys
+import itertools
import os
import textwrap
import argparse
@@ -32,11 +32,6 @@ from khmer.khmer_args import info
from khmer.utils import (write_record_pair, check_is_left, check_is_right,
check_is_pair)
-try:
- from itertools import zip_longest
-except ImportError:
- from itertools import izip_longest as zip_longest
-
def get_parser():
epilog = """
@@ -82,38 +77,38 @@ def main():
else:
s2_file = s1_file.replace('_R1_', '_R2_')
if s1_file == s2_file:
- print(("ERROR: given only one filename, that "
- "doesn't contain _R1_. Exiting."), file=sys.stderr)
+ print >>sys.stderr, ("ERROR: given only one filename, that "
+ "doesn't contain _R1_. Exiting.")
sys.exit(1)
- print(("given only one file; "
- "guessing that R2 file is %s" % s2_file), file=sys.stderr)
+ print >> sys.stderr, ("given only one file; "
+ "guessing that R2 file is %s" % s2_file)
fail = False
if not os.path.exists(s1_file):
- print("Error! R1 file %s does not exist" % s1_file, file=sys.stderr)
+ print >> sys.stderr, "Error! R1 file %s does not exist" % s1_file
fail = True
if not os.path.exists(s2_file):
- print("Error! R2 file %s does not exist" % s2_file, file=sys.stderr)
+ print >> sys.stderr, "Error! R2 file %s does not exist" % s2_file
fail = True
if fail and not args.force:
sys.exit(1)
- print("Interleaving:\n\t%s\n\t%s" % (s1_file, s2_file), file=sys.stderr)
+ print >> sys.stderr, "Interleaving:\n\t%s\n\t%s" % (s1_file, s2_file)
counter = 0
screed_iter_1 = screed.open(s1_file, parse_description=False)
screed_iter_2 = screed.open(s2_file, parse_description=False)
- for read1, read2 in zip_longest(screed_iter_1, screed_iter_2):
+ for read1, read2 in itertools.izip_longest(screed_iter_1, screed_iter_2):
if read1 is None or read2 is None:
- print(("ERROR: Input files contain different number"
- " of records."), file=sys.stderr)
+ print >>sys.stderr, ("ERROR: Input files contain different number"
+ " of records.")
sys.exit(1)
if counter % 100000 == 0:
- print('...', counter, 'pairs', file=sys.stderr)
+ print >> sys.stderr, '...', counter, 'pairs'
counter += 1
name1 = read1.name
@@ -127,14 +122,14 @@ def main():
read2.name = name2
if not check_is_pair(read1, read2):
- print("ERROR: This doesn't look like paired data! "
- "%s %s" % (read1.name, read2.name), file=sys.stderr)
+ print >>sys.stderr, "ERROR: This doesn't look like paired data! " \
+ "%s %s" % (read1.name, read2.name)
sys.exit(1)
write_record_pair(read1, read2, args.output)
- print('final: interleaved %d pairs' % counter, file=sys.stderr)
- print('output written to', args.output.name, file=sys.stderr)
+ print >> sys.stderr, 'final: interleaved %d pairs' % counter
+ print >> sys.stderr, 'output written to', args.output.name
if __name__ == '__main__':
main()
diff --git a/scripts/load-graph.py b/scripts/load-graph.py
index 999403e..9fbc7a3 100755
--- a/scripts/load-graph.py
+++ b/scripts/load-graph.py
@@ -1,6 +1,6 @@
-#! /usr/bin/env python
+#! /usr/bin/env python2
#
-# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
+# This file is part of khmer, http://github.com/ged-lab/khmer/, and is
# Copyright (C) Michigan State University, 2009-2015. It is licensed under
# the three-clause BSD license; see LICENSE.
# Contact: khmer-project at idyll.org
@@ -13,7 +13,6 @@ Build a graph from the given sequences, save in <ptname>.
Use '-h' for parameter help.
"""
-from __future__ import print_function, unicode_literals
import sys
import threading
@@ -23,21 +22,101 @@ from khmer.khmer_args import build_hashbits_args
from khmer.khmer_args import (report_on_config, info, add_threading_args)
from khmer.kfile import check_input_files, check_space
from khmer.kfile import check_space_for_hashtable
-from oxli import build_graph
def get_parser():
parser = build_hashbits_args(descr="Load sequences into the compressible "
- "graph format plus optional tagset.")
-
- parser = build_graph.build_parser(parser)
+ "graph format plus optional tagset.")
+ add_threading_args(parser)
+ parser.add_argument('--no-build-tagset', '-n', default=False,
+ action='store_true', dest='no_build_tagset',
+ help='Do NOT construct tagset while loading sequences')
+ parser.add_argument('output_filename',
+ metavar='output_presence_table_filename', help='output'
+ ' k-mer presence table filename.')
+ parser.add_argument('input_filenames', metavar='input_sequence_filename',
+ nargs='+', help='input FAST[AQ] sequence filename')
+ parser.add_argument('--report-total-kmers', '-t', action='store_true',
+ help="Prints the total number of k-mers to stderr")
+ parser.add_argument('--write-fp-rate', '-w', action='store_true',
+ help="Write false positive rate into .info file")
+ parser.add_argument('-f', '--force', default=False, action='store_true',
+ help='Overwrite output file if it exists')
return parser
+def main():
+ info('load-graph.py', ['graph', 'SeqAn'])
+ args = get_parser().parse_args()
+ report_on_config(args, hashtype='hashbits')
+
+ base = args.output_filename
+ filenames = args.input_filenames
+
+ for _ in args.input_filenames:
+ check_input_files(_, args.force)
+
+ check_space(args.input_filenames, args.force)
+ check_space_for_hashtable(
+ (float(args.n_tables * args.min_tablesize) / 8.), args.force)
+
+ print >>sys.stderr, 'Saving k-mer presence table to %s' % base
+ print >>sys.stderr, 'Loading kmers from sequences in %s' % repr(filenames)
+ if args.no_build_tagset:
+ print >>sys.stderr, 'We WILL NOT build the tagset.'
+ else:
+ print >>sys.stderr, 'We WILL build the tagset', \
+ ' (for partitioning/traversal).'
+
+ print >>sys.stderr, 'making k-mer presence table'
+ htable = khmer.new_hashbits(args.ksize, args.min_tablesize, args.n_tables)
+
+ if args.no_build_tagset:
+ target_method = htable.consume_fasta_with_reads_parser
+ else:
+ target_method = htable.consume_fasta_and_tag_with_reads_parser
+
+ for _, filename in enumerate(filenames):
+ rparser = khmer.ReadParser(filename)
+ threads = []
+ print >>sys.stderr, 'consuming input', filename
+ for num in xrange(args.threads):
+ cur_thread = threading.Thread(
+ target=target_method, args=(rparser,))
+ threads.append(cur_thread)
+ cur_thread.start()
+
+ for thread in threads:
+ thread.join()
+
+ if args.report_total_kmers:
+ print >> sys.stderr, 'Total number of unique k-mers: {0}'.format(
+ htable.n_unique_kmers())
+
+ print >>sys.stderr, 'saving k-mer presence table in', base + '.pt'
+ htable.save(base + '.pt')
+
+ if not args.no_build_tagset:
+ print >>sys.stderr, 'saving tagset in', base + '.tagset'
+ htable.save_tagset(base + '.tagset')
+
+ info_fp = open(base + '.info', 'w')
+ info_fp.write('%d unique k-mers' % htable.n_unique_kmers())
+
+ fp_rate = \
+ khmer.calc_expected_collisions(htable, args.force, max_false_pos=.15)
+ # 0.18 is ACTUAL MAX. Do not change.
+
+ print >>sys.stderr, 'fp rate estimated to be %1.3f' % fp_rate
+ if args.write_fp_rate:
+ print >> info_fp, \
+ '\nfalse positive rate estimated to be %1.3f' % fp_rate
+
+ print >> sys.stderr, 'wrote to', base + '.info and', base + '.pt'
+ if not args.no_build_tagset:
+ print >> sys.stderr, 'and ' + base + '.tagset'
+
if __name__ == '__main__':
- parser = get_parser()
- args = parser.parse_args()
- build_graph.main(args)
- sys.exit(0)
+ main()
# vim: set ft=python ts=4 sts=4 sw=4 et tw=79:
diff --git a/scripts/load-into-counting.py b/scripts/load-into-counting.py
index f907c36..b81e767 100755
--- a/scripts/load-into-counting.py
+++ b/scripts/load-into-counting.py
@@ -1,6 +1,6 @@
-#! /usr/bin/env python
+#! /usr/bin/env python2
#
-# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
+# This file is part of khmer, http://github.com/ged-lab/khmer/, and is
# Copyright (C) Michigan State University, 2009-2015. It is licensed under
# the three-clause BSD license; see LICENSE.
# Contact: khmer-project at idyll.org
@@ -12,7 +12,6 @@ Build a counting Bloom filter from the given sequences, save in <htname>.
Use '-h' for parameter help.
"""
-from __future__ import print_function, unicode_literals
import json
import os
@@ -20,7 +19,6 @@ import sys
import threading
import textwrap
import khmer
-from khmer import khmer_args
from khmer.khmer_args import build_counting_args, report_on_config, info,\
add_threading_args
from khmer.kfile import check_file_writable
@@ -60,8 +58,8 @@ def get_parser():
action='store_false', help="The default behaviour is "
"to count past 255 using bigcount. This flag turns "
"bigcount off, limiting counts to 255.")
- parser.add_argument('--summary-info', '-s', type=str, default=None,
- metavar="FORMAT", choices=[str('json'), str('tsv')],
+ parser.add_argument('--summary-info', '-s', default=None, metavar="FORMAT",
+ choices=['json', 'tsv'],
help="What format should the machine readable run "
"summary be in? (json or tsv, disabled by default)")
parser.add_argument('--report-total-kmers', '-t', action='store_true',
@@ -85,21 +83,21 @@ def main():
check_input_files(name, args.force)
check_space(args.input_sequence_filename, args.force)
- check_space_for_hashtable(args, 'countgraph', args.force)
+ check_space_for_hashtable(args.n_tables * args.min_tablesize, args.force)
check_file_writable(base)
check_file_writable(base + ".info")
- print('Saving k-mer counting table to %s' % base, file=sys.stderr)
- print('Loading kmers from sequences in %s' %
- repr(filenames), file=sys.stderr)
+ print >>sys.stderr, 'Saving k-mer counting table to %s' % base
+ print >>sys.stderr, 'Loading kmers from sequences in %s' % repr(filenames)
# clobber the '.info' file now, as we always open in append mode below
if os.path.exists(base + '.info'):
os.remove(base + '.info')
- print('making countgraph', file=sys.stderr)
- htable = khmer_args.create_countgraph(args)
+ print >>sys.stderr, 'making k-mer counting table'
+ htable = khmer.new_counting_hash(args.ksize, args.min_tablesize,
+ args.n_tables)
htable.set_use_bigcount(args.bigcount)
filename = None
@@ -110,8 +108,8 @@ def main():
rparser = khmer.ReadParser(filename)
threads = []
- print('consuming input', filename, file=sys.stderr)
- for _ in range(args.threads):
+ print >>sys.stderr, 'consuming input', filename
+ for _ in xrange(args.threads):
cur_thrd = \
threading.Thread(
target=htable.consume_fasta_with_reads_parser,
@@ -124,21 +122,21 @@ def main():
thread.join()
if index > 0 and index % 10 == 0:
- check_space_for_hashtable(args, 'countgraph', args.force)
- print('mid-save', base, file=sys.stderr)
-
+ check_space_for_hashtable(args.n_tables * args.min_tablesize,
+ args.force)
+ print >>sys.stderr, 'mid-save', base
htable.save(base)
with open(base + '.info', 'a') as info_fh:
- print('through', filename, file=info_fh)
+ print >> info_fh, 'through', filename
total_num_reads += rparser.num_reads
n_kmers = htable.n_unique_kmers()
if args.report_total_kmers:
- print('Total number of unique k-mers:', n_kmers, file=sys.stderr)
+ print >> sys.stderr, 'Total number of unique k-mers:', n_kmers
with open(base + '.info', 'a') as info_fp:
- print('Total number of unique k-mers:', n_kmers, file=info_fp)
+ print >>info_fp, 'Total number of unique k-mers:', n_kmers
- print('saving', base, file=sys.stderr)
+ print >>sys.stderr, 'saving', base
htable.save(base)
# Change max_false_pos=0.2 only if you really grok it. HINT: You don't
@@ -146,12 +144,12 @@ def main():
khmer.calc_expected_collisions(htable, args.force, max_false_pos=.2)
with open(base + '.info', 'a') as info_fp:
- print('fp rate estimated to be %1.3f\n' % fp_rate, file=info_fp)
+ print >> info_fp, 'fp rate estimated to be %1.3f\n' % fp_rate
if args.summary_info:
mr_fmt = args.summary_info.lower()
mr_file = base + '.info.' + mr_fmt
- print("Writing summmary info to", mr_file, file=sys.stderr)
+ print >> sys.stderr, "Writing summmary info to", mr_file
with open(mr_file, 'w') as mr_fh:
if mr_fmt == 'json':
mr_data = {
@@ -175,10 +173,10 @@ def main():
]
mr_fh.write("\t".join(vals) + "\n")
- print('fp rate estimated to be %1.3f' % fp_rate, file=sys.stderr)
+ print >> sys.stderr, 'fp rate estimated to be %1.3f' % fp_rate
- print('DONE.', file=sys.stderr)
- print('wrote to:', base + '.info', file=sys.stderr)
+ print >>sys.stderr, 'DONE.'
+ print >>sys.stderr, 'wrote to:', base + '.info'
if __name__ == '__main__':
main()
diff --git a/scripts/make-initial-stoptags.py b/scripts/make-initial-stoptags.py
index 29a08ef..48a2741 100755
--- a/scripts/make-initial-stoptags.py
+++ b/scripts/make-initial-stoptags.py
@@ -1,6 +1,6 @@
-#! /usr/bin/env python
+#! /usr/bin/env python2
#
-# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
+# This file is part of khmer, http://github.com/ged-lab/khmer/, and is
# Copyright (C) Michigan State University, 2009-2015. It is licensed under
# the three-clause BSD license; see LICENSE.
# Contact: khmer-project at idyll.org
@@ -11,12 +11,10 @@ Find an initial set of highly connected k-mers, to save on repartitioning time.
% python scripts/make-initial-stoptags.py <base>
"""
-from __future__ import print_function
import sys
import textwrap
import khmer
-from khmer import khmer_args
from khmer.khmer_args import (build_counting_args, info)
from khmer.kfile import check_input_files, check_space
@@ -85,19 +83,20 @@ def main():
check_space(infiles, args.force)
- print('loading htable %s.pt' % graphbase, file=sys.stderr)
+ print >>sys.stderr, 'loading htable %s.pt' % graphbase
htable = khmer.load_hashbits(graphbase + '.pt')
# do we want to load stop tags, and do they exist?
if args.stoptags:
- print('loading stoptags from', args.stoptags, file=sys.stderr)
+ print >>sys.stderr, 'loading stoptags from', args.stoptags
htable.load_stop_tags(args.stoptags)
- print('loading tagset %s.tagset...' % graphbase, file=sys.stderr)
+ print >>sys.stderr, 'loading tagset %s.tagset...' % graphbase
htable.load_tagset(graphbase + '.tagset')
ksize = htable.ksize()
- counting = khmer_args.create_countgraph(args)
+ counting = khmer.new_counting_hash(ksize, args.min_tablesize,
+ args.n_tables)
# divide up into SUBSET_SIZE fragments
divvy = htable.divide_tags_into_subsets(args.subset_size)
@@ -109,19 +108,19 @@ def main():
start, end = divvy[:2]
# partition!
- print('doing pre-partitioning from', start, 'to', end, file=sys.stderr)
+ print >>sys.stderr, 'doing pre-partitioning from', start, 'to', end
subset = htable.do_subset_partition(start, end)
# now, repartition...
- print('repartitioning to find HCKs.', file=sys.stderr)
+ print >>sys.stderr, 'repartitioning to find HCKs.'
htable.repartition_largest_partition(subset, counting,
EXCURSION_DISTANCE,
EXCURSION_KMER_THRESHOLD,
EXCURSION_KMER_COUNT_THRESHOLD)
- print('saving stop tags', file=sys.stderr)
+ print >>sys.stderr, 'saving stop tags'
htable.save_stop_tags(graphbase + '.stoptags')
- print('wrote to:', graphbase + '.stoptags', file=sys.stderr)
+ print >> sys.stderr, 'wrote to:', graphbase + '.stoptags'
if __name__ == '__main__':
main()
diff --git a/scripts/merge-partitions.py b/scripts/merge-partitions.py
index c77d822..99f6a84 100755
--- a/scripts/merge-partitions.py
+++ b/scripts/merge-partitions.py
@@ -1,6 +1,6 @@
-#! /usr/bin/env python
+#! /usr/bin/env python2
#
-# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
+# This file is part of khmer, http://github.com/ged-lab/khmer/, and is
# Copyright (C) Michigan State University, 2009-2015. It is licensed under
# the three-clause BSD license; see LICENSE.
# Contact: khmer-project at idyll.org
@@ -14,7 +14,6 @@ Merge multiple pmap files into a single one.
Load <base>.subset.*.pmap and merge into a single pmap file. Final
merged pmap file will be in <base>.pmap.merged.
"""
-from __future__ import print_function
import argparse
import glob
@@ -57,11 +56,11 @@ def main():
output_file = args.graphbase + '.pmap.merged'
pmap_files = glob.glob(args.graphbase + '.subset.*.pmap')
- print('loading %d pmap files (first one: %s)' %
- (len(pmap_files), pmap_files[0]), file=sys.stderr)
+ print >>sys.stderr, 'loading %d pmap files (first one: %s)' % \
+ (len(pmap_files), pmap_files[0])
ksize = args.ksize
- htable = khmer.Hashbits(ksize, 1, 1)
+ htable = khmer.new_hashbits(ksize, 1, 1)
for _ in pmap_files:
check_input_files(_, args.force)
@@ -69,14 +68,14 @@ def main():
check_space(pmap_files, args.force)
for pmap_file in pmap_files:
- print('merging', pmap_file, file=sys.stderr)
+ print >>sys.stderr, 'merging', pmap_file
htable.merge_subset_from_disk(pmap_file)
- print('saving merged to', output_file, file=sys.stderr)
+ print >>sys.stderr, 'saving merged to', output_file
htable.save_partitionmap(output_file)
if args.remove_subsets:
- print('removing pmap files', file=sys.stderr)
+ print >>sys.stderr, 'removing pmap files'
for pmap_file in pmap_files:
os.unlink(pmap_file)
diff --git a/scripts/normalize-by-median.py b/scripts/normalize-by-median.py
index 3bb2ba7..22c84dc 100755
--- a/scripts/normalize-by-median.py
+++ b/scripts/normalize-by-median.py
@@ -1,6 +1,6 @@
-#! /usr/bin/env python
+#! /usr/bin/env python2
#
-# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
+# This file is part of khmer, http://github.com/ged-lab/khmer/, and is
# Copyright (C) Michigan State University, 2009-2015. It is licensed under
# the three-clause BSD license; see LICENSE.
# Contact: khmer-project at idyll.org
@@ -17,139 +17,162 @@ option to output to STDOUT.
Use '-h' for parameter help.
"""
-from __future__ import print_function
import sys
import screed
import os
import khmer
import textwrap
-from khmer import khmer_args
-from contextlib import contextmanager
-
+from itertools import izip
from khmer.khmer_args import (build_counting_args, add_loadhash_args,
report_on_config, info)
import argparse
from khmer.kfile import (check_space, check_space_for_hashtable,
check_valid_file_exists)
-from khmer.utils import write_record, check_is_pair, broken_paired_reader
+from khmer.utils import write_record, check_is_pair
+DEFAULT_DESIRED_COVERAGE = 10
+# Iterate a collection in arbitrary batches
+# from: http://stackoverflow.com/questions/4628290/pairs-from-single-list
-DEFAULT_DESIRED_COVERAGE = 20
+def batchwise(coll, size):
+ iter_coll = iter(coll)
+ return izip(*[iter_coll] * size)
-def WithDiagnostics(ifilename, norm, reader, fp):
- """
- Generator/context manager to do boilerplate output of statistics using a
- Normalizer object.
- """
+# Returns true if the pair of records are properly pairs
- index = 0
- # per read diagnostic output
- for index, record in enumerate(norm(reader)):
+# pylint: disable=too-many-locals,too-many-branches
+def normalize_by_median(input_filename, outfp, htable, paired, cutoff,
+ report_fp=None):
- if norm.total % 100000 == 0:
- print('... kept {kept} of {total} or {perc:2}% so far'
- .format(kept=norm.total - norm.discarded,
- total=norm.total,
- perc=int(100. - norm.discarded /
- float(norm.total) * 100.)),
- file=sys.stderr)
+ desired_coverage = cutoff
+ ksize = htable.ksize()
- print('... in file ' + ifilename, file=sys.stderr)
+ # In paired mode we read two records at a time
+ batch_size = 1
+ if paired:
+ batch_size = 2
- yield record
+ index = -1
+ total = 0
+ discarded = 0
+ for index, batch in enumerate(batchwise(screed.open(
+ input_filename, parse_description=False), batch_size)):
+ if index > 0 and index % 100000 == 0:
+ print >>sys.stderr, '... kept {kept} of {total} or'\
+ ' {perc:2}%'.format(kept=total - discarded, total=total,
+ perc=int(100. - discarded /
+ float(total) * 100.))
+ print >>sys.stderr, '... in file', input_filename
- # per file diagnostic output
- if norm.total == 0:
- print('SKIPPED empty file ' + ifilename, file=sys.stderr)
- else:
- print('DONE with {inp}; kept {kept} of {total} or {perc:2}%'
- .format(inp=ifilename, kept=norm.total - norm.discarded,
- total=norm.total, perc=int(100. - norm.discarded /
- float(norm.total) * 100.)),
- file=sys.stderr)
+ if report_fp:
+ print >> report_fp, total, total - discarded, \
+ 1. - (discarded / float(total))
+ report_fp.flush()
- if fp:
- print("{total} {kept} {discarded}"
- .format(total=norm.total, kept=norm.total - norm.discarded,
- discarded=1. - (norm.discarded / float(norm.total))),
- file=fp)
- fp.flush()
+ total += batch_size
+ # If in paired mode, check that the reads are properly interleaved
-class Normalizer(object):
- """
- Digital normalization algorithm.
- """
+ if paired:
+ if not check_is_pair(batch[0], batch[1]):
+ raise IOError('Error: Improperly interleaved pairs \
+ {b0} {b1}'.format(b0=batch[0].name, b1=batch[1].name))
- def __init__(self, desired_coverage, htable):
- self.htable = htable
- self.desired_coverage = desired_coverage
+ # Emit the batch of reads if any read passes the filter
+ # and all reads are longer than K
+ passed_filter = False
+ passed_length = True
+ for record in batch:
+ if len(record.sequence) < ksize:
+ passed_length = False
+ continue
- self.total = 0
- self.discarded = 0
+ seq = record.sequence.replace('N', 'A')
+ med, _, _ = htable.get_median_count(seq)
- def __call__(self, reader):
- """
- Actually does digital normalization - the core algorithm.
+ if med < desired_coverage:
+ htable.consume(seq)
+ passed_filter = True
- * get one (unpaired) or two (paired) reads;
- * sanitize the sequences (convert Ns to As);
- * get the median k-mer count of one/both reads;
- * if any read's median k-mer count is below desired coverage, keep all;
- * consume and yield kept reads.
- """
+ # Emit records if any passed
+ if passed_length and passed_filter:
+ for record in batch:
+ write_record(record, outfp)
+ else:
+ discarded += batch_size
- desired_coverage = self.desired_coverage
+ if report_fp:
+ print >> report_fp, total, total - discarded, \
+ 1. - (discarded / float(total))
+ report_fp.flush()
- for index, is_paired, read0, read1 in reader:
- passed_filter = False
+ return total, discarded
- self.total += 1
- if is_paired:
- self.total += 1
+def handle_error(error, output_name, input_name, fail_save, htable):
+ print >> sys.stderr, '** ERROR:', error
+ print >> sys.stderr, '** Failed on {name}: '.format(name=input_name)
+ if fail_save:
+ tablename = os.path.basename(input_name) + '.ct.failed'
+ print >> sys.stderr, \
+ '** ...dumping k-mer counting table to {tn}'.format(tn=tablename)
+ htable.save(tablename)
+ try:
+ os.remove(output_name)
+ except: # pylint: disable=bare-except
+ print >> sys.stderr, '** ERROR: problem removing corrupt filtered file'
- batch = []
- batch.append(read0)
- if read1 is not None:
- batch.append(read1)
- for record in batch:
- seq = record.sequence.replace('N', 'A')
- if not self.htable.median_at_least(seq, desired_coverage):
- passed_filter = True
-
- if passed_filter:
- for record in batch:
- seq = record.sequence.replace('N', 'A')
- self.htable.consume(seq)
- yield record
- else:
- self.discarded += len(batch)
+def normalize_by_median_and_check(input_filename, htable, single_output_file,
+ fail_save, paired, cutoff, force,
+ corrupt_files, report_fp=None):
+ total = 0
+ discarded = 0
+ total_acc = None
+ discarded_acc = None
+
+ if single_output_file:
+ if single_output_file is sys.stdout:
+ output_name = '/dev/stdout'
+ else:
+ output_name = single_output_file.name
+ outfp = single_output_file
+
+ else:
+ output_name = os.path.basename(input_filename) + '.keep'
+ outfp = open(output_name, 'w')
- at contextmanager
-def CatchIOErrors(ifile, out, single_out, force, corrupt_files):
- """
- Context manager to do boilerplate handling of IOErrors.
- """
try:
- yield
- except (IOError, ValueError) as error:
- print('** ERROR: ' + str(error), file=sys.stderr)
- print('** Failed on {name}: '.format(name=ifile), file=sys.stderr)
- if not single_out:
- os.remove(out.name)
+ total_acc, discarded_acc = normalize_by_median(
+ input_filename, outfp, htable, paired, cutoff, report_fp=None)
+ except IOError as err:
+ handle_error(err, output_name, input_filename, fail_save,
+ htable)
if not force:
- print('** Exiting!', file=sys.stderr)
+ print >> sys.stderr, '** Exiting!'
sys.exit(1)
else:
- print('*** Skipping error file, moving on...', file=sys.stderr)
- corrupt_files.append(ifile)
+ print >> sys.stderr, '*** Skipping error file, moving on...'
+ corrupt_files.append(input_filename)
+ else:
+ if total_acc == 0 and discarded_acc == 0:
+ print >> sys.stderr, 'SKIPPED empty file', input_filename
+ else:
+ total += total_acc
+ discarded += discarded_acc
+ print >> sys.stderr, \
+ 'DONE with {inp}; kept {kept} of {total} or {perc:2}%'\
+ .format(inp=input_filename, kept=total - discarded,
+ total=total, perc=int(100. - discarded /
+ float(total) * 100.))
+ print >> sys.stderr, 'output in', output_name
+
+ return total_acc, discarded_acc, corrupt_files
def get_parser():
@@ -157,18 +180,12 @@ def get_parser():
Discard sequences based on whether or not their median k-mer abundance lies
above a specified cutoff. Kept sequences will be placed in <fileN>.keep.
- By default, paired end reads will be considered together; if
- either read should be kept, both will be kept. (This keeps both
- reads from a fragment, and helps with retention of repeats.)
- Unpaired reads are treated individually.
-
- If :option:`-p`/`--paired` is set, then proper pairing is required
- and the script will exit on unpaired reads, although
- :option:`--unpaired-reads` can be used to supply a file of orphan
- reads to be read after the paired reads.
-
- :option:`--force-single` will ignore all pairing information and treat
- reads individually.
+ Paired end reads will be considered together if :option:`-p` is set. If
+ either read will be kept, then both will be kept. This should result in
+ keeping (or discarding) each sequencing fragment. This helps with retention
+ of repeats, especially. With :option: `-u`/:option:`--unpaired-reads`,
+ unpaired reads from the specified file will be read after the paired data
+ is read.
With :option:`-s`/:option:`--savetable`, the k-mer counting table
will be saved to the specified file after all sequences have been
@@ -181,6 +198,11 @@ def get_parser():
produced by :program:`load-into-counting.py` and consumed by
:program:`abundance-dist.py`.
+ :option:`-f`/:option:`--fault-tolerant` will force the program to continue
+ upon encountering a formatting error in a sequence file; the k-mer counting
+ table up to that point will be dumped, and processing will continue on the
+ next file.
+
To append reads to an output file (rather than overwriting it), send output
to STDOUT with `--out -` and use UNIX file redirection syntax (`>>`) to
append to the file.
@@ -212,23 +234,24 @@ def get_parser():
epilog=textwrap.dedent(epilog))
parser.add_argument('-C', '--cutoff', type=int,
default=DEFAULT_DESIRED_COVERAGE)
- parser.add_argument('-p', '--paired', action='store_true',
- help='require that all sequences be properly paired')
- parser.add_argument('--force-single', dest='force_single',
- action='store_true',
- help='treat all sequences as single-ended/unpaired')
+ parser.add_argument('-p', '--paired', action='store_true')
parser.add_argument('-u', '--unpaired-reads',
- metavar="unpaired_reads_filename",
- help='include a file of unpaired reads to which '
- '-p/--paired does not apply.')
+ metavar="unpaired_reads_filename", help='with paired data only,\
+ include an unpaired file')
parser.add_argument('-s', '--savetable', metavar="filename", default='',
help='save the k-mer counting table to disk after all'
'reads are loaded.')
parser.add_argument('-R', '--report',
metavar='filename', type=argparse.FileType('w'))
- parser.add_argument('-f', '--force', dest='force',
+ parser.add_argument('-f', '--fault-tolerant', dest='force',
help='continue on next file if read errors are \
encountered', action='store_true')
+ parser.add_argument('--save-on-failure', dest='fail_save',
+ action='store_false', default=True,
+ help='Save k-mer counting table when an error occurs')
+ parser.add_argument('-d', '--dump-frequency', dest='dump_frequency',
+ type=int, help='dump k-mer counting table every d '
+ 'files', default=-1)
parser.add_argument('-o', '--out', metavar="filename",
dest='single_output_file',
type=argparse.FileType('w'),
@@ -238,6 +261,11 @@ def get_parser():
'terminal)')
parser.add_argument('input_filenames', metavar='input_sequence_filename',
help='Input FAST[AQ] sequence filename.', nargs='+')
+ parser.add_argument('--report-total-kmers', '-t', action='store_true',
+ help="Prints the total number of k-mers"
+ " post-normalization to stderr")
+ parser.add_argument('--force', default=False, action='store_true',
+ help='Overwrite output file if it exists')
add_loadhash_args(parser)
return parser
@@ -249,116 +277,88 @@ def main(): # pylint: disable=too-many-branches,too-many-statements
report_on_config(args)
report_fp = args.report
- force_single = args.force_single
# check for similar filenames
- # if we're using a single output file only check for identical filenames
- # otherwise, check for identical BASE names as well.
filenames = []
- basenames = []
for pathfilename in args.input_filenames:
- filenames.append(pathfilename)
- if args.single_output_file:
- continue # nothing more to worry about
-
- basename = os.path.basename(pathfilename)
- if basename in basenames:
- print('ERROR: Duplicate filename--Cannot handle this!',
- file=sys.stderr)
- print('** Exiting!', file=sys.stderr)
- sys.exit(1)
-
- basenames.append(basename)
+ filename = pathfilename.split('/')[-1]
+ if (filename in filenames):
+ print >>sys.stderr, "WARNING: At least two input files are named \
+%s . (The script normalize-by-median.py can not handle this, only one .keep \
+file for one of the input files will be generated.)" % filename
+ else:
+ filenames.append(filename)
- # check that files exist and there is sufficient output disk space.
+ # check for others
check_valid_file_exists(args.input_filenames)
check_space(args.input_filenames, args.force)
if args.savetable:
- check_space_for_hashtable(args, 'countgraph', args.force)
+ check_space_for_hashtable(
+ args.n_tables * args.min_tablesize, args.force)
+
+ # list to save error files along with throwing exceptions
+ corrupt_files = []
- # load or create counting table.
if args.loadtable:
- print('loading k-mer counting table from ' + args.loadtable,
- file=sys.stderr)
+ print 'loading k-mer counting table from', args.loadtable
htable = khmer.load_counting_hash(args.loadtable)
else:
- print('making countgraph', file=sys.stderr)
- htable = khmer_args.create_countgraph(args)
+ print >> sys.stderr, 'making k-mer counting table'
+ htable = khmer.new_counting_hash(args.ksize, args.min_tablesize,
+ args.n_tables)
input_filename = None
- # create an object to handle diginorm of all files
- norm = Normalizer(args.cutoff, htable)
-
- # make a list of all filenames and if they're paired or not;
- # if we don't know if they're paired, default to allowing but not
- # forcing pairing.
- files = []
- for e in filenames:
- files.append([e, args.paired])
- if args.unpaired_reads:
- files.append([args.unpaired_reads, False])
-
- corrupt_files = []
- outfp = None
- output_name = None
-
- if args.single_output_file:
- if args.single_output_file is sys.stdout:
- output_name = '/dev/stdout'
- else:
- output_name = args.single_output_file.name
- outfp = args.single_output_file
-
- #
- # main loop: iterate over all files given, do diginorm.
- #
+ for index, input_filename in enumerate(args.input_filenames):
+ total_acc, discarded_acc, corrupt_files = \
+ normalize_by_median_and_check(
+ input_filename, htable, args.single_output_file,
+ args.fail_save, args.paired, args.cutoff, args.force,
+ corrupt_files, report_fp)
+
+ if (args.dump_frequency > 0 and
+ index > 0 and index % args.dump_frequency == 0):
+ print 'Backup: Saving k-mer counting file through', input_filename
+ if args.savetable:
+ hashname = args.savetable
+ print '...saving to', hashname
+ else:
+ hashname = 'backup.ct'
+ print 'Nothing given for savetable, saving to', hashname
+ htable.save(hashname)
- for filename, require_paired in files:
+ if args.paired and args.unpaired_reads:
+ args.paired = False
+ output_name = args.unpaired_reads
if not args.single_output_file:
- output_name = os.path.basename(filename) + '.keep'
- outfp = open(output_name, 'w')
-
- # failsafe context manager in case an input file breaks
- with CatchIOErrors(filename, outfp, args.single_output_file,
- args.force, corrupt_files):
-
- screed_iter = screed.open(filename, parse_description=False)
- reader = broken_paired_reader(screed_iter, min_length=args.ksize,
- force_single=force_single,
- require_paired=require_paired)
-
- # actually do diginorm
- for record in WithDiagnostics(filename, norm, reader, report_fp):
- if record is not None:
- write_record(record, outfp)
-
- print('output in ' + output_name, file=sys.stderr)
- if output_name is not '/dev/stdout':
- outfp.close()
-
- # finished - print out some diagnostics.
-
- print('Total number of unique k-mers: {0}'
- .format(htable.n_unique_kmers()),
- file=sys.stderr)
+ output_name = os.path.basename(args.unpaired_reads) + '.keep'
+ outfp = open(output_name, 'w')
+ total_acc, discarded_acc, corrupt_files = \
+ normalize_by_median_and_check(
+ args.unpaired_reads, htable, args.single_output_file,
+ args.fail_save, args.paired, args.cutoff, args.force,
+ corrupt_files, report_fp)
+
+ if args.report_total_kmers:
+ print >> sys.stderr, 'Total number of unique k-mers: {0}'.format(
+ htable.n_unique_kmers())
if args.savetable:
- print('...saving to ' + args.savetable, file=sys.stderr)
+ print 'Saving k-mer counting table through', input_filename
+ print '...saving to', args.savetable
htable.save(args.savetable)
fp_rate = \
khmer.calc_expected_collisions(htable, args.force, max_false_pos=.8)
# for max_false_pos see Zhang et al., http://arxiv.org/abs/1309.2975
- print('fp rate estimated to be {fpr:1.3f}'.format(fpr=fp_rate),
- file=sys.stderr)
+ print >> sys.stderr, \
+ 'fp rate estimated to be {fpr:1.3f}'.format(fpr=fp_rate)
if args.force and len(corrupt_files) > 0:
- print("** WARNING: Finished with errors!", file=sys.stderr)
- print("** IOErrors occurred in the following files:", file=sys.stderr)
- print("\t", " ".join(corrupt_files), file=sys.stderr)
-
+ print >> sys.stderr, "** WARNING: Finished with errors!"
+ print >> sys.stderr, "** IOErrors occurred in the following files:"
+ print >> sys.stderr, "\t", " ".join(corrupt_files)
if __name__ == '__main__':
main()
diff --git a/scripts/partition-graph.py b/scripts/partition-graph.py
index 73666e2..63f1e1a 100755
--- a/scripts/partition-graph.py
+++ b/scripts/partition-graph.py
@@ -1,6 +1,6 @@
-#! /usr/bin/env python
+#! /usr/bin/env python2
#
-# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
+# This file is part of khmer, http://github.com/ged-lab/khmer/, and is
# Copyright (C) Michigan State University, 2009-2015. It is licensed under
# the three-clause BSD license; see LICENSE.
# Contact: khmer-project at idyll.org
@@ -15,9 +15,9 @@ This will output many <base>.subset.N.pmap files.
Use '-h' for parameter help.
"""
-from __future__ import print_function
import threading
+import Queue
import gc
import os.path
import argparse
@@ -31,19 +31,13 @@ import re
import platform
if "Linux" == platform.system():
def __debug_vm_usage(msg):
- print("===> DEBUG: " + msg, file=sys.stderr)
+ print >>sys.stderr, "===> DEBUG: " + msg
for vmstat in re.findall(r".*Vm.*", file("/proc/self/status").read()):
- print(vmstat, file=sys.stderr)
+ print >>sys.stderr, vmstat
else:
def __debug_vm_usage(msg): # pylint: disable=unused-argument
pass
-# stdlib queue module was renamed on Python 3
-try:
- import queue
-except ImportError:
- import Queue as queue
-
DEFAULT_SUBSET_SIZE = int(1e5)
DEFAULT_N_THREADS = 4
@@ -52,23 +46,23 @@ def worker(queue, basename, stop_big_traversals):
while True:
try:
(htable, index, start, stop) = queue.get(False)
- except queue.Empty:
- print('exiting', file=sys.stderr)
+ except Queue.Empty:
+ print >>sys.stderr, 'exiting'
return
outfile = basename + '.subset.%d.pmap' % (index,)
if os.path.exists(outfile):
- print('SKIPPING', outfile, ' -- already exists', file=sys.stderr)
+ print >>sys.stderr, 'SKIPPING', outfile, ' -- already exists'
continue
- print('starting:', basename, index, file=sys.stderr)
+ print >>sys.stderr, 'starting:', basename, index
# pay attention to stoptags when partitioning; take command line
# direction on whether or not to exhaustively traverse.
subset = htable.do_subset_partition(start, stop, True,
stop_big_traversals)
- print('saving:', basename, index, file=sys.stderr)
+ print >>sys.stderr, 'saving:', basename, index
htable.save_subset_partitionmap(subset, outfile)
del subset
gc.collect()
@@ -113,30 +107,30 @@ def main():
check_space(filenames, args.force)
- print('--', file=sys.stderr)
- print('SUBSET SIZE', args.subset_size, file=sys.stderr)
- print('N THREADS', args.threads, file=sys.stderr)
+ print >>sys.stderr, '--'
+ print >>sys.stderr, 'SUBSET SIZE', args.subset_size
+ print >>sys.stderr, 'N THREADS', args.threads
if args.stoptags:
- print('stoptag file:', args.stoptags, file=sys.stderr)
- print('--', file=sys.stderr)
+ print >>sys.stderr, 'stoptag file:', args.stoptags
+ print >>sys.stderr, '--'
- print('loading ht %s.pt' % basename, file=sys.stderr)
+ print >>sys.stderr, 'loading ht %s.pt' % basename
htable = khmer.load_hashbits(basename + '.pt')
htable.load_tagset(basename + '.tagset')
# do we want to load stop tags, and do they exist?
if args.stoptags:
- print('loading stoptags from', args.stoptags, file=sys.stderr)
+ print >>sys.stderr, 'loading stoptags from', args.stoptags
htable.load_stop_tags(args.stoptags)
# do we want to exhaustively traverse the graph?
stop_big_traversals = args.no_big_traverse
if stop_big_traversals:
- print('** This script brakes for lumps:',
- ' stop_big_traversals is true.', file=sys.stderr)
+ print >>sys.stderr, '** This script brakes for lumps:', \
+ ' stop_big_traversals is true.'
else:
- print('** Traverse all the things:',
- ' stop_big_traversals is false.', file=sys.stderr)
+ print >>sys.stderr, '** Traverse all the things:', \
+ ' stop_big_traversals is false.'
#
# now, partition!
@@ -148,7 +142,7 @@ def main():
divvy.append(0)
# build a queue of tasks:
- worker_q = queue.Queue()
+ worker_q = Queue.Queue()
# break up the subsets into a list of worker tasks
for _ in range(0, n_subsets):
@@ -156,7 +150,7 @@ def main():
end = divvy[_ + 1]
worker_q.put((htable, _, start, end))
- print('enqueued %d subset tasks' % n_subsets, file=sys.stderr)
+ print >>sys.stderr, 'enqueued %d subset tasks' % n_subsets
open('%s.info' % basename, 'w').write('%d subsets total\n' % (n_subsets))
n_threads = args.threads
@@ -164,8 +158,8 @@ def main():
n_threads = n_subsets
# start threads!
- print('starting %d threads' % n_threads, file=sys.stderr)
- print('---', file=sys.stderr)
+ print >>sys.stderr, 'starting %d threads' % n_threads
+ print >>sys.stderr, '---'
threads = []
for _ in range(n_threads):
@@ -174,15 +168,15 @@ def main():
threads.append(cur_thrd)
cur_thrd.start()
- print('done starting threads', file=sys.stderr)
+ print >>sys.stderr, 'done starting threads'
# wait for threads
for _ in threads:
_.join()
- print('---', file=sys.stderr)
- print('done making subsets! see %s.subset.*.pmap' %
- (basename,), file=sys.stderr)
+ print >>sys.stderr, '---'
+ print >>sys.stderr, 'done making subsets! see %s.subset.*.pmap' % \
+ (basename,)
if __name__ == '__main__':
main()
diff --git a/scripts/readstats.py b/scripts/readstats.py
index d8e995f..d3c5cd5 100755
--- a/scripts/readstats.py
+++ b/scripts/readstats.py
@@ -1,7 +1,7 @@
-#! /usr/bin/env python
+#! /usr/bin/env python2
#
-# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
-# Copyright (C) Michigan State University, 2009-2015. It is licensed under
+# This file is part of khmer, http://github.com/ged-lab/khmer/, and is
+# Copyright (C) Michigan State University, 2009-2013. It is licensed under
# the three-clause BSD license; see LICENSE.
# Contact: khmer-project at idyll.org
#
@@ -12,7 +12,6 @@ Display summary statistics for one or more FASTA/FASTQ files.
Use '-h' for parameter help.
"""
-from __future__ import print_function
import sys
import csv
@@ -27,7 +26,7 @@ def get_parser():
Report number of bases, number of sequences, and average sequence length
for one or more FASTA/FASTQ files; and report aggregate statistics at end.
- With :option:`-o`/:option:`--output`, the output will be saved to the
+ With :option:`-o`/:options:`--output`, the output will be saved to the
specified file.
Example::
@@ -131,7 +130,7 @@ def analyze_file(filename):
input_iter = screed.open(filename, parse_description=False)
for record in input_iter:
if seqs % 100000 == 0:
- print('...', filename, seqs, file=sys.stderr)
+ print >>sys.stderr, '...', filename, seqs
bps += len(record.sequence)
seqs += 1
return bps, seqs
@@ -151,8 +150,8 @@ def main():
try:
bps, seqs = analyze_file(filename)
except (IOError, OSError, EOFError) as exc:
- print('ERROR in opening %s:' % filename, file=sys.stderr)
- print(' ', str(exc), file=sys.stderr)
+ print >>sys.stderr, 'ERROR in opening %s:' % filename
+ print >>sys.stderr, ' ', str(exc)
continue
if seqs:
@@ -162,9 +161,11 @@ def main():
seqs,
avg,
filename)
- print('... found', msg, file=sys.stderr)
+
+ print >>sys.stderr, '... found', msg
+
else:
- print('No sequences found in %s' % filename, file=sys.stderr)
+ print >>sys.stderr, 'No sequences found in %s' % filename
if statistics:
if args.csv:
@@ -175,8 +176,8 @@ def main():
for stat in statistics:
out.append(*stat)
else:
- print('No sequences found in %d files' %
- len(args.filenames), file=args.outfp)
+ print >>args.outfp, \
+ 'No sequences found in %d files' % len(args.filenames)
if __name__ == '__main__':
diff --git a/scripts/sample-reads-randomly.py b/scripts/sample-reads-randomly.py
index 79b4777..64323e4 100755
--- a/scripts/sample-reads-randomly.py
+++ b/scripts/sample-reads-randomly.py
@@ -1,6 +1,6 @@
-#! /usr/bin/env python
+#! /usr/bin/env python2
#
-# This script is part of khmer, https://github.com/dib-lab/khmer/, and is
+# This script is part of khmer, http://github.com/ged-lab/khmer/, and is
# Copyright (C) Michigan State University, 2009-2015. It is licensed under
# the three-clause BSD license; see LICENSE.
# Contact: khmer-project at idyll.org
@@ -17,7 +17,6 @@ By default take one subsample, but take -S samples if specified.
Reads FASTQ and FASTA input, retains format for output.
"""
-from __future__ import print_function
import argparse
import screed
@@ -111,18 +110,17 @@ def main():
output_filename = os.path.basename(filename) + '.subset'
if num_samples == 1:
- print('Subsampling %d reads using reservoir sampling.' %
- args.num_reads, file=sys.stderr)
- print('Subsampled reads will be placed in %s' %
- output_filename, file=sys.stderr)
- print('', file=sys.stderr)
+ print >>sys.stderr, 'Subsampling %d reads using reservoir sampling.' %\
+ args.num_reads
+ print >>sys.stderr, 'Subsampled reads will be placed in %s' % \
+ output_filename
+ print >>sys.stderr, ''
else: # > 1
- print('Subsampling %d reads, %d times,'
- % (args.num_reads, num_samples), ' using reservoir sampling.',
- file=sys.stderr)
- print('Subsampled reads will be placed in %s.N'
- % output_filename, file=sys.stderr)
- print('', file=sys.stderr)
+ print >>sys.stderr, 'Subsampling %d reads, %d times,' \
+ % (args.num_reads, num_samples), ' using reservoir sampling.'
+ print >>sys.stderr, 'Subsampled reads will be placed in %s.N' \
+ % output_filename
+ print >>sys.stderr, ''
reads = []
for n in range(num_samples):
@@ -130,17 +128,17 @@ def main():
# read through all the sequences and load/resample the reservoir
for filename in args.filenames:
- print('opening', filename, 'for reading', file=sys.stderr)
+ print >>sys.stderr, 'opening', filename, 'for reading'
screed_iter = screed.open(filename, parse_description=False)
for count, (_, ispair, rcrd1, rcrd2) in enumerate(broken_paired_reader(
screed_iter,
force_single=args.force_single)):
if count % 10000 == 0:
- print('...', count, 'reads scanned', file=sys.stderr)
+ print >>sys.stderr, '...', count, 'reads scanned'
if count >= args.max_reads:
- print('reached upper limit of %d reads' %
- args.max_reads, '(see -M); exiting', file=sys.stderr)
+ print >>sys.stderr, 'reached upper limit of %d reads' % \
+ args.max_reads, '(see -M); exiting'
break
# collect first N reads
@@ -160,8 +158,8 @@ def main():
# output all the subsampled reads:
if len(reads) == 1:
- print('Writing %d sequences to %s' %
- (len(reads[0]), output_filename), file=sys.stderr)
+ print >>sys.stderr, 'Writing %d sequences to %s' % \
+ (len(reads[0]), output_filename)
if not output_file:
output_file = open(output_filename, 'w')
@@ -172,8 +170,8 @@ def main():
else:
for n in range(num_samples):
n_filename = output_filename + '.%d' % n
- print('Writing %d sequences to %s' %
- (len(reads[n]), n_filename), file=sys.stderr)
+ print >>sys.stderr, 'Writing %d sequences to %s' % \
+ (len(reads[n]), n_filename)
output_file = open(n_filename, 'w')
for records in reads[n]:
write_record(records[0], output_file)
diff --git a/scripts/split-paired-reads.py b/scripts/split-paired-reads.py
index e9eac94..f80cf65 100755
--- a/scripts/split-paired-reads.py
+++ b/scripts/split-paired-reads.py
@@ -1,6 +1,6 @@
-#! /usr/bin/env python
+#! /usr/bin/env python2
#
-# This script is part of khmer, https://github.com/dib-lab/khmer/, and is
+# This script is part of khmer, http://github.com/ged-lab/khmer/, and is
# Copyright (C) Michigan State University, 2009-2015. It is licensed under
# the three-clause BSD license; see LICENSE.
# Contact: khmer-project at idyll.org
@@ -16,7 +16,6 @@ files (.1 and .2).
Reads FASTQ and FASTA input, retains format for output.
"""
-from __future__ import print_function
import screed
import sys
import os
@@ -64,7 +63,7 @@ def get_parser():
epilog=textwrap.dedent(epilog),
formatter_class=argparse.ArgumentDefaultsHelpFormatter)
- parser.add_argument('infile', nargs='?', default='/dev/stdin')
+ parser.add_argument('infile')
parser.add_argument('-o', '--output-dir', metavar="output_directory",
dest='output_directory', default='', help='Output '
@@ -73,10 +72,10 @@ def get_parser():
parser.add_argument('-1', '--output-first', metavar='output_first',
default=None, help='Output "left" reads to this '
- 'file', type=argparse.FileType('w'))
+ 'file')
parser.add_argument('-2', '--output-second', metavar='output_second',
default=None, help='Output "right" reads to this '
- 'file', type=argparse.FileType('w'))
+ 'file')
parser.add_argument('-p', '--force-paired', action='store_true',
help='Require that reads be interleaved')
@@ -93,17 +92,12 @@ def main():
infile = args.infile
- filenames = [infile]
check_input_files(infile, args.force)
+ filenames = [infile]
check_space(filenames, args.force)
# decide where to put output files - specific directory? or just default?
- if infile == '/dev/stdin' or infile == '-':
- if not (args.output_first and args.output_second):
- print >>sys.stderr, ("Accepting input from stdin; "
- "output filenames must be provided.")
- sys.exit(1)
- elif args.output_directory:
+ if args.output_directory:
if not os.path.exists(args.output_directory):
os.makedirs(args.output_directory)
out1 = args.output_directory + '/' + os.path.basename(infile) + '.1'
@@ -114,17 +108,12 @@ def main():
# OVERRIDE output file locations with -1, -2
if args.output_first:
- fp_out1 = args.output_first
- out1 = fp_out1.name
- else:
- # Use default filename created above
- fp_out1 = open(out1, 'w')
+ out1 = args.output_first
if args.output_second:
- fp_out2 = args.output_second
- out2 = fp_out2.name
- else:
- # Use default filename created above
- fp_out2 = open(out2, 'w')
+ out2 = args.output_second
+
+ fp_out1 = open(out1, 'w')
+ fp_out2 = open(out2, 'w')
counter1 = 0
counter2 = 0
@@ -133,15 +122,14 @@ def main():
screed_iter = screed.open(infile, parse_description=False)
# walk through all the reads in broken-paired mode.
- paired_iter = broken_paired_reader(screed_iter)
- for index, is_pair, record1, record2 in paired_iter:
- if index % 10000 == 0:
- print('...', index, file=sys.stderr)
+ for index, is_pair, record1, record2 in broken_paired_reader(screed_iter):
+ if index % 100000 == 0 and index:
+ print >> sys.stderr, '...', index
# are we requiring pairs?
if args.force_paired and not is_pair:
- print('ERROR, %s is not part of a pair' %
- record1.name, file=sys.stderr)
+ print >>sys.stderr, 'ERROR, %s is not part of a pair' % \
+ record1.name
sys.exit(1)
if is_pair:
@@ -158,15 +146,15 @@ def main():
write_record(record1, fp_out2)
counter2 += 1
else:
- print("Unrecognized format for read pair information: %s" %
- name, file=sys.stderr)
- print("Exiting.", file=sys.stderr)
+ print >>sys.stderr, \
+ "Unrecognized format for read pair information: %s" % name
+ print >>sys.stderr, "Exiting."
sys.exit(1)
- print("DONE; split %d sequences (%d left, %d right)" %
- (counter1 + counter2, counter1, counter2), file=sys.stderr)
- print("/1 reads in %s" % out1, file=sys.stderr)
- print("/2 reads in %s" % out2, file=sys.stderr)
+ print >> sys.stderr, "DONE; split %d sequences (%d left, %d right)" % \
+ (counter1 + counter2, counter1, counter2)
+ print >> sys.stderr, "/1 reads in %s" % out1
+ print >> sys.stderr, "/2 reads in %s" % out2
if __name__ == '__main__':
main()
diff --git a/scripts/trim-low-abund.py b/scripts/trim-low-abund.py
index 741b181..564e24e 100755
--- a/scripts/trim-low-abund.py
+++ b/scripts/trim-low-abund.py
@@ -1,6 +1,6 @@
-#! /usr/bin/env python
+#! /usr/bin/env python2
#
-# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
+# This file is part of khmer, http://github.com/ged-lab/khmer/, and is
# Copyright (C) Michigan State University, 2009-2015. It is licensed under
# the three-clause BSD license; see LICENSE.
# Contact: khmer-project at idyll.org
@@ -14,7 +14,6 @@ Output sequences will be placed in 'infile.abundtrim'.
Use -h for parameter help.
"""
-from __future__ import print_function
import sys
import screed
import os
@@ -24,9 +23,7 @@ import shutil
import textwrap
import argparse
-from screed import Record
-from khmer import khmer_args
-
+from screed.screedRecord import _screed_record_dict
from khmer.khmer_args import (build_counting_args, info, add_loadhash_args,
report_on_config)
from khmer.utils import write_record, write_record_pair, broken_paired_reader
@@ -38,7 +35,7 @@ DEFAULT_CUTOFF = 2
def trim_record(read, trim_at):
- new_read = Record()
+ new_read = _screed_record_dict()
new_read.name = read.name
new_read.sequence = read.sequence[:trim_at]
if hasattr(read, 'quality'):
@@ -116,8 +113,8 @@ def main():
###
if len(set(args.input_filenames)) != len(args.input_filenames):
- print("Error: Cannot input the same filename multiple times.",
- file=sys.stderr)
+ print >>sys.stderr, \
+ "Error: Cannot input the same filename multiple times."
sys.exit(1)
###
@@ -126,22 +123,24 @@ def main():
check_valid_file_exists(args.input_filenames)
check_space(args.input_filenames, args.force)
if args.savetable:
- check_space_for_hashtable(args, 'countgraph', args.force)
+ check_space_for_hashtable(
+ args.n_tables * args.min_tablesize, args.force)
- if args.loadtable:
- print('loading countgraph from', args.loadtable, file=sys.stderr)
- ct = khmer.load_counting_hash(args.loadtable)
- else:
- print('making countgraph', file=sys.stderr)
- ct = khmer_args.create_countgraph(args)
+ K = args.ksize
- K = ct.ksize()
CUTOFF = args.cutoff
NORMALIZE_LIMIT = args.normalize_to
+ if args.loadtable:
+ print >>sys.stderr, 'loading k-mer counting table from', args.loadtable
+ ct = khmer.load_counting_hash(args.loadtable)
+ else:
+ print >>sys.stderr, 'making k-mer counting table'
+ ct = khmer.new_counting_hash(K, args.min_tablesize, args.n_tables)
+
tempdir = tempfile.mkdtemp('khmer', 'tmp', args.tempdir)
- print('created temporary directory %s; '
- 'use -T to change location' % tempdir, file=sys.stderr)
+ print >>sys.stderr, 'created temporary directory %s; ' \
+ 'use -T to change location' % tempdir
# ### FIRST PASS ###
@@ -174,8 +173,8 @@ def main():
force_single=args.ignore_pairs)
for n, is_pair, read1, read2 in paired_iter:
if n % 10000 == 0:
- print('...', n, filename, save_pass2, n_reads, n_bp,
- written_reads, written_bp, file=sys.stderr)
+ print >>sys.stderr, '...', n, filename, save_pass2, \
+ n_reads, n_bp, written_reads, written_bp
# we want to track paired reads here, to make sure that pairs
# are not split between first pass and second pass.
@@ -241,9 +240,8 @@ def main():
pass2fp.close()
- print('%s: kept aside %d of %d from first pass, in %s' %
- (filename, save_pass2, n, filename),
- file=sys.stderr)
+ print >>sys.stderr, '%s: kept aside %d of %d from first pass, in %s' \
+ % (filename, save_pass2, n, filename)
save_pass2_total += save_pass2
# ### SECOND PASS. ###
@@ -251,9 +249,8 @@ def main():
skipped_n = 0
skipped_bp = 0
for _, pass2filename, trimfp in pass2list:
- print('second pass: looking at sequences kept aside in %s' %
- pass2filename,
- file=sys.stderr)
+ print >>sys.stderr, ('second pass: looking at sequences kept aside '
+ 'in %s') % pass2filename
# note that for this second pass, we don't care about paired
# reads - they will be output in the same order they're read in,
@@ -263,8 +260,8 @@ def main():
for n, read in enumerate(screed.open(pass2filename,
parse_description=False)):
if n % 10000 == 0:
- print('... x 2', n, pass2filename,
- written_reads, written_bp, file=sys.stderr)
+ print >>sys.stderr, '... x 2', n, pass2filename, \
+ written_reads, written_bp
seq = read.sequence.replace('N', 'A')
med, _, _ = ct.get_median_count(seq)
@@ -291,45 +288,42 @@ def main():
if trim_at != len(read.sequence):
trimmed_reads += 1
- print('removing %s' % pass2filename, file=sys.stderr)
+ print >>sys.stderr, 'removing %s' % pass2filename
os.unlink(pass2filename)
- print('removing temp directory & contents (%s)' % tempdir, file=sys.stderr)
+ print >>sys.stderr, 'removing temp directory & contents (%s)' % tempdir
shutil.rmtree(tempdir)
n_passes = 1.0 + (float(save_pass2_total) / n_reads)
percent_reads_trimmed = float(trimmed_reads + (n_reads - written_reads)) /\
n_reads * 100.0
- print('read %d reads, %d bp' % (n_reads, n_bp,))
- print('wrote %d reads, %d bp' % (written_reads, written_bp,))
- print('looked at %d reads twice (%.2f passes)' % (save_pass2_total,
- n_passes))
- print('removed %d reads and trimmed %d reads (%.2f%%)' %
- (n_reads - written_reads, trimmed_reads, percent_reads_trimmed))
- print('trimmed or removed %.2f%% of bases (%d total)' %
- ((1 - (written_bp / float(n_bp))) * 100.0, n_bp - written_bp))
+ print >>sys.stderr, 'read %d reads, %d bp' % (n_reads, n_bp,)
+ print >>sys.stderr, 'wrote %d reads, %d bp' % (written_reads, written_bp,)
+ print >>sys.stderr, 'looked at %d reads twice (%.2f passes)' % \
+ (save_pass2_total, n_passes)
+ print >>sys.stderr, 'removed %d reads and trimmed %d reads (%.2f%%)' % \
+ (n_reads - written_reads, trimmed_reads, percent_reads_trimmed)
+ print >>sys.stderr, 'trimmed or removed %.2f%% of bases (%d total)' % \
+ ((1 - (written_bp / float(n_bp))) * 100.0, n_bp - written_bp)
if args.variable_coverage:
percent_reads_hicov = 100.0 * float(n_reads - skipped_n) / n_reads
- print('%d reads were high coverage (%.2f%%);' % (n_reads - skipped_n,
- percent_reads_hicov),
- file=sys.stderr)
- print('skipped %d reads/%d bases because of low coverage' %
- (skipped_n, skipped_bp),
- file=sys.stderr)
+ print >>sys.stderr, '%d reads were high coverage (%.2f%%);' % \
+ (n_reads - skipped_n, percent_reads_hicov)
+ print >>sys.stderr, ('skipped %d reads/%d bases because of low'
+ 'coverage') % (skipped_n, skipped_bp)
fp_rate = \
khmer.calc_expected_collisions(ct, args.force, max_false_pos=.8)
# for max_false_pos see Zhang et al., http://arxiv.org/abs/1309.2975
- print('fp rate estimated to be {fpr:1.3f}'.format(fpr=fp_rate),
- file=sys.stderr)
+ print >>sys.stderr, \
+ 'fp rate estimated to be {fpr:1.3f}'.format(fpr=fp_rate)
- print('output in *.abundtrim', file=sys.stderr)
+ print >>sys.stderr, 'output in *.abundtrim'
if args.savetable:
- print("Saving k-mer counting table to",
- args.savetable, file=sys.stderr)
+ print >>sys.stderr, "Saving k-mer counting table to", args.savetable
ct.save(args.savetable)
diff --git a/setup.cfg b/setup.cfg
index a04f6d1..d5e5068 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -1,7 +1,7 @@
[nosetests]
verbosity = 2
-stop = FALSE
-attr = !known_failing,!jenkins,!huge
+stop = TRUE
+attr = !known_failing,!jenkins,!linux
#processes = -1 # breaks xunit output
[build_ext]
diff --git a/setup.py b/setup.py
index c9d785e..5a21bdb 100755
--- a/setup.py
+++ b/setup.py
@@ -1,5 +1,5 @@
-#! /usr/bin/env python
-# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
+#! /usr/bin/env python2
+# This file is part of khmer, http://github.com/ged-lab/khmer/, and is
# Copyright (C) Michigan State University, 2009-2015. It is licensed under
# the three-clause BSD license; see doc/LICENSE.txt.
# Contact: khmer-project at idyll.org
@@ -104,7 +104,7 @@ BUILD_DEPENDS.extend(path_join("lib", bn + ".hh") for bn in [
"khmer", "kmer_hash", "hashtable", "counting", "hashbits", "labelhash",
"hllcounter", "khmer_exception", "read_aligner", "subset", "read_parsers"])
-SOURCES = ["khmer/_khmer.cc"]
+SOURCES = ["khmer/_khmermodule.cc"]
SOURCES.extend(path_join("lib", bn + ".cc") for bn in [
"trace_logger", "perf_metrics", "read_parsers", "kmer_hash", "hashtable",
"hashbits", "labelhash", "counting", "subset", "read_aligner",
@@ -134,7 +134,7 @@ EXTENSION_MOD_DICT = \
"define_macros": [("VERSION", versioneer.get_version()), ],
}
-EXTENSION_MOD = Extension("khmer._khmer", # pylint: disable=W0142
+EXTENSION_MOD = Extension("khmer._khmermodule", # pylint: disable=W0142
** EXTENSION_MOD_DICT)
SCRIPTS = []
SCRIPTS.extend([path_join("scripts", script)
@@ -150,9 +150,8 @@ CLASSIFIERS = [
"Operating System :: POSIX :: Linux",
"Operating System :: MacOS :: MacOS X",
"Programming Language :: C++",
+ "Programming Language :: Python :: 2 :: Only",
"Programming Language :: Python :: 2.7",
- "Programming Language :: Python :: 3.3",
- "Programming Language :: Python :: 3.4",
"Topic :: Scientific/Engineering :: Bio-Informatics",
]
if "-rc" in versioneer.get_version():
@@ -175,21 +174,16 @@ SETUP_METADATA = \
# "maintainer_email": 'mcrusoe at msu.edu', # so don't include it
# http://docs.python.org/2/distutils/setupscript.html
# additiona-meta-data note #3
- "url": 'https://khmer.readthedocs.org/',
- "packages": ['khmer', 'khmer.tests', 'oxli'],
+ "url": 'http://ged.msu.edu/',
+ "packages": ['khmer', 'khmer.tests'],
"package_dir": {'khmer.tests': 'tests'},
- "install_requires": ['screed >= 0.9'],
+ "install_requires": ['screed >= 0.8'],
# testing screed download link
"extras_require": {':python_version=="2.6"': ['argparse>=1.2.1'],
'docs': ['sphinx', 'sphinxcontrib-autoprogram'],
'tests': ['nose >= 1.0']},
"scripts": SCRIPTS,
- "entry_points": {
- 'console_scripts': [
- "oxli = oxli:main"
- ]
- },
"ext_modules": [EXTENSION_MOD, ],
# "platforms": '', # empty as is conveyed by the classifiers below
# "license": '', # empty as is conveyed by the classifier below
diff --git a/tests/__init__.py b/tests/__init__.py
index cee3cea..520b18d 100644
--- a/tests/__init__.py
+++ b/tests/__init__.py
@@ -1,5 +1,5 @@
#
-# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
-# Copyright (C) Michigan State University, 2009-2015. It is licensed under
+# This file is part of khmer, http://github.com/ged-lab/khmer/, and is
+# Copyright (C) Michigan State University, 2009-2013. It is licensed under
# the three-clause BSD license; see doc/LICENSE.txt.
# Contact: khmer-project at idyll.org
diff --git a/tests/khmer_tst_utils.py b/tests/khmer_tst_utils.py
index 0cbe36c..d52303f 100644
--- a/tests/khmer_tst_utils.py
+++ b/tests/khmer_tst_utils.py
@@ -1,6 +1,5 @@
-from __future__ import print_function
#
-# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
+# This file is part of khmer, http://github.com/ged-lab/khmer/, and is
# Copyright (C) Michigan State University, 2009-2015. It is licensed under
# the three-clause BSD license; see LICENSE.
# Contact: khmer-project at idyll.org
@@ -9,16 +8,11 @@ import tempfile
import os
import shutil
from pkg_resources import Requirement, resource_filename, ResolutionError
+from cStringIO import StringIO
import nose
import sys
import traceback
import subprocess
-from io import open
-
-try:
- from StringIO import StringIO
-except ImportError:
- from io import StringIO
def get_test_data(filename):
@@ -106,8 +100,8 @@ def runscript(scriptname, args, in_directory=None,
os.chdir(in_directory)
try:
- print('running:', scriptname, 'in:', in_directory)
- print('arguments', sysargs)
+ print 'running:', scriptname, 'in:', in_directory
+ print 'arguments', sysargs
status = _runscript(scriptname, sandbox=sandbox)
except nose.SkipTest:
raise
@@ -124,8 +118,8 @@ def runscript(scriptname, args, in_directory=None,
os.chdir(cwd)
if status != 0 and not fail_ok:
- print(out)
- print(err)
+ print out
+ print err
assert False, (status, out, err)
return status, out, err
@@ -154,12 +148,10 @@ def runscriptredirect(scriptname, args, stdinfilename, in_directory=None,
os.chdir(in_directory)
sysargs = 'cat ' + stdinfilename + ' | python ' + scriptfile + \
" " + args
- out = open(
- os.path.join(in_directory, "out"), 'w+', encoding='utf-8')
- err = open(
- os.path.join(in_directory, "err"), 'w+', encoding='utf-8')
- print('running:', scriptname, 'in:', in_directory)
- print('arguments', sysargs)
+ out = open(os.path.join(in_directory, "out"), 'w+b')
+ err = open(os.path.join(in_directory, "err"), 'w+b')
+ print 'running:', scriptname, 'in:', in_directory
+ print 'arguments', sysargs
status = subprocess.call(args=sysargs, stdout=out, stderr=err,
shell=True)
os.chdir(cwd)
@@ -168,8 +160,8 @@ def runscriptredirect(scriptname, args, stdinfilename, in_directory=None,
out = out.read()
err.seek(0)
err = err.read()
- print(out)
- print(err)
+ print out
+ print err
assert False, (status, out, err)
return status, out, err
diff --git a/tests/test-data/badversion-k32.tagset b/tests/test-data/badversion-k32.tagset
index a568d68..8a4e4b0 100644
Binary files a/tests/test-data/badversion-k32.tagset and b/tests/test-data/badversion-k32.tagset differ
diff --git a/tests/test-data/dn-test-all-paired-all-keep.fa b/tests/test-data/dn-test-all-paired-all-keep.fa
deleted file mode 100644
index 4584f4a..0000000
--- a/tests/test-data/dn-test-all-paired-all-keep.fa
+++ /dev/null
@@ -1,16 +0,0 @@
->a/1
-ACTTCATCGTAGCTTACCACCGAGCGATCATTCCTTCTATCGGAAGGCGTCAGAACCGAATTTGGAGTATGGTTCTGAGACGGGAACATGCCTTGACCAG
->a/2
-GGAGCTGGCAGCCACAGCACCGCAAGTTGATTTCGGGGCCGAATCACCAATATTAGAGGCAACGATGCATAACTCGTCTGTCGTAATGTTTAGCCGTTTTC
->b/1
-ACTTCATCGTAGCTTACCACCGAGCGATCATTCCTTCTATCGGAAGGCGTCAGAACCGAATTTGGAGTATGGTTCTGAGACGGGAACATGCCTTGACCAG
->b/2
-GTTAAAGCCGTGCGCGAGAGCGAACTGCAACATACCTTCCCTTATCCAGGAAAGGAGGTAGTTATACGGTCACTTTGTGGACTCTACCCGTAGATTCCGGT
->c/1
-GAATGCACCTTCCGTAGTGGAGTGTTCGTCCCCACCTACGAGACTTCAATTCAGATACCGGCGTGAGTCGCAGTTATGATAAGAGACAGTGCTCTAGTACG
->c/2
-ACTTCATCGTAGCTTACCACCGAGCGATCATTCCTTCTATCGGAAGGCGTCAGAACCGAATTTGGAGTATGGTTCTGAGACGGGAACATGCCTTGACCAG
->d/1
-ACTTCATCGTAGCTTACCACCGAGCGATCATTCCTTCTATCGGAAGGCGTCAGAACCGAATTTGGAGTATGGTTCTGAGACGGGAACATGCCTTGACCAG
->d/2
-GGCGTACATGCCTCACAATTTAGGCCCCGGGACCGCAGCACACGCCTAACAATATCTCAGATTAGGGAGTAATCCTGATATGGTTTGGTAGTGGCTATCTG
\ No newline at end of file
diff --git a/tests/test-data/dn-test-none-paired.fa b/tests/test-data/dn-test-none-paired.fa
deleted file mode 100644
index 9553d5d..0000000
--- a/tests/test-data/dn-test-none-paired.fa
+++ /dev/null
@@ -1,8 +0,0 @@
->a/1
-ACTTCATCGTAGCTTACCACCGAGCGATCATTCCTTCTATCGGAAGGCGTCAGAACCGAATTTGGAGTATGGTTCTGAGACGGGAACATGCCTTGACCAG
->b/2
-GTTAAAGCCGTGCGCGAGAGCGAACTGCAACATACCTTCCCTTATCCAGGAAAGGAGGTAGTTATACGGTCACTTTGTGGACTCTACCCGTAGATTCCGGT
->c/2
-ACTTCATCGTAGCTTACCACCGAGCGATCATTCCTTCTATCGGAAGGCGTCAGAACCGAATTTGGAGTATGGTTCTGAGACGGGAACATGCCTTGACCAG
->d/1
-GGCGTACATGCCTCACAATTTAGGCCCCGGGACCGCAGCACACGCCTAACAATATCTCAGATTAGGGAGTAATCCTGATATGGTTTGGTAGTGGCTATCTG
diff --git a/tests/test-data/dn-test-some-paired-all-keep.fa b/tests/test-data/dn-test-some-paired-all-keep.fa
deleted file mode 100644
index dc65521..0000000
--- a/tests/test-data/dn-test-some-paired-all-keep.fa
+++ /dev/null
@@ -1,12 +0,0 @@
->a/1
-ACTTCATCGTAGCTTACCACCGAGCGATCATTCCTTCTATCGGAAGGCGTCAGAACCGAATTTGGAGTATGGTTCTGAGACGGGAACATGCCTTGACCAG
->a/2
-GGAGCTGGCAGCCACAGCACCGCAAGTTGATTTCGGGGCCGAATCACCAATATTAGAGGCAACGATGCATAACTCGTCTGTCGTAATGTTTAGCCGTTTTC
->b/2
-GTTAAAGCCGTGCGCGAGAGCGAACTGCAACATACCTTCCCTTATCCAGGAAAGGAGGTAGTTATACGGTCACTTTGTGGACTCTACCCGTAGATTCCGGT
->c/1
-GAATGCACCTTCCGTAGTGGAGTGTTCGTCCCCACCTACGAGACTTCAATTCAGATACCGGCGTGAGTCGCAGTTATGATAAGAGACAGTGCTCTAGTACG
->c/2
-ACTTCATCGTAGCTTACCACCGAGCGATCATTCCTTCTATCGGAAGGCGTCAGAACCGAATTTGGAGTATGGTTCTGAGACGGGAACATGCCTTGACCAG
->d/2
-GGCGTACATGCCTCACAATTTAGGCCCCGGGACCGCAGCACACGCCTAACAATATCTCAGATTAGGGAGTAATCCTGATATGGTTTGGTAGTGGCTATCTG
diff --git a/tests/test-data/goodversion-k32.tagset b/tests/test-data/goodversion-k32.tagset
index 2fe701e..9d78e7a 100644
Binary files a/tests/test-data/goodversion-k32.tagset and b/tests/test-data/goodversion-k32.tagset differ
diff --git a/tests/test-data/normC20k20.ct b/tests/test-data/normC20k20.ct
index 1400ef9..9694a07 100644
Binary files a/tests/test-data/normC20k20.ct and b/tests/test-data/normC20k20.ct differ
diff --git a/tests/test-data/paired-slash1.fq b/tests/test-data/paired-slash1.fq
deleted file mode 100644
index 995c7c3..0000000
--- a/tests/test-data/paired-slash1.fq
+++ /dev/null
@@ -1,32 +0,0 @@
- at SRR797058.3 HWI-ST600:227:C0WR4ACXX:7:1101:17167:2000/1
-NCTACCAAAAAAATGCCCGATAATTCTGACCATTCCTTCCTCATTCTCGTCTGGCGTTTGGTCACGACGCACGATACCTTCTGCACTTGTCAAGACAGCGG
-+
-#00@#################################################################################################
- at SRR797058.3 HWI-ST600:227:C0WR4ACXX:7:1101:17167:2000/2
-CTTGACAAGAGCAGAAGTTATCTTGCCTCGGGACCAAACGCCAGACGAGCACGAGGGAGCGATCGTCCGCATTAGCCGGCATTCTTTTGCTAGCAGATCGG
-+
-=?###################################################################################################
- at SRR797058.3 HWI-ST600:227:C0WR4ACXX:7:1101:17167:2000/1
-NCTACCAAAAAAATGCCCGATAATTCTGACCATTCCTTCCTCATTCTCGTCTGGCGTTTGGTCACGACGCACGATACCTTCTGCACTTGTCAAGACAGCGG
-+
-#00@#################################################################################################
- at SRR797058.3 HWI-ST600:227:C0WR4ACXX:7:1101:17167:2000/2
-CTTGACAAGAGCAGAAGTTATCTTGCCTCGGGACCAAACGCCAGACGAGCACGAGGGAGCGATCGTCCGCATTAGCCGGCATTCTTTTGCTAGCAGATCGG
-+
-=?###################################################################################################
- at SRR797058.3 HWI-ST600:227:C0WR4ACXX:7:1101:17167:2000/1
-NCTACCAAAAAAATGCCCGATAATTCTGACCATTCCTTCCTCATTCTCGTCTGGCGTTTGGTCACGACGCACGATACCTTCTGCACTTGTCAAGACAGCGG
-+
-#00@#################################################################################################
- at SRR797058.3 HWI-ST600:227:C0WR4ACXX:7:1101:17167:2000/2
-CTTGACAAGAGCAGAAGTTATCTTGCCTCGGGACCAAACGCCAGACGAGCACGAGGGAGCGATCGTCCGCATTAGCCGGCATTCTTTTGCTAGCAGATCGG
-+
-=?###################################################################################################
- at SRR797058.3 HWI-ST600:227:C0WR4ACXX:7:1101:17167:2000/1
-NCTACCAAAAAAATGCCCGATAATTCTGACCATTCCTTCCTCATTCTCGTCTGGCGTTTGGTCACGACGCACGATACCTTCTGCACTTGTCAAGACAGCGG
-+
-#00@#################################################################################################
- at SRR797058.3 HWI-ST600:227:C0WR4ACXX:7:1101:17167:2000/2
-CTTGACAAGAGCAGAAGTTATCTTGCCTCGGGACCAAACGCCAGACGAGCACGAGGGAGCGATCGTCCGCATTAGCCGGCATTCTTTTGCTAGCAGATCGG
-+
-=?###################################################################################################
diff --git a/tests/test-data/paired-slash1.fq.1 b/tests/test-data/paired-slash1.fq.1
deleted file mode 100644
index 4c95773..0000000
--- a/tests/test-data/paired-slash1.fq.1
+++ /dev/null
@@ -1,16 +0,0 @@
- at SRR797058.3 HWI-ST600:227:C0WR4ACXX:7:1101:17167:2000/1
-NCTACCAAAAAAATGCCCGATAATTCTGACCATTCCTTCCTCATTCTCGTCTGGCGTTTGGTCACGACGCACGATACCTTCTGCACTTGTCAAGACAGCGG
-+
-#00@#################################################################################################
- at SRR797058.3 HWI-ST600:227:C0WR4ACXX:7:1101:17167:2000/1
-NCTACCAAAAAAATGCCCGATAATTCTGACCATTCCTTCCTCATTCTCGTCTGGCGTTTGGTCACGACGCACGATACCTTCTGCACTTGTCAAGACAGCGG
-+
-#00@#################################################################################################
- at SRR797058.3 HWI-ST600:227:C0WR4ACXX:7:1101:17167:2000/1
-NCTACCAAAAAAATGCCCGATAATTCTGACCATTCCTTCCTCATTCTCGTCTGGCGTTTGGTCACGACGCACGATACCTTCTGCACTTGTCAAGACAGCGG
-+
-#00@#################################################################################################
- at SRR797058.3 HWI-ST600:227:C0WR4ACXX:7:1101:17167:2000/1
-NCTACCAAAAAAATGCCCGATAATTCTGACCATTCCTTCCTCATTCTCGTCTGGCGTTTGGTCACGACGCACGATACCTTCTGCACTTGTCAAGACAGCGG
-+
-#00@#################################################################################################
diff --git a/tests/test-data/paired-slash1.fq.2 b/tests/test-data/paired-slash1.fq.2
deleted file mode 100644
index 46a8ba0..0000000
--- a/tests/test-data/paired-slash1.fq.2
+++ /dev/null
@@ -1,16 +0,0 @@
- at SRR797058.3 HWI-ST600:227:C0WR4ACXX:7:1101:17167:2000/2
-CTTGACAAGAGCAGAAGTTATCTTGCCTCGGGACCAAACGCCAGACGAGCACGAGGGAGCGATCGTCCGCATTAGCCGGCATTCTTTTGCTAGCAGATCGG
-+
-=?###################################################################################################
- at SRR797058.3 HWI-ST600:227:C0WR4ACXX:7:1101:17167:2000/2
-CTTGACAAGAGCAGAAGTTATCTTGCCTCGGGACCAAACGCCAGACGAGCACGAGGGAGCGATCGTCCGCATTAGCCGGCATTCTTTTGCTAGCAGATCGG
-+
-=?###################################################################################################
- at SRR797058.3 HWI-ST600:227:C0WR4ACXX:7:1101:17167:2000/2
-CTTGACAAGAGCAGAAGTTATCTTGCCTCGGGACCAAACGCCAGACGAGCACGAGGGAGCGATCGTCCGCATTAGCCGGCATTCTTTTGCTAGCAGATCGG
-+
-=?###################################################################################################
- at SRR797058.3 HWI-ST600:227:C0WR4ACXX:7:1101:17167:2000/2
-CTTGACAAGAGCAGAAGTTATCTTGCCTCGGGACCAAACGCCAGACGAGCACGAGGGAGCGATCGTCCGCATTAGCCGGCATTCTTTTGCTAGCAGATCGG
-+
-=?###################################################################################################
diff --git a/tests/test-data/paired_one.base.dif.fa b/tests/test-data/paired_one.base.dif.fa
deleted file mode 100644
index 1ea9040..0000000
--- a/tests/test-data/paired_one.base.dif.fa
+++ /dev/null
@@ -1,5 +0,0 @@
->895:1:37:17593:9954/1
-GGTTGACGGGGCTCAGGGGGCGGCTGACTCCGAGAGACAGCAGCCGCAGCTGTCGTCAGGGGATTTCCGGGGCGGAGGCCGCAGACGCGAGTGGTGGAGGGAGAAGGCCTGACA
->895:1:37:17593:9954/2
-GGTTGACGGGGCTCAGGGGGCGGCTGACTCCGAGAGACAGCAGCCGCAGCTGTCGTCAGGGGATTTCCGGGGCGGAGGCCGCAGACGCGAGTGGTGGAGGGAGAAGGCCTGACG
-
diff --git a/tests/test-data/test-filter-abund-Ns.fq b/tests/test-data/test-filter-abund-Ns.fq
deleted file mode 100644
index f80289f..0000000
--- a/tests/test-data/test-filter-abund-Ns.fq
+++ /dev/null
@@ -1,16 +0,0 @@
- at 895:1:37:17593:9954 1::FOO_withN
-GGTTGACGGGGCTCAGGGGGCGGCTGACTCCGAGNGACAGCAGCCGCAGCTGTCGTCAGGGGATTTCCGGGGCGGAGGCCGCAGACGCGAGTGGTGGAGGGAGAAGGCCTGACG
-+
-##################################################################################################################
- at 895:1:37:17593:9954 1::FOO
-GGTTGACGGGGCTCAGGGGGCGGCTGACTCCGAGAGACAGCAGCCGCAGCTGTCGTCAGGGGATTTCCGGGGCGGAGGCCGCAGACGCGAGTGGTGGAGGGAGAAGGCCTGACG
-+
-##################################################################################################################
- at 895:1:37:17593:9954 1::FOO
-GGTTGACGGGGCTCAGGGGGCGGCTGACTCCGAGAGACAGCAGCCGCAGCTGTCGTCAGGGGATTTCCGGGGCGGAGGCCGCAGACGCGAGTGGTGGAGGGAGAAGGCCTGACG
-+
-##################################################################################################################
- at 895:1:37:17593:9954 1::FOO
-GGTTGACGGGGCTCAGGGGGCGGCTGACTCCGAGAGACAGCAGCCGCAGCTGTCGTCAGGGGATTTCCGGGGCGGAGGCCGCAGACGCGAGTGGTGGAGGGAGAAGGCCTGACG
-+
-##################################################################################################################
diff --git a/tests/test_counting_hash.py b/tests/test_counting_hash.py
index 5e08aba..849eb21 100644
--- a/tests/test_counting_hash.py
+++ b/tests/test_counting_hash.py
@@ -1,19 +1,14 @@
-from __future__ import print_function
-from __future__ import absolute_import, unicode_literals
#
-# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
-# Copyright (C) Michigan State University, 2009-2015. It is licensed under
+# This file is part of khmer, http://github.com/ged-lab/khmer/, and is
+# Copyright (C) Michigan State University, 2009-2013. It is licensed under
# the three-clause BSD license; see LICENSE.
# Contact: khmer-project at idyll.org
#
# pylint: disable=missing-docstring,protected-access
import gzip
-import os
-import shutil
-
import khmer
-from . import khmer_tst_utils as utils
+import khmer_tst_utils as utils
from khmer import ReadParser
import screed
@@ -43,26 +38,11 @@ def teardown():
class Test_CountingHash(object):
def setup(self):
- self.hi = khmer._CountingHash(12, PRIMES_1m)
-
- def test_failed_get(self):
- GG = 'G' * 12 # forward_hash: 11184810
- GGhash = khmer.forward_hash(GG, 12)
- assert khmer.forward_hash(GG, 12) == 11184810
-
- hi = self.hi
- hi.consume(GG)
-
- try:
- hi.get(float(GGhash))
- assert "the previous statement should fail"
- except ValueError as err:
- print(str(err))
+ self.hi = khmer.CountingHash(12, PRIMES_1m)
def test_collision_1(self):
GG = 'G' * 12 # forward_hash: 11184810
- GGhash = khmer.forward_hash(GG, 12)
assert khmer.forward_hash(GG, 12) == 11184810
collision_1 = 'AAACGTATGACT'
@@ -79,7 +59,6 @@ class Test_CountingHash(object):
hi.consume(collision_1)
assert hi.get(GG) == 1
- assert hi.get(GGhash) == 1
def test_collision_2(self):
@@ -124,38 +103,47 @@ class Test_CountingHash(object):
def test_get_raw_tables():
- ht = khmer.CountingHash(20, 1e5, 4)
+ ht = khmer.new_counting_hash(20, 1e5, 4)
tables = ht.get_raw_tables()
for size, table in zip(ht.hashsizes(), tables):
- assert isinstance(table, memoryview)
+ assert isinstance(table, buffer)
assert size == len(table)
def test_get_raw_tables_view():
- ht = khmer.CountingHash(20, 1e5, 4)
+ try:
+ memoryview
+ except NameError:
+ raise nose.SkipTest("This test requires memoryview")
+ ht = khmer.new_counting_hash(20, 1e5, 4)
tables = ht.get_raw_tables()
for tab in tables:
- assert sum(tab.tolist()) == 0
+ try:
+ memv = memoryview(tab)
+ except TypeError:
+ raise nose.SkipTest("This test needs a higher version of Python.")
+ assert sum(memv.tolist()) == 0
ht.consume('AAAATTTTCCCCGGGGAAAA')
for tab in tables:
- assert sum(tab.tolist()) == 1
+ memv = memoryview(tab)
+ assert sum(memv.tolist()) == 1
- at attr('huge')
+ at attr('linux')
def test_toobig():
try:
- ct = khmer.CountingHash(30, 1e13, 1)
+ ct = khmer.new_counting_hash(30, 1e13, 1)
assert 0, "this should fail"
except MemoryError as err:
- print(str(err))
+ print str(err)
def test_3_tables():
x = list(PRIMES_1m)
x.append(1000005)
- hi = khmer._CountingHash(12, x)
+ hi = khmer.CountingHash(12, x)
GG = 'G' * 12 # forward_hash: 11184810
assert khmer.forward_hash(GG, 12) == 11184810
@@ -186,206 +174,64 @@ def test_3_tables():
def test_simple_median():
- hi = khmer.CountingHash(6, 1e6, 2)
+ hi = khmer.new_counting_hash(6, 1e6, 2)
hi.consume("AAAAAA")
(median, average, stddev) = hi.get_median_count("AAAAAA")
- print(median, average, stddev)
+ print median, average, stddev
assert median == 1
assert average == 1.0
assert stddev == 0.0
hi.consume("AAAAAA")
(median, average, stddev) = hi.get_median_count("AAAAAA")
- print(median, average, stddev)
+ print median, average, stddev
assert median == 2
assert average == 2.0
assert stddev == 0.0
hi.consume("AAAAAT")
(median, average, stddev) = hi.get_median_count("AAAAAAT")
- print(median, average, stddev)
+ print median, average, stddev
assert median == 2
assert average == 1.5
assert int(stddev * 100) == 50 # .5
hi.consume("AAAAAT")
(median, average, stddev) = hi.get_median_count("AAAAAAT")
- print(median, average, stddev)
+ print median, average, stddev
assert median == 2
assert average == 2.0
assert stddev == 0.0
hi.consume("AAAAAT")
(median, average, stddev) = hi.get_median_count("AAAAAAT")
- print(median, average, stddev)
+ print median, average, stddev
assert median == 3
assert average == 2.5
assert int(stddev * 100) == 50 # .5
-def test_median_too_short():
- hi = khmer.CountingHash(6, 1e6, 2)
-
- hi.consume("AAAAAA")
- try:
- hi.get_median_count("A")
- assert 0, "this should fail"
- except ValueError:
- pass
-
-
-def test_median_at_least():
- hi = khmer.CountingHash(6, 1e6, 2)
-
- hi.consume("AAAAAA")
- assert hi.median_at_least("AAAAAA", 1)
- assert hi.median_at_least("AAAAAA", 2) is False
-
- hi.consume("AAAAAA")
- assert hi.median_at_least("AAAAAA", 2)
- assert hi.median_at_least("AAAAAA", 3) is False
-
- hi.consume("AAAAAA")
- assert hi.median_at_least("AAAAAA", 3)
- assert hi.median_at_least("AAAAAA", 4) is False
-
- hi.consume("AAAAAA")
- assert hi.median_at_least("AAAAAA", 4)
- assert hi.median_at_least("AAAAAA", 5) is False
-
- hi.consume("AAAAAA")
- assert hi.median_at_least("AAAAAA", 5)
- assert hi.median_at_least("AAAAAA", 6) is False
-
-
-def test_median_at_least_single_gt():
- K = 20
- hi = khmer.CountingHash(K, 1e6, 2)
-
- kmers = ['ATCGATCGATCGATCGATCG',
- 'GTACGTACGTACGTACGTAC',
- 'TTAGTTAGTTAGTTAGTTAG']
-
- for kmer in kmers:
- hi.consume(kmer)
- assert hi.median_at_least(kmer, 1) is True
-
-
-def test_median_at_least_single_lt():
- K = 20
- hi = khmer.CountingHash(K, 1e6, 2)
-
- kmers = ['ATCGATCGATCGATCGATCG',
- 'GTACGTACGTACGTACGTAC',
- 'TTAGTTAGTTAGTTAGTTAG']
-
- for kmer in kmers:
- hi.consume(kmer)
- assert hi.median_at_least(kmer, 2) is False
-
-
-def test_median_at_least_odd_gt():
- # test w/odd number of k-mers
- K = 20
- hi = khmer.CountingHash(K, 1e6, 2)
-
- seqs = ['ATCGATCGATCGATCGATCGCC',
- 'GTACGTACGTACGTACGTACCC',
- 'TTAGTTAGTTAGTTAGTTAGCC']
-
- for seq in seqs:
- hi.consume(seq)
- assert hi.median_at_least(seq, 1) is True
-
-
-def test_median_at_least_odd_lt():
- K = 20
- hi = khmer.CountingHash(K, 1e6, 2)
-
- seqs = ['ATCGATCGATCGATCGATCGCC',
- 'GTACGTACGTACGTACGTACCC',
- 'TTAGTTAGTTAGTTAGTTAGCC']
-
- for seq in seqs:
- hi.consume(seq)
- assert hi.median_at_least(seq, 2) is False
-
-
-# Test median with even number of k-mers
-def test_median_at_least_even_gt():
- K = 20
- hi = khmer.CountingHash(K, 1e6, 2)
-
- seqs = ['ATCGATCGATCGATCGATCGCCC',
- 'GTACGTACGTACGTACGTACCCC',
- 'TTAGTTAGTTAGTTAGTTAGCCC']
-
- for seq in seqs:
- hi.consume(seq)
- assert hi.median_at_least(seq, 1) is True
-
-
-def test_median_at_least_even_lt():
- K = 20
- hi = khmer.CountingHash(K, 1e6, 2)
-
- seqs = ['ATCGATCGATCGATCGATCGCCC',
- 'GTACGTACGTACGTACGTACCCC',
- 'TTAGTTAGTTAGTTAGTTAGCCC']
-
- for seq in seqs:
- hi.consume(seq)
- assert hi.median_at_least(seq, 2) is False
-
-
-def test_median_at_least_comp():
- K = 20
- C = 4
- hi = khmer.CountingHash(K, 1e6, 2)
-
- seqs = ['ATCGATCGATCGATCGATCGCCC',
- 'GTACGTACGTACGTACGTACCCC',
- 'TTAGTTAGTTAGTTAGTTAGCCC']
-
- for seq in seqs:
- hi.consume(seq)
- hi.consume(seq)
- hi.consume(seq)
-
- med, _, _ = hi.get_median_count(seq)
- assert hi.median_at_least(seq, C) is (med >= C)
-
-
-def test_median_at_least_exception():
- ht = khmer.CountingHash(20, 1e6, 2)
- try:
- ht.median_at_least('ATGGCTGATCGAT', 1)
- assert 0, "should have thrown ValueError"
- except ValueError as e:
- pass
-
-
def test_simple_kadian():
- hi = khmer.CountingHash(6, 1e6, 2)
+ hi = khmer.new_counting_hash(6, 1e6, 2)
hi.consume("ACTGCTATCTCTAGAGCTATG")
assert hi.get_kadian_count("ACTGCTATCTCTAGAGCTATG") == 1
- hi = khmer.CountingHash(6, 1e6, 2)
+ hi = khmer.new_counting_hash(6, 1e6, 2)
hi.consume("ACTGCTATCTCTAGAGCTATG")
hi.consume("ACTGCTATCTCTAGAcCTATG")
# ---------------^
x = hi.get_kadian_count("ACTGCTATCTCTAGAGCTATG")
assert x == 2, x
- hi = khmer.CountingHash(6, 1e6, 2)
+ hi = khmer.new_counting_hash(6, 1e6, 2)
hi.consume("ACTGCTATCTCTAGAGCTATG")
hi.consume("ACTGCTATCTCTAGAcCTATG")
# ---------------^---^
x = hi.get_kadian_count("ACTGCTATCTCTAGAGCTATG")
assert x == 2
- hi = khmer.CountingHash(6, 1e6, 2)
+ hi = khmer.new_counting_hash(6, 1e6, 2)
hi.consume("ACTGCTATCTCTAGAGCTATG")
hi.consume("ACTGCTATCTCTAGtGCTAcG")
# --------------^^---^
@@ -394,11 +240,11 @@ def test_simple_kadian():
def test_simple_kadian_2():
- hi = khmer.CountingHash(6, 1e6, 2)
+ hi = khmer.new_counting_hash(6, 1e6, 2)
hi.consume("ACTGCTATCTCTAGAGCTATG")
assert hi.get_kadian_count("ACTGCTATCTCTAGAGCTATG") == 1
- hi = khmer.CountingHash(6, 1e6, 2)
+ hi = khmer.new_counting_hash(6, 1e6, 2)
hi.consume("ACTGCTATCTCTAGAGCTATG")
# hi.consume("ACaGCTATCTCTAGAGCTATG")
hi.consume("ACAGCTATCTCTAGAGCTATG")
@@ -406,7 +252,7 @@ def test_simple_kadian_2():
x = hi.get_kadian_count("ACTGCTATCTCTAGAGCTATG")
assert x == 2, x
- hi = khmer.CountingHash(6, 1e6, 2)
+ hi = khmer.new_counting_hash(6, 1e6, 2)
hi.consume("ACTGCTATCTCTAGAGCTATG")
# hi.consume("ACaGCTATCTCTAGAcCTATG")
hi.consume("ACAGCTATCTCTAGACCTATG")
@@ -414,7 +260,7 @@ def test_simple_kadian_2():
x = hi.get_kadian_count("ACTGCTATCTCTAGAGCTATG")
assert x == 1, x
- hi = khmer.CountingHash(6, 1e6, 2)
+ hi = khmer.new_counting_hash(6, 1e6, 2)
hi.consume("ACTGCTATCTCTAGAGCTATG")
# hi.consume("ACTGCTATCgCTAGAGCTATG")
hi.consume("ACTGCTATCGCTAGAGCTATG")
@@ -424,11 +270,11 @@ def test_simple_kadian_2():
def test_2_kadian():
- hi = khmer.CountingHash(6, 1e6, 2)
+ hi = khmer.new_counting_hash(6, 1e6, 2)
hi.consume("ACTGCTATCTCTAGAGCTATG")
assert hi.get_kadian_count("ACTGCTATCTCTAGAGCTATG", 2) == 1
- hi = khmer.CountingHash(6, 1e6, 2)
+ hi = khmer.new_counting_hash(6, 1e6, 2)
hi.consume("ACTGCTATCTCTAGAGCTATG")
# hi.consume("ACTGCTATCTCTAGAcCTATG")
hi.consume("ACTGCTATCTCTAGACCTATG")
@@ -436,14 +282,14 @@ def test_2_kadian():
x = hi.get_kadian_count("ACTGCTATCTCTAGAGCTATG", 2)
assert x == 2, x
- hi = khmer.CountingHash(6, 1e6, 2)
+ hi = khmer.new_counting_hash(6, 1e6, 2)
hi.consume("ACTGCTATCTCTAGAGCTATG")
# hi.consume("ACTGCTATCTCTAGAcCTAtG")
hi.consume("ACTGCTATCTCTAGACCTATG")
# ---------------^---^
assert hi.get_kadian_count("ACTGCTATCTCTAGAGCTATG", 2) == 2
- hi = khmer.CountingHash(6, 1e6, 2)
+ hi = khmer.new_counting_hash(6, 1e6, 2)
hi.consume("ACTGCTATCTCTAGAGCTATG")
# hi.consume("ACTGCTATCTCTACtcCTAtG")
hi.consume("ACTGCTATCTCTACTCCTATG")
@@ -451,7 +297,7 @@ def test_2_kadian():
x = hi.get_kadian_count("ACTGCTATCTCTAGAGCTATG", 2)
assert x == 2, x
- hi = khmer.CountingHash(6, 1e6, 2)
+ hi = khmer.new_counting_hash(6, 1e6, 2)
hi.consume("ACTGCTATCTCTAGAGCTATG")
# hi.consume("ACTGCTgTCTCTACtcCTAtG")
hi.consume("ACTGCTGTCTCTACTCCTATG")
@@ -460,137 +306,6 @@ def test_2_kadian():
assert x == 1, x
-def test_get_kmer_counts_too_short():
- hi = khmer.CountingHash(6, 1e6, 2)
-
- hi.consume("AAAAAA")
- counts = hi.get_kmer_counts("A")
- assert len(counts) == 0
-
-
-def test_get_kmer_hashes_too_short():
- hi = khmer.CountingHash(6, 1e6, 2)
-
- hi.consume("AAAAAA")
- hashes = hi.get_kmer_hashes("A")
- assert len(hashes) == 0
-
-
-def test_get_kmers_too_short():
- hi = khmer.CountingHash(6, 1e6, 2)
-
- hi.consume("AAAAAA")
- kmers = hi.get_kmers("A")
- assert len(kmers) == 0
-
-
-def test_get_kmer_counts():
- hi = khmer.CountingHash(6, 1e6, 2)
-
- hi.consume("AAAAAA")
- counts = hi.get_kmer_counts("AAAAAA")
- print(counts)
- assert len(counts) == 1
- assert counts[0] == 1
-
- hi.consume("AAAAAA")
- counts = hi.get_kmer_counts("AAAAAA")
- print(counts)
- assert len(counts) == 1
- assert counts[0] == 2
-
- hi.consume("AAAAAT")
- counts = hi.get_kmer_counts("AAAAAAT")
- print(counts)
- assert len(counts) == 2
- assert counts[0] == 2
- assert counts[1] == 1
-
- hi.consume("AAAAAT")
- counts = hi.get_kmer_counts("AAAAAAT")
- print(counts)
- assert len(counts) == 2
- assert counts[0] == 2
- assert counts[1] == 2
-
- hi.consume("AAAAAT")
- counts = hi.get_kmer_counts("AAAAAAT")
- print(counts)
- assert len(counts) == 2
- assert counts[0] == 2
- assert counts[1] == 3
-
-
-def test_get_kmer_hashes():
- hi = khmer.CountingHash(6, 1e6, 2)
-
- hi.consume("AAAAAA")
- hashes = hi.get_kmer_hashes("AAAAAA")
- print(hashes)
- assert len(hashes) == 1
- assert hi.get(hashes[0]) == 1
-
- hi.consume("AAAAAA")
- hashes = hi.get_kmer_hashes("AAAAAA")
- print(hashes)
- assert len(hashes) == 1
- assert hi.get(hashes[0]) == 2
-
- hi.consume("AAAAAT")
- hashes = hi.get_kmer_hashes("AAAAAAT")
- print(hashes)
- assert len(hashes) == 2
- assert hi.get(hashes[0]) == 2
- assert hi.get(hashes[1]) == 1
-
- hi.consume("AAAAAT")
- hashes = hi.get_kmer_hashes("AAAAAAT")
- print(hashes)
- assert len(hashes) == 2
- assert hi.get(hashes[0]) == 2
- assert hi.get(hashes[1]) == 2
-
- hi.consume("AAAAAT")
- hashes = hi.get_kmer_hashes("AAAAAAT")
- print(hashes)
- assert len(hashes) == 2
- assert hi.get(hashes[0]) == 2
- assert hi.get(hashes[1]) == 3
-
-
-def test_get_kmers():
- hi = khmer.CountingHash(6, 1e6, 2)
-
- kmers = hi.get_kmers("AAAAAA")
- assert kmers == ["AAAAAA"]
-
- kmers = hi.get_kmers("AAAAAAT")
- assert kmers == ["AAAAAA", "AAAAAT"]
-
-
- at attr("huge")
-def test_save_load_large():
- def do_test(ctfile):
- inpath = utils.get_test_data('random-20-a.fa')
- savepath = utils.get_temp_filename(ctfile)
-
- sizes = khmer.get_n_primes_near_x(1, 2**31 + 1000)
-
- orig = khmer._CountingHash(12, sizes)
- orig.consume_fasta(inpath)
- orig.save(savepath)
-
- loaded = khmer.load_counting_hash(savepath)
-
- orig_count = orig.n_occupied()
- loaded_count = loaded.n_occupied()
- assert orig_count == 3966, orig_count
- assert loaded_count == orig_count, loaded_count
-
- for ctfile in ['temp.ct.gz', 'temp.ct']:
- do_test(ctfile)
-
-
def test_save_load():
inpath = utils.get_test_data('random-20-a.fa')
savepath = utils.get_temp_filename('tempcountingsave0.ht')
@@ -598,15 +313,12 @@ def test_save_load():
sizes = list(PRIMES_1m)
sizes.append(1000005)
- hi = khmer._CountingHash(12, sizes)
+ hi = khmer.CountingHash(12, sizes)
hi.consume_fasta(inpath)
hi.save(savepath)
- ht = khmer._CountingHash(12, sizes)
- try:
- ht.load(savepath)
- except IOError as err:
- assert 0, 'Should not produce an IOError: ' + str(err)
+ ht = khmer.CountingHash(12, sizes)
+ ht.load(savepath)
tracking = khmer._Hashbits(12, sizes)
x = hi.abundance_distribution(inpath, tracking)
@@ -618,30 +330,6 @@ def test_save_load():
assert x == y, (x, y)
-def test_load_truncated():
- inpath = utils.get_test_data('random-20-a.fa')
- savepath = utils.get_temp_filename('save.ht')
- truncpath = utils.get_temp_filename('trunc.ht')
-
- sizes = khmer.get_n_primes_near_x(3, 200)
-
- hi = khmer._CountingHash(12, sizes)
- hi.consume_fasta(inpath)
- hi.save(savepath)
-
- data = open(savepath, 'rb').read()
- for i in range(len(data)):
- fp = open(truncpath, 'wb')
- fp.write(data[:i])
- fp.close()
-
- try:
- ht = khmer.load_counting_hash(truncpath)
- assert 0, "this should not be reached!"
- except IOError as err:
- print(str(err))
-
-
def test_load_gz():
inpath = utils.get_test_data('random-20-a.fa')
@@ -652,7 +340,7 @@ def test_load_gz():
sizes.append(1000005)
# save uncompressed hashtable.
- hi = khmer._CountingHash(12, sizes)
+ hi = khmer.CountingHash(12, sizes)
hi.consume_fasta(inpath)
hi.save(savepath)
@@ -664,11 +352,8 @@ def test_load_gz():
in_file.close()
# load compressed hashtable.
- ht = khmer._CountingHash(12, sizes)
- try:
- ht.load(loadpath)
- except IOError as err:
- assert 0, "Should not produce an IOError: " + str(err)
+ ht = khmer.CountingHash(12, sizes)
+ ht.load(loadpath)
tracking = khmer._Hashbits(12, sizes)
x = hi.abundance_distribution(inpath, tracking)
@@ -687,15 +372,12 @@ def test_save_load_gz():
sizes = list(PRIMES_1m)
sizes.append(1000005)
- hi = khmer._CountingHash(12, sizes)
+ hi = khmer.CountingHash(12, sizes)
hi.consume_fasta(inpath)
hi.save(savepath)
- ht = khmer._CountingHash(12, sizes)
- try:
- ht.load(savepath)
- except IOError as err:
- assert 0, 'Should not produce an IOError: ' + str(err)
+ ht = khmer.CountingHash(12, sizes)
+ ht.load(savepath)
tracking = khmer._Hashbits(12, sizes)
x = hi.abundance_distribution(inpath, tracking)
@@ -708,7 +390,7 @@ def test_save_load_gz():
def test_trim_full():
- hi = khmer.CountingHash(6, 1e6, 2)
+ hi = khmer.new_counting_hash(6, 1e6, 2)
hi.consume(DNA)
hi.consume(DNA)
@@ -718,7 +400,7 @@ def test_trim_full():
def test_trim_short():
- hi = khmer.CountingHash(6, 1e6, 2)
+ hi = khmer.new_counting_hash(6, 1e6, 2)
hi.consume(DNA)
hi.consume(DNA[:50])
@@ -730,20 +412,20 @@ def test_trim_short():
def test_find_spectral_error_positions_1():
- hi = khmer.CountingHash(8, 1e6, 2)
+ hi = khmer.new_counting_hash(8, 1e6, 2)
hi.consume(DNA)
hi.consume(DNA[:30])
for n in range(len(DNA) - 8 + 1):
- print(n, hi.get(DNA[n:n + 8]))
+ print n, hi.get(DNA[n:n + 8])
posns = hi.find_spectral_error_positions(DNA, 1)
assert posns == [30], posns
def test_find_spectral_error_positions_2():
- hi = khmer.CountingHash(8, 1e6, 2)
+ hi = khmer.new_counting_hash(8, 1e6, 2)
hi.consume(DNA)
hi.consume(DNA)
@@ -753,20 +435,20 @@ def test_find_spectral_error_positions_2():
def test_find_spectral_error_positions_6():
- hi = khmer.CountingHash(8, 1e6, 2)
+ hi = khmer.new_counting_hash(8, 1e6, 2)
hi.consume(DNA)
hi.consume(DNA[1:])
for n in range(len(DNA) - 8 + 1):
- print(n, hi.get(DNA[n:n + 8]))
+ print n, hi.get(DNA[n:n + 8])
posns = hi.find_spectral_error_positions(DNA, 1)
assert posns == [0], posns
def test_find_spectral_error_positions_4():
- hi = khmer.CountingHash(8, 1e6, 2)
+ hi = khmer.new_counting_hash(8, 1e6, 2)
hi.consume(DNA)
@@ -775,7 +457,7 @@ def test_find_spectral_error_positions_4():
def test_find_spectral_error_positions_5():
- hi = khmer.CountingHash(8, 1e6, 2)
+ hi = khmer.new_counting_hash(8, 1e6, 2)
hi.consume(DNA)
hi.consume(DNA[:10])
@@ -785,22 +467,22 @@ def test_find_spectral_error_positions_5():
assert posns == [10], posns
-def test_find_spectral_error_locs7():
+def test_find_spectral_error_positions_6():
K = 8
- hi = khmer.CountingHash(K, 1e6, 2)
+ hi = khmer.new_counting_hash(K, 1e6, 2)
hi.consume(DNA)
hi.consume(DNA[K:])
for n in range(len(DNA) - 8 + 1):
- print(n, hi.get(DNA[n:n + 8]))
+ print n, hi.get(DNA[n:n + 8])
posns = hi.find_spectral_error_positions(DNA, 1)
assert posns == [7], posns
def test_find_spectral_error_positions_err():
- hi = khmer.CountingHash(8, 1e6, 2)
+ hi = khmer.new_counting_hash(8, 1e6, 2)
try:
posns = hi.find_spectral_error_positions(DNA[:6], 1)
@@ -817,7 +499,7 @@ def test_find_spectral_error_positions_err():
def test_maxcount():
# hashtable should saturate at some point so as not to overflow counter
- kh = khmer.CountingHash(4, 4 ** 4, 4)
+ kh = khmer.new_counting_hash(4, 4 ** 4, 4)
kh.set_use_bigcount(False)
last_count = None
@@ -835,7 +517,7 @@ def test_maxcount():
def test_maxcount_with_bigcount():
# hashtable should not saturate, if use_bigcount is set.
- kh = khmer.CountingHash(4, 4 ** 4, 4)
+ kh = khmer.new_counting_hash(4, 4 ** 4, 4)
kh.set_use_bigcount(True)
last_count = None
@@ -853,7 +535,7 @@ def test_maxcount_with_bigcount():
def test_maxcount_with_bigcount_save():
# hashtable should not saturate, if use_bigcount is set.
- kh = khmer.CountingHash(4, 4 ** 4, 4)
+ kh = khmer.new_counting_hash(4, 4 ** 4, 4)
kh.set_use_bigcount(True)
for i in range(0, 1000):
@@ -863,11 +545,8 @@ def test_maxcount_with_bigcount_save():
savepath = utils.get_temp_filename('tempcountingsave.ht')
kh.save(savepath)
- kh = khmer.CountingHash(1, 1, 1)
- try:
- kh.load(savepath)
- except IOError as err:
- assert 0, "Should not produce an IOError: " + str(err)
+ kh = khmer.new_counting_hash(1, 1, 1)
+ kh.load(savepath)
c = kh.get('AAAA')
assert c == 1000, "should be able to count to 1000: %d" % c
@@ -876,17 +555,14 @@ def test_maxcount_with_bigcount_save():
def test_bigcount_save():
# hashtable should not saturate, if use_bigcount is set.
- kh = khmer.CountingHash(4, 4 ** 4, 4)
+ kh = khmer.new_counting_hash(4, 4 ** 4, 4)
kh.set_use_bigcount(True)
savepath = utils.get_temp_filename('tempcountingsave.ht')
kh.save(savepath)
- kh = khmer.CountingHash(1, 1, 1)
- try:
- kh.load(savepath)
- except IOError as err:
- assert 0, "Should not produce an IOError: " + str(err)
+ kh = khmer.new_counting_hash(1, 1, 1)
+ kh.load(savepath)
# set_use_bigcount should still be True after load (i.e. should be saved)
@@ -900,17 +576,14 @@ def test_bigcount_save():
def test_nobigcount_save():
- kh = khmer.CountingHash(4, 4 ** 4, 4)
+ kh = khmer.new_counting_hash(4, 4 ** 4, 4)
# kh.set_use_bigcount(False) <-- this is the default
savepath = utils.get_temp_filename('tempcountingsave.ht')
kh.save(savepath)
- kh = khmer.CountingHash(1, 1, 1)
- try:
- kh.load(savepath)
- except IOError as err:
- assert 0, 'Should not produce an IOError: ' + str(err)
+ kh = khmer.new_counting_hash(1, 1, 1)
+ kh.load(savepath)
# set_use_bigcount should still be False after load (i.e. should be saved)
@@ -924,8 +597,8 @@ def test_nobigcount_save():
def test_bigcount_abund_dist():
- kh = khmer.CountingHash(18, 1e2, 4)
- tracking = khmer.Hashbits(18, 1e2, 4)
+ kh = khmer.new_counting_hash(18, 1e2, 4)
+ tracking = khmer.new_hashbits(18, 1e2, 4)
kh.set_use_bigcount(True)
seqpath = utils.get_test_data('test-abund-read-2.fa')
@@ -933,15 +606,15 @@ def test_bigcount_abund_dist():
kh.consume_fasta(seqpath)
dist = kh.abundance_distribution(seqpath, tracking)
- print(kh.get('GGTTGACGGGGCTCAGGG'))
+ print kh.get('GGTTGACGGGGCTCAGGG')
pdist = [(i, dist[i]) for i in range(len(dist)) if dist[i]]
- assert dist[1002] == 1, pdist
+ assert dist[1001] == 1, pdist
def test_bigcount_abund_dist_2():
- kh = khmer.CountingHash(18, 1e7, 4)
- tracking = khmer.Hashbits(18, 1e7, 4)
+ kh = khmer.new_counting_hash(18, 1e7, 4)
+ tracking = khmer.new_hashbits(18, 1e7, 4)
kh.set_use_bigcount(True)
seqpath = utils.get_test_data('test-abund-read.fa')
@@ -951,14 +624,14 @@ def test_bigcount_abund_dist_2():
kh.count('GGTTGACGGGGCTCAGGG')
dist = kh.abundance_distribution(seqpath, tracking)
- print(kh.get('GGTTGACGGGGCTCAGGG'))
+ print kh.get('GGTTGACGGGGCTCAGGG')
pdist = [(i, dist[i]) for i in range(len(dist)) if dist[i]]
assert dist[1001] == 1, pdist
def test_bigcount_overflow():
- kh = khmer.CountingHash(18, 1e7, 4)
+ kh = khmer.new_counting_hash(18, 1e7, 4)
kh.set_use_bigcount(True)
for i in range(0, 70000):
@@ -968,18 +641,18 @@ def test_bigcount_overflow():
def test_get_ksize():
- kh = khmer.CountingHash(22, 1, 1)
+ kh = khmer.new_counting_hash(22, 1, 1)
assert kh.ksize() == 22
def test_get_hashsizes():
- kh = khmer.CountingHash(22, 100, 4)
- assert kh.hashsizes() == [97L, 89L, 83L, 79L], kh.hashsizes()
+ kh = khmer.new_counting_hash(22, 100, 4)
+ assert kh.hashsizes() == [101, 103, 107, 109], kh.hashsizes()
# def test_collect_high_abundance_kmers():
# seqpath = utils.get_test_data('test-abund-read-2.fa')
#
-# kh = khmer.CountingHash(18, 1e6, 4)
+# kh = khmer.new_counting_hash(18, 1e6, 4)
# hb = kh.collect_high_abundance_kmers(seqpath, 2, 4)
@@ -989,19 +662,19 @@ def test_get_hashsizes():
def test_load_notexist_should_fail():
savepath = utils.get_temp_filename('tempcountingsave0.ht')
- hi = khmer.CountingHash(12, 1000, 2)
+ hi = khmer.new_counting_hash(12, 1000)
try:
hi.load(savepath)
assert 0, "load should fail"
except IOError as e:
- print(str(e))
+ print str(e)
def test_load_truncated_should_fail():
inpath = utils.get_test_data('random-20-a.fa')
savepath = utils.get_temp_filename('tempcountingsave0.ht')
- hi = khmer.CountingHash(12, 1000, 2)
+ hi = khmer.new_counting_hash(12, 1000)
hi.consume_fasta(inpath)
hi.save(savepath)
@@ -1013,30 +686,30 @@ def test_load_truncated_should_fail():
fp.write(data[:1000])
fp.close()
- hi = khmer._CountingHash(12, [1])
+ hi = khmer.new_counting_hash(12, 1)
try:
hi.load(savepath)
assert 0, "load should fail"
except IOError as e:
- print(str(e))
+ print str(e)
def test_load_gz_notexist_should_fail():
savepath = utils.get_temp_filename('tempcountingsave0.ht.gz')
- hi = khmer.CountingHash(12, 1000, 2)
+ hi = khmer.new_counting_hash(12, 1000)
try:
hi.load(savepath)
assert 0, "load should fail"
except IOError as e:
- print(str(e))
+ print str(e)
def test_load_gz_truncated_should_fail():
inpath = utils.get_test_data('random-20-a.fa')
savepath = utils.get_temp_filename('tempcountingsave0.ht.gz')
- hi = khmer.CountingHash(12, 1000, 2)
+ hi = khmer.new_counting_hash(12, 1000)
hi.consume_fasta(inpath)
hi.save(savepath)
@@ -1048,16 +721,16 @@ def test_load_gz_truncated_should_fail():
fp.write(data[:1000])
fp.close()
- hi = khmer._CountingHash(12, [1])
+ hi = khmer.new_counting_hash(12, 1)
try:
hi.load(savepath)
assert 0, "load should fail"
except IOError as e:
- print(str(e))
+ print str(e)
def test_counting_file_version_check():
- ht = khmer.CountingHash(12, 1, 1)
+ ht = khmer.new_counting_hash(12, 1, 1)
inpath = utils.get_test_data('badversion-k12.ct')
@@ -1065,11 +738,11 @@ def test_counting_file_version_check():
ht.load(inpath)
assert 0, "this should fail"
except IOError as e:
- print(str(e))
+ print str(e)
def test_counting_gz_file_version_check():
- ht = khmer.CountingHash(12, 1, 1)
+ ht = khmer.new_counting_hash(12, 1, 1)
inpath = utils.get_test_data('badversion-k12.ct.gz')
@@ -1077,161 +750,161 @@ def test_counting_gz_file_version_check():
ht.load(inpath)
assert 0, "this should fail"
except IOError as e:
- print(str(e))
+ print str(e)
def test_counting_file_type_check():
inpath = utils.get_test_data('goodversion-k12.ht')
- kh = khmer.CountingHash(12, 1, 1)
+ kh = khmer.new_counting_hash(12, 1, 1)
try:
kh.load(inpath)
assert 0, "this should fail"
except IOError as e:
- print(str(e))
+ print str(e)
def test_counting_gz_file_type_check():
- ht = khmer.Hashbits(12, 1, 1)
+ ht = khmer.new_hashbits(12, 1, 1)
inpath = utils.get_test_data('goodversion-k12.ht.gz')
- kh = khmer.CountingHash(12, 1, 1)
+ kh = khmer.new_counting_hash(12, 1, 1)
try:
kh.load(inpath)
assert 0, "this should fail"
except IOError as e:
- print(str(e))
+ print str(e)
def test_counting_bad_primes_list():
try:
- ht = khmer._CountingHash(12, ["a", "b", "c"], 1)
+ ht = khmer.CountingHash(12, ["a", "b", "c"], 1)
assert 0, "bad list of primes should fail"
except TypeError as e:
- print(str(e))
+ print str(e)
def test_bad_use_bigcount():
- countingtable = khmer.CountingHash(4, 4 ** 4, 4)
+ countingtable = khmer.new_counting_hash(4, 4 ** 4, 4)
countingtable.set_use_bigcount(True)
assert countingtable.get_use_bigcount()
try:
countingtable.get_use_bigcount(True)
assert 0, "this should fail"
except TypeError as err:
- print(str(err))
+ print str(err)
def test_consume_absentfasta():
- countingtable = khmer.CountingHash(4, 4 ** 4, 4)
+ countingtable = khmer.new_counting_hash(4, 4 ** 4, 4)
try:
countingtable.consume_fasta("absent_file.fa")
assert 0, "This should fail"
except IOError as err:
- print(str(err))
+ print str(err)
def test_consume_absentfasta_with_reads_parser():
- countingtable = khmer.CountingHash(4, 4 ** 4, 4)
+ countingtable = khmer.new_counting_hash(4, 4 ** 4, 4)
try:
countingtable.consume_fasta_with_reads_parser()
assert 0, "this should fail"
except TypeError as err:
- print(str(err))
+ print str(err)
try:
readparser = ReadParser(utils.get_test_data('empty-file'))
countingtable.consume_fasta_with_reads_parser(readparser)
assert 0, "this should fail"
except IOError as err:
- print(str(err))
+ print str(err)
except ValueError as err:
- print(str(err))
+ print str(err)
def test_badconsume():
- countingtable = khmer.CountingHash(4, 4 ** 4, 4)
+ countingtable = khmer.new_counting_hash(4, 4 ** 4, 4)
try:
countingtable.consume()
assert 0, "this should fail"
except TypeError as err:
- print(str(err))
+ print str(err)
try:
countingtable.consume("AAA")
assert 0, "this should fail"
except ValueError as err:
- print(str(err))
+ print str(err)
def test_get_badmin_count():
- countingtable = khmer.CountingHash(4, 4 ** 4, 4)
+ countingtable = khmer.new_counting_hash(4, 4 ** 4, 4)
try:
countingtable.get_min_count()
assert 0, "this should fail"
except TypeError as err:
- print(str(err))
+ print str(err)
try:
countingtable.get_min_count("AAA")
assert 0, "this should fail"
except ValueError as err:
- print(str(err))
+ print str(err)
def test_get_badmax_count():
- countingtable = khmer.CountingHash(4, 4 ** 4, 4)
+ countingtable = khmer.new_counting_hash(4, 4 ** 4, 4)
try:
countingtable.get_max_count()
assert 0, "this should fail"
except TypeError as err:
- print(str(err))
+ print str(err)
try:
countingtable.get_max_count("AAA")
assert 0, "this should fail"
except ValueError as err:
- print(str(err))
+ print str(err)
def test_get_badmedian_count():
- countingtable = khmer.CountingHash(4, 4 ** 4, 4)
+ countingtable = khmer.new_counting_hash(4, 4 ** 4, 4)
try:
countingtable.get_median_count()
assert 0, "this should fail"
except TypeError as err:
- print(str(err))
+ print str(err)
try:
countingtable.get_median_count("AAA")
assert 0, "this should fail"
except ValueError as err:
- print(str(err))
+ print str(err)
def test_get_badkadian_count():
- countingtable = khmer.CountingHash(4, 4 ** 4, 4)
+ countingtable = khmer.new_counting_hash(4, 4 ** 4, 4)
try:
countingtable.get_kadian_count()
assert 0, "this should fail"
except TypeError as err:
- print(str(err))
+ print str(err)
try:
countingtable.get_kadian_count("AAA")
assert 0, "this should fail"
except ValueError as err:
- print(str(err))
+ print str(err)
def test_badget():
- countingtable = khmer.CountingHash(4, 4 ** 4, 4)
+ countingtable = khmer.new_counting_hash(4, 4 ** 4, 4)
try:
countingtable.get()
assert 0, "this should fail"
except TypeError as err:
- print(str(err))
+ print str(err)
def test_badget_2():
- countingtable = khmer.CountingHash(6, 1e6, 2)
+ countingtable = khmer.new_counting_hash(6, 1e6)
countingtable.consume(DNA)
@@ -1243,98 +916,98 @@ def test_badget_2():
countingtable.get("AGCTT")
assert 0, "this should fail"
except ValueError as err:
- print(str(err))
+ print str(err)
def test_badtrim():
- countingtable = khmer.CountingHash(6, 1e6, 2)
+ countingtable = khmer.new_counting_hash(6, 1e6, 2)
countingtable.consume(DNA)
try:
countingtable.trim_on_abundance()
assert 0, "this should fail"
except TypeError as err:
- print(str(err))
+ print str(err)
countingtable.trim_on_abundance("AAAAAA", 1)
def test_badfasta_count_kmers_by_position():
- countingtable = khmer.CountingHash(4, 4 ** 4, 4)
+ countingtable = khmer.new_counting_hash(4, 4 ** 4, 4)
try:
countingtable.fasta_count_kmers_by_position()
except TypeError as err:
- print(str(err))
+ print str(err)
filename = utils.get_test_data("test-short.fa")
try:
countingtable.fasta_count_kmers_by_position(filename, -1, 0)
assert 0, "this should fail"
except ValueError as err:
- print(str(err))
+ print str(err)
try:
countingtable.fasta_count_kmers_by_position(filename, 0, -1)
assert 0, "this should fail"
except ValueError as err:
- print(str(err))
+ print str(err)
def test_badload():
- countingtable = khmer.CountingHash(4, 4 ** 4, 4)
+ countingtable = khmer.new_counting_hash(4, 4 ** 4, 4)
try:
countingtable.load()
assert 0, "this should fail"
except TypeError as err:
- print(str(err))
+ print str(err)
def test_badsave():
- countingtable = khmer.CountingHash(4, 4 ** 4, 4)
+ countingtable = khmer.new_counting_hash(4, 4 ** 4, 4)
try:
countingtable.save()
assert 0, "this should fail"
except TypeError as err:
- print(str(err))
+ print str(err)
def test_badksize():
- countingtable = khmer.CountingHash(4, 4 ** 4, 4)
+ countingtable = khmer.new_counting_hash(4, 4 ** 4, 4)
try:
countingtable.ksize(True)
assert 0, "this should fail"
except TypeError as err:
- print(str(err))
+ print str(err)
def test_badhashsizes():
- countingtable = khmer.CountingHash(4, 4 ** 4, 4)
+ countingtable = khmer.new_counting_hash(4, 4 ** 4, 4)
try:
countingtable.hashsizes(True)
assert 0, "this should fail"
except TypeError as err:
- print(str(err))
+ print str(err)
def test_badconsume_and_tag():
- countingtable = khmer.CountingHash(4, 4 ** 4, 4)
+ countingtable = khmer.new_counting_hash(4, 4 ** 4, 4)
try:
countingtable.consume_and_tag()
assert 0, "this should fail"
except TypeError as err:
- print(str(err))
+ print str(err)
def test_consume_fasta_and_tag():
- countingtable = khmer.CountingHash(4, 4 ** 4, 4)
+ countingtable = khmer.new_counting_hash(4, 4 ** 4, 4)
try:
countingtable.consume_fasta_and_tag()
assert 0, "this should fail"
except TypeError as err:
- print(str(err))
+ print str(err)
countingtable.consume_fasta_and_tag(utils.get_test_data("test-graph2.fa"))
def test_consume_and_retrieve_tags_1():
- ct = khmer.CountingHash(4, 4 ** 4, 4)
+ ct = khmer.new_counting_hash(4, 4 ** 4, 4)
# first, for each sequence, build tags.
for record in screed.open(utils.get_test_data('test-graph2.fa')):
@@ -1357,7 +1030,7 @@ def test_consume_and_retrieve_tags_1():
def test_consume_and_retrieve_tags_empty():
- ct = khmer.CountingHash(4, 4 ** 4, 4)
+ ct = khmer.new_counting_hash(4, 4 ** 4, 4)
# load each sequence but do not build tags - everything should be empty.
for record in screed.open(utils.get_test_data('test-graph2.fa')):
@@ -1381,7 +1054,7 @@ def test_consume_and_retrieve_tags_empty():
def test_find_all_tags_list_error():
- ct = khmer.CountingHash(4, 4 ** 4, 4)
+ ct = khmer.new_counting_hash(4, 4 ** 4, 4)
# load each sequence but do not build tags - everything should be empty.
for record in screed.open(utils.get_test_data('test-graph2.fa')):
@@ -1398,46 +1071,3 @@ def test_find_all_tags_list_error():
assert False, "a ValueError should be raised for incorrect k-mer size"
except ValueError:
pass
-
-
-def test_abund_dist_gz_bigcount():
- infile = utils.get_temp_filename('test.fa')
- shutil.copyfile(utils.get_test_data('test-abund-read-2.fa'), infile)
- outfile = utils.get_temp_filename('test_ct.gz')
- script = 'load-into-counting.py'
- htfile = utils.get_temp_filename('test_ct')
- args = ['-x', str(1e7), '-N', str(2), '-k', str(2), htfile, infile]
- utils.runscript(script, args) # create a bigcount table
- assert os.path.exists(htfile)
- data = open(htfile, 'rb').read()
- f_out = gzip.open(outfile, 'wb') # compress the created bigcount table
- f_out.write(data)
- f_out.close()
- # load the compressed bigcount table
- try:
- counting_hash = khmer.load_counting_hash(outfile)
- except IOError as err:
- assert 0, 'Should not produce IOError: ' + str(err)
- hashsizes = counting_hash.hashsizes()
- kmer_size = counting_hash.ksize()
- tracking = khmer._Hashbits(kmer_size, hashsizes)
- abundances = counting_hash.abundance_distribution(infile, tracking)
- # calculate abundance distribution for compressed bigcount table
- flag = False
- # check if abundance is > 255
- # if ok gzipped bigcount was loaded correctly
- for _, i in enumerate(abundances):
- print(_, i)
- if _ > 255 and i > 0:
- flag = True
- break
- assert flag
-
-
-def test_counting_load_bigcount():
- count_table = khmer.CountingHash(10, 1e5, 4)
- count_table.set_use_bigcount(True)
- for i in range(500):
- print(i, count_table.count('ATATATATAT'))
- count = count_table.get('ATATATATAT')
- assert count == 500
diff --git a/tests/test_counting_single.py b/tests/test_counting_single.py
index a76e63c..7fd348a 100644
--- a/tests/test_counting_single.py
+++ b/tests/test_counting_single.py
@@ -1,8 +1,6 @@
-from __future__ import print_function
-from __future__ import absolute_import
#
-# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
-# Copyright (C) Michigan State University, 2009-2015. It is licensed under
+# This file is part of khmer, http://github.com/ged-lab/khmer/, and is
+# Copyright (C) Michigan State University, 2009-2013. It is licensed under
# the three-clause BSD license; see LICENSE.
# Contact: khmer-project at idyll.org
#
@@ -10,14 +8,14 @@ from __future__ import absolute_import
# pylint: disable=C0111,C0103
import khmer
-from . import khmer_tst_utils as utils
+import khmer_tst_utils as utils
from nose.plugins.attrib import attr
MAX_COUNT = 255
def test_no_collision():
- kh = khmer._CountingHash(4, [5])
+ kh = khmer.new_hashtable(4, 4)
kh.count('AAAA')
assert kh.get('AAAA') == 1
@@ -26,17 +24,17 @@ def test_no_collision():
assert kh.get('TTTT') == 2
- at attr('huge')
+ at attr('linux')
def test_toobig():
try:
- ct = khmer.CountingHash(4, 1000000000000, 1)
+ ct = khmer.new_hashtable(4, 1000000000000)
assert 0, "this should fail"
except MemoryError as err:
- print(str(err))
+ print str(err)
def test_collision():
- kh = khmer._CountingHash(4, [5])
+ kh = khmer.new_hashtable(4, 4)
kh.count('AAAA')
assert kh.get('AAAA') == 1
@@ -46,30 +44,30 @@ def test_collision():
def test_badcount():
- countingtable = khmer._CountingHash(4, [5])
+ countingtable = khmer.new_hashtable(4, 4)
try:
countingtable.count()
assert 0, "count should require one argument"
except TypeError as err:
- print(str(err))
+ print str(err)
try:
countingtable.count('ABCDE')
assert 0, "count should require k-mer size to be equal"
except ValueError as err:
- print(str(err))
+ print str(err)
def test_hashtable_n_entries():
- countingtable = khmer._CountingHash(4, [5])
+ countingtable = khmer.new_hashtable(4, 4)
try:
countingtable.n_entries("nope")
assert 0, "n_entries should accept no arguments"
except TypeError as err:
- print(str(err))
+ print str(err)
def test_complete_no_collision():
- kh = khmer._CountingHash(4, [4**4])
+ kh = khmer.new_hashtable(4, 4 ** 2)
for i in range(0, kh.n_entries()):
s = khmer.reverse_hash(i, 4)
@@ -89,13 +87,13 @@ def test_complete_no_collision():
n_fwd_filled += 1
assert n_rc_filled == kh.n_entries(), n_rc_filled
- assert n_palindromes == 16, n_palindromes
+ assert n_palindromes == 16, n_palindromes # @CTB check this
assert n_fwd_filled == kh.n_entries() // 2 + n_palindromes // 2, \
n_fwd_filled
def test_complete_2_collision():
- kh = khmer._CountingHash(4, [5])
+ kh = khmer.new_hashtable(4, 4)
for i in range(0, kh.n_entries()):
s = khmer.reverse_hash(i, 4)
@@ -116,7 +114,7 @@ def test_complete_2_collision():
def test_complete_4_collision():
- kh = khmer._CountingHash(4, [3])
+ kh = khmer.new_hashtable(4, 2)
for i in range(0, kh.n_entries()):
s = khmer.reverse_hash(i, 4)
@@ -138,14 +136,14 @@ def test_complete_4_collision():
def test_maxcount():
# hashtable should saturate at some point so as not to overflow counter
- kh = khmer._CountingHash(4, [5])
+ kh = khmer.new_hashtable(4, 4)
last_count = None
for _ in range(0, 10000):
kh.count('AAAA')
c = kh.get('AAAA')
- print(last_count, c)
+ print last_count, c
if c == last_count:
break
last_count = c
@@ -156,7 +154,7 @@ def test_maxcount():
def test_maxcount_with_bigcount():
# hashtable should not saturate, if use_bigcount is set.
- kh = khmer._CountingHash(4, [5])
+ kh = khmer.new_hashtable(4, 4)
kh.set_use_bigcount(True)
last_count = None
@@ -164,7 +162,7 @@ def test_maxcount_with_bigcount():
kh.count('AAAA')
c = kh.get('AAAA')
- print(last_count, c)
+ print last_count, c
if c == last_count:
break
last_count = c
@@ -174,7 +172,7 @@ def test_maxcount_with_bigcount():
def test_consume_uniqify_first():
- kh = khmer._CountingHash(4, [5])
+ kh = khmer.new_hashtable(4, 4)
s = "TTTT"
s_rc = "AAAA"
@@ -186,7 +184,7 @@ def test_consume_uniqify_first():
def test_maxcount_consume():
# hashtable should saturate at some point so as not to overflow counter
- kh = khmer._CountingHash(4, [5])
+ kh = khmer.new_hashtable(4, 4)
s = "A" * 10000
kh.consume(s)
@@ -197,7 +195,7 @@ def test_maxcount_consume():
def test_maxcount_consume_with_bigcount():
# use the bigcount hack to avoid saturating the hashtable.
- kh = khmer._CountingHash(4, [5])
+ kh = khmer.new_hashtable(4, 4)
kh.set_use_bigcount(True)
s = "A" * 10000
@@ -208,21 +206,21 @@ def test_maxcount_consume_with_bigcount():
def test_get_mincount():
- kh = khmer._CountingHash(4, [5])
+ kh = khmer.new_hashtable(4, 4)
s = "AAAAACGT"
kh.consume(s)
x = kh.get_min_count(s)
- assert x == 1, x
+ assert x == 1
kh.consume(s)
x = kh.get_min_count(s)
- assert x == 2, x
+ assert x == 2
def test_get_maxcount():
- kh = khmer._CountingHash(4, [7])
+ kh = khmer.new_hashtable(4, 4)
s = "AAAAACGT"
kh.consume(s)
@@ -236,29 +234,29 @@ def test_get_maxcount():
def test_get_maxcount_rc():
- kh = khmer._CountingHash(4, [7])
+ kh = khmer.new_hashtable(4, 4)
s = "AAAAACGT"
src = "ACGTTTTT"
kh.consume(s)
x = kh.get_max_count(s)
- assert x == 2, x
+ assert x == 2
kh.consume(src)
x = kh.get_max_count(s)
- assert x == 4, x
+ assert x == 4
def test_get_mincount_rc():
- kh = khmer._CountingHash(4, [5])
+ kh = khmer.new_hashtable(4, 4)
s = "AAAAACGT"
src = "ACGTTTTT"
kh.consume(s)
x = kh.get_min_count(s)
- assert x == 1, x
+ assert x == 1
kh.consume(src)
x = kh.get_min_count(s)
@@ -266,7 +264,7 @@ def test_get_mincount_rc():
def test_badget():
- kh = khmer.CountingHash(6, 4 ** 10, 1)
+ kh = khmer.new_hashtable(6, 4 ** 10)
DNA = "AGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTCTGATAG"
@@ -280,11 +278,11 @@ def test_badget():
kh.get("AGCTT")
assert 0, "this should fail"
except ValueError as err:
- print(str(err))
+ print str(err)
def test_64bitshift():
- kh = khmer.CountingHash(25, 4, 1)
+ kh = khmer.new_hashtable(25, 4)
fullstr = "GTATGCCAGCTCCAACTGGGCCGGTACGAGCAGGCCATTGCCTCTTGCCGCGATGCGTCGGCG"
substr = "ATGCCAGCTCCAACTGGGCCGGTACGAGCAGGCCATTGCCTCTTGC"
@@ -293,7 +291,7 @@ def test_64bitshift():
def test_64bitshift_2():
- kh = khmer.CountingHash(25, 4, 1)
+ kh = khmer.new_hashtable(25, 4)
fullstr = "GTATGCCAGCTCCAACTGGGCCGGTACGAGCAGGCCATTGCCTCTTGCCGCGATGCGTCGGCG"
kh.consume(fullstr)
@@ -304,12 +302,12 @@ def test_64bitshift_2():
def test_very_short_read():
short_filename = utils.get_test_data('test-short.fa')
- kh = khmer.CountingHash(9, 4, 1)
+ kh = khmer.new_hashtable(9, 4)
n_reads, n_kmers = kh.consume_fasta(short_filename)
assert n_reads == 1, n_reads
assert n_kmers == 0, n_kmers
- kh = khmer.CountingHash(8, 4, 1)
+ kh = khmer.new_hashtable(8, 4)
n_reads, n_kmers = kh.consume_fasta(short_filename)
assert n_reads == 1, n_reads
assert n_kmers == 1, n_kmers
@@ -318,7 +316,7 @@ def test_very_short_read():
class Test_ConsumeString(object):
def setup(self):
- self.kh = khmer._CountingHash(4, [4**4])
+ self.kh = khmer.new_hashtable(4, 4 ** 4)
def test_n_occupied(self):
assert self.kh.n_occupied() == 0
@@ -330,7 +328,7 @@ class Test_ConsumeString(object):
self.kh.n_occupied("MU", 1, 3)
assert 0, "n_occupied shouldn't accept three arguments"
except TypeError as err:
- print(str(err))
+ print str(err)
def test_abundance_by_pos(self):
kh = self.kh
@@ -375,7 +373,7 @@ class Test_ConsumeString(object):
assert self.kh.n_occupied() == 0
self.kh.consume('AAAA')
assert self.kh.n_occupied(0, 1) == 1
- assert self.kh.n_occupied(1, 4 ** 4) == 0, self.kh.n_occupied()
+ assert self.kh.n_occupied(1, 4 ** 4) == 0
hashvalue = khmer.forward_hash('AACT', 4)
self.kh.consume('AACT')
@@ -414,14 +412,14 @@ class Test_ConsumeString(object):
class Test_AbundanceDistribution(object):
def setup(self):
- self.kh = khmer._CountingHash(4, [5])
+ self.kh = khmer.new_hashtable(4, 4)
A_filename = utils.get_test_data('all-A.fa')
self.kh.consume_fasta(A_filename)
def test_count_A(self):
A_filename = utils.get_test_data('all-A.fa')
- tracking = khmer._Hashbits(4, [5])
+ tracking = khmer.new_hashbits(4, 4, 1)
dist = self.kh.abundance_distribution(A_filename, tracking)
assert sum(dist) == 1
diff --git a/tests/test_filter.py b/tests/test_filter.py
index 2ff9091..28b87ae 100644
--- a/tests/test_filter.py
+++ b/tests/test_filter.py
@@ -1,8 +1,6 @@
-from __future__ import print_function
-from __future__ import absolute_import
#
-# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
-# Copyright (C) Michigan State University, 2009-2015. It is licensed under
+# This file is part of khmer, http://github.com/ged-lab/khmer/, and is
+# Copyright (C) Michigan State University, 2009-2013. It is licensed under
# the three-clause BSD license; see LICENSE.
# Contact: khmer-project at idyll.org
#
@@ -10,7 +8,7 @@ import khmer
from screed.fasta import fasta_iter
from nose.plugins.attrib import attr
-from . import khmer_tst_utils as utils
+import khmer_tst_utils as utils
def teardown():
@@ -27,7 +25,7 @@ def load_fa_seq_names(filename):
class Test_Filter(object):
def test_abund(self):
- ht = khmer.CountingHash(10, 4 ** 10, 1)
+ ht = khmer.new_hashtable(10, 4 ** 10)
filename = utils.get_test_data('test-abund-read.fa')
outname = utils.get_temp_filename('test_abund.out')
@@ -37,18 +35,18 @@ class Test_Filter(object):
ht.consume_fasta()
assert 0, "should fail"
except TypeError as err:
- print(str(err))
+ print str(err)
try:
ht.consume_fasta("nonexistent")
assert 0, "should fail"
except IOError as err:
- print(str(err))
+ print str(err)
ht.output_fasta_kmer_pos_freq(filename, outname)
try:
ht.output_fasta_kmer_pos_freq()
assert 0, "should fail"
except TypeError as err:
- print(str(err))
+ print str(err)
fd = open(outname, "r")
diff --git a/tests/test_functions.py b/tests/test_functions.py
index 32f3f99..edf0c8d 100644
--- a/tests/test_functions.py
+++ b/tests/test_functions.py
@@ -1,20 +1,17 @@
-from __future__ import print_function
-from __future__ import absolute_import
#
-# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
+# This file is part of khmer, http://github.com/ged-lab/khmer/, and is
# Copyright (C) Michigan State University, 2009-2015. It is licensed under
# the three-clause BSD license; see LICENSE.
# Contact: khmer-project at idyll.org
#
import khmer
+from nose.plugins.attrib import attr
import os
-import sys
+import khmer_tst_utils as utils
import collections
-from . import khmer_tst_utils as utils
from khmer.utils import (check_is_pair, broken_paired_reader, check_is_left,
check_is_right)
from khmer.kfile import check_input_files
-from cStringIO import StringIO
def test_forward_hash():
@@ -79,37 +76,15 @@ def test_get_primes():
assert primes == [19, 17, 13, 11, 7, 5, 3]
-def test_get_primes_fal():
- try:
- primes = khmer.get_n_primes_near_x(5, 5)
- assert 0, "previous statement should fail"
- except AssertionError:
- raise
- except Exception as err:
- assert "unable to find 5 prime numbers < 5" in str(err)
-
-
-def test_extract_countinghash_info_badfile():
- try:
- khmer.extract_countinghash_info(
- utils.get_test_data('test-abund-read-2.fa'))
- assert 0, 'this should fail'
- except ValueError:
- pass
-
-
def test_extract_countinghash_info():
fn = utils.get_temp_filename('test_extract_counting.ct')
for size in [1e6, 2e6, 5e6, 1e7]:
- ht = khmer.CountingHash(25, size, 4)
+ ht = khmer.new_counting_hash(25, size, 4)
ht.save(fn)
- try:
- info = khmer.extract_countinghash_info(fn)
- except ValueError as err:
- assert 0, 'Should not throw a ValueErorr: ' + str(err)
+ info = khmer.extract_countinghash_info(fn)
ksize, table_size, n_tables, _, _, _ = info
- print(ksize, table_size, n_tables)
+ print ksize, table_size, n_tables
assert(ksize) == 25
assert table_size == size
@@ -117,17 +92,8 @@ def test_extract_countinghash_info():
try:
os.remove(fn)
- except OSError as err:
- assert 0, '...failed to remove ' + fn + str(err)
-
-
-def test_extract_hashbits_info_badfile():
- try:
- khmer.extract_hashbits_info(
- utils.get_test_data('test-abund-read-2.fa'))
- assert 0, 'this should fail'
- except ValueError:
- pass
+ except OSError as e:
+ print >>sys.stder, '...failed to remove {fn}'.format(fn)
def test_extract_hashbits_info():
@@ -138,7 +104,7 @@ def test_extract_hashbits_info():
info = khmer.extract_hashbits_info(fn)
ksize, table_size, n_tables, _, _ = info
- print(ksize, table_size, n_tables)
+ print ksize, table_size, n_tables
assert(ksize) == 25
assert table_size == size
@@ -146,40 +112,26 @@ def test_extract_hashbits_info():
try:
os.remove(fn)
- except OSError as err:
- print('...failed to remove {fn}'.format(fn) + str(err),
- file=sys.stderr)
+ except OSError as e:
+ print >>sys.stderr, '...failed to remove {fn}'.format(fn)
def test_check_file_status_kfile():
fn = utils.get_temp_filename('thisfiledoesnotexist')
check_file_status_exited = False
-
- old_stderr = sys.stderr
- sys.stderr = capture = StringIO()
-
try:
check_input_files(fn, False)
except SystemExit:
- assert "does not exist" in capture.getvalue(), capture.getvalue()
- finally:
- sys.stderr = old_stderr
+ check_file_status_exited = True
+ assert check_file_status_exited
def test_check_file_status_kfile_force():
fn = utils.get_temp_filename('thisfiledoesnotexist')
-
- old_stderr = sys.stderr
- sys.stderr = capture = StringIO()
-
try:
check_input_files(fn, True)
- except OSError:
+ except OSError as e:
assert False
- finally:
- sys.stderr = old_stderr
-
- assert "does not exist" in capture.getvalue(), capture.getvalue()
FakeFQRead = collections.namedtuple('Read', ['name', 'quality', 'sequence'])
diff --git a/tests/test_graph.py b/tests/test_graph.py
index 5afcb92..9b05c48 100644
--- a/tests/test_graph.py
+++ b/tests/test_graph.py
@@ -1,15 +1,13 @@
-from __future__ import print_function
-from __future__ import absolute_import
#
-# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
-# Copyright (C) Michigan State University, 2009-2015. It is licensed under
+# This file is part of khmer, http://github.com/ged-lab/khmer/, and is
+# Copyright (C) Michigan State University, 2009-2013. It is licensed under
# the three-clause BSD license; see LICENSE.
# Contact: khmer-project at idyll.org
#
import khmer
import screed
-from . import khmer_tst_utils as utils
+import khmer_tst_utils as utils
from nose.plugins.attrib import attr
@@ -21,7 +19,7 @@ def teardown():
class Test_ExactGraphFu(object):
def setup(self):
- self.ht = khmer.Hashbits(12, 1e4, 2)
+ self.ht = khmer.new_hashbits(12, 1e4)
def test_counts(self):
ht = self.ht
@@ -115,7 +113,7 @@ class Test_ExactGraphFu(object):
class Test_InexactGraphFu(object):
def setup(self):
- self.ht = khmer.Hashbits(12, 4 ** 3 + 1, 2)
+ self.ht = khmer.new_hashbits(12, 4 ** 2 + 1)
def test_graph_links_next_a(self):
ht = self.ht
@@ -133,7 +131,7 @@ class Test_InexactGraphFu(object):
ht.consume(word[1:] + "C")
x = ht.calc_connected_graph_size(word)
- assert x == 2, x
+ assert x == 2
def test_graph_links_next_g(self):
ht = self.ht
@@ -199,7 +197,7 @@ class Test_Partitioning(object):
filename = utils.get_test_data('random-20-a.fa')
- ht = khmer._Hashbits(21, [5, 7, 11, 13])
+ ht = khmer.new_hashbits(21, 4, 4)
ht.consume_fasta_and_tag(filename)
output_file = utils.get_temp_filename('part0test')
@@ -216,7 +214,7 @@ class Test_Partitioning(object):
filename = utils.get_test_data('random-20-a.fa')
- ht = khmer._Hashbits(21, [5, 7, 11, 13])
+ ht = khmer.new_hashbits(21, 4, 4)
ht.consume_fasta_and_tag(filename)
output_file = utils.get_temp_filename('parttest')
@@ -231,7 +229,7 @@ class Test_Partitioning(object):
def test_output_fq(self):
filename = utils.get_test_data('random-20-a.fq')
- ht = khmer.Hashbits(20, 1e4, 4)
+ ht = khmer.new_hashbits(20, 1e4, 4)
ht.consume_fasta_and_tag(filename)
subset = ht.do_subset_partition(0, 0)
ht.merge_subset(subset)
@@ -239,7 +237,7 @@ class Test_Partitioning(object):
output_file = utils.get_temp_filename('parttest')
ht.output_partitions(filename, output_file, False)
- print(open(output_file).read())
+ print open(output_file).read()
x = set([r.quality for r in screed.open(output_file)])
assert x, x
@@ -247,7 +245,7 @@ class Test_Partitioning(object):
def test_disconnected_20_a(self):
filename = utils.get_test_data('random-20-a.fa')
- ht = khmer.Hashbits(21, 1e5, 4)
+ ht = khmer.new_hashbits(21, 1e5, 4)
ht.consume_fasta_and_tag(filename)
subset = ht.do_subset_partition(0, 0)
@@ -257,7 +255,7 @@ class Test_Partitioning(object):
def test_connected_20_a(self):
filename = utils.get_test_data('random-20-a.fa')
- ht = khmer.Hashbits(20, 1e4, 4)
+ ht = khmer.new_hashbits(20, 1e4, 4)
ht.consume_fasta_and_tag(filename)
subset = ht.do_subset_partition(0, 0)
@@ -267,7 +265,7 @@ class Test_Partitioning(object):
def test_disconnected_20_b(self):
filename = utils.get_test_data('random-20-b.fa')
- ht = khmer.Hashbits(21, 1e4, 4)
+ ht = khmer.new_hashbits(21, 1e4, 4)
ht.consume_fasta_and_tag(filename)
subset = ht.do_subset_partition(0, 0)
@@ -277,7 +275,7 @@ class Test_Partitioning(object):
def test_connected_20_b(self):
filename = utils.get_test_data('random-20-b.fa')
- ht = khmer.Hashbits(20, 1e4, 4)
+ ht = khmer.new_hashbits(20, 1e4, 4)
ht.consume_fasta_and_tag(filename)
subset = ht.do_subset_partition(0, 0)
@@ -287,7 +285,7 @@ class Test_Partitioning(object):
def test_disconnected_31_c(self):
filename = utils.get_test_data('random-31-c.fa')
- ht = khmer.Hashbits(32, 1e6, 4)
+ ht = khmer.new_hashbits(32, 1e6, 4)
ht.consume_fasta_and_tag(filename)
subset = ht.do_subset_partition(0, 0)
@@ -297,7 +295,7 @@ class Test_Partitioning(object):
def test_connected_31_c(self):
filename = utils.get_test_data('random-31-c.fa')
- ht = khmer.Hashbits(31, 1e5, 4)
+ ht = khmer.new_hashbits(31, 1e5, 4)
ht.consume_fasta_and_tag(filename)
subset = ht.do_subset_partition(0, 0)
@@ -310,13 +308,13 @@ class Test_Partitioning(object):
class Test_PythonAPI(object):
def test_find_all_tags_kmersize(self):
- ht = khmer.Hashbits(20, 4 ** 4 + 1, 2)
+ ht = khmer.new_hashbits(20, 4 ** 4 + 1)
a = "ATTGGGACTCTGGGAGCACTTATCATGGAGAT"
b = "GAGCACTTTAACCCTGCAGAGTGGCCAAGGCT"
c = "GGAGCACTTATCATGGAGATATATCCCGTGCTTAAACATCGCACTTTAACCCTGCAGAGT"
- print(ht.consume(a))
+ print ht.consume(a)
try:
ppi = ht.find_all_tags(c[:19])
assert False, "should raise a ValueError for wrong k-mer size"
@@ -330,23 +328,23 @@ class Test_PythonAPI(object):
pass
def test_ordered_connect(self):
- ht = khmer.Hashbits(20, 4 ** 4 + 1, 2)
+ ht = khmer.new_hashbits(20, 4 ** 4 + 1)
a = "ATTGGGACTCTGGGAGCACTTATCATGGAGAT"
b = "GAGCACTTTAACCCTGCAGAGTGGCCAAGGCT"
c = "GGAGCACTTATCATGGAGATATATCCCGTGCTTAAACATCGCACTTTAACCCTGCAGAGT"
- print(ht.consume(a))
+ print ht.consume(a)
ppi = ht.find_all_tags(a[:20])
pid = ht.assign_partition_id(ppi)
assert pid == 0, pid
- print(ht.consume(b))
+ print ht.consume(b)
ppi = ht.find_all_tags(b[:20])
pid = ht.assign_partition_id(ppi)
assert pid == 0, pid
- print(ht.consume(c))
+ print ht.consume(c)
ppi = ht.find_all_tags(c[:20])
pid = ht.assign_partition_id(ppi)
assert pid == 2, pid
diff --git a/tests/test_hashbits.py b/tests/test_hashbits.py
index 12a4f09..40b8d71 100644
--- a/tests/test_hashbits.py
+++ b/tests/test_hashbits.py
@@ -1,8 +1,6 @@
-from __future__ import print_function
-from __future__ import absolute_import
#
-# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
-# Copyright (C) Michigan State University, 2009-2015. It is licensed under
+# This file is part of khmer, http://github.com/ged-lab/khmer/, and is
+# Copyright (C) Michigan State University, 2009-2013. It is licensed under
# the three-clause BSD license; see LICENSE.
# Contact: khmer-project at idyll.org
#
@@ -13,7 +11,7 @@ from khmer import ReadParser
from screed.fasta import fasta_iter
import screed
-from . import khmer_tst_utils as utils
+import khmer_tst_utils as utils
from nose.plugins.attrib import attr
@@ -21,17 +19,8 @@ def teardown():
utils.cleanup()
- at attr('huge')
-def test_toobig():
- try:
- pt = khmer.Hashbits(32, 1e13, 1)
- assert 0, "This should fail"
- except MemoryError as err:
- print(str(err))
-
-
def test__get_set_tag_density():
- ht = khmer._Hashbits(32, [1])
+ ht = khmer.new_hashbits(32, 1, 1)
orig = ht._get_tag_density()
assert orig != 2
@@ -39,76 +28,6 @@ def test__get_set_tag_density():
assert ht._get_tag_density() == 2
-def test_update_from():
- ht = khmer.Hashbits(5, 1000, 4)
- ht2 = khmer.Hashbits(5, 1000, 4)
-
- assert ht.get('AAAAA') == 0
- assert ht.get('GCGCG') == 0
- assert ht2.get('AAAAA') == 0
- assert ht2.get('GCGCG') == 0
-
- ht2.count('AAAAA')
-
- assert ht.get('AAAAA') == 0
- assert ht.get('GCGCG') == 0
- assert ht2.get('AAAAA') == 1
- assert ht2.get('GCGCG') == 0
-
- ht.count('GCGCG')
-
- assert ht.get('AAAAA') == 0
- assert ht.get('GCGCG') == 1
- assert ht2.get('AAAAA') == 1
- assert ht2.get('GCGCG') == 0
-
- ht.update(ht2)
-
- assert ht.get('AAAAA') == 1
- assert ht.get('GCGCG') == 1
- assert ht2.get('AAAAA') == 1
- assert ht2.get('GCGCG') == 0
-
-
-def test_update_from_diff_ksize_2():
- ht = khmer.Hashbits(5, 1000, 4)
- ht2 = khmer.Hashbits(4, 1000, 4)
-
- try:
- ht.update(ht2)
- assert 0, "should not be reached"
- except ValueError as err:
- print(str(err))
-
- try:
- ht2.update(ht)
- assert 0, "should not be reached"
- except ValueError as err:
- print(str(err))
-
-
-def test_update_from_diff_tablesize():
- ht = khmer.Hashbits(5, 100, 4)
- ht2 = khmer.Hashbits(5, 1000, 4)
-
- try:
- ht.update(ht2)
- assert 0, "should not be reached"
- except ValueError as err:
- print(str(err))
-
-
-def test_update_from_diff_num_tables():
- ht = khmer.Hashbits(5, 1000, 3)
- ht2 = khmer.Hashbits(5, 1000, 4)
-
- try:
- ht.update(ht2)
- assert 0, "should not be reached"
- except ValueError as err:
- print(str(err))
-
-
def test_n_occupied_1():
filename = utils.get_test_data('random-20-a.fa')
@@ -117,13 +36,13 @@ def test_n_occupied_1():
N_HT = 1 # number of hashtables
# test modified c++ n_occupied code
- ht1 = khmer.Hashbits(K, HT_SIZE, N_HT)
+ ht1 = khmer.new_hashbits(K, HT_SIZE, N_HT)
for n, record in enumerate(fasta_iter(open(filename))):
ht1.consume(record['sequence'])
# this number calculated independently
- assert ht1.n_occupied() == 3884, ht1.n_occupied()
+ assert ht1.n_occupied() == 3877
def test_bloom_python_1():
@@ -134,7 +53,7 @@ def test_bloom_python_1():
HT_SIZE = 100000 # size of hashtable
N_HT = 3 # number of hashtables
- ht2 = khmer.Hashbits(K, HT_SIZE, N_HT)
+ ht2 = khmer.new_hashbits(K, HT_SIZE, N_HT)
n_unique = 0
for n, record in enumerate(fasta_iter(open(filename))):
@@ -147,10 +66,8 @@ def test_bloom_python_1():
ht2.count(kmer)
assert n_unique == 3960
- assert ht2.n_occupied() == 3885, ht2.n_occupied()
-
- # this number equals n_unique
- assert ht2.n_unique_kmers() == 3960, ht2.n_unique_kmers()
+ assert ht2.n_occupied() == 3882
+ assert ht2.n_unique_kmers() == 3960 # this number equals to n_unique
def test_bloom_c_1():
@@ -162,12 +79,12 @@ def test_bloom_c_1():
HT_SIZE = 100000 # size of hashtable
N_HT = 3 # number of hashtables
- ht3 = khmer.Hashbits(K, HT_SIZE, N_HT)
+ ht3 = khmer.new_hashbits(K, HT_SIZE, N_HT)
for n, record in enumerate(fasta_iter(open(filename))):
ht3.consume(record['sequence'])
- assert ht3.n_occupied() == 3885
+ assert ht3.n_occupied() == 3882
assert ht3.n_unique_kmers() == 3960
@@ -176,7 +93,7 @@ def test_n_occupied_2(): # simple one
HT_SIZE = 10 # use 11
N_HT = 1
- ht1 = khmer._Hashbits(K, [11])
+ ht1 = khmer.new_hashbits(K, HT_SIZE, N_HT)
ht1.count('AAAA') # 00 00 00 00 = 0
assert ht1.n_occupied() == 1
@@ -187,14 +104,17 @@ def test_n_occupied_2(): # simple one
assert ht1.n_occupied() == 2
ht1.count('AGAC') # 00 11 00 10 # collision 2
- assert ht1.n_occupied() == 2, ht1.n_occupied()
+ assert ht1.n_occupied() == 2
def test_bloom_c_2(): # simple one
K = 4
+ HT_SIZE = 10 # use 11
+ N_HT1 = 1 # hashtable size = 11
+ N_HT2 = 2 # hashtable size = 11,13
# use only 1 hashtable, no bloom filter
- ht1 = khmer._Hashbits(K, [11])
+ ht1 = khmer.new_hashbits(K, HT_SIZE, N_HT1)
ht1.count('AAAA') # 00 00 00 00 = 0
ht1.count('ACTG') # 00 10 01 11 =
assert ht1.n_unique_kmers() == 2
@@ -204,7 +124,7 @@ def test_bloom_c_2(): # simple one
assert ht1.n_unique_kmers() == 2
# use two hashtables with 11,13
- ht2 = khmer._Hashbits(K, [11, 13])
+ ht2 = khmer.new_hashbits(K, HT_SIZE, N_HT2)
ht2.count('AAAA') # 00 00 00 00 = 0
ht2.count('ACTG') # 00 10 01 11 = 2*16 +4 +3 = 39
@@ -218,7 +138,7 @@ def test_bloom_c_2(): # simple one
def test_filter_if_present():
- ht = khmer._Hashbits(32, [3, 5])
+ ht = khmer.new_hashbits(32, 2, 2)
maskfile = utils.get_test_data('filter-test-A.fa')
inputfile = utils.get_test_data('filter-test-B.fa')
@@ -234,7 +154,7 @@ def test_filter_if_present():
def test_combine_pe():
inpfile = utils.get_test_data('combine_parts_1.fa')
- ht = khmer._Hashbits(32, [1])
+ ht = khmer.new_hashbits(32, 1, 1)
ht.consume_partitioned_fasta(inpfile)
assert ht.count_partitions() == (2, 0)
@@ -259,7 +179,7 @@ def test_combine_pe():
def test_load_partitioned():
inpfile = utils.get_test_data('combine_parts_1.fa')
- ht = khmer._Hashbits(32, [1])
+ ht = khmer.new_hashbits(32, 1, 1)
ht.consume_partitioned_fasta(inpfile)
assert ht.count_partitions() == (2, 0)
@@ -276,9 +196,9 @@ def test_load_partitioned():
def test_count_within_radius_simple():
inpfile = utils.get_test_data('all-A.fa')
- ht = khmer._Hashbits(4, [3, 5])
+ ht = khmer.new_hashbits(4, 2, 2)
- print(ht.consume_fasta(inpfile))
+ print ht.consume_fasta(inpfile)
n = ht.count_kmers_within_radius('AAAA', 1)
assert n == 1
@@ -288,13 +208,13 @@ def test_count_within_radius_simple():
def test_count_within_radius_big():
inpfile = utils.get_test_data('random-20-a.fa')
- ht = khmer.Hashbits(20, 1e5, 4)
+ ht = khmer.new_hashbits(20, 1e5, 4)
ht.consume_fasta(inpfile)
n = ht.count_kmers_within_radius('CGCAGGCTGGATTCTAGAGG', int(1e6))
- assert n == 3961, n
+ assert n == 3960
- ht = khmer.Hashbits(21, 1e5, 4)
+ ht = khmer.new_hashbits(21, 1e5, 4)
ht.consume_fasta(inpfile)
n = ht.count_kmers_within_radius('CGCAGGCTGGATTCTAGAGGC', int(1e6))
assert n == 39
@@ -302,7 +222,7 @@ def test_count_within_radius_big():
def test_count_kmer_degree():
inpfile = utils.get_test_data('all-A.fa')
- ht = khmer._Hashbits(4, [3, 5])
+ ht = khmer.new_hashbits(4, 2, 2)
ht.consume_fasta(inpfile)
assert ht.kmer_degree('AAAA') == 2
@@ -312,7 +232,7 @@ def test_count_kmer_degree():
def test_save_load_tagset():
- ht = khmer._Hashbits(32, [1])
+ ht = khmer.new_hashbits(32, 1, 1)
outfile = utils.get_temp_filename('tagset')
@@ -330,11 +250,11 @@ def test_save_load_tagset():
fp = open(outfile, 'rb')
data = fp.read()
fp.close()
- assert len(data) == 30, len(data)
+ assert len(data) == 26, len(data)
def test_save_load_tagset_noclear():
- ht = khmer._Hashbits(32, [1])
+ ht = khmer.new_hashbits(32, 1, 1)
outfile = utils.get_temp_filename('tagset')
@@ -352,7 +272,7 @@ def test_save_load_tagset_noclear():
fp = open(outfile, 'rb')
data = fp.read()
fp.close()
- assert len(data) == 38, len(data)
+ assert len(data) == 34, len(data)
def test_stop_traverse():
@@ -362,7 +282,7 @@ def test_stop_traverse():
HT_SIZE = 1e4 # size of hashtable
N_HT = 3 # number of hashtables
- ht = khmer.Hashbits(K, HT_SIZE, N_HT)
+ ht = khmer.new_hashbits(K, HT_SIZE, N_HT)
# without tagging/joining across consume, this breaks into two partition;
# with, it is one partition.
@@ -383,7 +303,7 @@ def test_tag_across_stoptraverse():
HT_SIZE = 1e4 # size of hashtable
N_HT = 3 # number of hashtables
- ht = khmer.Hashbits(K, HT_SIZE, N_HT)
+ ht = khmer.new_hashbits(K, HT_SIZE, N_HT)
# without tagging/joining across consume, this breaks into two partition;
# with, it is one partition.
@@ -411,7 +331,7 @@ def test_notag_across_stoptraverse():
HT_SIZE = 1e4 # size of hashtable
N_HT = 3 # number of hashtables
- ht = khmer.Hashbits(K, HT_SIZE, N_HT)
+ ht = khmer.new_hashbits(K, HT_SIZE, N_HT)
# connecting k-mer at the beginning/end of a read: breaks up into two.
ht.add_stop_tag('TTGCATACGTTGAGCCAGCG')
@@ -426,7 +346,7 @@ def test_notag_across_stoptraverse():
def test_find_stoptags():
- ht = khmer._Hashbits(5, [1])
+ ht = khmer.new_hashbits(5, 1, 1)
ht.add_stop_tag("AAAAA")
assert ht.identify_stoptags_by_position("AAAAA") == [0]
@@ -436,7 +356,7 @@ def test_find_stoptags():
def test_find_stoptags2():
- ht = khmer._Hashbits(4, [1])
+ ht = khmer.new_hashbits(4, 1, 1)
ht.add_stop_tag("ATGC")
x = ht.identify_stoptags_by_position("ATGCATGCGCAT")
@@ -444,17 +364,17 @@ def test_find_stoptags2():
def test_get_ksize():
- kh = khmer._Hashbits(22, [1])
+ kh = khmer.new_hashbits(22, 1, 1)
assert kh.ksize() == 22
def test_get_hashsizes():
- kh = khmer.Hashbits(22, 100, 4)
- assert kh.hashsizes() == [97L, 89L, 83L, 79L], kh.hashsizes()
+ kh = khmer.new_hashbits(22, 100, 4)
+ assert kh.hashsizes() == [101, 103, 107, 109], kh.hashsizes()
def test_extract_unique_paths_0():
- kh = khmer._Hashbits(10, [5, 7, 11, 13])
+ kh = khmer.new_hashbits(10, 4, 4)
x = kh.extract_unique_paths('ATGGAGAGACACAGATAGACAGGAGTGGCGATG', 10, 1)
assert x == ['ATGGAGAGACACAGATAGACAGGAGTGGCGATG']
@@ -465,36 +385,36 @@ def test_extract_unique_paths_0():
def test_extract_unique_paths_1():
- kh = khmer._Hashbits(10, [5, 7, 11, 13])
+ kh = khmer.new_hashbits(10, 4, 4)
kh.consume('AGTGGCGATG')
x = kh.extract_unique_paths('ATGGAGAGACACAGATAGACAGGAGTGGCGATG', 10, 1)
- print(x)
+ print x
assert x == ['ATGGAGAGACACAGATAGACAGGAGTGGCGAT'] # all but the last k-mer
def test_extract_unique_paths_2():
- kh = khmer._Hashbits(10, [5, 7, 11, 13])
+ kh = khmer.new_hashbits(10, 4, 4)
kh.consume('ATGGAGAGAC')
x = kh.extract_unique_paths('ATGGAGAGACACAGATAGACAGGAGTGGCGATG', 10, 1)
- print(x)
+ print x
assert x == ['TGGAGAGACACAGATAGACAGGAGTGGCGATG'] # all but the 1st k-mer
def test_extract_unique_paths_3():
- kh = khmer._Hashbits(10, [5, 7, 11, 13])
+ kh = khmer.new_hashbits(10, 4, 4)
kh.consume('ATGGAGAGAC')
kh.consume('AGTGGCGATG')
x = kh.extract_unique_paths('ATGGAGAGACACAGATAGACAGGAGTGGCGATG', 10, 1)
- print(x)
+ print x
# all but the 1st/last k-mer
assert x == ['TGGAGAGACACAGATAGACAGGAGTGGCGAT']
def test_extract_unique_paths_4():
- kh = khmer.Hashbits(10, 1e6, 4)
+ kh = khmer.new_hashbits(10, 4, 4)
kh.consume('ATGGAGAGAC')
kh.consume('AGTGGCGATG')
@@ -502,7 +422,7 @@ def test_extract_unique_paths_4():
kh.consume('ATAGACAGGA')
x = kh.extract_unique_paths('ATGGAGAGACACAGATAGACAGGAGTGGCGATG', 10, 1)
- print(x)
+ print x
assert x == ['TGGAGAGACACAGATAGACAGG', 'TAGACAGGAGTGGCGAT']
@@ -514,7 +434,7 @@ def test_find_unpart():
HT_SIZE = 1e4 # size of hashtable
N_HT = 3 # number of hashtables
- ht = khmer.Hashbits(K, HT_SIZE, N_HT)
+ ht = khmer.new_hashbits(K, HT_SIZE, N_HT)
ht.consume_fasta_and_tag(filename)
subset = ht.do_subset_partition(0, 0)
@@ -536,7 +456,7 @@ def test_find_unpart_notraverse():
HT_SIZE = 1e4 # size of hashtable
N_HT = 3 # number of hashtables
- ht = khmer.Hashbits(K, HT_SIZE, N_HT)
+ ht = khmer.new_hashbits(K, HT_SIZE, N_HT)
ht.consume_fasta_and_tag(filename)
subset = ht.do_subset_partition(0, 0)
@@ -558,7 +478,7 @@ def test_find_unpart_fail():
HT_SIZE = 1e4 # size of hashtable
N_HT = 3 # number of hashtables
- ht = khmer.Hashbits(K, HT_SIZE, N_HT)
+ ht = khmer.new_hashbits(K, HT_SIZE, N_HT)
ht.consume_fasta_and_tag(filename)
subset = ht.do_subset_partition(0, 0)
@@ -573,24 +493,24 @@ def test_find_unpart_fail():
def test_simple_median():
- hi = khmer.Hashbits(6, 1e5, 2)
+ hi = khmer.new_hashbits(6, 2, 2)
(median, average, stddev) = hi.get_median_count("AAAAAA")
- print(median, average, stddev)
+ print median, average, stddev
assert median == 0
assert average == 0.0
assert stddev == 0.0
hi.consume("AAAAAA")
(median, average, stddev) = hi.get_median_count("AAAAAA")
- print(median, average, stddev)
+ print median, average, stddev
assert median == 1
assert average == 1.0
assert stddev == 0.0
def test_badget():
- hbts = khmer.Hashbits(6, 1e6, 1)
+ hbts = khmer.new_hashbits(6, 1e6, 1)
dna = "AGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTCTGATAG"
@@ -601,16 +521,10 @@ def test_badget():
assert hbts.get("GATGAG") == 0
try:
- hbts.get(b"AGCTT")
- assert 0, "this should fail"
- except ValueError as err:
- print(str(err))
-
- try:
- hbts.get(u"AGCTT")
+ hbts.get("AGCTT")
assert 0, "this should fail"
except ValueError as err:
- print(str(err))
+ print str(err)
#
@@ -619,7 +533,7 @@ def test_badget():
def test_load_notexist_should_fail():
savepath = utils.get_temp_filename('temphashbitssave0.ht')
- hi = khmer._CountingHash(12, [1])
+ hi = khmer.new_counting_hash(12, 2)
try:
hi.load(savepath)
assert 0, "load should fail"
@@ -631,8 +545,7 @@ def test_load_truncated_should_fail():
inpath = utils.get_test_data('random-20-a.fa')
savepath = utils.get_temp_filename('temphashbitssave0.ct')
- hi = khmer.CountingHash(12, 1000, 2)
-
+ hi = khmer.new_counting_hash(12, 1000)
hi.consume_fasta(inpath)
hi.save(savepath)
@@ -644,27 +557,27 @@ def test_load_truncated_should_fail():
fp.write(data[:1000])
fp.close()
- hi = khmer._CountingHash(12, [1])
+ hi = khmer.new_counting_hash(12, 1)
try:
hi.load(savepath)
assert 0, "load should fail"
except IOError as e:
- print(str(e))
+ print str(e)
def test_save_load_tagset_notexist():
- ht = khmer._Hashbits(32, [1])
+ ht = khmer.new_hashbits(32, 1, 1)
outfile = utils.get_temp_filename('tagset')
try:
ht.load_tagset(outfile)
assert 0, "this test should fail"
except IOError as e:
- print(str(e))
+ print str(e)
def test_save_load_tagset_trunc():
- ht = khmer._Hashbits(32, [1])
+ ht = khmer.new_hashbits(32, 1, 1)
outfile = utils.get_temp_filename('tagset')
@@ -677,18 +590,16 @@ def test_save_load_tagset_trunc():
data = fp.read()
fp.close()
- for i in range(len(data)):
- fp = open(outfile, 'wb')
- fp.write(data[:i])
- fp.close()
-
- # try loading it...
- try:
- ht.load_tagset(outfile)
- assert 0, "this test should fail"
- except IOError as err:
- print(str(err), i)
+ fp = open(outfile, 'wb')
+ fp.write(data[:26])
+ fp.close()
+ # try loading it...
+ try:
+ ht.load_tagset(outfile)
+ assert 0, "this test should fail"
+ except IOError:
+ pass
# to build the test files used below, add 'test' to this function
# and then look in /tmp. You will need to tweak the version info in
@@ -699,13 +610,13 @@ def _build_testfiles():
# hashbits file
inpath = utils.get_test_data('random-20-a.fa')
- hi = khmer.Hashbits(12, 2)
+ hi = khmer.new_hashbits(12, 2)
hi.consume_fasta(inpath)
hi.save('/tmp/goodversion-k12.ht')
# tagset file
- ht = khmer._Hashbits(32, [1])
+ ht = khmer.new_hashbits(32, 1, 1)
ht.add_tag('A' * 32)
ht.add_tag('G' * 32)
@@ -715,7 +626,7 @@ def _build_testfiles():
fakelump_fa = utils.get_test_data('fakelump.fa')
- ht = khmer.Hashbits(32, 4, 4)
+ ht = khmer.new_hashbits(32, 4, 4)
ht.consume_fasta_and_tag(fakelump_fa)
subset = ht.do_subset_partition(0, 0)
@@ -724,7 +635,7 @@ def _build_testfiles():
EXCURSION_DISTANCE = 40
EXCURSION_KMER_THRESHOLD = 82
EXCURSION_KMER_COUNT_THRESHOLD = 1
- counting = khmer.CountingHash(32, 4, 4)
+ counting = khmer.new_counting_hash(32, 4, 4)
ht.repartition_largest_partition(None, counting,
EXCURSION_DISTANCE,
@@ -735,7 +646,7 @@ def _build_testfiles():
def test_hashbits_file_version_check():
- ht = khmer._Hashbits(12, [1])
+ ht = khmer.new_hashbits(12, 1, 1)
inpath = utils.get_test_data('badversion-k12.ht')
@@ -743,25 +654,25 @@ def test_hashbits_file_version_check():
ht.load(inpath)
assert 0, "this should fail"
except IOError as e:
- print(str(e))
+ print str(e)
def test_hashbits_file_type_check():
- kh = khmer._CountingHash(12, [1])
+ kh = khmer.new_counting_hash(12, 1, 1)
savepath = utils.get_temp_filename('tempcountingsave0.ct')
kh.save(savepath)
- ht = khmer._Hashbits(12, [1])
+ ht = khmer.new_hashbits(12, 1, 1)
try:
ht.load(savepath)
assert 0, "this should fail"
except IOError as e:
- print(str(e))
+ print str(e)
def test_stoptags_file_version_check():
- ht = khmer._Hashbits(32, [1])
+ ht = khmer.new_hashbits(32, 1, 1)
inpath = utils.get_test_data('badversion-k32.stoptags')
@@ -769,33 +680,33 @@ def test_stoptags_file_version_check():
ht.load_stop_tags(inpath)
assert 0, "this should fail"
except IOError as e:
- print(str(e))
+ print str(e)
def test_stoptags_ksize_check():
- ht = khmer._Hashbits(31, [1])
+ ht = khmer.new_hashbits(31, 1, 1)
inpath = utils.get_test_data('goodversion-k32.stoptags')
try:
ht.load_stop_tags(inpath)
assert 0, "this should fail"
except IOError as e:
- print(str(e))
+ print str(e)
def test_stop_tags_filetype_check():
- ht = khmer._Hashbits(31, [1])
+ ht = khmer.new_hashbits(31, 1, 1)
inpath = utils.get_test_data('goodversion-k32.tagset')
try:
ht.load_stop_tags(inpath)
assert 0, "this should fail"
except IOError as e:
- print(str(e))
+ print str(e)
def test_tagset_file_version_check():
- ht = khmer._Hashbits(32, [1])
+ ht = khmer.new_hashbits(32, 1, 1)
inpath = utils.get_test_data('badversion-k32.tagset')
@@ -803,48 +714,29 @@ def test_tagset_file_version_check():
ht.load_tagset(inpath)
assert 0, "this should fail"
except IOError as e:
- print(str(e))
-
-
-def test_stop_tags_truncate_check():
- ht = khmer._Hashbits(32, [1])
-
- inpath = utils.get_test_data('goodversion-k32.tagset')
- data = open(inpath, 'rb').read()
-
- truncpath = utils.get_temp_filename('zzz')
- for i in range(len(data)):
- fp = open(truncpath, 'wb')
- fp.write(data[:i])
- fp.close()
-
- try:
- ht.load_stop_tags(truncpath)
- assert 0, "expect failure of previous command"
- except IOError as e:
- print(i, str(e))
+ print str(e)
def test_tagset_ksize_check():
- ht = khmer._Hashbits(31, [1])
+ ht = khmer.new_hashbits(31, 1, 1)
inpath = utils.get_test_data('goodversion-k32.tagset')
try:
ht.load_tagset(inpath)
assert 0, "this should fail"
except IOError as e:
- print(str(e))
+ print str(e)
def test_tagset_filetype_check():
- ht = khmer._Hashbits(31, [1])
+ ht = khmer.new_hashbits(31, 1, 1)
inpath = utils.get_test_data('goodversion-k32.stoptags')
try:
ht.load_tagset(inpath)
assert 0, "this should fail"
except IOError as e:
- print(str(e))
+ print str(e)
def test_bad_primes_list():
@@ -852,42 +744,21 @@ def test_bad_primes_list():
coutingtable = khmer._Hashbits(31, ["a", "b", "c"], 1)
assert 0, "Bad primes list should fail"
except TypeError as e:
- print(str(e))
+ print str(e)
def test_consume_absentfasta_with_reads_parser():
- presencetable = khmer._Hashbits(31, [1])
+ presencetable = khmer.new_hashbits(31, 1, 1)
try:
presencetable.consume_fasta_with_reads_parser()
assert 0, "this should fail"
except TypeError as err:
- print(str(err))
+ print str(err)
try:
readparser = ReadParser(utils.get_test_data('empty-file'))
presencetable.consume_fasta_with_reads_parser(readparser)
assert 0, "this should fail"
except IOError as err:
- print(str(err))
+ print str(err)
except ValueError as err:
- print(str(err))
-
-
-def test_bad_primes():
- try:
- countingtable = khmer._Hashbits.__new__(
- khmer._Hashbits, 6, ["a", "b", "c"])
- assert 0, "this should fail"
- except TypeError as e:
- print(str(e))
-
-
-def test_consume_fasta_and_tag_with_badreads_parser():
- presencetable = khmer.Hashbits(6, 1e6, 2)
- try:
- readsparser = khmer.ReadParser(utils.get_test_data("test-empty.fa"))
- presencetable.consume_fasta_and_tag_with_reads_parser(readsparser)
- assert 0, "this should fail"
- except IOError as e:
- print(str(e))
- except ValueError as e:
- print(str(e))
+ print str(err)
diff --git a/tests/test_hashbits.py b/tests/test_hashbits_obj.py
similarity index 56%
copy from tests/test_hashbits.py
copy to tests/test_hashbits_obj.py
index 12a4f09..2d3ebd1 100644
--- a/tests/test_hashbits.py
+++ b/tests/test_hashbits_obj.py
@@ -1,19 +1,23 @@
-from __future__ import print_function
-from __future__ import absolute_import
#
-# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
-# Copyright (C) Michigan State University, 2009-2015. It is licensed under
+# This file is part of khmer, http://github.com/ged-lab/khmer/, and is
+# Copyright (C) Michigan State University, 2009-2013. It is licensed under
# the three-clause BSD license; see LICENSE.
# Contact: khmer-project at idyll.org
#
# pylint: disable=missing-docstring,protected-access
+
+#
+# This is an exact copy of test_hashbits, with all invocations of
+# khmer.new_hashbits replaced by khmer.Hashbits constructor calls
+#
+
import khmer
-from khmer import ReadParser
+from khmer import Hashbits
from screed.fasta import fasta_iter
import screed
-from . import khmer_tst_utils as utils
+import khmer_tst_utils as utils
from nose.plugins.attrib import attr
@@ -21,17 +25,17 @@ def teardown():
utils.cleanup()
- at attr('huge')
+ at attr('linux')
def test_toobig():
try:
pt = khmer.Hashbits(32, 1e13, 1)
assert 0, "This should fail"
except MemoryError as err:
- print(str(err))
+ print str(err)
def test__get_set_tag_density():
- ht = khmer._Hashbits(32, [1])
+ ht = khmer.Hashbits(32, 1, 1)
orig = ht._get_tag_density()
assert orig != 2
@@ -39,76 +43,6 @@ def test__get_set_tag_density():
assert ht._get_tag_density() == 2
-def test_update_from():
- ht = khmer.Hashbits(5, 1000, 4)
- ht2 = khmer.Hashbits(5, 1000, 4)
-
- assert ht.get('AAAAA') == 0
- assert ht.get('GCGCG') == 0
- assert ht2.get('AAAAA') == 0
- assert ht2.get('GCGCG') == 0
-
- ht2.count('AAAAA')
-
- assert ht.get('AAAAA') == 0
- assert ht.get('GCGCG') == 0
- assert ht2.get('AAAAA') == 1
- assert ht2.get('GCGCG') == 0
-
- ht.count('GCGCG')
-
- assert ht.get('AAAAA') == 0
- assert ht.get('GCGCG') == 1
- assert ht2.get('AAAAA') == 1
- assert ht2.get('GCGCG') == 0
-
- ht.update(ht2)
-
- assert ht.get('AAAAA') == 1
- assert ht.get('GCGCG') == 1
- assert ht2.get('AAAAA') == 1
- assert ht2.get('GCGCG') == 0
-
-
-def test_update_from_diff_ksize_2():
- ht = khmer.Hashbits(5, 1000, 4)
- ht2 = khmer.Hashbits(4, 1000, 4)
-
- try:
- ht.update(ht2)
- assert 0, "should not be reached"
- except ValueError as err:
- print(str(err))
-
- try:
- ht2.update(ht)
- assert 0, "should not be reached"
- except ValueError as err:
- print(str(err))
-
-
-def test_update_from_diff_tablesize():
- ht = khmer.Hashbits(5, 100, 4)
- ht2 = khmer.Hashbits(5, 1000, 4)
-
- try:
- ht.update(ht2)
- assert 0, "should not be reached"
- except ValueError as err:
- print(str(err))
-
-
-def test_update_from_diff_num_tables():
- ht = khmer.Hashbits(5, 1000, 3)
- ht2 = khmer.Hashbits(5, 1000, 4)
-
- try:
- ht.update(ht2)
- assert 0, "should not be reached"
- except ValueError as err:
- print(str(err))
-
-
def test_n_occupied_1():
filename = utils.get_test_data('random-20-a.fa')
@@ -123,7 +57,7 @@ def test_n_occupied_1():
ht1.consume(record['sequence'])
# this number calculated independently
- assert ht1.n_occupied() == 3884, ht1.n_occupied()
+ assert ht1.n_occupied() == 3877
def test_bloom_python_1():
@@ -147,10 +81,8 @@ def test_bloom_python_1():
ht2.count(kmer)
assert n_unique == 3960
- assert ht2.n_occupied() == 3885, ht2.n_occupied()
-
- # this number equals n_unique
- assert ht2.n_unique_kmers() == 3960, ht2.n_unique_kmers()
+ assert ht2.n_occupied() == 3882
+ assert ht2.n_unique_kmers() == 3960 # this number equals to n_unique
def test_bloom_c_1():
@@ -167,7 +99,7 @@ def test_bloom_c_1():
for n, record in enumerate(fasta_iter(open(filename))):
ht3.consume(record['sequence'])
- assert ht3.n_occupied() == 3885
+ assert ht3.n_occupied() == 3882
assert ht3.n_unique_kmers() == 3960
@@ -176,7 +108,7 @@ def test_n_occupied_2(): # simple one
HT_SIZE = 10 # use 11
N_HT = 1
- ht1 = khmer._Hashbits(K, [11])
+ ht1 = khmer.Hashbits(K, HT_SIZE, N_HT)
ht1.count('AAAA') # 00 00 00 00 = 0
assert ht1.n_occupied() == 1
@@ -187,14 +119,17 @@ def test_n_occupied_2(): # simple one
assert ht1.n_occupied() == 2
ht1.count('AGAC') # 00 11 00 10 # collision 2
- assert ht1.n_occupied() == 2, ht1.n_occupied()
+ assert ht1.n_occupied() == 2
def test_bloom_c_2(): # simple one
K = 4
+ HT_SIZE = 10 # use 11
+ N_HT1 = 1 # hashtable size = 11
+ N_HT2 = 2 # hashtable size = 11,13
# use only 1 hashtable, no bloom filter
- ht1 = khmer._Hashbits(K, [11])
+ ht1 = khmer.Hashbits(K, HT_SIZE, N_HT1)
ht1.count('AAAA') # 00 00 00 00 = 0
ht1.count('ACTG') # 00 10 01 11 =
assert ht1.n_unique_kmers() == 2
@@ -204,7 +139,7 @@ def test_bloom_c_2(): # simple one
assert ht1.n_unique_kmers() == 2
# use two hashtables with 11,13
- ht2 = khmer._Hashbits(K, [11, 13])
+ ht2 = khmer.Hashbits(K, HT_SIZE, N_HT2)
ht2.count('AAAA') # 00 00 00 00 = 0
ht2.count('ACTG') # 00 10 01 11 = 2*16 +4 +3 = 39
@@ -218,7 +153,7 @@ def test_bloom_c_2(): # simple one
def test_filter_if_present():
- ht = khmer._Hashbits(32, [3, 5])
+ ht = khmer.Hashbits(32, 1e6, 2)
maskfile = utils.get_test_data('filter-test-A.fa')
inputfile = utils.get_test_data('filter-test-B.fa')
@@ -234,7 +169,7 @@ def test_filter_if_present():
def test_combine_pe():
inpfile = utils.get_test_data('combine_parts_1.fa')
- ht = khmer._Hashbits(32, [1])
+ ht = khmer.Hashbits(32, 1, 1)
ht.consume_partitioned_fasta(inpfile)
assert ht.count_partitions() == (2, 0)
@@ -259,7 +194,7 @@ def test_combine_pe():
def test_load_partitioned():
inpfile = utils.get_test_data('combine_parts_1.fa')
- ht = khmer._Hashbits(32, [1])
+ ht = khmer.Hashbits(32, 1, 1)
ht.consume_partitioned_fasta(inpfile)
assert ht.count_partitions() == (2, 0)
@@ -276,9 +211,9 @@ def test_load_partitioned():
def test_count_within_radius_simple():
inpfile = utils.get_test_data('all-A.fa')
- ht = khmer._Hashbits(4, [3, 5])
+ ht = khmer.Hashbits(4, 1e6, 2)
- print(ht.consume_fasta(inpfile))
+ print ht.consume_fasta(inpfile)
n = ht.count_kmers_within_radius('AAAA', 1)
assert n == 1
@@ -288,13 +223,13 @@ def test_count_within_radius_simple():
def test_count_within_radius_big():
inpfile = utils.get_test_data('random-20-a.fa')
- ht = khmer.Hashbits(20, 1e5, 4)
+ ht = khmer.Hashbits(20, 1e6, 4)
ht.consume_fasta(inpfile)
n = ht.count_kmers_within_radius('CGCAGGCTGGATTCTAGAGG', int(1e6))
- assert n == 3961, n
+ assert n == 3960
- ht = khmer.Hashbits(21, 1e5, 4)
+ ht = khmer.Hashbits(21, 1e6, 4)
ht.consume_fasta(inpfile)
n = ht.count_kmers_within_radius('CGCAGGCTGGATTCTAGAGGC', int(1e6))
assert n == 39
@@ -302,7 +237,7 @@ def test_count_within_radius_big():
def test_count_kmer_degree():
inpfile = utils.get_test_data('all-A.fa')
- ht = khmer._Hashbits(4, [3, 5])
+ ht = khmer.Hashbits(4, 1e6, 2)
ht.consume_fasta(inpfile)
assert ht.kmer_degree('AAAA') == 2
@@ -312,7 +247,7 @@ def test_count_kmer_degree():
def test_save_load_tagset():
- ht = khmer._Hashbits(32, [1])
+ ht = khmer.Hashbits(32, 1, 1)
outfile = utils.get_temp_filename('tagset')
@@ -330,11 +265,11 @@ def test_save_load_tagset():
fp = open(outfile, 'rb')
data = fp.read()
fp.close()
- assert len(data) == 30, len(data)
+ assert len(data) == 26, len(data)
def test_save_load_tagset_noclear():
- ht = khmer._Hashbits(32, [1])
+ ht = khmer.Hashbits(32, 1, 1)
outfile = utils.get_temp_filename('tagset')
@@ -352,14 +287,14 @@ def test_save_load_tagset_noclear():
fp = open(outfile, 'rb')
data = fp.read()
fp.close()
- assert len(data) == 38, len(data)
+ assert len(data) == 34, len(data)
def test_stop_traverse():
filename = utils.get_test_data('random-20-a.fa')
K = 20 # size of kmer
- HT_SIZE = 1e4 # size of hashtable
+ HT_SIZE = 100000 # size of hashtable
N_HT = 3 # number of hashtables
ht = khmer.Hashbits(K, HT_SIZE, N_HT)
@@ -380,7 +315,7 @@ def test_tag_across_stoptraverse():
filename = utils.get_test_data('random-20-a.fa')
K = 20 # size of kmer
- HT_SIZE = 1e4 # size of hashtable
+ HT_SIZE = 100000 # size of hashtable
N_HT = 3 # number of hashtables
ht = khmer.Hashbits(K, HT_SIZE, N_HT)
@@ -408,7 +343,7 @@ def test_notag_across_stoptraverse():
filename = utils.get_test_data('random-20-a.fa')
K = 20 # size of kmer
- HT_SIZE = 1e4 # size of hashtable
+ HT_SIZE = 100000 # size of hashtable
N_HT = 3 # number of hashtables
ht = khmer.Hashbits(K, HT_SIZE, N_HT)
@@ -426,7 +361,7 @@ def test_notag_across_stoptraverse():
def test_find_stoptags():
- ht = khmer._Hashbits(5, [1])
+ ht = khmer.Hashbits(5, 1, 1)
ht.add_stop_tag("AAAAA")
assert ht.identify_stoptags_by_position("AAAAA") == [0]
@@ -436,7 +371,7 @@ def test_find_stoptags():
def test_find_stoptags2():
- ht = khmer._Hashbits(4, [1])
+ ht = khmer.Hashbits(4, 1, 1)
ht.add_stop_tag("ATGC")
x = ht.identify_stoptags_by_position("ATGCATGCGCAT")
@@ -444,17 +379,17 @@ def test_find_stoptags2():
def test_get_ksize():
- kh = khmer._Hashbits(22, [1])
+ kh = khmer.Hashbits(22, 1, 1)
assert kh.ksize() == 22
def test_get_hashsizes():
kh = khmer.Hashbits(22, 100, 4)
- assert kh.hashsizes() == [97L, 89L, 83L, 79L], kh.hashsizes()
+ assert kh.hashsizes() == [101, 103, 107, 109], kh.hashsizes()
def test_extract_unique_paths_0():
- kh = khmer._Hashbits(10, [5, 7, 11, 13])
+ kh = khmer.Hashbits(10, 1e5, 4)
x = kh.extract_unique_paths('ATGGAGAGACACAGATAGACAGGAGTGGCGATG', 10, 1)
assert x == ['ATGGAGAGACACAGATAGACAGGAGTGGCGATG']
@@ -465,36 +400,36 @@ def test_extract_unique_paths_0():
def test_extract_unique_paths_1():
- kh = khmer._Hashbits(10, [5, 7, 11, 13])
+ kh = khmer.Hashbits(10, 1e5, 4)
kh.consume('AGTGGCGATG')
x = kh.extract_unique_paths('ATGGAGAGACACAGATAGACAGGAGTGGCGATG', 10, 1)
- print(x)
+ print x
assert x == ['ATGGAGAGACACAGATAGACAGGAGTGGCGAT'] # all but the last k-mer
def test_extract_unique_paths_2():
- kh = khmer._Hashbits(10, [5, 7, 11, 13])
+ kh = khmer.Hashbits(10, 1e5, 4)
kh.consume('ATGGAGAGAC')
x = kh.extract_unique_paths('ATGGAGAGACACAGATAGACAGGAGTGGCGATG', 10, 1)
- print(x)
+ print x
assert x == ['TGGAGAGACACAGATAGACAGGAGTGGCGATG'] # all but the 1st k-mer
def test_extract_unique_paths_3():
- kh = khmer._Hashbits(10, [5, 7, 11, 13])
+ kh = khmer.Hashbits(10, 1e5, 4)
kh.consume('ATGGAGAGAC')
kh.consume('AGTGGCGATG')
x = kh.extract_unique_paths('ATGGAGAGACACAGATAGACAGGAGTGGCGATG', 10, 1)
- print(x)
+ print x
# all but the 1st/last k-mer
assert x == ['TGGAGAGACACAGATAGACAGGAGTGGCGAT']
def test_extract_unique_paths_4():
- kh = khmer.Hashbits(10, 1e6, 4)
+ kh = khmer.Hashbits(10, 1e5, 4)
kh.consume('ATGGAGAGAC')
kh.consume('AGTGGCGATG')
@@ -502,7 +437,7 @@ def test_extract_unique_paths_4():
kh.consume('ATAGACAGGA')
x = kh.extract_unique_paths('ATGGAGAGACACAGATAGACAGGAGTGGCGATG', 10, 1)
- print(x)
+ print x
assert x == ['TGGAGAGACACAGATAGACAGG', 'TAGACAGGAGTGGCGAT']
@@ -511,7 +446,7 @@ def test_find_unpart():
filename2 = utils.get_test_data('random-20-a.even.fa')
K = 20 # size of kmer
- HT_SIZE = 1e4 # size of hashtable
+ HT_SIZE = 100000 # size of hashtable
N_HT = 3 # number of hashtables
ht = khmer.Hashbits(K, HT_SIZE, N_HT)
@@ -533,7 +468,7 @@ def test_find_unpart_notraverse():
filename2 = utils.get_test_data('random-20-a.even.fa')
K = 20 # size of kmer
- HT_SIZE = 1e4 # size of hashtable
+ HT_SIZE = 100000 # size of hashtable
N_HT = 3 # number of hashtables
ht = khmer.Hashbits(K, HT_SIZE, N_HT)
@@ -555,7 +490,7 @@ def test_find_unpart_fail():
filename2 = utils.get_test_data('random-20-a.odd.fa') # <- switch to odd
K = 20 # size of kmer
- HT_SIZE = 1e4 # size of hashtable
+ HT_SIZE = 100000 # size of hashtable
N_HT = 3 # number of hashtables
ht = khmer.Hashbits(K, HT_SIZE, N_HT)
@@ -573,17 +508,17 @@ def test_find_unpart_fail():
def test_simple_median():
- hi = khmer.Hashbits(6, 1e5, 2)
+ hi = khmer.Hashbits(6, 1e6, 2)
(median, average, stddev) = hi.get_median_count("AAAAAA")
- print(median, average, stddev)
+ print median, average, stddev
assert median == 0
assert average == 0.0
assert stddev == 0.0
hi.consume("AAAAAA")
(median, average, stddev) = hi.get_median_count("AAAAAA")
- print(median, average, stddev)
+ print median, average, stddev
assert median == 1
assert average == 1.0
assert stddev == 0.0
@@ -601,275 +536,10 @@ def test_badget():
assert hbts.get("GATGAG") == 0
try:
- hbts.get(b"AGCTT")
- assert 0, "this should fail"
- except ValueError as err:
- print(str(err))
-
- try:
- hbts.get(u"AGCTT")
- assert 0, "this should fail"
- except ValueError as err:
- print(str(err))
-
-
-#
-
-
-def test_load_notexist_should_fail():
- savepath = utils.get_temp_filename('temphashbitssave0.ht')
-
- hi = khmer._CountingHash(12, [1])
- try:
- hi.load(savepath)
- assert 0, "load should fail"
- except IOError:
- pass
-
-
-def test_load_truncated_should_fail():
- inpath = utils.get_test_data('random-20-a.fa')
- savepath = utils.get_temp_filename('temphashbitssave0.ct')
-
- hi = khmer.CountingHash(12, 1000, 2)
-
- hi.consume_fasta(inpath)
- hi.save(savepath)
-
- fp = open(savepath, 'rb')
- data = fp.read()
- fp.close()
-
- fp = open(savepath, 'wb')
- fp.write(data[:1000])
- fp.close()
-
- hi = khmer._CountingHash(12, [1])
- try:
- hi.load(savepath)
- assert 0, "load should fail"
- except IOError as e:
- print(str(e))
-
-
-def test_save_load_tagset_notexist():
- ht = khmer._Hashbits(32, [1])
-
- outfile = utils.get_temp_filename('tagset')
- try:
- ht.load_tagset(outfile)
- assert 0, "this test should fail"
- except IOError as e:
- print(str(e))
-
-
-def test_save_load_tagset_trunc():
- ht = khmer._Hashbits(32, [1])
-
- outfile = utils.get_temp_filename('tagset')
-
- ht.add_tag('A' * 32)
- ht.add_tag('G' * 32)
- ht.save_tagset(outfile)
-
- # truncate tagset file...
- fp = open(outfile, 'rb')
- data = fp.read()
- fp.close()
-
- for i in range(len(data)):
- fp = open(outfile, 'wb')
- fp.write(data[:i])
- fp.close()
-
- # try loading it...
- try:
- ht.load_tagset(outfile)
- assert 0, "this test should fail"
- except IOError as err:
- print(str(err), i)
-
-
-# to build the test files used below, add 'test' to this function
-# and then look in /tmp. You will need to tweak the version info in
-# khmer.hh in order to create "bad" versions, of course. -CTB
-
-
-def _build_testfiles():
- # hashbits file
-
- inpath = utils.get_test_data('random-20-a.fa')
- hi = khmer.Hashbits(12, 2)
- hi.consume_fasta(inpath)
- hi.save('/tmp/goodversion-k12.ht')
-
- # tagset file
-
- ht = khmer._Hashbits(32, [1])
-
- ht.add_tag('A' * 32)
- ht.add_tag('G' * 32)
- ht.save_tagset('/tmp/goodversion-k32.tagset')
-
- # stoptags file
-
- fakelump_fa = utils.get_test_data('fakelump.fa')
-
- ht = khmer.Hashbits(32, 4, 4)
- ht.consume_fasta_and_tag(fakelump_fa)
-
- subset = ht.do_subset_partition(0, 0)
- ht.merge_subset(subset)
-
- EXCURSION_DISTANCE = 40
- EXCURSION_KMER_THRESHOLD = 82
- EXCURSION_KMER_COUNT_THRESHOLD = 1
- counting = khmer.CountingHash(32, 4, 4)
-
- ht.repartition_largest_partition(None, counting,
- EXCURSION_DISTANCE,
- EXCURSION_KMER_THRESHOLD,
- EXCURSION_KMER_COUNT_THRESHOLD)
-
- ht.save_stop_tags('/tmp/goodversion-k32.stoptags')
-
-
-def test_hashbits_file_version_check():
- ht = khmer._Hashbits(12, [1])
-
- inpath = utils.get_test_data('badversion-k12.ht')
-
- try:
- ht.load(inpath)
- assert 0, "this should fail"
- except IOError as e:
- print(str(e))
-
-
-def test_hashbits_file_type_check():
- kh = khmer._CountingHash(12, [1])
- savepath = utils.get_temp_filename('tempcountingsave0.ct')
- kh.save(savepath)
-
- ht = khmer._Hashbits(12, [1])
-
- try:
- ht.load(savepath)
- assert 0, "this should fail"
- except IOError as e:
- print(str(e))
-
-
-def test_stoptags_file_version_check():
- ht = khmer._Hashbits(32, [1])
-
- inpath = utils.get_test_data('badversion-k32.stoptags')
-
- try:
- ht.load_stop_tags(inpath)
- assert 0, "this should fail"
- except IOError as e:
- print(str(e))
-
-
-def test_stoptags_ksize_check():
- ht = khmer._Hashbits(31, [1])
-
- inpath = utils.get_test_data('goodversion-k32.stoptags')
- try:
- ht.load_stop_tags(inpath)
- assert 0, "this should fail"
- except IOError as e:
- print(str(e))
-
-
-def test_stop_tags_filetype_check():
- ht = khmer._Hashbits(31, [1])
-
- inpath = utils.get_test_data('goodversion-k32.tagset')
- try:
- ht.load_stop_tags(inpath)
- assert 0, "this should fail"
- except IOError as e:
- print(str(e))
-
-
-def test_tagset_file_version_check():
- ht = khmer._Hashbits(32, [1])
-
- inpath = utils.get_test_data('badversion-k32.tagset')
-
- try:
- ht.load_tagset(inpath)
- assert 0, "this should fail"
- except IOError as e:
- print(str(e))
-
-
-def test_stop_tags_truncate_check():
- ht = khmer._Hashbits(32, [1])
-
- inpath = utils.get_test_data('goodversion-k32.tagset')
- data = open(inpath, 'rb').read()
-
- truncpath = utils.get_temp_filename('zzz')
- for i in range(len(data)):
- fp = open(truncpath, 'wb')
- fp.write(data[:i])
- fp.close()
-
- try:
- ht.load_stop_tags(truncpath)
- assert 0, "expect failure of previous command"
- except IOError as e:
- print(i, str(e))
-
-
-def test_tagset_ksize_check():
- ht = khmer._Hashbits(31, [1])
-
- inpath = utils.get_test_data('goodversion-k32.tagset')
- try:
- ht.load_tagset(inpath)
- assert 0, "this should fail"
- except IOError as e:
- print(str(e))
-
-
-def test_tagset_filetype_check():
- ht = khmer._Hashbits(31, [1])
-
- inpath = utils.get_test_data('goodversion-k32.stoptags')
- try:
- ht.load_tagset(inpath)
- assert 0, "this should fail"
- except IOError as e:
- print(str(e))
-
-
-def test_bad_primes_list():
- try:
- coutingtable = khmer._Hashbits(31, ["a", "b", "c"], 1)
- assert 0, "Bad primes list should fail"
- except TypeError as e:
- print(str(e))
-
-
-def test_consume_absentfasta_with_reads_parser():
- presencetable = khmer._Hashbits(31, [1])
- try:
- presencetable.consume_fasta_with_reads_parser()
- assert 0, "this should fail"
- except TypeError as err:
- print(str(err))
- try:
- readparser = ReadParser(utils.get_test_data('empty-file'))
- presencetable.consume_fasta_with_reads_parser(readparser)
+ hbts.get("AGCTT")
assert 0, "this should fail"
- except IOError as err:
- print(str(err))
except ValueError as err:
- print(str(err))
+ print str(err)
def test_bad_primes():
@@ -878,7 +548,7 @@ def test_bad_primes():
khmer._Hashbits, 6, ["a", "b", "c"])
assert 0, "this should fail"
except TypeError as e:
- print(str(e))
+ print str(e)
def test_consume_fasta_and_tag_with_badreads_parser():
@@ -888,6 +558,6 @@ def test_consume_fasta_and_tag_with_badreads_parser():
presencetable.consume_fasta_and_tag_with_reads_parser(readsparser)
assert 0, "this should fail"
except IOError as e:
- print(str(e))
+ print str(e)
except ValueError as e:
- print(str(e))
+ print str(e)
diff --git a/tests/test_hll.py b/tests/test_hll.py
index ebde12d..266ce5d 100644
--- a/tests/test_hll.py
+++ b/tests/test_hll.py
@@ -1,7 +1,5 @@
-from __future__ import division, print_function, unicode_literals
-from __future__ import absolute_import
#
-# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
+# This file is part of khmer, http://github.com/ged-lab/khmer/, and is
# Copyright (C) Michigan State University, 2014-2015. It is licensed under
# the three-clause BSD license; see LICENSE.
# Contact: khmer-project at idyll.org
@@ -9,19 +7,20 @@ from __future__ import absolute_import
# pylint: disable=missing-docstring,protected-access
import math
+import string
import khmer
from screed.fasta import fasta_iter
-from . import khmer_tst_utils as utils
+import khmer_tst_utils as utils
from nose.tools import assert_raises
+TT = string.maketrans('ACGT', 'TGCA')
K = 20 # size of kmer
ERR_RATE = 0.01
N_UNIQUE = 3960
-TRANSLATE = {'A': 'T', 'C': 'G', 'T': 'A', 'G': 'C'}
def teardown():
@@ -42,7 +41,7 @@ def test_hll_add_python():
seq_len = len(sequence)
for n in range(0, seq_len + 1 - K):
kmer = sequence[n:n + K]
- rc = "".join(TRANSLATE[c] for c in kmer[::-1])
+ rc = kmer[::-1].translate(TT)
hllcpp.add(kmer)
@@ -62,12 +61,9 @@ def test_hll_consume_string():
filename = utils.get_test_data('random-20-a.fa')
hllcpp = khmer.HLLCounter(ERR_RATE, K)
- n_consumed = 0
- for n, record in enumerate(fasta_iter(open(filename)), 1):
- n_consumed += hllcpp.consume_string(record['sequence'])
+ for n, record in enumerate(fasta_iter(open(filename))):
+ hllcpp.consume_string(record['sequence'])
- assert n == 99
- assert n_consumed == 3960
assert abs(1 - float(hllcpp.estimate_cardinality()) / N_UNIQUE) < ERR_RATE
@@ -83,10 +79,8 @@ def test_hll_consume_fasta():
filename = utils.get_test_data('random-20-a.fa')
hllcpp = khmer.HLLCounter(ERR_RATE, K)
- n, n_consumed = hllcpp.consume_fasta(filename)
+ hllcpp.consume_fasta(filename)
- assert n == 99
- assert n_consumed == 3960
assert abs(1 - float(hllcpp.estimate_cardinality()) / N_UNIQUE) < ERR_RATE
@@ -96,12 +90,10 @@ def test_hll_consume_fasta_ep():
filename = utils.get_test_data('paired-mixed.fa')
hll = khmer.HLLCounter(0.36, 32)
- n, n_consumed = hll.consume_fasta(filename)
+ hll.consume_fasta(filename)
assert all(c != 0 for c in hll.counters)
assert len(hll) == 236
- assert n == 11
- assert n_consumed == 575
def test_hll_consume_fasta_estimate_bias():
@@ -112,21 +104,17 @@ def test_hll_consume_fasta_estimate_bias():
filename = utils.get_test_data("test-abund-read-3.fa")
hll = khmer.HLLCounter(0.36, K)
- n, n_consumed = hll.consume_fasta(filename)
+ hll.consume_fasta(filename)
assert all(c != 0 for c in hll.counters)
assert len(hll) == 79
- assert n == 21
- assert n_consumed == 1176
def test_hll_len():
filename = utils.get_test_data('random-20-a.fa')
hllcpp = khmer.HLLCounter(ERR_RATE, K)
- n, n_consumed = hllcpp.consume_fasta(filename)
+ hllcpp.consume_fasta(filename)
- assert n == 99
- assert n_consumed == 3960
assert hllcpp.estimate_cardinality() == len(hllcpp)
@@ -237,7 +225,7 @@ def test_hll_change_ksize():
hllcpp.ksize = 24
assert hllcpp.ksize == 24
- hllcpp.ksize = 12
+ hllcpp.ksize = 12L
assert hllcpp.ksize == 12
with assert_raises(ValueError):
@@ -260,43 +248,3 @@ def test_hll_get_counters():
counters = hll.counters
assert len(counters) == 2 ** 4
assert all(c == 0 for c in counters)
-
-
-def test_hll_merge_1():
- hll = khmer.HLLCounter(0.36, K)
- hll2 = khmer.HLLCounter(0.36, K - 1)
-
- try:
- hll.merge(hll2)
- assert 0, "previous statement should fail with a ValueError"
- except ValueError as err:
- print(str(err))
-
-
-def test_hll_merge_2():
- hll = khmer.HLLCounter(0.10, K)
- hll2 = khmer.HLLCounter(0.36, K)
-
- try:
- hll.merge(hll2)
- assert 0, "previous statement should fail with a ValueError"
- except ValueError as err:
- print(str(err))
-
-
-def test_hll_merge_3():
- hll = khmer.HLLCounter(0.36, 32)
- hll2 = khmer.HLLCounter(0.36, 32)
-
- filename = utils.get_test_data('paired-mixed.fa')
- hll = khmer.HLLCounter(0.36, 32)
- hll.consume_fasta(filename)
-
- hll2 = khmer.HLLCounter(0.36, 32)
- hll2.consume_fasta(filename)
-
- assert len(hll) == 236
- assert len(hll2) == 236
-
- hll.merge(hll2)
- assert len(hll) == 236
diff --git a/tests/test_labelhash.py b/tests/test_labelhash.py
index 59a56b0..36c9e7b 100644
--- a/tests/test_labelhash.py
+++ b/tests/test_labelhash.py
@@ -1,19 +1,16 @@
-from __future__ import print_function
-from __future__ import absolute_import
#
-# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
-# Copyright (C) Michigan State University, 2009-2015. It is licensed under
+# This file is part of khmer, http://github.com/ged-lab/khmer/, and is
+# Copyright (C) Michigan State University, 2009-2013. It is licensed under
# the three-clause BSD license; see LICENSE.
# Contact: khmer-project at idyll.org
#
# pylint: disable=missing-docstring,protected-access
-import os
import khmer
-from khmer import LabelHash, CountingLabelHash
+from khmer import LabelHash
from screed.fasta import fasta_iter
import screed
-from . import khmer_tst_utils as utils
+import khmer_tst_utils as utils
from nose.plugins.attrib import attr
@@ -25,22 +22,13 @@ def teardown():
# * thread-safety
- at attr('huge')
+ at attr('linux')
def test_toobig():
try:
lh = LabelHash(20, 1e13, 1)
assert 0, "This should fail."
except MemoryError as err:
- print(str(err))
-
-
-def test_error_create():
- from khmer import _LabelHash
- try:
- lh = _LabelHash(None)
- assert 0, "This should fail."
- except ValueError as err:
- print(str(err))
+ print str(err)
def test_n_labels():
@@ -48,7 +36,7 @@ def test_n_labels():
filename = utils.get_test_data('test-labels.fa')
lh.consume_fasta_and_tag_with_labels(filename)
- print(lh.n_labels())
+ print lh.n_labels()
assert lh.n_labels() == 4
@@ -65,100 +53,6 @@ def test_get_label_dict():
assert a_label in expected
-def test_get_label_dict_save_load():
- lb_pre = LabelHash(20, 1e7, 4)
- filename = utils.get_test_data('test-labels.fa')
- lb_pre.consume_fasta_and_tag_with_labels(filename)
-
- # save labels to a file
- savepath = utils.get_temp_filename('saved.labels')
- lb_pre.save_labels_and_tags(savepath)
-
- # trash the old LabelHash
- del lb_pre
-
- # create new, load labels & tags
- lb = LabelHash(20, 1e7, 4)
- lb.load_labels_and_tags(savepath)
-
- labels = lb.get_label_dict()
- expected = [0, 1, 2, 3]
- for e_label in expected:
- assert e_label in labels
- for a_label in labels:
- assert a_label in expected
-
-
-def test_get_label_dict_save_load_wrong_ksize():
- lb_pre = LabelHash(19, 1e7, 4)
- filename = utils.get_test_data('test-labels.fa')
- lb_pre.consume_fasta_and_tag_with_labels(filename)
-
- # save labels to a file
- savepath = utils.get_temp_filename('saved.labels')
- lb_pre.save_labels_and_tags(savepath)
-
- # trash the old LabelHash
- del lb_pre
-
- # create new, load labels & tags
- lb = LabelHash(20, 1e7, 4)
- try:
- lb.load_labels_and_tags(savepath)
- assert 0, "this should not succeed - different ksize"
- except IOError as err:
- print(str(err))
- assert "Incorrect k-mer size 19" in str(err)
-
-
-def test_save_load_corrupted():
- lb_pre = LabelHash(20, 1e7, 4)
- filename = utils.get_test_data('test-labels.fa')
- lb_pre.consume_fasta_and_tag_with_labels(filename)
-
- # save labels to a file
- savepath = utils.get_temp_filename('saved.labels')
- lb_pre.save_labels_and_tags(savepath)
-
- # trash the old LabelHash
- del lb_pre
-
- lb = LabelHash(20, 1e7, 4)
-
- # produce all possible truncated versions of this file
- data = open(savepath, 'rb').read()
- for i in range(len(data)):
- truncated = utils.get_temp_filename('trunc.labels')
- fp = open(truncated, 'wb')
- fp.write(data[:i])
- fp.close()
-
- try:
- lb.load_labels_and_tags(truncated)
- assert 0, "this should not succeed -- truncated file len %d" % (i,)
- except IOError as err:
- print('expected failure for', i, ': ', str(err))
-
-
-def test_save_fail_readonly():
- lb_pre = LabelHash(20, 1e7, 4)
- filename = utils.get_test_data('test-labels.fa')
- lb_pre.consume_fasta_and_tag_with_labels(filename)
-
- # save labels to a file
- savepath = utils.get_temp_filename('saved.labels')
- fp = open(savepath, 'w')
- fp.close()
-
- os.chmod(savepath, 0x444)
-
- try:
- lb_pre.save_labels_and_tags(savepath)
- assert 0, "this should fail: read-only file"
- except IOError as err:
- print(str(err))
-
-
def test_get_tag_labels():
lb = LabelHash(20, 1e7, 4)
filename = utils.get_test_data('single-read.fq')
@@ -176,22 +70,22 @@ def test_consume_fasta_and_tag_with_labels():
filename = utils.get_test_data('test-transcript.fa')
total_reads, n_consumed = lb.consume_fasta_and_tag_with_labels(filename)
- print("doing get")
- assert lb.graph.get(read_1[:20])
+ print "doing get"
+ assert lb.get(read_1[:20])
assert total_reads == 3
- print("doing n_labels")
- print(lb.n_labels())
- print("doing label dict")
- print(lb.get_label_dict())
- print("get tagset")
- for tag in lb.graph.get_tagset():
- print("forward hash")
- print(tag, khmer.forward_hash(tag, 20))
+ print "doing n_labels"
+ print lb.n_labels()
+ print "doing label dict"
+ print lb.get_label_dict()
+ print "get tagset"
+ for tag in lb.get_tagset():
+ print "forward hash"
+ print tag, khmer.forward_hash(tag, 20)
for record in screed.open(filename):
- print("Sweeping tags")
- print(lb.sweep_tag_neighborhood(record.sequence, 40))
- print("Sweeping labels...")
- print(lb.sweep_label_neighborhood(record.sequence, 40))
+ print "Sweeping tags"
+ print lb.sweep_tag_neighborhood(record.sequence, 40)
+ print "Sweeping labels..."
+ print lb.sweep_label_neighborhood(record.sequence, 40)
assert lb.n_labels() == 3
@@ -205,8 +99,8 @@ def test_consume_partitioned_fasta_and_tag_with_labels():
for record in screed.open(filename):
seq = record.sequence
labels.update(lb.sweep_label_neighborhood(seq, 0, False, False))
- # print(lb.n_labels())
- # print(labels)
+ # print lb.n_labels()
+ # print labels
assert len(labels) == 1
assert labels.pop() == 2
assert lb.n_labels() == 1
@@ -228,7 +122,7 @@ def test_consume_sequence_and_tag_with_labels():
def test_sweep_tag_neighborhood():
lb = LabelHash(20, 1e7, 4)
filename = utils.get_test_data('single-read.fq')
- lb.graph.consume_fasta_and_tag(filename)
+ lb.consume_fasta_and_tag(filename)
tags = lb.sweep_tag_neighborhood('CAGGCGCCCACCACCGTGCCCTCCAACCTGATGGT')
assert len(tags) == 1
@@ -262,11 +156,11 @@ def test_label_tag_correctness():
labels = lb.sweep_label_neighborhood(
'ATCGTGTAAGCTATCGTAATCGTAAGCTCTGCCTAGAGCTAGGCTAGGCTCTGCCTAGAG'
'CTAGGCTAGGTGTGCTCTGCCTAGAGCTAGGCTAGGTGT')
- print(lb.sweep_tag_neighborhood(
+ print lb.sweep_tag_neighborhood(
'TTCGTGTAAGCTATCGTAATCGTAAGCTCTGCCTAGAGCTAGGCTAGGCTCTGCCTAGAG'
- 'CTAGGCTAGGTGTGCTCTGCTAGAGCTAGGCTAGGTGT'))
- print(labels)
- print(len('ATCGTGTAAGCTATCGTAATCGTAAGCTCTGCCTAGAGCTAGGCTAG') - 19)
+ 'CTAGGCTAGGTGTGCTCTGCTAGAGCTAGGCTAGGTGT')
+ print labels
+ print len('ATCGTGTAAGCTATCGTAATCGTAAGCTCTGCCTAGAGCTAGGCTAG') - 19
assert len(labels) == 2
assert 0 in labels
assert 1 in labels
@@ -275,7 +169,7 @@ def test_label_tag_correctness():
labels = lb.sweep_label_neighborhood(
'GCGTAATCGTAAGCTCTGCCTAGAGCTAGGCTAGCTCTGCCTAGAGCTAGGCTAGGTGTTGGGGATAG'
'ATAGATAGATGACCTAGAGCTAGGCTAGGTGTTGGGGATAGATAGATAGATGA')
- print(labels)
+ print labels
assert len(labels) == 3
assert 0 in labels
assert 1 in labels
@@ -286,7 +180,7 @@ def test_label_tag_correctness():
'TGGGATAGATAGATAGATGACCTAGAGCTAGGCTAGGTGTTGGGGATAGATAGATAGATGACCTAGAG'
'CTAGGCTAGGTGTTGGGGATAGATAGATAGATGAGTTGGGGATAGATAGATAGATGAGTGTAGATCCA'
'ACAACACATACA')
- print(labels)
+ print labels
assert len(labels) == 2
assert 1 in labels
assert 2 in labels
@@ -294,144 +188,508 @@ def test_label_tag_correctness():
# read D
labels = lb.sweep_label_neighborhood(
'TATATATATAGCTAGCTAGCTAACTAGCTAGCATCGATCGATCGATC')
- print(labels)
+ print labels
assert len(labels) == 1
assert 3 in labels
+#
+# Begin Hashbits tests
+#
-def test_counting_label_tag_correctness():
- lb = CountingLabelHash(20, 1e7, 4)
- filename = utils.get_test_data('test-labels.fa')
- lb.consume_fasta_and_tag_with_labels(filename)
- # read A
- labels = lb.sweep_label_neighborhood(
- 'ATCGTGTAAGCTATCGTAATCGTAAGCTCTGCCTAGAGCTAGGCTAGGCTCTGCCTAGAG'
- 'CTAGGCTAGGTGTGCTCTGCCTAGAGCTAGGCTAGGTGT')
- print(lb.sweep_tag_neighborhood(
- 'TTCGTGTAAGCTATCGTAATCGTAAGCTCTGCCTAGAGCTAGGCTAGGCTCTGCCTAGAG'
- 'CTAGGCTAGGTGTGCTCTGCTAGAGCTAGGCTAGGTGT'))
- print(labels)
- print(len('ATCGTGTAAGCTATCGTAATCGTAAGCTCTGCCTAGAGCTAGGCTAG') - 19)
- assert len(labels) == 2
- assert 0 in labels
- assert 1 in labels
+def test__get_set_tag_density():
+ ht = khmer.LabelHash(32, 1, 1)
- # read B
- labels = lb.sweep_label_neighborhood(
- 'GCGTAATCGTAAGCTCTGCCTAGAGCTAGGCTAGCTCTGCCTAGAGCTAGGCTAGGTGTTGGGGATAG'
- 'ATAGATAGATGACCTAGAGCTAGGCTAGGTGTTGGGGATAGATAGATAGATGA')
- print(labels)
- assert len(labels) == 3
- assert 0 in labels
- assert 1 in labels
- assert 2 in labels
+ orig = ht._get_tag_density()
+ assert orig != 2
+ ht._set_tag_density(2)
+ assert ht._get_tag_density() == 2
- # read C
- labels = lb.sweep_label_neighborhood(
- 'TGGGATAGATAGATAGATGACCTAGAGCTAGGCTAGGTGTTGGGGATAGATAGATAGATGACCTAGAG'
- 'CTAGGCTAGGTGTTGGGGATAGATAGATAGATGAGTTGGGGATAGATAGATAGATGAGTGTAGATCCA'
- 'ACAACACATACA')
- print(labels)
- assert len(labels) == 2
- assert 1 in labels
- assert 2 in labels
- # read D
- labels = lb.sweep_label_neighborhood(
- 'TATATATATAGCTAGCTAGCTAACTAGCTAGCATCGATCGATCGATC')
- print(labels)
- assert len(labels) == 1
- assert 3 in labels
+def test_n_occupied_1():
+ filename = utils.get_test_data('random-20-a.fa')
+ K = 20 # size of kmer
+ HT_SIZE = 100000 # size of hashtable
+ N_HT = 1 # number of hashtables
-def test_label_tag_correctness_save_load():
- lb_pre = LabelHash(20, 1e7, 4)
- filename = utils.get_test_data('test-labels.fa')
- lb_pre.consume_fasta_and_tag_with_labels(filename)
+ # test modified c++ n_occupied code
+ ht1 = khmer.LabelHash(K, HT_SIZE, N_HT)
- # save labels to a file
- savepath = utils.get_temp_filename('saved.labels')
- lb_pre.save_labels_and_tags(savepath)
+ for n, record in enumerate(fasta_iter(open(filename))):
+ ht1.consume(record['sequence'])
- # trash the old LabelHash
- del lb_pre
+ # this number calculated independently
+ assert ht1.n_occupied() == 3877
- # create new, load labels & tags
- lb = LabelHash(20, 1e7, 4)
- lb.load_labels_and_tags(savepath)
- # read A
- labels = lb.sweep_label_neighborhood(
- 'ATCGTGTAAGCTATCGTAATCGTAAGCTCTGCCTAGAGCTAGGCTAGGCTCTGCCTAGAG'
- 'CTAGGCTAGGTGTGCTCTGCCTAGAGCTAGGCTAGGTGT')
- print(lb.sweep_tag_neighborhood(
- 'TTCGTGTAAGCTATCGTAATCGTAAGCTCTGCCTAGAGCTAGGCTAGGCTCTGCCTAGAG'
- 'CTAGGCTAGGTGTGCTCTGCTAGAGCTAGGCTAGGTGT'))
- print(labels)
- print(len('ATCGTGTAAGCTATCGTAATCGTAAGCTCTGCCTAGAGCTAGGCTAG') - 19)
- assert len(labels) == 2
- assert 0 in labels
- assert 1 in labels
+def test_bloom_python_1():
+ # test python code to count unique kmers using bloom filter
+ filename = utils.get_test_data('random-20-a.fa')
- # read B
- labels = lb.sweep_label_neighborhood(
- 'GCGTAATCGTAAGCTCTGCCTAGAGCTAGGCTAGCTCTGCCTAGAGCTAGGCTAGGTGTTGGGGATAG'
- 'ATAGATAGATGACCTAGAGCTAGGCTAGGTGTTGGGGATAGATAGATAGATGA')
- print(labels)
- assert len(labels) == 3
- assert 0 in labels
- assert 1 in labels
- assert 2 in labels
+ K = 20 # size of kmer
+ HT_SIZE = 100000 # size of hashtable
+ N_HT = 3 # number of hashtables
- # read C
- labels = lb.sweep_label_neighborhood(
- 'TGGGATAGATAGATAGATGACCTAGAGCTAGGCTAGGTGTTGGGGATAGATAGATAGATGACCTAGAG'
- 'CTAGGCTAGGTGTTGGGGATAGATAGATAGATGAGTTGGGGATAGATAGATAGATGAGTGTAGATCCA'
- 'ACAACACATACA')
- print(labels)
- assert len(labels) == 2
- assert 1 in labels
- assert 2 in labels
+ ht2 = khmer.LabelHash(K, HT_SIZE, N_HT)
- # read D
- labels = lb.sweep_label_neighborhood(
- 'TATATATATAGCTAGCTAGCTAACTAGCTAGCATCGATCGATCGATC')
- print(labels)
- assert len(labels) == 1
- assert 3 in labels
+ n_unique = 0
+ for n, record in enumerate(fasta_iter(open(filename))):
+ sequence = record['sequence']
+ seq_len = len(sequence)
+ for n in range(0, seq_len + 1 - K):
+ kmer = sequence[n:n + K]
+ if (not ht2.get(kmer)):
+ n_unique += 1
+ ht2.count(kmer)
+ assert n_unique == 3960
+ assert ht2.n_occupied() == 3882
+ assert ht2.n_unique_kmers() == 3960 # this number equals to n_unique
-def test_load_wrong_filetype():
- lb = LabelHash(20, 1e7, 4)
- # try to load a tagset
- filename = utils.get_test_data('goodversion-k32.tagset')
- try:
- lb.load_labels_and_tags(filename)
- assert 0, "this should not succeed - bad file type"
- except IOError as err:
- print(str(err))
- assert "Incorrect file format type" in str(err)
-
- # try to load a nonsense file
- filename = utils.get_test_data('all-A.fa')
- try:
- lb.load_labels_and_tags(filename)
- assert 0, "this should not succeed - bad file signature"
- except IOError as err:
- print(str(err))
- assert "Incorrect file signature" in str(err)
+def test_bloom_c_1():
+ # test c++ code to count unique kmers using bloom filter
+ filename = utils.get_test_data('random-20-a.fa')
+
+ K = 20 # size of kmer
+ HT_SIZE = 100000 # size of hashtable
+ N_HT = 3 # number of hashtables
+
+ ht3 = khmer.LabelHash(K, HT_SIZE, N_HT)
+
+ for n, record in enumerate(fasta_iter(open(filename))):
+ ht3.consume(record['sequence'])
+
+ assert ht3.n_occupied() == 3882
+ assert ht3.n_unique_kmers() == 3960
+
+
+def test_n_occupied_2(): # simple one
+ K = 4
+ HT_SIZE = 10 # use 11
+ N_HT = 1
+
+ ht1 = khmer.LabelHash(K, HT_SIZE, N_HT)
+ ht1.count('AAAA') # 00 00 00 00 = 0
+ assert ht1.n_occupied() == 1
+
+ ht1.count('ACTG') # 00 10 01 11 =
+ assert ht1.n_occupied() == 2
+
+ ht1.count('AACG') # 00 00 10 11 = 11 # collision 1
+
+ assert ht1.n_occupied() == 2
+ ht1.count('AGAC') # 00 11 00 10 # collision 2
+ assert ht1.n_occupied() == 2
+
+
+def test_bloom_c_2(): # simple one
+ K = 4
+ HT_SIZE = 10 # use 11
+ N_HT1 = 1 # hashtable size = 11
+ N_HT2 = 2 # hashtable size = 11,13
+
+ # use only 1 hashtable, no bloom filter
+ ht1 = khmer.LabelHash(K, HT_SIZE, N_HT1)
+ ht1.count('AAAA') # 00 00 00 00 = 0
+ ht1.count('ACTG') # 00 10 01 11 =
+ assert ht1.n_unique_kmers() == 2
+ ht1.count('AACG') # 00 00 10 11 = 11 # collision with 1st kmer
+ assert ht1.n_unique_kmers() == 2
+ ht1.count('AGAC') # 00 11 00 10 # collision with 2nd kmer
+ assert ht1.n_unique_kmers() == 2
+
+ # use two hashtables with 11,13
+ ht2 = khmer.LabelHash(K, HT_SIZE, N_HT2)
+ ht2.count('AAAA') # 00 00 00 00 = 0
+
+ ht2.count('ACTG') # 00 10 01 11 = 2*16 +4 +3 = 39
+ assert ht2.n_unique_kmers() == 2
+ ht2.count('AACG') # 00 00 10 11 = 11 # collision with only 1st kmer
+ assert ht2.n_unique_kmers() == 3
+ ht2.count('AGAC') # 00 11 00 10 3*16 +2 = 50
+ # collision with both 2nd and 3rd kmers
+
+ assert ht2.n_unique_kmers() == 3
+
+
+def test_filter_if_present():
+ ht = khmer.LabelHash(32, 1e6, 2)
+
+ maskfile = utils.get_test_data('filter-test-A.fa')
+ inputfile = utils.get_test_data('filter-test-B.fa')
+ outfile = utils.get_temp_filename('filter')
+
+ ht.consume_fasta(maskfile)
+ ht.filter_if_present(inputfile, outfile)
+
+ records = list(fasta_iter(open(outfile)))
+ assert len(records) == 1
+ assert records[0]['name'] == '3'
+
+
+def test_combine_pe():
+ inpfile = utils.get_test_data('combine_parts_1.fa')
+ ht = khmer.LabelHash(32, 1, 1)
+
+ ht.consume_partitioned_fasta(inpfile)
+ assert ht.count_partitions() == (2, 0)
+
+ s1 = "CATGCAGAAGTTCCGCAACCATACCGTTCAGT"
+ pid1 = ht.get_partition_id(s1)
+
+ s2 = "CAAATGTACATGCACTTAAAATCATCCAGCCG"
+ pid2 = ht.get_partition_id(s2)
+
+ assert pid1 == 2
+ assert pid2 == 80293
+
+ ht.join_partitions(pid1, pid2)
+
+ pid1 = ht.get_partition_id(s1)
+ pid2 = ht.get_partition_id(s2)
+
+ assert pid1 == pid2
+ assert ht.count_partitions() == (1, 0)
+
+
+def test_load_partitioned():
+ inpfile = utils.get_test_data('combine_parts_1.fa')
+ ht = khmer.LabelHash(32, 1, 1)
+
+ ht.consume_partitioned_fasta(inpfile)
+ assert ht.count_partitions() == (2, 0)
+
+ s1 = "CATGCAGAAGTTCCGCAACCATACCGTTCAGT"
+ assert ht.get(s1)
+
+ s2 = "CAAATGTACATGCACTTAAAATCATCCAGCCG"
+ assert ht.get(s2)
+
+ s3 = "CATGCAGAAGTTCCGCAACCATACCGTTCAGTTCCTGGTGGCTA"[-32:]
+ assert ht.get(s3)
+
+
+def test_count_within_radius_simple():
+ inpfile = utils.get_test_data('all-A.fa')
+ ht = khmer.LabelHash(4, 1e6, 2)
+
+ print ht.consume_fasta(inpfile)
+ n = ht.count_kmers_within_radius('AAAA', 1)
+ assert n == 1
+
+ n = ht.count_kmers_within_radius('AAAA', 10)
+ assert n == 1
+
+
+def test_count_within_radius_big():
+ inpfile = utils.get_test_data('random-20-a.fa')
+ ht = khmer.LabelHash(20, 1e6, 4)
+
+ ht.consume_fasta(inpfile)
+ n = ht.count_kmers_within_radius('CGCAGGCTGGATTCTAGAGG', int(1e6))
+ assert n == 3960
+
+ ht = khmer.LabelHash(21, 1e6, 4)
+ ht.consume_fasta(inpfile)
+ n = ht.count_kmers_within_radius('CGCAGGCTGGATTCTAGAGGC', int(1e6))
+ assert n == 39
+
+
+def test_count_kmer_degree():
+ inpfile = utils.get_test_data('all-A.fa')
+ ht = khmer.LabelHash(4, 1e6, 2)
+ ht.consume_fasta(inpfile)
+
+ assert ht.kmer_degree('AAAA') == 2
+ assert ht.kmer_degree('AAAT') == 1
+ assert ht.kmer_degree('AATA') == 0
+ assert ht.kmer_degree('TAAA') == 1
+
+
+def test_save_load_tagset():
+ ht = khmer.LabelHash(32, 1, 1)
+
+ outfile = utils.get_temp_filename('tagset')
+
+ ht.add_tag('A' * 32)
+ ht.save_tagset(outfile)
+
+ ht.add_tag('G' * 32)
+
+ ht.load_tagset(outfile) # implicitly => clear_tags=True
+ ht.save_tagset(outfile)
+
+ # if tags have been cleared, then the new tagfile will be larger (34 bytes)
+ # else smaller (26 bytes).
+
+ fp = open(outfile, 'rb')
+ data = fp.read()
+ fp.close()
+ assert len(data) == 26, len(data)
+
+
+def test_save_load_tagset_noclear():
+ ht = khmer.LabelHash(32, 1, 1)
+
+ outfile = utils.get_temp_filename('tagset')
+
+ ht.add_tag('A' * 32)
+ ht.save_tagset(outfile)
+
+ ht.add_tag('G' * 32)
+
+ ht.load_tagset(outfile, False) # set clear_tags => False; zero tags
+ ht.save_tagset(outfile)
+
+ # if tags have been cleared, then the new tagfile will be large (34 bytes);
+ # else small (26 bytes).
+
+ fp = open(outfile, 'rb')
+ data = fp.read()
+ fp.close()
+ assert len(data) == 34, len(data)
+
+
+def test_stop_traverse():
+ filename = utils.get_test_data('random-20-a.fa')
+
+ K = 20 # size of kmer
+ HT_SIZE = 100000 # size of hashtable
+ N_HT = 3 # number of hashtables
+
+ ht = khmer.LabelHash(K, HT_SIZE, N_HT)
+
+ # without tagging/joining across consume, this breaks into two partition;
+ # with, it is one partition.
+ ht.add_stop_tag('TTGCATACGTTGAGCCAGCG')
+
+ ht.consume_fasta_and_tag(filename) # DO NOT join reads across stoptags
+ subset = ht.do_subset_partition(0, 0, True)
+ ht.merge_subset(subset)
+
+ n, _ = ht.count_partitions()
+ assert n == 2, n
+
+
+def test_tag_across_stoptraverse():
+ filename = utils.get_test_data('random-20-a.fa')
+
+ K = 20 # size of kmer
+ HT_SIZE = 100000 # size of hashtable
+ N_HT = 3 # number of hashtables
+
+ ht = khmer.LabelHash(K, HT_SIZE, N_HT)
+
+ # without tagging/joining across consume, this breaks into two partition;
+ # with, it is one partition.
+ ht.add_stop_tag('CCGAATATATAACAGCGACG')
+
+ ht.consume_fasta_and_tag_with_stoptags(filename) # DO join reads across
+
+ subset = ht.do_subset_partition(0, 0)
+ n, _ = ht.count_partitions()
+ assert n == 99 # reads only connected by traversal...
+
+ n, _ = ht.subset_count_partitions(subset)
+ assert n == 2 # but need main to cross stoptags.
+
+ ht.merge_subset(subset)
+
+ n, _ = ht.count_partitions() # ta-da!
+ assert n == 1, n
+
+
+def test_notag_across_stoptraverse():
+ filename = utils.get_test_data('random-20-a.fa')
+
+ K = 20 # size of kmer
+ HT_SIZE = 100000 # size of hashtable
+ N_HT = 3 # number of hashtables
+
+ ht = khmer.LabelHash(K, HT_SIZE, N_HT)
+
+ # connecting k-mer at the beginning/end of a read: breaks up into two.
+ ht.add_stop_tag('TTGCATACGTTGAGCCAGCG')
+
+ ht.consume_fasta_and_tag_with_stoptags(filename)
+
+ subset = ht.do_subset_partition(0, 0)
+ ht.merge_subset(subset)
+
+ n, _ = ht.count_partitions()
+ assert n == 2, n
+
+
+def test_find_stoptags():
+ ht = khmer.LabelHash(5, 1, 1)
+ ht.add_stop_tag("AAAAA")
+
+ assert ht.identify_stoptags_by_position("AAAAA") == [0]
+ assert ht.identify_stoptags_by_position("AAAAAA") == [0, 1]
+ assert ht.identify_stoptags_by_position("TTTTT") == [0]
+ assert ht.identify_stoptags_by_position("TTTTTT") == [0, 1]
+
+
+def test_find_stoptags2():
+ ht = khmer.LabelHash(4, 1, 1)
+ ht.add_stop_tag("ATGC")
+
+ x = ht.identify_stoptags_by_position("ATGCATGCGCAT")
+ assert x == [0, 2, 4, 8], x
+
+
+def test_get_ksize():
+ kh = khmer.LabelHash(22, 1, 1)
+ assert kh.ksize() == 22
+
+
+def test_get_hashsizes():
+ kh = khmer.LabelHash(22, 100, 4)
+ assert kh.hashsizes() == [101, 103, 107, 109], kh.hashsizes()
+
+
+def test_extract_unique_paths_0():
+ kh = khmer.LabelHash(10, 1e5, 4)
+
+ x = kh.extract_unique_paths('ATGGAGAGACACAGATAGACAGGAGTGGCGATG', 10, 1)
+ assert x == ['ATGGAGAGACACAGATAGACAGGAGTGGCGATG']
+
+ kh.consume('ATGGAGAGACACAGATAGACAGGAGTGGCGATG')
+ x = kh.extract_unique_paths('ATGGAGAGACACAGATAGACAGGAGTGGCGATG', 10, 1)
+ assert not x
+
+
+def test_extract_unique_paths_1():
+ kh = khmer.LabelHash(10, 1e5, 4)
+
+ kh.consume('AGTGGCGATG')
+ x = kh.extract_unique_paths('ATGGAGAGACACAGATAGACAGGAGTGGCGATG', 10, 1)
+ print x
+ assert x == ['ATGGAGAGACACAGATAGACAGGAGTGGCGAT'] # all but the last k-mer
+
+
+def test_extract_unique_paths_2():
+ kh = khmer.LabelHash(10, 1e5, 4)
+
+ kh.consume('ATGGAGAGAC')
+ x = kh.extract_unique_paths('ATGGAGAGACACAGATAGACAGGAGTGGCGATG', 10, 1)
+ print x
+ assert x == ['TGGAGAGACACAGATAGACAGGAGTGGCGATG'] # all but the 1st k-mer
+
+
+def test_extract_unique_paths_3():
+ kh = khmer.LabelHash(10, 1e5, 4)
+
+ kh.consume('ATGGAGAGAC')
+ kh.consume('AGTGGCGATG')
+ x = kh.extract_unique_paths('ATGGAGAGACACAGATAGACAGGAGTGGCGATG', 10, 1)
+ print x
+ # all but the 1st/last k-mer
+ assert x == ['TGGAGAGACACAGATAGACAGGAGTGGCGAT']
+
+
+def test_extract_unique_paths_4():
+ kh = khmer.LabelHash(10, 1e5, 4)
+
+ kh.consume('ATGGAGAGAC')
+ kh.consume('AGTGGCGATG')
+
+ kh.consume('ATAGACAGGA')
+
+ x = kh.extract_unique_paths('ATGGAGAGACACAGATAGACAGGAGTGGCGATG', 10, 1)
+ print x
+ assert x == ['TGGAGAGACACAGATAGACAGG', 'TAGACAGGAGTGGCGAT']
+
+
+def test_find_unpart():
+ filename = utils.get_test_data('random-20-a.odd.fa')
+ filename2 = utils.get_test_data('random-20-a.even.fa')
+
+ K = 20 # size of kmer
+ HT_SIZE = 100000 # size of hashtable
+ N_HT = 3 # number of hashtables
+
+ ht = khmer.LabelHash(K, HT_SIZE, N_HT)
+ ht.consume_fasta_and_tag(filename)
+
+ subset = ht.do_subset_partition(0, 0)
+ ht.merge_subset(subset)
+
+ n, _ = ht.count_partitions()
+ assert n == 49
+
+ ht.find_unpart(filename2, True, False)
+ n, _ = ht.count_partitions()
+ assert n == 1, n # all sequences connect
+
+
+def test_find_unpart_notraverse():
+ filename = utils.get_test_data('random-20-a.odd.fa')
+ filename2 = utils.get_test_data('random-20-a.even.fa')
+
+ K = 20 # size of kmer
+ HT_SIZE = 100000 # size of hashtable
+ N_HT = 3 # number of hashtables
+
+ ht = khmer.LabelHash(K, HT_SIZE, N_HT)
+ ht.consume_fasta_and_tag(filename)
+
+ subset = ht.do_subset_partition(0, 0)
+ ht.merge_subset(subset)
+
+ n, _ = ht.count_partitions()
+ assert n == 49
+
+ ht.find_unpart(filename2, False, False) # <-- don't traverse
+ n, _ = ht.count_partitions()
+ assert n == 99, n # all sequences disconnected
+
+
+def test_find_unpart_fail():
+ filename = utils.get_test_data('random-20-a.odd.fa')
+ filename2 = utils.get_test_data('random-20-a.odd.fa') # <- switch to odd
+
+ K = 20 # size of kmer
+ HT_SIZE = 100000 # size of hashtable
+ N_HT = 3 # number of hashtables
+
+ ht = khmer.LabelHash(K, HT_SIZE, N_HT)
+ ht.consume_fasta_and_tag(filename)
+
+ subset = ht.do_subset_partition(0, 0)
+ ht.merge_subset(subset)
+
+ n, _ = ht.count_partitions()
+ assert n == 49
+
+ ht.find_unpart(filename2, True, False)
+ n, _ = ht.count_partitions()
+ assert n == 49, n # only 49 sequences worth of tags
+
+
+def test_simple_median():
+ hi = khmer.LabelHash(6, 1e6, 2)
+
+ (median, average, stddev) = hi.get_median_count("AAAAAA")
+ print median, average, stddev
+ assert median == 0
+ assert average == 0.0
+ assert stddev == 0.0
+
+ hi.consume("AAAAAA")
+ (median, average, stddev) = hi.get_median_count("AAAAAA")
+ print median, average, stddev
+ assert median == 1
+ assert average == 1.0
+ assert stddev == 0.0
-def test_load_wrong_fileversion():
- lb = LabelHash(20, 1e7, 4)
- # try to load a tagset from an old version
- filename = utils.get_test_data('badversion-k32.tagset')
+def test_bad_primes():
try:
- lb.load_labels_and_tags(filename)
- assert 0, "this should not succeed - bad file type"
- except IOError as err:
- print(str(err))
- assert "Incorrect file format version" in str(err)
+ hi = khmer._LabelHash.__new__(khmer.LabelHash, 6, ["a", "b", "c"])
+ assert 0, "Non number prime list should fail"
+ except TypeError as e:
+ print str(e)
diff --git a/tests/test_lump.py b/tests/test_lump.py
index c7eeb0d..3d82471 100644
--- a/tests/test_lump.py
+++ b/tests/test_lump.py
@@ -1,7 +1,6 @@
-from __future__ import absolute_import
#
-# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
-# Copyright (C) Michigan State University, 2009-2015. It is licensed under
+# This file is part of khmer, http://github.com/ged-lab/khmer/, and is
+# Copyright (C) Michigan State University, 2009-2013. It is licensed under
# the three-clause BSD license; see LICENSE.
# Contact: khmer-project at idyll.org
#
@@ -9,7 +8,7 @@ from __future__ import absolute_import
import khmer
import screed
-from . import khmer_tst_utils as utils
+import khmer_tst_utils as utils
from nose.plugins.attrib import attr
# Below, 'fakelump.fa' is an artificial data set of 3x1 kb sequences in
@@ -19,7 +18,7 @@ from nose.plugins.attrib import attr
def test_fakelump_together():
fakelump_fa = utils.get_test_data('fakelump.fa')
- ht = khmer.Hashbits(32, 1e5, 4)
+ ht = khmer.new_hashbits(32, 1e5, 4)
ht.consume_fasta_and_tag(fakelump_fa)
subset = ht.do_subset_partition(0, 0)
@@ -35,7 +34,7 @@ def test_fakelump_stop():
fakelump_fa = utils.get_test_data('fakelump.fa')
fakelump_stoptags_txt = utils.get_test_data('fakelump.fa.stoptags.txt')
- ht = khmer.Hashbits(32, 1e5, 4)
+ ht = khmer.new_hashbits(32, 1e5, 4)
ht.consume_fasta_and_tag(fakelump_fa)
for line in open(fakelump_stoptags_txt):
@@ -53,7 +52,7 @@ def test_fakelump_stop():
def test_fakelump_stop2():
fakelump_fa = utils.get_test_data('fakelump.fa')
- ht = khmer.Hashbits(32, 1e5, 4)
+ ht = khmer.new_hashbits(32, 1e5, 4)
ht.consume_fasta_and_tag(fakelump_fa)
ht.add_stop_tag('GGGGAGGGGTGCAGTTGTGACTTGCTCGAGAG')
@@ -71,7 +70,7 @@ def test_fakelump_repartitioning():
fakelump_fa = utils.get_test_data('fakelump.fa')
fakelump_fa_foo = utils.get_temp_filename('fakelump.fa.stopfoo')
- ht = khmer.Hashbits(32, 1e5, 4)
+ ht = khmer.new_hashbits(32, 1e5, 4)
ht.consume_fasta_and_tag(fakelump_fa)
subset = ht.do_subset_partition(0, 0)
@@ -88,7 +87,7 @@ def test_fakelump_repartitioning():
EXCURSION_DISTANCE = 40
EXCURSION_KMER_THRESHOLD = 82
EXCURSION_KMER_COUNT_THRESHOLD = 1
- counting = khmer.CountingHash(32, 1e5, 4)
+ counting = khmer.new_counting_hash(32, 1e4, 4)
ht.repartition_largest_partition(None, counting,
EXCURSION_DISTANCE,
@@ -99,7 +98,7 @@ def test_fakelump_repartitioning():
# ok, now re-do everything with these stop tags, specifically.
- ht = khmer.Hashbits(32, 1e5, 4)
+ ht = khmer.new_hashbits(32, 1e5, 4)
ht.consume_fasta_and_tag(fakelump_fa)
ht.load_stop_tags(fakelump_fa_foo)
@@ -107,14 +106,14 @@ def test_fakelump_repartitioning():
ht.merge_subset(subset)
(n_partitions, n_singletons) = ht.count_partitions()
- assert n_partitions == 6, n_partitions
+ assert n_partitions == 3, n_partitions
def test_fakelump_load_stop_tags_trunc():
fakelump_fa = utils.get_test_data('fakelump.fa')
fakelump_fa_foo = utils.get_temp_filename('fakelump.fa.stopfoo')
- ht = khmer.Hashbits(32, 1e5, 4)
+ ht = khmer.new_hashbits(32, 1e5, 4)
ht.consume_fasta_and_tag(fakelump_fa)
subset = ht.do_subset_partition(0, 0)
@@ -131,7 +130,7 @@ def test_fakelump_load_stop_tags_trunc():
EXCURSION_DISTANCE = 40
EXCURSION_KMER_THRESHOLD = 82
EXCURSION_KMER_COUNT_THRESHOLD = 1
- counting = khmer._CountingHash(32, [5, 7, 11, 13])
+ counting = khmer.new_counting_hash(32, 4, 4)
ht.repartition_largest_partition(None, counting,
EXCURSION_DISTANCE,
@@ -139,14 +138,14 @@ def test_fakelump_load_stop_tags_trunc():
EXCURSION_KMER_COUNT_THRESHOLD)
ht.save_stop_tags(fakelump_fa_foo)
- data = open(fakelump_fa_foo, 'rb').read()
+ data = open(fakelump_fa_foo).read()
fp = open(fakelump_fa_foo, 'wb')
fp.write(data[:10])
fp.close()
# ok, now try loading these stop tags; should fail.
- ht = khmer._Hashbits(32, [5, 7, 11, 13])
+ ht = khmer.new_hashbits(32, 4, 4)
ht.consume_fasta_and_tag(fakelump_fa)
try:
@@ -160,7 +159,7 @@ def test_fakelump_load_stop_tags_notexist():
fakelump_fa_foo = utils.get_temp_filename('fakelump.fa.stopfoo')
# ok, now try loading these stop tags; should fail.
- ht = khmer._Hashbits(32, [5, 7, 11, 13])
+ ht = khmer.new_hashbits(32, 4, 4)
try:
ht.load_stop_tags(fakelump_fa_foo)
diff --git a/tests/test_normalize_by_median.py b/tests/test_normalize_by_median.py
deleted file mode 100644
index abdcc58..0000000
--- a/tests/test_normalize_by_median.py
+++ /dev/null
@@ -1,627 +0,0 @@
-from __future__ import print_function
-from __future__ import absolute_import
-from __future__ import unicode_literals
-#
-# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
-# Copyright (C) Michigan State University, 2009-2015. It is licensed under
-# the three-clause BSD license; see LICENSE.
-# Contact: khmer-project at idyll.org
-#
-
-import os
-import shutil
-import threading
-import io
-
-import screed
-import khmer
-
-from . import khmer_tst_utils as utils
-from nose.plugins.attrib import attr
-from .test_scripts import _make_counting
-
-
-def test_normalize_by_median_indent():
- infile = utils.get_test_data('paired-mixed.fa.pe')
- hashfile = utils.get_test_data('normC20k20.ct')
- outfile = utils.get_temp_filename('paired-mixed.fa.pe.keep')
- script = 'normalize-by-median.py'
- args = ['--loadtable', hashfile, '-o', outfile, infile]
- (status, out, err) = utils.runscript(script, args)
- assert status == 0, (out, err)
- assert os.path.exists(outfile)
-
-
-def test_normalize_by_median():
- CUTOFF = '1'
-
- infile = utils.get_temp_filename('test.fa')
- in_dir = os.path.dirname(infile)
-
- shutil.copyfile(utils.get_test_data('test-abund-read-2.fa'), infile)
-
- script = 'normalize-by-median.py'
- args = ['-C', CUTOFF, '-k', '17', infile]
- (status, out, err) = utils.runscript(script, args, in_dir)
-
- assert 'Total number of unique k-mers: 98' in err, err
-
- outfile = infile + '.keep'
- assert os.path.exists(outfile), outfile
-
- seqs = [r.sequence for r in screed.open(outfile)]
- assert len(seqs) == 1, seqs
- assert seqs[0].startswith('GGTTGACGGGGCTCAGGGGG'), seqs
- assert "IOErrors" not in err
-
-
-def test_normalize_by_median_unpaired_final_read():
- CUTOFF = '1'
-
- infile = utils.get_temp_filename('test.fa')
- in_dir = os.path.dirname(infile)
-
- shutil.copyfile(utils.get_test_data('single-read.fq'), infile)
-
- script = 'normalize-by-median.py'
- args = ['-C', CUTOFF, '-k', '17', '-p', infile]
- try:
- (status, out, err) = utils.runscript(script, args, in_dir)
- raise Exception("Shouldn't get to this")
- except AssertionError as e:
- out = str(e)
- assert "ERROR: Unpaired reads when require_paired" in out, out
-
-
-def test_normalize_by_median_unforced_badfile():
- CUTOFF = '1'
-
- infile = utils.get_temp_filename("potatoes")
- outfile = infile + '.keep'
- in_dir = os.path.dirname(infile)
- script = 'normalize-by-median.py'
- args = ['-C', CUTOFF, '-k', '17', infile]
- try:
- (status, out, err) = utils.runscript(script, args, in_dir)
- raise Exception("Shouldn't get to this")
- except AssertionError as e:
- out = str(e)
- assert "ERROR: [Errno 2] No such file or directory:" in out, out
-
- if os.path.exists(outfile):
- assert False, '.keep file should have been removed: '
-
-
-def test_normalize_by_median_contradictory_args():
- infile = utils.get_temp_filename('test.fa')
- in_dir = os.path.dirname(infile)
- outfile = utils.get_temp_filename('report.out')
-
- shutil.copyfile(utils.get_test_data('test-large.fa'), infile)
-
- script = 'normalize-by-median.py'
- args = ['-C', '1', '-k', '17', '--force-single', '-p', '-R',
- outfile, infile]
- try:
- (status, out, err) = utils.runscript(script, args, in_dir)
- raise Exception("Shouldn't get to this")
- except AssertionError as e:
- out = str(e)
- assert "cannot both be set" in out, out
-
-
-def test_normalize_by_median_stdout_3():
- CUTOFF = '1'
-
- infile = utils.get_temp_filename('test.fa')
- in_dir = os.path.dirname(infile)
-
- shutil.copyfile(utils.get_test_data('test-abund-read-2.fa'), infile)
-
- script = 'normalize-by-median.py'
- args = ['-C', CUTOFF, '-k', '17', infile, '--out', '-']
- (status, out, err) = utils.runscript(script, args, in_dir)
-
- assert 'Total number of unique k-mers: 98' in err, err
- assert 'in /dev/stdout' in err, err
- assert "IOErrors" not in err
-
-
- at attr('known_failing')
-def test_normalize_by_median_known_good():
- CUTOFF = '2'
-
- infile = utils.get_temp_filename('test.fa.gz')
- in_dir = os.path.dirname(infile)
- shutil.copyfile(utils.get_test_data('100k-filtered.fa.gz'), infile)
-
- script = 'normalize-by-median.py'
- args = ['-C', CUTOFF, '-k', '20', '-x', '4e6', infile]
- (status, out, err) = utils.runscript(script, args, in_dir)
-
- outfile = infile + '.keep'
- assert os.path.exists(outfile), outfile
- iter_known = screed.open(utils.get_test_data('100k-filtered.fa.keep.gz'))
- iter_out = screed.open(outfile)
- try:
- for rknown, rout in zip(iter_known, iter_out):
- assert rknown.name == rout.name
- except Exception as e:
- print(e)
- assert False
-
-
- at attr('huge')
-def test_normalize_by_median_report_fp():
- infile = utils.get_temp_filename('test.fa')
- in_dir = os.path.dirname(infile)
- outfile = utils.get_temp_filename('report.out')
-
- shutil.copyfile(utils.get_test_data('test-large.fa'), infile)
-
- script = 'normalize-by-median.py'
- args = ['-C', '1', '-k', '17', '-R', outfile, infile]
- (status, out, err) = utils.runscript(script, args, in_dir)
-
- assert "fp rate estimated to be 0.623" in err, err
- report = open(outfile, 'r')
- line = report.readline()
- assert "100000 25261 0.25261" in line, line
-
-
-def test_normalize_by_median_unpaired_and_paired():
- CUTOFF = '1'
-
- infile = utils.get_temp_filename('test.fa')
- in_dir = os.path.dirname(infile)
-
- shutil.copyfile(utils.get_test_data('test-abund-read-paired.fa'), infile)
-
- unpairedfile = utils.get_temp_filename('test1.fa', tempdir=in_dir)
- shutil.copyfile(utils.get_test_data('random-20-a.fa'), unpairedfile)
-
- script = 'normalize-by-median.py'
- args = ['-C', CUTOFF, '-k', '17', '-u', unpairedfile, '-p', infile]
- (status, out, err) = utils.runscript(script, args, in_dir)
-
- assert 'Total number of unique k-mers: 4030' in err, err
-
- outfile = infile + '.keep'
- assert os.path.exists(outfile), outfile
-
-
-def test_normalize_by_median_count_kmers_PE():
- CUTOFF = '1'
- infile = utils.get_temp_filename('test.fa')
- in_dir = os.path.dirname(infile)
- # The test file has one pair of identical read except for the last base
- # The 2nd read should be discarded in the unpaired mode
- # but kept in the paired end mode adding only one more unique kmer
- shutil.copyfile(utils.get_test_data('paired_one.base.dif.fa'), infile)
- script = 'normalize-by-median.py'
-
- args = ['-C', CUTOFF, '-k', '17', '--force-single', infile]
- (status, out, err) = utils.runscript(script, args, in_dir)
- assert 'Total number of unique k-mers: 98' in err, err
- assert 'kept 1 of 2 or 50%' in err, err
-
- args = ['-C', CUTOFF, '-k', '17', '-p', infile]
- (status, out, err) = utils.runscript(script, args, in_dir)
- assert 'Total number of unique k-mers: 99' in err, err
- assert 'kept 2 of 2 or 100%' in err, err
-
-
-def test_normalize_by_median_double_file_name():
- infile = utils.get_temp_filename('test-abund-read-2.fa')
- in_dir = os.path.dirname(infile)
-
- shutil.copyfile(utils.get_test_data('test-abund-read-2.fa'), infile)
-
- script = 'normalize-by-median.py'
- args = [utils.get_test_data('test-abund-read-2.fa'), infile]
-
- try:
- (status, out, err) = utils.runscript(script, args, in_dir)
- except AssertionError as e:
- assert "Duplicate filename--Cannot handle this!" in str(e), str(e)
-
-
-def test_normalize_by_median_overwrite():
- outfile = utils.get_temp_filename('test.fa.keep')
- shutil.copyfile(utils.get_test_data('test-abund-read.fa'), outfile)
- in_dir = os.path.dirname(outfile)
-
- CUTOFF = '1'
- infile = utils.get_temp_filename('test.fa', in_dir)
- shutil.copyfile(utils.get_test_data('test-abund-read-3.fa'), infile)
- script = 'normalize-by-median.py'
-
- args = ['-C', CUTOFF, '-k', '17', '-o', outfile, infile]
- (status, out, err) = utils.runscript(script, args, in_dir)
- assert os.path.exists(outfile), outfile
- seqs = [r.sequence for r in screed.open(outfile)]
- assert len(seqs) == 1, seqs
- assert 'GACAGCgtgCCGCA' in seqs[0], seqs
-
-
-def test_normalize_by_median_version():
- script = 'normalize-by-median.py'
- args = ['--version']
- status, out, err = utils.runscript(script, args)
-
- errlines = err.splitlines()
- for err in errlines:
- if err.startswith('||') or \
- not err.strip():
- continue
- break
-
- print(errlines)
- print(err)
-
- assert err.startswith('khmer ')
-
-
-def test_normalize_by_median_2():
- CUTOFF = '2'
-
- infile = utils.get_temp_filename('test.fa')
- in_dir = os.path.dirname(infile)
-
- shutil.copyfile(utils.get_test_data('test-abund-read-2.fa'), infile)
-
- script = 'normalize-by-median.py'
- args = ['-C', CUTOFF, '-k', '17', infile]
- utils.runscript(script, args, in_dir)
-
- outfile = infile + '.keep'
- assert os.path.exists(outfile), outfile
-
- seqs = [r.sequence for r in screed.open(outfile)]
- assert len(seqs) == 2, seqs
- assert seqs[0].startswith('GGTTGACGGGGCTCAGGGGG'), seqs
- assert seqs[1] == 'GGTTGACGGGGCTCAGGG', seqs
-
-
-def test_normalize_by_median_paired():
- CUTOFF = '1'
-
- infile = utils.get_temp_filename('test.fa')
- in_dir = os.path.dirname(infile)
-
- shutil.copyfile(utils.get_test_data('test-abund-read-paired.fa'), infile)
-
- script = 'normalize-by-median.py'
- args = ['-C', CUTOFF, '-p', '-k', '17', infile]
- utils.runscript(script, args, in_dir)
-
- outfile = infile + '.keep'
- assert os.path.exists(outfile), outfile
-
- seqs = [r.sequence for r in screed.open(outfile)]
- assert len(seqs) == 2, seqs
- assert seqs[0].startswith('GGTTGACGGGGCTCAGGGGG'), seqs
- assert seqs[1].startswith('GGTTGACGGGGCTCAGGG'), seqs
-
-
-def test_normalize_by_median_paired_fq():
- CUTOFF = '20'
-
- infile = utils.get_temp_filename('test.fa')
- in_dir = os.path.dirname(infile)
-
- shutil.copyfile(utils.get_test_data('test-abund-read-paired.fq'), infile)
-
- script = 'normalize-by-median.py'
- args = ['-C', CUTOFF, '-p', '-k', '17', infile]
- _, out, err = utils.runscript(script, args, in_dir)
- print(out)
- print(err)
-
- outfile = infile + '.keep'
- assert os.path.exists(outfile), outfile
-
- seqs = [r.sequence for r in screed.open(outfile)]
- assert len(seqs) == 6, len(seqs)
- assert seqs[0].startswith('GGTTGACGGGGCTCAGGGGG'), seqs
- assert seqs[1].startswith('GGTTGACGGGGCTCAGGG'), seqs
-
- names = [r.name for r in screed.open(outfile, parse_description=False)]
- assert len(names) == 6, names
- assert '895:1:37:17593:9954 1::FOO' in names, names
- assert '895:1:37:17593:9954 2::FOO' in names, names
-
-
-def test_normalize_by_median_impaired():
- CUTOFF = '1'
-
- infile = utils.get_temp_filename('test.fa')
- in_dir = os.path.dirname(infile)
-
- shutil.copyfile(utils.get_test_data('test-abund-read-impaired.fa'), infile)
-
- script = 'normalize-by-median.py'
- args = ['-C', CUTOFF, '-p', '-k', '17', infile]
- _, out, err = utils.runscript(script, args, in_dir, fail_ok=True)
- assert 'ERROR: Unpaired reads ' in err, err
-
-
-def test_normalize_by_median_force():
- CUTOFF = '1'
-
- corrupt_infile = utils.get_temp_filename('test-corrupt.fq')
- good_infile = utils.get_temp_filename('test-good.fq',
- tempdir=os.path.dirname(
- corrupt_infile))
-
- in_dir = os.path.dirname(good_infile)
-
- shutil.copyfile(utils.get_test_data('test-error-reads.fq'), corrupt_infile)
- shutil.copyfile(utils.get_test_data('test-fastq-reads.fq'), good_infile)
-
- script = 'normalize-by-median.py'
- args = ['-f', '-C', CUTOFF, '-k', '17', corrupt_infile, good_infile]
-
- (status, out, err) = utils.runscript(script, args, in_dir)
-
- assert '*** Skipping' in err
- assert '** IOErrors' in err
-
-
-def test_normalize_by_median_no_bigcount():
- infile = utils.get_temp_filename('test.fa')
- hashfile = utils.get_temp_filename('test-out.ct')
- outfile = infile + '.keep'
- in_dir = os.path.dirname(infile)
-
- shutil.copyfile(utils.get_test_data('test-abund-read-2.fa'), infile)
- counting_ht = _make_counting(infile, K=8)
-
- script = 'normalize-by-median.py'
- args = ['-C', '1000', '-k 8', '--savetable', hashfile, infile]
-
- (status, out, err) = utils.runscript(script, args, in_dir)
- assert status == 0, (out, err)
- print((out, err))
-
- assert os.path.exists(hashfile), hashfile
- kh = khmer.load_counting_hash(hashfile)
-
- assert kh.get('GGTTGACG') == 255
-
-
-def test_normalize_by_median_empty():
- CUTOFF = '1'
-
- infile = utils.get_temp_filename('test.fa')
- in_dir = os.path.dirname(infile)
-
- shutil.copyfile(utils.get_test_data('test-empty.fa'), infile)
-
- script = 'normalize-by-median.py'
- args = ['-C', CUTOFF, '-k', '17', infile]
- utils.runscript(script, args, in_dir)
-
- outfile = infile + '.keep'
- assert os.path.exists(outfile), outfile
-
-
-def test_normalize_by_median_emptycountingtable():
- CUTOFF = '1'
-
- infile = utils.get_temp_filename('test.fa')
- in_dir = os.path.dirname(infile)
-
- shutil.copyfile(utils.get_test_data('test-empty.fa'), infile)
-
- script = 'normalize-by-median.py'
- args = ['-C', CUTOFF, '--loadtable', infile, infile]
- (status, out, err) = utils.runscript(script, args, in_dir, fail_ok=True)
- assert 'ValueError' in err, (status, out, err)
-
-
-def test_normalize_by_median_fpr():
- MAX_TABLESIZE_PARAM = 12
-
- infile = utils.get_temp_filename('test-fpr.fq')
- in_dir = os.path.dirname(infile)
- shutil.copyfile(utils.get_test_data('test-fastq-reads.fq'), infile)
-
- script = 'normalize-by-median.py'
- args = ['-f', '-k 17', '-x ' + str(MAX_TABLESIZE_PARAM), infile]
-
- (status, out, err) = utils.runscript(script, args, in_dir, fail_ok=True)
-
- print(out)
- print(err)
-
- assert os.path.exists(infile + '.keep'), infile
- assert '** ERROR: the graph structure is too small' in err, err
-
-
-def write_by_chunks(infile, outfile, CHUNKSIZE=8192):
- ifile = io.open(infile, 'rb')
- ofile = io.open(outfile, 'wb')
- chunk = ifile.read(CHUNKSIZE)
- while len(chunk) > 0:
- ofile.write(chunk)
- chunk = ifile.read(CHUNKSIZE)
- ifile.close()
- ofile.close()
-
-
-def test_normalize_by_median_streaming():
- CUTOFF = '20'
-
- infile = utils.get_test_data('100-reads.fq.gz')
- in_dir = os.path.dirname(infile)
- fifo = utils.get_temp_filename('fifo')
- outfile = utils.get_temp_filename('outfile')
-
- # Use a fifo to copy stdout to a file for checking
- os.mkfifo(fifo)
- thread = threading.Thread(target=write_by_chunks, args=(fifo, outfile))
- thread.start()
-
- # Execute diginorm
- script = 'normalize-by-median.py'
- args = ['-C', CUTOFF, '-k', '17', '-o', fifo, infile]
- (status, out, err) = utils.runscript(script, args, in_dir)
-
- # Merge the thread
- thread.join()
-
- assert os.path.exists(outfile), outfile
- with open(outfile) as fp:
- linecount = sum(1 for _ in fp)
- assert linecount == 400
-
-
-def test_diginorm_basic_functionality_1():
- # each of these pairs has both a multicopy sequence ('ACTTCA...') and
- # a random sequence. With 'C=1' and '-p', all should be kept.
- CUTOFF = ['-C', '1']
- PAIRING = ['-p']
-
- infile = utils.get_temp_filename('test.fa')
- in_dir = os.path.dirname(infile)
-
- shutil.copyfile(utils.get_test_data('dn-test-all-paired-all-keep.fa'),
- infile)
-
- script = 'normalize-by-median.py'
- args = list(CUTOFF) + list(PAIRING) + ['-k', '15', infile]
- _, out, err = utils.runscript(script, args, in_dir)
- print(out)
- print(err)
-
- outfile = infile + '.keep'
- assert os.path.exists(outfile), outfile
-
- seqs = set([r.name for r in screed.open(outfile)])
-
- assert seqs == set(['a/1', 'a/2',
- 'b/1', 'b/2',
- 'c/1', 'c/2',
- 'd/1', 'd/2']), seqs
-
-
-def test_diginorm_basic_functionality_2():
- # each of these pairs has both a multicopy sequence ('ACTTCA...')
- # and a random sequence ('G...'). With 'C=1' and '--force-
- # single', only random seqs should be kept, together with one copy
- # of the multicopy sequence.
- CUTOFF = ['-C', '1']
- PAIRING = ['--force-single']
-
- infile = utils.get_temp_filename('test.fa')
- in_dir = os.path.dirname(infile)
-
- shutil.copyfile(utils.get_test_data('dn-test-all-paired-all-keep.fa'),
- infile)
-
- script = 'normalize-by-median.py'
- args = list(CUTOFF) + list(PAIRING) + ['-k', '15', infile]
- _, out, err = utils.runscript(script, args, in_dir)
- print(out)
- print(err)
-
- outfile = infile + '.keep'
- assert os.path.exists(outfile), outfile
-
- seqs = set([r.name for r in screed.open(outfile)])
-
- assert seqs == set(['a/1', 'a/2',
- 'b/2',
- 'c/1',
- 'd/2']), seqs
-
-
-def test_diginorm_basic_functionality_3():
- # This data is entirely unpaired, but with one duplicate ('A...').
- # and a random sequence ('G...'). With 'C=1' only three seqs should
- # be left, with no other complaints.
-
- CUTOFF = ['-C', '1']
- PAIRING = []
-
- infile = utils.get_temp_filename('test.fa')
- in_dir = os.path.dirname(infile)
-
- shutil.copyfile(utils.get_test_data('dn-test-none-paired.fa'),
- infile)
-
- script = 'normalize-by-median.py'
- args = list(CUTOFF) + list(PAIRING) + ['-k', '15', infile]
- _, out, err = utils.runscript(script, args, in_dir)
- print(out)
- print(err)
-
- outfile = infile + '.keep'
- assert os.path.exists(outfile), outfile
-
- seqs = set([r.name for r in screed.open(outfile)])
-
- assert seqs == set(['a/1',
- 'b/2',
- 'd/1']), seqs
-
-
-def test_diginorm_basic_functionality_4():
- # This data is mixed paired/unpaired, but with one duplicate ('A...').
- # and a random sequence ('G...'). With 'C=2' all of the sequences
- # should be kept.
-
- CUTOFF = ['-C', '1']
-
- infile = utils.get_temp_filename('test.fa')
- in_dir = os.path.dirname(infile)
-
- shutil.copyfile(utils.get_test_data('dn-test-some-paired-all-keep.fa'),
- infile)
-
- script = 'normalize-by-median.py'
- args = list(CUTOFF) + ['-k', '15', infile]
-
- _, out, err = utils.runscript(script, args, in_dir)
- print(out)
- print(err)
-
- outfile = infile + '.keep'
- assert os.path.exists(outfile), outfile
-
- seqs = set([r.name for r in screed.open(outfile)])
-
- assert seqs == set(['a/1', 'a/2',
- 'b/2',
- 'c/1', 'c/2',
- 'd/2']), seqs
-
-
-def test_diginorm_basic_functionality_5():
- # each of these pairs has both a multicopy sequence ('ACTTCA...') and
- # a random sequence. With 'C=1' and '-p', all should be
- CUTOFF = ['-C', '1']
- PAIRING = ['-p']
-
- infile = utils.get_temp_filename('test.fa')
- in_dir = os.path.dirname(infile)
-
- shutil.copyfile(utils.get_test_data('dn-test-all-paired-all-keep.fa'),
- infile)
-
- script = 'normalize-by-median.py'
- args = list(CUTOFF) + list(PAIRING) + ['-k', '15', infile]
- _, out, err = utils.runscript(script, args, in_dir)
- print(out)
- print(err)
-
- outfile = infile + '.keep'
- assert os.path.exists(outfile), outfile
-
- seqs = set([r.name for r in screed.open(outfile)])
-
- assert seqs == set(['a/1', 'a/2',
- 'b/1', 'b/2',
- 'c/1', 'c/2',
- 'd/1', 'd/2']), seqs
diff --git a/tests/test_oxli_functions.py b/tests/test_oxli_functions.py
deleted file mode 100644
index 63ad48c..0000000
--- a/tests/test_oxli_functions.py
+++ /dev/null
@@ -1,60 +0,0 @@
-from __future__ import print_function
-from __future__ import absolute_import
-from __future__ import unicode_literals
-#
-# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
-# Copyright (C) Michigan State University, 2009-2015. It is licensed under
-# the three-clause BSD license; see LICENSE.
-# Contact: khmer-project at idyll.org
-#
-
-# pylint: disable=C0111,C0103,E1103,W0612
-
-from . import khmer_tst_utils as utils
-import khmer
-from oxli import functions
-
-
-def test_estimate_functions_1():
- res = functions.estimate_optimal_with_N_and_M(99, 1024)
- assert res[0] == 7, res[0]
- assert res[1] == 146, res[1]
- assert res[2] == 1022, res[2]
- assert abs(.008 - res[3]) < .001, res[3]
-
- res = functions.estimate_optimal_with_N_and_f(99, 0.00701925498897)
- assert res[0] == 7, res[0]
- assert res[1] == 145, res[1]
- assert res[2] == 1015, res[2]
- assert abs(.008 - res[3]) < .002, res[3]
-
- res = functions.estimate_optimal_with_N_and_M(1024, 2)
- assert res[0] == 1, res[0]
- assert res[1] == 2, res[1]
- assert res[2] == 2, res[2]
- assert res[3] == 1.0, res[3]
-
- # using a crazy high FP rate just for coverage
- res = functions.estimate_optimal_with_N_and_f(1024, 0.7)
- assert res[0] == 1, res[0]
- assert res[1] == 850, res[1]
- assert res[2] == 850, res[2]
- assert abs(.7 - res[3]) < 0.0022, abs(.7 - res[3])
-
-
-def test_estimate_functions_namedtup():
- res = functions.estimate_optimal_with_N_and_M(99, 1024)
- assert res.num_htables == 7, res[0]
- assert res.htable_size == 146, res[1]
- assert res.mem_use == 1022, res[2]
- assert abs(.008 - res.fp_rate) < .001, res[3]
-
- res = functions.estimate_optimal_with_N_and_f(99, 0.00701925498897)
- assert res.num_htables == 7, res[0]
- assert res.htable_size == 145, res[1]
- assert res.mem_use == 1015, res[2]
- assert abs(.008 - res.fp_rate) < .002, res[3]
-
-
-def test_output_gen():
- res = functions.optimal_args_output_gen(99, 0.00701925498897)
diff --git a/tests/test_read_aligner.py b/tests/test_read_aligner.py
index 0fa9eec..b5ce9b5 100644
--- a/tests/test_read_aligner.py
+++ b/tests/test_read_aligner.py
@@ -1,10 +1,8 @@
#
-# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
-# Copyright (C) Michigan State University, 2009-2015. It is licensed under
+# This file is part of khmer, http://github.com/ged-lab/khmer/, and is
+# Copyright (C) Michigan State University, 2009-2013. It is licensed under
# the three-clause BSD license; see LICENSE. Contact: ctb at msu.edu
#
-from __future__ import print_function
-
import khmer
from nose.tools import assert_almost_equals
@@ -15,7 +13,7 @@ def eq_(v1, v2):
def test_alignnocov():
- ch = khmer.CountingHash(10, 1048576, 1)
+ ch = khmer.new_counting_hash(10, 1048576, 1)
read = "ACCTAGGTTCGACATGTACC"
aligner = khmer.ReadAligner(ch, 0, 0)
for i in range(20):
@@ -29,7 +27,7 @@ def test_alignnocov():
def test_simple_readalign():
- ch = khmer.CountingHash(10, 1048576, 1)
+ ch = khmer.new_counting_hash(10, 1048576, 1)
aligner = khmer.ReadAligner(ch, 2, 0)
for i in range(20):
ch.consume("AGAGGGAAAGCTAGGTTCGACATGTCCTTGACAGAT")
@@ -48,7 +46,7 @@ def test_simple_readalign():
def test_readalign():
- ch = khmer.CountingHash(10, 1048576, 1)
+ ch = khmer.new_counting_hash(10, 1048576, 1)
aligner = khmer.ReadAligner(ch, 1, 0)
for i in range(20):
ch.consume("AGAGGGAAAGCTAGGTTCGACAAGTCCTTGACAGAT")
@@ -209,15 +207,15 @@ queries = [
def test_readalign_new():
- ch = khmer.CountingHash(32, 1048576, 1)
+ ch = khmer.new_counting_hash(32, 1048576, 1)
aligner = khmer.ReadAligner(ch, 1, 0)
for seq in ht_seqs:
ch.consume(seq)
for query in queries:
score, graphAlign, readAlign, trunc = aligner.align(query["seq"])
- print(graphAlign)
- print(readAlign)
+ print graphAlign
+ print readAlign
eq_(graphAlign, query["graph_aln"])
eq_(readAlign, query["read_aln"])
eq_(trunc, query["truncated"])
diff --git a/tests/test_read_parsers.py b/tests/test_read_parsers.py
index c785772..f2ae329 100644
--- a/tests/test_read_parsers.py
+++ b/tests/test_read_parsers.py
@@ -1,8 +1,6 @@
-from __future__ import print_function
-from __future__ import absolute_import
#
-# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
-# Copyright (C) Michigan State University, 2009-2015. It is licensed under
+# This file is part of khmer, http://github.com/ged-lab/khmer/, and is
+# Copyright (C) Michigan State University, 2009-2013. It is licensed under
# the three-clause BSD license; see LICENSE.
# Contact: khmer-project at idyll.org
#
@@ -12,7 +10,7 @@ from __future__ import absolute_import
import khmer
from khmer import ReadParser
-from . import khmer_tst_utils as utils
+import khmer_tst_utils as utils
from nose.plugins.attrib import attr
from functools import reduce
@@ -70,7 +68,7 @@ def test_num_reads_threads():
n_threads = 4
threads = []
rparser = ReadParser(utils.get_test_data("100-reads.fq.gz"))
- for _ in range(n_threads):
+ for _ in xrange(n_threads):
thr = threading.Thread(target=count_reads, args=[rparser, ])
threads.append(thr)
thr.start()
@@ -110,7 +108,7 @@ def test_gzip_decompression_truncated():
pass
assert 0, "this should fail"
except IOError as err:
- print(str(err))
+ print str(err)
def test_gzip_decompression_truncated_pairiter():
@@ -121,7 +119,7 @@ def test_gzip_decompression_truncated_pairiter():
pass
assert 0, "this should fail"
except IOError as err:
- print(str(err))
+ print str(err)
def test_bzip2_decompression():
@@ -142,7 +140,7 @@ def test_bzip2_decompression_truncated():
pass
assert 0, "this should fail"
except IOError as err:
- print(str(err))
+ print str(err)
def test_bzip2_decompression_truncated_pairiter():
@@ -153,7 +151,7 @@ def test_bzip2_decompression_truncated_pairiter():
pass
assert 0, "this should fail"
except IOError as err:
- print(str(err))
+ print str(err)
def test_badbzip2():
@@ -163,9 +161,9 @@ def test_badbzip2():
pass
assert 0, "this should fail"
except IOError as err:
- print(str(err))
+ print str(err)
except ValueError as err:
- print(str(err))
+ print str(err)
@attr('multithread')
@@ -186,7 +184,7 @@ def test_with_multiple_threads(testfile="test-reads.fq.bz2"):
threads = []
reads_counts_per_thread = [0] * N_THREADS
rparser = ReadParser(utils.get_test_data(testfile))
- for tnum in range(N_THREADS):
+ for tnum in xrange(N_THREADS):
t = \
threading.Thread(
target=count_reads,
@@ -310,10 +308,10 @@ def test_read_pair_iterator_in_error_mode():
in rparser.iter_read_pairs(ReadParser.PAIR_MODE_ERROR_ON_UNPAIRED):
read_pairs_2.append([read_1, read_2])
matches = \
- list(map(
+ map(
lambda rp1, rp2: rp1[0].name == rp2[0].name,
read_pairs_1, read_pairs_2
- ))
+ )
assert all(matches) # Assert ALL the matches. :-]
@@ -355,12 +353,12 @@ def test_constructor():
assert 0, ("ReadParser's constructor shouldn't accept a character for "
"the number of threads")
except TypeError as err:
- print(str(err))
+ print str(err)
try:
rparser = ReadParser("non-existent-file-name")
assert 0, "ReadParser shouldn't accept a non-existant file name"
except ValueError as err:
- print(str(err))
+ print str(err)
def test_iternext():
@@ -371,7 +369,7 @@ def test_iternext():
read_pairs.append(read_1, read_2)
assert 0, "Shouldn't be able to iterate over non FASTA file"
except IOError as err:
- print(str(err))
+ print str(err)
except ValueError as err:
- print(str(err))
+ print str(err)
# vim: set ft=python ts=4 sts=4 sw=4 et tw=79:
diff --git a/tests/test_sandbox_scripts.py b/tests/test_sandbox_scripts.py
index ef85a82..c2ab6fc 100644
--- a/tests/test_sandbox_scripts.py
+++ b/tests/test_sandbox_scripts.py
@@ -1,7 +1,5 @@
-from __future__ import print_function
-from __future__ import absolute_import
#
-# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
+# This file is part of khmer, http://github.com/ged-lab/khmer/, and is
# Copyright (C) Michigan State University, 2015. It is licensed under
# the three-clause BSD license; see LICENSE.
# Contact: khmer-project at idyll.org
@@ -13,14 +11,13 @@ import sys
import os
import os.path
import shutil
-from io import StringIO
+from cStringIO import StringIO
import traceback
import nose
-from nose.plugins.attrib import attr
import glob
import imp
-from . import khmer_tst_utils as utils
+import khmer_tst_utils as utils
import khmer
import screed
@@ -57,7 +54,7 @@ class _checkImportSucceeds(object):
try:
mod = imp.load_source('__zzz', self.filename)
except:
- print(traceback.format_exc())
+ print traceback.format_exc()
raise AssertionError("%s cannot be imported" % (self.filename,))
#
@@ -75,10 +72,9 @@ class _checkImportSucceeds(object):
exec(
compile(open(self.filename).read(), self.filename, 'exec'),
global_dict)
- except (ImportError, SyntaxError) as err:
- print("{0}".format(err))
- raise AssertionError("%s cannot be exec'd" % (self.filename),
- "{0}".format(traceback))
+ except (ImportError, SyntaxError):
+ print traceback.format_exc()
+ raise AssertionError("%s cannot be exec'd" % (self.filename,))
except:
pass # other failures are expected :)
finally:
@@ -111,7 +107,7 @@ def test_sweep_reads():
mout = os.path.join(in_dir, 'test_multi.fa')
oout = os.path.join(in_dir, 'test_orphaned.fa')
- print(os.listdir(in_dir))
+ print os.listdir(in_dir)
assert os.path.exists(out1)
assert os.path.exists(out2)
@@ -122,10 +118,10 @@ def test_sweep_reads():
seqsm = set([r.name for r in screed.open(mout)])
seqso = set([r.name for r in screed.open(oout)])
- print(seqs1)
- print(seqs2)
- print(seqsm)
- print(seqso)
+ print seqs1
+ print seqs2
+ print seqsm
+ print seqso
assert seqs1 == set(['read1_p0\t0', 'read2_p0\t0'])
assert seqs2 == set(['read3_p1\t1'])
assert (seqsm == set(['read4_multi\t0\t1']) or
@@ -161,19 +157,19 @@ def test_sweep_reads_fq():
assert os.path.exists(out2)
assert os.path.exists(mout)
assert os.path.exists(oout)
- print(open(out1).read())
+ print open(out1).read()
- print(os.listdir(in_dir))
+ print os.listdir(in_dir)
seqs1 = set([r.name for r in screed.open(out1)])
seqs2 = set([r.name for r in screed.open(out2)])
seqsm = set([r.name for r in screed.open(mout)])
seqso = set([r.name for r in screed.open(oout)])
- print(seqs1)
- print(seqs2)
- print(seqsm)
- print(seqso)
+ print seqs1
+ print seqs2
+ print seqsm
+ print seqso
assert seqs1 == set(['read1_p0\t0', 'read2_p0\t0'])
assert seqs2 == set(['read3_p1\t1'])
assert (seqsm == set(['read4_multi\t0\t1']) or
@@ -198,9 +194,9 @@ def test_sweep_reads_2():
'test', '--label-by-seq', inref, infile]
status, out, err = utils.runscript(script, args, wdir, sandbox=True)
- for i in range(99):
+ for i in xrange(99):
p = os.path.join(wdir, 'test_{i}.fa'.format(i=i))
- print(p, err, out)
+ print p, err, out
assert os.path.exists(p)
os.remove(p)
assert os.path.exists(os.path.join(wdir, 'test.counts.csv'))
@@ -218,9 +214,9 @@ def test_sweep_reads_3():
'test', '--label-by-group', '10', infile, infile]
status, out, err = utils.runscript(script, args, wdir, sandbox=True)
- for i in range(10):
+ for i in xrange(10):
p = os.path.join(wdir, 'test_{i}.fa'.format(i=i))
- print(p, err, out)
+ print p, err, out
assert os.path.exists(p)
os.remove(p)
@@ -233,25 +229,3 @@ def test_sweep_reads_3():
assert os.path.exists(counts_fn)
assert os.path.exists(os.path.join(wdir, 'test.dist.txt'))
assert not os.path.exists(os.path.join(wdir, 'test_multi.fa'))
-
-
-def test_collect_reads():
- outfile = utils.get_temp_filename('out.graph')
- infile = utils.get_test_data('test-reads.fa')
- script = 'collect-reads.py'
- args = ['-M', '1e7', outfile, infile]
-
- status, out, err = utils.runscript(script, args, sandbox=True)
-
- assert status == 0
- assert os.path.exists(outfile)
-
-
-def test_saturate_by_median():
- infile = utils.get_test_data('test-reads.fa')
- script = 'saturate-by-median.py'
- args = ['-M', '1e7', infile]
-
- status, out, err = utils.runscript(script, args, sandbox=True)
-
- assert status == 0
diff --git a/tests/test_script_arguments.py b/tests/test_script_arguments.py
index e7cdc8d..bc0e132 100644
--- a/tests/test_script_arguments.py
+++ b/tests/test_script_arguments.py
@@ -1,5 +1,5 @@
#
-# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
+# This file is part of khmer, http://github.com/ged-lab/khmer/, and is
# Copyright (C) Michigan State University, 2014-2015. It is licensed under
# the three-clause BSD license; see LICENSE.
# Contact: khmer-project at idyll.org
@@ -7,46 +7,36 @@
"""
Tests for various argument-handling code.
"""
-from __future__ import print_function, unicode_literals
-from __future__ import absolute_import
import sys
-import io
-import collections
-from . import khmer_tst_utils as utils
+import cStringIO
+import khmer_tst_utils as utils
-import argparse
import khmer.kfile
-from khmer import khmer_args
-from cStringIO import StringIO
def test_check_space():
fakelump_fa = utils.get_test_data('fakelump.fa')
- save_stderr, sys.stderr = sys.stderr, io.StringIO()
+ save_stderr, sys.stderr = sys.stderr, cStringIO.StringIO()
try:
khmer.kfile.check_space(
[fakelump_fa], force=False, _testhook_free_space=0)
assert 0, "this should fail"
except SystemExit as e:
- print(str(e))
+ print str(e)
finally:
sys.stderr = save_stderr
def test_check_tablespace():
- save_stderr, sys.stderr = sys.stderr, io.StringIO()
-
- parser = khmer_args.build_counting_args()
- args = parser.parse_args(['-M', '1e9'])
-
+ save_stderr, sys.stderr = sys.stderr, cStringIO.StringIO()
try:
- khmer.kfile.check_space_for_hashtable(args, 'countgraph', force=False,
- _testhook_free_space=0)
+ khmer.kfile.check_space_for_hashtable(
+ 1e9, force=False, _testhook_free_space=0)
assert 0, "this should fail"
except SystemExit as e:
- print(str(e))
+ print str(e)
finally:
sys.stderr = save_stderr
@@ -54,208 +44,36 @@ def test_check_tablespace():
def test_check_space_force():
fakelump_fa = utils.get_test_data('fakelump.fa')
- save_stderr, sys.stderr = sys.stderr, io.StringIO()
+ save_stderr, sys.stderr = sys.stderr, cStringIO.StringIO()
try:
khmer.kfile.check_space(
[fakelump_fa], force=True, _testhook_free_space=0)
assert True, "this should pass"
except SystemExit as e:
- print(str(e))
+ print str(e)
finally:
sys.stderr = save_stderr
def test_check_tablespace_force():
- save_stderr, sys.stderr = sys.stderr, io.StringIO()
-
- parser = khmer_args.build_counting_args()
- args = parser.parse_args(['-M', '1e9'])
-
+ save_stderr, sys.stderr = sys.stderr, cStringIO.StringIO()
try:
- khmer.kfile.check_space_for_hashtable(args, 'countgraph', True,
- _testhook_free_space=0)
+ khmer.kfile.check_space_for_hashtable(
+ 1e9, force=True, _testhook_free_space=0)
assert True, "this should pass"
except SystemExit as e:
- print(str(e))
+ print str(e)
finally:
sys.stderr = save_stderr
def test_invalid_file_warn():
- save_stderr, sys.stderr = sys.stderr, io.StringIO()
+ save_stderr, sys.stderr = sys.stderr, cStringIO.StringIO()
try:
khmer.kfile.check_valid_file_exists(["nonexistent", "nonexistent2"])
assert sys.stderr.getvalue().count("\n") == 2, \
"Should produce two warning lines"
- except SystemExit as e:
- print(str(e))
+ except SystemExit, e:
+ print str(e)
finally:
sys.stderr = save_stderr
-
-
-FakeArgparseObject = collections.namedtuple('FakeArgs',
- ['ksize', 'n_tables',
- 'max_tablesize',
- 'max_memory_usage'])
-
-
-def test_create_countgraph_1():
- ksize = khmer_args.DEFAULT_K
- n_tables = khmer_args.DEFAULT_N_TABLES
- max_tablesize = khmer_args.DEFAULT_MAX_TABLESIZE
- max_mem = 1e7
-
- args = FakeArgparseObject(ksize, n_tables, max_tablesize, max_mem)
-
- countgraph = khmer_args.create_countgraph(args)
- assert countgraph.hashsizes() == [2499997L, 2499989L, 2499983L, 2499967L]
- assert sum(countgraph.hashsizes()) < max_mem, sum(countgraph.hashsizes())
-
-
-def test_create_countgraph_2():
- # tests overriding ksize by passing into create_nodegraph explicitly.
-
- ksize = khmer_args.DEFAULT_K
- n_tables = khmer_args.DEFAULT_N_TABLES
- max_tablesize = khmer_args.DEFAULT_MAX_TABLESIZE
- max_mem = 1e7
-
- args = FakeArgparseObject(ksize, n_tables, max_tablesize, max_mem)
-
- countgraph = khmer_args.create_countgraph(args, ksize=15)
- assert countgraph.ksize() == 15
-
-
-def test_create_countgraph_3():
- # tests too-big ksize
-
- ksize = khmer_args.DEFAULT_K
- n_tables = khmer_args.DEFAULT_N_TABLES
- max_tablesize = khmer_args.DEFAULT_MAX_TABLESIZE
- max_mem = 1e7
-
- args = FakeArgparseObject(ksize, n_tables, max_tablesize, max_mem)
-
- old_stderr = sys.stderr
- sys.stderr = capture = StringIO()
-
- try:
- countgraph = khmer_args.create_countgraph(args, ksize=35)
- assert 0, "should not reach this"
- except SystemExit:
- err = capture.getvalue()
- assert 'khmer only supports k-mer sizes <= 32.' in err, err
- finally:
- sys.stderr = old_stderr
-
-
-def test_create_countgraph_4_multiplier():
- ksize = khmer_args.DEFAULT_K
- n_tables = khmer_args.DEFAULT_N_TABLES
- max_tablesize = khmer_args.DEFAULT_MAX_TABLESIZE
- max_mem = 1e7
-
- args = FakeArgparseObject(ksize, n_tables, max_tablesize, max_mem)
-
- countgraph = khmer_args.create_countgraph(args, multiplier=2.0)
- assert sum(countgraph.hashsizes()) < max_mem / 2.0, \
- sum(countgraph.hashsizes())
-
-
-def test_create_nodegraph_1():
- ksize = khmer_args.DEFAULT_K
- n_tables = khmer_args.DEFAULT_N_TABLES
- max_tablesize = khmer_args.DEFAULT_MAX_TABLESIZE
- max_mem = 1e7
-
- args = FakeArgparseObject(ksize, n_tables, max_tablesize, max_mem)
-
- nodegraph = khmer_args.create_nodegraph(args)
- assert nodegraph.hashsizes() == [19999999L, 19999981L,
- 19999963L, 19999927L]
-
- assert sum(nodegraph.hashsizes())/8.0 < max_mem, sum(nodegraph.hashsizes())
-
-
-def test_create_nodegraph_2():
- # tests overriding ksize by passing into create_nodegraph explicitly.
-
- ksize = khmer_args.DEFAULT_K
- n_tables = khmer_args.DEFAULT_N_TABLES
- max_tablesize = khmer_args.DEFAULT_MAX_TABLESIZE
- max_mem = 1e7
-
- args = FakeArgparseObject(ksize, n_tables, max_tablesize, max_mem)
-
- nodegraph = khmer_args.create_nodegraph(args, ksize=15)
- assert nodegraph.ksize() == 15
-
-
-def test_create_nodegraph_3():
- # tests too-big ksize
-
- ksize = khmer_args.DEFAULT_K
- n_tables = khmer_args.DEFAULT_N_TABLES
- max_tablesize = khmer_args.DEFAULT_MAX_TABLESIZE
- max_mem = 1e7
-
- args = FakeArgparseObject(ksize, n_tables, max_tablesize, max_mem)
-
- old_stderr = sys.stderr
- sys.stderr = capture = StringIO()
-
- try:
- nodegraph = khmer_args.create_nodegraph(args, ksize=35)
- assert 0, "should not reach this"
- except SystemExit:
- err = capture.getvalue()
- assert 'khmer only supports k-mer sizes <= 32.' in err, err
-
-
-def test_create_nodegraph_4_multiplier():
- ksize = khmer_args.DEFAULT_K
- n_tables = khmer_args.DEFAULT_N_TABLES
- max_tablesize = khmer_args.DEFAULT_MAX_TABLESIZE
- max_mem = 1e7
-
- args = FakeArgparseObject(ksize, n_tables, max_tablesize, max_mem)
-
- nodegraph = khmer_args.create_nodegraph(args, multiplier=2.0)
- assert sum(nodegraph.hashsizes())/8.0 < max_mem / 2.0, \
- sum(nodegraph.hashsizes())
-
-
-def test_report_on_config_bad_hashtype():
- ksize = khmer_args.DEFAULT_K
- n_tables = khmer_args.DEFAULT_N_TABLES
- max_tablesize = khmer_args.DEFAULT_MAX_TABLESIZE
- max_mem = 1e7
-
- args = FakeArgparseObject(ksize, n_tables, max_tablesize, max_mem)
-
- try:
- khmer_args.report_on_config(args, 'foograph')
- assert 0, "the previous statement should raise an exception"
- except AssertionError:
- raise
- except Exception as err:
- assert "unknown graph type: foograph" in str(err), str(err)
-
-
-def test_fail_calculate_foograph_size():
- # tests unknown graph type
-
- ksize = khmer_args.DEFAULT_K
- n_tables = khmer_args.DEFAULT_N_TABLES
- max_tablesize = khmer_args.DEFAULT_MAX_TABLESIZE
- max_mem = 1e7
-
- args = FakeArgparseObject(ksize, n_tables, max_tablesize, max_mem)
-
- try:
- nodegraph = khmer_args._calculate_tablesize(args, 'foograph')
- assert 0, "previous statement should fail"
- except AssertionError:
- raise
- except Exception as err:
- assert "unknown graph type: foograph" in str(err), str(err)
diff --git a/tests/test_scripts.py b/tests/test_scripts.py
index ffbbb81..2f4a75d 100644
--- a/tests/test_scripts.py
+++ b/tests/test_scripts.py
@@ -1,8 +1,5 @@
-from __future__ import print_function
-from __future__ import absolute_import
-from __future__ import unicode_literals
#
-# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
+# This file is part of khmer, http://github.com/ged-lab/khmer/, and is
# Copyright (C) Michigan State University, 2009-2015. It is licensed under
# the three-clause BSD license; see LICENSE.
# Contact: khmer-project at idyll.org
@@ -15,7 +12,7 @@ import sys
import os
import stat
import shutil
-from io import StringIO
+from cStringIO import StringIO
import traceback
from nose.plugins.attrib import attr
import subprocess
@@ -23,12 +20,16 @@ import threading
import bz2
import io
-from . import khmer_tst_utils as utils
+import khmer_tst_utils as utils
import khmer
import khmer.kfile
import screed
+def scriptpath(script):
+ return script
+
+
def teardown():
utils.cleanup()
@@ -41,7 +42,7 @@ def test_check_space():
def test_load_into_counting():
- script = 'load-into-counting.py'
+ script = scriptpath('load-into-counting.py')
args = ['-x', '1e3', '-N', '2', '-k', '20', '-t']
outfile = utils.get_temp_filename('out.ct')
@@ -50,65 +51,12 @@ def test_load_into_counting():
args.extend([outfile, infile])
(status, out, err) = utils.runscript(script, args)
- assert 'Total number of unique k-mers: 83' in err, err
- assert os.path.exists(outfile)
-
-
-def test_load_into_counting_tablesize_warning():
- script = 'load-into-counting.py'
- args = ['-k', '20', '-t']
-
- outfile = utils.get_temp_filename('out.ct')
- infile = utils.get_test_data('test-abund-read-2.fa')
-
- args.extend([outfile, infile])
-
- (status, out, err) = utils.runscript(script, args)
- assert os.path.exists(outfile)
- assert "WARNING: tablesize is default!" in err
-
-
-def test_load_into_counting_max_memory_usage_parameter():
- script = 'load-into-counting.py'
- args = ['-M', '2e3', '-k', '20', '-t']
-
- outfile = utils.get_temp_filename('out.ct')
- infile = utils.get_test_data('test-abund-read-2.fa')
-
- args.extend([outfile, infile])
-
- (status, out, err) = utils.runscript(script, args)
- assert os.path.exists(outfile)
- assert "WARNING: tablesize is default!" not in err
-
- kh = khmer.load_counting_hash(outfile)
- assert sum(kh.hashsizes()) < 3e8
-
-
-def test_load_into_counting_abundance_dist_nobig():
- script = 'load-into-counting.py'
- args = ['-x', '1e3', '-N', '2', '-k', '20', '-t', '-b']
-
- outfile = utils.get_temp_filename('out.ct')
- infile = utils.get_test_data('test-abund-read-2.fa')
-
- args.extend([outfile, infile])
-
- (status, out, err) = utils.runscript(script, args)
- assert 'Total number of unique k-mers: 83' in err, err
+ assert 'Total number of unique k-mers: 89' in err, err
assert os.path.exists(outfile)
- htfile = outfile
- outfile = utils.get_temp_filename('out')
- script2 = 'abundance-dist.py'
- args = ['-z', htfile, infile, outfile]
- (status, out, err) = utils.runscript(script2, args)
- assert 'WARNING: The loaded graph has bigcount' in err, err
- assert 'bigcount' in err, err
-
def test_load_into_counting_nonwritable():
- script = 'load-into-counting.py'
+ script = scriptpath('load-into-counting.py')
args = ['-x', '1e3', '-N', '2', '-k', '20', '-t']
outfile = utils.get_temp_filename('test-nonwritable')
@@ -125,9 +73,9 @@ def test_load_into_counting_nonwritable():
assert status == 1, status
- at attr('huge')
+ at attr('linux')
def test_load_into_counting_toobig():
- script = 'load-into-counting.py'
+ script = scriptpath('load-into-counting.py')
args = ['-x', '1e12', '-N', '2', '-k', '20', '-t', '--force']
outfile = utils.get_temp_filename('out.kh')
@@ -141,7 +89,7 @@ def test_load_into_counting_toobig():
def test_load_into_counting_fail():
- script = 'load-into-counting.py'
+ script = scriptpath('load-into-counting.py')
args = ['-x', '1e2', '-N', '2', '-k', '20'] # use small HT
outfile = utils.get_temp_filename('out.ct')
@@ -151,12 +99,12 @@ def test_load_into_counting_fail():
(status, out, err) = utils.runscript(script, args, fail_ok=True)
assert status == 1, status
- print(err)
+ print err
assert "** ERROR: the graph structure is too small" in err
def test_load_into_counting_multifile():
- script = 'load-into-counting.py'
+ script = scriptpath('load-into-counting.py')
args = ['-x', '1e7', '-N', '2', '-k', '20', '-t']
outfile = utils.get_temp_filename('out.kh')
@@ -171,7 +119,7 @@ def test_load_into_counting_multifile():
def test_load_into_counting_tsv():
- script = 'load-into-counting.py'
+ script = scriptpath('load-into-counting.py')
args = ['-x', '1e7', '-N', '2', '-k', '20', '-t', '-s', 'tsv']
outfile = utils.get_temp_filename('out.ct')
@@ -194,7 +142,7 @@ def test_load_into_counting_tsv():
def test_load_into_counting_json():
- script = 'load-into-counting.py'
+ script = scriptpath('load-into-counting.py')
args = ['-x', '1e7', '-N', '2', '-k', '20', '-t', '-s', 'json']
outfile = utils.get_temp_filename('out.ct')
@@ -211,21 +159,20 @@ def test_load_into_counting_json():
with open(jsonfile) as jsonfh:
got_json = json.load(jsonfh)
outbase = os.path.basename(outfile)
-
expected_json = {
- u"files": [infile],
- u"ht_name": outbase,
- u"num_kmers": 95,
- u"num_reads": 1001,
- u"fpr": 9.025048735197377e-11,
- u"mrinfo_version": "0.2.0",
+ "files": [infile],
+ "ht_name": outbase,
+ "num_kmers": 95,
+ "num_reads": 1001,
+ "fpr": 9.024965705097741e-11,
+ "mrinfo_version": "0.2.0",
}
assert got_json == expected_json, got_json
def test_load_into_counting_bad_summary_fmt():
- script = 'load-into-counting.py'
+ script = scriptpath('load-into-counting.py')
args = ['-x', '1e7', '-N', '2', '-k', '20', '-s', 'badfmt']
outfile = utils.get_temp_filename('out.ct')
@@ -239,7 +186,7 @@ def test_load_into_counting_bad_summary_fmt():
def _make_counting(infilename, SIZE=1e7, N=2, K=20, BIGCOUNT=True):
- script = 'load-into-counting.py'
+ script = scriptpath('load-into-counting.py')
args = ['-x', str(SIZE), '-N', str(N), '-k', str(K)]
if not BIGCOUNT:
@@ -256,7 +203,7 @@ def _make_counting(infilename, SIZE=1e7, N=2, K=20, BIGCOUNT=True):
def test_filter_abund_1():
- script = 'filter-abund.py'
+ script = scriptpath('filter-abund.py')
infile = utils.get_temp_filename('test.fa')
n_infile = utils.get_temp_filename('test-fastq-n-reads.fq')
@@ -302,7 +249,7 @@ def test_filter_abund_2():
shutil.copyfile(utils.get_test_data('test-abund-read-2.fa'), infile)
counting_ht = _make_counting(infile, K=17)
- script = 'filter-abund.py'
+ script = scriptpath('filter-abund.py')
args = ['-C', '1', counting_ht, infile, infile]
utils.runscript(script, args, in_dir)
@@ -323,7 +270,7 @@ def test_filter_abund_3_fq_retained():
shutil.copyfile(utils.get_test_data('test-abund-read-2.fq'), infile)
counting_ht = _make_counting(infile, K=17)
- script = 'filter-abund.py'
+ script = scriptpath('filter-abund.py')
args = ['-C', '1', counting_ht, infile, infile]
utils.runscript(script, args, in_dir)
@@ -351,7 +298,7 @@ def test_filter_abund_4_fq_casava_18():
infile)
counting_ht = _make_counting(infile, K=17)
- script = 'filter-abund.py'
+ script = scriptpath('filter-abund.py')
args = [counting_ht, infile, infile]
utils.runscript(script, args, in_dir)
@@ -368,7 +315,7 @@ def test_filter_abund_1_singlefile():
shutil.copyfile(utils.get_test_data('test-abund-read-2.fa'), infile)
- script = 'filter-abund-single.py'
+ script = scriptpath('filter-abund-single.py')
args = ['-x', '1e7', '-N', '2', '-k', '17', '-t', infile]
(status, out, err) = utils.runscript(script, args, in_dir)
@@ -389,7 +336,7 @@ def test_filter_abund_2_singlefile():
shutil.copyfile(utils.get_test_data('test-abund-read-2.fa'), infile)
- script = 'filter-abund-single.py'
+ script = scriptpath('filter-abund-single.py')
args = ['-x', '1e7', '-N', '2', '-k', '17', '-t', '--savetable',
tabfile, infile]
(status, out, err) = utils.runscript(script, args, in_dir)
@@ -411,7 +358,7 @@ def test_filter_abund_2_singlefile_fq_casava_18():
shutil.copyfile(utils.get_test_data('test-abund-read-2.paired2.fq'),
infile)
- script = 'filter-abund-single.py'
+ script = scriptpath('filter-abund-single.py')
args = ['-x', '1e7', '-N', '2', '-k', '17', infile]
(status, out, err) = utils.runscript(script, args, in_dir)
@@ -430,7 +377,7 @@ def test_filter_abund_4_retain_low_abund():
shutil.copyfile(utils.get_test_data('test-abund-read-2.fa'), infile)
counting_ht = _make_counting(infile, K=17)
- script = 'filter-abund.py'
+ script = scriptpath('filter-abund.py')
args = ['-V', counting_ht, infile]
utils.runscript(script, args, in_dir)
@@ -441,16 +388,17 @@ def test_filter_abund_4_retain_low_abund():
assert len(seqs) == 2, seqs
assert 'GGTTGACGGGGCTCAGGG' in seqs
+# test that the -V option *does* trim sequences that are low abundance
+
def test_filter_abund_5_trim_high_abund():
- # test that the -V option *does* trim sequences that are high abundance
infile = utils.get_temp_filename('test.fa')
in_dir = os.path.dirname(infile)
shutil.copyfile(utils.get_test_data('test-abund-read-3.fa'), infile)
counting_ht = _make_counting(infile, K=17)
- script = 'filter-abund.py'
+ script = scriptpath('filter-abund.py')
args = ['-V', counting_ht, infile]
utils.runscript(script, args, in_dir)
@@ -463,18 +411,17 @@ def test_filter_abund_5_trim_high_abund():
# trimmed sequence @ error
assert 'GGTTGACGGGGCTCAGGGGGCGGCTGACTCCGAGAGACAGC' in seqs
+# test that -V/-Z setting - should not trip if -Z is set high enough.
+
def test_filter_abund_6_trim_high_abund_Z():
- # test that -V/-Z settings interact properly -
- # trimming should not happen if -Z is set high enough.
-
infile = utils.get_temp_filename('test.fa')
in_dir = os.path.dirname(infile)
shutil.copyfile(utils.get_test_data('test-abund-read-3.fa'), infile)
counting_ht = _make_counting(infile, K=17)
- script = 'filter-abund.py'
+ script = scriptpath('filter-abund.py')
args = ['-V', '-Z', '25', counting_ht, infile]
utils.runscript(script, args, in_dir)
@@ -490,72 +437,6 @@ def test_filter_abund_6_trim_high_abund_Z():
assert badseq in seqs # should be there, untrimmed
-def test_filter_abund_7_retain_Ns():
- # check that filter-abund retains sequences with Ns, and treats them as As.
-
- infile = utils.get_temp_filename('test.fq')
- in_dir = os.path.dirname(infile)
-
- # copy test file over to test.fq & load into counting table
- shutil.copyfile(utils.get_test_data('test-filter-abund-Ns.fq'), infile)
- counting_ht = _make_counting(infile, K=17)
-
- script = 'filter-abund.py'
- args = ['-C', '3', counting_ht, infile]
- utils.runscript(script, args, in_dir)
-
- outfile = infile + '.abundfilt'
- assert os.path.exists(outfile), outfile
-
- # test for a sequence with an 'N' in it --
- names = set([r.name for r in screed.open(outfile, parse_description=0)])
- assert '895:1:37:17593:9954 1::FOO_withN' in names, names
-
- # check to see if that 'N' was properly changed to an 'A'
- seqs = set([r.sequence for r in screed.open(outfile)])
- assert 'GGTTGACGGGGCTCAGGGGGCGGCTGACTCCGAG' not in seqs, seqs
-
- # ...and that an 'N' remains in the output sequences
- found_N = False
- for s in seqs:
- if 'N' in s:
- found_N = True
- assert found_N, seqs
-
-
-def test_filter_abund_single_8_retain_Ns():
- # check that filter-abund-single retains
- # sequences with Ns, and treats them as As.
-
- infile = utils.get_temp_filename('test.fq')
- in_dir = os.path.dirname(infile)
-
- # copy test file over to test.fq & load into counting table
- shutil.copyfile(utils.get_test_data('test-filter-abund-Ns.fq'), infile)
-
- script = 'filter-abund-single.py'
- args = ['-k', '17', '-x', '1e7', '-N', '2', '-C', '3', infile]
- utils.runscript(script, args, in_dir)
-
- outfile = infile + '.abundfilt'
- assert os.path.exists(outfile), outfile
-
- # test for a sequence with an 'N' in it --
- names = set([r.name for r in screed.open(outfile, parse_description=0)])
- assert '895:1:37:17593:9954 1::FOO_withN' in names, names
-
- # check to see if that 'N' was properly changed to an 'A'
- seqs = set([r.sequence for r in screed.open(outfile)])
- assert 'GGTTGACGGGGCTCAGGGGGCGGCTGACTCCGAG' not in seqs, seqs
-
- # ...and that an 'N' remains in the output sequences
- found_N = False
- for s in seqs:
- if 'N' in s:
- found_N = True
- assert found_N, seqs
-
-
def test_filter_stoptags():
infile = utils.get_temp_filename('test.fa')
in_dir = os.path.dirname(infile)
@@ -566,13 +447,13 @@ def test_filter_stoptags():
# now, create a file with some stop tags in it --
K = 18
- kh = khmer._Hashbits(K, [1])
+ kh = khmer.new_hashbits(K, 1, 1)
kh.add_stop_tag('GTTGACGGGGCTCAGGGG')
kh.save_stop_tags(stopfile)
del kh
# finally, run filter-stoptags.
- script = 'filter-stoptags.py'
+ script = scriptpath('filter-stoptags.py')
args = ['-k', str(K), stopfile, infile, infile]
utils.runscript(script, args, in_dir)
@@ -597,13 +478,13 @@ def test_filter_stoptags_fq():
# now, create a file with some stop tags in it --
K = 18
- kh = khmer._Hashbits(K, [1])
+ kh = khmer.new_hashbits(K, 1, 1)
kh.add_stop_tag('GTTGACGGGGCTCAGGGG')
kh.save_stop_tags(stopfile)
del kh
# finally, run filter-stoptags.
- script = 'filter-stoptags.py'
+ script = scriptpath('filter-stoptags.py')
args = ['-k', str(K), stopfile, infile, infile]
utils.runscript(script, args, in_dir)
@@ -623,6 +504,356 @@ def test_filter_stoptags_fq():
assert 'seq 1::BAR' in names
+def test_normalize_by_median_indent():
+ infile = utils.get_test_data('paired-mixed.fa.pe')
+ hashfile = utils.get_test_data('normC20k20.ct')
+ outfile = utils.get_temp_filename('paired-mixed.fa.pe.keep')
+ script = scriptpath('normalize-by-median.py')
+ args = ['--loadtable', hashfile, '-o', outfile, infile]
+ (status, out, err) = utils.runscript(script, args)
+ assert status == 0, (out, err)
+ assert os.path.exists(outfile)
+
+
+def test_normalize_by_median():
+ CUTOFF = '1'
+
+ infile = utils.get_temp_filename('test.fa')
+ in_dir = os.path.dirname(infile)
+
+ shutil.copyfile(utils.get_test_data('test-abund-read-2.fa'), infile)
+
+ script = scriptpath('normalize-by-median.py')
+ args = ['-C', CUTOFF, '-k', '17', '-t', infile]
+ (status, out, err) = utils.runscript(script, args, in_dir)
+
+ assert 'Total number of unique k-mers: 98' in err, err
+
+ outfile = infile + '.keep'
+ assert os.path.exists(outfile), outfile
+
+ seqs = [r.sequence for r in screed.open(outfile)]
+ assert len(seqs) == 1, seqs
+ assert seqs[0].startswith('GGTTGACGGGGCTCAGGGGG'), seqs
+
+
+def test_normalize_by_median_unpaired_and_paired():
+ CUTOFF = '1'
+
+ infile = utils.get_temp_filename('test.fa')
+ in_dir = os.path.dirname(infile)
+
+ shutil.copyfile(utils.get_test_data('test-abund-read-paired.fa'), infile)
+
+ unpairedfile = utils.get_temp_filename('test1.fa', tempdir=in_dir)
+ shutil.copyfile(utils.get_test_data('random-20-a.fa'), unpairedfile)
+
+ script = scriptpath('normalize-by-median.py')
+ args = ['-C', CUTOFF, '-k', '17', '-t', '-u', unpairedfile, '-p', infile]
+ (status, out, err) = utils.runscript(script, args, in_dir)
+
+ assert 'Total number of unique k-mers: 4029' in err, err
+
+ outfile = infile + '.keep'
+ assert os.path.exists(outfile), outfile
+
+
+def test_normalize_by_median_double_file_name():
+ infile = utils.get_temp_filename('test-abund-read-2.fa')
+ in_dir = os.path.dirname(infile)
+
+ shutil.copyfile(utils.get_test_data('test-abund-read-2.fa'), infile)
+
+ script = scriptpath('normalize-by-median.py')
+ args = [utils.get_test_data('test-abund-read-2.fa'), infile]
+ (status, out, err) = utils.runscript(script, args, in_dir)
+
+ assert "WARNING: At least two input files are named" in err, err
+
+
+def test_normalize_by_median_overwrite():
+ outfile = utils.get_temp_filename('test.fa.keep')
+ shutil.copyfile(utils.get_test_data('test-abund-read.fa'), outfile)
+ in_dir = os.path.dirname(outfile)
+
+ CUTOFF = '1'
+ infile = utils.get_temp_filename('test.fa', in_dir)
+ shutil.copyfile(utils.get_test_data('test-abund-read-3.fa'), infile)
+ script = scriptpath('normalize-by-median.py')
+
+ args = ['-C', CUTOFF, '-k', '17', '-t', '-o', outfile, infile]
+ (status, out, err) = utils.runscript(script, args, in_dir)
+ assert os.path.exists(outfile), outfile
+ seqs = [r.sequence for r in screed.open(outfile)]
+ assert len(seqs) == 1, seqs
+ assert 'GACAGCgtgCCGCA' in seqs[0], seqs
+
+
+def test_normalize_by_median_version():
+ script = scriptpath('normalize-by-median.py')
+ args = ['--version']
+ status, out, err = utils.runscript(script, args)
+
+ errlines = err.splitlines()
+ for err in errlines:
+ if err.startswith('||') or \
+ not err.strip():
+ continue
+ break
+
+ print errlines
+ print err
+
+ assert err.startswith('khmer ')
+
+
+def test_normalize_by_median_2():
+ CUTOFF = '2'
+
+ infile = utils.get_temp_filename('test.fa')
+ in_dir = os.path.dirname(infile)
+
+ shutil.copyfile(utils.get_test_data('test-abund-read-2.fa'), infile)
+
+ script = scriptpath('normalize-by-median.py')
+ args = ['-C', CUTOFF, '-k', '17', infile]
+ utils.runscript(script, args, in_dir)
+
+ outfile = infile + '.keep'
+ assert os.path.exists(outfile), outfile
+
+ seqs = [r.sequence for r in screed.open(outfile)]
+ assert len(seqs) == 2, seqs
+ assert seqs[0].startswith('GGTTGACGGGGCTCAGGGGG'), seqs
+ assert seqs[1] == 'GGTTGACGGGGCTCAGGG', seqs
+
+
+def test_normalize_by_median_paired():
+ CUTOFF = '1'
+
+ infile = utils.get_temp_filename('test.fa')
+ in_dir = os.path.dirname(infile)
+
+ shutil.copyfile(utils.get_test_data('test-abund-read-paired.fa'), infile)
+
+ script = scriptpath('normalize-by-median.py')
+ args = ['-C', CUTOFF, '-p', '-k', '17', infile]
+ utils.runscript(script, args, in_dir)
+
+ outfile = infile + '.keep'
+ assert os.path.exists(outfile), outfile
+
+ seqs = [r.sequence for r in screed.open(outfile)]
+ assert len(seqs) == 2, seqs
+ assert seqs[0].startswith('GGTTGACGGGGCTCAGGGGG'), seqs
+ assert seqs[1].startswith('GGTTGACGGGGCTCAGGG'), seqs
+
+
+def test_normalize_by_median_paired_fq():
+ CUTOFF = '20'
+
+ infile = utils.get_temp_filename('test.fa')
+ in_dir = os.path.dirname(infile)
+
+ shutil.copyfile(utils.get_test_data('test-abund-read-paired.fq'), infile)
+
+ script = scriptpath('normalize-by-median.py')
+ args = ['-C', CUTOFF, '-p', '-k', '17', infile]
+ _, out, err = utils.runscript(script, args, in_dir)
+ print out
+ print err
+
+ outfile = infile + '.keep'
+ assert os.path.exists(outfile), outfile
+
+ seqs = [r.sequence for r in screed.open(outfile)]
+ assert len(seqs) == 6, len(seqs)
+ assert seqs[0].startswith('GGTTGACGGGGCTCAGGGGG'), seqs
+ assert seqs[1].startswith('GGTTGACGGGGCTCAGGG'), seqs
+
+ names = [r.name for r in screed.open(outfile, parse_description=False)]
+ assert len(names) == 6, names
+ assert '895:1:37:17593:9954 1::FOO' in names, names
+ assert '895:1:37:17593:9954 2::FOO' in names, names
+
+
+def test_normalize_by_median_impaired():
+ CUTOFF = '1'
+
+ infile = utils.get_temp_filename('test.fa')
+ in_dir = os.path.dirname(infile)
+
+ shutil.copyfile(utils.get_test_data('test-abund-read-impaired.fa'), infile)
+
+ script = scriptpath('normalize-by-median.py')
+ args = ['-C', CUTOFF, '-p', '-k', '17', infile]
+ _, out, err = utils.runscript(script, args, in_dir, fail_ok=True)
+ assert '** ERROR: Error: Improperly interleaved pairs ' in err
+
+
+def test_normalize_by_median_force():
+ CUTOFF = '1'
+
+ corrupt_infile = utils.get_temp_filename('test-corrupt.fq')
+ good_infile = utils.get_temp_filename('test-good.fq',
+ tempdir=os.path.dirname(
+ corrupt_infile))
+
+ in_dir = os.path.dirname(good_infile)
+
+ shutil.copyfile(utils.get_test_data('test-error-reads.fq'), corrupt_infile)
+ shutil.copyfile(utils.get_test_data('test-fastq-reads.fq'), good_infile)
+
+ script = scriptpath('normalize-by-median.py')
+ args = ['-f', '-C', CUTOFF, '-k', '17', corrupt_infile, good_infile]
+
+ (status, out, err) = utils.runscript(script, args, in_dir)
+
+ test_ht = khmer.load_counting_hash(corrupt_infile + '.ct.failed')
+ test_good_read = 'CAGGCGCCCACCACCGTGCCCTCCAACCTGATGGT'
+ test_good_read2 = 'TAGTATCATCAAGGTTCAAGATGTTAATGAATAACAATTGCGCAGCAA'
+ assert test_ht.count(test_good_read[:17]) > 0
+ assert test_ht.count(test_good_read2[:17]) > 0
+ assert os.path.exists(corrupt_infile + '.ct.failed')
+ assert '*** Skipping' in err
+ assert '** IOErrors' in err
+
+
+def test_normalize_by_median_no_bigcount():
+ infile = utils.get_temp_filename('test.fa')
+ hashfile = utils.get_temp_filename('test-out.ct')
+ outfile = infile + '.keep'
+ in_dir = os.path.dirname(infile)
+
+ shutil.copyfile(utils.get_test_data('test-abund-read-2.fa'), infile)
+ counting_ht = _make_counting(infile, K=8)
+
+ script = scriptpath('normalize-by-median.py')
+ args = ['-C', '1000', '-k 8', '--savetable', hashfile, infile]
+
+ (status, out, err) = utils.runscript(script, args, in_dir)
+ assert status == 0, (out, err)
+ print(out, err)
+
+ assert os.path.exists(hashfile), hashfile
+ kh = khmer.load_counting_hash(hashfile)
+
+ assert kh.get('GGTTGACG') == 255
+
+
+def test_normalize_by_median_dumpfrequency():
+ CUTOFF = '1'
+
+ infiles = [utils.get_temp_filename('test-0.fq')]
+ in_dir = os.path.dirname(infiles[0])
+ for x in range(1, 5):
+ infiles.append(utils.get_temp_filename('test-{x}.fq'.format(x=x),
+ tempdir=in_dir))
+
+ for infile in infiles:
+ shutil.copyfile(utils.get_test_data('test-fastq-reads.fq'), infile)
+
+ script = scriptpath('normalize-by-median.py')
+ args = ['-d', '2', '-C', CUTOFF, '-k', '17']
+ args.extend(infiles)
+
+ (status, out, err) = utils.runscript(script, args, in_dir)
+
+ test_ht = khmer.load_counting_hash(os.path.join(in_dir, 'backup.ct'))
+ test_good_read = 'CAGGCGCCCACCACCGTGCCCTCCAACCTGATGGT'
+ test_good_read2 = 'TAGTATCATCAAGGTTCAAGATGTTAATGAATAACAATTGCGCAGCAA'
+ assert test_ht.count(test_good_read[:17]) > 0
+ assert test_ht.count(test_good_read2[:17]) > 0
+
+ assert os.path.exists(os.path.join(in_dir, 'backup.ct'))
+ assert out.count('Backup: Saving') == 2
+ assert 'Nothing' in out
+
+
+def test_normalize_by_median_empty():
+ CUTOFF = '1'
+
+ infile = utils.get_temp_filename('test.fa')
+ in_dir = os.path.dirname(infile)
+
+ shutil.copyfile(utils.get_test_data('test-empty.fa'), infile)
+
+ script = scriptpath('normalize-by-median.py')
+ args = ['-C', CUTOFF, '-k', '17', infile]
+ utils.runscript(script, args, in_dir)
+
+ outfile = infile + '.keep'
+ assert os.path.exists(outfile), outfile
+
+
+def test_normalize_by_median_emptycountingtable():
+ CUTOFF = '1'
+
+ infile = utils.get_temp_filename('test.fa')
+ in_dir = os.path.dirname(infile)
+
+ shutil.copyfile(utils.get_test_data('test-empty.fa'), infile)
+
+ script = scriptpath('normalize-by-median.py')
+ args = ['-C', CUTOFF, '--loadtable', infile, infile]
+ (status, out, err) = utils.runscript(script, args, in_dir, fail_ok=True)
+ assert 'ValueError' in err, (status, out, err)
+
+
+def test_normalize_by_median_fpr():
+ MIN_TABLESIZE_PARAM = 1
+
+ infile = utils.get_temp_filename('test-fpr.fq')
+ in_dir = os.path.dirname(infile)
+ shutil.copyfile(utils.get_test_data('test-fastq-reads.fq'), infile)
+
+ script = scriptpath('normalize-by-median.py')
+ args = ['-f', '-k 17', '-x ' + str(MIN_TABLESIZE_PARAM), infile]
+
+ (status, out, err) = utils.runscript(script, args, in_dir, fail_ok=True)
+
+ assert os.path.exists(infile + '.keep')
+ assert '** ERROR: the graph structure is too small' in err, err
+
+
+def write_by_chunks(infile, outfile, CHUNKSIZE=8192):
+ ifile = io.open(infile, 'rb')
+ ofile = io.open(outfile, 'wb')
+ chunk = ifile.read(CHUNKSIZE)
+ while len(chunk) > 0:
+ ofile.write(chunk)
+ chunk = ifile.read(CHUNKSIZE)
+ ifile.close()
+ ofile.close()
+
+
+def test_normalize_by_median_stdout():
+ CUTOFF = '20'
+
+ infile = utils.get_test_data('100-reads.fq.gz')
+ in_dir = os.path.dirname(infile)
+ fifo = utils.get_temp_filename('fifo')
+ outfile = utils.get_temp_filename('outfile')
+
+ # Use a fifo to copy stdout to a file for checking
+ os.mkfifo(fifo)
+ thread = threading.Thread(target=write_by_chunks, args=(fifo, outfile))
+ thread.start()
+
+ # Execute diginorm
+ script = scriptpath('normalize-by-median.py')
+ args = ['-C', CUTOFF, '-k', '17', '-o', fifo, infile]
+ (status, out, err) = utils.runscript(script, args, in_dir)
+
+ # Merge the thread
+ thread.join()
+
+ assert os.path.exists(outfile), outfile
+ with open(outfile) as fp:
+ linecount = sum(1 for _ in fp)
+ assert linecount == 400
+
+
def test_count_median():
infile = utils.get_temp_filename('test.fa')
outfile = infile + '.counts'
@@ -630,7 +861,7 @@ def test_count_median():
shutil.copyfile(utils.get_test_data('test-abund-read-2.fa'), infile)
counting_ht = _make_counting(infile, K=8)
- script = 'count-median.py'
+ script = scriptpath('count-median.py')
args = [counting_ht, infile, outfile]
utils.runscript(script, args)
@@ -650,7 +881,7 @@ def test_count_median_fq():
shutil.copyfile(utils.get_test_data('test-abund-read-2.fq'), infile)
counting_ht = _make_counting(infile, K=8)
- script = 'count-median.py'
+ script = scriptpath('count-median.py')
args = [counting_ht, infile, outfile]
utils.runscript(script, args)
@@ -670,7 +901,7 @@ def test_count_median_fq_csv():
shutil.copyfile(utils.get_test_data('test-abund-read-2.fq'), infile)
counting_ht = _make_counting(infile, K=8)
- script = 'count-median.py'
+ script = scriptpath('count-median.py')
args = ['--csv', counting_ht, infile, outfile]
utils.runscript(script, args)
@@ -686,43 +917,12 @@ def test_count_median_fq_csv():
names = set([line.split(',')[0] for line in data])
assert '895:1:37:17593:9954 1::FOO' in names, names
-
-def test_load_graph():
- script = 'load-graph.py'
- args = ['-x', '1e7', '-N', '2', '-k', '20']
-
- outfile = utils.get_temp_filename('out')
- infile = utils.get_test_data('random-20-a.fa')
-
- args.extend([outfile, infile])
-
- (status, out, err) = utils.runscript(script, args)
-
- assert 'Total number of unique k-mers: 3960' in err, err
-
- ht_file = outfile + '.pt'
- assert os.path.exists(ht_file), ht_file
-
- tagset_file = outfile + '.tagset'
- assert os.path.exists(tagset_file), tagset_file
-
- try:
- ht = khmer.load_hashbits(ht_file)
- except IOError as err:
- assert 0, str(err)
- ht.load_tagset(tagset_file)
-
- # check to make sure we get the expected result for this data set
- # upon partitioning (all in one partition). This is kind of a
- # roundabout way of checking that load-graph worked :)
- subset = ht.do_subset_partition(0, 0)
- x = ht.subset_count_partitions(subset)
- assert x == (1, 0), x
+#
-def test_oxli_build_graph():
- script = 'oxli'
- args = ['build-graph', '-x', '1e7', '-N', '2', '-k', '20']
+def test_load_graph():
+ script = scriptpath('load-graph.py')
+ args = ['-x', '1e7', '-N', '2', '-k', '20', '-t']
outfile = utils.get_temp_filename('out')
infile = utils.get_test_data('random-20-a.fa')
@@ -751,7 +951,7 @@ def test_oxli_build_graph():
def test_load_graph_no_tags():
- script = 'load-graph.py'
+ script = scriptpath('load-graph.py')
args = ['-x', '1e7', '-N', '2', '-k', '20', '-n']
outfile = utils.get_temp_filename('out')
@@ -773,31 +973,8 @@ def test_load_graph_no_tags():
# loading the ht file...
-def test_oxli_build_graph_no_tags():
- script = 'oxli'
- args = ['build-graph', '-x', '1e7', '-N', '2', '-k', '20', '-n']
-
- outfile = utils.get_temp_filename('out')
- infile = utils.get_test_data('random-20-a.fa')
-
- args.extend([outfile, infile])
-
- utils.runscript(script, args)
-
- ht_file = outfile + '.pt'
- assert os.path.exists(ht_file), ht_file
-
- tagset_file = outfile + '.tagset'
- assert not os.path.exists(tagset_file), tagset_file
-
- assert khmer.load_hashbits(ht_file)
-
- # can't think of a good way to make sure this worked, beyond just
- # loading the ht file...
-
-
def test_load_graph_fail():
- script = 'load-graph.py'
+ script = scriptpath('load-graph.py')
args = ['-x', '1e3', '-N', '2', '-k', '20'] # use small HT
outfile = utils.get_temp_filename('out')
@@ -810,46 +987,9 @@ def test_load_graph_fail():
assert "** ERROR: the graph structure is too small" in err
-def test_oxli_build_graph_fail():
- script = 'oxli'
- args = ['build-graph', '-x', '1e3', '-N', '2', '-k', '20'] # use small HT
-
- outfile = utils.get_temp_filename('out')
- infile = utils.get_test_data('random-20-a.fa')
-
- args.extend([outfile, infile])
-
- (status, out, err) = utils.runscript(script, args, fail_ok=True)
- assert status == 1, status
- assert "** ERROR: the graph structure is too small" in err
-
-
def test_load_graph_write_fp():
- script = 'load-graph.py'
- args = ['-x', '1e5', '-N', '2', '-k', '20'] # use small HT
-
- outfile = utils.get_temp_filename('out')
- infile = utils.get_test_data('random-20-a.fa')
-
- args.extend([outfile, infile])
-
- (status, out, err) = utils.runscript(script, args)
-
- ht_file = outfile + '.pt'
- assert os.path.exists(ht_file), ht_file
-
- info_file = outfile + '.info'
- assert os.path.exists(info_file), info_file
- data = [x.strip() for x in open(info_file)]
- data = set(data)
- assert '3959 unique k-mers' in data, data
- assert 'false positive rate estimated to be 0.002' in data
-
-
-def test_oxli_build_graph_write_fp():
- script = 'oxli'
- # use small HT
- args = ['build-graph', '-x', '1e5', '-N', '2', '-k', '20']
+ script = scriptpath('load-graph.py')
+ args = ['-x', '1e5', '-N', '2', '-k', '20', '-w'] # use small HT
outfile = utils.get_temp_filename('out')
infile = utils.get_test_data('random-20-a.fa')
@@ -870,7 +1010,7 @@ def test_oxli_build_graph_write_fp():
def test_load_graph_multithread():
- script = 'load-graph.py'
+ script = scriptpath('load-graph.py')
outfile = utils.get_temp_filename('test')
infile = utils.get_test_data('test-reads.fa')
@@ -880,46 +1020,11 @@ def test_load_graph_multithread():
(status, out, err) = utils.runscript(script, args)
-def test_oxli_build_graph_multithread():
- script = 'oxli'
-
- outfile = utils.get_temp_filename('test')
- infile = utils.get_test_data('test-reads.fa')
-
- args = ['build-graph', '-N', '4', '-x', '1e7', '-T', '8', outfile, infile]
-
- (status, out, err) = utils.runscript(script, args)
-
-
-def test_load_graph_max_memory_usage_parameter():
- script = 'load-graph.py'
- args = ['-M', '2e7', '-k', '20', '-n']
-
- outfile = utils.get_temp_filename('out')
- infile = utils.get_test_data('random-20-a.fa')
-
- args.extend([outfile, infile])
-
- (status, out, err) = utils.runscript(script, args)
-
- assert 'Total number of unique k-mers: 3960' in err, err
-
- ht_file = outfile + '.pt'
- assert os.path.exists(ht_file), ht_file
-
- try:
- ht = khmer.load_hashbits(ht_file)
- except IOError as err:
- assert 0, str(err)
-
- assert (sum(ht.hashsizes()) / 8.) < 2e7, ht.hashsizes()
-
-
def _make_graph(infilename, min_hashsize=1e7, n_hashes=2, ksize=20,
do_partition=False,
annotate_partitions=False,
stop_big_traverse=False):
- script = 'load-graph.py'
+ script = scriptpath('load-graph.py')
args = ['-x', str(min_hashsize), '-N', str(n_hashes), '-k', str(ksize)]
outfile = utils.get_temp_filename('out')
@@ -936,13 +1041,13 @@ def _make_graph(infilename, min_hashsize=1e7, n_hashes=2, ksize=20,
assert os.path.exists(tagset_file), tagset_file
if do_partition:
- script = 'partition-graph.py'
+ script = scriptpath('partition-graph.py')
args = [outfile]
if stop_big_traverse:
args.insert(0, '--no-big-traverse')
utils.runscript(script, args)
- script = 'merge-partitions.py'
+ script = scriptpath('merge-partitions.py')
args = [outfile, '-k', str(ksize)]
utils.runscript(script, args)
@@ -950,7 +1055,7 @@ def _make_graph(infilename, min_hashsize=1e7, n_hashes=2, ksize=20,
assert os.path.exists(final_pmap_file)
if annotate_partitions:
- script = 'annotate-partitions.py'
+ script = scriptpath('annotate-partitions.py')
args = ["-k", str(ksize), outfile, infilename]
in_dir = os.path.dirname(outfile)
@@ -966,7 +1071,7 @@ def _DEBUG_make_graph(infilename, min_hashsize=1e7, n_hashes=2, ksize=20,
do_partition=False,
annotate_partitions=False,
stop_big_traverse=False):
- script = 'load-graph.py'
+ script = scriptpath('load-graph.py')
args = ['-x', str(min_hashsize), '-N', str(n_hashes), '-k', str(ksize)]
outfile = utils.get_temp_filename('out')
@@ -983,15 +1088,15 @@ def _DEBUG_make_graph(infilename, min_hashsize=1e7, n_hashes=2, ksize=20,
assert os.path.exists(tagset_file), tagset_file
if do_partition:
- print(">>>> DEBUG: Partitioning <<<")
- script = 'partition-graph.py'
+ print ">>>> DEBUG: Partitioning <<<"
+ script = scriptpath('partition-graph.py')
args = [outfile]
if stop_big_traverse:
args.insert(0, '--no-big-traverse')
utils.runscript(script, args)
- print(">>>> DEBUG: Merging Partitions <<<")
- script = 'merge-partitions.py'
+ print ">>>> DEBUG: Merging Partitions <<<"
+ script = scriptpath('merge-partitions.py')
args = [outfile, '-k', str(ksize)]
utils.runscript(script, args)
@@ -999,8 +1104,8 @@ def _DEBUG_make_graph(infilename, min_hashsize=1e7, n_hashes=2, ksize=20,
assert os.path.exists(final_pmap_file)
if annotate_partitions:
- print(">>>> DEBUG: Annotating Partitions <<<")
- script = 'annotate-partitions.py'
+ print ">>>> DEBUG: Annotating Partitions <<<"
+ script = scriptpath('annotate-partitions.py')
args = ["-k", str(ksize), outfile, infilename]
in_dir = os.path.dirname(outfile)
@@ -1015,12 +1120,12 @@ def _DEBUG_make_graph(infilename, min_hashsize=1e7, n_hashes=2, ksize=20,
def test_partition_graph_1():
graphbase = _make_graph(utils.get_test_data('random-20-a.fa'))
- script = 'partition-graph.py'
+ script = scriptpath('partition-graph.py')
args = [graphbase]
utils.runscript(script, args)
- script = 'merge-partitions.py'
+ script = scriptpath('merge-partitions.py')
args = [graphbase, '-k', str(20)]
utils.runscript(script, args)
@@ -1039,12 +1144,12 @@ def test_partition_graph_nojoin_k21():
# test with K=21
graphbase = _make_graph(utils.get_test_data('random-20-a.fa'), ksize=21)
- script = 'partition-graph.py'
+ script = scriptpath('partition-graph.py')
args = [graphbase]
utils.runscript(script, args)
- script = 'merge-partitions.py'
+ script = scriptpath('merge-partitions.py')
args = [graphbase, '-k', str(21)]
utils.runscript(script, args)
@@ -1071,12 +1176,12 @@ def test_partition_graph_nojoin_stoptags():
del ht
# run script with stoptags option
- script = 'partition-graph.py'
+ script = scriptpath('partition-graph.py')
args = ['--stoptags', stoptags_file, graphbase]
utils.runscript(script, args)
- script = 'merge-partitions.py'
+ script = scriptpath('merge-partitions.py')
args = [graphbase, '-k', str(20)]
utils.runscript(script, args)
@@ -1122,22 +1227,6 @@ def test_partition_graph_no_big_traverse():
assert x[0] == 4, x # should be four partitions, broken at knot.
-def test_partition_find_knots_execute():
- graphbase = _make_graph(utils.get_test_data('random-20-a.fa'))
-
- script = 'partition-graph.py'
- args = [graphbase]
-
- utils.runscript(script, args)
-
- script = 'find-knots.py'
- args = [graphbase]
- utils.runscript(script, args)
-
- stoptags_file = graphbase + '.stoptags'
- assert os.path.exists(stoptags_file)
-
-
def test_annotate_partitions():
seqfile = utils.get_test_data('random-20-a.fa')
graphbase = _make_graph(seqfile, do_partition=True)
@@ -1147,7 +1236,7 @@ def test_annotate_partitions():
final_pmap_file = graphbase + '.pmap.merged'
assert os.path.exists(final_pmap_file)
- script = 'annotate-partitions.py'
+ script = scriptpath('annotate-partitions.py')
args = ["-k", "20", graphbase, seqfile]
utils.runscript(script, args, in_dir)
@@ -1170,7 +1259,7 @@ def test_annotate_partitions_2():
final_pmap_file = graphbase + '.pmap.merged'
assert os.path.exists(final_pmap_file)
- script = 'annotate-partitions.py'
+ script = scriptpath('annotate-partitions.py')
args = ["-k", "21", graphbase, seqfile]
utils.runscript(script, args, in_dir)
@@ -1178,7 +1267,7 @@ def test_annotate_partitions_2():
parts = [r.name.split('\t')[1] for r in screed.open(partfile)]
parts = set(parts)
- print(parts)
+ print parts
assert len(parts) == 99, len(parts)
@@ -1192,7 +1281,7 @@ def test_extract_partitions():
partfile = os.path.join(in_dir, 'random-20-a.fa.part')
# ok, now run extract-partitions.
- script = 'extract-partitions.py'
+ script = scriptpath('extract-partitions.py')
args = ['extracted', partfile]
utils.runscript(script, args, in_dir)
@@ -1221,7 +1310,7 @@ def test_extract_partitions_header_whitespace():
partfile = os.path.join(in_dir, 'test-overlap2.fa.part')
# ok, now run extract-partitions.
- script = 'extract-partitions.py'
+ script = scriptpath('extract-partitions.py')
args = ['extracted', partfile]
utils.runscript(script, args, in_dir)
@@ -1232,13 +1321,13 @@ def test_extract_partitions_header_whitespace():
assert os.path.exists(groupfile)
dist = open(distfile).readline()
- assert dist.strip() == '1 11960 11960 11960', dist.strip()
+ assert dist.strip() == '1 11957 11957 11957'
parts = [r.name.split('\t')[1]
for r in screed.open(partfile, parse_description=False)]
assert len(parts) == 13538, len(parts)
parts = set(parts)
- assert len(parts) == 12602, len(parts)
+ assert len(parts) == 12601, len(parts)
def test_extract_partitions_fq():
@@ -1251,7 +1340,7 @@ def test_extract_partitions_fq():
partfile = os.path.join(in_dir, 'random-20-a.fq.part')
# ok, now run extract-partitions.
- script = 'extract-partitions.py'
+ script = scriptpath('extract-partitions.py')
args = ['extracted', partfile]
utils.runscript(script, args, in_dir)
@@ -1291,7 +1380,7 @@ def test_extract_partitions_output_unassigned():
partfile = os.path.join(in_dir, 'random-20-a.fa.part')
# ok, now run extract-partitions.
- script = 'extract-partitions.py'
+ script = scriptpath('extract-partitions.py')
args = ['-U', 'extracted', partfile]
utils.runscript(script, args, in_dir)
@@ -1322,7 +1411,7 @@ def test_extract_partitions_no_output_groups():
partfile = os.path.join(in_dir, 'random-20-a.fq.part')
# ok, now run extract-partitions.
- script = 'extract-partitions.py'
+ script = scriptpath('extract-partitions.py')
args = ['-n', 'extracted', partfile]
# We expect a sys.exit -> we need the test to be tolerant
@@ -1341,7 +1430,7 @@ def test_extract_partitions_pid_0():
in_dir = os.path.dirname(partfile)
# ok, now run extract-partitions.
- script = 'extract-partitions.py'
+ script = scriptpath('extract-partitions.py')
args = ['-U', 'extracted', partfile]
utils.runscript(script, args, in_dir)
@@ -1366,7 +1455,7 @@ def test_extract_partitions_multi_groups():
in_dir = os.path.dirname(partfile)
# ok, now run extract-partitions.
- script = 'extract-partitions.py'
+ script = scriptpath('extract-partitions.py')
args = ['-m', '1', '-X', '1', 'extracted', partfile]
utils.runscript(script, args, in_dir)
@@ -1388,7 +1477,7 @@ def test_extract_partitions_no_groups():
in_dir = os.path.dirname(empty_file)
# ok, now run extract-partitions.
- script = 'extract-partitions.py'
+ script = scriptpath('extract-partitions.py')
args = ['extracted', empty_file]
_, _, err = utils.runscript(script, args, in_dir, fail_ok=True)
@@ -1408,27 +1497,27 @@ def test_abundance_dist():
htfile = _make_counting(infile, K=17)
- script = 'abundance-dist.py'
+ script = scriptpath('abundance-dist.py')
args = ['-z', htfile, infile, outfile]
utils.runscript(script, args, in_dir)
- with open(outfile) as fp:
- line = fp.readline().strip()
- assert line == '1 96 96 0.98', line
- line = fp.readline().strip()
- assert line == '1001 2 98 1.0', line
+ fp = iter(open(outfile))
+ line = fp.next().strip()
+ assert line == '1 96 96 0.98', line
+ line = fp.next().strip()
+ assert line == '1001 2 98 1.0', line
os.remove(outfile)
args = ['-z', '--csv', htfile, infile, outfile]
utils.runscript(script, args, in_dir)
- with open(outfile) as fp:
- line = fp.readline().strip()
- assert (line == 'abundance,count,cumulative,cumulative_fraction'), line
- line = fp.readline().strip()
- assert line == '1,96,96,0.98', line
- line = fp.readline().strip()
- assert line == '1001,2,98,1.0', line
+ fp = iter(open(outfile))
+ line = fp.next().strip()
+ assert (line == 'abundance,count,cumulative,cumulative_fraction'), line
+ line = fp.next().strip()
+ assert line == '1,96,96,0.98', line
+ line = fp.next().strip()
+ assert line == '1001,2,98,1.0', line
def test_abundance_dist_nobigcount():
@@ -1438,17 +1527,17 @@ def test_abundance_dist_nobigcount():
shutil.copyfile(utils.get_test_data('test-abund-read-2.fa'), infile)
- htfile = _make_counting(infile, K=17)
+ htfile = _make_counting(infile, K=17, BIGCOUNT=False)
- script = 'abundance-dist.py'
- args = ['-b', '-z', htfile, infile, outfile]
+ script = scriptpath('abundance-dist.py')
+ args = ['-z', htfile, infile, outfile]
utils.runscript(script, args, in_dir)
- with open(outfile) as fp:
- line = fp.readline().strip()
- assert line == '1 96 96 0.98', line
- line = fp.readline().strip()
- assert line == '255 2 98 1.0', line
+ fp = iter(open(outfile))
+ line = fp.next().strip()
+ assert line == '1 96 96 0.98', line
+ line = fp.next().strip()
+ assert line == '255 2 98 1.0', line
def test_abundance_dist_single():
@@ -1458,18 +1547,18 @@ def test_abundance_dist_single():
shutil.copyfile(utils.get_test_data('test-abund-read-2.fa'), infile)
- script = 'abundance-dist-single.py'
+ script = scriptpath('abundance-dist-single.py')
args = ['-x', '1e7', '-N', '2', '-k', '17', '-z', '-t', infile,
outfile]
(status, out, err) = utils.runscript(script, args, in_dir)
assert 'Total number of unique k-mers: 98' in err, err
- with open(outfile) as fp:
- line = fp.readline().strip()
- assert line == '1 96 96 0.98', line
- line = fp.readline().strip()
- assert line == '1001 2 98 1.0', line
+ fp = iter(open(outfile))
+ line = fp.next().strip()
+ assert line == '1 96 96 0.98', line
+ line = fp.next().strip()
+ assert line == '1001 2 98 1.0', line
def test_abundance_dist_threaded():
@@ -1479,18 +1568,18 @@ def test_abundance_dist_threaded():
shutil.copyfile(utils.get_test_data('test-abund-read-2.fa'), infile)
- script = 'abundance-dist-single.py'
+ script = scriptpath('abundance-dist-single.py')
args = ['-x', '1e7', '-N', '2', '-k', '17', '-z', '-t', '--threads', '18',
infile, outfile]
(status, out, err) = utils.runscript(script, args, in_dir)
assert 'Total number of unique k-mers: 98' in err, err
- with open(outfile) as fp:
- line = fp.readline().strip()
- assert line == '1 96 96 0.98', line
- line = fp.readline().strip()
- assert line == '1001 2 98 1.0', line
+ fp = iter(open(outfile))
+ line = fp.next().strip()
+ assert line == '1 96 96 0.98', line
+ line = fp.next().strip()
+ assert line == '1001 2 98 1.0', line
def test_abundance_dist_single_csv():
@@ -1500,18 +1589,18 @@ def test_abundance_dist_single_csv():
shutil.copyfile(utils.get_test_data('test-abund-read-2.fa'), infile)
- script = 'abundance-dist-single.py'
+ script = scriptpath('abundance-dist-single.py')
args = ['-x', '1e7', '-N', '2', '-k', '17', '-z', '--csv', infile,
outfile]
(status, out, err) = utils.runscript(script, args, in_dir)
- with open(outfile) as fp:
- line = fp.readline().strip()
- assert (line == 'abundance,count,cumulative,cumulative_fraction'), line
- line = fp.readline().strip()
- assert line == '1,96,96,0.98', line
- line = fp.readline().strip()
- assert line == '1001,2,98,1.0', line
+ fp = iter(open(outfile))
+ line = fp.next().strip()
+ assert (line == 'abundance,count,cumulative,cumulative_fraction'), line
+ line = fp.next().strip()
+ assert line == '1,96,96,0.98', line
+ line = fp.next().strip()
+ assert line == '1001,2,98,1.0', line
def test_abundance_dist_single_nobigcount():
@@ -1521,15 +1610,15 @@ def test_abundance_dist_single_nobigcount():
shutil.copyfile(utils.get_test_data('test-abund-read-2.fa'), infile)
- script = 'abundance-dist-single.py'
+ script = scriptpath('abundance-dist-single.py')
args = ['-x', '1e7', '-N', '2', '-k', '17', '-z', '-b', infile, outfile]
utils.runscript(script, args, in_dir)
- with open(outfile) as fp:
- line = fp.readline().strip()
- assert line == '1 96 96 0.98', line
- line = fp.readline().strip()
- assert line == '255 2 98 1.0', line
+ fp = iter(open(outfile))
+ line = fp.next().strip()
+ assert line == '1 96 96 0.98', line
+ line = fp.next().strip()
+ assert line == '255 2 98 1.0', line
def test_abundance_dist_single_nosquash():
@@ -1539,15 +1628,15 @@ def test_abundance_dist_single_nosquash():
shutil.copyfile(utils.get_test_data('test-abund-read-2.fa'), infile)
- script = 'abundance-dist-single.py'
+ script = scriptpath('abundance-dist-single.py')
args = ['-x', '1e7', '-N', '2', '-k', '17', '-z', '-t', infile, outfile]
utils.runscript(script, args, in_dir)
- with open(outfile) as fp:
- line = fp.readline().strip()
- assert line == '1 96 96 0.98', line
- line = fp.readline().strip()
- assert line == '1001 2 98 1.0', line
+ fp = iter(open(outfile))
+ line = fp.next().strip()
+ assert line == '1 96 96 0.98', line
+ line = fp.next().strip()
+ assert line == '1001 2 98 1.0', line
def test_abundance_dist_single_savetable():
@@ -1558,16 +1647,16 @@ def test_abundance_dist_single_savetable():
shutil.copyfile(utils.get_test_data('test-abund-read-2.fa'), infile)
- script = 'abundance-dist-single.py'
+ script = scriptpath('abundance-dist-single.py')
args = ['-x', '1e7', '-N', '2', '-k', '17', '-z', '-t', '--savetable',
tabfile, infile, outfile]
utils.runscript(script, args, in_dir)
- with open(outfile) as fp:
- line = fp.readline().strip()
- assert line == '1 96 96 0.98', line
- line = fp.readline().strip()
- assert line == '1001 2 98 1.0', line
+ fp = iter(open(outfile))
+ line = fp.next().strip()
+ assert line == '1 96 96 0.98', line
+ line = fp.next().strip()
+ assert line == '1001 2 98 1.0', line
def test_do_partition():
@@ -1575,7 +1664,7 @@ def test_do_partition():
graphbase = utils.get_temp_filename('out')
in_dir = os.path.dirname(graphbase)
- script = 'do-partition.py'
+ script = scriptpath('do-partition.py')
args = ["-k", "20", graphbase, seqfile]
utils.runscript(script, args, in_dir)
@@ -1594,7 +1683,7 @@ def test_do_partition_2():
graphbase = utils.get_temp_filename('out')
in_dir = os.path.dirname(graphbase)
- script = 'do-partition.py'
+ script = scriptpath('do-partition.py')
args = ["-k", "21", graphbase, seqfile]
utils.runscript(script, args, in_dir)
@@ -1613,7 +1702,7 @@ def test_do_partition_2_fq():
graphbase = utils.get_temp_filename('out')
in_dir = os.path.dirname(graphbase)
- script = 'do-partition.py'
+ script = scriptpath('do-partition.py')
args = ["-k", "21", graphbase, seqfile]
utils.runscript(script, args, in_dir)
@@ -1626,30 +1715,6 @@ def test_do_partition_2_fq():
assert '46 1::FIZ' in names
-def test_interleave_read_seq1_fq():
- # create input files
- infile1 = utils.get_test_data('paired-slash1.fq.1')
- infile2 = utils.get_test_data('paired-slash1.fq.2')
-
- # correct output
- ex_outfile = utils.get_test_data('paired-slash1.fq')
-
- # actual output file
- outfile = utils.get_temp_filename('out.fq')
-
- script = 'interleave-reads.py'
- args = [infile1, infile2, '-o', outfile]
-
- utils.runscript(script, args)
-
- n = 0
- for r, q in zip(screed.open(ex_outfile), screed.open(outfile)):
- n += 1
- assert r.name == q.name
- assert r.sequence == q.sequence
- assert n > 0
-
-
def test_interleave_reads_1_fq():
# test input files
infile1 = utils.get_test_data('paired.fq.1')
@@ -1661,7 +1726,7 @@ def test_interleave_reads_1_fq():
# actual output file
outfile = utils.get_temp_filename('out.fq')
- script = 'interleave-reads.py'
+ script = scriptpath('interleave-reads.py')
args = [infile1, infile2, '-o', outfile]
utils.runscript(script, args)
@@ -1680,7 +1745,7 @@ def test_interleave_reads_broken_fq():
# actual output file
outfile = utils.get_temp_filename('out.fq')
- script = 'interleave-reads.py'
+ script = scriptpath('interleave-reads.py')
args = [infile1, infile2, '-o', outfile]
status, out, err = utils.runscript(script, args, fail_ok=True)
@@ -1696,7 +1761,7 @@ def test_interleave_reads_broken_fq_2():
# actual output file
outfile = utils.get_temp_filename('out.fq')
- script = 'interleave-reads.py'
+ script = scriptpath('interleave-reads.py')
args = [infile1, infile2, '-o', outfile]
status, out, err = utils.runscript(script, args, fail_ok=True)
@@ -1712,7 +1777,7 @@ def test_interleave_reads_broken_fq_3():
# actual output file
outfile = utils.get_temp_filename('out.fq')
- script = 'interleave-reads.py'
+ script = scriptpath('interleave-reads.py')
args = [infile1, infile2, '-o', outfile]
status, out, err = utils.runscript(script, args, fail_ok=True)
@@ -1727,7 +1792,7 @@ def test_interleave_reads_broken_fq_4():
# actual output file
outfile = utils.get_temp_filename('out.fq')
- script = 'interleave-reads.py'
+ script = scriptpath('interleave-reads.py')
args = [infile1, '-o', outfile]
status, out, err = utils.runscript(script, args, fail_ok=True)
@@ -1746,7 +1811,7 @@ def test_interleave_reads_2_fa():
# actual output file
outfile = utils.get_temp_filename('out.fa')
- script = 'interleave-reads.py'
+ script = scriptpath('interleave-reads.py')
args = [infile1, infile2, '-o', outfile]
utils.runscript(script, args)
@@ -1768,8 +1833,8 @@ def test_make_initial_stoptags():
shutil.copyfile(utils.get_test_data('test-reads.fq.bz2'), bzinfile)
in_dir = os.path.dirname(bzinfile)
- genscript = 'load-graph.py'
- genscriptargs = ['test-reads', 'test-reads.fq.bz2']
+ genscript = scriptpath('load-graph.py')
+ genscriptargs = ['-t', 'test-reads', 'test-reads.fq.bz2']
utils.runscript(genscript, genscriptargs, in_dir)
# test input file gen'd by load-graphs
@@ -1782,7 +1847,7 @@ def test_make_initial_stoptags():
# actual output file
outfile1 = utils.get_temp_filename('test-reads.stoptags', in_dir)
- script = 'make-initial-stoptags.py'
+ script = scriptpath('make-initial-stoptags.py')
# make-initial-stoptags has weird file argument syntax
# read the code before modifying
args = ['test-reads']
@@ -1803,7 +1868,7 @@ def test_extract_paired_reads_1_fa():
in_dir = os.path.dirname(outfile1)
outfile2 = utils.get_temp_filename('paired-mixed.fa.se', in_dir)
- script = 'extract-paired-reads.py'
+ script = scriptpath('extract-paired-reads.py')
args = [infile]
utils.runscript(script, args, in_dir)
@@ -1838,7 +1903,7 @@ def test_extract_paired_reads_2_fq():
in_dir = os.path.dirname(outfile1)
outfile2 = utils.get_temp_filename('paired-mixed.fq.se', in_dir)
- script = 'extract-paired-reads.py'
+ script = scriptpath('extract-paired-reads.py')
args = [infile]
utils.runscript(script, args, in_dir)
@@ -1865,145 +1930,6 @@ def test_extract_paired_reads_2_fq():
assert n > 0
-def test_extract_paired_reads_3_output_dir():
- # test input file
- infile = utils.get_test_data('paired-mixed.fa')
-
- ex_outfile1 = utils.get_test_data('paired-mixed.fa.pe')
- ex_outfile2 = utils.get_test_data('paired-mixed.fa.se')
-
- # output directory
- out_dir = utils.get_temp_filename('output')
-
- script = 'extract-paired-reads.py'
- args = [infile, '-o', out_dir]
-
- utils.runscript(script, args)
-
- outfile1 = os.path.join(out_dir, 'paired-mixed.fa.pe')
- outfile2 = os.path.join(out_dir, 'paired-mixed.fa.se')
- assert os.path.exists(outfile1), outfile1
- assert os.path.exists(outfile2), outfile2
-
- n = 0
- for r, q in zip(screed.open(ex_outfile1), screed.open(outfile1)):
- n += 1
- assert r.name == q.name
- assert r.sequence == q.sequence
- assert n > 0
-
- n = 0
- for r, q in zip(screed.open(ex_outfile2), screed.open(outfile2)):
- n += 1
- assert r.name == q.name
- assert r.sequence == q.sequence
- assert n > 0
-
-
-def test_extract_paired_reads_4_output_files():
- # test input file
- infile = utils.get_test_data('paired-mixed.fa')
-
- ex_outfile1 = utils.get_test_data('paired-mixed.fa.pe')
- ex_outfile2 = utils.get_test_data('paired-mixed.fa.se')
-
- # actual output files...
- outfile1 = utils.get_temp_filename('out_pe')
- outfile2 = utils.get_temp_filename('out_se')
-
- script = 'extract-paired-reads.py'
- args = [infile, '-p', outfile1, '-s', outfile2]
-
- utils.runscript(script, args)
-
- assert os.path.exists(outfile1), outfile1
- assert os.path.exists(outfile2), outfile2
-
- n = 0
- for r, q in zip(screed.open(ex_outfile1), screed.open(outfile1)):
- n += 1
- assert r.name == q.name
- assert r.sequence == q.sequence
- assert n > 0
-
- n = 0
- for r, q in zip(screed.open(ex_outfile2), screed.open(outfile2)):
- n += 1
- assert r.name == q.name
- assert r.sequence == q.sequence
- assert n > 0
-
-
-def test_extract_paired_reads_5_stdin_error():
- script = 'extract-paired-reads.py'
- args = ['-f', '/dev/stdin']
-
- status, out, err = utils.runscript(script, args, fail_ok=True)
- assert status == 1
- assert "output filenames must be provided." in err
-
-
-def execute_extract_paired_streaming(ifilename):
- fifo = utils.get_temp_filename('fifo')
- in_dir = os.path.dirname(fifo)
- outfile1 = utils.get_temp_filename('paired.pe')
- outfile2 = utils.get_temp_filename('paired.se')
- script = 'extract-paired-reads.py'
- args = [fifo, '-p', outfile1, '-s', outfile2]
-
- # make a fifo to simulate streaming
- os.mkfifo(fifo)
-
- thread = threading.Thread(target=utils.runscript,
- args=(script, args, in_dir))
- thread.start()
- ifile = open(ifilename, 'r')
- fifofile = open(fifo, 'w')
- chunk = ifile.read(4)
- while len(chunk) > 0:
- fifofile.write(chunk)
- chunk = ifile.read(4)
- fifofile.close()
- thread.join()
- assert os.path.exists(outfile1), outfile1
- assert os.path.exists(outfile2), outfile2
-
-
-def test_extract_paired_streaming():
- testinput = utils.get_test_data('paired-mixed.fa')
- o = execute_extract_paired_streaming(testinput)
-
-
-def execute_split_paired_streaming(ifilename):
- fifo = utils.get_temp_filename('fifo')
- in_dir = os.path.dirname(fifo)
- outfile1 = utils.get_temp_filename('paired-1.fa')
- outfile2 = utils.get_temp_filename('paired-2.fa')
- script = 'split-paired-reads.py'
- args = [fifo, '-1', outfile1, '-2', outfile2]
-
- # make a fifo to simulate streaming
- os.mkfifo(fifo)
-
- thread = threading.Thread(target=utils.runscript,
- args=(script, args, in_dir))
- thread.start()
- ifile = open(ifilename, 'r')
- fifofile = open(fifo, 'w')
- chunk = ifile.read(4)
- while len(chunk) > 0:
- fifofile.write(chunk)
- chunk = ifile.read(4)
- fifofile.close()
- thread.join()
- assert os.path.exists(outfile1), outfile1
- assert os.path.exists(outfile2), outfile2
-
-
-def test_split_paired_streaming():
- o = execute_split_paired_streaming(utils.get_test_data('paired.fa'))
-
-
def test_split_paired_reads_1_fa():
# test input file
infile = utils.get_test_data('paired.fa')
@@ -2016,7 +1942,7 @@ def test_split_paired_reads_1_fa():
in_dir = os.path.dirname(outfile1)
outfile2 = utils.get_temp_filename('paired.fa.2', in_dir)
- script = 'split-paired-reads.py'
+ script = scriptpath('split-paired-reads.py')
args = [infile]
utils.runscript(script, args, in_dir)
@@ -2051,7 +1977,7 @@ def test_split_paired_reads_2_fq():
in_dir = os.path.dirname(outfile1)
outfile2 = utils.get_temp_filename('paired.fq.2', in_dir)
- script = 'split-paired-reads.py'
+ script = scriptpath('split-paired-reads.py')
args = [infile]
utils.runscript(script, args, in_dir)
@@ -2082,7 +2008,7 @@ def test_split_paired_reads_2_mixed_fq_require_pair():
shutil.copyfile(utils.get_test_data('paired-mixed.fq'), infile)
in_dir = os.path.dirname(infile)
- script = 'split-paired-reads.py'
+ script = scriptpath('split-paired-reads.py')
args = ['-p', infile]
status, out, err = utils.runscript(script, args, in_dir, fail_ok=True)
@@ -2096,7 +2022,7 @@ def test_split_paired_reads_2_mixed_fq():
shutil.copyfile(utils.get_test_data('paired-mixed-2.fq'), infile)
in_dir = os.path.dirname(infile)
- script = 'split-paired-reads.py'
+ script = scriptpath('split-paired-reads.py')
args = [infile]
status, out, err = utils.runscript(script, args, in_dir)
@@ -2110,7 +2036,7 @@ def test_split_paired_reads_2_mixed_fq_broken_pairing_format():
shutil.copyfile(utils.get_test_data('paired-mixed-broken.fq'), infile)
in_dir = os.path.dirname(infile)
- script = 'split-paired-reads.py'
+ script = scriptpath('split-paired-reads.py')
args = [infile]
status, out, err = utils.runscript(script, args, in_dir, fail_ok=True)
@@ -2130,7 +2056,7 @@ def test_split_paired_reads_3_output_dir():
output_dir = os.path.dirname(outfile1)
outfile2 = utils.get_temp_filename('paired.fq.2', output_dir)
- script = 'split-paired-reads.py'
+ script = scriptpath('split-paired-reads.py')
args = ['--output-dir', output_dir, infile]
utils.runscript(script, args)
@@ -2167,7 +2093,7 @@ def test_split_paired_reads_3_output_files():
output_dir = os.path.dirname(outfile1)
outfile2 = utils.get_temp_filename('yyy', output_dir)
- script = 'split-paired-reads.py'
+ script = scriptpath('split-paired-reads.py')
args = ['-1', outfile1, '-2', outfile2, infile]
utils.runscript(script, args)
@@ -2204,7 +2130,7 @@ def test_split_paired_reads_3_output_files_left():
output_dir = os.path.dirname(outfile1)
outfile2 = utils.get_temp_filename('paired.fq.2', output_dir)
- script = 'split-paired-reads.py'
+ script = scriptpath('split-paired-reads.py')
args = ['-o', output_dir, '-1', outfile1, infile]
utils.runscript(script, args)
@@ -2241,7 +2167,7 @@ def test_split_paired_reads_3_output_files_right():
output_dir = os.path.dirname(outfile1)
outfile2 = utils.get_temp_filename('yyy', output_dir)
- script = 'split-paired-reads.py'
+ script = scriptpath('split-paired-reads.py')
args = ['-2', outfile2, '-o', output_dir, infile]
utils.runscript(script, args)
@@ -2272,7 +2198,7 @@ def test_sample_reads_randomly():
shutil.copyfile(utils.get_test_data('test-reads.fa'), infile)
- script = 'sample-reads-randomly.py'
+ script = scriptpath('sample-reads-randomly.py')
# fix random number seed for reproducibility
args = ['-N', '10', '-M', '12000', '-R', '1']
args.append(infile)
@@ -2282,32 +2208,18 @@ def test_sample_reads_randomly():
assert os.path.exists(outfile), outfile
seqs = set([r.name for r in screed.open(outfile)])
- print(list(sorted(seqs)))
-
- if sys.version_info.major == 2:
- answer = {'850:2:1:1859:11742/1', '850:2:1:1859:11742/2',
- '850:2:1:2131:17360/1', '850:2:1:2131:17360/2',
- '850:2:1:2416:7565/1', '850:2:1:2416:7565/2',
- '850:2:1:2490:13491/1', '850:2:1:2490:13491/2',
- '850:2:1:2962:3999/1', '850:2:1:2962:3999/2',
- '850:2:1:3096:20321/1', '850:2:1:3096:20321/2',
- '850:2:1:3164:6414/1', '850:2:1:3164:6414/2',
- '850:2:1:3206:13876/1', '850:2:1:3206:13876/2',
- '850:2:1:3631:20919/1', '850:2:1:3631:20919/2',
- '850:2:1:3655:15581/1', '850:2:1:3655:15581/2'}
- else:
- answer = {'850:2:1:1257:3404/1', '850:2:1:1257:3404/2',
- '850:2:1:1362:19357/1', '850:2:1:1362:19357/2',
- '850:2:1:1396:5659/1', '850:2:1:1396:5659/2',
- '850:2:1:2063:11124/1', '850:2:1:2063:11124/2',
- '850:2:1:2121:12070/1', '850:2:1:2121:12070/2',
- '850:2:1:2528:15779/1', '850:2:1:2528:15779/2',
- '850:2:1:2581:12886/1', '850:2:1:2581:12886/2',
- '850:2:1:2864:8505/1', '850:2:1:2864:8505/2',
- '850:2:1:3000:2015/1', '850:2:1:3000:2015/2',
- '850:2:1:3302:5025/1', '850:2:1:3302:5025/2'}
-
- assert seqs == answer
+ print list(sorted(seqs))
+
+ assert seqs == set(['850:2:1:1859:11742/1', '850:2:1:1859:11742/2',
+ '850:2:1:2131:17360/1', '850:2:1:2131:17360/2',
+ '850:2:1:2416:7565/1', '850:2:1:2416:7565/2',
+ '850:2:1:2490:13491/1', '850:2:1:2490:13491/2',
+ '850:2:1:2962:3999/1', '850:2:1:2962:3999/2',
+ '850:2:1:3096:20321/1', '850:2:1:3096:20321/2',
+ '850:2:1:3164:6414/1', '850:2:1:3164:6414/2',
+ '850:2:1:3206:13876/1', '850:2:1:3206:13876/2',
+ '850:2:1:3631:20919/1', '850:2:1:3631:20919/2',
+ '850:2:1:3655:15581/1', '850:2:1:3655:15581/2'])
def test_sample_reads_randomly_force_single():
@@ -2316,7 +2228,7 @@ def test_sample_reads_randomly_force_single():
shutil.copyfile(utils.get_test_data('test-reads.fa'), infile)
- script = 'sample-reads-randomly.py'
+ script = scriptpath('sample-reads-randomly.py')
# fix random number seed for reproducibility
args = ['-N', '10', '-M', '12000', '-R', '1', '--force_single']
args.append(infile)
@@ -2326,32 +2238,17 @@ def test_sample_reads_randomly_force_single():
assert os.path.exists(outfile), outfile
seqs = set([r.name for r in screed.open(outfile)])
- print(list(sorted(seqs)))
-
- if sys.version_info.major == 2:
- answer = {'850:2:1:2399:20086/2',
- '850:2:1:2273:13309/1',
- '850:2:1:2065:16816/1',
- '850:2:1:1984:7162/2',
- '850:2:1:2691:14602/1',
- '850:2:1:1762:5439/1',
- '850:2:1:2503:4494/2',
- '850:2:1:2263:11143/2',
- '850:2:1:1792:15774/2',
- '850:2:1:2084:17145/1'}
- else:
- answer = {'850:2:1:1199:4197/1',
- '850:2:1:1251:16575/2',
- '850:2:1:1267:6790/2',
- '850:2:1:1601:4443/1',
- '850:2:1:1625:19325/1',
- '850:2:1:1832:14607/2',
- '850:2:1:1946:20852/2',
- '850:2:1:2401:4896/2',
- '850:2:1:2562:1308/1',
- '850:2:1:3123:15968/2'}
-
- assert seqs == answer
+ print list(sorted(seqs))
+ assert seqs == set(['850:2:1:2399:20086/2',
+ '850:2:1:2273:13309/1',
+ '850:2:1:2065:16816/1',
+ '850:2:1:1984:7162/2',
+ '850:2:1:2691:14602/1',
+ '850:2:1:1762:5439/1',
+ '850:2:1:2503:4494/2',
+ '850:2:1:2263:11143/2',
+ '850:2:1:1792:15774/2',
+ '850:2:1:2084:17145/1'])
def test_sample_reads_randomly_fq():
@@ -2360,7 +2257,7 @@ def test_sample_reads_randomly_fq():
shutil.copyfile(utils.get_test_data('test-reads.fq.gz'), infile)
- script = 'sample-reads-randomly.py'
+ script = scriptpath('sample-reads-randomly.py')
# fix random number seed for reproducibility
args = ['-N', '10', '-M', '12000', '-R', '1']
args.append(infile)
@@ -2369,38 +2266,25 @@ def test_sample_reads_randomly_fq():
outfile = infile + '.subset'
assert os.path.exists(outfile), outfile
- if sys.version_info.major == 2:
- answer = {'850:2:1:2399:20086/2',
- '850:2:1:1762:5439 1::FOO',
- '850:2:1:2065:16816/1',
- '850:2:1:2263:11143/2',
- '850:2:1:1792:15774/2',
- '850:2:1:2691:14602/1',
- '850:2:1:2503:4494 1::FOO',
- '850:2:1:2084:17145/1',
- '850:2:1:1984:7162 1::FOO',
- '850:2:1:2273:13309 1::FOO'}
- else:
- answer = {'850:2:1:1199:4197 1::FOO',
- '850:2:1:1251:16575/2',
- '850:2:1:1267:6790/2',
- '850:2:1:1601:4443 1::FOO',
- '850:2:1:1625:1932 1::FOO1',
- '850:2:1:1832:14607 1::FOO',
- '850:2:1:1946:20852 1::FOO',
- '850:2:1:2401:4896/2',
- '850:2:1:2562:1308/1',
- '850:2:1:3123:15968/2'}
-
seqs = set([r.name for r in screed.open(outfile,
parse_description=False)])
- print(list(sorted(seqs)))
- assert seqs == answer
+
+ print list(sorted(seqs))
+ assert seqs == set(['850:2:1:2399:20086/2',
+ '850:2:1:1762:5439 1::FOO',
+ '850:2:1:2065:16816/1',
+ '850:2:1:2263:11143/2',
+ '850:2:1:1792:15774/2',
+ '850:2:1:2691:14602/1',
+ '850:2:1:2503:4494 1::FOO',
+ '850:2:1:2084:17145/1',
+ '850:2:1:1984:7162 1::FOO',
+ '850:2:1:2273:13309 1::FOO'])
def test_fastq_to_fasta():
- script = 'fastq-to-fasta.py'
+ script = scriptpath('fastq-to-fasta.py')
clean_infile = utils.get_temp_filename('test-clean.fq')
n_infile = utils.get_temp_filename('test-n.fq')
@@ -2450,7 +2334,7 @@ def test_fastq_to_fasta():
def test_extract_long_sequences_fa():
- script = 'extract-long-sequences.py'
+ script = scriptpath('extract-long-sequences.py')
fa_infile = utils.get_temp_filename('test.fa')
shutil.copyfile(utils.get_test_data('paired-mixed.fa'), fa_infile)
@@ -2472,7 +2356,7 @@ def test_extract_long_sequences_fa():
def test_extract_long_sequences_fq():
- script = 'extract-long-sequences.py'
+ script = scriptpath('extract-long-sequences.py')
fq_infile = utils.get_temp_filename('test.fq')
shutil.copyfile(utils.get_test_data('paired-mixed.fq'), fq_infile)
@@ -2498,7 +2382,7 @@ def test_sample_reads_randomly_S():
shutil.copyfile(utils.get_test_data('test-fastq-reads.fq'), infile)
- script = 'sample-reads-randomly.py'
+ script = scriptpath('sample-reads-randomly.py')
# fix random number seed for reproducibility
args = ['-N', '10', '-R', '1', '-S', '3']
@@ -2516,63 +2400,38 @@ def test_sample_reads_randomly_S():
outfile = infile + '.subset.0'
assert os.path.exists(outfile), outfile
- seqs = set([r.name for r in screed.open(outfile, parse_description=True)])
- print(list(sorted(seqs)))
-
- print(seqs)
- if sys.version_info.major == 2:
- answer = {'895:1:1:1303:14389', '895:1:1:1347:3237',
- '895:1:1:1295:6189', '895:1:1:1308:20421',
- '895:1:1:1320:11648', '895:1:1:1352:5369',
- '895:1:1:1318:10532', '895:1:1:1363:11839',
- '895:1:1:1355:13535', '895:1:1:1349:15165'}
- else:
- answer = {'895:1:1:1290:11501', '895:1:1:1303:14389',
- '895:1:1:1307:4308', '895:1:1:1308:2539',
- '895:1:1:1331:1766', '895:1:1:1333:2512',
- '895:1:1:1347:3237', '895:1:1:1363:11839',
- '895:1:1:1378:18986', '895:1:1:1383:3089'}
-
- assert seqs == answer
+ seqs = set([r.name for r in screed.open(outfile)])
+ print list(sorted(seqs))
+
+ assert seqs == set(['895:1:1:1303:14389', '895:1:1:1347:3237',
+ '895:1:1:1295:6189', '895:1:1:1308:20421',
+ '895:1:1:1320:11648', '895:1:1:1352:5369',
+ '895:1:1:1318:10532', '895:1:1:1363:11839',
+ '895:1:1:1355:13535', '895:1:1:1349:15165'])
outfile = infile + '.subset.1'
assert os.path.exists(outfile), outfile
- seqs = set([r.name for r in screed.open(outfile, parse_description=True)])
- print(list(sorted(seqs)))
-
- if sys.version_info.major == 2:
- answer = set(['895:1:1:1303:14389', '895:1:1:1373:4848',
- '895:1:1:1357:19736', '895:1:1:1347:3237',
- '895:1:1:1338:7557', '895:1:1:1388:11093',
- '895:1:1:1296:1784', '895:1:1:1290:11501',
- '895:1:1:1355:13535', '895:1:1:1303:6251'])
- else:
- answer = {'895:1:1:1255:18861', '895:1:1:1276:16426',
- '895:1:1:1303:6251', '895:1:1:1308:20421',
- '895:1:1:1314:10430', '895:1:1:1351:14718',
- '895:1:1:1355:13535', '895:1:1:1358:4953',
- '895:1:1:1362:3983', '895:1:1:1363:9988'}
- assert seqs == answer
-
- seqs = set([r.name for r in screed.open(outfile, parse_description=True)])
- print(list(sorted(seqs)))
-
- if sys.version_info.major == 2:
- answer = {'895:1:1:1303:14389', '895:1:1:1373:4848',
- '895:1:1:1357:19736', '895:1:1:1347:3237',
- '895:1:1:1338:7557', '895:1:1:1388:11093',
- '895:1:1:1296:1784', '895:1:1:1290:11501',
- '895:1:1:1355:13535', '895:1:1:1303:6251'}
-
- else:
- answer = {'895:1:1:1362:3983', '895:1:1:1363:9988',
- '895:1:1:1314:10430', '895:1:1:1255:18861',
- '895:1:1:1308:20421', '895:1:1:1358:4953',
- '895:1:1:1351:14718', '895:1:1:1303:6251',
- '895:1:1:1276:16426', '895:1:1:1355:13535'}
-
- assert seqs == answer
+ seqs = set([r.name for r in screed.open(outfile)])
+ print list(sorted(seqs))
+
+ assert seqs == set(['895:1:1:1303:14389', '895:1:1:1373:4848',
+ '895:1:1:1357:19736', '895:1:1:1347:3237',
+ '895:1:1:1338:7557', '895:1:1:1388:11093',
+ '895:1:1:1296:1784', '895:1:1:1290:11501',
+ '895:1:1:1355:13535', '895:1:1:1303:6251'])
+
+ outfile = infile + '.subset.2'
+ assert os.path.exists(outfile), outfile
+
+ seqs = set([r.name for r in screed.open(outfile)])
+ print list(sorted(seqs))
+
+ assert seqs == set(['895:1:1:1298:13380', '895:1:1:1348:18672',
+ '895:1:1:1309:4153', '895:1:1:1252:19493',
+ '895:1:1:1368:4434', '895:1:1:1348:1257',
+ '895:1:1:1383:3089', '895:1:1:1355:13535',
+ '895:1:1:1303:6251', '895:1:1:1349:15165'])
def test_count_overlap_invalid_datafile():
@@ -2581,14 +2440,11 @@ def test_count_overlap_invalid_datafile():
shutil.copy(utils.get_test_data('test-overlap1.fa'), seqfile1)
htfile = _make_graph(seqfile1, ksize=20)
outfile = utils.get_temp_filename('overlap.out', in_dir)
- script = 'count-overlap.py'
- args = ['--ksize', '20', '--n_tables', '2', '--max-tablesize', '10000000',
+ script = scriptpath('count-overlap.py')
+ args = ['--ksize', '20', '--n_tables', '2', '--min-tablesize', '10000000',
htfile + '.pt', htfile + '.pt', outfile]
(status, out, err) = utils.runscript(script, args, in_dir, fail_ok=True)
- if sys.version_info.major == 2:
- assert "IOError" in err
- else:
- assert "OSError" in err
+ assert "IOError" in err
def test_count_overlap():
@@ -2600,22 +2456,22 @@ def test_count_overlap():
shutil.copy(utils.get_test_data('test-overlap1.fa'), seqfile1)
shutil.copy(utils.get_test_data('test-overlap2.fa'), seqfile2)
htfile = _make_graph(seqfile1, ksize=20)
- script = 'count-overlap.py'
- args = ['--ksize', '20', '--n_tables', '2', '--max-tablesize', '10000000',
+ script = scriptpath('count-overlap.py')
+ args = ['--ksize', '20', '--n_tables', '2', '--min-tablesize', '10000000',
htfile + '.pt', seqfile2, outfile]
(status, out, err) = utils.runscript(script, args, in_dir)
assert status == 0
assert os.path.exists(outfile), outfile
data = [x.strip() for x in open(outfile)]
data = set(data)
- assert '# of unique k-mers in dataset2: 759020' in data, data
- assert '# of overlap unique k-mers: 245547' in data
+ assert '# of unique k-mers in dataset2: 759047' in data
+ assert '# of overlap unique k-mers: 245621' in data
assert os.path.exists(curvefile), curvefile
data = [x.strip() for x in open(curvefile)]
data = set(data)
- assert '178630 1134' in data, data
- assert '496280 2904' in data
- assert '752031 238558' in data
+ assert '178633 1155' in data
+ assert '496285 2970' in data
+ assert '752053 238627' in data
def test_count_overlap_csv():
@@ -2627,22 +2483,22 @@ def test_count_overlap_csv():
shutil.copy(utils.get_test_data('test-overlap1.fa'), seqfile1)
shutil.copy(utils.get_test_data('test-overlap2.fa'), seqfile2)
htfile = _make_graph(seqfile1, ksize=20)
- script = 'count-overlap.py'
- args = ['--ksize', '20', '--n_tables', '2', '--max-tablesize',
+ script = scriptpath('count-overlap.py')
+ args = ['--ksize', '20', '--n_tables', '2', '--min-tablesize',
'10000000', '--csv', htfile + '.pt', seqfile2, outfile]
(status, out, err) = utils.runscript(script, args, in_dir)
assert status == 0
assert os.path.exists(outfile), outfile
data = [x.strip() for x in open(outfile)]
data = set(data)
- assert '# of unique k-mers in dataset2: 759020' in data
- assert '# of overlap unique k-mers: 245547' in data
+ assert '# of unique k-mers in dataset2: 759047' in data
+ assert '# of overlap unique k-mers: 245621' in data
assert os.path.exists(curvefile), curvefile
data = [x.strip() for x in open(curvefile)]
data = set(data)
- assert '178630,1134' in data, data
- assert '496280,2904' in data
- assert '752031,238558' in data
+ assert '178633,1155' in data
+ assert '496285,2970' in data
+ assert '752053,238627' in data
def execute_streaming_diginorm(ifilename):
@@ -2654,7 +2510,7 @@ def execute_streaming_diginorm(ifilename):
# Get temp filenames, etc.
fifo = utils.get_temp_filename('fifo')
in_dir = os.path.dirname(fifo)
- script = 'normalize-by-median.py'
+ script = scriptpath('normalize-by-median.py')
args = ['-C', '1', '-k', '17', '-o', 'outfile', fifo]
# make a fifo to simulate streaming
@@ -2687,8 +2543,8 @@ def execute_load_graph_streaming(filename):
This is not directly executed but is run by the tests themselves
'''
- script = 'load-graph.py'
- args = '-x 1e7 -N 2 -k 20 out -'
+ script = scriptpath('load-graph.py')
+ args = '-x 1e7 -N 2 -k 20 -t out -'
infile = utils.get_temp_filename('temp')
in_dir = os.path.dirname(infile)
@@ -2697,9 +2553,9 @@ def execute_load_graph_streaming(filename):
if status != 0:
for line in out:
- print(out)
+ print out
for line in err:
- print(err)
+ print err
assert status == 0, status
err.seek(0)
err = err.read()
@@ -2722,6 +2578,7 @@ def execute_load_graph_streaming(filename):
assert x == (1, 0), x
+ at attr('known_failing')
def test_screed_streaming_ufa():
# uncompressed fa
o = execute_streaming_diginorm(utils.get_test_data('test-abund-read-2.fa'))
@@ -2732,6 +2589,7 @@ def test_screed_streaming_ufa():
assert seqs[0].startswith('GGTTGACGGGGCTCAGGGGG')
+ at attr('known_failing')
def test_screed_streaming_ufq():
# uncompressed fq
o = execute_streaming_diginorm(utils.get_test_data('test-fastq-reads.fq'))
@@ -2740,6 +2598,7 @@ def test_screed_streaming_ufq():
assert seqs[0].startswith('CAGGCGCCCACCACCGTGCCCTCCAACCTGATGGT')
+ at attr('known_failing')
def test_screed_streaming_bzipfq():
# bzip compressed fq
o = execute_streaming_diginorm(utils.get_test_data('100-reads.fq.bz2'))
@@ -2748,6 +2607,7 @@ def test_screed_streaming_bzipfq():
assert seqs[0].startswith('CAGGCGCCCACCACCGTGCCCTCCAACCTGATGGT'), seqs
+ at attr('known_failing')
def test_screed_streaming_bzipfa():
# bzip compressed fa
o = execute_streaming_diginorm(
@@ -3070,15 +2930,15 @@ def test_trim_low_abund_trimtest():
for record in screed.open(outfile):
if record.name == 'seqtrim/1':
- print(record.name, record.sequence)
+ print record.name, record.sequence
assert record.sequence == \
'GGTTGACGGGGCTCAGGGGGCGGCTGACTCCGAGAGACAGCAGCC'
elif record.name == 'seqtrim/2':
- print(record.name, record.sequence)
+ print record.name, record.sequence
assert record.sequence == \
'GGTTGACGGGGCTCAGGGGGCGGCTGACTCCGAGAGACAGCAGCCGC'
elif record.name == 'seqtrim2/1':
- print(record.name, record.sequence)
+ print record.name, record.sequence
assert record.sequence == \
'GGTTGACGGGGCTCAGGGGGCGGCTGACTCCGAGAGACAGCA'
@@ -3102,15 +2962,15 @@ def test_trim_low_abund_trimtest_after_load():
for record in screed.open(outfile):
if record.name == 'seqtrim/1':
- print(record.name, record.sequence)
+ print record.name, record.sequence
assert record.sequence == \
'GGTTGACGGGGCTCAGGGGGCGGCTGACTCCGAGAGACAGCAGCC'
elif record.name == 'seqtrim/2':
- print(record.name, record.sequence)
+ print record.name, record.sequence
assert record.sequence == \
'GGTTGACGGGGCTCAGGGGGCGGCTGACTCCGAGAGACAGCAGCCGC'
elif record.name == 'seqtrim2/1':
- print(record.name, record.sequence)
+ print record.name, record.sequence
assert record.sequence == \
'GGTTGACGGGGCTCAGGGGGCGGCTGACTCCGAGAGACAGCA'
@@ -3133,15 +2993,15 @@ def test_trim_low_abund_trimtest_savetable():
for record in screed.open(outfile):
if record.name == 'seqtrim/1':
- print(record.name, record.sequence)
+ print record.name, record.sequence
assert record.sequence == \
'GGTTGACGGGGCTCAGGGGGCGGCTGACTCCGAGAGACAGCAGCC'
elif record.name == 'seqtrim/2':
- print(record.name, record.sequence)
+ print record.name, record.sequence
assert record.sequence == \
'GGTTGACGGGGCTCAGGGGGCGGCTGACTCCGAGAGACAGCAGCCGC'
elif record.name == 'seqtrim2/1':
- print(record.name, record.sequence)
+ print record.name, record.sequence
assert record.sequence == \
'GGTTGACGGGGCTCAGGGGGCGGCTGACTCCGAGAGACAGCA'
diff --git a/tests/test_subset_graph.py b/tests/test_subset_graph.py
index b5a4209..97f9ba6 100644
--- a/tests/test_subset_graph.py
+++ b/tests/test_subset_graph.py
@@ -1,8 +1,6 @@
-from __future__ import print_function
-from __future__ import absolute_import
#
-# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
-# Copyright (C) Michigan State University, 2009-2015. It is licensed under
+# This file is part of khmer, http://github.com/ged-lab/khmer/, and is
+# Copyright (C) Michigan State University, 2009-2013. It is licensed under
# the three-clause BSD license; see LICENSE.
# Contact: khmer-project at idyll.org
#
@@ -10,8 +8,8 @@ from __future__ import absolute_import
import khmer
import screed
+import khmer_tst_utils as utils
import os
-from . import khmer_tst_utils as utils
def teardown():
@@ -21,7 +19,7 @@ def teardown():
class Test_RandomData(object):
def test_3_merge_013(self):
- ht = khmer.Hashbits(20, 4 ** 4 + 1, 2)
+ ht = khmer.new_hashbits(20, 4 ** 4 + 1)
filename = utils.get_test_data('test-graph2.fa')
@@ -43,7 +41,7 @@ class Test_RandomData(object):
assert n_partitions == 1, n_partitions # combined.
def test_3_merge_023(self):
- ht = khmer.Hashbits(20, 4 ** 4 + 1, 2)
+ ht = khmer.new_hashbits(20, 4 ** 4 + 1)
filename = utils.get_test_data('test-graph2.fa')
(total_reads, total_kmers) = ht.consume_fasta_and_tag(filename)
@@ -64,7 +62,7 @@ class Test_RandomData(object):
assert n_partitions == 1, n_partitions # combined.
def test_5_merge_046(self):
- ht = khmer.Hashbits(20, 4 ** 4 + 1, 2)
+ ht = khmer.new_hashbits(20, 4 ** 4 + 1)
filename = utils.get_test_data('test-graph5.fa')
(total_reads, total_kmers) = ht.consume_fasta_and_tag(filename)
@@ -83,7 +81,7 @@ class Test_RandomData(object):
assert n_partitions == 1, n_partitions # combined.
def test_random_20_a_succ(self):
- ht = khmer.Hashbits(20, 4 ** 7 + 1, 2)
+ ht = khmer.new_hashbits(20, 4 ** 7 + 1)
filename = utils.get_test_data('random-20-a.fa')
outfile = utils.get_temp_filename('out')
@@ -102,7 +100,7 @@ class Test_RandomData(object):
assert n_partitions == 1, n_partitions
def test_random_20_a_succ_II(self):
- ht = khmer.Hashbits(20, 4 ** 7 + 1, 2)
+ ht = khmer.new_hashbits(20, 4 ** 7 + 1)
filename = utils.get_test_data('random-20-a.fa')
outfile = utils.get_temp_filename('out')
@@ -121,7 +119,7 @@ class Test_RandomData(object):
assert n_partitions == 1, n_partitions
def test_random_20_a_succ_III(self):
- ht = khmer.Hashbits(20, 4 ** 7 + 1, 2)
+ ht = khmer.new_hashbits(20, 4 ** 7 + 1)
filename = utils.get_test_data('random-20-a.fa')
outfile = utils.get_temp_filename('out')
@@ -144,7 +142,7 @@ class Test_RandomData(object):
assert n_partitions == 1, n_partitions
def test_random_20_a_succ_IV(self):
- ht = khmer.Hashbits(20, 4 ** 7 + 1, 2)
+ ht = khmer.new_hashbits(20, 4 ** 7 + 1)
filename = utils.get_test_data('random-20-a.fa')
outfile = utils.get_temp_filename('out')
@@ -164,7 +162,7 @@ class Test_RandomData(object):
assert n_partitions == 1, n_partitions
def test_random_20_a_succ_IV_save(self):
- ht = khmer.Hashbits(20, 4 ** 7 + 1, 2)
+ ht = khmer.new_hashbits(20, 4 ** 7 + 1)
filename = utils.get_test_data('random-20-a.fa')
savefile_ht = utils.get_temp_filename('ht')
@@ -177,7 +175,7 @@ class Test_RandomData(object):
ht.save_tagset(savefile_tags)
del ht
- ht = khmer.Hashbits(20, 4 ** 7 + 1, 2)
+ ht = khmer.new_hashbits(20, 4 ** 7 + 1)
ht.load(savefile_ht)
ht.load_tagset(savefile_tags)
@@ -200,15 +198,15 @@ class Test_RandomData(object):
class Test_SaveLoadPmap(object):
def test_save_load_merge(self):
- ht = khmer.Hashbits(20, 4 ** 4 + 1, 2)
+ ht = khmer.new_hashbits(20, 4 ** 4 + 1)
filename = utils.get_test_data('test-graph2.fa')
(total_reads, total_kmers) = ht.consume_fasta_and_tag(filename)
assert total_reads == 3, total_reads
divvy = ht.divide_tags_into_subsets(1)
- print(divvy)
- assert len(divvy) == 3
+ print divvy
+ assert len(divvy) is 3
(a, b, c) = divvy
outfile1 = utils.get_temp_filename('x.pmap')
@@ -232,45 +230,8 @@ class Test_SaveLoadPmap(object):
n_partitions = ht.output_partitions(filename, outfile)
assert n_partitions == 1, n_partitions # combined.
- def test_save_load_merge_truncate(self):
- ht = khmer.Hashbits(20, 4 ** 4 + 1, 2)
- filename = utils.get_test_data('test-graph2.fa')
-
- (total_reads, total_kmers) = ht.consume_fasta_and_tag(filename)
- assert total_reads == 3, total_reads
-
- divvy = ht.divide_tags_into_subsets(1)
- print(divvy)
- assert len(divvy) is 3
- (a, b, c) = divvy
-
- outfile1 = utils.get_temp_filename('x.pmap')
- outfile2 = utils.get_temp_filename('y.pmap')
-
- x = ht.do_subset_partition(a, b)
- ht.save_subset_partitionmap(x, outfile1)
- del x
-
- y = ht.do_subset_partition(b, 0)
- ht.save_subset_partitionmap(y, outfile2)
- del y
-
- outfile3 = utils.get_temp_filename('z.pmap')
- data = open(outfile1, 'rb').read()
-
- for i in range(len(data)):
- fp = open(outfile3, 'wb')
- fp.write(data[:i])
- fp.close()
-
- try:
- a = ht.load_subset_partitionmap(outfile3)
- assert 0, "this should not pass"
- except IOError as err:
- print(str(err), i)
-
def test_save_load_merge_2(self):
- ht = khmer.Hashbits(20, 4 ** 8 + 1, 2)
+ ht = khmer.new_hashbits(20, 4 ** 8 + 1)
filename = utils.get_test_data('random-20-a.fa')
(total_reads, total_kmers) = ht.consume_fasta_and_tag(filename)
@@ -302,22 +263,23 @@ class Test_SaveLoadPmap(object):
assert n_partitions == 1, n_partitions # combined.
def test_save_load_merge_nexist(self):
- ht = khmer._Hashbits(20, [1])
+ ht = khmer.new_hashbits(20, 1)
try:
a = ht.load_subset_partitionmap('this does not exist')
assert 0, "this should not succeed"
except IOError as e:
- print(str(e))
+ print str(e)
def test_save_merge_from_disk(self):
- ht = khmer.Hashbits(20, 4 ** 4 + 1, 2)
+ ht = khmer.new_hashbits(20, 4 ** 4 + 1)
filename = utils.get_test_data('test-graph2.fa')
(total_reads, total_kmers) = ht.consume_fasta_and_tag(filename)
assert total_reads == 3, total_reads
divvy = ht.divide_tags_into_subsets(1)
- print(divvy)
+ print divvy
+ assert len(divvy) is 3
(a, b, c) = divvy
outfile1 = utils.get_temp_filename('x.pmap')
@@ -339,7 +301,7 @@ class Test_SaveLoadPmap(object):
assert n_partitions == 1, n_partitions # combined.
def test_save_merge_from_disk_2(self):
- ht = khmer.Hashbits(20, 4 ** 7 + 1, 2)
+ ht = khmer.new_hashbits(20, 4 ** 7 + 1)
filename = utils.get_test_data('random-20-a.fa')
(total_reads, total_kmers) = ht.consume_fasta_and_tag(filename)
@@ -368,14 +330,15 @@ class Test_SaveLoadPmap(object):
assert n_partitions == 1, n_partitions # combined.
def test_save_merge_from_disk_file_not_exist(self):
- ht = khmer.Hashbits(20, 4 ** 4 + 1, 2)
+ ht = khmer.new_hashbits(20, 4 ** 4 + 1)
filename = utils.get_test_data('test-graph2.fa')
(total_reads, total_kmers) = ht.consume_fasta_and_tag(filename)
assert total_reads == 3, total_reads
divvy = ht.divide_tags_into_subsets(1)
- print(divvy)
+ print divvy
+ assert len(divvy) is 3
(a, b, c) = divvy
outfile1 = utils.get_temp_filename('x.pmap')
@@ -386,37 +349,38 @@ class Test_SaveLoadPmap(object):
ht.merge_subset_from_disk(outfile1)
assert 0, "this should fail"
except IOError as e:
- print(str(e))
+ print str(e)
def test_merge_from_disk_file_bad_type(self):
- ht = khmer.Hashbits(20, 4 ** 4 + 1, 2)
+ ht = khmer.new_hashbits(20, 4 ** 4 + 1)
infile = utils.get_test_data('goodversion-k12.ht')
try:
ht.merge_subset_from_disk(infile)
assert 0, "this should fail"
except IOError as e:
- print(str(e))
+ print str(e)
def test_merge_from_disk_file_version(self):
- ht = khmer.Hashbits(20, 4 ** 4 + 1, 2)
+ ht = khmer.new_hashbits(20, 4 ** 4 + 1)
infile = utils.get_test_data('badversion-k12.ht')
try:
ht.merge_subset_from_disk(infile)
assert 0, "this should fail"
except IOError as e:
- print(str(e))
+ print str(e)
def test_save_merge_from_disk_ksize(self):
- ht = khmer.Hashbits(20, 4 ** 4 + 1, 2)
+ ht = khmer.new_hashbits(20, 4 ** 4 + 1)
filename = utils.get_test_data('test-graph2.fa')
(total_reads, total_kmers) = ht.consume_fasta_and_tag(filename)
assert total_reads == 3, total_reads
divvy = ht.divide_tags_into_subsets(1)
- print(divvy)
+ print divvy
+ assert len(divvy) is 3
(a, b, c) = divvy
outfile1 = utils.get_temp_filename('x.pmap')
@@ -424,89 +388,18 @@ class Test_SaveLoadPmap(object):
ht.save_subset_partitionmap(x, outfile1)
del x
- ht = khmer._Hashbits(19, [1])
+ ht = khmer.new_hashbits(19, 1, 1)
try:
ht.merge_subset_from_disk(outfile1)
assert 0, "this should fail"
except IOError as e:
- print(str(e))
-
-
-def test_save_load_merge_on_graph():
- ht = khmer.Hashbits(20, 4 ** 4 + 1, 2)
- filename = utils.get_test_data('test-graph2.fa')
-
- (total_reads, total_kmers) = ht.consume_fasta_and_tag(filename)
- assert total_reads == 3, total_reads
-
- divvy = ht.divide_tags_into_subsets(1)
- print(divvy)
- assert len(divvy) is 3
- (a, b, c) = divvy
-
- outfile1 = utils.get_temp_filename('x.pmap')
- outfile2 = utils.get_temp_filename('y.pmap')
-
- x = ht.do_subset_partition(a, b)
- ht.save_subset_partitionmap(x, outfile1)
- del x
-
- y = ht.do_subset_partition(b, 0)
- ht.save_subset_partitionmap(y, outfile2)
- del y
-
- a = ht.load_partitionmap(outfile1) # <-- this is different
- b = ht.load_subset_partitionmap(outfile2)
-
- ht.merge_subset(b)
-
- outfile = utils.get_temp_filename('out.part')
- n_partitions = ht.output_partitions(filename, outfile)
- assert n_partitions == 1, n_partitions # combined.
-
-
-def test_save_load_on_graph_truncate():
- ht = khmer.Hashbits(20, 4 ** 4 + 1, 2)
- filename = utils.get_test_data('test-graph2.fa')
-
- (total_reads, total_kmers) = ht.consume_fasta_and_tag(filename)
- assert total_reads == 3, total_reads
-
- divvy = ht.divide_tags_into_subsets(1)
- print(divvy)
- assert len(divvy) is 3
- (a, b, c) = divvy
-
- outfile1 = utils.get_temp_filename('x.pmap')
- outfile2 = utils.get_temp_filename('y.pmap')
-
- x = ht.do_subset_partition(a, b)
- ht.save_subset_partitionmap(x, outfile1)
- del x
-
- y = ht.do_subset_partition(b, 0)
- ht.save_subset_partitionmap(y, outfile2)
- del y
-
- outfile3 = utils.get_temp_filename('z.pmap')
- data = open(outfile1, 'rb').read()
-
- for i in range(len(data)):
- fp = open(outfile3, 'wb')
- fp.write(data[:i])
- fp.close()
-
- try:
- a = ht.load_partitionmap(outfile3)
- assert 0, "this should not pass"
- except IOError as err:
- print(str(err), i)
+ print str(e)
def test_output_partitions():
filename = utils.get_test_data('test-output-partitions.fa')
- ht = khmer._Hashbits(10, [1])
+ ht = khmer.new_hashbits(10, 1, 1)
ht.set_partition_id('TTAGGACTGC', 2)
ht.set_partition_id('TGCGTTTCAA', 3)
ht.set_partition_id('ATACTGTAAA', 4)
@@ -531,7 +424,7 @@ test_output_partitions.runme = True
def test_tiny_real_partitions():
filename = utils.get_test_data('real-partition-tiny.fa')
- ht = khmer.Hashbits(32, 8e2, 4)
+ ht = khmer.new_hashbits(32, 8e1, 4)
ht.consume_fasta_and_tag(filename)
subset = ht.do_subset_partition(0, 0)
@@ -558,7 +451,7 @@ def test_tiny_real_partitions():
def test_small_real_partitions():
filename = utils.get_test_data('real-partition-small.fa')
- ht = khmer.Hashbits(32, 2e3, 4)
+ ht = khmer.new_hashbits(32, 2e2, 4)
ht.consume_fasta_and_tag(filename)
subset = ht.do_subset_partition(0, 0)
@@ -598,14 +491,14 @@ CCTCGGGCCTTTCCGTTCCGTTGCCGCCCAAGCTCTCTAGCATCGAATCGGTCAAGCGGT\
def test_partition_on_abundance_1():
- print((a,))
- print((b,))
- kh = khmer.CountingHash(20, 1e3, 4)
+ print(a,)
+ print(b,)
+ kh = khmer.new_counting_hash(20, 1e3, 4)
for i in range(10):
- print(kh.consume_and_tag(a))
+ print kh.consume_and_tag(a)
for i in range(10):
- print(kh.consume_and_tag(b))
+ print kh.consume_and_tag(b)
# all paths in 'a' and 'b'
p = kh.do_subset_partition_with_abundance(10, 50)
@@ -614,12 +507,12 @@ def test_partition_on_abundance_1():
def test_partition_on_abundance_2():
- kh = khmer.CountingHash(20, 1e3, 4)
+ kh = khmer.new_counting_hash(20, 1e3, 4)
for i in range(10):
- print(kh.consume_and_tag(a))
+ print kh.consume_and_tag(a)
for i in range(5):
- print(kh.consume_and_tag(b))
+ print kh.consume_and_tag(b)
# all paths in 'a'
p = kh.do_subset_partition_with_abundance(10, 50)
@@ -628,12 +521,12 @@ def test_partition_on_abundance_2():
def test_partition_on_abundance_3():
- kh = khmer.CountingHash(20, 1e4, 4)
+ kh = khmer.new_counting_hash(20, 1e4, 4)
for i in range(10):
- print(kh.consume_and_tag(a))
+ print kh.consume_and_tag(a)
for i in range(5):
- print(kh.consume_and_tag(b))
+ print kh.consume_and_tag(b)
# this will get paths only in 'a'
p = kh.do_subset_partition_with_abundance(10, 50)
@@ -642,12 +535,12 @@ def test_partition_on_abundance_3():
p = kh.do_subset_partition_with_abundance(5, 10)
x = p.count_partitions()
- print(x)
+ print x
assert x == (2, 2) # two partitions, two ignored tags
def test_partition_overlap_1():
- kh = khmer.CountingHash(20, 1e3, 4)
+ kh = khmer.new_counting_hash(20, 1e3, 4)
for i in range(10):
kh.consume_and_tag(a)
@@ -668,7 +561,7 @@ def test_partition_overlap_1():
def test_partition_overlap_2():
- kh = khmer.CountingHash(20, 1e4, 4)
+ kh = khmer.new_counting_hash(20, 1e4, 4)
for i in range(10):
kh.consume_and_tag(a)
diff --git a/tests/test_threaded_sequence_processor.py b/tests/test_threaded_sequence_processor.py
index 854a3fc..5aac0f4 100644
--- a/tests/test_threaded_sequence_processor.py
+++ b/tests/test_threaded_sequence_processor.py
@@ -1,16 +1,11 @@
import sys
from khmer.thread_utils import ThreadedSequenceProcessor, SequenceGroup
-from io import StringIO
+from cStringIO import StringIO
from screed.fasta import fasta_iter
from screed.fastq import fastq_iter
+import Queue
from nose.plugins.attrib import attr
-# stdlib queue module was renamed on Python 3
-try:
- import queue
-except ImportError:
- import Queue as queue
-
def load_records(stringio_fp):
records = list(fasta_iter(StringIO(stringio_fp.getvalue())))
@@ -116,7 +111,7 @@ def test_paired_2thread():
while not self.done or not inq.empty():
try:
g = inq.get(True, 1)
- except queue.Empty:
+ except Queue.Empty:
continue
assert len(g.seqlist) == 2
@@ -165,7 +160,7 @@ def test_paired_2thread_more_seq():
while not self.done or not inq.empty():
try:
g = inq.get(True, 1)
- except queue.Empty:
+ except Queue.Empty:
continue
if len(g.seqlist) == 2:
diff --git a/tests/test_version.py b/tests/test_version.py
index f8a8901..775edbe 100644
--- a/tests/test_version.py
+++ b/tests/test_version.py
@@ -1,7 +1,6 @@
-from __future__ import print_function, unicode_literals
#
-# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
-# Copyright (C) Michigan State University, 2014-2015. It is licensed under
+# This file is part of khmer, http://github.com/ged-lab/khmer/, and is
+# Copyright (C) Michigan State University, 2014. It is licensed under
# the three-clause BSD license; see LICENSE.
# Contact: khmer-project at idyll.org
#
@@ -13,8 +12,8 @@ from nose.plugins.attrib import attr
def test_python_and_c_match():
# checks c++ compiler option version against versioneer version
# (respectively)
- print('c++ version {0}:'.format(khmer.__version_cpp__()))
- print('versioneer (python) version: {0}'.format(khmer.__version__))
+ print 'c++ version {0}:'.format(khmer.__version_cpp__())
+ print 'versioneer (python) version: {0}'.format(khmer.__version__)
assert khmer.__version_cpp__() == khmer.__version__
@@ -23,9 +22,9 @@ def test_python_and_c_match_base():
# it's a hash based on git commits which can get out-of-sync too easily
cppver = '-'.join(khmer.__version_cpp__().split('-')[0:2])
pyver = '-'.join(khmer.__version__.split('-')[0:2])
- print('c++ version {0}'.format(cppver))
- print('python version: {0}'.format(pyver))
- print('if you are seeing this, the version compiled into your cpp')
- print('objects and your versioneer stuff is out-of-sync.')
- print('try doing: make clean; make')
+ print 'c++ version {0}'.format(cppver)
+ print 'python version: {0}'.format(pyver)
+ print 'if you are seeing this, the version compiled into your cpp'
+ print 'objects and your versioneer stuff is out-of-sync.'
+ print 'try doing: make clean; make'
assert cppver == pyver
diff --git a/third-party/bzip2/.gitignore b/third-party/bzip2/.gitignore
deleted file mode 100644
index 0dadbab..0000000
--- a/third-party/bzip2/.gitignore
+++ /dev/null
@@ -1,2 +0,0 @@
-bzip2-shared
-libbz2.so.*
diff --git a/third-party/bzip2/CHANGES b/third-party/bzip2/CHANGES
deleted file mode 100644
index 81e97ca..0000000
--- a/third-party/bzip2/CHANGES
+++ /dev/null
@@ -1,327 +0,0 @@
- ------------------------------------------------------------------
- This file is part of bzip2/libbzip2, a program and library for
- lossless, block-sorting data compression.
-
- bzip2/libbzip2 version 1.0.6 of 6 September 2010
- Copyright (C) 1996-2010 Julian Seward <jseward at bzip.org>
-
- Please read the WARNING, DISCLAIMER and PATENTS sections in the
- README file.
-
- This program is released under the terms of the license contained
- in the file LICENSE.
- ------------------------------------------------------------------
-
-
-0.9.0
-~~~~~
-First version.
-
-
-0.9.0a
-~~~~~~
-Removed 'ranlib' from Makefile, since most modern Unix-es
-don't need it, or even know about it.
-
-
-0.9.0b
-~~~~~~
-Fixed a problem with error reporting in bzip2.c. This does not effect
-the library in any way. Problem is: versions 0.9.0 and 0.9.0a (of the
-program proper) compress and decompress correctly, but give misleading
-error messages (internal panics) when an I/O error occurs, instead of
-reporting the problem correctly. This shouldn't give any data loss
-(as far as I can see), but is confusing.
-
-Made the inline declarations disappear for non-GCC compilers.
-
-
-0.9.0c
-~~~~~~
-Fixed some problems in the library pertaining to some boundary cases.
-This makes the library behave more correctly in those situations. The
-fixes apply only to features (calls and parameters) not used by
-bzip2.c, so the non-fixedness of them in previous versions has no
-effect on reliability of bzip2.c.
-
-In bzlib.c:
- * made zero-length BZ_FLUSH work correctly in bzCompress().
- * fixed bzWrite/bzRead to ignore zero-length requests.
- * fixed bzread to correctly handle read requests after EOF.
- * wrong parameter order in call to bzDecompressInit in
- bzBuffToBuffDecompress. Fixed.
-
-In compress.c:
- * changed setting of nGroups in sendMTFValues() so as to
- do a bit better on small files. This _does_ effect
- bzip2.c.
-
-
-0.9.5a
-~~~~~~
-Major change: add a fallback sorting algorithm (blocksort.c)
-to give reasonable behaviour even for very repetitive inputs.
-Nuked --repetitive-best and --repetitive-fast since they are
-no longer useful.
-
-Minor changes: mostly a whole bunch of small changes/
-bugfixes in the driver (bzip2.c). Changes pertaining to the
-user interface are:
-
- allow decompression of symlink'd files to stdout
- decompress/test files even without .bz2 extension
- give more accurate error messages for I/O errors
- when compressing/decompressing to stdout, don't catch control-C
- read flags from BZIP2 and BZIP environment variables
- decline to break hard links to a file unless forced with -f
- allow -c flag even with no filenames
- preserve file ownerships as far as possible
- make -s -1 give the expected block size (100k)
- add a flag -q --quiet to suppress nonessential warnings
- stop decoding flags after --, so files beginning in - can be handled
- resolved inconsistent naming: bzcat or bz2cat ?
- bzip2 --help now returns 0
-
-Programming-level changes are:
-
- fixed syntax error in GET_LL4 for Borland C++ 5.02
- let bzBuffToBuffDecompress return BZ_DATA_ERROR{_MAGIC}
- fix overshoot of mode-string end in bzopen_or_bzdopen
- wrapped bzlib.h in #ifdef __cplusplus ... extern "C" { ... }
- close file handles under all error conditions
- added minor mods so it compiles with DJGPP out of the box
- fixed Makefile so it doesn't give problems with BSD make
- fix uninitialised memory reads in dlltest.c
-
-0.9.5b
-~~~~~~
-Open stdin/stdout in binary mode for DJGPP.
-
-0.9.5c
-~~~~~~
-Changed BZ_N_OVERSHOOT to be ... + 2 instead of ... + 1. The + 1
-version could cause the sorted order to be wrong in some extremely
-obscure cases. Also changed setting of quadrant in blocksort.c.
-
-0.9.5d
-~~~~~~
-The only functional change is to make bzlibVersion() in the library
-return the correct string. This has no effect whatsoever on the
-functioning of the bzip2 program or library. Added a couple of casts
-so the library compiles without warnings at level 3 in MS Visual
-Studio 6.0. Included a Y2K statement in the file Y2K_INFO. All other
-changes are minor documentation changes.
-
-1.0
-~~~
-Several minor bugfixes and enhancements:
-
-* Large file support. The library uses 64-bit counters to
- count the volume of data passing through it. bzip2.c
- is now compiled with -D_FILE_OFFSET_BITS=64 to get large
- file support from the C library. -v correctly prints out
- file sizes greater than 4 gigabytes. All these changes have
- been made without assuming a 64-bit platform or a C compiler
- which supports 64-bit ints, so, except for the C library
- aspect, they are fully portable.
-
-* Decompression robustness. The library/program should be
- robust to any corruption of compressed data, detecting and
- handling _all_ corruption, instead of merely relying on
- the CRCs. What this means is that the program should
- never crash, given corrupted data, and the library should
- always return BZ_DATA_ERROR.
-
-* Fixed an obscure race-condition bug only ever observed on
- Solaris, in which, if you were very unlucky and issued
- control-C at exactly the wrong time, both input and output
- files would be deleted.
-
-* Don't run out of file handles on test/decompression when
- large numbers of files have invalid magic numbers.
-
-* Avoid library namespace pollution. Prefix all exported
- symbols with BZ2_.
-
-* Minor sorting enhancements from my DCC2000 paper.
-
-* Advance the version number to 1.0, so as to counteract the
- (false-in-this-case) impression some people have that programs
- with version numbers less than 1.0 are in some way, experimental,
- pre-release versions.
-
-* Create an initial Makefile-libbz2_so to build a shared library.
- Yes, I know I should really use libtool et al ...
-
-* Make the program exit with 2 instead of 0 when decompression
- fails due to a bad magic number (ie, an invalid bzip2 header).
- Also exit with 1 (as the manual claims :-) whenever a diagnostic
- message would have been printed AND the corresponding operation
- is aborted, for example
- bzip2: Output file xx already exists.
- When a diagnostic message is printed but the operation is not
- aborted, for example
- bzip2: Can't guess original name for wurble -- using wurble.out
- then the exit value 0 is returned, unless some other problem is
- also detected.
-
- I think it corresponds more closely to what the manual claims now.
-
-
-1.0.1
-~~~~~
-* Modified dlltest.c so it uses the new BZ2_ naming scheme.
-* Modified makefile-msc to fix minor build probs on Win2k.
-* Updated README.COMPILATION.PROBLEMS.
-
-There are no functionality changes or bug fixes relative to version
-1.0.0. This is just a documentation update + a fix for minor Win32
-build problems. For almost everyone, upgrading from 1.0.0 to 1.0.1 is
-utterly pointless. Don't bother.
-
-
-1.0.2
-~~~~~
-A bug fix release, addressing various minor issues which have appeared
-in the 18 or so months since 1.0.1 was released. Most of the fixes
-are to do with file-handling or documentation bugs. To the best of my
-knowledge, there have been no data-loss-causing bugs reported in the
-compression/decompression engine of 1.0.0 or 1.0.1.
-
-Note that this release does not improve the rather crude build system
-for Unix platforms. The general plan here is to autoconfiscate/
-libtoolise 1.0.2 soon after release, and release the result as 1.1.0
-or perhaps 1.2.0. That, however, is still just a plan at this point.
-
-Here are the changes in 1.0.2. Bug-reporters and/or patch-senders in
-parentheses.
-
-* Fix an infinite segfault loop in 1.0.1 when a directory is
- encountered in -f (force) mode.
- (Trond Eivind Glomsrod, Nicholas Nethercote, Volker Schmidt)
-
-* Avoid double fclose() of output file on certain I/O error paths.
- (Solar Designer)
-
-* Don't fail with internal error 1007 when fed a long stream (> 48MB)
- of byte 251. Also print useful message suggesting that 1007s may be
- caused by bad memory.
- (noticed by Juan Pedro Vallejo, fixed by me)
-
-* Fix uninitialised variable silly bug in demo prog dlltest.c.
- (Jorj Bauer)
-
-* Remove 512-MB limitation on recovered file size for bzip2recover
- on selected platforms which support 64-bit ints. At the moment
- all GCC supported platforms, and Win32.
- (me, Alson van der Meulen)
-
-* Hard-code header byte values, to give correct operation on platforms
- using EBCDIC as their native character set (IBM's OS/390).
- (Leland Lucius)
-
-* Copy file access times correctly.
- (Marty Leisner)
-
-* Add distclean and check targets to Makefile.
- (Michael Carmack)
-
-* Parameterise use of ar and ranlib in Makefile. Also add $(LDFLAGS).
- (Rich Ireland, Bo Thorsen)
-
-* Pass -p (create parent dirs as needed) to mkdir during make install.
- (Jeremy Fusco)
-
-* Dereference symlinks when copying file permissions in -f mode.
- (Volker Schmidt)
-
-* Majorly simplify implementation of uInt64_qrm10.
- (Bo Lindbergh)
-
-* Check the input file still exists before deleting the output one,
- when aborting in cleanUpAndFail().
- (Joerg Prante, Robert Linden, Matthias Krings)
-
-Also a bunch of patches courtesy of Philippe Troin, the Debian maintainer
-of bzip2:
-
-* Wrapper scripts (with manpages): bzdiff, bzgrep, bzmore.
-
-* Spelling changes and minor enhancements in bzip2.1.
-
-* Avoid race condition between creating the output file and setting its
- interim permissions safely, by using fopen_output_safely().
- No changes to bzip2recover since there is no issue with file
- permissions there.
-
-* do not print senseless report with -v when compressing an empty
- file.
-
-* bzcat -f works on non-bzip2 files.
-
-* do not try to escape shell meta-characters on unix (the shell takes
- care of these).
-
-* added --fast and --best aliases for -1 -9 for gzip compatibility.
-
-
-1.0.3 (15 Feb 05)
-~~~~~~~~~~~~~~~~~
-Fixes some minor bugs since the last version, 1.0.2.
-
-* Further robustification against corrupted compressed data.
- There are currently no known bitstreams which can cause the
- decompressor to crash, loop or access memory which does not
- belong to it. If you are using bzip2 or the library to
- decompress bitstreams from untrusted sources, an upgrade
- to 1.0.3 is recommended. This fixes CAN-2005-1260.
-
-* The documentation has been converted to XML, from which html
- and pdf can be derived.
-
-* Various minor bugs in the documentation have been fixed.
-
-* Fixes for various compilation warnings with newer versions of
- gcc, and on 64-bit platforms.
-
-* The BZ_NO_STDIO cpp symbol was not properly observed in 1.0.2.
- This has been fixed.
-
-
-1.0.4 (20 Dec 06)
-~~~~~~~~~~~~~~~~~
-Fixes some minor bugs since the last version, 1.0.3.
-
-* Fix file permissions race problem (CAN-2005-0953).
-
-* Avoid possible segfault in BZ2_bzclose. From Coverity's NetBSD
- scan.
-
-* 'const'/prototype cleanups in the C code.
-
-* Change default install location to /usr/local, and handle multiple
- 'make install's without error.
-
-* Sanitise file names more carefully in bzgrep. Fixes CAN-2005-0758
- to the extent that applies to bzgrep.
-
-* Use 'mktemp' rather than 'tempfile' in bzdiff.
-
-* Tighten up a couple of assertions in blocksort.c following automated
- analysis.
-
-* Fix minor doc/comment bugs.
-
-
-1.0.5 (10 Dec 07)
-~~~~~~~~~~~~~~~~~
-Security fix only. Fixes CERT-FI 20469 as it applies to bzip2.
-
-
-1.0.6 (6 Sept 10)
-~~~~~~~~~~~~~~~~~
-
-* Security fix for CVE-2010-0405. This was reported by Mikolaj
- Izdebski.
-
-* Make the documentation build on Ubuntu 10.04
diff --git a/third-party/bzip2/LICENSE b/third-party/bzip2/LICENSE
deleted file mode 100644
index cc61417..0000000
--- a/third-party/bzip2/LICENSE
+++ /dev/null
@@ -1,42 +0,0 @@
-
---------------------------------------------------------------------------
-
-This program, "bzip2", the associated library "libbzip2", and all
-documentation, are copyright (C) 1996-2010 Julian R Seward. All
-rights reserved.
-
-Redistribution and use in source and binary forms, with or without
-modification, are permitted provided that the following conditions
-are met:
-
-1. Redistributions of source code must retain the above copyright
- notice, this list of conditions and the following disclaimer.
-
-2. The origin of this software must not be misrepresented; you must
- not claim that you wrote the original software. If you use this
- software in a product, an acknowledgment in the product
- documentation would be appreciated but is not required.
-
-3. Altered source versions must be plainly marked as such, and must
- not be misrepresented as being the original software.
-
-4. The name of the author may not be used to endorse or promote
- products derived from this software without specific prior written
- permission.
-
-THIS SOFTWARE IS PROVIDED BY THE AUTHOR ``AS IS'' AND ANY EXPRESS
-OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
-WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
-ARE DISCLAIMED. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY
-DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
-DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE
-GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
-INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
-WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
-NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
-SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-
-Julian Seward, jseward at bzip.org
-bzip2/libbzip2 version 1.0.6 of 6 September 2010
-
---------------------------------------------------------------------------
diff --git a/third-party/bzip2/Makefile b/third-party/bzip2/Makefile
deleted file mode 100644
index 9754ddf..0000000
--- a/third-party/bzip2/Makefile
+++ /dev/null
@@ -1,217 +0,0 @@
-# ------------------------------------------------------------------
-# This file is part of bzip2/libbzip2, a program and library for
-# lossless, block-sorting data compression.
-#
-# bzip2/libbzip2 version 1.0.6 of 6 September 2010
-# Copyright (C) 1996-2010 Julian Seward <jseward at bzip.org>
-#
-# Please read the WARNING, DISCLAIMER and PATENTS sections in the
-# README file.
-#
-# This program is released under the terms of the license contained
-# in the file LICENSE.
-# ------------------------------------------------------------------
-
-SHELL=/bin/sh
-
-# To assist in cross-compiling
-CC=gcc
-AR=ar
-RANLIB=ranlib
-LDFLAGS=
-
-BIGFILES=-D_FILE_OFFSET_BITS=64
-CFLAGS=-Wall -Winline -O2 -g $(BIGFILES)
-
-# Where you want it installed when you do 'make install'
-PREFIX=/usr/local
-
-
-OBJS= blocksort.o \
- huffman.o \
- crctable.o \
- randtable.o \
- compress.o \
- decompress.o \
- bzlib.o
-
-all: libbz2.a bzip2 bzip2recover test
-
-bzip2: libbz2.a bzip2.o
- $(CC) $(CFLAGS) $(LDFLAGS) -o bzip2 bzip2.o -L. -lbz2
-
-bzip2recover: bzip2recover.o
- $(CC) $(CFLAGS) $(LDFLAGS) -o bzip2recover bzip2recover.o
-
-libbz2.a: $(OBJS)
- rm -f libbz2.a
- $(AR) cq libbz2.a $(OBJS)
- @if ( test -f $(RANLIB) -o -f /usr/bin/ranlib -o \
- -f /bin/ranlib -o -f /usr/ccs/bin/ranlib ) ; then \
- echo $(RANLIB) libbz2.a ; \
- $(RANLIB) libbz2.a ; \
- fi
-
-check: test
-test: bzip2
- @cat words1
- ./bzip2 -1 < sample1.ref > sample1.rb2
- ./bzip2 -2 < sample2.ref > sample2.rb2
- ./bzip2 -3 < sample3.ref > sample3.rb2
- ./bzip2 -d < sample1.bz2 > sample1.tst
- ./bzip2 -d < sample2.bz2 > sample2.tst
- ./bzip2 -ds < sample3.bz2 > sample3.tst
- cmp sample1.bz2 sample1.rb2
- cmp sample2.bz2 sample2.rb2
- cmp sample3.bz2 sample3.rb2
- cmp sample1.tst sample1.ref
- cmp sample2.tst sample2.ref
- cmp sample3.tst sample3.ref
- @cat words3
-
-install: bzip2 bzip2recover
- if ( test ! -d $(PREFIX)/bin ) ; then mkdir -p $(PREFIX)/bin ; fi
- if ( test ! -d $(PREFIX)/lib ) ; then mkdir -p $(PREFIX)/lib ; fi
- if ( test ! -d $(PREFIX)/man ) ; then mkdir -p $(PREFIX)/man ; fi
- if ( test ! -d $(PREFIX)/man/man1 ) ; then mkdir -p $(PREFIX)/man/man1 ; fi
- if ( test ! -d $(PREFIX)/include ) ; then mkdir -p $(PREFIX)/include ; fi
- cp -f bzip2 $(PREFIX)/bin/bzip2
- cp -f bzip2 $(PREFIX)/bin/bunzip2
- cp -f bzip2 $(PREFIX)/bin/bzcat
- cp -f bzip2recover $(PREFIX)/bin/bzip2recover
- chmod a+x $(PREFIX)/bin/bzip2
- chmod a+x $(PREFIX)/bin/bunzip2
- chmod a+x $(PREFIX)/bin/bzcat
- chmod a+x $(PREFIX)/bin/bzip2recover
- cp -f bzip2.1 $(PREFIX)/man/man1
- chmod a+r $(PREFIX)/man/man1/bzip2.1
- cp -f bzlib.h $(PREFIX)/include
- chmod a+r $(PREFIX)/include/bzlib.h
- cp -f libbz2.a $(PREFIX)/lib
- chmod a+r $(PREFIX)/lib/libbz2.a
- cp -f bzgrep $(PREFIX)/bin/bzgrep
- ln -s -f $(PREFIX)/bin/bzgrep $(PREFIX)/bin/bzegrep
- ln -s -f $(PREFIX)/bin/bzgrep $(PREFIX)/bin/bzfgrep
- chmod a+x $(PREFIX)/bin/bzgrep
- cp -f bzmore $(PREFIX)/bin/bzmore
- ln -s -f $(PREFIX)/bin/bzmore $(PREFIX)/bin/bzless
- chmod a+x $(PREFIX)/bin/bzmore
- cp -f bzdiff $(PREFIX)/bin/bzdiff
- ln -s -f $(PREFIX)/bin/bzdiff $(PREFIX)/bin/bzcmp
- chmod a+x $(PREFIX)/bin/bzdiff
- cp -f bzgrep.1 bzmore.1 bzdiff.1 $(PREFIX)/man/man1
- chmod a+r $(PREFIX)/man/man1/bzgrep.1
- chmod a+r $(PREFIX)/man/man1/bzmore.1
- chmod a+r $(PREFIX)/man/man1/bzdiff.1
- echo ".so man1/bzgrep.1" > $(PREFIX)/man/man1/bzegrep.1
- echo ".so man1/bzgrep.1" > $(PREFIX)/man/man1/bzfgrep.1
- echo ".so man1/bzmore.1" > $(PREFIX)/man/man1/bzless.1
- echo ".so man1/bzdiff.1" > $(PREFIX)/man/man1/bzcmp.1
-
-clean:
- rm -f *.o libbz2.a bzip2 bzip2recover \
- sample1.rb2 sample2.rb2 sample3.rb2 \
- sample1.tst sample2.tst sample3.tst
-
-blocksort.o: blocksort.c
- @cat words0
- $(CC) $(CFLAGS) -c blocksort.c
-huffman.o: huffman.c
- $(CC) $(CFLAGS) -c huffman.c
-crctable.o: crctable.c
- $(CC) $(CFLAGS) -c crctable.c
-randtable.o: randtable.c
- $(CC) $(CFLAGS) -c randtable.c
-compress.o: compress.c
- $(CC) $(CFLAGS) -c compress.c
-decompress.o: decompress.c
- $(CC) $(CFLAGS) -c decompress.c
-bzlib.o: bzlib.c
- $(CC) $(CFLAGS) -c bzlib.c
-bzip2.o: bzip2.c
- $(CC) $(CFLAGS) -c bzip2.c
-bzip2recover.o: bzip2recover.c
- $(CC) $(CFLAGS) -c bzip2recover.c
-
-
-distclean: clean
- rm -f manual.ps manual.html manual.pdf
-
-DISTNAME=bzip2-1.0.6
-dist: check manual
- rm -f $(DISTNAME)
- ln -s -f . $(DISTNAME)
- tar cvf $(DISTNAME).tar \
- $(DISTNAME)/blocksort.c \
- $(DISTNAME)/huffman.c \
- $(DISTNAME)/crctable.c \
- $(DISTNAME)/randtable.c \
- $(DISTNAME)/compress.c \
- $(DISTNAME)/decompress.c \
- $(DISTNAME)/bzlib.c \
- $(DISTNAME)/bzip2.c \
- $(DISTNAME)/bzip2recover.c \
- $(DISTNAME)/bzlib.h \
- $(DISTNAME)/bzlib_private.h \
- $(DISTNAME)/Makefile \
- $(DISTNAME)/LICENSE \
- $(DISTNAME)/bzip2.1 \
- $(DISTNAME)/bzip2.1.preformatted \
- $(DISTNAME)/bzip2.txt \
- $(DISTNAME)/words0 \
- $(DISTNAME)/words1 \
- $(DISTNAME)/words2 \
- $(DISTNAME)/words3 \
- $(DISTNAME)/sample1.ref \
- $(DISTNAME)/sample2.ref \
- $(DISTNAME)/sample3.ref \
- $(DISTNAME)/sample1.bz2 \
- $(DISTNAME)/sample2.bz2 \
- $(DISTNAME)/sample3.bz2 \
- $(DISTNAME)/dlltest.c \
- $(DISTNAME)/manual.html \
- $(DISTNAME)/manual.pdf \
- $(DISTNAME)/manual.ps \
- $(DISTNAME)/README \
- $(DISTNAME)/README.COMPILATION.PROBLEMS \
- $(DISTNAME)/README.XML.STUFF \
- $(DISTNAME)/CHANGES \
- $(DISTNAME)/libbz2.def \
- $(DISTNAME)/libbz2.dsp \
- $(DISTNAME)/dlltest.dsp \
- $(DISTNAME)/makefile.msc \
- $(DISTNAME)/unzcrash.c \
- $(DISTNAME)/spewG.c \
- $(DISTNAME)/mk251.c \
- $(DISTNAME)/bzdiff \
- $(DISTNAME)/bzdiff.1 \
- $(DISTNAME)/bzmore \
- $(DISTNAME)/bzmore.1 \
- $(DISTNAME)/bzgrep \
- $(DISTNAME)/bzgrep.1 \
- $(DISTNAME)/Makefile-libbz2_so \
- $(DISTNAME)/bz-common.xsl \
- $(DISTNAME)/bz-fo.xsl \
- $(DISTNAME)/bz-html.xsl \
- $(DISTNAME)/bzip.css \
- $(DISTNAME)/entities.xml \
- $(DISTNAME)/manual.xml \
- $(DISTNAME)/format.pl \
- $(DISTNAME)/xmlproc.sh
- gzip -v $(DISTNAME).tar
-
-# For rebuilding the manual from sources on my SuSE 9.1 box
-
-MANUAL_SRCS= bz-common.xsl bz-fo.xsl bz-html.xsl bzip.css \
- entities.xml manual.xml
-
-manual: manual.html manual.ps manual.pdf
-
-manual.ps: $(MANUAL_SRCS)
- ./xmlproc.sh -ps manual.xml
-
-manual.pdf: $(MANUAL_SRCS)
- ./xmlproc.sh -pdf manual.xml
-
-manual.html: $(MANUAL_SRCS)
- ./xmlproc.sh -html manual.xml
diff --git a/third-party/bzip2/Makefile-libbz2_so b/third-party/bzip2/Makefile-libbz2_so
deleted file mode 100644
index e1a09f5..0000000
--- a/third-party/bzip2/Makefile-libbz2_so
+++ /dev/null
@@ -1,59 +0,0 @@
-
-# This Makefile builds a shared version of the library,
-# libbz2.so.1.0.6, with soname libbz2.so.1.0,
-# at least on x86-Linux (RedHat 7.2),
-# with gcc-2.96 20000731 (Red Hat Linux 7.1 2.96-98).
-# Please see the README file for some important info
-# about building the library like this.
-
-# ------------------------------------------------------------------
-# This file is part of bzip2/libbzip2, a program and library for
-# lossless, block-sorting data compression.
-#
-# bzip2/libbzip2 version 1.0.6 of 6 September 2010
-# Copyright (C) 1996-2010 Julian Seward <jseward at bzip.org>
-#
-# Please read the WARNING, DISCLAIMER and PATENTS sections in the
-# README file.
-#
-# This program is released under the terms of the license contained
-# in the file LICENSE.
-# ------------------------------------------------------------------
-
-
-SHELL=/bin/sh
-CC=gcc
-BIGFILES=-D_FILE_OFFSET_BITS=64
-CFLAGS=-fpic -fPIC -Wall -Winline -O2 -g $(BIGFILES)
-
-OBJS= blocksort.o \
- huffman.o \
- crctable.o \
- randtable.o \
- compress.o \
- decompress.o \
- bzlib.o
-
-all: $(OBJS)
- #$(CC) -shared -Wl,-soname -Wl,libbz2.so.1.0 -o libbz2.so.1.0.6 $(OBJS)
- #$(CC) $(CFLAGS) -o bzip2-shared bzip2.c libbz2.so.1.0.6
- #rm -f libbz2.so.1.0
- #ln -s libbz2.so.1.0.6 libbz2.so.1.0
-
-clean:
- rm -f $(OBJS) bzip2.o libbz2.so.1.0.6 libbz2.so.1.0 bzip2-shared
-
-blocksort.o: blocksort.c
- $(CC) $(CFLAGS) -c blocksort.c
-huffman.o: huffman.c
- $(CC) $(CFLAGS) -c huffman.c
-crctable.o: crctable.c
- $(CC) $(CFLAGS) -c crctable.c
-randtable.o: randtable.c
- $(CC) $(CFLAGS) -c randtable.c
-compress.o: compress.c
- $(CC) $(CFLAGS) -c compress.c
-decompress.o: decompress.c
- $(CC) $(CFLAGS) -c decompress.c
-bzlib.o: bzlib.c
- $(CC) $(CFLAGS) -c bzlib.c
diff --git a/third-party/bzip2/README b/third-party/bzip2/README
deleted file mode 100644
index 9fb0f63..0000000
--- a/third-party/bzip2/README
+++ /dev/null
@@ -1,215 +0,0 @@
-
-This is the README for bzip2/libzip2.
-This version is fully compatible with the previous public releases.
-
-------------------------------------------------------------------
-This file is part of bzip2/libbzip2, a program and library for
-lossless, block-sorting data compression.
-
-bzip2/libbzip2 version 1.0.6 of 6 September 2010
-Copyright (C) 1996-2010 Julian Seward <jseward at bzip.org>
-
-Please read the WARNING, DISCLAIMER and PATENTS sections in this file.
-
-This program is released under the terms of the license contained
-in the file LICENSE.
-------------------------------------------------------------------
-
-Complete documentation is available in Postscript form (manual.ps),
-PDF (manual.pdf) or html (manual.html). A plain-text version of the
-manual page is available as bzip2.txt.
-
-
-HOW TO BUILD -- UNIX
-
-Type 'make'. This builds the library libbz2.a and then the programs
-bzip2 and bzip2recover. Six self-tests are run. If the self-tests
-complete ok, carry on to installation:
-
-To install in /usr/local/bin, /usr/local/lib, /usr/local/man and
-/usr/local/include, type
-
- make install
-
-To install somewhere else, eg, /xxx/yyy/{bin,lib,man,include}, type
-
- make install PREFIX=/xxx/yyy
-
-If you are (justifiably) paranoid and want to see what 'make install'
-is going to do, you can first do
-
- make -n install or
- make -n install PREFIX=/xxx/yyy respectively.
-
-The -n instructs make to show the commands it would execute, but not
-actually execute them.
-
-
-HOW TO BUILD -- UNIX, shared library libbz2.so.
-
-Do 'make -f Makefile-libbz2_so'. This Makefile seems to work for
-Linux-ELF (RedHat 7.2 on an x86 box), with gcc. I make no claims
-that it works for any other platform, though I suspect it probably
-will work for most platforms employing both ELF and gcc.
-
-bzip2-shared, a client of the shared library, is also built, but not
-self-tested. So I suggest you also build using the normal Makefile,
-since that conducts a self-test. A second reason to prefer the
-version statically linked to the library is that, on x86 platforms,
-building shared objects makes a valuable register (%ebx) unavailable
-to gcc, resulting in a slowdown of 10%-20%, at least for bzip2.
-
-Important note for people upgrading .so's from 0.9.0/0.9.5 to version
-1.0.X. All the functions in the library have been renamed, from (eg)
-bzCompress to BZ2_bzCompress, to avoid namespace pollution.
-Unfortunately this means that the libbz2.so created by
-Makefile-libbz2_so will not work with any program which used an older
-version of the library. I do encourage library clients to make the
-effort to upgrade to use version 1.0, since it is both faster and more
-robust than previous versions.
-
-
-HOW TO BUILD -- Windows 95, NT, DOS, Mac, etc.
-
-It's difficult for me to support compilation on all these platforms.
-My approach is to collect binaries for these platforms, and put them
-on the master web site (http://www.bzip.org). Look there. However
-(FWIW), bzip2-1.0.X is very standard ANSI C and should compile
-unmodified with MS Visual C. If you have difficulties building, you
-might want to read README.COMPILATION.PROBLEMS.
-
-At least using MS Visual C++ 6, you can build from the unmodified
-sources by issuing, in a command shell:
-
- nmake -f makefile.msc
-
-(you may need to first run the MSVC-provided script VCVARS32.BAT
- so as to set up paths to the MSVC tools correctly).
-
-
-VALIDATION
-
-Correct operation, in the sense that a compressed file can always be
-decompressed to reproduce the original, is obviously of paramount
-importance. To validate bzip2, I used a modified version of Mark
-Nelson's churn program. Churn is an automated test driver which
-recursively traverses a directory structure, using bzip2 to compress
-and then decompress each file it encounters, and checking that the
-decompressed data is the same as the original.
-
-
-
-Please read and be aware of the following:
-
-WARNING:
-
- This program and library (attempts to) compress data by
- performing several non-trivial transformations on it.
- Unless you are 100% familiar with *all* the algorithms
- contained herein, and with the consequences of modifying them,
- you should NOT meddle with the compression or decompression
- machinery. Incorrect changes can and very likely *will*
- lead to disastrous loss of data.
-
-
-DISCLAIMER:
-
- I TAKE NO RESPONSIBILITY FOR ANY LOSS OF DATA ARISING FROM THE
- USE OF THIS PROGRAM/LIBRARY, HOWSOEVER CAUSED.
-
- Every compression of a file implies an assumption that the
- compressed file can be decompressed to reproduce the original.
- Great efforts in design, coding and testing have been made to
- ensure that this program works correctly. However, the complexity
- of the algorithms, and, in particular, the presence of various
- special cases in the code which occur with very low but non-zero
- probability make it impossible to rule out the possibility of bugs
- remaining in the program. DO NOT COMPRESS ANY DATA WITH THIS
- PROGRAM UNLESS YOU ARE PREPARED TO ACCEPT THE POSSIBILITY, HOWEVER
- SMALL, THAT THE DATA WILL NOT BE RECOVERABLE.
-
- That is not to say this program is inherently unreliable.
- Indeed, I very much hope the opposite is true. bzip2/libbzip2
- has been carefully constructed and extensively tested.
-
-
-PATENTS:
-
- To the best of my knowledge, bzip2/libbzip2 does not use any
- patented algorithms. However, I do not have the resources
- to carry out a patent search. Therefore I cannot give any
- guarantee of the above statement.
-
-
-
-WHAT'S NEW IN 0.9.0 (as compared to 0.1pl2) ?
-
- * Approx 10% faster compression, 30% faster decompression
- * -t (test mode) is a lot quicker
- * Can decompress concatenated compressed files
- * Programming interface, so programs can directly read/write .bz2 files
- * Less restrictive (BSD-style) licensing
- * Flag handling more compatible with GNU gzip
- * Much more documentation, i.e., a proper user manual
- * Hopefully, improved portability (at least of the library)
-
-WHAT'S NEW IN 0.9.5 ?
-
- * Compression speed is much less sensitive to the input
- data than in previous versions. Specifically, the very
- slow performance caused by repetitive data is fixed.
- * Many small improvements in file and flag handling.
- * A Y2K statement.
-
-WHAT'S NEW IN 1.0.0 ?
-
- See the CHANGES file.
-
-WHAT'S NEW IN 1.0.2 ?
-
- See the CHANGES file.
-
-WHAT'S NEW IN 1.0.3 ?
-
- See the CHANGES file.
-
-WHAT'S NEW IN 1.0.4 ?
-
- See the CHANGES file.
-
-WHAT'S NEW IN 1.0.5 ?
-
- See the CHANGES file.
-
-WHAT'S NEW IN 1.0.6 ?
-
- See the CHANGES file.
-
-
-I hope you find bzip2 useful. Feel free to contact me at
- jseward at bzip.org
-if you have any suggestions or queries. Many people mailed me with
-comments, suggestions and patches after the releases of bzip-0.15,
-bzip-0.21, and bzip2 versions 0.1pl2, 0.9.0, 0.9.5, 1.0.0, 1.0.1,
-1.0.2 and 1.0.3, and the changes in bzip2 are largely a result of this
-feedback. I thank you for your comments.
-
-bzip2's "home" is http://www.bzip.org/
-
-Julian Seward
-jseward at bzip.org
-Cambridge, UK.
-
-18 July 1996 (version 0.15)
-25 August 1996 (version 0.21)
- 7 August 1997 (bzip2, version 0.1)
-29 August 1997 (bzip2, version 0.1pl2)
-23 August 1998 (bzip2, version 0.9.0)
- 8 June 1999 (bzip2, version 0.9.5)
- 4 Sept 1999 (bzip2, version 0.9.5d)
- 5 May 2000 (bzip2, version 1.0pre8)
-30 December 2001 (bzip2, version 1.0.2pre1)
-15 February 2005 (bzip2, version 1.0.3)
-20 December 2006 (bzip2, version 1.0.4)
-10 December 2007 (bzip2, version 1.0.5)
- 6 Sept 2010 (bzip2, version 1.0.6)
diff --git a/third-party/bzip2/README.COMPILATION.PROBLEMS b/third-party/bzip2/README.COMPILATION.PROBLEMS
deleted file mode 100644
index 667d0d6..0000000
--- a/third-party/bzip2/README.COMPILATION.PROBLEMS
+++ /dev/null
@@ -1,58 +0,0 @@
-------------------------------------------------------------------
-This file is part of bzip2/libbzip2, a program and library for
-lossless, block-sorting data compression.
-
-bzip2/libbzip2 version 1.0.6 of 6 September 2010
-Copyright (C) 1996-2010 Julian Seward <jseward at bzip.org>
-
-Please read the WARNING, DISCLAIMER and PATENTS sections in the
-README file.
-
-This program is released under the terms of the license contained
-in the file LICENSE.
-------------------------------------------------------------------
-
-bzip2-1.0.6 should compile without problems on the vast majority of
-platforms. Using the supplied Makefile, I've built and tested it
-myself for x86-linux and amd64-linux. With makefile.msc, Visual C++
-6.0 and nmake, you can build a native Win32 version too. Large file
-support seems to work correctly on at least on amd64-linux.
-
-When I say "large file" I mean a file of size 2,147,483,648 (2^31)
-bytes or above. Many older OSs can't handle files above this size,
-but many newer ones can. Large files are pretty huge -- most files
-you'll encounter are not Large Files.
-
-Early versions of bzip2 (0.1, 0.9.0, 0.9.5) compiled on a wide variety
-of platforms without difficulty, and I hope this version will continue
-in that tradition. However, in order to support large files, I've had
-to include the define -D_FILE_OFFSET_BITS=64 in the Makefile. This
-can cause problems.
-
-The technique of adding -D_FILE_OFFSET_BITS=64 to get large file
-support is, as far as I know, the Recommended Way to get correct large
-file support. For more details, see the Large File Support
-Specification, published by the Large File Summit, at
-
- http://ftp.sas.com/standards/large.file
-
-As a general comment, if you get compilation errors which you think
-are related to large file support, try removing the above define from
-the Makefile, ie, delete the line
-
- BIGFILES=-D_FILE_OFFSET_BITS=64
-
-from the Makefile, and do 'make clean ; make'. This will give you a
-version of bzip2 without large file support, which, for most
-applications, is probably not a problem.
-
-Alternatively, try some of the platform-specific hints listed below.
-
-You can use the spewG.c program to generate huge files to test bzip2's
-large file support, if you are feeling paranoid. Be aware though that
-any compilation problems which affect bzip2 will also affect spewG.c,
-alas.
-
-AIX: I have reports that for large file support, you need to specify
--D_LARGE_FILES rather than -D_FILE_OFFSET_BITS=64. I have not tested
-this myself.
diff --git a/third-party/bzip2/README.XML.STUFF b/third-party/bzip2/README.XML.STUFF
deleted file mode 100644
index 3a57f3f..0000000
--- a/third-party/bzip2/README.XML.STUFF
+++ /dev/null
@@ -1,45 +0,0 @@
- ----------------------------------------------------------------
- This file is part of bzip2/libbzip2, a program and library for
- lossless, block-sorting data compression.
-
- bzip2/libbzip2 version 1.0.6 of 6 September 2010
- Copyright (C) 1996-2010 Julian Seward <jseward at bzip.org>
-
- Please read the WARNING, DISCLAIMER and PATENTS sections in the
- README file.
-
- This program is released under the terms of the license contained
- in the file LICENSE.
- ----------------------------------------------------------------
-
-The script xmlproc.sh takes an xml file as input,
-and processes it to create .pdf, .html or .ps output.
-It uses format.pl, a perl script to format <pre> blocks nicely,
- and add CDATA tags so writers do not have to use eg. <
-
-The file "entities.xml" must be edited to reflect current
-version, year, etc.
-
-
-Usage:
-
- ./xmlproc.sh -v manual.xml
- Validates an xml file to ensure no dtd-compliance errors
-
- ./xmlproc.sh -html manual.xml
- Output: manual.html
-
- ./xmlproc.sh -pdf manual.xml
- Output: manual.pdf
-
- ./xmlproc.sh -ps manual.xml
- Output: manual.ps
-
-
-Notum bene:
-- pdfxmltex barfs if given a filename with an underscore in it
-
-- xmltex won't work yet - there's a bug in passivetex
- which we are all waiting for Sebastian to fix.
- So we are going the xml -> pdf -> ps route for the time being,
- using pdfxmltex.
diff --git a/third-party/bzip2/blocksort.c b/third-party/bzip2/blocksort.c
deleted file mode 100644
index d0d662c..0000000
--- a/third-party/bzip2/blocksort.c
+++ /dev/null
@@ -1,1094 +0,0 @@
-
-/*-------------------------------------------------------------*/
-/*--- Block sorting machinery ---*/
-/*--- blocksort.c ---*/
-/*-------------------------------------------------------------*/
-
-/* ------------------------------------------------------------------
- This file is part of bzip2/libbzip2, a program and library for
- lossless, block-sorting data compression.
-
- bzip2/libbzip2 version 1.0.6 of 6 September 2010
- Copyright (C) 1996-2010 Julian Seward <jseward at bzip.org>
-
- Please read the WARNING, DISCLAIMER and PATENTS sections in the
- README file.
-
- This program is released under the terms of the license contained
- in the file LICENSE.
- ------------------------------------------------------------------ */
-
-
-#include "bzlib_private.h"
-
-/*---------------------------------------------*/
-/*--- Fallback O(N log(N)^2) sorting ---*/
-/*--- algorithm, for repetitive blocks ---*/
-/*---------------------------------------------*/
-
-/*---------------------------------------------*/
-static
-__inline__
-void fallbackSimpleSort ( UInt32* fmap,
- UInt32* eclass,
- Int32 lo,
- Int32 hi )
-{
- Int32 i, j, tmp;
- UInt32 ec_tmp;
-
- if (lo == hi) return;
-
- if (hi - lo > 3) {
- for ( i = hi-4; i >= lo; i-- ) {
- tmp = fmap[i];
- ec_tmp = eclass[tmp];
- for ( j = i+4; j <= hi && ec_tmp > eclass[fmap[j]]; j += 4 )
- fmap[j-4] = fmap[j];
- fmap[j-4] = tmp;
- }
- }
-
- for ( i = hi-1; i >= lo; i-- ) {
- tmp = fmap[i];
- ec_tmp = eclass[tmp];
- for ( j = i+1; j <= hi && ec_tmp > eclass[fmap[j]]; j++ )
- fmap[j-1] = fmap[j];
- fmap[j-1] = tmp;
- }
-}
-
-
-/*---------------------------------------------*/
-#define fswap(zz1, zz2) \
- { Int32 zztmp = zz1; zz1 = zz2; zz2 = zztmp; }
-
-#define fvswap(zzp1, zzp2, zzn) \
-{ \
- Int32 yyp1 = (zzp1); \
- Int32 yyp2 = (zzp2); \
- Int32 yyn = (zzn); \
- while (yyn > 0) { \
- fswap(fmap[yyp1], fmap[yyp2]); \
- yyp1++; yyp2++; yyn--; \
- } \
-}
-
-
-#define fmin(a,b) ((a) < (b)) ? (a) : (b)
-
-#define fpush(lz,hz) { stackLo[sp] = lz; \
- stackHi[sp] = hz; \
- sp++; }
-
-#define fpop(lz,hz) { sp--; \
- lz = stackLo[sp]; \
- hz = stackHi[sp]; }
-
-#define FALLBACK_QSORT_SMALL_THRESH 10
-#define FALLBACK_QSORT_STACK_SIZE 100
-
-
-static
-void fallbackQSort3 ( UInt32* fmap,
- UInt32* eclass,
- Int32 loSt,
- Int32 hiSt )
-{
- Int32 unLo, unHi, ltLo, gtHi, n, m;
- Int32 sp, lo, hi;
- UInt32 med, r, r3;
- Int32 stackLo[FALLBACK_QSORT_STACK_SIZE];
- Int32 stackHi[FALLBACK_QSORT_STACK_SIZE];
-
- r = 0;
-
- sp = 0;
- fpush ( loSt, hiSt );
-
- while (sp > 0) {
-
- AssertH ( sp < FALLBACK_QSORT_STACK_SIZE - 1, 1004 );
-
- fpop ( lo, hi );
- if (hi - lo < FALLBACK_QSORT_SMALL_THRESH) {
- fallbackSimpleSort ( fmap, eclass, lo, hi );
- continue;
- }
-
- /* Random partitioning. Median of 3 sometimes fails to
- avoid bad cases. Median of 9 seems to help but
- looks rather expensive. This too seems to work but
- is cheaper. Guidance for the magic constants
- 7621 and 32768 is taken from Sedgewick's algorithms
- book, chapter 35.
- */
- r = ((r * 7621) + 1) % 32768;
- r3 = r % 3;
- if (r3 == 0) med = eclass[fmap[lo]]; else
- if (r3 == 1) med = eclass[fmap[(lo+hi)>>1]]; else
- med = eclass[fmap[hi]];
-
- unLo = ltLo = lo;
- unHi = gtHi = hi;
-
- while (1) {
- while (1) {
- if (unLo > unHi) break;
- n = (Int32)eclass[fmap[unLo]] - (Int32)med;
- if (n == 0) {
- fswap(fmap[unLo], fmap[ltLo]);
- ltLo++; unLo++;
- continue;
- };
- if (n > 0) break;
- unLo++;
- }
- while (1) {
- if (unLo > unHi) break;
- n = (Int32)eclass[fmap[unHi]] - (Int32)med;
- if (n == 0) {
- fswap(fmap[unHi], fmap[gtHi]);
- gtHi--; unHi--;
- continue;
- };
- if (n < 0) break;
- unHi--;
- }
- if (unLo > unHi) break;
- fswap(fmap[unLo], fmap[unHi]); unLo++; unHi--;
- }
-
- AssertD ( unHi == unLo-1, "fallbackQSort3(2)" );
-
- if (gtHi < ltLo) continue;
-
- n = fmin(ltLo-lo, unLo-ltLo); fvswap(lo, unLo-n, n);
- m = fmin(hi-gtHi, gtHi-unHi); fvswap(unLo, hi-m+1, m);
-
- n = lo + unLo - ltLo - 1;
- m = hi - (gtHi - unHi) + 1;
-
- if (n - lo > hi - m) {
- fpush ( lo, n );
- fpush ( m, hi );
- } else {
- fpush ( m, hi );
- fpush ( lo, n );
- }
- }
-}
-
-#undef fmin
-#undef fpush
-#undef fpop
-#undef fswap
-#undef fvswap
-#undef FALLBACK_QSORT_SMALL_THRESH
-#undef FALLBACK_QSORT_STACK_SIZE
-
-
-/*---------------------------------------------*/
-/* Pre:
- nblock > 0
- eclass exists for [0 .. nblock-1]
- ((UChar*)eclass) [0 .. nblock-1] holds block
- ptr exists for [0 .. nblock-1]
-
- Post:
- ((UChar*)eclass) [0 .. nblock-1] holds block
- All other areas of eclass destroyed
- fmap [0 .. nblock-1] holds sorted order
- bhtab [ 0 .. 2+(nblock/32) ] destroyed
-*/
-
-#define SET_BH(zz) bhtab[(zz) >> 5] |= (1 << ((zz) & 31))
-#define CLEAR_BH(zz) bhtab[(zz) >> 5] &= ~(1 << ((zz) & 31))
-#define ISSET_BH(zz) (bhtab[(zz) >> 5] & (1 << ((zz) & 31)))
-#define WORD_BH(zz) bhtab[(zz) >> 5]
-#define UNALIGNED_BH(zz) ((zz) & 0x01f)
-
-static
-void fallbackSort ( UInt32* fmap,
- UInt32* eclass,
- UInt32* bhtab,
- Int32 nblock,
- Int32 verb )
-{
- Int32 ftab[257];
- Int32 ftabCopy[256];
- Int32 H, i, j, k, l, r, cc, cc1;
- Int32 nNotDone;
- Int32 nBhtab;
- UChar* eclass8 = (UChar*)eclass;
-
- /*--
- Initial 1-char radix sort to generate
- initial fmap and initial BH bits.
- --*/
- if (verb >= 4)
- VPrintf0 ( " bucket sorting ...\n" );
- for (i = 0; i < 257; i++) ftab[i] = 0;
- for (i = 0; i < nblock; i++) ftab[eclass8[i]]++;
- for (i = 0; i < 256; i++) ftabCopy[i] = ftab[i];
- for (i = 1; i < 257; i++) ftab[i] += ftab[i-1];
-
- for (i = 0; i < nblock; i++) {
- j = eclass8[i];
- k = ftab[j] - 1;
- ftab[j] = k;
- fmap[k] = i;
- }
-
- nBhtab = 2 + (nblock / 32);
- for (i = 0; i < nBhtab; i++) bhtab[i] = 0;
- for (i = 0; i < 256; i++) SET_BH(ftab[i]);
-
- /*--
- Inductively refine the buckets. Kind-of an
- "exponential radix sort" (!), inspired by the
- Manber-Myers suffix array construction algorithm.
- --*/
-
- /*-- set sentinel bits for block-end detection --*/
- for (i = 0; i < 32; i++) {
- SET_BH(nblock + 2*i);
- CLEAR_BH(nblock + 2*i + 1);
- }
-
- /*-- the log(N) loop --*/
- H = 1;
- while (1) {
-
- if (verb >= 4)
- VPrintf1 ( " depth %6d has ", H );
-
- j = 0;
- for (i = 0; i < nblock; i++) {
- if (ISSET_BH(i)) j = i;
- k = fmap[i] - H; if (k < 0) k += nblock;
- eclass[k] = j;
- }
-
- nNotDone = 0;
- r = -1;
- while (1) {
-
- /*-- find the next non-singleton bucket --*/
- k = r + 1;
- while (ISSET_BH(k) && UNALIGNED_BH(k)) k++;
- if (ISSET_BH(k)) {
- while (WORD_BH(k) == 0xffffffff) k += 32;
- while (ISSET_BH(k)) k++;
- }
- l = k - 1;
- if (l >= nblock) break;
- while (!ISSET_BH(k) && UNALIGNED_BH(k)) k++;
- if (!ISSET_BH(k)) {
- while (WORD_BH(k) == 0x00000000) k += 32;
- while (!ISSET_BH(k)) k++;
- }
- r = k - 1;
- if (r >= nblock) break;
-
- /*-- now [l, r] bracket current bucket --*/
- if (r > l) {
- nNotDone += (r - l + 1);
- fallbackQSort3 ( fmap, eclass, l, r );
-
- /*-- scan bucket and generate header bits-- */
- cc = -1;
- for (i = l; i <= r; i++) {
- cc1 = eclass[fmap[i]];
- if (cc != cc1) { SET_BH(i); cc = cc1; };
- }
- }
- }
-
- if (verb >= 4)
- VPrintf1 ( "%6d unresolved strings\n", nNotDone );
-
- H *= 2;
- if (H > nblock || nNotDone == 0) break;
- }
-
- /*--
- Reconstruct the original block in
- eclass8 [0 .. nblock-1], since the
- previous phase destroyed it.
- --*/
- if (verb >= 4)
- VPrintf0 ( " reconstructing block ...\n" );
- j = 0;
- for (i = 0; i < nblock; i++) {
- while (ftabCopy[j] == 0) j++;
- ftabCopy[j]--;
- eclass8[fmap[i]] = (UChar)j;
- }
- AssertH ( j < 256, 1005 );
-}
-
-#undef SET_BH
-#undef CLEAR_BH
-#undef ISSET_BH
-#undef WORD_BH
-#undef UNALIGNED_BH
-
-
-/*---------------------------------------------*/
-/*--- The main, O(N^2 log(N)) sorting ---*/
-/*--- algorithm. Faster for "normal" ---*/
-/*--- non-repetitive blocks. ---*/
-/*---------------------------------------------*/
-
-/*---------------------------------------------*/
-static
-__inline__
-Bool mainGtU ( UInt32 i1,
- UInt32 i2,
- UChar* block,
- UInt16* quadrant,
- UInt32 nblock,
- Int32* budget )
-{
- Int32 k;
- UChar c1, c2;
- UInt16 s1, s2;
-
- AssertD ( i1 != i2, "mainGtU" );
- /* 1 */
- c1 = block[i1]; c2 = block[i2];
- if (c1 != c2) return (c1 > c2);
- i1++; i2++;
- /* 2 */
- c1 = block[i1]; c2 = block[i2];
- if (c1 != c2) return (c1 > c2);
- i1++; i2++;
- /* 3 */
- c1 = block[i1]; c2 = block[i2];
- if (c1 != c2) return (c1 > c2);
- i1++; i2++;
- /* 4 */
- c1 = block[i1]; c2 = block[i2];
- if (c1 != c2) return (c1 > c2);
- i1++; i2++;
- /* 5 */
- c1 = block[i1]; c2 = block[i2];
- if (c1 != c2) return (c1 > c2);
- i1++; i2++;
- /* 6 */
- c1 = block[i1]; c2 = block[i2];
- if (c1 != c2) return (c1 > c2);
- i1++; i2++;
- /* 7 */
- c1 = block[i1]; c2 = block[i2];
- if (c1 != c2) return (c1 > c2);
- i1++; i2++;
- /* 8 */
- c1 = block[i1]; c2 = block[i2];
- if (c1 != c2) return (c1 > c2);
- i1++; i2++;
- /* 9 */
- c1 = block[i1]; c2 = block[i2];
- if (c1 != c2) return (c1 > c2);
- i1++; i2++;
- /* 10 */
- c1 = block[i1]; c2 = block[i2];
- if (c1 != c2) return (c1 > c2);
- i1++; i2++;
- /* 11 */
- c1 = block[i1]; c2 = block[i2];
- if (c1 != c2) return (c1 > c2);
- i1++; i2++;
- /* 12 */
- c1 = block[i1]; c2 = block[i2];
- if (c1 != c2) return (c1 > c2);
- i1++; i2++;
-
- k = nblock + 8;
-
- do {
- /* 1 */
- c1 = block[i1]; c2 = block[i2];
- if (c1 != c2) return (c1 > c2);
- s1 = quadrant[i1]; s2 = quadrant[i2];
- if (s1 != s2) return (s1 > s2);
- i1++; i2++;
- /* 2 */
- c1 = block[i1]; c2 = block[i2];
- if (c1 != c2) return (c1 > c2);
- s1 = quadrant[i1]; s2 = quadrant[i2];
- if (s1 != s2) return (s1 > s2);
- i1++; i2++;
- /* 3 */
- c1 = block[i1]; c2 = block[i2];
- if (c1 != c2) return (c1 > c2);
- s1 = quadrant[i1]; s2 = quadrant[i2];
- if (s1 != s2) return (s1 > s2);
- i1++; i2++;
- /* 4 */
- c1 = block[i1]; c2 = block[i2];
- if (c1 != c2) return (c1 > c2);
- s1 = quadrant[i1]; s2 = quadrant[i2];
- if (s1 != s2) return (s1 > s2);
- i1++; i2++;
- /* 5 */
- c1 = block[i1]; c2 = block[i2];
- if (c1 != c2) return (c1 > c2);
- s1 = quadrant[i1]; s2 = quadrant[i2];
- if (s1 != s2) return (s1 > s2);
- i1++; i2++;
- /* 6 */
- c1 = block[i1]; c2 = block[i2];
- if (c1 != c2) return (c1 > c2);
- s1 = quadrant[i1]; s2 = quadrant[i2];
- if (s1 != s2) return (s1 > s2);
- i1++; i2++;
- /* 7 */
- c1 = block[i1]; c2 = block[i2];
- if (c1 != c2) return (c1 > c2);
- s1 = quadrant[i1]; s2 = quadrant[i2];
- if (s1 != s2) return (s1 > s2);
- i1++; i2++;
- /* 8 */
- c1 = block[i1]; c2 = block[i2];
- if (c1 != c2) return (c1 > c2);
- s1 = quadrant[i1]; s2 = quadrant[i2];
- if (s1 != s2) return (s1 > s2);
- i1++; i2++;
-
- if (i1 >= nblock) i1 -= nblock;
- if (i2 >= nblock) i2 -= nblock;
-
- k -= 8;
- (*budget)--;
- }
- while (k >= 0);
-
- return False;
-}
-
-
-/*---------------------------------------------*/
-/*--
- Knuth's increments seem to work better
- than Incerpi-Sedgewick here. Possibly
- because the number of elems to sort is
- usually small, typically <= 20.
---*/
-static
-Int32 incs[14] = { 1, 4, 13, 40, 121, 364, 1093, 3280,
- 9841, 29524, 88573, 265720,
- 797161, 2391484 };
-
-static
-void mainSimpleSort ( UInt32* ptr,
- UChar* block,
- UInt16* quadrant,
- Int32 nblock,
- Int32 lo,
- Int32 hi,
- Int32 d,
- Int32* budget )
-{
- Int32 i, j, h, bigN, hp;
- UInt32 v;
-
- bigN = hi - lo + 1;
- if (bigN < 2) return;
-
- hp = 0;
- while (incs[hp] < bigN) hp++;
- hp--;
-
- for (; hp >= 0; hp--) {
- h = incs[hp];
-
- i = lo + h;
- while (True) {
-
- /*-- copy 1 --*/
- if (i > hi) break;
- v = ptr[i];
- j = i;
- while ( mainGtU (
- ptr[j-h]+d, v+d, block, quadrant, nblock, budget
- ) ) {
- ptr[j] = ptr[j-h];
- j = j - h;
- if (j <= (lo + h - 1)) break;
- }
- ptr[j] = v;
- i++;
-
- /*-- copy 2 --*/
- if (i > hi) break;
- v = ptr[i];
- j = i;
- while ( mainGtU (
- ptr[j-h]+d, v+d, block, quadrant, nblock, budget
- ) ) {
- ptr[j] = ptr[j-h];
- j = j - h;
- if (j <= (lo + h - 1)) break;
- }
- ptr[j] = v;
- i++;
-
- /*-- copy 3 --*/
- if (i > hi) break;
- v = ptr[i];
- j = i;
- while ( mainGtU (
- ptr[j-h]+d, v+d, block, quadrant, nblock, budget
- ) ) {
- ptr[j] = ptr[j-h];
- j = j - h;
- if (j <= (lo + h - 1)) break;
- }
- ptr[j] = v;
- i++;
-
- if (*budget < 0) return;
- }
- }
-}
-
-
-/*---------------------------------------------*/
-/*--
- The following is an implementation of
- an elegant 3-way quicksort for strings,
- described in a paper "Fast Algorithms for
- Sorting and Searching Strings", by Robert
- Sedgewick and Jon L. Bentley.
---*/
-
-#define mswap(zz1, zz2) \
- { Int32 zztmp = zz1; zz1 = zz2; zz2 = zztmp; }
-
-#define mvswap(zzp1, zzp2, zzn) \
-{ \
- Int32 yyp1 = (zzp1); \
- Int32 yyp2 = (zzp2); \
- Int32 yyn = (zzn); \
- while (yyn > 0) { \
- mswap(ptr[yyp1], ptr[yyp2]); \
- yyp1++; yyp2++; yyn--; \
- } \
-}
-
-static
-__inline__
-UChar mmed3 ( UChar a, UChar b, UChar c )
-{
- UChar t;
- if (a > b) { t = a; a = b; b = t; };
- if (b > c) {
- b = c;
- if (a > b) b = a;
- }
- return b;
-}
-
-#define mmin(a,b) ((a) < (b)) ? (a) : (b)
-
-#define mpush(lz,hz,dz) { stackLo[sp] = lz; \
- stackHi[sp] = hz; \
- stackD [sp] = dz; \
- sp++; }
-
-#define mpop(lz,hz,dz) { sp--; \
- lz = stackLo[sp]; \
- hz = stackHi[sp]; \
- dz = stackD [sp]; }
-
-
-#define mnextsize(az) (nextHi[az]-nextLo[az])
-
-#define mnextswap(az,bz) \
- { Int32 tz; \
- tz = nextLo[az]; nextLo[az] = nextLo[bz]; nextLo[bz] = tz; \
- tz = nextHi[az]; nextHi[az] = nextHi[bz]; nextHi[bz] = tz; \
- tz = nextD [az]; nextD [az] = nextD [bz]; nextD [bz] = tz; }
-
-
-#define MAIN_QSORT_SMALL_THRESH 20
-#define MAIN_QSORT_DEPTH_THRESH (BZ_N_RADIX + BZ_N_QSORT)
-#define MAIN_QSORT_STACK_SIZE 100
-
-static
-void mainQSort3 ( UInt32* ptr,
- UChar* block,
- UInt16* quadrant,
- Int32 nblock,
- Int32 loSt,
- Int32 hiSt,
- Int32 dSt,
- Int32* budget )
-{
- Int32 unLo, unHi, ltLo, gtHi, n, m, med;
- Int32 sp, lo, hi, d;
-
- Int32 stackLo[MAIN_QSORT_STACK_SIZE];
- Int32 stackHi[MAIN_QSORT_STACK_SIZE];
- Int32 stackD [MAIN_QSORT_STACK_SIZE];
-
- Int32 nextLo[3];
- Int32 nextHi[3];
- Int32 nextD [3];
-
- sp = 0;
- mpush ( loSt, hiSt, dSt );
-
- while (sp > 0) {
-
- AssertH ( sp < MAIN_QSORT_STACK_SIZE - 2, 1001 );
-
- mpop ( lo, hi, d );
- if (hi - lo < MAIN_QSORT_SMALL_THRESH ||
- d > MAIN_QSORT_DEPTH_THRESH) {
- mainSimpleSort ( ptr, block, quadrant, nblock, lo, hi, d, budget );
- if (*budget < 0) return;
- continue;
- }
-
- med = (Int32)
- mmed3 ( block[ptr[ lo ]+d],
- block[ptr[ hi ]+d],
- block[ptr[ (lo+hi)>>1 ]+d] );
-
- unLo = ltLo = lo;
- unHi = gtHi = hi;
-
- while (True) {
- while (True) {
- if (unLo > unHi) break;
- n = ((Int32)block[ptr[unLo]+d]) - med;
- if (n == 0) {
- mswap(ptr[unLo], ptr[ltLo]);
- ltLo++; unLo++; continue;
- };
- if (n > 0) break;
- unLo++;
- }
- while (True) {
- if (unLo > unHi) break;
- n = ((Int32)block[ptr[unHi]+d]) - med;
- if (n == 0) {
- mswap(ptr[unHi], ptr[gtHi]);
- gtHi--; unHi--; continue;
- };
- if (n < 0) break;
- unHi--;
- }
- if (unLo > unHi) break;
- mswap(ptr[unLo], ptr[unHi]); unLo++; unHi--;
- }
-
- AssertD ( unHi == unLo-1, "mainQSort3(2)" );
-
- if (gtHi < ltLo) {
- mpush(lo, hi, d+1 );
- continue;
- }
-
- n = mmin(ltLo-lo, unLo-ltLo); mvswap(lo, unLo-n, n);
- m = mmin(hi-gtHi, gtHi-unHi); mvswap(unLo, hi-m+1, m);
-
- n = lo + unLo - ltLo - 1;
- m = hi - (gtHi - unHi) + 1;
-
- nextLo[0] = lo; nextHi[0] = n; nextD[0] = d;
- nextLo[1] = m; nextHi[1] = hi; nextD[1] = d;
- nextLo[2] = n+1; nextHi[2] = m-1; nextD[2] = d+1;
-
- if (mnextsize(0) < mnextsize(1)) mnextswap(0,1);
- if (mnextsize(1) < mnextsize(2)) mnextswap(1,2);
- if (mnextsize(0) < mnextsize(1)) mnextswap(0,1);
-
- AssertD (mnextsize(0) >= mnextsize(1), "mainQSort3(8)" );
- AssertD (mnextsize(1) >= mnextsize(2), "mainQSort3(9)" );
-
- mpush (nextLo[0], nextHi[0], nextD[0]);
- mpush (nextLo[1], nextHi[1], nextD[1]);
- mpush (nextLo[2], nextHi[2], nextD[2]);
- }
-}
-
-#undef mswap
-#undef mvswap
-#undef mpush
-#undef mpop
-#undef mmin
-#undef mnextsize
-#undef mnextswap
-#undef MAIN_QSORT_SMALL_THRESH
-#undef MAIN_QSORT_DEPTH_THRESH
-#undef MAIN_QSORT_STACK_SIZE
-
-
-/*---------------------------------------------*/
-/* Pre:
- nblock > N_OVERSHOOT
- block32 exists for [0 .. nblock-1 +N_OVERSHOOT]
- ((UChar*)block32) [0 .. nblock-1] holds block
- ptr exists for [0 .. nblock-1]
-
- Post:
- ((UChar*)block32) [0 .. nblock-1] holds block
- All other areas of block32 destroyed
- ftab [0 .. 65536 ] destroyed
- ptr [0 .. nblock-1] holds sorted order
- if (*budget < 0), sorting was abandoned
-*/
-
-#define BIGFREQ(b) (ftab[((b)+1) << 8] - ftab[(b) << 8])
-#define SETMASK (1 << 21)
-#define CLEARMASK (~(SETMASK))
-
-static
-void mainSort ( UInt32* ptr,
- UChar* block,
- UInt16* quadrant,
- UInt32* ftab,
- Int32 nblock,
- Int32 verb,
- Int32* budget )
-{
- Int32 i, j, k, ss, sb;
- Int32 runningOrder[256];
- Bool bigDone[256];
- Int32 copyStart[256];
- Int32 copyEnd [256];
- UChar c1;
- Int32 numQSorted;
- UInt16 s;
- if (verb >= 4) VPrintf0 ( " main sort initialise ...\n" );
-
- /*-- set up the 2-byte frequency table --*/
- for (i = 65536; i >= 0; i--) ftab[i] = 0;
-
- j = block[0] << 8;
- i = nblock-1;
- for (; i >= 3; i -= 4) {
- quadrant[i] = 0;
- j = (j >> 8) | ( ((UInt16)block[i]) << 8);
- ftab[j]++;
- quadrant[i-1] = 0;
- j = (j >> 8) | ( ((UInt16)block[i-1]) << 8);
- ftab[j]++;
- quadrant[i-2] = 0;
- j = (j >> 8) | ( ((UInt16)block[i-2]) << 8);
- ftab[j]++;
- quadrant[i-3] = 0;
- j = (j >> 8) | ( ((UInt16)block[i-3]) << 8);
- ftab[j]++;
- }
- for (; i >= 0; i--) {
- quadrant[i] = 0;
- j = (j >> 8) | ( ((UInt16)block[i]) << 8);
- ftab[j]++;
- }
-
- /*-- (emphasises close relationship of block & quadrant) --*/
- for (i = 0; i < BZ_N_OVERSHOOT; i++) {
- block [nblock+i] = block[i];
- quadrant[nblock+i] = 0;
- }
-
- if (verb >= 4) VPrintf0 ( " bucket sorting ...\n" );
-
- /*-- Complete the initial radix sort --*/
- for (i = 1; i <= 65536; i++) ftab[i] += ftab[i-1];
-
- s = block[0] << 8;
- i = nblock-1;
- for (; i >= 3; i -= 4) {
- s = (s >> 8) | (block[i] << 8);
- j = ftab[s] -1;
- ftab[s] = j;
- ptr[j] = i;
- s = (s >> 8) | (block[i-1] << 8);
- j = ftab[s] -1;
- ftab[s] = j;
- ptr[j] = i-1;
- s = (s >> 8) | (block[i-2] << 8);
- j = ftab[s] -1;
- ftab[s] = j;
- ptr[j] = i-2;
- s = (s >> 8) | (block[i-3] << 8);
- j = ftab[s] -1;
- ftab[s] = j;
- ptr[j] = i-3;
- }
- for (; i >= 0; i--) {
- s = (s >> 8) | (block[i] << 8);
- j = ftab[s] -1;
- ftab[s] = j;
- ptr[j] = i;
- }
-
- /*--
- Now ftab contains the first loc of every small bucket.
- Calculate the running order, from smallest to largest
- big bucket.
- --*/
- for (i = 0; i <= 255; i++) {
- bigDone [i] = False;
- runningOrder[i] = i;
- }
-
- {
- Int32 vv;
- Int32 h = 1;
- do h = 3 * h + 1; while (h <= 256);
- do {
- h = h / 3;
- for (i = h; i <= 255; i++) {
- vv = runningOrder[i];
- j = i;
- while ( BIGFREQ(runningOrder[j-h]) > BIGFREQ(vv) ) {
- runningOrder[j] = runningOrder[j-h];
- j = j - h;
- if (j <= (h - 1)) goto zero;
- }
- zero:
- runningOrder[j] = vv;
- }
- } while (h != 1);
- }
-
- /*--
- The main sorting loop.
- --*/
-
- numQSorted = 0;
-
- for (i = 0; i <= 255; i++) {
-
- /*--
- Process big buckets, starting with the least full.
- Basically this is a 3-step process in which we call
- mainQSort3 to sort the small buckets [ss, j], but
- also make a big effort to avoid the calls if we can.
- --*/
- ss = runningOrder[i];
-
- /*--
- Step 1:
- Complete the big bucket [ss] by quicksorting
- any unsorted small buckets [ss, j], for j != ss.
- Hopefully previous pointer-scanning phases have already
- completed many of the small buckets [ss, j], so
- we don't have to sort them at all.
- --*/
- for (j = 0; j <= 255; j++) {
- if (j != ss) {
- sb = (ss << 8) + j;
- if ( ! (ftab[sb] & SETMASK) ) {
- Int32 lo = ftab[sb] & CLEARMASK;
- Int32 hi = (ftab[sb+1] & CLEARMASK) - 1;
- if (hi > lo) {
- if (verb >= 4)
- VPrintf4 ( " qsort [0x%x, 0x%x] "
- "done %d this %d\n",
- ss, j, numQSorted, hi - lo + 1 );
- mainQSort3 (
- ptr, block, quadrant, nblock,
- lo, hi, BZ_N_RADIX, budget
- );
- numQSorted += (hi - lo + 1);
- if (*budget < 0) return;
- }
- }
- ftab[sb] |= SETMASK;
- }
- }
-
- AssertH ( !bigDone[ss], 1006 );
-
- /*--
- Step 2:
- Now scan this big bucket [ss] so as to synthesise the
- sorted order for small buckets [t, ss] for all t,
- including, magically, the bucket [ss,ss] too.
- This will avoid doing Real Work in subsequent Step 1's.
- --*/
- {
- for (j = 0; j <= 255; j++) {
- copyStart[j] = ftab[(j << 8) + ss] & CLEARMASK;
- copyEnd [j] = (ftab[(j << 8) + ss + 1] & CLEARMASK) - 1;
- }
- for (j = ftab[ss << 8] & CLEARMASK; j < copyStart[ss]; j++) {
- k = ptr[j]-1; if (k < 0) k += nblock;
- c1 = block[k];
- if (!bigDone[c1])
- ptr[ copyStart[c1]++ ] = k;
- }
- for (j = (ftab[(ss+1) << 8] & CLEARMASK) - 1; j > copyEnd[ss]; j--) {
- k = ptr[j]-1; if (k < 0) k += nblock;
- c1 = block[k];
- if (!bigDone[c1])
- ptr[ copyEnd[c1]-- ] = k;
- }
- }
-
- AssertH ( (copyStart[ss]-1 == copyEnd[ss])
- ||
- /* Extremely rare case missing in bzip2-1.0.0 and 1.0.1.
- Necessity for this case is demonstrated by compressing
- a sequence of approximately 48.5 million of character
- 251; 1.0.0/1.0.1 will then die here. */
- (copyStart[ss] == 0 && copyEnd[ss] == nblock-1),
- 1007 )
-
- for (j = 0; j <= 255; j++) ftab[(j << 8) + ss] |= SETMASK;
-
- /*--
- Step 3:
- The [ss] big bucket is now done. Record this fact,
- and update the quadrant descriptors. Remember to
- update quadrants in the overshoot area too, if
- necessary. The "if (i < 255)" test merely skips
- this updating for the last bucket processed, since
- updating for the last bucket is pointless.
-
- The quadrant array provides a way to incrementally
- cache sort orderings, as they appear, so as to
- make subsequent comparisons in fullGtU() complete
- faster. For repetitive blocks this makes a big
- difference (but not big enough to be able to avoid
- the fallback sorting mechanism, exponential radix sort).
-
- The precise meaning is: at all times:
-
- for 0 <= i < nblock and 0 <= j <= nblock
-
- if block[i] != block[j],
-
- then the relative values of quadrant[i] and
- quadrant[j] are meaningless.
-
- else {
- if quadrant[i] < quadrant[j]
- then the string starting at i lexicographically
- precedes the string starting at j
-
- else if quadrant[i] > quadrant[j]
- then the string starting at j lexicographically
- precedes the string starting at i
-
- else
- the relative ordering of the strings starting
- at i and j has not yet been determined.
- }
- --*/
- bigDone[ss] = True;
-
- if (i < 255) {
- Int32 bbStart = ftab[ss << 8] & CLEARMASK;
- Int32 bbSize = (ftab[(ss+1) << 8] & CLEARMASK) - bbStart;
- Int32 shifts = 0;
-
- while ((bbSize >> shifts) > 65534) shifts++;
-
- for (j = bbSize-1; j >= 0; j--) {
- Int32 a2update = ptr[bbStart + j];
- UInt16 qVal = (UInt16)(j >> shifts);
- quadrant[a2update] = qVal;
- if (a2update < BZ_N_OVERSHOOT)
- quadrant[a2update + nblock] = qVal;
- }
- AssertH ( ((bbSize-1) >> shifts) <= 65535, 1002 );
- }
-
- }
-
- if (verb >= 4)
- VPrintf3 ( " %d pointers, %d sorted, %d scanned\n",
- nblock, numQSorted, nblock - numQSorted );
-}
-
-#undef BIGFREQ
-#undef SETMASK
-#undef CLEARMASK
-
-
-/*---------------------------------------------*/
-/* Pre:
- nblock > 0
- arr2 exists for [0 .. nblock-1 +N_OVERSHOOT]
- ((UChar*)arr2) [0 .. nblock-1] holds block
- arr1 exists for [0 .. nblock-1]
-
- Post:
- ((UChar*)arr2) [0 .. nblock-1] holds block
- All other areas of block destroyed
- ftab [ 0 .. 65536 ] destroyed
- arr1 [0 .. nblock-1] holds sorted order
-*/
-void BZ2_blockSort ( EState* s )
-{
- UInt32* ptr = s->ptr;
- UChar* block = s->block;
- UInt32* ftab = s->ftab;
- Int32 nblock = s->nblock;
- Int32 verb = s->verbosity;
- Int32 wfact = s->workFactor;
- UInt16* quadrant;
- Int32 budget;
- Int32 budgetInit;
- Int32 i;
-
- if (nblock < 10000) {
- fallbackSort ( s->arr1, s->arr2, ftab, nblock, verb );
- } else {
- /* Calculate the location for quadrant, remembering to get
- the alignment right. Assumes that &(block[0]) is at least
- 2-byte aligned -- this should be ok since block is really
- the first section of arr2.
- */
- i = nblock+BZ_N_OVERSHOOT;
- if (i & 1) i++;
- quadrant = (UInt16*)(&(block[i]));
-
- /* (wfact-1) / 3 puts the default-factor-30
- transition point at very roughly the same place as
- with v0.1 and v0.9.0.
- Not that it particularly matters any more, since the
- resulting compressed stream is now the same regardless
- of whether or not we use the main sort or fallback sort.
- */
- if (wfact < 1 ) wfact = 1;
- if (wfact > 100) wfact = 100;
- budgetInit = nblock * ((wfact-1) / 3);
- budget = budgetInit;
-
- mainSort ( ptr, block, quadrant, ftab, nblock, verb, &budget );
- if (verb >= 3)
- VPrintf3 ( " %d work, %d block, ratio %5.2f\n",
- budgetInit - budget,
- nblock,
- (float)(budgetInit - budget) /
- (float)(nblock==0 ? 1 : nblock) );
- if (budget < 0) {
- if (verb >= 2)
- VPrintf0 ( " too repetitive; using fallback"
- " sorting algorithm\n" );
- fallbackSort ( s->arr1, s->arr2, ftab, nblock, verb );
- }
- }
-
- s->origPtr = -1;
- for (i = 0; i < s->nblock; i++)
- if (ptr[i] == 0)
- { s->origPtr = i; break; };
-
- AssertH( s->origPtr != -1, 1003 );
-}
-
-
-/*-------------------------------------------------------------*/
-/*--- end blocksort.c ---*/
-/*-------------------------------------------------------------*/
diff --git a/third-party/bzip2/bz-common.xsl b/third-party/bzip2/bz-common.xsl
deleted file mode 100644
index 66fcd6f..0000000
--- a/third-party/bzip2/bz-common.xsl
+++ /dev/null
@@ -1,39 +0,0 @@
-<?xml version="1.0"?> <!-- -*- sgml -*- -->
-<xsl:stylesheet
- xmlns:xsl="http://www.w3.org/1999/XSL/Transform" version="1.0">
-
-<!-- we like '1.2 Title' -->
-<xsl:param name="section.autolabel" select="'1'"/>
-<xsl:param name="section.label.includes.component.label" select="'1'"/>
-
-<!-- Do not put 'Chapter' at the start of eg 'Chapter 1. Doing This' -->
-<xsl:param name="local.l10n.xml" select="document('')"/>
-<l:i18n xmlns:l="http://docbook.sourceforge.net/xmlns/l10n/1.0">
- <l:l10n language="en">
- <l:context name="title-numbered">
- <l:template name="chapter" text="%n. %t"/>
- </l:context>
- </l:l10n>
-</l:i18n>
-
-<!-- don't generate sub-tocs for qanda sets -->
-<xsl:param name="generate.toc">
-set toc,title
-book toc,title,figure,table,example,equation
-chapter toc,title
-section toc
-sect1 toc
-sect2 toc
-sect3 toc
-sect4 nop
-sect5 nop
-qandaset toc
-qandadiv nop
-appendix toc,title
-article/appendix nop
-article toc,title
-preface toc,title
-reference toc,title
-</xsl:param>
-
-</xsl:stylesheet>
diff --git a/third-party/bzip2/bz-fo.xsl b/third-party/bzip2/bz-fo.xsl
deleted file mode 100644
index ba3e301..0000000
--- a/third-party/bzip2/bz-fo.xsl
+++ /dev/null
@@ -1,276 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?> <!-- -*- sgml -*- -->
-<xsl:stylesheet xmlns:xsl="http://www.w3.org/1999/XSL/Transform"
- xmlns:fo="http://www.w3.org/1999/XSL/Format" version="1.0">
-
-<xsl:import href="http://docbook.sourceforge.net/release/xsl/current/fo/docbook.xsl"/>
-<xsl:import href="bz-common.xsl"/>
-
-<!-- set indent = yes while debugging, then change to NO -->
-<xsl:output method="xml" indent="yes"/>
-
-<!-- ensure only passivetex extensions are on -->
-<xsl:param name="stylesheet.result.type" select="'fo'"/>
-<!-- fo extensions: PDF bookmarks and index terms -->
-<xsl:param name="use.extensions" select="'1'"/>
-<xsl:param name="xep.extensions" select="0"/>
-<xsl:param name="fop.extensions" select="0"/>
-<xsl:param name="saxon.extensions" select="0"/>
-<xsl:param name="passivetex.extensions" select="1"/>
-<xsl:param name="tablecolumns.extension" select="'1'"/>
-
-<!-- ensure we are using single sided -->
-<xsl:param name="double.sided" select="'0'"/>
-
-<!-- insert cross references to page numbers -->
-<xsl:param name="insert.xref.page.number" select="1"/>
-
-<!-- <?custom-pagebreak?> inserts a page break at this point -->
-<xsl:template match="processing-instruction('custom-pagebreak')">
- <fo:block break-before='page'/>
-</xsl:template>
-
-<!-- show links in color -->
-<xsl:attribute-set name="xref.properties">
- <xsl:attribute name="color">blue</xsl:attribute>
-</xsl:attribute-set>
-
-<!-- make pre listings indented a bit + a bg colour -->
-<xsl:template match="programlisting | screen">
- <fo:block start-indent="0.25in" wrap-option="no-wrap"
- white-space-collapse="false" text-align="start"
- font-family="monospace" background-color="#f2f2f9"
- linefeed-treatment="preserve"
- xsl:use-attribute-sets="normal.para.spacing">
- <xsl:apply-templates/>
- </fo:block>
-</xsl:template>
-<!-- make verbatim output prettier -->
-<xsl:template match="literallayout">
- <fo:block start-indent="0.25in" wrap-option="no-wrap"
- white-space-collapse="false" text-align="start"
- font-family="monospace" background-color="#edf7f4"
- linefeed-treatment="preserve"
- space-before="0em" space-after="0em">
- <xsl:apply-templates/>
- </fo:block>
-</xsl:template>
-
-<!-- workaround bug in passivetex fo output for itemizedlist -->
-<xsl:template match="itemizedlist/listitem">
- <xsl:variable name="id">
- <xsl:call-template name="object.id"/></xsl:variable>
- <xsl:variable name="itemsymbol">
- <xsl:call-template name="list.itemsymbol">
- <xsl:with-param name="node" select="parent::itemizedlist"/>
- </xsl:call-template>
- </xsl:variable>
- <xsl:variable name="item.contents">
- <fo:list-item-label end-indent="label-end()">
- <fo:block>
- <xsl:choose>
- <xsl:when test="$itemsymbol='disc'">•</xsl:when>
- <xsl:when test="$itemsymbol='bullet'">•</xsl:when>
- <xsl:otherwise>•</xsl:otherwise>
- </xsl:choose>
- </fo:block>
- </fo:list-item-label>
- <fo:list-item-body start-indent="body-start()">
- <xsl:apply-templates/> <!-- removed extra block wrapper -->
- </fo:list-item-body>
- </xsl:variable>
- <xsl:choose>
- <xsl:when test="parent::*/@spacing = 'compact'">
- <fo:list-item id="{$id}"
- xsl:use-attribute-sets="compact.list.item.spacing">
- <xsl:copy-of select="$item.contents"/>
- </fo:list-item>
- </xsl:when>
- <xsl:otherwise>
- <fo:list-item id="{$id}" xsl:use-attribute-sets="list.item.spacing">
- <xsl:copy-of select="$item.contents"/>
- </fo:list-item>
- </xsl:otherwise>
- </xsl:choose>
-</xsl:template>
-
-<!-- workaround bug in passivetex fo output for orderedlist -->
-<xsl:template match="orderedlist/listitem">
- <xsl:variable name="id">
- <xsl:call-template name="object.id"/></xsl:variable>
- <xsl:variable name="item.contents">
- <fo:list-item-label end-indent="label-end()">
- <fo:block>
- <xsl:apply-templates select="." mode="item-number"/>
- </fo:block>
- </fo:list-item-label>
- <fo:list-item-body start-indent="body-start()">
- <xsl:apply-templates/> <!-- removed extra block wrapper -->
- </fo:list-item-body>
- </xsl:variable>
- <xsl:choose>
- <xsl:when test="parent::*/@spacing = 'compact'">
- <fo:list-item id="{$id}"
- xsl:use-attribute-sets="compact.list.item.spacing">
- <xsl:copy-of select="$item.contents"/>
- </fo:list-item>
- </xsl:when>
- <xsl:otherwise>
- <fo:list-item id="{$id}" xsl:use-attribute-sets="list.item.spacing">
- <xsl:copy-of select="$item.contents"/>
- </fo:list-item>
- </xsl:otherwise>
- </xsl:choose>
-</xsl:template>
-
-<!-- workaround bug in passivetex fo output for variablelist -->
-<xsl:param name="variablelist.as.blocks" select="1"/>
-<xsl:template match="varlistentry" mode="vl.as.blocks">
- <xsl:variable name="id">
- <xsl:call-template name="object.id"/></xsl:variable>
- <fo:block id="{$id}" xsl:use-attribute-sets="list.item.spacing"
- keep-together.within-column="always"
- keep-with-next.within-column="always">
- <xsl:apply-templates select="term"/>
- </fo:block>
- <fo:block start-indent="0.5in" end-indent="0in"
- space-after.minimum="0.2em"
- space-after.optimum="0.4em"
- space-after.maximum="0.6em">
- <fo:block>
- <xsl:apply-templates select="listitem"/>
- </fo:block>
- </fo:block>
-</xsl:template>
-
-
-<!-- workaround bug in footers: force right-align w/two 80|30 cols -->
-<xsl:template name="footer.table">
- <xsl:param name="pageclass" select="''"/>
- <xsl:param name="sequence" select="''"/>
- <xsl:param name="gentext-key" select="''"/>
- <xsl:choose>
- <xsl:when test="$pageclass = 'index'">
- <xsl:attribute name="margin-left">0pt</xsl:attribute>
- </xsl:when>
- </xsl:choose>
- <xsl:variable name="candidate">
- <fo:table table-layout="fixed" width="100%">
- <fo:table-column column-number="1" column-width="80%"/>
- <fo:table-column column-number="2" column-width="20%"/>
- <fo:table-body>
- <fo:table-row height="14pt">
- <fo:table-cell text-align="left" display-align="after">
- <xsl:attribute name="relative-align">baseline</xsl:attribute>
- <fo:block>
- <fo:block> </fo:block><!-- empty cell -->
- </fo:block>
- </fo:table-cell>
- <fo:table-cell text-align="center" display-align="after">
- <xsl:attribute name="relative-align">baseline</xsl:attribute>
- <fo:block>
- <xsl:call-template name="footer.content">
- <xsl:with-param name="pageclass" select="$pageclass"/>
- <xsl:with-param name="sequence" select="$sequence"/>
- <xsl:with-param name="position" select="'center'"/>
- <xsl:with-param name="gentext-key" select="$gentext-key"/>
- </xsl:call-template>
- </fo:block>
- </fo:table-cell>
- </fo:table-row>
- </fo:table-body>
- </fo:table>
- </xsl:variable>
- <!-- Really output a footer? -->
- <xsl:choose>
- <xsl:when test="$pageclass='titlepage' and $gentext-key='book'
- and $sequence='first'">
- <!-- no, book titlepages have no footers at all -->
- </xsl:when>
- <xsl:when test="$sequence = 'blank' and $footers.on.blank.pages = 0">
- <!-- no output -->
- </xsl:when>
- <xsl:otherwise>
- <xsl:copy-of select="$candidate"/>
- </xsl:otherwise>
- </xsl:choose>
-</xsl:template>
-
-
-<!-- fix bug in headers: force right-align w/two 40|60 cols -->
-<xsl:template name="header.table">
- <xsl:param name="pageclass" select="''"/>
- <xsl:param name="sequence" select="''"/>
- <xsl:param name="gentext-key" select="''"/>
- <xsl:choose>
- <xsl:when test="$pageclass = 'index'">
- <xsl:attribute name="margin-left">0pt</xsl:attribute>
- </xsl:when>
- </xsl:choose>
- <xsl:variable name="candidate">
- <fo:table table-layout="fixed" width="100%">
- <xsl:call-template name="head.sep.rule">
- <xsl:with-param name="pageclass" select="$pageclass"/>
- <xsl:with-param name="sequence" select="$sequence"/>
- <xsl:with-param name="gentext-key" select="$gentext-key"/>
- </xsl:call-template>
- <fo:table-column column-number="1" column-width="40%"/>
- <fo:table-column column-number="2" column-width="60%"/>
- <fo:table-body>
- <fo:table-row height="14pt">
- <fo:table-cell text-align="left" display-align="before">
- <xsl:attribute name="relative-align">baseline</xsl:attribute>
- <fo:block>
- <fo:block> </fo:block><!-- empty cell -->
- </fo:block>
- </fo:table-cell>
- <fo:table-cell text-align="center" display-align="before">
- <xsl:attribute name="relative-align">baseline</xsl:attribute>
- <fo:block>
- <xsl:call-template name="header.content">
- <xsl:with-param name="pageclass" select="$pageclass"/>
- <xsl:with-param name="sequence" select="$sequence"/>
- <xsl:with-param name="position" select="'center'"/>
- <xsl:with-param name="gentext-key" select="$gentext-key"/>
- </xsl:call-template>
- </fo:block>
- </fo:table-cell>
- </fo:table-row>
- </fo:table-body>
- </fo:table>
- </xsl:variable>
- <!-- Really output a header? -->
- <xsl:choose>
- <xsl:when test="$pageclass = 'titlepage' and $gentext-key = 'book'
- and $sequence='first'">
- <!-- no, book titlepages have no headers at all -->
- </xsl:when>
- <xsl:when test="$sequence = 'blank' and $headers.on.blank.pages = 0">
- <!-- no output -->
- </xsl:when>
- <xsl:otherwise>
- <xsl:copy-of select="$candidate"/>
- </xsl:otherwise>
- </xsl:choose>
-</xsl:template>
-
-
-<!-- Bug-fix for Suse 10 PassiveTex version -->
-<!-- Precompute attribute values 'cos PassiveTex is too stupid: -->
-<xsl:attribute-set name="component.title.properties">
- <xsl:attribute name="keep-with-next.within-column">always</xsl:attribute>
- <xsl:attribute name="space-before.optimum">
- <xsl:value-of select="concat($body.font.master, 'pt')"/>
- </xsl:attribute>
- <xsl:attribute name="space-before.minimum">
- <xsl:value-of select="$body.font.master * 0.8"/>
- <xsl:text>pt</xsl:text>
- </xsl:attribute>
- <xsl:attribute name="space-before.maximum">
- <xsl:value-of select="$body.font.master * 1.2"/>
- <xsl:text>pt</xsl:text>
- </xsl:attribute>
- <xsl:attribute name="hyphenate">false</xsl:attribute>
-</xsl:attribute-set>
-
-
-</xsl:stylesheet>
diff --git a/third-party/bzip2/bz-html.xsl b/third-party/bzip2/bz-html.xsl
deleted file mode 100644
index 1785fff..0000000
--- a/third-party/bzip2/bz-html.xsl
+++ /dev/null
@@ -1,20 +0,0 @@
-<?xml version="1.0"?> <!-- -*- sgml -*- -->
-<!DOCTYPE xsl:stylesheet [ <!ENTITY bz-css SYSTEM "./bzip.css"> ]>
-
-<xsl:stylesheet
- xmlns:xsl="http://www.w3.org/1999/XSL/Transform" version="1.0">
-
-<xsl:import href="http://docbook.sourceforge.net/release/xsl/current/html/docbook.xsl"/>
-<xsl:import href="bz-common.xsl"/>
-
-<!-- use 8859-1 encoding -->
-<xsl:output method="html" encoding="ISO-8859-1" indent="yes"/>
-
-<!-- we include the css directly when generating one large file -->
-<xsl:template name="user.head.content">
- <style type="text/css" media="screen">
- <xsl:text>&bz-css;</xsl:text>
- </style>
-</xsl:template>
-
-</xsl:stylesheet>
diff --git a/third-party/bzip2/bzdiff b/third-party/bzip2/bzdiff
deleted file mode 100644
index 6fc38f9..0000000
--- a/third-party/bzip2/bzdiff
+++ /dev/null
@@ -1,76 +0,0 @@
-#!/bin/sh
-# sh is buggy on RS/6000 AIX 3.2. Replace above line with #!/bin/ksh
-
-# Bzcmp/diff wrapped for bzip2,
-# adapted from zdiff by Philippe Troin <phil at fifi.org> for Debian GNU/Linux.
-
-# Bzcmp and bzdiff are used to invoke the cmp or the diff pro-
-# gram on compressed files. All options specified are passed
-# directly to cmp or diff. If only 1 file is specified, then
-# the files compared are file1 and an uncompressed file1.gz.
-# If two files are specified, then they are uncompressed (if
-# necessary) and fed to cmp or diff. The exit status from cmp
-# or diff is preserved.
-
-PATH="/usr/bin:/bin:$PATH"; export PATH
-prog=`echo $0 | sed 's|.*/||'`
-case "$prog" in
- *cmp) comp=${CMP-cmp} ;;
- *) comp=${DIFF-diff} ;;
-esac
-
-OPTIONS=
-FILES=
-for ARG
-do
- case "$ARG" in
- -*) OPTIONS="$OPTIONS $ARG";;
- *) if test -f "$ARG"; then
- FILES="$FILES $ARG"
- else
- echo "${prog}: $ARG not found or not a regular file"
- exit 1
- fi ;;
- esac
-done
-if test -z "$FILES"; then
- echo "Usage: $prog [${comp}_options] file [file]"
- exit 1
-fi
-tmp=`mktemp ${TMPDIR:-/tmp}/bzdiff.XXXXXXXXXX` || {
- echo 'cannot create a temporary file' >&2
- exit 1
-}
-set $FILES
-if test $# -eq 1; then
- FILE=`echo "$1" | sed 's/.bz2$//'`
- bzip2 -cd "$FILE.bz2" | $comp $OPTIONS - "$FILE"
- STAT="$?"
-
-elif test $# -eq 2; then
- case "$1" in
- *.bz2)
- case "$2" in
- *.bz2)
- F=`echo "$2" | sed 's|.*/||;s|.bz2$||'`
- bzip2 -cdfq "$2" > $tmp
- bzip2 -cdfq "$1" | $comp $OPTIONS - $tmp
- STAT="$?"
- /bin/rm -f $tmp;;
-
- *) bzip2 -cdfq "$1" | $comp $OPTIONS - "$2"
- STAT="$?";;
- esac;;
- *) case "$2" in
- *.bz2)
- bzip2 -cdfq "$2" | $comp $OPTIONS "$1" -
- STAT="$?";;
- *) $comp $OPTIONS "$1" "$2"
- STAT="$?";;
- esac;;
- esac
- exit "$STAT"
-else
- echo "Usage: $prog [${comp}_options] file [file]"
- exit 1
-fi
diff --git a/third-party/bzip2/bzdiff.1 b/third-party/bzip2/bzdiff.1
deleted file mode 100644
index adb7a8e..0000000
--- a/third-party/bzip2/bzdiff.1
+++ /dev/null
@@ -1,47 +0,0 @@
-\"Shamelessly copied from zmore.1 by Philippe Troin <phil at fifi.org>
-\"for Debian GNU/Linux
-.TH BZDIFF 1
-.SH NAME
-bzcmp, bzdiff \- compare bzip2 compressed files
-.SH SYNOPSIS
-.B bzcmp
-[ cmp_options ] file1
-[ file2 ]
-.br
-.B bzdiff
-[ diff_options ] file1
-[ file2 ]
-.SH DESCRIPTION
-.I Bzcmp
-and
-.I bzdiff
-are used to invoke the
-.I cmp
-or the
-.I diff
-program on bzip2 compressed files. All options specified are passed
-directly to
-.I cmp
-or
-.IR diff "."
-If only 1 file is specified, then the files compared are
-.I file1
-and an uncompressed
-.IR file1 ".bz2."
-If two files are specified, then they are uncompressed if necessary and fed to
-.I cmp
-or
-.IR diff "."
-The exit status from
-.I cmp
-or
-.I diff
-is preserved.
-.SH "SEE ALSO"
-cmp(1), diff(1), bzmore(1), bzless(1), bzgrep(1), bzip2(1)
-.SH BUGS
-Messages from the
-.I cmp
-or
-.I diff
-programs refer to temporary filenames instead of those specified.
diff --git a/third-party/bzip2/bzgrep b/third-party/bzip2/bzgrep
deleted file mode 100644
index 9a04b83..0000000
--- a/third-party/bzip2/bzgrep
+++ /dev/null
@@ -1,75 +0,0 @@
-#!/bin/sh
-
-# Bzgrep wrapped for bzip2,
-# adapted from zgrep by Philippe Troin <phil at fifi.org> for Debian GNU/Linux.
-## zgrep notice:
-## zgrep -- a wrapper around a grep program that decompresses files as needed
-## Adapted from a version sent by Charles Levert <charles at comm.polymtl.ca>
-
-PATH="/usr/bin:$PATH"; export PATH
-
-prog=`echo $0 | sed 's|.*/||'`
-case "$prog" in
- *egrep) grep=${EGREP-egrep} ;;
- *fgrep) grep=${FGREP-fgrep} ;;
- *) grep=${GREP-grep} ;;
-esac
-pat=""
-while test $# -ne 0; do
- case "$1" in
- -e | -f) opt="$opt $1"; shift; pat="$1"
- if test "$grep" = grep; then # grep is buggy with -e on SVR4
- grep=egrep
- fi;;
- -A | -B) opt="$opt $1 $2"; shift;;
- -*) opt="$opt $1";;
- *) if test -z "$pat"; then
- pat="$1"
- else
- break;
- fi;;
- esac
- shift
-done
-
-if test -z "$pat"; then
- echo "grep through bzip2 files"
- echo "usage: $prog [grep_options] pattern [files]"
- exit 1
-fi
-
-list=0
-silent=0
-op=`echo "$opt" | sed -e 's/ //g' -e 's/-//g'`
-case "$op" in
- *l*) list=1
-esac
-case "$op" in
- *h*) silent=1
-esac
-
-if test $# -eq 0; then
- bzip2 -cdfq | $grep $opt "$pat"
- exit $?
-fi
-
-res=0
-for i do
- if test -f "$i"; then :; else if test -f "$i.bz2"; then i="$i.bz2"; fi; fi
- if test $list -eq 1; then
- bzip2 -cdfq "$i" | $grep $opt "$pat" 2>&1 > /dev/null && echo $i
- r=$?
- elif test $# -eq 1 -o $silent -eq 1; then
- bzip2 -cdfq "$i" | $grep $opt "$pat"
- r=$?
- else
- j=${i//\\/\\\\}
- j=${j//|/\\|}
- j=${j//&/\\&}
- j=`printf "%s" "$j" | tr '\n' ' '`
- bzip2 -cdfq "$i" | $grep $opt "$pat" | sed "s|^|${j}:|"
- r=$?
- fi
- test "$r" -ne 0 && res="$r"
-done
-exit $res
diff --git a/third-party/bzip2/bzgrep.1 b/third-party/bzip2/bzgrep.1
deleted file mode 100644
index 930af8c..0000000
--- a/third-party/bzip2/bzgrep.1
+++ /dev/null
@@ -1,56 +0,0 @@
-\"Shamelessly copied from zmore.1 by Philippe Troin <phil at fifi.org>
-\"for Debian GNU/Linux
-.TH BZGREP 1
-.SH NAME
-bzgrep, bzfgrep, bzegrep \- search possibly bzip2 compressed files for a regular expression
-.SH SYNOPSIS
-.B bzgrep
-[ grep_options ]
-.BI [\ -e\ ] " pattern"
-.IR filename ".\|.\|."
-.br
-.B bzegrep
-[ egrep_options ]
-.BI [\ -e\ ] " pattern"
-.IR filename ".\|.\|."
-.br
-.B bzfgrep
-[ fgrep_options ]
-.BI [\ -e\ ] " pattern"
-.IR filename ".\|.\|."
-.SH DESCRIPTION
-.IR Bzgrep
-is used to invoke the
-.I grep
-on bzip2-compressed files. All options specified are passed directly to
-.I grep.
-If no file is specified, then the standard input is decompressed
-if necessary and fed to grep.
-Otherwise the given files are uncompressed if necessary and fed to
-.I grep.
-.PP
-If
-.I bzgrep
-is invoked as
-.I bzegrep
-or
-.I bzfgrep
-then
-.I egrep
-or
-.I fgrep
-is used instead of
-.I grep.
-If the GREP environment variable is set,
-.I bzgrep
-uses it as the
-.I grep
-program to be invoked. For example:
-
- for sh: GREP=fgrep bzgrep string files
- for csh: (setenv GREP fgrep; bzgrep string files)
-.SH AUTHOR
-Charles Levert (charles at comm.polymtl.ca). Adapted to bzip2 by Philippe
-Troin <phil at fifi.org> for Debian GNU/Linux.
-.SH "SEE ALSO"
-grep(1), egrep(1), fgrep(1), bzdiff(1), bzmore(1), bzless(1), bzip2(1)
diff --git a/third-party/bzip2/bzip.css b/third-party/bzip2/bzip.css
deleted file mode 100644
index 43193d8..0000000
--- a/third-party/bzip2/bzip.css
+++ /dev/null
@@ -1,74 +0,0 @@
-/* Colours:
-#74240f dark brown h1, h2, h3, h4
-#336699 medium blue links
-#339999 turquoise link hover colour
-#202020 almost black general text
-#761596 purple md5sum text
-#626262 dark gray pre border
-#eeeeee very light gray pre background
-#f2f2f9 very light blue nav table background
-#3366cc medium blue nav table border
-*/
-
-a, a:link, a:visited, a:active { color: #336699; }
-a:hover { color: #339999; }
-
-body { font: 80%/126% sans-serif; }
-h1, h2, h3, h4 { color: #74240f; }
-
-dt { color: #336699; font-weight: bold }
-dd {
- margin-left: 1.5em;
- padding-bottom: 0.8em;
-}
-
-/* -- ruler -- */
-div.hr_blue {
- height: 3px;
- background:#ffffff url("/images/hr_blue.png") repeat-x; }
-div.hr_blue hr { display:none; }
-
-/* release styles */
-#release p { margin-top: 0.4em; }
-#release .md5sum { color: #761596; }
-
-
-/* ------ styles for docs|manuals|howto ------ */
-/* -- lists -- */
-ul {
- margin: 0px 4px 16px 16px;
- padding: 0px;
- list-style: url("/images/li-blue.png");
-}
-ul li {
- margin-bottom: 10px;
-}
-ul ul {
- list-style-type: none;
- list-style-image: none;
- margin-left: 0px;
-}
-
-/* header / footer nav tables */
-table.nav {
- border: solid 1px #3366cc;
- background: #f2f2f9;
- background-color: #f2f2f9;
- margin-bottom: 0.5em;
-}
-/* don't have underlined links in chunked nav menus */
-table.nav a { text-decoration: none; }
-table.nav a:hover { text-decoration: underline; }
-table.nav td { font-size: 85%; }
-
-code, tt, pre { font-size: 120%; }
-code, tt { color: #761596; }
-
-div.literallayout, pre.programlisting, pre.screen {
- color: #000000;
- padding: 0.5em;
- background: #eeeeee;
- border: 1px solid #626262;
- background-color: #eeeeee;
- margin: 4px 0px 4px 0px;
-}
diff --git a/third-party/bzip2/bzip2.1 b/third-party/bzip2/bzip2.1
deleted file mode 100644
index ce3a78e..0000000
--- a/third-party/bzip2/bzip2.1
+++ /dev/null
@@ -1,454 +0,0 @@
-.PU
-.TH bzip2 1
-.SH NAME
-bzip2, bunzip2 \- a block-sorting file compressor, v1.0.6
-.br
-bzcat \- decompresses files to stdout
-.br
-bzip2recover \- recovers data from damaged bzip2 files
-
-.SH SYNOPSIS
-.ll +8
-.B bzip2
-.RB [ " \-cdfkqstvzVL123456789 " ]
-[
-.I "filenames \&..."
-]
-.ll -8
-.br
-.B bunzip2
-.RB [ " \-fkvsVL " ]
-[
-.I "filenames \&..."
-]
-.br
-.B bzcat
-.RB [ " \-s " ]
-[
-.I "filenames \&..."
-]
-.br
-.B bzip2recover
-.I "filename"
-
-.SH DESCRIPTION
-.I bzip2
-compresses files using the Burrows-Wheeler block sorting
-text compression algorithm, and Huffman coding. Compression is
-generally considerably better than that achieved by more conventional
-LZ77/LZ78-based compressors, and approaches the performance of the PPM
-family of statistical compressors.
-
-The command-line options are deliberately very similar to
-those of
-.I GNU gzip,
-but they are not identical.
-
-.I bzip2
-expects a list of file names to accompany the
-command-line flags. Each file is replaced by a compressed version of
-itself, with the name "original_name.bz2".
-Each compressed file
-has the same modification date, permissions, and, when possible,
-ownership as the corresponding original, so that these properties can
-be correctly restored at decompression time. File name handling is
-naive in the sense that there is no mechanism for preserving original
-file names, permissions, ownerships or dates in filesystems which lack
-these concepts, or have serious file name length restrictions, such as
-MS-DOS.
-
-.I bzip2
-and
-.I bunzip2
-will by default not overwrite existing
-files. If you want this to happen, specify the \-f flag.
-
-If no file names are specified,
-.I bzip2
-compresses from standard
-input to standard output. In this case,
-.I bzip2
-will decline to
-write compressed output to a terminal, as this would be entirely
-incomprehensible and therefore pointless.
-
-.I bunzip2
-(or
-.I bzip2 \-d)
-decompresses all
-specified files. Files which were not created by
-.I bzip2
-will be detected and ignored, and a warning issued.
-.I bzip2
-attempts to guess the filename for the decompressed file
-from that of the compressed file as follows:
-
- filename.bz2 becomes filename
- filename.bz becomes filename
- filename.tbz2 becomes filename.tar
- filename.tbz becomes filename.tar
- anyothername becomes anyothername.out
-
-If the file does not end in one of the recognised endings,
-.I .bz2,
-.I .bz,
-.I .tbz2
-or
-.I .tbz,
-.I bzip2
-complains that it cannot
-guess the name of the original file, and uses the original name
-with
-.I .out
-appended.
-
-As with compression, supplying no
-filenames causes decompression from
-standard input to standard output.
-
-.I bunzip2
-will correctly decompress a file which is the
-concatenation of two or more compressed files. The result is the
-concatenation of the corresponding uncompressed files. Integrity
-testing (\-t)
-of concatenated
-compressed files is also supported.
-
-You can also compress or decompress files to the standard output by
-giving the \-c flag. Multiple files may be compressed and
-decompressed like this. The resulting outputs are fed sequentially to
-stdout. Compression of multiple files
-in this manner generates a stream
-containing multiple compressed file representations. Such a stream
-can be decompressed correctly only by
-.I bzip2
-version 0.9.0 or
-later. Earlier versions of
-.I bzip2
-will stop after decompressing
-the first file in the stream.
-
-.I bzcat
-(or
-.I bzip2 -dc)
-decompresses all specified files to
-the standard output.
-
-.I bzip2
-will read arguments from the environment variables
-.I BZIP2
-and
-.I BZIP,
-in that order, and will process them
-before any arguments read from the command line. This gives a
-convenient way to supply default arguments.
-
-Compression is always performed, even if the compressed
-file is slightly
-larger than the original. Files of less than about one hundred bytes
-tend to get larger, since the compression mechanism has a constant
-overhead in the region of 50 bytes. Random data (including the output
-of most file compressors) is coded at about 8.05 bits per byte, giving
-an expansion of around 0.5%.
-
-As a self-check for your protection,
-.I
-bzip2
-uses 32-bit CRCs to
-make sure that the decompressed version of a file is identical to the
-original. This guards against corruption of the compressed data, and
-against undetected bugs in
-.I bzip2
-(hopefully very unlikely). The
-chances of data corruption going undetected is microscopic, about one
-chance in four billion for each file processed. Be aware, though, that
-the check occurs upon decompression, so it can only tell you that
-something is wrong. It can't help you
-recover the original uncompressed
-data. You can use
-.I bzip2recover
-to try to recover data from
-damaged files.
-
-Return values: 0 for a normal exit, 1 for environmental problems (file
-not found, invalid flags, I/O errors, &c), 2 to indicate a corrupt
-compressed file, 3 for an internal consistency error (eg, bug) which
-caused
-.I bzip2
-to panic.
-
-.SH OPTIONS
-.TP
-.B \-c --stdout
-Compress or decompress to standard output.
-.TP
-.B \-d --decompress
-Force decompression.
-.I bzip2,
-.I bunzip2
-and
-.I bzcat
-are
-really the same program, and the decision about what actions to take is
-done on the basis of which name is used. This flag overrides that
-mechanism, and forces
-.I bzip2
-to decompress.
-.TP
-.B \-z --compress
-The complement to \-d: forces compression, regardless of the
-invocation name.
-.TP
-.B \-t --test
-Check integrity of the specified file(s), but don't decompress them.
-This really performs a trial decompression and throws away the result.
-.TP
-.B \-f --force
-Force overwrite of output files. Normally,
-.I bzip2
-will not overwrite
-existing output files. Also forces
-.I bzip2
-to break hard links
-to files, which it otherwise wouldn't do.
-
-bzip2 normally declines to decompress files which don't have the
-correct magic header bytes. If forced (-f), however, it will pass
-such files through unmodified. This is how GNU gzip behaves.
-.TP
-.B \-k --keep
-Keep (don't delete) input files during compression
-or decompression.
-.TP
-.B \-s --small
-Reduce memory usage, for compression, decompression and testing. Files
-are decompressed and tested using a modified algorithm which only
-requires 2.5 bytes per block byte. This means any file can be
-decompressed in 2300k of memory, albeit at about half the normal speed.
-
-During compression, \-s selects a block size of 200k, which limits
-memory use to around the same figure, at the expense of your compression
-ratio. In short, if your machine is low on memory (8 megabytes or
-less), use \-s for everything. See MEMORY MANAGEMENT below.
-.TP
-.B \-q --quiet
-Suppress non-essential warning messages. Messages pertaining to
-I/O errors and other critical events will not be suppressed.
-.TP
-.B \-v --verbose
-Verbose mode -- show the compression ratio for each file processed.
-Further \-v's increase the verbosity level, spewing out lots of
-information which is primarily of interest for diagnostic purposes.
-.TP
-.B \-L --license -V --version
-Display the software version, license terms and conditions.
-.TP
-.B \-1 (or \-\-fast) to \-9 (or \-\-best)
-Set the block size to 100 k, 200 k .. 900 k when compressing. Has no
-effect when decompressing. See MEMORY MANAGEMENT below.
-The \-\-fast and \-\-best aliases are primarily for GNU gzip
-compatibility. In particular, \-\-fast doesn't make things
-significantly faster.
-And \-\-best merely selects the default behaviour.
-.TP
-.B \--
-Treats all subsequent arguments as file names, even if they start
-with a dash. This is so you can handle files with names beginning
-with a dash, for example: bzip2 \-- \-myfilename.
-.TP
-.B \--repetitive-fast --repetitive-best
-These flags are redundant in versions 0.9.5 and above. They provided
-some coarse control over the behaviour of the sorting algorithm in
-earlier versions, which was sometimes useful. 0.9.5 and above have an
-improved algorithm which renders these flags irrelevant.
-
-.SH MEMORY MANAGEMENT
-.I bzip2
-compresses large files in blocks. The block size affects
-both the compression ratio achieved, and the amount of memory needed for
-compression and decompression. The flags \-1 through \-9
-specify the block size to be 100,000 bytes through 900,000 bytes (the
-default) respectively. At decompression time, the block size used for
-compression is read from the header of the compressed file, and
-.I bunzip2
-then allocates itself just enough memory to decompress
-the file. Since block sizes are stored in compressed files, it follows
-that the flags \-1 to \-9 are irrelevant to and so ignored
-during decompression.
-
-Compression and decompression requirements,
-in bytes, can be estimated as:
-
- Compression: 400k + ( 8 x block size )
-
- Decompression: 100k + ( 4 x block size ), or
- 100k + ( 2.5 x block size )
-
-Larger block sizes give rapidly diminishing marginal returns. Most of
-the compression comes from the first two or three hundred k of block
-size, a fact worth bearing in mind when using
-.I bzip2
-on small machines.
-It is also important to appreciate that the decompression memory
-requirement is set at compression time by the choice of block size.
-
-For files compressed with the default 900k block size,
-.I bunzip2
-will require about 3700 kbytes to decompress. To support decompression
-of any file on a 4 megabyte machine,
-.I bunzip2
-has an option to
-decompress using approximately half this amount of memory, about 2300
-kbytes. Decompression speed is also halved, so you should use this
-option only where necessary. The relevant flag is -s.
-
-In general, try and use the largest block size memory constraints allow,
-since that maximises the compression achieved. Compression and
-decompression speed are virtually unaffected by block size.
-
-Another significant point applies to files which fit in a single block
--- that means most files you'd encounter using a large block size. The
-amount of real memory touched is proportional to the size of the file,
-since the file is smaller than a block. For example, compressing a file
-20,000 bytes long with the flag -9 will cause the compressor to
-allocate around 7600k of memory, but only touch 400k + 20000 * 8 = 560
-kbytes of it. Similarly, the decompressor will allocate 3700k but only
-touch 100k + 20000 * 4 = 180 kbytes.
-
-Here is a table which summarises the maximum memory usage for different
-block sizes. Also recorded is the total compressed size for 14 files of
-the Calgary Text Compression Corpus totalling 3,141,622 bytes. This
-column gives some feel for how compression varies with block size.
-These figures tend to understate the advantage of larger block sizes for
-larger files, since the Corpus is dominated by smaller files.
-
- Compress Decompress Decompress Corpus
- Flag usage usage -s usage Size
-
- -1 1200k 500k 350k 914704
- -2 2000k 900k 600k 877703
- -3 2800k 1300k 850k 860338
- -4 3600k 1700k 1100k 846899
- -5 4400k 2100k 1350k 845160
- -6 5200k 2500k 1600k 838626
- -7 6100k 2900k 1850k 834096
- -8 6800k 3300k 2100k 828642
- -9 7600k 3700k 2350k 828642
-
-.SH RECOVERING DATA FROM DAMAGED FILES
-.I bzip2
-compresses files in blocks, usually 900kbytes long. Each
-block is handled independently. If a media or transmission error causes
-a multi-block .bz2
-file to become damaged, it may be possible to
-recover data from the undamaged blocks in the file.
-
-The compressed representation of each block is delimited by a 48-bit
-pattern, which makes it possible to find the block boundaries with
-reasonable certainty. Each block also carries its own 32-bit CRC, so
-damaged blocks can be distinguished from undamaged ones.
-
-.I bzip2recover
-is a simple program whose purpose is to search for
-blocks in .bz2 files, and write each block out into its own .bz2
-file. You can then use
-.I bzip2
-\-t
-to test the
-integrity of the resulting files, and decompress those which are
-undamaged.
-
-.I bzip2recover
-takes a single argument, the name of the damaged file,
-and writes a number of files "rec00001file.bz2",
-"rec00002file.bz2", etc, containing the extracted blocks.
-The output filenames are designed so that the use of
-wildcards in subsequent processing -- for example,
-"bzip2 -dc rec*file.bz2 > recovered_data" -- processes the files in
-the correct order.
-
-.I bzip2recover
-should be of most use dealing with large .bz2
-files, as these will contain many blocks. It is clearly
-futile to use it on damaged single-block files, since a
-damaged block cannot be recovered. If you wish to minimise
-any potential data loss through media or transmission errors,
-you might consider compressing with a smaller
-block size.
-
-.SH PERFORMANCE NOTES
-The sorting phase of compression gathers together similar strings in the
-file. Because of this, files containing very long runs of repeated
-symbols, like "aabaabaabaab ..." (repeated several hundred times) may
-compress more slowly than normal. Versions 0.9.5 and above fare much
-better than previous versions in this respect. The ratio between
-worst-case and average-case compression time is in the region of 10:1.
-For previous versions, this figure was more like 100:1. You can use the
-\-vvvv option to monitor progress in great detail, if you want.
-
-Decompression speed is unaffected by these phenomena.
-
-.I bzip2
-usually allocates several megabytes of memory to operate
-in, and then charges all over it in a fairly random fashion. This means
-that performance, both for compressing and decompressing, is largely
-determined by the speed at which your machine can service cache misses.
-Because of this, small changes to the code to reduce the miss rate have
-been observed to give disproportionately large performance improvements.
-I imagine
-.I bzip2
-will perform best on machines with very large caches.
-
-.SH CAVEATS
-I/O error messages are not as helpful as they could be.
-.I bzip2
-tries hard to detect I/O errors and exit cleanly, but the details of
-what the problem is sometimes seem rather misleading.
-
-This manual page pertains to version 1.0.6 of
-.I bzip2.
-Compressed data created by this version is entirely forwards and
-backwards compatible with the previous public releases, versions
-0.1pl2, 0.9.0, 0.9.5, 1.0.0, 1.0.1, 1.0.2 and above, but with the following
-exception: 0.9.0 and above can correctly decompress multiple
-concatenated compressed files. 0.1pl2 cannot do this; it will stop
-after decompressing just the first file in the stream.
-
-.I bzip2recover
-versions prior to 1.0.2 used 32-bit integers to represent
-bit positions in compressed files, so they could not handle compressed
-files more than 512 megabytes long. Versions 1.0.2 and above use
-64-bit ints on some platforms which support them (GNU supported
-targets, and Windows). To establish whether or not bzip2recover was
-built with such a limitation, run it without arguments. In any event
-you can build yourself an unlimited version if you can recompile it
-with MaybeUInt64 set to be an unsigned 64-bit integer.
-
-
-
-.SH AUTHOR
-Julian Seward, jsewardbzip.org.
-
-http://www.bzip.org
-
-The ideas embodied in
-.I bzip2
-are due to (at least) the following
-people: Michael Burrows and David Wheeler (for the block sorting
-transformation), David Wheeler (again, for the Huffman coder), Peter
-Fenwick (for the structured coding model in the original
-.I bzip,
-and many refinements), and Alistair Moffat, Radford Neal and Ian Witten
-(for the arithmetic coder in the original
-.I bzip).
-I am much
-indebted for their help, support and advice. See the manual in the
-source distribution for pointers to sources of documentation. Christian
-von Roques encouraged me to look for faster sorting algorithms, so as to
-speed up compression. Bela Lubkin encouraged me to improve the
-worst-case compression performance.
-Donna Robinson XMLised the documentation.
-The bz* scripts are derived from those of GNU gzip.
-Many people sent patches, helped
-with portability problems, lent machines, gave advice and were generally
-helpful.
diff --git a/third-party/bzip2/bzip2.1.preformatted b/third-party/bzip2/bzip2.1.preformatted
deleted file mode 100644
index 63c33be..0000000
--- a/third-party/bzip2/bzip2.1.preformatted
+++ /dev/null
@@ -1,399 +0,0 @@
-bzip2(1) bzip2(1)
-
-
-
-NNAAMMEE
- bzip2, bunzip2 − a block‐sorting file compressor, v1.0.6
- bzcat − decompresses files to stdout
- bzip2recover − recovers data from damaged bzip2 files
-
-
-SSYYNNOOPPSSIISS
- bbzziipp22 [ −−ccddffkkqqssttvvzzVVLL112233445566778899 ] [ _f_i_l_e_n_a_m_e_s _._._. ]
- bbuunnzziipp22 [ −−ffkkvvssVVLL ] [ _f_i_l_e_n_a_m_e_s _._._. ]
- bbzzccaatt [ −−ss ] [ _f_i_l_e_n_a_m_e_s _._._. ]
- bbzziipp22rreeccoovveerr _f_i_l_e_n_a_m_e
-
-
-DDEESSCCRRIIPPTTIIOONN
- _b_z_i_p_2 compresses files using the Burrows‐Wheeler block
- sorting text compression algorithm, and Huffman coding.
- Compression is generally considerably better than that
- achieved by more conventional LZ77/LZ78‐based compressors,
- and approaches the performance of the PPM family of sta
- tistical compressors.
-
- The command‐line options are deliberately very similar to
- those of _G_N_U _g_z_i_p_, but they are not identical.
-
- _b_z_i_p_2 expects a list of file names to accompany the com
- mand‐line flags. Each file is replaced by a compressed
- version of itself, with the name "original_name.bz2".
- Each compressed file has the same modification date, per
- missions, and, when possible, ownership as the correspond
- ing original, so that these properties can be correctly
- restored at decompression time. File name handling is
- naive in the sense that there is no mechanism for preserv
- ing original file names, permissions, ownerships or dates
- in filesystems which lack these concepts, or have serious
- file name length restrictions, such as MS‐DOS.
-
- _b_z_i_p_2 and _b_u_n_z_i_p_2 will by default not overwrite existing
- files. If you want this to happen, specify the −f flag.
-
- If no file names are specified, _b_z_i_p_2 compresses from
- standard input to standard output. In this case, _b_z_i_p_2
- will decline to write compressed output to a terminal, as
- this would be entirely incomprehensible and therefore
- pointless.
-
- _b_u_n_z_i_p_2 (or _b_z_i_p_2 _−_d_) decompresses all specified files.
- Files which were not created by _b_z_i_p_2 will be detected and
- ignored, and a warning issued. _b_z_i_p_2 attempts to guess
- the filename for the decompressed file from that of the
- compressed file as follows:
-
- filename.bz2 becomes filename
- filename.bz becomes filename
- filename.tbz2 becomes filename.tar
- filename.tbz becomes filename.tar
- anyothername becomes anyothername.out
-
- If the file does not end in one of the recognised endings,
- _._b_z_2_, _._b_z_, _._t_b_z_2 or _._t_b_z_, _b_z_i_p_2 complains that it cannot
- guess the name of the original file, and uses the original
- name with _._o_u_t appended.
-
- As with compression, supplying no filenames causes decom
- pression from standard input to standard output.
-
- _b_u_n_z_i_p_2 will correctly decompress a file which is the con
- catenation of two or more compressed files. The result is
- the concatenation of the corresponding uncompressed files.
- Integrity testing (−t) of concatenated compressed files is
- also supported.
-
- You can also compress or decompress files to the standard
- output by giving the −c flag. Multiple files may be com
- pressed and decompressed like this. The resulting outputs
- are fed sequentially to stdout. Compression of multiple
- files in this manner generates a stream containing multi
- ple compressed file representations. Such a stream can be
- decompressed correctly only by _b_z_i_p_2 version 0.9.0 or
- later. Earlier versions of _b_z_i_p_2 will stop after decom
- pressing the first file in the stream.
-
- _b_z_c_a_t (or _b_z_i_p_2 _‐_d_c_) decompresses all specified files to
- the standard output.
-
- _b_z_i_p_2 will read arguments from the environment variables
- _B_Z_I_P_2 and _B_Z_I_P_, in that order, and will process them
- before any arguments read from the command line. This
- gives a convenient way to supply default arguments.
-
- Compression is always performed, even if the compressed
- file is slightly larger than the original. Files of less
- than about one hundred bytes tend to get larger, since the
- compression mechanism has a constant overhead in the
- region of 50 bytes. Random data (including the output of
- most file compressors) is coded at about 8.05 bits per
- byte, giving an expansion of around 0.5%.
-
- As a self‐check for your protection, _b_z_i_p_2 uses 32‐bit
- CRCs to make sure that the decompressed version of a file
- is identical to the original. This guards against corrup
- tion of the compressed data, and against undetected bugs
- in _b_z_i_p_2 (hopefully very unlikely). The chances of data
- corruption going undetected is microscopic, about one
- chance in four billion for each file processed. Be aware,
- though, that the check occurs upon decompression, so it
- can only tell you that something is wrong. It can’t help
- you recover the original uncompressed data. You can use
- _b_z_i_p_2_r_e_c_o_v_e_r to try to recover data from damaged files.
-
- Return values: 0 for a normal exit, 1 for environmental
- problems (file not found, invalid flags, I/O errors, &c),
- 2 to indicate a corrupt compressed file, 3 for an internal
- consistency error (eg, bug) which caused _b_z_i_p_2 to panic.
-
-
-OOPPTTIIOONNSS
- −−cc ‐‐‐‐ssttddoouutt
- Compress or decompress to standard output.
-
- −−dd ‐‐‐‐ddeeccoommpprreessss
- Force decompression. _b_z_i_p_2_, _b_u_n_z_i_p_2 and _b_z_c_a_t are
- really the same program, and the decision about
- what actions to take is done on the basis of which
- name is used. This flag overrides that mechanism,
- and forces _b_z_i_p_2 to decompress.
-
- −−zz ‐‐‐‐ccoommpprreessss
- The complement to −d: forces compression,
- regardless of the invocation name.
-
- −−tt ‐‐‐‐tteesstt
- Check integrity of the specified file(s), but don’t
- decompress them. This really performs a trial
- decompression and throws away the result.
-
- −−ff ‐‐‐‐ffoorrccee
- Force overwrite of output files. Normally, _b_z_i_p_2
- will not overwrite existing output files. Also
- forces _b_z_i_p_2 to break hard links to files, which it
- otherwise wouldn’t do.
-
- bzip2 normally declines to decompress files which
- don’t have the correct magic header bytes. If
- forced (‐f), however, it will pass such files
- through unmodified. This is how GNU gzip behaves.
-
- −−kk ‐‐‐‐kkeeeepp
- Keep (don’t delete) input files during compression
- or decompression.
-
- −−ss ‐‐‐‐ssmmaallll
- Reduce memory usage, for compression, decompression
- and testing. Files are decompressed and tested
- using a modified algorithm which only requires 2.5
- bytes per block byte. This means any file can be
- decompressed in 2300k of memory, albeit at about
- half the normal speed.
-
- During compression, −s selects a block size of
- 200k, which limits memory use to around the same
- figure, at the expense of your compression ratio.
- In short, if your machine is low on memory (8
- megabytes or less), use −s for everything. See
- MEMORY MANAGEMENT below.
-
- −−qq ‐‐‐‐qquuiieett
- Suppress non‐essential warning messages. Messages
- pertaining to I/O errors and other critical events
- will not be suppressed.
-
- −−vv ‐‐‐‐vveerrbboossee
- Verbose mode ‐‐ show the compression ratio for each
- file processed. Further −v’s increase the ver
- bosity level, spewing out lots of information which
- is primarily of interest for diagnostic purposes.
-
- −−LL ‐‐‐‐lliicceennssee ‐‐VV ‐‐‐‐vveerrssiioonn
- Display the software version, license terms and
- conditions.
-
- −−11 ((oorr −−−−ffaasstt)) ttoo −−99 ((oorr −−−−bbeesstt))
- Set the block size to 100 k, 200 k .. 900 k when
- compressing. Has no effect when decompressing.
- See MEMORY MANAGEMENT below. The −−fast and −−best
- aliases are primarily for GNU gzip compatibility.
- In particular, −−fast doesn’t make things signifi
- cantly faster. And −−best merely selects the
- default behaviour.
-
- −−‐‐ Treats all subsequent arguments as file names, even
- if they start with a dash. This is so you can han
- dle files with names beginning with a dash, for
- example: bzip2 −‐ −myfilename.
-
- −−‐‐rreeppeettiittiivvee‐‐ffaasstt ‐‐‐‐rreeppeettiittiivvee‐‐bbeesstt
- These flags are redundant in versions 0.9.5 and
- above. They provided some coarse control over the
- behaviour of the sorting algorithm in earlier ver
- sions, which was sometimes useful. 0.9.5 and above
- have an improved algorithm which renders these
- flags irrelevant.
-
-
-MMEEMMOORRYY MMAANNAAGGEEMMEENNTT
- _b_z_i_p_2 compresses large files in blocks. The block size
- affects both the compression ratio achieved, and the
- amount of memory needed for compression and decompression.
- The flags −1 through −9 specify the block size to be
- 100,000 bytes through 900,000 bytes (the default) respec
- tively. At decompression time, the block size used for
- compression is read from the header of the compressed
- file, and _b_u_n_z_i_p_2 then allocates itself just enough memory
- to decompress the file. Since block sizes are stored in
- compressed files, it follows that the flags −1 to −9 are
- irrelevant to and so ignored during decompression.
-
- Compression and decompression requirements, in bytes, can
- be estimated as:
-
- Compression: 400k + ( 8 x block size )
-
- Decompression: 100k + ( 4 x block size ), or
- 100k + ( 2.5 x block size )
-
- Larger block sizes give rapidly diminishing marginal
- returns. Most of the compression comes from the first two
- or three hundred k of block size, a fact worth bearing in
- mind when using _b_z_i_p_2 on small machines. It is also
- important to appreciate that the decompression memory
- requirement is set at compression time by the choice of
- block size.
-
- For files compressed with the default 900k block size,
- _b_u_n_z_i_p_2 will require about 3700 kbytes to decompress. To
- support decompression of any file on a 4 megabyte machine,
- _b_u_n_z_i_p_2 has an option to decompress using approximately
- half this amount of memory, about 2300 kbytes. Decompres
- sion speed is also halved, so you should use this option
- only where necessary. The relevant flag is ‐s.
-
- In general, try and use the largest block size memory con
- straints allow, since that maximises the compression
- achieved. Compression and decompression speed are virtu
- ally unaffected by block size.
-
- Another significant point applies to files which fit in a
- single block ‐‐ that means most files you’d encounter
- using a large block size. The amount of real memory
- touched is proportional to the size of the file, since the
- file is smaller than a block. For example, compressing a
- file 20,000 bytes long with the flag ‐9 will cause the
- compressor to allocate around 7600k of memory, but only
- touch 400k + 20000 * 8 = 560 kbytes of it. Similarly, the
- decompressor will allocate 3700k but only touch 100k +
- 20000 * 4 = 180 kbytes.
-
- Here is a table which summarises the maximum memory usage
- for different block sizes. Also recorded is the total
- compressed size for 14 files of the Calgary Text Compres
- sion Corpus totalling 3,141,622 bytes. This column gives
- some feel for how compression varies with block size.
- These figures tend to understate the advantage of larger
- block sizes for larger files, since the Corpus is domi
- nated by smaller files.
-
- Compress Decompress Decompress Corpus
- Flag usage usage ‐s usage Size
-
- ‐1 1200k 500k 350k 914704
- ‐2 2000k 900k 600k 877703
- ‐3 2800k 1300k 850k 860338
- ‐4 3600k 1700k 1100k 846899
- ‐5 4400k 2100k 1350k 845160
- ‐6 5200k 2500k 1600k 838626
- ‐7 6100k 2900k 1850k 834096
- ‐8 6800k 3300k 2100k 828642
- ‐9 7600k 3700k 2350k 828642
-
-
-RREECCOOVVEERRIINNGG DDAATTAA FFRROOMM DDAAMMAAGGEEDD FFIILLEESS
- _b_z_i_p_2 compresses files in blocks, usually 900kbytes long.
- Each block is handled independently. If a media or trans
- mission error causes a multi‐block .bz2 file to become
- damaged, it may be possible to recover data from the
- undamaged blocks in the file.
-
- The compressed representation of each block is delimited
- by a 48‐bit pattern, which makes it possible to find the
- block boundaries with reasonable certainty. Each block
- also carries its own 32‐bit CRC, so damaged blocks can be
- distinguished from undamaged ones.
-
- _b_z_i_p_2_r_e_c_o_v_e_r is a simple program whose purpose is to
- search for blocks in .bz2 files, and write each block out
- into its own .bz2 file. You can then use _b_z_i_p_2 −t to test
- the integrity of the resulting files, and decompress those
- which are undamaged.
-
- _b_z_i_p_2_r_e_c_o_v_e_r takes a single argument, the name of the dam
- aged file, and writes a number of files
- "rec00001file.bz2", "rec00002file.bz2", etc, containing
- the extracted blocks. The output filenames are
- designed so that the use of wildcards in subsequent pro
- cessing ‐‐ for example, "bzip2 ‐dc rec*file.bz2 > recov
- ered_data" ‐‐ processes the files in the correct order.
-
- _b_z_i_p_2_r_e_c_o_v_e_r should be of most use dealing with large .bz2
- files, as these will contain many blocks. It is clearly
- futile to use it on damaged single‐block files, since a
- damaged block cannot be recovered. If you wish to min
- imise any potential data loss through media or transmis
- sion errors, you might consider compressing with a smaller
- block size.
-
-
-PPEERRFFOORRMMAANNCCEE NNOOTTEESS
- The sorting phase of compression gathers together similar
- strings in the file. Because of this, files containing
- very long runs of repeated symbols, like "aabaabaabaab
- ..." (repeated several hundred times) may compress more
- slowly than normal. Versions 0.9.5 and above fare much
- better than previous versions in this respect. The ratio
- between worst‐case and average‐case compression time is in
- the region of 10:1. For previous versions, this figure
- was more like 100:1. You can use the −vvvv option to mon
- itor progress in great detail, if you want.
-
- Decompression speed is unaffected by these phenomena.
-
- _b_z_i_p_2 usually allocates several megabytes of memory to
- operate in, and then charges all over it in a fairly ran
- dom fashion. This means that performance, both for com
- pressing and decompressing, is largely determined by the
- speed at which your machine can service cache misses.
- Because of this, small changes to the code to reduce the
- miss rate have been observed to give disproportionately
- large performance improvements. I imagine _b_z_i_p_2 will per
- form best on machines with very large caches.
-
-
-CCAAVVEEAATTSS
- I/O error messages are not as helpful as they could be.
- _b_z_i_p_2 tries hard to detect I/O errors and exit cleanly,
- but the details of what the problem is sometimes seem
- rather misleading.
-
- This manual page pertains to version 1.0.6 of _b_z_i_p_2_. Com
- pressed data created by this version is entirely forwards
- and backwards compatible with the previous public
- releases, versions 0.1pl2, 0.9.0, 0.9.5, 1.0.0, 1.0.1,
- 1.0.2 and above, but with the following exception: 0.9.0
- and above can correctly decompress multiple concatenated
- compressed files. 0.1pl2 cannot do this; it will stop
- after decompressing just the first file in the stream.
-
- _b_z_i_p_2_r_e_c_o_v_e_r versions prior to 1.0.2 used 32‐bit integers
- to represent bit positions in compressed files, so they
- could not handle compressed files more than 512 megabytes
- long. Versions 1.0.2 and above use 64‐bit ints on some
- platforms which support them (GNU supported targets, and
- Windows). To establish whether or not bzip2recover was
- built with such a limitation, run it without arguments.
- In any event you can build yourself an unlimited version
- if you can recompile it with MaybeUInt64 set to be an
- unsigned 64‐bit integer.
-
-
-
-
-AAUUTTHHOORR
- Julian Seward, jsewardbzip.org.
-
- http://www.bzip.org
-
- The ideas embodied in _b_z_i_p_2 are due to (at least) the fol
- lowing people: Michael Burrows and David Wheeler (for the
- block sorting transformation), David Wheeler (again, for
- the Huffman coder), Peter Fenwick (for the structured cod
- ing model in the original _b_z_i_p_, and many refinements), and
- Alistair Moffat, Radford Neal and Ian Witten (for the
- arithmetic coder in the original _b_z_i_p_)_. I am much
- indebted for their help, support and advice. See the man
- ual in the source distribution for pointers to sources of
- documentation. Christian von Roques encouraged me to look
- for faster sorting algorithms, so as to speed up compres
- sion. Bela Lubkin encouraged me to improve the worst‐case
- compression performance. Donna Robinson XMLised the docu
- mentation. The bz* scripts are derived from those of GNU
- gzip. Many people sent patches, helped with portability
- problems, lent machines, gave advice and were generally
- helpful.
-
-
-
- bzip2(1)
diff --git a/third-party/bzip2/bzip2.c b/third-party/bzip2/bzip2.c
deleted file mode 100644
index 6de9d1d..0000000
--- a/third-party/bzip2/bzip2.c
+++ /dev/null
@@ -1,2034 +0,0 @@
-
-/*-----------------------------------------------------------*/
-/*--- A block-sorting, lossless compressor bzip2.c ---*/
-/*-----------------------------------------------------------*/
-
-/* ------------------------------------------------------------------
- This file is part of bzip2/libbzip2, a program and library for
- lossless, block-sorting data compression.
-
- bzip2/libbzip2 version 1.0.6 of 6 September 2010
- Copyright (C) 1996-2010 Julian Seward <jseward at bzip.org>
-
- Please read the WARNING, DISCLAIMER and PATENTS sections in the
- README file.
-
- This program is released under the terms of the license contained
- in the file LICENSE.
- ------------------------------------------------------------------ */
-
-
-/* Place a 1 beside your platform, and 0 elsewhere.
- Generic 32-bit Unix.
- Also works on 64-bit Unix boxes.
- This is the default.
-*/
-#define BZ_UNIX 1
-
-/*--
- Win32, as seen by Jacob Navia's excellent
- port of (Chris Fraser & David Hanson)'s excellent
- lcc compiler. Or with MS Visual C.
- This is selected automatically if compiled by a compiler which
- defines _WIN32, not including the Cygwin GCC.
---*/
-#define BZ_LCCWIN32 0
-
-#if defined(_WIN32) && !defined(__CYGWIN__)
-#undef BZ_LCCWIN32
-#define BZ_LCCWIN32 1
-#undef BZ_UNIX
-#define BZ_UNIX 0
-#endif
-
-
-/*---------------------------------------------*/
-/*--
- Some stuff for all platforms.
---*/
-
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
-#include <signal.h>
-#include <math.h>
-#include <errno.h>
-#include <ctype.h>
-#include "bzlib.h"
-
-#define ERROR_IF_EOF(i) { if ((i) == EOF) ioError(); }
-#define ERROR_IF_NOT_ZERO(i) { if ((i) != 0) ioError(); }
-#define ERROR_IF_MINUS_ONE(i) { if ((i) == (-1)) ioError(); }
-
-
-/*---------------------------------------------*/
-/*--
- Platform-specific stuff.
---*/
-
-#if BZ_UNIX
-# include <fcntl.h>
-# include <sys/types.h>
-# include <utime.h>
-# include <unistd.h>
-# include <sys/stat.h>
-# include <sys/times.h>
-
-# define PATH_SEP '/'
-# define MY_LSTAT lstat
-# define MY_STAT stat
-# define MY_S_ISREG S_ISREG
-# define MY_S_ISDIR S_ISDIR
-
-# define APPEND_FILESPEC(root, name) \
- root=snocString((root), (name))
-
-# define APPEND_FLAG(root, name) \
- root=snocString((root), (name))
-
-# define SET_BINARY_MODE(fd) /**/
-
-# ifdef __GNUC__
-# define NORETURN __attribute__ ((noreturn))
-# else
-# define NORETURN /**/
-# endif
-
-# ifdef __DJGPP__
-# include <io.h>
-# include <fcntl.h>
-# undef MY_LSTAT
-# undef MY_STAT
-# define MY_LSTAT stat
-# define MY_STAT stat
-# undef SET_BINARY_MODE
-# define SET_BINARY_MODE(fd) \
- do { \
- int retVal = setmode ( fileno ( fd ), \
- O_BINARY ); \
- ERROR_IF_MINUS_ONE ( retVal ); \
- } while ( 0 )
-# endif
-
-# ifdef __CYGWIN__
-# include <io.h>
-# include <fcntl.h>
-# undef SET_BINARY_MODE
-# define SET_BINARY_MODE(fd) \
- do { \
- int retVal = setmode ( fileno ( fd ), \
- O_BINARY ); \
- ERROR_IF_MINUS_ONE ( retVal ); \
- } while ( 0 )
-# endif
-#endif /* BZ_UNIX */
-
-
-
-#if BZ_LCCWIN32
-# include <io.h>
-# include <fcntl.h>
-# include <sys\stat.h>
-
-# define NORETURN /**/
-# define PATH_SEP '\\'
-# define MY_LSTAT _stat
-# define MY_STAT _stat
-# define MY_S_ISREG(x) ((x) & _S_IFREG)
-# define MY_S_ISDIR(x) ((x) & _S_IFDIR)
-
-# define APPEND_FLAG(root, name) \
- root=snocString((root), (name))
-
-# define APPEND_FILESPEC(root, name) \
- root = snocString ((root), (name))
-
-# define SET_BINARY_MODE(fd) \
- do { \
- int retVal = setmode ( fileno ( fd ), \
- O_BINARY ); \
- ERROR_IF_MINUS_ONE ( retVal ); \
- } while ( 0 )
-
-#endif /* BZ_LCCWIN32 */
-
-
-/*---------------------------------------------*/
-/*--
- Some more stuff for all platforms :-)
---*/
-
-typedef char Char;
-typedef unsigned char Bool;
-typedef unsigned char UChar;
-typedef int Int32;
-typedef unsigned int UInt32;
-typedef short Int16;
-typedef unsigned short UInt16;
-
-#define True ((Bool)1)
-#define False ((Bool)0)
-
-/*--
- IntNative is your platform's `native' int size.
- Only here to avoid probs with 64-bit platforms.
---*/
-typedef int IntNative;
-
-
-/*---------------------------------------------------*/
-/*--- Misc (file handling) data decls ---*/
-/*---------------------------------------------------*/
-
-Int32 verbosity;
-Bool keepInputFiles, smallMode, deleteOutputOnInterrupt;
-Bool forceOverwrite, testFailsExist, unzFailsExist, noisy;
-Int32 numFileNames, numFilesProcessed, blockSize100k;
-Int32 exitValue;
-
-/*-- source modes; F==file, I==stdin, O==stdout --*/
-#define SM_I2O 1
-#define SM_F2O 2
-#define SM_F2F 3
-
-/*-- operation modes --*/
-#define OM_Z 1
-#define OM_UNZ 2
-#define OM_TEST 3
-
-Int32 opMode;
-Int32 srcMode;
-
-#define FILE_NAME_LEN 1034
-
-Int32 longestFileName;
-Char inName [FILE_NAME_LEN];
-Char outName[FILE_NAME_LEN];
-Char tmpName[FILE_NAME_LEN];
-Char *progName;
-Char progNameReally[FILE_NAME_LEN];
-FILE *outputHandleJustInCase;
-Int32 workFactor;
-
-static void panic ( const Char* ) NORETURN;
-static void ioError ( void ) NORETURN;
-static void outOfMemory ( void ) NORETURN;
-static void configError ( void ) NORETURN;
-static void crcError ( void ) NORETURN;
-static void cleanUpAndFail ( Int32 ) NORETURN;
-static void compressedStreamEOF ( void ) NORETURN;
-
-static void copyFileName ( Char*, Char* );
-static void* myMalloc ( Int32 );
-static void applySavedFileAttrToOutputFile ( IntNative fd );
-
-
-
-/*---------------------------------------------------*/
-/*--- An implementation of 64-bit ints. Sigh. ---*/
-/*--- Roll on widespread deployment of ANSI C9X ! ---*/
-/*---------------------------------------------------*/
-
-typedef
- struct { UChar b[8]; }
- UInt64;
-
-
-static
-void uInt64_from_UInt32s ( UInt64* n, UInt32 lo32, UInt32 hi32 )
-{
- n->b[7] = (UChar)((hi32 >> 24) & 0xFF);
- n->b[6] = (UChar)((hi32 >> 16) & 0xFF);
- n->b[5] = (UChar)((hi32 >> 8) & 0xFF);
- n->b[4] = (UChar) (hi32 & 0xFF);
- n->b[3] = (UChar)((lo32 >> 24) & 0xFF);
- n->b[2] = (UChar)((lo32 >> 16) & 0xFF);
- n->b[1] = (UChar)((lo32 >> 8) & 0xFF);
- n->b[0] = (UChar) (lo32 & 0xFF);
-}
-
-
-static
-double uInt64_to_double ( UInt64* n )
-{
- Int32 i;
- double base = 1.0;
- double sum = 0.0;
- for (i = 0; i < 8; i++) {
- sum += base * (double)(n->b[i]);
- base *= 256.0;
- }
- return sum;
-}
-
-
-static
-Bool uInt64_isZero ( UInt64* n )
-{
- Int32 i;
- for (i = 0; i < 8; i++)
- if (n->b[i] != 0) return 0;
- return 1;
-}
-
-
-/* Divide *n by 10, and return the remainder. */
-static
-Int32 uInt64_qrm10 ( UInt64* n )
-{
- UInt32 rem, tmp;
- Int32 i;
- rem = 0;
- for (i = 7; i >= 0; i--) {
- tmp = rem * 256 + n->b[i];
- n->b[i] = tmp / 10;
- rem = tmp % 10;
- }
- return rem;
-}
-
-
-/* ... and the Whole Entire Point of all this UInt64 stuff is
- so that we can supply the following function.
-*/
-static
-void uInt64_toAscii ( char* outbuf, UInt64* n )
-{
- Int32 i, q;
- UChar buf[32];
- Int32 nBuf = 0;
- UInt64 n_copy = *n;
- do {
- q = uInt64_qrm10 ( &n_copy );
- buf[nBuf] = q + '0';
- nBuf++;
- } while (!uInt64_isZero(&n_copy));
- outbuf[nBuf] = 0;
- for (i = 0; i < nBuf; i++)
- outbuf[i] = buf[nBuf-i-1];
-}
-
-
-/*---------------------------------------------------*/
-/*--- Processing of complete files and streams ---*/
-/*---------------------------------------------------*/
-
-/*---------------------------------------------*/
-static
-Bool myfeof ( FILE* f )
-{
- Int32 c = fgetc ( f );
- if (c == EOF) return True;
- ungetc ( c, f );
- return False;
-}
-
-
-/*---------------------------------------------*/
-static
-void compressStream ( FILE *stream, FILE *zStream )
-{
- BZFILE* bzf = NULL;
- UChar ibuf[5000];
- Int32 nIbuf;
- UInt32 nbytes_in_lo32, nbytes_in_hi32;
- UInt32 nbytes_out_lo32, nbytes_out_hi32;
- Int32 bzerr, bzerr_dummy, ret;
-
- SET_BINARY_MODE(stream);
- SET_BINARY_MODE(zStream);
-
- if (ferror(stream)) goto errhandler_io;
- if (ferror(zStream)) goto errhandler_io;
-
- bzf = BZ2_bzWriteOpen ( &bzerr, zStream,
- blockSize100k, verbosity, workFactor );
- if (bzerr != BZ_OK) goto errhandler;
-
- if (verbosity >= 2) fprintf ( stderr, "\n" );
-
- while (True) {
-
- if (myfeof(stream)) break;
- nIbuf = fread ( ibuf, sizeof(UChar), 5000, stream );
- if (ferror(stream)) goto errhandler_io;
- if (nIbuf > 0) BZ2_bzWrite ( &bzerr, bzf, (void*)ibuf, nIbuf );
- if (bzerr != BZ_OK) goto errhandler;
-
- }
-
- BZ2_bzWriteClose64 ( &bzerr, bzf, 0,
- &nbytes_in_lo32, &nbytes_in_hi32,
- &nbytes_out_lo32, &nbytes_out_hi32 );
- if (bzerr != BZ_OK) goto errhandler;
-
- if (ferror(zStream)) goto errhandler_io;
- ret = fflush ( zStream );
- if (ret == EOF) goto errhandler_io;
- if (zStream != stdout) {
- Int32 fd = fileno ( zStream );
- if (fd < 0) goto errhandler_io;
- applySavedFileAttrToOutputFile ( fd );
- ret = fclose ( zStream );
- outputHandleJustInCase = NULL;
- if (ret == EOF) goto errhandler_io;
- }
- outputHandleJustInCase = NULL;
- if (ferror(stream)) goto errhandler_io;
- ret = fclose ( stream );
- if (ret == EOF) goto errhandler_io;
-
- if (verbosity >= 1) {
- if (nbytes_in_lo32 == 0 && nbytes_in_hi32 == 0) {
- fprintf ( stderr, " no data compressed.\n");
- } else {
- Char buf_nin[32], buf_nout[32];
- UInt64 nbytes_in, nbytes_out;
- double nbytes_in_d, nbytes_out_d;
- uInt64_from_UInt32s ( &nbytes_in,
- nbytes_in_lo32, nbytes_in_hi32 );
- uInt64_from_UInt32s ( &nbytes_out,
- nbytes_out_lo32, nbytes_out_hi32 );
- nbytes_in_d = uInt64_to_double ( &nbytes_in );
- nbytes_out_d = uInt64_to_double ( &nbytes_out );
- uInt64_toAscii ( buf_nin, &nbytes_in );
- uInt64_toAscii ( buf_nout, &nbytes_out );
- fprintf ( stderr, "%6.3f:1, %6.3f bits/byte, "
- "%5.2f%% saved, %s in, %s out.\n",
- nbytes_in_d / nbytes_out_d,
- (8.0 * nbytes_out_d) / nbytes_in_d,
- 100.0 * (1.0 - nbytes_out_d / nbytes_in_d),
- buf_nin,
- buf_nout
- );
- }
- }
-
- return;
-
- errhandler:
- BZ2_bzWriteClose64 ( &bzerr_dummy, bzf, 1,
- &nbytes_in_lo32, &nbytes_in_hi32,
- &nbytes_out_lo32, &nbytes_out_hi32 );
- switch (bzerr) {
- case BZ_CONFIG_ERROR:
- configError(); break;
- case BZ_MEM_ERROR:
- outOfMemory (); break;
- case BZ_IO_ERROR:
- errhandler_io:
- ioError(); break;
- default:
- panic ( "compress:unexpected error" );
- }
-
- panic ( "compress:end" );
- /*notreached*/
-}
-
-
-
-/*---------------------------------------------*/
-static
-Bool uncompressStream ( FILE *zStream, FILE *stream )
-{
- BZFILE* bzf = NULL;
- Int32 bzerr, bzerr_dummy, ret, nread, streamNo, i;
- UChar obuf[5000];
- UChar unused[BZ_MAX_UNUSED];
- Int32 nUnused;
- void* unusedTmpV;
- UChar* unusedTmp;
-
- nUnused = 0;
- streamNo = 0;
-
- SET_BINARY_MODE(stream);
- SET_BINARY_MODE(zStream);
-
- if (ferror(stream)) goto errhandler_io;
- if (ferror(zStream)) goto errhandler_io;
-
- while (True) {
-
- bzf = BZ2_bzReadOpen (
- &bzerr, zStream, verbosity,
- (int)smallMode, unused, nUnused
- );
- if (bzf == NULL || bzerr != BZ_OK) goto errhandler;
- streamNo++;
-
- while (bzerr == BZ_OK) {
- nread = BZ2_bzRead ( &bzerr, bzf, obuf, 5000 );
- if (bzerr == BZ_DATA_ERROR_MAGIC) goto trycat;
- if ((bzerr == BZ_OK || bzerr == BZ_STREAM_END) && nread > 0)
- fwrite ( obuf, sizeof(UChar), nread, stream );
- if (ferror(stream)) goto errhandler_io;
- }
- if (bzerr != BZ_STREAM_END) goto errhandler;
-
- BZ2_bzReadGetUnused ( &bzerr, bzf, &unusedTmpV, &nUnused );
- if (bzerr != BZ_OK) panic ( "decompress:bzReadGetUnused" );
-
- unusedTmp = (UChar*)unusedTmpV;
- for (i = 0; i < nUnused; i++) unused[i] = unusedTmp[i];
-
- BZ2_bzReadClose ( &bzerr, bzf );
- if (bzerr != BZ_OK) panic ( "decompress:bzReadGetUnused" );
-
- if (nUnused == 0 && myfeof(zStream)) break;
- }
-
- closeok:
- if (ferror(zStream)) goto errhandler_io;
- if (stream != stdout) {
- Int32 fd = fileno ( stream );
- if (fd < 0) goto errhandler_io;
- applySavedFileAttrToOutputFile ( fd );
- }
- ret = fclose ( zStream );
- if (ret == EOF) goto errhandler_io;
-
- if (ferror(stream)) goto errhandler_io;
- ret = fflush ( stream );
- if (ret != 0) goto errhandler_io;
- if (stream != stdout) {
- ret = fclose ( stream );
- outputHandleJustInCase = NULL;
- if (ret == EOF) goto errhandler_io;
- }
- outputHandleJustInCase = NULL;
- if (verbosity >= 2) fprintf ( stderr, "\n " );
- return True;
-
- trycat:
- if (forceOverwrite) {
- rewind(zStream);
- while (True) {
- if (myfeof(zStream)) break;
- nread = fread ( obuf, sizeof(UChar), 5000, zStream );
- if (ferror(zStream)) goto errhandler_io;
- if (nread > 0) fwrite ( obuf, sizeof(UChar), nread, stream );
- if (ferror(stream)) goto errhandler_io;
- }
- goto closeok;
- }
-
- errhandler:
- BZ2_bzReadClose ( &bzerr_dummy, bzf );
- switch (bzerr) {
- case BZ_CONFIG_ERROR:
- configError(); break;
- case BZ_IO_ERROR:
- errhandler_io:
- ioError(); break;
- case BZ_DATA_ERROR:
- crcError();
- case BZ_MEM_ERROR:
- outOfMemory();
- case BZ_UNEXPECTED_EOF:
- compressedStreamEOF();
- case BZ_DATA_ERROR_MAGIC:
- if (zStream != stdin) fclose(zStream);
- if (stream != stdout) fclose(stream);
- if (streamNo == 1) {
- return False;
- } else {
- if (noisy)
- fprintf ( stderr,
- "\n%s: %s: trailing garbage after EOF ignored\n",
- progName, inName );
- return True;
- }
- default:
- panic ( "decompress:unexpected error" );
- }
-
- panic ( "decompress:end" );
- return True; /*notreached*/
-}
-
-
-/*---------------------------------------------*/
-static
-Bool testStream ( FILE *zStream )
-{
- BZFILE* bzf = NULL;
- Int32 bzerr, bzerr_dummy, ret, nread, streamNo, i;
- UChar obuf[5000];
- UChar unused[BZ_MAX_UNUSED];
- Int32 nUnused;
- void* unusedTmpV;
- UChar* unusedTmp;
-
- nUnused = 0;
- streamNo = 0;
-
- SET_BINARY_MODE(zStream);
- if (ferror(zStream)) goto errhandler_io;
-
- while (True) {
-
- bzf = BZ2_bzReadOpen (
- &bzerr, zStream, verbosity,
- (int)smallMode, unused, nUnused
- );
- if (bzf == NULL || bzerr != BZ_OK) goto errhandler;
- streamNo++;
-
- while (bzerr == BZ_OK) {
- nread = BZ2_bzRead ( &bzerr, bzf, obuf, 5000 );
- if (bzerr == BZ_DATA_ERROR_MAGIC) goto errhandler;
- }
- if (bzerr != BZ_STREAM_END) goto errhandler;
-
- BZ2_bzReadGetUnused ( &bzerr, bzf, &unusedTmpV, &nUnused );
- if (bzerr != BZ_OK) panic ( "test:bzReadGetUnused" );
-
- unusedTmp = (UChar*)unusedTmpV;
- for (i = 0; i < nUnused; i++) unused[i] = unusedTmp[i];
-
- BZ2_bzReadClose ( &bzerr, bzf );
- if (bzerr != BZ_OK) panic ( "test:bzReadGetUnused" );
- if (nUnused == 0 && myfeof(zStream)) break;
-
- }
-
- if (ferror(zStream)) goto errhandler_io;
- ret = fclose ( zStream );
- if (ret == EOF) goto errhandler_io;
-
- if (verbosity >= 2) fprintf ( stderr, "\n " );
- return True;
-
- errhandler:
- BZ2_bzReadClose ( &bzerr_dummy, bzf );
- if (verbosity == 0)
- fprintf ( stderr, "%s: %s: ", progName, inName );
- switch (bzerr) {
- case BZ_CONFIG_ERROR:
- configError(); break;
- case BZ_IO_ERROR:
- errhandler_io:
- ioError(); break;
- case BZ_DATA_ERROR:
- fprintf ( stderr,
- "data integrity (CRC) error in data\n" );
- return False;
- case BZ_MEM_ERROR:
- outOfMemory();
- case BZ_UNEXPECTED_EOF:
- fprintf ( stderr,
- "file ends unexpectedly\n" );
- return False;
- case BZ_DATA_ERROR_MAGIC:
- if (zStream != stdin) fclose(zStream);
- if (streamNo == 1) {
- fprintf ( stderr,
- "bad magic number (file not created by bzip2)\n" );
- return False;
- } else {
- if (noisy)
- fprintf ( stderr,
- "trailing garbage after EOF ignored\n" );
- return True;
- }
- default:
- panic ( "test:unexpected error" );
- }
-
- panic ( "test:end" );
- return True; /*notreached*/
-}
-
-
-/*---------------------------------------------------*/
-/*--- Error [non-] handling grunge ---*/
-/*---------------------------------------------------*/
-
-/*---------------------------------------------*/
-static
-void setExit ( Int32 v )
-{
- if (v > exitValue) exitValue = v;
-}
-
-
-/*---------------------------------------------*/
-static
-void cadvise ( void )
-{
- if (noisy)
- fprintf (
- stderr,
- "\nIt is possible that the compressed file(s) have become corrupted.\n"
- "You can use the -tvv option to test integrity of such files.\n\n"
- "You can use the `bzip2recover' program to attempt to recover\n"
- "data from undamaged sections of corrupted files.\n\n"
- );
-}
-
-
-/*---------------------------------------------*/
-static
-void showFileNames ( void )
-{
- if (noisy)
- fprintf (
- stderr,
- "\tInput file = %s, output file = %s\n",
- inName, outName
- );
-}
-
-
-/*---------------------------------------------*/
-static
-void cleanUpAndFail ( Int32 ec )
-{
- IntNative retVal;
- struct MY_STAT statBuf;
-
- if ( srcMode == SM_F2F
- && opMode != OM_TEST
- && deleteOutputOnInterrupt ) {
-
- /* Check whether input file still exists. Delete output file
- only if input exists to avoid loss of data. Joerg Prante, 5
- January 2002. (JRS 06-Jan-2002: other changes in 1.0.2 mean
- this is less likely to happen. But to be ultra-paranoid, we
- do the check anyway.) */
- retVal = MY_STAT ( inName, &statBuf );
- if (retVal == 0) {
- if (noisy)
- fprintf ( stderr,
- "%s: Deleting output file %s, if it exists.\n",
- progName, outName );
- if (outputHandleJustInCase != NULL)
- fclose ( outputHandleJustInCase );
- retVal = remove ( outName );
- if (retVal != 0)
- fprintf ( stderr,
- "%s: WARNING: deletion of output file "
- "(apparently) failed.\n",
- progName );
- } else {
- fprintf ( stderr,
- "%s: WARNING: deletion of output file suppressed\n",
- progName );
- fprintf ( stderr,
- "%s: since input file no longer exists. Output file\n",
- progName );
- fprintf ( stderr,
- "%s: `%s' may be incomplete.\n",
- progName, outName );
- fprintf ( stderr,
- "%s: I suggest doing an integrity test (bzip2 -tv)"
- " of it.\n",
- progName );
- }
- }
-
- if (noisy && numFileNames > 0 && numFilesProcessed < numFileNames) {
- fprintf ( stderr,
- "%s: WARNING: some files have not been processed:\n"
- "%s: %d specified on command line, %d not processed yet.\n\n",
- progName, progName,
- numFileNames, numFileNames - numFilesProcessed );
- }
- setExit(ec);
- exit(exitValue);
-}
-
-
-/*---------------------------------------------*/
-static
-void panic ( const Char* s )
-{
- fprintf ( stderr,
- "\n%s: PANIC -- internal consistency error:\n"
- "\t%s\n"
- "\tThis is a BUG. Please report it to me at:\n"
- "\tjseward at bzip.org\n",
- progName, s );
- showFileNames();
- cleanUpAndFail( 3 );
-}
-
-
-/*---------------------------------------------*/
-static
-void crcError ( void )
-{
- fprintf ( stderr,
- "\n%s: Data integrity error when decompressing.\n",
- progName );
- showFileNames();
- cadvise();
- cleanUpAndFail( 2 );
-}
-
-
-/*---------------------------------------------*/
-static
-void compressedStreamEOF ( void )
-{
- if (noisy) {
- fprintf ( stderr,
- "\n%s: Compressed file ends unexpectedly;\n\t"
- "perhaps it is corrupted? *Possible* reason follows.\n",
- progName );
- perror ( progName );
- showFileNames();
- cadvise();
- }
- cleanUpAndFail( 2 );
-}
-
-
-/*---------------------------------------------*/
-static
-void ioError ( void )
-{
- fprintf ( stderr,
- "\n%s: I/O or other error, bailing out. "
- "Possible reason follows.\n",
- progName );
- perror ( progName );
- showFileNames();
- cleanUpAndFail( 1 );
-}
-
-
-/*---------------------------------------------*/
-static
-void mySignalCatcher ( IntNative n )
-{
- fprintf ( stderr,
- "\n%s: Control-C or similar caught, quitting.\n",
- progName );
- cleanUpAndFail(1);
-}
-
-
-/*---------------------------------------------*/
-static
-void mySIGSEGVorSIGBUScatcher ( IntNative n )
-{
- if (opMode == OM_Z)
- fprintf (
- stderr,
- "\n%s: Caught a SIGSEGV or SIGBUS whilst compressing.\n"
- "\n"
- " Possible causes are (most likely first):\n"
- " (1) This computer has unreliable memory or cache hardware\n"
- " (a surprisingly common problem; try a different machine.)\n"
- " (2) A bug in the compiler used to create this executable\n"
- " (unlikely, if you didn't compile bzip2 yourself.)\n"
- " (3) A real bug in bzip2 -- I hope this should never be the case.\n"
- " The user's manual, Section 4.3, has more info on (1) and (2).\n"
- " \n"
- " If you suspect this is a bug in bzip2, or are unsure about (1)\n"
- " or (2), feel free to report it to me at: jseward at bzip.org.\n"
- " Section 4.3 of the user's manual describes the info a useful\n"
- " bug report should have. If the manual is available on your\n"
- " system, please try and read it before mailing me. If you don't\n"
- " have the manual or can't be bothered to read it, mail me anyway.\n"
- "\n",
- progName );
- else
- fprintf (
- stderr,
- "\n%s: Caught a SIGSEGV or SIGBUS whilst decompressing.\n"
- "\n"
- " Possible causes are (most likely first):\n"
- " (1) The compressed data is corrupted, and bzip2's usual checks\n"
- " failed to detect this. Try bzip2 -tvv my_file.bz2.\n"
- " (2) This computer has unreliable memory or cache hardware\n"
- " (a surprisingly common problem; try a different machine.)\n"
- " (3) A bug in the compiler used to create this executable\n"
- " (unlikely, if you didn't compile bzip2 yourself.)\n"
- " (4) A real bug in bzip2 -- I hope this should never be the case.\n"
- " The user's manual, Section 4.3, has more info on (2) and (3).\n"
- " \n"
- " If you suspect this is a bug in bzip2, or are unsure about (2)\n"
- " or (3), feel free to report it to me at: jseward at bzip.org.\n"
- " Section 4.3 of the user's manual describes the info a useful\n"
- " bug report should have. If the manual is available on your\n"
- " system, please try and read it before mailing me. If you don't\n"
- " have the manual or can't be bothered to read it, mail me anyway.\n"
- "\n",
- progName );
-
- showFileNames();
- if (opMode == OM_Z)
- cleanUpAndFail( 3 ); else
- { cadvise(); cleanUpAndFail( 2 ); }
-}
-
-
-/*---------------------------------------------*/
-static
-void outOfMemory ( void )
-{
- fprintf ( stderr,
- "\n%s: couldn't allocate enough memory\n",
- progName );
- showFileNames();
- cleanUpAndFail(1);
-}
-
-
-/*---------------------------------------------*/
-static
-void configError ( void )
-{
- fprintf ( stderr,
- "bzip2: I'm not configured correctly for this platform!\n"
- "\tI require Int32, Int16 and Char to have sizes\n"
- "\tof 4, 2 and 1 bytes to run properly, and they don't.\n"
- "\tProbably you can fix this by defining them correctly,\n"
- "\tand recompiling. Bye!\n" );
- setExit(3);
- exit(exitValue);
-}
-
-
-/*---------------------------------------------------*/
-/*--- The main driver machinery ---*/
-/*---------------------------------------------------*/
-
-/* All rather crufty. The main problem is that input files
- are stat()d multiple times before use. This should be
- cleaned up.
-*/
-
-/*---------------------------------------------*/
-static
-void pad ( Char *s )
-{
- Int32 i;
- if ( (Int32)strlen(s) >= longestFileName ) return;
- for (i = 1; i <= longestFileName - (Int32)strlen(s); i++)
- fprintf ( stderr, " " );
-}
-
-
-/*---------------------------------------------*/
-static
-void copyFileName ( Char* to, Char* from )
-{
- if ( strlen(from) > FILE_NAME_LEN-10 ) {
- fprintf (
- stderr,
- "bzip2: file name\n`%s'\n"
- "is suspiciously (more than %d chars) long.\n"
- "Try using a reasonable file name instead. Sorry! :-)\n",
- from, FILE_NAME_LEN-10
- );
- setExit(1);
- exit(exitValue);
- }
-
- strncpy(to,from,FILE_NAME_LEN-10);
- to[FILE_NAME_LEN-10]='\0';
-}
-
-
-/*---------------------------------------------*/
-static
-Bool fileExists ( Char* name )
-{
- FILE *tmp = fopen ( name, "rb" );
- Bool exists = (tmp != NULL);
- if (tmp != NULL) fclose ( tmp );
- return exists;
-}
-
-
-/*---------------------------------------------*/
-/* Open an output file safely with O_EXCL and good permissions.
- This avoids a race condition in versions < 1.0.2, in which
- the file was first opened and then had its interim permissions
- set safely. We instead use open() to create the file with
- the interim permissions required. (--- --- rw-).
-
- For non-Unix platforms, if we are not worrying about
- security issues, simple this simply behaves like fopen.
-*/
-static
-FILE* fopen_output_safely ( Char* name, const char* mode )
-{
-# if BZ_UNIX
- FILE* fp;
- IntNative fh;
- fh = open(name, O_WRONLY|O_CREAT|O_EXCL, S_IWUSR|S_IRUSR);
- if (fh == -1) return NULL;
- fp = fdopen(fh, mode);
- if (fp == NULL) close(fh);
- return fp;
-# else
- return fopen(name, mode);
-# endif
-}
-
-
-/*---------------------------------------------*/
-/*--
- if in doubt, return True
---*/
-static
-Bool notAStandardFile ( Char* name )
-{
- IntNative i;
- struct MY_STAT statBuf;
-
- i = MY_LSTAT ( name, &statBuf );
- if (i != 0) return True;
- if (MY_S_ISREG(statBuf.st_mode)) return False;
- return True;
-}
-
-
-/*---------------------------------------------*/
-/*--
- rac 11/21/98 see if file has hard links to it
---*/
-static
-Int32 countHardLinks ( Char* name )
-{
- IntNative i;
- struct MY_STAT statBuf;
-
- i = MY_LSTAT ( name, &statBuf );
- if (i != 0) return 0;
- return (statBuf.st_nlink - 1);
-}
-
-
-/*---------------------------------------------*/
-/* Copy modification date, access date, permissions and owner from the
- source to destination file. We have to copy this meta-info off
- into fileMetaInfo before starting to compress / decompress it,
- because doing it afterwards means we get the wrong access time.
-
- To complicate matters, in compress() and decompress() below, the
- sequence of tests preceding the call to saveInputFileMetaInfo()
- involves calling fileExists(), which in turn establishes its result
- by attempting to fopen() the file, and if successful, immediately
- fclose()ing it again. So we have to assume that the fopen() call
- does not cause the access time field to be updated.
-
- Reading of the man page for stat() (man 2 stat) on RedHat 7.2 seems
- to imply that merely doing open() will not affect the access time.
- Therefore we merely need to hope that the C library only does
- open() as a result of fopen(), and not any kind of read()-ahead
- cleverness.
-
- It sounds pretty fragile to me. Whether this carries across
- robustly to arbitrary Unix-like platforms (or even works robustly
- on this one, RedHat 7.2) is unknown to me. Nevertheless ...
-*/
-#if BZ_UNIX
-static
-struct MY_STAT fileMetaInfo;
-#endif
-
-static
-void saveInputFileMetaInfo ( Char *srcName )
-{
-# if BZ_UNIX
- IntNative retVal;
- /* Note use of stat here, not lstat. */
- retVal = MY_STAT( srcName, &fileMetaInfo );
- ERROR_IF_NOT_ZERO ( retVal );
-# endif
-}
-
-
-static
-void applySavedTimeInfoToOutputFile ( Char *dstName )
-{
-# if BZ_UNIX
- IntNative retVal;
- struct utimbuf uTimBuf;
-
- uTimBuf.actime = fileMetaInfo.st_atime;
- uTimBuf.modtime = fileMetaInfo.st_mtime;
-
- retVal = utime ( dstName, &uTimBuf );
- ERROR_IF_NOT_ZERO ( retVal );
-# endif
-}
-
-static
-void applySavedFileAttrToOutputFile ( IntNative fd )
-{
-# if BZ_UNIX
- IntNative retVal;
-
- retVal = fchmod ( fd, fileMetaInfo.st_mode );
- ERROR_IF_NOT_ZERO ( retVal );
-
- (void) fchown ( fd, fileMetaInfo.st_uid, fileMetaInfo.st_gid );
- /* chown() will in many cases return with EPERM, which can
- be safely ignored.
- */
-# endif
-}
-
-
-/*---------------------------------------------*/
-static
-Bool containsDubiousChars ( Char* name )
-{
-# if BZ_UNIX
- /* On unix, files can contain any characters and the file expansion
- * is performed by the shell.
- */
- return False;
-# else /* ! BZ_UNIX */
- /* On non-unix (Win* platforms), wildcard characters are not allowed in
- * filenames.
- */
- for (; *name != '\0'; name++)
- if (*name == '?' || *name == '*') return True;
- return False;
-# endif /* BZ_UNIX */
-}
-
-
-/*---------------------------------------------*/
-#define BZ_N_SUFFIX_PAIRS 4
-
-const Char* zSuffix[BZ_N_SUFFIX_PAIRS]
- = { ".bz2", ".bz", ".tbz2", ".tbz" };
-const Char* unzSuffix[BZ_N_SUFFIX_PAIRS]
- = { "", "", ".tar", ".tar" };
-
-static
-Bool hasSuffix ( Char* s, const Char* suffix )
-{
- Int32 ns = strlen(s);
- Int32 nx = strlen(suffix);
- if (ns < nx) return False;
- if (strcmp(s + ns - nx, suffix) == 0) return True;
- return False;
-}
-
-static
-Bool mapSuffix ( Char* name,
- const Char* oldSuffix,
- const Char* newSuffix )
-{
- if (!hasSuffix(name,oldSuffix)) return False;
- name[strlen(name)-strlen(oldSuffix)] = 0;
- strcat ( name, newSuffix );
- return True;
-}
-
-
-/*---------------------------------------------*/
-static
-void compress ( Char *name )
-{
- FILE *inStr;
- FILE *outStr;
- Int32 n, i;
- struct MY_STAT statBuf;
-
- deleteOutputOnInterrupt = False;
-
- if (name == NULL && srcMode != SM_I2O)
- panic ( "compress: bad modes\n" );
-
- switch (srcMode) {
- case SM_I2O:
- copyFileName ( inName, (Char*)"(stdin)" );
- copyFileName ( outName, (Char*)"(stdout)" );
- break;
- case SM_F2F:
- copyFileName ( inName, name );
- copyFileName ( outName, name );
- strcat ( outName, ".bz2" );
- break;
- case SM_F2O:
- copyFileName ( inName, name );
- copyFileName ( outName, (Char*)"(stdout)" );
- break;
- }
-
- if ( srcMode != SM_I2O && containsDubiousChars ( inName ) ) {
- if (noisy)
- fprintf ( stderr, "%s: There are no files matching `%s'.\n",
- progName, inName );
- setExit(1);
- return;
- }
- if ( srcMode != SM_I2O && !fileExists ( inName ) ) {
- fprintf ( stderr, "%s: Can't open input file %s: %s.\n",
- progName, inName, strerror(errno) );
- setExit(1);
- return;
- }
- for (i = 0; i < BZ_N_SUFFIX_PAIRS; i++) {
- if (hasSuffix(inName, zSuffix[i])) {
- if (noisy)
- fprintf ( stderr,
- "%s: Input file %s already has %s suffix.\n",
- progName, inName, zSuffix[i] );
- setExit(1);
- return;
- }
- }
- if ( srcMode == SM_F2F || srcMode == SM_F2O ) {
- MY_STAT(inName, &statBuf);
- if ( MY_S_ISDIR(statBuf.st_mode) ) {
- fprintf( stderr,
- "%s: Input file %s is a directory.\n",
- progName,inName);
- setExit(1);
- return;
- }
- }
- if ( srcMode == SM_F2F && !forceOverwrite && notAStandardFile ( inName )) {
- if (noisy)
- fprintf ( stderr, "%s: Input file %s is not a normal file.\n",
- progName, inName );
- setExit(1);
- return;
- }
- if ( srcMode == SM_F2F && fileExists ( outName ) ) {
- if (forceOverwrite) {
- remove(outName);
- } else {
- fprintf ( stderr, "%s: Output file %s already exists.\n",
- progName, outName );
- setExit(1);
- return;
- }
- }
- if ( srcMode == SM_F2F && !forceOverwrite &&
- (n=countHardLinks ( inName )) > 0) {
- fprintf ( stderr, "%s: Input file %s has %d other link%s.\n",
- progName, inName, n, n > 1 ? "s" : "" );
- setExit(1);
- return;
- }
-
- if ( srcMode == SM_F2F ) {
- /* Save the file's meta-info before we open it. Doing it later
- means we mess up the access times. */
- saveInputFileMetaInfo ( inName );
- }
-
- switch ( srcMode ) {
-
- case SM_I2O:
- inStr = stdin;
- outStr = stdout;
- if ( isatty ( fileno ( stdout ) ) ) {
- fprintf ( stderr,
- "%s: I won't write compressed data to a terminal.\n",
- progName );
- fprintf ( stderr, "%s: For help, type: `%s --help'.\n",
- progName, progName );
- setExit(1);
- return;
- };
- break;
-
- case SM_F2O:
- inStr = fopen ( inName, "rb" );
- outStr = stdout;
- if ( isatty ( fileno ( stdout ) ) ) {
- fprintf ( stderr,
- "%s: I won't write compressed data to a terminal.\n",
- progName );
- fprintf ( stderr, "%s: For help, type: `%s --help'.\n",
- progName, progName );
- if ( inStr != NULL ) fclose ( inStr );
- setExit(1);
- return;
- };
- if ( inStr == NULL ) {
- fprintf ( stderr, "%s: Can't open input file %s: %s.\n",
- progName, inName, strerror(errno) );
- setExit(1);
- return;
- };
- break;
-
- case SM_F2F:
- inStr = fopen ( inName, "rb" );
- outStr = fopen_output_safely ( outName, "wb" );
- if ( outStr == NULL) {
- fprintf ( stderr, "%s: Can't create output file %s: %s.\n",
- progName, outName, strerror(errno) );
- if ( inStr != NULL ) fclose ( inStr );
- setExit(1);
- return;
- }
- if ( inStr == NULL ) {
- fprintf ( stderr, "%s: Can't open input file %s: %s.\n",
- progName, inName, strerror(errno) );
- if ( outStr != NULL ) fclose ( outStr );
- setExit(1);
- return;
- };
- break;
-
- default:
- panic ( "compress: bad srcMode" );
- break;
- }
-
- if (verbosity >= 1) {
- fprintf ( stderr, " %s: ", inName );
- pad ( inName );
- fflush ( stderr );
- }
-
- /*--- Now the input and output handles are sane. Do the Biz. ---*/
- outputHandleJustInCase = outStr;
- deleteOutputOnInterrupt = True;
- compressStream ( inStr, outStr );
- outputHandleJustInCase = NULL;
-
- /*--- If there was an I/O error, we won't get here. ---*/
- if ( srcMode == SM_F2F ) {
- applySavedTimeInfoToOutputFile ( outName );
- deleteOutputOnInterrupt = False;
- if ( !keepInputFiles ) {
- IntNative retVal = remove ( inName );
- ERROR_IF_NOT_ZERO ( retVal );
- }
- }
-
- deleteOutputOnInterrupt = False;
-}
-
-
-/*---------------------------------------------*/
-static
-void uncompress ( Char *name )
-{
- FILE *inStr;
- FILE *outStr;
- Int32 n, i;
- Bool magicNumberOK;
- Bool cantGuess;
- struct MY_STAT statBuf;
-
- deleteOutputOnInterrupt = False;
-
- if (name == NULL && srcMode != SM_I2O)
- panic ( "uncompress: bad modes\n" );
-
- cantGuess = False;
- switch (srcMode) {
- case SM_I2O:
- copyFileName ( inName, (Char*)"(stdin)" );
- copyFileName ( outName, (Char*)"(stdout)" );
- break;
- case SM_F2F:
- copyFileName ( inName, name );
- copyFileName ( outName, name );
- for (i = 0; i < BZ_N_SUFFIX_PAIRS; i++)
- if (mapSuffix(outName,zSuffix[i],unzSuffix[i]))
- goto zzz;
- cantGuess = True;
- strcat ( outName, ".out" );
- break;
- case SM_F2O:
- copyFileName ( inName, name );
- copyFileName ( outName, (Char*)"(stdout)" );
- break;
- }
-
- zzz:
- if ( srcMode != SM_I2O && containsDubiousChars ( inName ) ) {
- if (noisy)
- fprintf ( stderr, "%s: There are no files matching `%s'.\n",
- progName, inName );
- setExit(1);
- return;
- }
- if ( srcMode != SM_I2O && !fileExists ( inName ) ) {
- fprintf ( stderr, "%s: Can't open input file %s: %s.\n",
- progName, inName, strerror(errno) );
- setExit(1);
- return;
- }
- if ( srcMode == SM_F2F || srcMode == SM_F2O ) {
- MY_STAT(inName, &statBuf);
- if ( MY_S_ISDIR(statBuf.st_mode) ) {
- fprintf( stderr,
- "%s: Input file %s is a directory.\n",
- progName,inName);
- setExit(1);
- return;
- }
- }
- if ( srcMode == SM_F2F && !forceOverwrite && notAStandardFile ( inName )) {
- if (noisy)
- fprintf ( stderr, "%s: Input file %s is not a normal file.\n",
- progName, inName );
- setExit(1);
- return;
- }
- if ( /* srcMode == SM_F2F implied && */ cantGuess ) {
- if (noisy)
- fprintf ( stderr,
- "%s: Can't guess original name for %s -- using %s\n",
- progName, inName, outName );
- /* just a warning, no return */
- }
- if ( srcMode == SM_F2F && fileExists ( outName ) ) {
- if (forceOverwrite) {
- remove(outName);
- } else {
- fprintf ( stderr, "%s: Output file %s already exists.\n",
- progName, outName );
- setExit(1);
- return;
- }
- }
- if ( srcMode == SM_F2F && !forceOverwrite &&
- (n=countHardLinks ( inName ) ) > 0) {
- fprintf ( stderr, "%s: Input file %s has %d other link%s.\n",
- progName, inName, n, n > 1 ? "s" : "" );
- setExit(1);
- return;
- }
-
- if ( srcMode == SM_F2F ) {
- /* Save the file's meta-info before we open it. Doing it later
- means we mess up the access times. */
- saveInputFileMetaInfo ( inName );
- }
-
- switch ( srcMode ) {
-
- case SM_I2O:
- inStr = stdin;
- outStr = stdout;
- if ( isatty ( fileno ( stdin ) ) ) {
- fprintf ( stderr,
- "%s: I won't read compressed data from a terminal.\n",
- progName );
- fprintf ( stderr, "%s: For help, type: `%s --help'.\n",
- progName, progName );
- setExit(1);
- return;
- };
- break;
-
- case SM_F2O:
- inStr = fopen ( inName, "rb" );
- outStr = stdout;
- if ( inStr == NULL ) {
- fprintf ( stderr, "%s: Can't open input file %s:%s.\n",
- progName, inName, strerror(errno) );
- if ( inStr != NULL ) fclose ( inStr );
- setExit(1);
- return;
- };
- break;
-
- case SM_F2F:
- inStr = fopen ( inName, "rb" );
- outStr = fopen_output_safely ( outName, "wb" );
- if ( outStr == NULL) {
- fprintf ( stderr, "%s: Can't create output file %s: %s.\n",
- progName, outName, strerror(errno) );
- if ( inStr != NULL ) fclose ( inStr );
- setExit(1);
- return;
- }
- if ( inStr == NULL ) {
- fprintf ( stderr, "%s: Can't open input file %s: %s.\n",
- progName, inName, strerror(errno) );
- if ( outStr != NULL ) fclose ( outStr );
- setExit(1);
- return;
- };
- break;
-
- default:
- panic ( "uncompress: bad srcMode" );
- break;
- }
-
- if (verbosity >= 1) {
- fprintf ( stderr, " %s: ", inName );
- pad ( inName );
- fflush ( stderr );
- }
-
- /*--- Now the input and output handles are sane. Do the Biz. ---*/
- outputHandleJustInCase = outStr;
- deleteOutputOnInterrupt = True;
- magicNumberOK = uncompressStream ( inStr, outStr );
- outputHandleJustInCase = NULL;
-
- /*--- If there was an I/O error, we won't get here. ---*/
- if ( magicNumberOK ) {
- if ( srcMode == SM_F2F ) {
- applySavedTimeInfoToOutputFile ( outName );
- deleteOutputOnInterrupt = False;
- if ( !keepInputFiles ) {
- IntNative retVal = remove ( inName );
- ERROR_IF_NOT_ZERO ( retVal );
- }
- }
- } else {
- unzFailsExist = True;
- deleteOutputOnInterrupt = False;
- if ( srcMode == SM_F2F ) {
- IntNative retVal = remove ( outName );
- ERROR_IF_NOT_ZERO ( retVal );
- }
- }
- deleteOutputOnInterrupt = False;
-
- if ( magicNumberOK ) {
- if (verbosity >= 1)
- fprintf ( stderr, "done\n" );
- } else {
- setExit(2);
- if (verbosity >= 1)
- fprintf ( stderr, "not a bzip2 file.\n" ); else
- fprintf ( stderr,
- "%s: %s is not a bzip2 file.\n",
- progName, inName );
- }
-
-}
-
-
-/*---------------------------------------------*/
-static
-void testf ( Char *name )
-{
- FILE *inStr;
- Bool allOK;
- struct MY_STAT statBuf;
-
- deleteOutputOnInterrupt = False;
-
- if (name == NULL && srcMode != SM_I2O)
- panic ( "testf: bad modes\n" );
-
- copyFileName ( outName, (Char*)"(none)" );
- switch (srcMode) {
- case SM_I2O: copyFileName ( inName, (Char*)"(stdin)" ); break;
- case SM_F2F: copyFileName ( inName, name ); break;
- case SM_F2O: copyFileName ( inName, name ); break;
- }
-
- if ( srcMode != SM_I2O && containsDubiousChars ( inName ) ) {
- if (noisy)
- fprintf ( stderr, "%s: There are no files matching `%s'.\n",
- progName, inName );
- setExit(1);
- return;
- }
- if ( srcMode != SM_I2O && !fileExists ( inName ) ) {
- fprintf ( stderr, "%s: Can't open input %s: %s.\n",
- progName, inName, strerror(errno) );
- setExit(1);
- return;
- }
- if ( srcMode != SM_I2O ) {
- MY_STAT(inName, &statBuf);
- if ( MY_S_ISDIR(statBuf.st_mode) ) {
- fprintf( stderr,
- "%s: Input file %s is a directory.\n",
- progName,inName);
- setExit(1);
- return;
- }
- }
-
- switch ( srcMode ) {
-
- case SM_I2O:
- if ( isatty ( fileno ( stdin ) ) ) {
- fprintf ( stderr,
- "%s: I won't read compressed data from a terminal.\n",
- progName );
- fprintf ( stderr, "%s: For help, type: `%s --help'.\n",
- progName, progName );
- setExit(1);
- return;
- };
- inStr = stdin;
- break;
-
- case SM_F2O: case SM_F2F:
- inStr = fopen ( inName, "rb" );
- if ( inStr == NULL ) {
- fprintf ( stderr, "%s: Can't open input file %s:%s.\n",
- progName, inName, strerror(errno) );
- setExit(1);
- return;
- };
- break;
-
- default:
- panic ( "testf: bad srcMode" );
- break;
- }
-
- if (verbosity >= 1) {
- fprintf ( stderr, " %s: ", inName );
- pad ( inName );
- fflush ( stderr );
- }
-
- /*--- Now the input handle is sane. Do the Biz. ---*/
- outputHandleJustInCase = NULL;
- allOK = testStream ( inStr );
-
- if (allOK && verbosity >= 1) fprintf ( stderr, "ok\n" );
- if (!allOK) testFailsExist = True;
-}
-
-
-/*---------------------------------------------*/
-static
-void license ( void )
-{
- fprintf ( stderr,
-
- "bzip2, a block-sorting file compressor. "
- "Version %s.\n"
- " \n"
- " Copyright (C) 1996-2010 by Julian Seward.\n"
- " \n"
- " This program is free software; you can redistribute it and/or modify\n"
- " it under the terms set out in the LICENSE file, which is included\n"
- " in the bzip2-1.0.6 source distribution.\n"
- " \n"
- " This program is distributed in the hope that it will be useful,\n"
- " but WITHOUT ANY WARRANTY; without even the implied warranty of\n"
- " MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\n"
- " LICENSE file for more details.\n"
- " \n",
- BZ2_bzlibVersion()
- );
-}
-
-
-/*---------------------------------------------*/
-static
-void usage ( Char *fullProgName )
-{
- fprintf (
- stderr,
- "bzip2, a block-sorting file compressor. "
- "Version %s.\n"
- "\n usage: %s [flags and input files in any order]\n"
- "\n"
- " -h --help print this message\n"
- " -d --decompress force decompression\n"
- " -z --compress force compression\n"
- " -k --keep keep (don't delete) input files\n"
- " -f --force overwrite existing output files\n"
- " -t --test test compressed file integrity\n"
- " -c --stdout output to standard out\n"
- " -q --quiet suppress noncritical error messages\n"
- " -v --verbose be verbose (a 2nd -v gives more)\n"
- " -L --license display software version & license\n"
- " -V --version display software version & license\n"
- " -s --small use less memory (at most 2500k)\n"
- " -1 .. -9 set block size to 100k .. 900k\n"
- " --fast alias for -1\n"
- " --best alias for -9\n"
- "\n"
- " If invoked as `bzip2', default action is to compress.\n"
- " as `bunzip2', default action is to decompress.\n"
- " as `bzcat', default action is to decompress to stdout.\n"
- "\n"
- " If no file names are given, bzip2 compresses or decompresses\n"
- " from standard input to standard output. You can combine\n"
- " short flags, so `-v -4' means the same as -v4 or -4v, &c.\n"
-# if BZ_UNIX
- "\n"
-# endif
- ,
-
- BZ2_bzlibVersion(),
- fullProgName
- );
-}
-
-
-/*---------------------------------------------*/
-static
-void redundant ( Char* flag )
-{
- fprintf (
- stderr,
- "%s: %s is redundant in versions 0.9.5 and above\n",
- progName, flag );
-}
-
-
-/*---------------------------------------------*/
-/*--
- All the garbage from here to main() is purely to
- implement a linked list of command-line arguments,
- into which main() copies argv[1 .. argc-1].
-
- The purpose of this exercise is to facilitate
- the expansion of wildcard characters * and ? in
- filenames for OSs which don't know how to do it
- themselves, like MSDOS, Windows 95 and NT.
-
- The actual Dirty Work is done by the platform-
- specific macro APPEND_FILESPEC.
---*/
-
-typedef
- struct zzzz {
- Char *name;
- struct zzzz *link;
- }
- Cell;
-
-
-/*---------------------------------------------*/
-static
-void *myMalloc ( Int32 n )
-{
- void* p;
-
- p = malloc ( (size_t)n );
- if (p == NULL) outOfMemory ();
- return p;
-}
-
-
-/*---------------------------------------------*/
-static
-Cell *mkCell ( void )
-{
- Cell *c;
-
- c = (Cell*) myMalloc ( sizeof ( Cell ) );
- c->name = NULL;
- c->link = NULL;
- return c;
-}
-
-
-/*---------------------------------------------*/
-static
-Cell *snocString ( Cell *root, Char *name )
-{
- if (root == NULL) {
- Cell *tmp = mkCell();
- tmp->name = (Char*) myMalloc ( 5 + strlen(name) );
- strcpy ( tmp->name, name );
- return tmp;
- } else {
- Cell *tmp = root;
- while (tmp->link != NULL) tmp = tmp->link;
- tmp->link = snocString ( tmp->link, name );
- return root;
- }
-}
-
-
-/*---------------------------------------------*/
-static
-void addFlagsFromEnvVar ( Cell** argList, Char* varName )
-{
- Int32 i, j, k;
- Char *envbase, *p;
-
- envbase = getenv(varName);
- if (envbase != NULL) {
- p = envbase;
- i = 0;
- while (True) {
- if (p[i] == 0) break;
- p += i;
- i = 0;
- while (isspace((Int32)(p[0]))) p++;
- while (p[i] != 0 && !isspace((Int32)(p[i]))) i++;
- if (i > 0) {
- k = i; if (k > FILE_NAME_LEN-10) k = FILE_NAME_LEN-10;
- for (j = 0; j < k; j++) tmpName[j] = p[j];
- tmpName[k] = 0;
- APPEND_FLAG(*argList, tmpName);
- }
- }
- }
-}
-
-
-/*---------------------------------------------*/
-#define ISFLAG(s) (strcmp(aa->name, (s))==0)
-
-IntNative main ( IntNative argc, Char *argv[] )
-{
- Int32 i, j;
- Char *tmp;
- Cell *argList;
- Cell *aa;
- Bool decode;
-
- /*-- Be really really really paranoid :-) --*/
- if (sizeof(Int32) != 4 || sizeof(UInt32) != 4 ||
- sizeof(Int16) != 2 || sizeof(UInt16) != 2 ||
- sizeof(Char) != 1 || sizeof(UChar) != 1)
- configError();
-
- /*-- Initialise --*/
- outputHandleJustInCase = NULL;
- smallMode = False;
- keepInputFiles = False;
- forceOverwrite = False;
- noisy = True;
- verbosity = 0;
- blockSize100k = 9;
- testFailsExist = False;
- unzFailsExist = False;
- numFileNames = 0;
- numFilesProcessed = 0;
- workFactor = 30;
- deleteOutputOnInterrupt = False;
- exitValue = 0;
- i = j = 0; /* avoid bogus warning from egcs-1.1.X */
-
- /*-- Set up signal handlers for mem access errors --*/
- signal (SIGSEGV, mySIGSEGVorSIGBUScatcher);
-# if BZ_UNIX
-# ifndef __DJGPP__
- signal (SIGBUS, mySIGSEGVorSIGBUScatcher);
-# endif
-# endif
-
- copyFileName ( inName, (Char*)"(none)" );
- copyFileName ( outName, (Char*)"(none)" );
-
- copyFileName ( progNameReally, argv[0] );
- progName = &progNameReally[0];
- for (tmp = &progNameReally[0]; *tmp != '\0'; tmp++)
- if (*tmp == PATH_SEP) progName = tmp + 1;
-
-
- /*-- Copy flags from env var BZIP2, and
- expand filename wildcards in arg list.
- --*/
- argList = NULL;
- addFlagsFromEnvVar ( &argList, (Char*)"BZIP2" );
- addFlagsFromEnvVar ( &argList, (Char*)"BZIP" );
- for (i = 1; i <= argc-1; i++)
- APPEND_FILESPEC(argList, argv[i]);
-
-
- /*-- Find the length of the longest filename --*/
- longestFileName = 7;
- numFileNames = 0;
- decode = True;
- for (aa = argList; aa != NULL; aa = aa->link) {
- if (ISFLAG("--")) { decode = False; continue; }
- if (aa->name[0] == '-' && decode) continue;
- numFileNames++;
- if (longestFileName < (Int32)strlen(aa->name) )
- longestFileName = (Int32)strlen(aa->name);
- }
-
-
- /*-- Determine source modes; flag handling may change this too. --*/
- if (numFileNames == 0)
- srcMode = SM_I2O; else srcMode = SM_F2F;
-
-
- /*-- Determine what to do (compress/uncompress/test/cat). --*/
- /*-- Note that subsequent flag handling may change this. --*/
- opMode = OM_Z;
-
- if ( (strstr ( progName, "unzip" ) != 0) ||
- (strstr ( progName, "UNZIP" ) != 0) )
- opMode = OM_UNZ;
-
- if ( (strstr ( progName, "z2cat" ) != 0) ||
- (strstr ( progName, "Z2CAT" ) != 0) ||
- (strstr ( progName, "zcat" ) != 0) ||
- (strstr ( progName, "ZCAT" ) != 0) ) {
- opMode = OM_UNZ;
- srcMode = (numFileNames == 0) ? SM_I2O : SM_F2O;
- }
-
-
- /*-- Look at the flags. --*/
- for (aa = argList; aa != NULL; aa = aa->link) {
- if (ISFLAG("--")) break;
- if (aa->name[0] == '-' && aa->name[1] != '-') {
- for (j = 1; aa->name[j] != '\0'; j++) {
- switch (aa->name[j]) {
- case 'c': srcMode = SM_F2O; break;
- case 'd': opMode = OM_UNZ; break;
- case 'z': opMode = OM_Z; break;
- case 'f': forceOverwrite = True; break;
- case 't': opMode = OM_TEST; break;
- case 'k': keepInputFiles = True; break;
- case 's': smallMode = True; break;
- case 'q': noisy = False; break;
- case '1': blockSize100k = 1; break;
- case '2': blockSize100k = 2; break;
- case '3': blockSize100k = 3; break;
- case '4': blockSize100k = 4; break;
- case '5': blockSize100k = 5; break;
- case '6': blockSize100k = 6; break;
- case '7': blockSize100k = 7; break;
- case '8': blockSize100k = 8; break;
- case '9': blockSize100k = 9; break;
- case 'V':
- case 'L': license(); break;
- case 'v': verbosity++; break;
- case 'h': usage ( progName );
- exit ( 0 );
- break;
- default: fprintf ( stderr, "%s: Bad flag `%s'\n",
- progName, aa->name );
- usage ( progName );
- exit ( 1 );
- break;
- }
- }
- }
- }
-
- /*-- And again ... --*/
- for (aa = argList; aa != NULL; aa = aa->link) {
- if (ISFLAG("--")) break;
- if (ISFLAG("--stdout")) srcMode = SM_F2O; else
- if (ISFLAG("--decompress")) opMode = OM_UNZ; else
- if (ISFLAG("--compress")) opMode = OM_Z; else
- if (ISFLAG("--force")) forceOverwrite = True; else
- if (ISFLAG("--test")) opMode = OM_TEST; else
- if (ISFLAG("--keep")) keepInputFiles = True; else
- if (ISFLAG("--small")) smallMode = True; else
- if (ISFLAG("--quiet")) noisy = False; else
- if (ISFLAG("--version")) license(); else
- if (ISFLAG("--license")) license(); else
- if (ISFLAG("--exponential")) workFactor = 1; else
- if (ISFLAG("--repetitive-best")) redundant(aa->name); else
- if (ISFLAG("--repetitive-fast")) redundant(aa->name); else
- if (ISFLAG("--fast")) blockSize100k = 1; else
- if (ISFLAG("--best")) blockSize100k = 9; else
- if (ISFLAG("--verbose")) verbosity++; else
- if (ISFLAG("--help")) { usage ( progName ); exit ( 0 ); }
- else
- if (strncmp ( aa->name, "--", 2) == 0) {
- fprintf ( stderr, "%s: Bad flag `%s'\n", progName, aa->name );
- usage ( progName );
- exit ( 1 );
- }
- }
-
- if (verbosity > 4) verbosity = 4;
- if (opMode == OM_Z && smallMode && blockSize100k > 2)
- blockSize100k = 2;
-
- if (opMode == OM_TEST && srcMode == SM_F2O) {
- fprintf ( stderr, "%s: -c and -t cannot be used together.\n",
- progName );
- exit ( 1 );
- }
-
- if (srcMode == SM_F2O && numFileNames == 0)
- srcMode = SM_I2O;
-
- if (opMode != OM_Z) blockSize100k = 0;
-
- if (srcMode == SM_F2F) {
- signal (SIGINT, mySignalCatcher);
- signal (SIGTERM, mySignalCatcher);
-# if BZ_UNIX
- signal (SIGHUP, mySignalCatcher);
-# endif
- }
-
- if (opMode == OM_Z) {
- if (srcMode == SM_I2O) {
- compress ( NULL );
- } else {
- decode = True;
- for (aa = argList; aa != NULL; aa = aa->link) {
- if (ISFLAG("--")) { decode = False; continue; }
- if (aa->name[0] == '-' && decode) continue;
- numFilesProcessed++;
- compress ( aa->name );
- }
- }
- }
- else
-
- if (opMode == OM_UNZ) {
- unzFailsExist = False;
- if (srcMode == SM_I2O) {
- uncompress ( NULL );
- } else {
- decode = True;
- for (aa = argList; aa != NULL; aa = aa->link) {
- if (ISFLAG("--")) { decode = False; continue; }
- if (aa->name[0] == '-' && decode) continue;
- numFilesProcessed++;
- uncompress ( aa->name );
- }
- }
- if (unzFailsExist) {
- setExit(2);
- exit(exitValue);
- }
- }
-
- else {
- testFailsExist = False;
- if (srcMode == SM_I2O) {
- testf ( NULL );
- } else {
- decode = True;
- for (aa = argList; aa != NULL; aa = aa->link) {
- if (ISFLAG("--")) { decode = False; continue; }
- if (aa->name[0] == '-' && decode) continue;
- numFilesProcessed++;
- testf ( aa->name );
- }
- }
- if (testFailsExist && noisy) {
- fprintf ( stderr,
- "\n"
- "You can use the `bzip2recover' program to attempt to recover\n"
- "data from undamaged sections of corrupted files.\n\n"
- );
- setExit(2);
- exit(exitValue);
- }
- }
-
- /* Free the argument list memory to mollify leak detectors
- (eg) Purify, Checker. Serves no other useful purpose.
- */
- aa = argList;
- while (aa != NULL) {
- Cell* aa2 = aa->link;
- if (aa->name != NULL) free(aa->name);
- free(aa);
- aa = aa2;
- }
-
- return exitValue;
-}
-
-
-/*-----------------------------------------------------------*/
-/*--- end bzip2.c ---*/
-/*-----------------------------------------------------------*/
diff --git a/third-party/bzip2/bzip2.txt b/third-party/bzip2/bzip2.txt
deleted file mode 100644
index d2deb39..0000000
--- a/third-party/bzip2/bzip2.txt
+++ /dev/null
@@ -1,391 +0,0 @@
-
-NAME
- bzip2, bunzip2 - a block-sorting file compressor, v1.0.6
- bzcat - decompresses files to stdout
- bzip2recover - recovers data from damaged bzip2 files
-
-
-SYNOPSIS
- bzip2 [ -cdfkqstvzVL123456789 ] [ filenames ... ]
- bunzip2 [ -fkvsVL ] [ filenames ... ]
- bzcat [ -s ] [ filenames ... ]
- bzip2recover filename
-
-
-DESCRIPTION
- bzip2 compresses files using the Burrows-Wheeler block
- sorting text compression algorithm, and Huffman coding.
- Compression is generally considerably better than that
- achieved by more conventional LZ77/LZ78-based compressors,
- and approaches the performance of the PPM family of sta-
- tistical compressors.
-
- The command-line options are deliberately very similar to
- those of GNU gzip, but they are not identical.
-
- bzip2 expects a list of file names to accompany the com-
- mand-line flags. Each file is replaced by a compressed
- version of itself, with the name "original_name.bz2".
- Each compressed file has the same modification date, per-
- missions, and, when possible, ownership as the correspond-
- ing original, so that these properties can be correctly
- restored at decompression time. File name handling is
- naive in the sense that there is no mechanism for preserv-
- ing original file names, permissions, ownerships or dates
- in filesystems which lack these concepts, or have serious
- file name length restrictions, such as MS-DOS.
-
- bzip2 and bunzip2 will by default not overwrite existing
- files. If you want this to happen, specify the -f flag.
-
- If no file names are specified, bzip2 compresses from
- standard input to standard output. In this case, bzip2
- will decline to write compressed output to a terminal, as
- this would be entirely incomprehensible and therefore
- pointless.
-
- bunzip2 (or bzip2 -d) decompresses all specified files.
- Files which were not created by bzip2 will be detected and
- ignored, and a warning issued. bzip2 attempts to guess
- the filename for the decompressed file from that of the
- compressed file as follows:
-
- filename.bz2 becomes filename
- filename.bz becomes filename
- filename.tbz2 becomes filename.tar
- filename.tbz becomes filename.tar
- anyothername becomes anyothername.out
-
- If the file does not end in one of the recognised endings,
- .bz2, .bz, .tbz2 or .tbz, bzip2 complains that it cannot
- guess the name of the original file, and uses the original
- name with .out appended.
-
- As with compression, supplying no filenames causes decom-
- pression from standard input to standard output.
-
- bunzip2 will correctly decompress a file which is the con-
- catenation of two or more compressed files. The result is
- the concatenation of the corresponding uncompressed files.
- Integrity testing (-t) of concatenated compressed files is
- also supported.
-
- You can also compress or decompress files to the standard
- output by giving the -c flag. Multiple files may be com-
- pressed and decompressed like this. The resulting outputs
- are fed sequentially to stdout. Compression of multiple
- files in this manner generates a stream containing multi-
- ple compressed file representations. Such a stream can be
- decompressed correctly only by bzip2 version 0.9.0 or
- later. Earlier versions of bzip2 will stop after decom-
- pressing the first file in the stream.
-
- bzcat (or bzip2 -dc) decompresses all specified files to
- the standard output.
-
- bzip2 will read arguments from the environment variables
- BZIP2 and BZIP, in that order, and will process them
- before any arguments read from the command line. This
- gives a convenient way to supply default arguments.
-
- Compression is always performed, even if the compressed
- file is slightly larger than the original. Files of less
- than about one hundred bytes tend to get larger, since the
- compression mechanism has a constant overhead in the
- region of 50 bytes. Random data (including the output of
- most file compressors) is coded at about 8.05 bits per
- byte, giving an expansion of around 0.5%.
-
- As a self-check for your protection, bzip2 uses 32-bit
- CRCs to make sure that the decompressed version of a file
- is identical to the original. This guards against corrup-
- tion of the compressed data, and against undetected bugs
- in bzip2 (hopefully very unlikely). The chances of data
- corruption going undetected is microscopic, about one
- chance in four billion for each file processed. Be aware,
- though, that the check occurs upon decompression, so it
- can only tell you that something is wrong. It can't help
- you recover the original uncompressed data. You can use
- bzip2recover to try to recover data from damaged files.
-
- Return values: 0 for a normal exit, 1 for environmental
- problems (file not found, invalid flags, I/O errors, &c),
- 2 to indicate a corrupt compressed file, 3 for an internal
- consistency error (eg, bug) which caused bzip2 to panic.
-
-
-OPTIONS
- -c --stdout
- Compress or decompress to standard output.
-
- -d --decompress
- Force decompression. bzip2, bunzip2 and bzcat are
- really the same program, and the decision about
- what actions to take is done on the basis of which
- name is used. This flag overrides that mechanism,
- and forces bzip2 to decompress.
-
- -z --compress
- The complement to -d: forces compression,
- regardless of the invocation name.
-
- -t --test
- Check integrity of the specified file(s), but don't
- decompress them. This really performs a trial
- decompression and throws away the result.
-
- -f --force
- Force overwrite of output files. Normally, bzip2
- will not overwrite existing output files. Also
- forces bzip2 to break hard links to files, which it
- otherwise wouldn't do.
-
- bzip2 normally declines to decompress files which
- don't have the correct magic header bytes. If
- forced (-f), however, it will pass such files
- through unmodified. This is how GNU gzip behaves.
-
- -k --keep
- Keep (don't delete) input files during compression
- or decompression.
-
- -s --small
- Reduce memory usage, for compression, decompression
- and testing. Files are decompressed and tested
- using a modified algorithm which only requires 2.5
- bytes per block byte. This means any file can be
- decompressed in 2300k of memory, albeit at about
- half the normal speed.
-
- During compression, -s selects a block size of
- 200k, which limits memory use to around the same
- figure, at the expense of your compression ratio.
- In short, if your machine is low on memory (8
- megabytes or less), use -s for everything. See
- MEMORY MANAGEMENT below.
-
- -q --quiet
- Suppress non-essential warning messages. Messages
- pertaining to I/O errors and other critical events
- will not be suppressed.
-
- -v --verbose
- Verbose mode -- show the compression ratio for each
- file processed. Further -v's increase the ver-
- bosity level, spewing out lots of information which
- is primarily of interest for diagnostic purposes.
-
- -L --license -V --version
- Display the software version, license terms and
- conditions.
-
- -1 (or --fast) to -9 (or --best)
- Set the block size to 100 k, 200 k .. 900 k when
- compressing. Has no effect when decompressing.
- See MEMORY MANAGEMENT below. The --fast and --best
- aliases are primarily for GNU gzip compatibility.
- In particular, --fast doesn't make things signifi-
- cantly faster. And --best merely selects the
- default behaviour.
-
- -- Treats all subsequent arguments as file names, even
- if they start with a dash. This is so you can han-
- dle files with names beginning with a dash, for
- example: bzip2 -- -myfilename.
-
- --repetitive-fast --repetitive-best
- These flags are redundant in versions 0.9.5 and
- above. They provided some coarse control over the
- behaviour of the sorting algorithm in earlier ver-
- sions, which was sometimes useful. 0.9.5 and above
- have an improved algorithm which renders these
- flags irrelevant.
-
-
-MEMORY MANAGEMENT
- bzip2 compresses large files in blocks. The block size
- affects both the compression ratio achieved, and the
- amount of memory needed for compression and decompression.
- The flags -1 through -9 specify the block size to be
- 100,000 bytes through 900,000 bytes (the default) respec-
- tively. At decompression time, the block size used for
- compression is read from the header of the compressed
- file, and bunzip2 then allocates itself just enough memory
- to decompress the file. Since block sizes are stored in
- compressed files, it follows that the flags -1 to -9 are
- irrelevant to and so ignored during decompression.
-
- Compression and decompression requirements, in bytes, can
- be estimated as:
-
- Compression: 400k + ( 8 x block size )
-
- Decompression: 100k + ( 4 x block size ), or
- 100k + ( 2.5 x block size )
-
- Larger block sizes give rapidly diminishing marginal
- returns. Most of the compression comes from the first two
- or three hundred k of block size, a fact worth bearing in
- mind when using bzip2 on small machines. It is also
- important to appreciate that the decompression memory
- requirement is set at compression time by the choice of
- block size.
-
- For files compressed with the default 900k block size,
- bunzip2 will require about 3700 kbytes to decompress. To
- support decompression of any file on a 4 megabyte machine,
- bunzip2 has an option to decompress using approximately
- half this amount of memory, about 2300 kbytes. Decompres-
- sion speed is also halved, so you should use this option
- only where necessary. The relevant flag is -s.
-
- In general, try and use the largest block size memory con-
- straints allow, since that maximises the compression
- achieved. Compression and decompression speed are virtu-
- ally unaffected by block size.
-
- Another significant point applies to files which fit in a
- single block -- that means most files you'd encounter
- using a large block size. The amount of real memory
- touched is proportional to the size of the file, since the
- file is smaller than a block. For example, compressing a
- file 20,000 bytes long with the flag -9 will cause the
- compressor to allocate around 7600k of memory, but only
- touch 400k + 20000 * 8 = 560 kbytes of it. Similarly, the
- decompressor will allocate 3700k but only touch 100k +
- 20000 * 4 = 180 kbytes.
-
- Here is a table which summarises the maximum memory usage
- for different block sizes. Also recorded is the total
- compressed size for 14 files of the Calgary Text Compres-
- sion Corpus totalling 3,141,622 bytes. This column gives
- some feel for how compression varies with block size.
- These figures tend to understate the advantage of larger
- block sizes for larger files, since the Corpus is domi-
- nated by smaller files.
-
- Compress Decompress Decompress Corpus
- Flag usage usage -s usage Size
-
- -1 1200k 500k 350k 914704
- -2 2000k 900k 600k 877703
- -3 2800k 1300k 850k 860338
- -4 3600k 1700k 1100k 846899
- -5 4400k 2100k 1350k 845160
- -6 5200k 2500k 1600k 838626
- -7 6100k 2900k 1850k 834096
- -8 6800k 3300k 2100k 828642
- -9 7600k 3700k 2350k 828642
-
-
-RECOVERING DATA FROM DAMAGED FILES
- bzip2 compresses files in blocks, usually 900kbytes long.
- Each block is handled independently. If a media or trans-
- mission error causes a multi-block .bz2 file to become
- damaged, it may be possible to recover data from the
- undamaged blocks in the file.
-
- The compressed representation of each block is delimited
- by a 48-bit pattern, which makes it possible to find the
- block boundaries with reasonable certainty. Each block
- also carries its own 32-bit CRC, so damaged blocks can be
- distinguished from undamaged ones.
-
- bzip2recover is a simple program whose purpose is to
- search for blocks in .bz2 files, and write each block out
- into its own .bz2 file. You can then use bzip2 -t to test
- the integrity of the resulting files, and decompress those
- which are undamaged.
-
- bzip2recover takes a single argument, the name of the dam-
- aged file, and writes a number of files
- "rec00001file.bz2", "rec00002file.bz2", etc, containing
- the extracted blocks. The output filenames are
- designed so that the use of wildcards in subsequent pro-
- cessing -- for example, "bzip2 -dc rec*file.bz2 > recov-
- ered_data" -- processes the files in the correct order.
-
- bzip2recover should be of most use dealing with large .bz2
- files, as these will contain many blocks. It is clearly
- futile to use it on damaged single-block files, since a
- damaged block cannot be recovered. If you wish to min-
- imise any potential data loss through media or transmis-
- sion errors, you might consider compressing with a smaller
- block size.
-
-
-PERFORMANCE NOTES
- The sorting phase of compression gathers together similar
- strings in the file. Because of this, files containing
- very long runs of repeated symbols, like "aabaabaabaab
- ..." (repeated several hundred times) may compress more
- slowly than normal. Versions 0.9.5 and above fare much
- better than previous versions in this respect. The ratio
- between worst-case and average-case compression time is in
- the region of 10:1. For previous versions, this figure
- was more like 100:1. You can use the -vvvv option to mon-
- itor progress in great detail, if you want.
-
- Decompression speed is unaffected by these phenomena.
-
- bzip2 usually allocates several megabytes of memory to
- operate in, and then charges all over it in a fairly ran-
- dom fashion. This means that performance, both for com-
- pressing and decompressing, is largely determined by the
- speed at which your machine can service cache misses.
- Because of this, small changes to the code to reduce the
- miss rate have been observed to give disproportionately
- large performance improvements. I imagine bzip2 will per-
- form best on machines with very large caches.
-
-
-CAVEATS
- I/O error messages are not as helpful as they could be.
- bzip2 tries hard to detect I/O errors and exit cleanly,
- but the details of what the problem is sometimes seem
- rather misleading.
-
- This manual page pertains to version 1.0.6 of bzip2. Com-
- pressed data created by this version is entirely forwards
- and backwards compatible with the previous public
- releases, versions 0.1pl2, 0.9.0, 0.9.5, 1.0.0, 1.0.1,
- 1.0.2 and above, but with the following exception: 0.9.0
- and above can correctly decompress multiple concatenated
- compressed files. 0.1pl2 cannot do this; it will stop
- after decompressing just the first file in the stream.
-
- bzip2recover versions prior to 1.0.2 used 32-bit integers
- to represent bit positions in compressed files, so they
- could not handle compressed files more than 512 megabytes
- long. Versions 1.0.2 and above use 64-bit ints on some
- platforms which support them (GNU supported targets, and
- Windows). To establish whether or not bzip2recover was
- built with such a limitation, run it without arguments.
- In any event you can build yourself an unlimited version
- if you can recompile it with MaybeUInt64 set to be an
- unsigned 64-bit integer.
-
-
-AUTHOR
- Julian Seward, jsewardbzip.org.
-
- http://www.bzip.org
-
- The ideas embodied in bzip2 are due to (at least) the fol-
- lowing people: Michael Burrows and David Wheeler (for the
- block sorting transformation), David Wheeler (again, for
- the Huffman coder), Peter Fenwick (for the structured cod-
- ing model in the original bzip, and many refinements), and
- Alistair Moffat, Radford Neal and Ian Witten (for the
- arithmetic coder in the original bzip). I am much
- indebted for their help, support and advice. See the man-
- ual in the source distribution for pointers to sources of
- documentation. Christian von Roques encouraged me to look
- for faster sorting algorithms, so as to speed up compres-
- sion. Bela Lubkin encouraged me to improve the worst-case
- compression performance. Donna Robinson XMLised the docu-
- mentation. The bz* scripts are derived from those of GNU
- gzip. Many people sent patches, helped with portability
- problems, lent machines, gave advice and were generally
- helpful.
-
diff --git a/third-party/bzip2/bzip2recover.c b/third-party/bzip2/bzip2recover.c
deleted file mode 100644
index f9de049..0000000
--- a/third-party/bzip2/bzip2recover.c
+++ /dev/null
@@ -1,514 +0,0 @@
-/*-----------------------------------------------------------*/
-/*--- Block recoverer program for bzip2 ---*/
-/*--- bzip2recover.c ---*/
-/*-----------------------------------------------------------*/
-
-/* ------------------------------------------------------------------
- This file is part of bzip2/libbzip2, a program and library for
- lossless, block-sorting data compression.
-
- bzip2/libbzip2 version 1.0.6 of 6 September 2010
- Copyright (C) 1996-2010 Julian Seward <jseward at bzip.org>
-
- Please read the WARNING, DISCLAIMER and PATENTS sections in the
- README file.
-
- This program is released under the terms of the license contained
- in the file LICENSE.
- ------------------------------------------------------------------ */
-
-/* This program is a complete hack and should be rewritten properly.
- It isn't very complicated. */
-
-#include <stdio.h>
-#include <errno.h>
-#include <stdlib.h>
-#include <string.h>
-
-
-/* This program records bit locations in the file to be recovered.
- That means that if 64-bit ints are not supported, we will not
- be able to recover .bz2 files over 512MB (2^32 bits) long.
- On GNU supported platforms, we take advantage of the 64-bit
- int support to circumvent this problem. Ditto MSVC.
-
- This change occurred in version 1.0.2; all prior versions have
- the 512MB limitation.
-*/
-#ifdef __GNUC__
- typedef unsigned long long int MaybeUInt64;
-# define MaybeUInt64_FMT "%Lu"
-#else
-#ifdef _MSC_VER
- typedef unsigned __int64 MaybeUInt64;
-# define MaybeUInt64_FMT "%I64u"
-#else
- typedef unsigned int MaybeUInt64;
-# define MaybeUInt64_FMT "%u"
-#endif
-#endif
-
-typedef unsigned int UInt32;
-typedef int Int32;
-typedef unsigned char UChar;
-typedef char Char;
-typedef unsigned char Bool;
-#define True ((Bool)1)
-#define False ((Bool)0)
-
-
-#define BZ_MAX_FILENAME 2000
-
-Char inFileName[BZ_MAX_FILENAME];
-Char outFileName[BZ_MAX_FILENAME];
-Char progName[BZ_MAX_FILENAME];
-
-MaybeUInt64 bytesOut = 0;
-MaybeUInt64 bytesIn = 0;
-
-
-/*---------------------------------------------------*/
-/*--- Header bytes ---*/
-/*---------------------------------------------------*/
-
-#define BZ_HDR_B 0x42 /* 'B' */
-#define BZ_HDR_Z 0x5a /* 'Z' */
-#define BZ_HDR_h 0x68 /* 'h' */
-#define BZ_HDR_0 0x30 /* '0' */
-
-
-/*---------------------------------------------------*/
-/*--- I/O errors ---*/
-/*---------------------------------------------------*/
-
-/*---------------------------------------------*/
-static void readError ( void )
-{
- fprintf ( stderr,
- "%s: I/O error reading `%s', possible reason follows.\n",
- progName, inFileName );
- perror ( progName );
- fprintf ( stderr, "%s: warning: output file(s) may be incomplete.\n",
- progName );
- exit ( 1 );
-}
-
-
-/*---------------------------------------------*/
-static void writeError ( void )
-{
- fprintf ( stderr,
- "%s: I/O error reading `%s', possible reason follows.\n",
- progName, inFileName );
- perror ( progName );
- fprintf ( stderr, "%s: warning: output file(s) may be incomplete.\n",
- progName );
- exit ( 1 );
-}
-
-
-/*---------------------------------------------*/
-static void mallocFail ( Int32 n )
-{
- fprintf ( stderr,
- "%s: malloc failed on request for %d bytes.\n",
- progName, n );
- fprintf ( stderr, "%s: warning: output file(s) may be incomplete.\n",
- progName );
- exit ( 1 );
-}
-
-
-/*---------------------------------------------*/
-static void tooManyBlocks ( Int32 max_handled_blocks )
-{
- fprintf ( stderr,
- "%s: `%s' appears to contain more than %d blocks\n",
- progName, inFileName, max_handled_blocks );
- fprintf ( stderr,
- "%s: and cannot be handled. To fix, increase\n",
- progName );
- fprintf ( stderr,
- "%s: BZ_MAX_HANDLED_BLOCKS in bzip2recover.c, and recompile.\n",
- progName );
- exit ( 1 );
-}
-
-
-
-/*---------------------------------------------------*/
-/*--- Bit stream I/O ---*/
-/*---------------------------------------------------*/
-
-typedef
- struct {
- FILE* handle;
- Int32 buffer;
- Int32 buffLive;
- Char mode;
- }
- BitStream;
-
-
-/*---------------------------------------------*/
-static BitStream* bsOpenReadStream ( FILE* stream )
-{
- BitStream *bs = malloc ( sizeof(BitStream) );
- if (bs == NULL) mallocFail ( sizeof(BitStream) );
- bs->handle = stream;
- bs->buffer = 0;
- bs->buffLive = 0;
- bs->mode = 'r';
- return bs;
-}
-
-
-/*---------------------------------------------*/
-static BitStream* bsOpenWriteStream ( FILE* stream )
-{
- BitStream *bs = malloc ( sizeof(BitStream) );
- if (bs == NULL) mallocFail ( sizeof(BitStream) );
- bs->handle = stream;
- bs->buffer = 0;
- bs->buffLive = 0;
- bs->mode = 'w';
- return bs;
-}
-
-
-/*---------------------------------------------*/
-static void bsPutBit ( BitStream* bs, Int32 bit )
-{
- if (bs->buffLive == 8) {
- Int32 retVal = putc ( (UChar) bs->buffer, bs->handle );
- if (retVal == EOF) writeError();
- bytesOut++;
- bs->buffLive = 1;
- bs->buffer = bit & 0x1;
- } else {
- bs->buffer = ( (bs->buffer << 1) | (bit & 0x1) );
- bs->buffLive++;
- };
-}
-
-
-/*---------------------------------------------*/
-/*--
- Returns 0 or 1, or 2 to indicate EOF.
---*/
-static Int32 bsGetBit ( BitStream* bs )
-{
- if (bs->buffLive > 0) {
- bs->buffLive --;
- return ( ((bs->buffer) >> (bs->buffLive)) & 0x1 );
- } else {
- Int32 retVal = getc ( bs->handle );
- if ( retVal == EOF ) {
- if (errno != 0) readError();
- return 2;
- }
- bs->buffLive = 7;
- bs->buffer = retVal;
- return ( ((bs->buffer) >> 7) & 0x1 );
- }
-}
-
-
-/*---------------------------------------------*/
-static void bsClose ( BitStream* bs )
-{
- Int32 retVal;
-
- if ( bs->mode == 'w' ) {
- while ( bs->buffLive < 8 ) {
- bs->buffLive++;
- bs->buffer <<= 1;
- };
- retVal = putc ( (UChar) (bs->buffer), bs->handle );
- if (retVal == EOF) writeError();
- bytesOut++;
- retVal = fflush ( bs->handle );
- if (retVal == EOF) writeError();
- }
- retVal = fclose ( bs->handle );
- if (retVal == EOF) {
- if (bs->mode == 'w') writeError(); else readError();
- }
- free ( bs );
-}
-
-
-/*---------------------------------------------*/
-static void bsPutUChar ( BitStream* bs, UChar c )
-{
- Int32 i;
- for (i = 7; i >= 0; i--)
- bsPutBit ( bs, (((UInt32) c) >> i) & 0x1 );
-}
-
-
-/*---------------------------------------------*/
-static void bsPutUInt32 ( BitStream* bs, UInt32 c )
-{
- Int32 i;
-
- for (i = 31; i >= 0; i--)
- bsPutBit ( bs, (c >> i) & 0x1 );
-}
-
-
-/*---------------------------------------------*/
-static Bool endsInBz2 ( Char* name )
-{
- Int32 n = strlen ( name );
- if (n <= 4) return False;
- return
- (name[n-4] == '.' &&
- name[n-3] == 'b' &&
- name[n-2] == 'z' &&
- name[n-1] == '2');
-}
-
-
-/*---------------------------------------------------*/
-/*--- ---*/
-/*---------------------------------------------------*/
-
-/* This logic isn't really right when it comes to Cygwin. */
-#ifdef _WIN32
-# define BZ_SPLIT_SYM '\\' /* path splitter on Windows platform */
-#else
-# define BZ_SPLIT_SYM '/' /* path splitter on Unix platform */
-#endif
-
-#define BLOCK_HEADER_HI 0x00003141UL
-#define BLOCK_HEADER_LO 0x59265359UL
-
-#define BLOCK_ENDMARK_HI 0x00001772UL
-#define BLOCK_ENDMARK_LO 0x45385090UL
-
-/* Increase if necessary. However, a .bz2 file with > 50000 blocks
- would have an uncompressed size of at least 40GB, so the chances
- are low you'll need to up this.
-*/
-#define BZ_MAX_HANDLED_BLOCKS 50000
-
-MaybeUInt64 bStart [BZ_MAX_HANDLED_BLOCKS];
-MaybeUInt64 bEnd [BZ_MAX_HANDLED_BLOCKS];
-MaybeUInt64 rbStart[BZ_MAX_HANDLED_BLOCKS];
-MaybeUInt64 rbEnd [BZ_MAX_HANDLED_BLOCKS];
-
-Int32 main ( Int32 argc, Char** argv )
-{
- FILE* inFile;
- FILE* outFile;
- BitStream* bsIn, *bsWr;
- Int32 b, wrBlock, currBlock, rbCtr;
- MaybeUInt64 bitsRead;
-
- UInt32 buffHi, buffLo, blockCRC;
- Char* p;
-
- strcpy ( progName, argv[0] );
- inFileName[0] = outFileName[0] = 0;
-
- fprintf ( stderr,
- "bzip2recover 1.0.6: extracts blocks from damaged .bz2 files.\n" );
-
- if (argc != 2) {
- fprintf ( stderr, "%s: usage is `%s damaged_file_name'.\n",
- progName, progName );
- switch (sizeof(MaybeUInt64)) {
- case 8:
- fprintf(stderr,
- "\trestrictions on size of recovered file: None\n");
- break;
- case 4:
- fprintf(stderr,
- "\trestrictions on size of recovered file: 512 MB\n");
- fprintf(stderr,
- "\tto circumvent, recompile with MaybeUInt64 as an\n"
- "\tunsigned 64-bit int.\n");
- break;
- default:
- fprintf(stderr,
- "\tsizeof(MaybeUInt64) is not 4 or 8 -- "
- "configuration error.\n");
- break;
- }
- exit(1);
- }
-
- if (strlen(argv[1]) >= BZ_MAX_FILENAME-20) {
- fprintf ( stderr,
- "%s: supplied filename is suspiciously (>= %d chars) long. Bye!\n",
- progName, (int)strlen(argv[1]) );
- exit(1);
- }
-
- strcpy ( inFileName, argv[1] );
-
- inFile = fopen ( inFileName, "rb" );
- if (inFile == NULL) {
- fprintf ( stderr, "%s: can't read `%s'\n", progName, inFileName );
- exit(1);
- }
-
- bsIn = bsOpenReadStream ( inFile );
- fprintf ( stderr, "%s: searching for block boundaries ...\n", progName );
-
- bitsRead = 0;
- buffHi = buffLo = 0;
- currBlock = 0;
- bStart[currBlock] = 0;
-
- rbCtr = 0;
-
- while (True) {
- b = bsGetBit ( bsIn );
- bitsRead++;
- if (b == 2) {
- if (bitsRead >= bStart[currBlock] &&
- (bitsRead - bStart[currBlock]) >= 40) {
- bEnd[currBlock] = bitsRead-1;
- if (currBlock > 0)
- fprintf ( stderr, " block %d runs from " MaybeUInt64_FMT
- " to " MaybeUInt64_FMT " (incomplete)\n",
- currBlock, bStart[currBlock], bEnd[currBlock] );
- } else
- currBlock--;
- break;
- }
- buffHi = (buffHi << 1) | (buffLo >> 31);
- buffLo = (buffLo << 1) | (b & 1);
- if ( ( (buffHi & 0x0000ffff) == BLOCK_HEADER_HI
- && buffLo == BLOCK_HEADER_LO)
- ||
- ( (buffHi & 0x0000ffff) == BLOCK_ENDMARK_HI
- && buffLo == BLOCK_ENDMARK_LO)
- ) {
- if (bitsRead > 49) {
- bEnd[currBlock] = bitsRead-49;
- } else {
- bEnd[currBlock] = 0;
- }
- if (currBlock > 0 &&
- (bEnd[currBlock] - bStart[currBlock]) >= 130) {
- fprintf ( stderr, " block %d runs from " MaybeUInt64_FMT
- " to " MaybeUInt64_FMT "\n",
- rbCtr+1, bStart[currBlock], bEnd[currBlock] );
- rbStart[rbCtr] = bStart[currBlock];
- rbEnd[rbCtr] = bEnd[currBlock];
- rbCtr++;
- }
- if (currBlock >= BZ_MAX_HANDLED_BLOCKS)
- tooManyBlocks(BZ_MAX_HANDLED_BLOCKS);
- currBlock++;
-
- bStart[currBlock] = bitsRead;
- }
- }
-
- bsClose ( bsIn );
-
- /*-- identified blocks run from 1 to rbCtr inclusive. --*/
-
- if (rbCtr < 1) {
- fprintf ( stderr,
- "%s: sorry, I couldn't find any block boundaries.\n",
- progName );
- exit(1);
- };
-
- fprintf ( stderr, "%s: splitting into blocks\n", progName );
-
- inFile = fopen ( inFileName, "rb" );
- if (inFile == NULL) {
- fprintf ( stderr, "%s: can't open `%s'\n", progName, inFileName );
- exit(1);
- }
- bsIn = bsOpenReadStream ( inFile );
-
- /*-- placate gcc's dataflow analyser --*/
- blockCRC = 0; bsWr = 0;
-
- bitsRead = 0;
- outFile = NULL;
- wrBlock = 0;
- while (True) {
- b = bsGetBit(bsIn);
- if (b == 2) break;
- buffHi = (buffHi << 1) | (buffLo >> 31);
- buffLo = (buffLo << 1) | (b & 1);
- if (bitsRead == 47+rbStart[wrBlock])
- blockCRC = (buffHi << 16) | (buffLo >> 16);
-
- if (outFile != NULL && bitsRead >= rbStart[wrBlock]
- && bitsRead <= rbEnd[wrBlock]) {
- bsPutBit ( bsWr, b );
- }
-
- bitsRead++;
-
- if (bitsRead == rbEnd[wrBlock]+1) {
- if (outFile != NULL) {
- bsPutUChar ( bsWr, 0x17 ); bsPutUChar ( bsWr, 0x72 );
- bsPutUChar ( bsWr, 0x45 ); bsPutUChar ( bsWr, 0x38 );
- bsPutUChar ( bsWr, 0x50 ); bsPutUChar ( bsWr, 0x90 );
- bsPutUInt32 ( bsWr, blockCRC );
- bsClose ( bsWr );
- }
- if (wrBlock >= rbCtr) break;
- wrBlock++;
- } else
- if (bitsRead == rbStart[wrBlock]) {
- /* Create the output file name, correctly handling leading paths.
- (31.10.2001 by Sergey E. Kusikov) */
- Char* split;
- Int32 ofs, k;
- for (k = 0; k < BZ_MAX_FILENAME; k++)
- outFileName[k] = 0;
- strcpy (outFileName, inFileName);
- split = strrchr (outFileName, BZ_SPLIT_SYM);
- if (split == NULL) {
- split = outFileName;
- } else {
- ++split;
- }
- /* Now split points to the start of the basename. */
- ofs = split - outFileName;
- sprintf (split, "rec%5d", wrBlock+1);
- for (p = split; *p != 0; p++) if (*p == ' ') *p = '0';
- strcat (outFileName, inFileName + ofs);
-
- if ( !endsInBz2(outFileName)) strcat ( outFileName, ".bz2" );
-
- fprintf ( stderr, " writing block %d to `%s' ...\n",
- wrBlock+1, outFileName );
-
- outFile = fopen ( outFileName, "wb" );
- if (outFile == NULL) {
- fprintf ( stderr, "%s: can't write `%s'\n",
- progName, outFileName );
- exit(1);
- }
- bsWr = bsOpenWriteStream ( outFile );
- bsPutUChar ( bsWr, BZ_HDR_B );
- bsPutUChar ( bsWr, BZ_HDR_Z );
- bsPutUChar ( bsWr, BZ_HDR_h );
- bsPutUChar ( bsWr, BZ_HDR_0 + 9 );
- bsPutUChar ( bsWr, 0x31 ); bsPutUChar ( bsWr, 0x41 );
- bsPutUChar ( bsWr, 0x59 ); bsPutUChar ( bsWr, 0x26 );
- bsPutUChar ( bsWr, 0x53 ); bsPutUChar ( bsWr, 0x59 );
- }
- }
-
- fprintf ( stderr, "%s: finished\n", progName );
- return 0;
-}
-
-
-
-/*-----------------------------------------------------------*/
-/*--- end bzip2recover.c ---*/
-/*-----------------------------------------------------------*/
diff --git a/third-party/bzip2/bzlib.c b/third-party/bzip2/bzlib.c
deleted file mode 100644
index bd358a7..0000000
--- a/third-party/bzip2/bzlib.c
+++ /dev/null
@@ -1,1572 +0,0 @@
-
-/*-------------------------------------------------------------*/
-/*--- Library top-level functions. ---*/
-/*--- bzlib.c ---*/
-/*-------------------------------------------------------------*/
-
-/* ------------------------------------------------------------------
- This file is part of bzip2/libbzip2, a program and library for
- lossless, block-sorting data compression.
-
- bzip2/libbzip2 version 1.0.6 of 6 September 2010
- Copyright (C) 1996-2010 Julian Seward <jseward at bzip.org>
-
- Please read the WARNING, DISCLAIMER and PATENTS sections in the
- README file.
-
- This program is released under the terms of the license contained
- in the file LICENSE.
- ------------------------------------------------------------------ */
-
-/* CHANGES
- 0.9.0 -- original version.
- 0.9.0a/b -- no changes in this file.
- 0.9.0c -- made zero-length BZ_FLUSH work correctly in bzCompress().
- fixed bzWrite/bzRead to ignore zero-length requests.
- fixed bzread to correctly handle read requests after EOF.
- wrong parameter order in call to bzDecompressInit in
- bzBuffToBuffDecompress. Fixed.
-*/
-
-#include "bzlib_private.h"
-
-
-/*---------------------------------------------------*/
-/*--- Compression stuff ---*/
-/*---------------------------------------------------*/
-
-
-/*---------------------------------------------------*/
-#ifndef BZ_NO_STDIO
-void BZ2_bz__AssertH__fail ( int errcode )
-{
- fprintf(stderr,
- "\n\nbzip2/libbzip2: internal error number %d.\n"
- "This is a bug in bzip2/libbzip2, %s.\n"
- "Please report it to me at: jseward at bzip.org. If this happened\n"
- "when you were using some program which uses libbzip2 as a\n"
- "component, you should also report this bug to the author(s)\n"
- "of that program. Please make an effort to report this bug;\n"
- "timely and accurate bug reports eventually lead to higher\n"
- "quality software. Thanks. Julian Seward, 10 December 2007.\n\n",
- errcode,
- BZ2_bzlibVersion()
- );
-
- if (errcode == 1007) {
- fprintf(stderr,
- "\n*** A special note about internal error number 1007 ***\n"
- "\n"
- "Experience suggests that a common cause of i.e. 1007\n"
- "is unreliable memory or other hardware. The 1007 assertion\n"
- "just happens to cross-check the results of huge numbers of\n"
- "memory reads/writes, and so acts (unintendedly) as a stress\n"
- "test of your memory system.\n"
- "\n"
- "I suggest the following: try compressing the file again,\n"
- "possibly monitoring progress in detail with the -vv flag.\n"
- "\n"
- "* If the error cannot be reproduced, and/or happens at different\n"
- " points in compression, you may have a flaky memory system.\n"
- " Try a memory-test program. I have used Memtest86\n"
- " (www.memtest86.com). At the time of writing it is free (GPLd).\n"
- " Memtest86 tests memory much more thorougly than your BIOSs\n"
- " power-on test, and may find failures that the BIOS doesn't.\n"
- "\n"
- "* If the error can be repeatably reproduced, this is a bug in\n"
- " bzip2, and I would very much like to hear about it. Please\n"
- " let me know, and, ideally, save a copy of the file causing the\n"
- " problem -- without which I will be unable to investigate it.\n"
- "\n"
- );
- }
-
- exit(3);
-}
-#endif
-
-
-/*---------------------------------------------------*/
-static
-int bz_config_ok ( void )
-{
- if (sizeof(int) != 4) return 0;
- if (sizeof(short) != 2) return 0;
- if (sizeof(char) != 1) return 0;
- return 1;
-}
-
-
-/*---------------------------------------------------*/
-static
-void* default_bzalloc ( void* opaque, Int32 items, Int32 size )
-{
- void* v = malloc ( items * size );
- return v;
-}
-
-static
-void default_bzfree ( void* opaque, void* addr )
-{
- if (addr != NULL) free ( addr );
-}
-
-
-/*---------------------------------------------------*/
-static
-void prepare_new_block ( EState* s )
-{
- Int32 i;
- s->nblock = 0;
- s->numZ = 0;
- s->state_out_pos = 0;
- BZ_INITIALISE_CRC ( s->blockCRC );
- for (i = 0; i < 256; i++) s->inUse[i] = False;
- s->blockNo++;
-}
-
-
-/*---------------------------------------------------*/
-static
-void init_RL ( EState* s )
-{
- s->state_in_ch = 256;
- s->state_in_len = 0;
-}
-
-
-static
-Bool isempty_RL ( EState* s )
-{
- if (s->state_in_ch < 256 && s->state_in_len > 0)
- return False; else
- return True;
-}
-
-
-/*---------------------------------------------------*/
-int BZ_API(BZ2_bzCompressInit)
- ( bz_stream* strm,
- int blockSize100k,
- int verbosity,
- int workFactor )
-{
- Int32 n;
- EState* s;
-
- if (!bz_config_ok()) return BZ_CONFIG_ERROR;
-
- if (strm == NULL ||
- blockSize100k < 1 || blockSize100k > 9 ||
- workFactor < 0 || workFactor > 250)
- return BZ_PARAM_ERROR;
-
- if (workFactor == 0) workFactor = 30;
- if (strm->bzalloc == NULL) strm->bzalloc = default_bzalloc;
- if (strm->bzfree == NULL) strm->bzfree = default_bzfree;
-
- s = BZALLOC( sizeof(EState) );
- if (s == NULL) return BZ_MEM_ERROR;
- s->strm = strm;
-
- s->arr1 = NULL;
- s->arr2 = NULL;
- s->ftab = NULL;
-
- n = 100000 * blockSize100k;
- s->arr1 = BZALLOC( n * sizeof(UInt32) );
- s->arr2 = BZALLOC( (n+BZ_N_OVERSHOOT) * sizeof(UInt32) );
- s->ftab = BZALLOC( 65537 * sizeof(UInt32) );
-
- if (s->arr1 == NULL || s->arr2 == NULL || s->ftab == NULL) {
- if (s->arr1 != NULL) BZFREE(s->arr1);
- if (s->arr2 != NULL) BZFREE(s->arr2);
- if (s->ftab != NULL) BZFREE(s->ftab);
- if (s != NULL) BZFREE(s);
- return BZ_MEM_ERROR;
- }
-
- s->blockNo = 0;
- s->state = BZ_S_INPUT;
- s->mode = BZ_M_RUNNING;
- s->combinedCRC = 0;
- s->blockSize100k = blockSize100k;
- s->nblockMAX = 100000 * blockSize100k - 19;
- s->verbosity = verbosity;
- s->workFactor = workFactor;
-
- s->block = (UChar*)s->arr2;
- s->mtfv = (UInt16*)s->arr1;
- s->zbits = NULL;
- s->ptr = (UInt32*)s->arr1;
-
- strm->state = s;
- strm->total_in_lo32 = 0;
- strm->total_in_hi32 = 0;
- strm->total_out_lo32 = 0;
- strm->total_out_hi32 = 0;
- init_RL ( s );
- prepare_new_block ( s );
- return BZ_OK;
-}
-
-
-/*---------------------------------------------------*/
-static
-void add_pair_to_block ( EState* s )
-{
- Int32 i;
- UChar ch = (UChar)(s->state_in_ch);
- for (i = 0; i < s->state_in_len; i++) {
- BZ_UPDATE_CRC( s->blockCRC, ch );
- }
- s->inUse[s->state_in_ch] = True;
- switch (s->state_in_len) {
- case 1:
- s->block[s->nblock] = (UChar)ch; s->nblock++;
- break;
- case 2:
- s->block[s->nblock] = (UChar)ch; s->nblock++;
- s->block[s->nblock] = (UChar)ch; s->nblock++;
- break;
- case 3:
- s->block[s->nblock] = (UChar)ch; s->nblock++;
- s->block[s->nblock] = (UChar)ch; s->nblock++;
- s->block[s->nblock] = (UChar)ch; s->nblock++;
- break;
- default:
- s->inUse[s->state_in_len-4] = True;
- s->block[s->nblock] = (UChar)ch; s->nblock++;
- s->block[s->nblock] = (UChar)ch; s->nblock++;
- s->block[s->nblock] = (UChar)ch; s->nblock++;
- s->block[s->nblock] = (UChar)ch; s->nblock++;
- s->block[s->nblock] = ((UChar)(s->state_in_len-4));
- s->nblock++;
- break;
- }
-}
-
-
-/*---------------------------------------------------*/
-static
-void flush_RL ( EState* s )
-{
- if (s->state_in_ch < 256) add_pair_to_block ( s );
- init_RL ( s );
-}
-
-
-/*---------------------------------------------------*/
-#define ADD_CHAR_TO_BLOCK(zs,zchh0) \
-{ \
- UInt32 zchh = (UInt32)(zchh0); \
- /*-- fast track the common case --*/ \
- if (zchh != zs->state_in_ch && \
- zs->state_in_len == 1) { \
- UChar ch = (UChar)(zs->state_in_ch); \
- BZ_UPDATE_CRC( zs->blockCRC, ch ); \
- zs->inUse[zs->state_in_ch] = True; \
- zs->block[zs->nblock] = (UChar)ch; \
- zs->nblock++; \
- zs->state_in_ch = zchh; \
- } \
- else \
- /*-- general, uncommon cases --*/ \
- if (zchh != zs->state_in_ch || \
- zs->state_in_len == 255) { \
- if (zs->state_in_ch < 256) \
- add_pair_to_block ( zs ); \
- zs->state_in_ch = zchh; \
- zs->state_in_len = 1; \
- } else { \
- zs->state_in_len++; \
- } \
-}
-
-
-/*---------------------------------------------------*/
-static
-Bool copy_input_until_stop ( EState* s )
-{
- Bool progress_in = False;
-
- if (s->mode == BZ_M_RUNNING) {
-
- /*-- fast track the common case --*/
- while (True) {
- /*-- block full? --*/
- if (s->nblock >= s->nblockMAX) break;
- /*-- no input? --*/
- if (s->strm->avail_in == 0) break;
- progress_in = True;
- ADD_CHAR_TO_BLOCK ( s, (UInt32)(*((UChar*)(s->strm->next_in))) );
- s->strm->next_in++;
- s->strm->avail_in--;
- s->strm->total_in_lo32++;
- if (s->strm->total_in_lo32 == 0) s->strm->total_in_hi32++;
- }
-
- } else {
-
- /*-- general, uncommon case --*/
- while (True) {
- /*-- block full? --*/
- if (s->nblock >= s->nblockMAX) break;
- /*-- no input? --*/
- if (s->strm->avail_in == 0) break;
- /*-- flush/finish end? --*/
- if (s->avail_in_expect == 0) break;
- progress_in = True;
- ADD_CHAR_TO_BLOCK ( s, (UInt32)(*((UChar*)(s->strm->next_in))) );
- s->strm->next_in++;
- s->strm->avail_in--;
- s->strm->total_in_lo32++;
- if (s->strm->total_in_lo32 == 0) s->strm->total_in_hi32++;
- s->avail_in_expect--;
- }
- }
- return progress_in;
-}
-
-
-/*---------------------------------------------------*/
-static
-Bool copy_output_until_stop ( EState* s )
-{
- Bool progress_out = False;
-
- while (True) {
-
- /*-- no output space? --*/
- if (s->strm->avail_out == 0) break;
-
- /*-- block done? --*/
- if (s->state_out_pos >= s->numZ) break;
-
- progress_out = True;
- *(s->strm->next_out) = s->zbits[s->state_out_pos];
- s->state_out_pos++;
- s->strm->avail_out--;
- s->strm->next_out++;
- s->strm->total_out_lo32++;
- if (s->strm->total_out_lo32 == 0) s->strm->total_out_hi32++;
- }
-
- return progress_out;
-}
-
-
-/*---------------------------------------------------*/
-static
-Bool handle_compress ( bz_stream* strm )
-{
- Bool progress_in = False;
- Bool progress_out = False;
- EState* s = strm->state;
-
- while (True) {
-
- if (s->state == BZ_S_OUTPUT) {
- progress_out |= copy_output_until_stop ( s );
- if (s->state_out_pos < s->numZ) break;
- if (s->mode == BZ_M_FINISHING &&
- s->avail_in_expect == 0 &&
- isempty_RL(s)) break;
- prepare_new_block ( s );
- s->state = BZ_S_INPUT;
- if (s->mode == BZ_M_FLUSHING &&
- s->avail_in_expect == 0 &&
- isempty_RL(s)) break;
- }
-
- if (s->state == BZ_S_INPUT) {
- progress_in |= copy_input_until_stop ( s );
- if (s->mode != BZ_M_RUNNING && s->avail_in_expect == 0) {
- flush_RL ( s );
- BZ2_compressBlock ( s, (Bool)(s->mode == BZ_M_FINISHING) );
- s->state = BZ_S_OUTPUT;
- }
- else
- if (s->nblock >= s->nblockMAX) {
- BZ2_compressBlock ( s, False );
- s->state = BZ_S_OUTPUT;
- }
- else
- if (s->strm->avail_in == 0) {
- break;
- }
- }
-
- }
-
- return progress_in || progress_out;
-}
-
-
-/*---------------------------------------------------*/
-int BZ_API(BZ2_bzCompress) ( bz_stream *strm, int action )
-{
- Bool progress;
- EState* s;
- if (strm == NULL) return BZ_PARAM_ERROR;
- s = strm->state;
- if (s == NULL) return BZ_PARAM_ERROR;
- if (s->strm != strm) return BZ_PARAM_ERROR;
-
- preswitch:
- switch (s->mode) {
-
- case BZ_M_IDLE:
- return BZ_SEQUENCE_ERROR;
-
- case BZ_M_RUNNING:
- if (action == BZ_RUN) {
- progress = handle_compress ( strm );
- return progress ? BZ_RUN_OK : BZ_PARAM_ERROR;
- }
- else
- if (action == BZ_FLUSH) {
- s->avail_in_expect = strm->avail_in;
- s->mode = BZ_M_FLUSHING;
- goto preswitch;
- }
- else
- if (action == BZ_FINISH) {
- s->avail_in_expect = strm->avail_in;
- s->mode = BZ_M_FINISHING;
- goto preswitch;
- }
- else
- return BZ_PARAM_ERROR;
-
- case BZ_M_FLUSHING:
- if (action != BZ_FLUSH) return BZ_SEQUENCE_ERROR;
- if (s->avail_in_expect != s->strm->avail_in)
- return BZ_SEQUENCE_ERROR;
- progress = handle_compress ( strm );
- if (s->avail_in_expect > 0 || !isempty_RL(s) ||
- s->state_out_pos < s->numZ) return BZ_FLUSH_OK;
- s->mode = BZ_M_RUNNING;
- return BZ_RUN_OK;
-
- case BZ_M_FINISHING:
- if (action != BZ_FINISH) return BZ_SEQUENCE_ERROR;
- if (s->avail_in_expect != s->strm->avail_in)
- return BZ_SEQUENCE_ERROR;
- progress = handle_compress ( strm );
- if (!progress) return BZ_SEQUENCE_ERROR;
- if (s->avail_in_expect > 0 || !isempty_RL(s) ||
- s->state_out_pos < s->numZ) return BZ_FINISH_OK;
- s->mode = BZ_M_IDLE;
- return BZ_STREAM_END;
- }
- return BZ_OK; /*--not reached--*/
-}
-
-
-/*---------------------------------------------------*/
-int BZ_API(BZ2_bzCompressEnd) ( bz_stream *strm )
-{
- EState* s;
- if (strm == NULL) return BZ_PARAM_ERROR;
- s = strm->state;
- if (s == NULL) return BZ_PARAM_ERROR;
- if (s->strm != strm) return BZ_PARAM_ERROR;
-
- if (s->arr1 != NULL) BZFREE(s->arr1);
- if (s->arr2 != NULL) BZFREE(s->arr2);
- if (s->ftab != NULL) BZFREE(s->ftab);
- BZFREE(strm->state);
-
- strm->state = NULL;
-
- return BZ_OK;
-}
-
-
-/*---------------------------------------------------*/
-/*--- Decompression stuff ---*/
-/*---------------------------------------------------*/
-
-/*---------------------------------------------------*/
-int BZ_API(BZ2_bzDecompressInit)
- ( bz_stream* strm,
- int verbosity,
- int small )
-{
- DState* s;
-
- if (!bz_config_ok()) return BZ_CONFIG_ERROR;
-
- if (strm == NULL) return BZ_PARAM_ERROR;
- if (small != 0 && small != 1) return BZ_PARAM_ERROR;
- if (verbosity < 0 || verbosity > 4) return BZ_PARAM_ERROR;
-
- if (strm->bzalloc == NULL) strm->bzalloc = default_bzalloc;
- if (strm->bzfree == NULL) strm->bzfree = default_bzfree;
-
- s = BZALLOC( sizeof(DState) );
- if (s == NULL) return BZ_MEM_ERROR;
- s->strm = strm;
- strm->state = s;
- s->state = BZ_X_MAGIC_1;
- s->bsLive = 0;
- s->bsBuff = 0;
- s->calculatedCombinedCRC = 0;
- strm->total_in_lo32 = 0;
- strm->total_in_hi32 = 0;
- strm->total_out_lo32 = 0;
- strm->total_out_hi32 = 0;
- s->smallDecompress = (Bool)small;
- s->ll4 = NULL;
- s->ll16 = NULL;
- s->tt = NULL;
- s->currBlockNo = 0;
- s->verbosity = verbosity;
-
- return BZ_OK;
-}
-
-
-/*---------------------------------------------------*/
-/* Return True iff data corruption is discovered.
- Returns False if there is no problem.
-*/
-static
-Bool unRLE_obuf_to_output_FAST ( DState* s )
-{
- UChar k1;
-
- if (s->blockRandomised) {
-
- while (True) {
- /* try to finish existing run */
- while (True) {
- if (s->strm->avail_out == 0) return False;
- if (s->state_out_len == 0) break;
- *( (UChar*)(s->strm->next_out) ) = s->state_out_ch;
- BZ_UPDATE_CRC ( s->calculatedBlockCRC, s->state_out_ch );
- s->state_out_len--;
- s->strm->next_out++;
- s->strm->avail_out--;
- s->strm->total_out_lo32++;
- if (s->strm->total_out_lo32 == 0) s->strm->total_out_hi32++;
- }
-
- /* can a new run be started? */
- if (s->nblock_used == s->save_nblock+1) return False;
-
- /* Only caused by corrupt data stream? */
- if (s->nblock_used > s->save_nblock+1)
- return True;
-
- s->state_out_len = 1;
- s->state_out_ch = s->k0;
- BZ_GET_FAST(k1); BZ_RAND_UPD_MASK;
- k1 ^= BZ_RAND_MASK; s->nblock_used++;
- if (s->nblock_used == s->save_nblock+1) continue;
- if (k1 != s->k0) { s->k0 = k1; continue; };
-
- s->state_out_len = 2;
- BZ_GET_FAST(k1); BZ_RAND_UPD_MASK;
- k1 ^= BZ_RAND_MASK; s->nblock_used++;
- if (s->nblock_used == s->save_nblock+1) continue;
- if (k1 != s->k0) { s->k0 = k1; continue; };
-
- s->state_out_len = 3;
- BZ_GET_FAST(k1); BZ_RAND_UPD_MASK;
- k1 ^= BZ_RAND_MASK; s->nblock_used++;
- if (s->nblock_used == s->save_nblock+1) continue;
- if (k1 != s->k0) { s->k0 = k1; continue; };
-
- BZ_GET_FAST(k1); BZ_RAND_UPD_MASK;
- k1 ^= BZ_RAND_MASK; s->nblock_used++;
- s->state_out_len = ((Int32)k1) + 4;
- BZ_GET_FAST(s->k0); BZ_RAND_UPD_MASK;
- s->k0 ^= BZ_RAND_MASK; s->nblock_used++;
- }
-
- } else {
-
- /* restore */
- UInt32 c_calculatedBlockCRC = s->calculatedBlockCRC;
- UChar c_state_out_ch = s->state_out_ch;
- Int32 c_state_out_len = s->state_out_len;
- Int32 c_nblock_used = s->nblock_used;
- Int32 c_k0 = s->k0;
- UInt32* c_tt = s->tt;
- UInt32 c_tPos = s->tPos;
- char* cs_next_out = s->strm->next_out;
- unsigned int cs_avail_out = s->strm->avail_out;
- Int32 ro_blockSize100k = s->blockSize100k;
- /* end restore */
-
- UInt32 avail_out_INIT = cs_avail_out;
- Int32 s_save_nblockPP = s->save_nblock+1;
- unsigned int total_out_lo32_old;
-
- while (True) {
-
- /* try to finish existing run */
- if (c_state_out_len > 0) {
- while (True) {
- if (cs_avail_out == 0) goto return_notr;
- if (c_state_out_len == 1) break;
- *( (UChar*)(cs_next_out) ) = c_state_out_ch;
- BZ_UPDATE_CRC ( c_calculatedBlockCRC, c_state_out_ch );
- c_state_out_len--;
- cs_next_out++;
- cs_avail_out--;
- }
- s_state_out_len_eq_one:
- {
- if (cs_avail_out == 0) {
- c_state_out_len = 1; goto return_notr;
- };
- *( (UChar*)(cs_next_out) ) = c_state_out_ch;
- BZ_UPDATE_CRC ( c_calculatedBlockCRC, c_state_out_ch );
- cs_next_out++;
- cs_avail_out--;
- }
- }
- /* Only caused by corrupt data stream? */
- if (c_nblock_used > s_save_nblockPP)
- return True;
-
- /* can a new run be started? */
- if (c_nblock_used == s_save_nblockPP) {
- c_state_out_len = 0; goto return_notr;
- };
- c_state_out_ch = c_k0;
- BZ_GET_FAST_C(k1); c_nblock_used++;
- if (k1 != c_k0) {
- c_k0 = k1; goto s_state_out_len_eq_one;
- };
- if (c_nblock_used == s_save_nblockPP)
- goto s_state_out_len_eq_one;
-
- c_state_out_len = 2;
- BZ_GET_FAST_C(k1); c_nblock_used++;
- if (c_nblock_used == s_save_nblockPP) continue;
- if (k1 != c_k0) { c_k0 = k1; continue; };
-
- c_state_out_len = 3;
- BZ_GET_FAST_C(k1); c_nblock_used++;
- if (c_nblock_used == s_save_nblockPP) continue;
- if (k1 != c_k0) { c_k0 = k1; continue; };
-
- BZ_GET_FAST_C(k1); c_nblock_used++;
- c_state_out_len = ((Int32)k1) + 4;
- BZ_GET_FAST_C(c_k0); c_nblock_used++;
- }
-
- return_notr:
- total_out_lo32_old = s->strm->total_out_lo32;
- s->strm->total_out_lo32 += (avail_out_INIT - cs_avail_out);
- if (s->strm->total_out_lo32 < total_out_lo32_old)
- s->strm->total_out_hi32++;
-
- /* save */
- s->calculatedBlockCRC = c_calculatedBlockCRC;
- s->state_out_ch = c_state_out_ch;
- s->state_out_len = c_state_out_len;
- s->nblock_used = c_nblock_used;
- s->k0 = c_k0;
- s->tt = c_tt;
- s->tPos = c_tPos;
- s->strm->next_out = cs_next_out;
- s->strm->avail_out = cs_avail_out;
- /* end save */
- }
- return False;
-}
-
-
-
-/*---------------------------------------------------*/
-__inline__ Int32 BZ2_indexIntoF ( Int32 indx, Int32 *cftab )
-{
- Int32 nb, na, mid;
- nb = 0;
- na = 256;
- do {
- mid = (nb + na) >> 1;
- if (indx >= cftab[mid]) nb = mid; else na = mid;
- }
- while (na - nb != 1);
- return nb;
-}
-
-
-/*---------------------------------------------------*/
-/* Return True iff data corruption is discovered.
- Returns False if there is no problem.
-*/
-static
-Bool unRLE_obuf_to_output_SMALL ( DState* s )
-{
- UChar k1;
-
- if (s->blockRandomised) {
-
- while (True) {
- /* try to finish existing run */
- while (True) {
- if (s->strm->avail_out == 0) return False;
- if (s->state_out_len == 0) break;
- *( (UChar*)(s->strm->next_out) ) = s->state_out_ch;
- BZ_UPDATE_CRC ( s->calculatedBlockCRC, s->state_out_ch );
- s->state_out_len--;
- s->strm->next_out++;
- s->strm->avail_out--;
- s->strm->total_out_lo32++;
- if (s->strm->total_out_lo32 == 0) s->strm->total_out_hi32++;
- }
-
- /* can a new run be started? */
- if (s->nblock_used == s->save_nblock+1) return False;
-
- /* Only caused by corrupt data stream? */
- if (s->nblock_used > s->save_nblock+1)
- return True;
-
- s->state_out_len = 1;
- s->state_out_ch = s->k0;
- BZ_GET_SMALL(k1); BZ_RAND_UPD_MASK;
- k1 ^= BZ_RAND_MASK; s->nblock_used++;
- if (s->nblock_used == s->save_nblock+1) continue;
- if (k1 != s->k0) { s->k0 = k1; continue; };
-
- s->state_out_len = 2;
- BZ_GET_SMALL(k1); BZ_RAND_UPD_MASK;
- k1 ^= BZ_RAND_MASK; s->nblock_used++;
- if (s->nblock_used == s->save_nblock+1) continue;
- if (k1 != s->k0) { s->k0 = k1; continue; };
-
- s->state_out_len = 3;
- BZ_GET_SMALL(k1); BZ_RAND_UPD_MASK;
- k1 ^= BZ_RAND_MASK; s->nblock_used++;
- if (s->nblock_used == s->save_nblock+1) continue;
- if (k1 != s->k0) { s->k0 = k1; continue; };
-
- BZ_GET_SMALL(k1); BZ_RAND_UPD_MASK;
- k1 ^= BZ_RAND_MASK; s->nblock_used++;
- s->state_out_len = ((Int32)k1) + 4;
- BZ_GET_SMALL(s->k0); BZ_RAND_UPD_MASK;
- s->k0 ^= BZ_RAND_MASK; s->nblock_used++;
- }
-
- } else {
-
- while (True) {
- /* try to finish existing run */
- while (True) {
- if (s->strm->avail_out == 0) return False;
- if (s->state_out_len == 0) break;
- *( (UChar*)(s->strm->next_out) ) = s->state_out_ch;
- BZ_UPDATE_CRC ( s->calculatedBlockCRC, s->state_out_ch );
- s->state_out_len--;
- s->strm->next_out++;
- s->strm->avail_out--;
- s->strm->total_out_lo32++;
- if (s->strm->total_out_lo32 == 0) s->strm->total_out_hi32++;
- }
-
- /* can a new run be started? */
- if (s->nblock_used == s->save_nblock+1) return False;
-
- /* Only caused by corrupt data stream? */
- if (s->nblock_used > s->save_nblock+1)
- return True;
-
- s->state_out_len = 1;
- s->state_out_ch = s->k0;
- BZ_GET_SMALL(k1); s->nblock_used++;
- if (s->nblock_used == s->save_nblock+1) continue;
- if (k1 != s->k0) { s->k0 = k1; continue; };
-
- s->state_out_len = 2;
- BZ_GET_SMALL(k1); s->nblock_used++;
- if (s->nblock_used == s->save_nblock+1) continue;
- if (k1 != s->k0) { s->k0 = k1; continue; };
-
- s->state_out_len = 3;
- BZ_GET_SMALL(k1); s->nblock_used++;
- if (s->nblock_used == s->save_nblock+1) continue;
- if (k1 != s->k0) { s->k0 = k1; continue; };
-
- BZ_GET_SMALL(k1); s->nblock_used++;
- s->state_out_len = ((Int32)k1) + 4;
- BZ_GET_SMALL(s->k0); s->nblock_used++;
- }
-
- }
-}
-
-
-/*---------------------------------------------------*/
-int BZ_API(BZ2_bzDecompress) ( bz_stream *strm )
-{
- Bool corrupt;
- DState* s;
- if (strm == NULL) return BZ_PARAM_ERROR;
- s = strm->state;
- if (s == NULL) return BZ_PARAM_ERROR;
- if (s->strm != strm) return BZ_PARAM_ERROR;
-
- while (True) {
- if (s->state == BZ_X_IDLE) return BZ_SEQUENCE_ERROR;
- if (s->state == BZ_X_OUTPUT) {
- if (s->smallDecompress)
- corrupt = unRLE_obuf_to_output_SMALL ( s ); else
- corrupt = unRLE_obuf_to_output_FAST ( s );
- if (corrupt) return BZ_DATA_ERROR;
- if (s->nblock_used == s->save_nblock+1 && s->state_out_len == 0) {
- BZ_FINALISE_CRC ( s->calculatedBlockCRC );
- if (s->verbosity >= 3)
- VPrintf2 ( " {0x%08x, 0x%08x}", s->storedBlockCRC,
- s->calculatedBlockCRC );
- if (s->verbosity >= 2) VPrintf0 ( "]" );
- if (s->calculatedBlockCRC != s->storedBlockCRC)
- return BZ_DATA_ERROR;
- s->calculatedCombinedCRC
- = (s->calculatedCombinedCRC << 1) |
- (s->calculatedCombinedCRC >> 31);
- s->calculatedCombinedCRC ^= s->calculatedBlockCRC;
- s->state = BZ_X_BLKHDR_1;
- } else {
- return BZ_OK;
- }
- }
- if (s->state >= BZ_X_MAGIC_1) {
- Int32 r = BZ2_decompress ( s );
- if (r == BZ_STREAM_END) {
- if (s->verbosity >= 3)
- VPrintf2 ( "\n combined CRCs: stored = 0x%08x, computed = 0x%08x",
- s->storedCombinedCRC, s->calculatedCombinedCRC );
- if (s->calculatedCombinedCRC != s->storedCombinedCRC)
- return BZ_DATA_ERROR;
- return r;
- }
- if (s->state != BZ_X_OUTPUT) return r;
- }
- }
-
- AssertH ( 0, 6001 );
-
- return 0; /*NOTREACHED*/
-}
-
-
-/*---------------------------------------------------*/
-int BZ_API(BZ2_bzDecompressEnd) ( bz_stream *strm )
-{
- DState* s;
- if (strm == NULL) return BZ_PARAM_ERROR;
- s = strm->state;
- if (s == NULL) return BZ_PARAM_ERROR;
- if (s->strm != strm) return BZ_PARAM_ERROR;
-
- if (s->tt != NULL) BZFREE(s->tt);
- if (s->ll16 != NULL) BZFREE(s->ll16);
- if (s->ll4 != NULL) BZFREE(s->ll4);
-
- BZFREE(strm->state);
- strm->state = NULL;
-
- return BZ_OK;
-}
-
-
-#ifndef BZ_NO_STDIO
-/*---------------------------------------------------*/
-/*--- File I/O stuff ---*/
-/*---------------------------------------------------*/
-
-#define BZ_SETERR(eee) \
-{ \
- if (bzerror != NULL) *bzerror = eee; \
- if (bzf != NULL) bzf->lastErr = eee; \
-}
-
-typedef
- struct {
- FILE* handle;
- Char buf[BZ_MAX_UNUSED];
- Int32 bufN;
- Bool writing;
- bz_stream strm;
- Int32 lastErr;
- Bool initialisedOk;
- }
- bzFile;
-
-
-/*---------------------------------------------*/
-static Bool myfeof ( FILE* f )
-{
- Int32 c = fgetc ( f );
- if (c == EOF) return True;
- ungetc ( c, f );
- return False;
-}
-
-
-/*---------------------------------------------------*/
-BZFILE* BZ_API(BZ2_bzWriteOpen)
- ( int* bzerror,
- FILE* f,
- int blockSize100k,
- int verbosity,
- int workFactor )
-{
- Int32 ret;
- bzFile* bzf = NULL;
-
- BZ_SETERR(BZ_OK);
-
- if (f == NULL ||
- (blockSize100k < 1 || blockSize100k > 9) ||
- (workFactor < 0 || workFactor > 250) ||
- (verbosity < 0 || verbosity > 4))
- { BZ_SETERR(BZ_PARAM_ERROR); return NULL; };
-
- if (ferror(f))
- { BZ_SETERR(BZ_IO_ERROR); return NULL; };
-
- bzf = malloc ( sizeof(bzFile) );
- if (bzf == NULL)
- { BZ_SETERR(BZ_MEM_ERROR); return NULL; };
-
- BZ_SETERR(BZ_OK);
- bzf->initialisedOk = False;
- bzf->bufN = 0;
- bzf->handle = f;
- bzf->writing = True;
- bzf->strm.bzalloc = NULL;
- bzf->strm.bzfree = NULL;
- bzf->strm.opaque = NULL;
-
- if (workFactor == 0) workFactor = 30;
- ret = BZ2_bzCompressInit ( &(bzf->strm), blockSize100k,
- verbosity, workFactor );
- if (ret != BZ_OK)
- { BZ_SETERR(ret); free(bzf); return NULL; };
-
- bzf->strm.avail_in = 0;
- bzf->initialisedOk = True;
- return bzf;
-}
-
-
-
-/*---------------------------------------------------*/
-void BZ_API(BZ2_bzWrite)
- ( int* bzerror,
- BZFILE* b,
- void* buf,
- int len )
-{
- Int32 n, n2, ret;
- bzFile* bzf = (bzFile*)b;
-
- BZ_SETERR(BZ_OK);
- if (bzf == NULL || buf == NULL || len < 0)
- { BZ_SETERR(BZ_PARAM_ERROR); return; };
- if (!(bzf->writing))
- { BZ_SETERR(BZ_SEQUENCE_ERROR); return; };
- if (ferror(bzf->handle))
- { BZ_SETERR(BZ_IO_ERROR); return; };
-
- if (len == 0)
- { BZ_SETERR(BZ_OK); return; };
-
- bzf->strm.avail_in = len;
- bzf->strm.next_in = buf;
-
- while (True) {
- bzf->strm.avail_out = BZ_MAX_UNUSED;
- bzf->strm.next_out = bzf->buf;
- ret = BZ2_bzCompress ( &(bzf->strm), BZ_RUN );
- if (ret != BZ_RUN_OK)
- { BZ_SETERR(ret); return; };
-
- if (bzf->strm.avail_out < BZ_MAX_UNUSED) {
- n = BZ_MAX_UNUSED - bzf->strm.avail_out;
- n2 = fwrite ( (void*)(bzf->buf), sizeof(UChar),
- n, bzf->handle );
- if (n != n2 || ferror(bzf->handle))
- { BZ_SETERR(BZ_IO_ERROR); return; };
- }
-
- if (bzf->strm.avail_in == 0)
- { BZ_SETERR(BZ_OK); return; };
- }
-}
-
-
-/*---------------------------------------------------*/
-void BZ_API(BZ2_bzWriteClose)
- ( int* bzerror,
- BZFILE* b,
- int abandon,
- unsigned int* nbytes_in,
- unsigned int* nbytes_out )
-{
- BZ2_bzWriteClose64 ( bzerror, b, abandon,
- nbytes_in, NULL, nbytes_out, NULL );
-}
-
-
-void BZ_API(BZ2_bzWriteClose64)
- ( int* bzerror,
- BZFILE* b,
- int abandon,
- unsigned int* nbytes_in_lo32,
- unsigned int* nbytes_in_hi32,
- unsigned int* nbytes_out_lo32,
- unsigned int* nbytes_out_hi32 )
-{
- Int32 n, n2, ret;
- bzFile* bzf = (bzFile*)b;
-
- if (bzf == NULL)
- { BZ_SETERR(BZ_OK); return; };
- if (!(bzf->writing))
- { BZ_SETERR(BZ_SEQUENCE_ERROR); return; };
- if (ferror(bzf->handle))
- { BZ_SETERR(BZ_IO_ERROR); return; };
-
- if (nbytes_in_lo32 != NULL) *nbytes_in_lo32 = 0;
- if (nbytes_in_hi32 != NULL) *nbytes_in_hi32 = 0;
- if (nbytes_out_lo32 != NULL) *nbytes_out_lo32 = 0;
- if (nbytes_out_hi32 != NULL) *nbytes_out_hi32 = 0;
-
- if ((!abandon) && bzf->lastErr == BZ_OK) {
- while (True) {
- bzf->strm.avail_out = BZ_MAX_UNUSED;
- bzf->strm.next_out = bzf->buf;
- ret = BZ2_bzCompress ( &(bzf->strm), BZ_FINISH );
- if (ret != BZ_FINISH_OK && ret != BZ_STREAM_END)
- { BZ_SETERR(ret); return; };
-
- if (bzf->strm.avail_out < BZ_MAX_UNUSED) {
- n = BZ_MAX_UNUSED - bzf->strm.avail_out;
- n2 = fwrite ( (void*)(bzf->buf), sizeof(UChar),
- n, bzf->handle );
- if (n != n2 || ferror(bzf->handle))
- { BZ_SETERR(BZ_IO_ERROR); return; };
- }
-
- if (ret == BZ_STREAM_END) break;
- }
- }
-
- if ( !abandon && !ferror ( bzf->handle ) ) {
- fflush ( bzf->handle );
- if (ferror(bzf->handle))
- { BZ_SETERR(BZ_IO_ERROR); return; };
- }
-
- if (nbytes_in_lo32 != NULL)
- *nbytes_in_lo32 = bzf->strm.total_in_lo32;
- if (nbytes_in_hi32 != NULL)
- *nbytes_in_hi32 = bzf->strm.total_in_hi32;
- if (nbytes_out_lo32 != NULL)
- *nbytes_out_lo32 = bzf->strm.total_out_lo32;
- if (nbytes_out_hi32 != NULL)
- *nbytes_out_hi32 = bzf->strm.total_out_hi32;
-
- BZ_SETERR(BZ_OK);
- BZ2_bzCompressEnd ( &(bzf->strm) );
- free ( bzf );
-}
-
-
-/*---------------------------------------------------*/
-BZFILE* BZ_API(BZ2_bzReadOpen)
- ( int* bzerror,
- FILE* f,
- int verbosity,
- int small,
- void* unused,
- int nUnused )
-{
- bzFile* bzf = NULL;
- int ret;
-
- BZ_SETERR(BZ_OK);
-
- if (f == NULL ||
- (small != 0 && small != 1) ||
- (verbosity < 0 || verbosity > 4) ||
- (unused == NULL && nUnused != 0) ||
- (unused != NULL && (nUnused < 0 || nUnused > BZ_MAX_UNUSED)))
- { BZ_SETERR(BZ_PARAM_ERROR); return NULL; };
-
- if (ferror(f))
- { BZ_SETERR(BZ_IO_ERROR); return NULL; };
-
- bzf = malloc ( sizeof(bzFile) );
- if (bzf == NULL)
- { BZ_SETERR(BZ_MEM_ERROR); return NULL; };
-
- BZ_SETERR(BZ_OK);
-
- bzf->initialisedOk = False;
- bzf->handle = f;
- bzf->bufN = 0;
- bzf->writing = False;
- bzf->strm.bzalloc = NULL;
- bzf->strm.bzfree = NULL;
- bzf->strm.opaque = NULL;
-
- while (nUnused > 0) {
- bzf->buf[bzf->bufN] = *((UChar*)(unused)); bzf->bufN++;
- unused = ((void*)( 1 + ((UChar*)(unused)) ));
- nUnused--;
- }
-
- ret = BZ2_bzDecompressInit ( &(bzf->strm), verbosity, small );
- if (ret != BZ_OK)
- { BZ_SETERR(ret); free(bzf); return NULL; };
-
- bzf->strm.avail_in = bzf->bufN;
- bzf->strm.next_in = bzf->buf;
-
- bzf->initialisedOk = True;
- return bzf;
-}
-
-
-/*---------------------------------------------------*/
-void BZ_API(BZ2_bzReadClose) ( int *bzerror, BZFILE *b )
-{
- bzFile* bzf = (bzFile*)b;
-
- BZ_SETERR(BZ_OK);
- if (bzf == NULL)
- { BZ_SETERR(BZ_OK); return; };
-
- if (bzf->writing)
- { BZ_SETERR(BZ_SEQUENCE_ERROR); return; };
-
- if (bzf->initialisedOk)
- (void)BZ2_bzDecompressEnd ( &(bzf->strm) );
- free ( bzf );
-}
-
-
-/*---------------------------------------------------*/
-int BZ_API(BZ2_bzRead)
- ( int* bzerror,
- BZFILE* b,
- void* buf,
- int len )
-{
- Int32 n, ret;
- bzFile* bzf = (bzFile*)b;
-
- BZ_SETERR(BZ_OK);
-
- if (bzf == NULL || buf == NULL || len < 0)
- { BZ_SETERR(BZ_PARAM_ERROR); return 0; };
-
- if (bzf->writing)
- { BZ_SETERR(BZ_SEQUENCE_ERROR); return 0; };
-
- if (len == 0)
- { BZ_SETERR(BZ_OK); return 0; };
-
- bzf->strm.avail_out = len;
- bzf->strm.next_out = buf;
-
- while (True) {
-
- if (ferror(bzf->handle))
- { BZ_SETERR(BZ_IO_ERROR); return 0; };
-
- if (bzf->strm.avail_in == 0 && !myfeof(bzf->handle)) {
- n = fread ( bzf->buf, sizeof(UChar),
- BZ_MAX_UNUSED, bzf->handle );
- if (ferror(bzf->handle))
- { BZ_SETERR(BZ_IO_ERROR); return 0; };
- bzf->bufN = n;
- bzf->strm.avail_in = bzf->bufN;
- bzf->strm.next_in = bzf->buf;
- }
-
- ret = BZ2_bzDecompress ( &(bzf->strm) );
-
- if (ret != BZ_OK && ret != BZ_STREAM_END)
- { BZ_SETERR(ret); return 0; };
-
- if (ret == BZ_OK && myfeof(bzf->handle) &&
- bzf->strm.avail_in == 0 && bzf->strm.avail_out > 0)
- { BZ_SETERR(BZ_UNEXPECTED_EOF); return 0; };
-
- if (ret == BZ_STREAM_END)
- { BZ_SETERR(BZ_STREAM_END);
- return len - bzf->strm.avail_out; };
- if (bzf->strm.avail_out == 0)
- { BZ_SETERR(BZ_OK); return len; };
-
- }
-
- return 0; /*not reached*/
-}
-
-
-/*---------------------------------------------------*/
-void BZ_API(BZ2_bzReadGetUnused)
- ( int* bzerror,
- BZFILE* b,
- void** unused,
- int* nUnused )
-{
- bzFile* bzf = (bzFile*)b;
- if (bzf == NULL)
- { BZ_SETERR(BZ_PARAM_ERROR); return; };
- if (bzf->lastErr != BZ_STREAM_END)
- { BZ_SETERR(BZ_SEQUENCE_ERROR); return; };
- if (unused == NULL || nUnused == NULL)
- { BZ_SETERR(BZ_PARAM_ERROR); return; };
-
- BZ_SETERR(BZ_OK);
- *nUnused = bzf->strm.avail_in;
- *unused = bzf->strm.next_in;
-}
-#endif
-
-
-/*---------------------------------------------------*/
-/*--- Misc convenience stuff ---*/
-/*---------------------------------------------------*/
-
-/*---------------------------------------------------*/
-int BZ_API(BZ2_bzBuffToBuffCompress)
- ( char* dest,
- unsigned int* destLen,
- char* source,
- unsigned int sourceLen,
- int blockSize100k,
- int verbosity,
- int workFactor )
-{
- bz_stream strm;
- int ret;
-
- if (dest == NULL || destLen == NULL ||
- source == NULL ||
- blockSize100k < 1 || blockSize100k > 9 ||
- verbosity < 0 || verbosity > 4 ||
- workFactor < 0 || workFactor > 250)
- return BZ_PARAM_ERROR;
-
- if (workFactor == 0) workFactor = 30;
- strm.bzalloc = NULL;
- strm.bzfree = NULL;
- strm.opaque = NULL;
- ret = BZ2_bzCompressInit ( &strm, blockSize100k,
- verbosity, workFactor );
- if (ret != BZ_OK) return ret;
-
- strm.next_in = source;
- strm.next_out = dest;
- strm.avail_in = sourceLen;
- strm.avail_out = *destLen;
-
- ret = BZ2_bzCompress ( &strm, BZ_FINISH );
- if (ret == BZ_FINISH_OK) goto output_overflow;
- if (ret != BZ_STREAM_END) goto errhandler;
-
- /* normal termination */
- *destLen -= strm.avail_out;
- BZ2_bzCompressEnd ( &strm );
- return BZ_OK;
-
- output_overflow:
- BZ2_bzCompressEnd ( &strm );
- return BZ_OUTBUFF_FULL;
-
- errhandler:
- BZ2_bzCompressEnd ( &strm );
- return ret;
-}
-
-
-/*---------------------------------------------------*/
-int BZ_API(BZ2_bzBuffToBuffDecompress)
- ( char* dest,
- unsigned int* destLen,
- char* source,
- unsigned int sourceLen,
- int small,
- int verbosity )
-{
- bz_stream strm;
- int ret;
-
- if (dest == NULL || destLen == NULL ||
- source == NULL ||
- (small != 0 && small != 1) ||
- verbosity < 0 || verbosity > 4)
- return BZ_PARAM_ERROR;
-
- strm.bzalloc = NULL;
- strm.bzfree = NULL;
- strm.opaque = NULL;
- ret = BZ2_bzDecompressInit ( &strm, verbosity, small );
- if (ret != BZ_OK) return ret;
-
- strm.next_in = source;
- strm.next_out = dest;
- strm.avail_in = sourceLen;
- strm.avail_out = *destLen;
-
- ret = BZ2_bzDecompress ( &strm );
- if (ret == BZ_OK) goto output_overflow_or_eof;
- if (ret != BZ_STREAM_END) goto errhandler;
-
- /* normal termination */
- *destLen -= strm.avail_out;
- BZ2_bzDecompressEnd ( &strm );
- return BZ_OK;
-
- output_overflow_or_eof:
- if (strm.avail_out > 0) {
- BZ2_bzDecompressEnd ( &strm );
- return BZ_UNEXPECTED_EOF;
- } else {
- BZ2_bzDecompressEnd ( &strm );
- return BZ_OUTBUFF_FULL;
- };
-
- errhandler:
- BZ2_bzDecompressEnd ( &strm );
- return ret;
-}
-
-
-/*---------------------------------------------------*/
-/*--
- Code contributed by Yoshioka Tsuneo (tsuneo at rr.iij4u.or.jp)
- to support better zlib compatibility.
- This code is not _officially_ part of libbzip2 (yet);
- I haven't tested it, documented it, or considered the
- threading-safeness of it.
- If this code breaks, please contact both Yoshioka and me.
---*/
-/*---------------------------------------------------*/
-
-/*---------------------------------------------------*/
-/*--
- return version like "0.9.5d, 4-Sept-1999".
---*/
-const char * BZ_API(BZ2_bzlibVersion)(void)
-{
- return BZ_VERSION;
-}
-
-
-#ifndef BZ_NO_STDIO
-/*---------------------------------------------------*/
-
-#if defined(_WIN32) || defined(OS2) || defined(MSDOS)
-# include <fcntl.h>
-# include <io.h>
-# define SET_BINARY_MODE(file) setmode(fileno(file),O_BINARY)
-#else
-# define SET_BINARY_MODE(file)
-#endif
-static
-BZFILE * bzopen_or_bzdopen
- ( const char *path, /* no use when bzdopen */
- int fd, /* no use when bzdopen */
- const char *mode,
- int open_mode) /* bzopen: 0, bzdopen:1 */
-{
- int bzerr;
- char unused[BZ_MAX_UNUSED];
- int blockSize100k = 9;
- int writing = 0;
- char mode2[10] = "";
- FILE *fp = NULL;
- BZFILE *bzfp = NULL;
- int verbosity = 0;
- int workFactor = 30;
- int smallMode = 0;
- int nUnused = 0;
-
- if (mode == NULL) return NULL;
- while (*mode) {
- switch (*mode) {
- case 'r':
- writing = 0; break;
- case 'w':
- writing = 1; break;
- case 's':
- smallMode = 1; break;
- default:
- if (isdigit((int)(*mode))) {
- blockSize100k = *mode-BZ_HDR_0;
- }
- }
- mode++;
- }
- strcat(mode2, writing ? "w" : "r" );
- strcat(mode2,"b"); /* binary mode */
-
- if (open_mode==0) {
- if (path==NULL || strcmp(path,"")==0) {
- fp = (writing ? stdout : stdin);
- SET_BINARY_MODE(fp);
- } else {
- fp = fopen(path,mode2);
- }
- } else {
-#ifdef BZ_STRICT_ANSI
- fp = NULL;
-#else
- fp = fdopen(fd,mode2);
-#endif
- }
- if (fp == NULL) return NULL;
-
- if (writing) {
- /* Guard against total chaos and anarchy -- JRS */
- if (blockSize100k < 1) blockSize100k = 1;
- if (blockSize100k > 9) blockSize100k = 9;
- bzfp = BZ2_bzWriteOpen(&bzerr,fp,blockSize100k,
- verbosity,workFactor);
- } else {
- bzfp = BZ2_bzReadOpen(&bzerr,fp,verbosity,smallMode,
- unused,nUnused);
- }
- if (bzfp == NULL) {
- if (fp != stdin && fp != stdout) fclose(fp);
- return NULL;
- }
- return bzfp;
-}
-
-
-/*---------------------------------------------------*/
-/*--
- open file for read or write.
- ex) bzopen("file","w9")
- case path="" or NULL => use stdin or stdout.
---*/
-BZFILE * BZ_API(BZ2_bzopen)
- ( const char *path,
- const char *mode )
-{
- return bzopen_or_bzdopen(path,-1,mode,/*bzopen*/0);
-}
-
-
-/*---------------------------------------------------*/
-BZFILE * BZ_API(BZ2_bzdopen)
- ( int fd,
- const char *mode )
-{
- return bzopen_or_bzdopen(NULL,fd,mode,/*bzdopen*/1);
-}
-
-
-/*---------------------------------------------------*/
-int BZ_API(BZ2_bzread) (BZFILE* b, void* buf, int len )
-{
- int bzerr, nread;
- if (((bzFile*)b)->lastErr == BZ_STREAM_END) return 0;
- nread = BZ2_bzRead(&bzerr,b,buf,len);
- if (bzerr == BZ_OK || bzerr == BZ_STREAM_END) {
- return nread;
- } else {
- return -1;
- }
-}
-
-
-/*---------------------------------------------------*/
-int BZ_API(BZ2_bzwrite) (BZFILE* b, void* buf, int len )
-{
- int bzerr;
-
- BZ2_bzWrite(&bzerr,b,buf,len);
- if(bzerr == BZ_OK){
- return len;
- }else{
- return -1;
- }
-}
-
-
-/*---------------------------------------------------*/
-int BZ_API(BZ2_bzflush) (BZFILE *b)
-{
- /* do nothing now... */
- return 0;
-}
-
-
-/*---------------------------------------------------*/
-void BZ_API(BZ2_bzclose) (BZFILE* b)
-{
- int bzerr;
- FILE *fp;
-
- if (b==NULL) {return;}
- fp = ((bzFile *)b)->handle;
- if(((bzFile*)b)->writing){
- BZ2_bzWriteClose(&bzerr,b,0,NULL,NULL);
- if(bzerr != BZ_OK){
- BZ2_bzWriteClose(NULL,b,1,NULL,NULL);
- }
- }else{
- BZ2_bzReadClose(&bzerr,b);
- }
- if(fp!=stdin && fp!=stdout){
- fclose(fp);
- }
-}
-
-
-/*---------------------------------------------------*/
-/*--
- return last error code
---*/
-static const char *bzerrorstrings[] = {
- "OK"
- ,"SEQUENCE_ERROR"
- ,"PARAM_ERROR"
- ,"MEM_ERROR"
- ,"DATA_ERROR"
- ,"DATA_ERROR_MAGIC"
- ,"IO_ERROR"
- ,"UNEXPECTED_EOF"
- ,"OUTBUFF_FULL"
- ,"CONFIG_ERROR"
- ,"???" /* for future */
- ,"???" /* for future */
- ,"???" /* for future */
- ,"???" /* for future */
- ,"???" /* for future */
- ,"???" /* for future */
-};
-
-
-const char * BZ_API(BZ2_bzerror) (BZFILE *b, int *errnum)
-{
- int err = ((bzFile *)b)->lastErr;
-
- if(err>0) err = 0;
- *errnum = err;
- return bzerrorstrings[err*-1];
-}
-#endif
-
-
-/*-------------------------------------------------------------*/
-/*--- end bzlib.c ---*/
-/*-------------------------------------------------------------*/
diff --git a/third-party/bzip2/bzlib.h b/third-party/bzip2/bzlib.h
deleted file mode 100644
index 8277123..0000000
--- a/third-party/bzip2/bzlib.h
+++ /dev/null
@@ -1,282 +0,0 @@
-
-/*-------------------------------------------------------------*/
-/*--- Public header file for the library. ---*/
-/*--- bzlib.h ---*/
-/*-------------------------------------------------------------*/
-
-/* ------------------------------------------------------------------
- This file is part of bzip2/libbzip2, a program and library for
- lossless, block-sorting data compression.
-
- bzip2/libbzip2 version 1.0.6 of 6 September 2010
- Copyright (C) 1996-2010 Julian Seward <jseward at bzip.org>
-
- Please read the WARNING, DISCLAIMER and PATENTS sections in the
- README file.
-
- This program is released under the terms of the license contained
- in the file LICENSE.
- ------------------------------------------------------------------ */
-
-
-#ifndef _BZLIB_H
-#define _BZLIB_H
-
-#ifdef __cplusplus
-extern "C" {
-#endif
-
-#define BZ_RUN 0
-#define BZ_FLUSH 1
-#define BZ_FINISH 2
-
-#define BZ_OK 0
-#define BZ_RUN_OK 1
-#define BZ_FLUSH_OK 2
-#define BZ_FINISH_OK 3
-#define BZ_STREAM_END 4
-#define BZ_SEQUENCE_ERROR (-1)
-#define BZ_PARAM_ERROR (-2)
-#define BZ_MEM_ERROR (-3)
-#define BZ_DATA_ERROR (-4)
-#define BZ_DATA_ERROR_MAGIC (-5)
-#define BZ_IO_ERROR (-6)
-#define BZ_UNEXPECTED_EOF (-7)
-#define BZ_OUTBUFF_FULL (-8)
-#define BZ_CONFIG_ERROR (-9)
-
-typedef
- struct {
- char *next_in;
- unsigned int avail_in;
- unsigned int total_in_lo32;
- unsigned int total_in_hi32;
-
- char *next_out;
- unsigned int avail_out;
- unsigned int total_out_lo32;
- unsigned int total_out_hi32;
-
- void *state;
-
- void *(*bzalloc)(void *,int,int);
- void (*bzfree)(void *,void *);
- void *opaque;
- }
- bz_stream;
-
-
-#ifndef BZ_IMPORT
-#define BZ_EXPORT
-#endif
-
-#ifndef BZ_NO_STDIO
-/* Need a definitition for FILE */
-#include <stdio.h>
-#endif
-
-#ifdef _WIN32
-# include <windows.h>
-# ifdef small
- /* windows.h define small to char */
-# undef small
-# endif
-# ifdef BZ_EXPORT
-# define BZ_API(func) WINAPI func
-# define BZ_EXTERN extern
-# else
- /* import windows dll dynamically */
-# define BZ_API(func) (WINAPI * func)
-# define BZ_EXTERN
-# endif
-#else
-# define BZ_API(func) func
-# define BZ_EXTERN extern
-#endif
-
-
-/*-- Core (low-level) library functions --*/
-
-BZ_EXTERN int BZ_API(BZ2_bzCompressInit) (
- bz_stream* strm,
- int blockSize100k,
- int verbosity,
- int workFactor
- );
-
-BZ_EXTERN int BZ_API(BZ2_bzCompress) (
- bz_stream* strm,
- int action
- );
-
-BZ_EXTERN int BZ_API(BZ2_bzCompressEnd) (
- bz_stream* strm
- );
-
-BZ_EXTERN int BZ_API(BZ2_bzDecompressInit) (
- bz_stream *strm,
- int verbosity,
- int small
- );
-
-BZ_EXTERN int BZ_API(BZ2_bzDecompress) (
- bz_stream* strm
- );
-
-BZ_EXTERN int BZ_API(BZ2_bzDecompressEnd) (
- bz_stream *strm
- );
-
-
-
-/*-- High(er) level library functions --*/
-
-#ifndef BZ_NO_STDIO
-#define BZ_MAX_UNUSED 5000
-
-typedef void BZFILE;
-
-BZ_EXTERN BZFILE* BZ_API(BZ2_bzReadOpen) (
- int* bzerror,
- FILE* f,
- int verbosity,
- int small,
- void* unused,
- int nUnused
- );
-
-BZ_EXTERN void BZ_API(BZ2_bzReadClose) (
- int* bzerror,
- BZFILE* b
- );
-
-BZ_EXTERN void BZ_API(BZ2_bzReadGetUnused) (
- int* bzerror,
- BZFILE* b,
- void** unused,
- int* nUnused
- );
-
-BZ_EXTERN int BZ_API(BZ2_bzRead) (
- int* bzerror,
- BZFILE* b,
- void* buf,
- int len
- );
-
-BZ_EXTERN BZFILE* BZ_API(BZ2_bzWriteOpen) (
- int* bzerror,
- FILE* f,
- int blockSize100k,
- int verbosity,
- int workFactor
- );
-
-BZ_EXTERN void BZ_API(BZ2_bzWrite) (
- int* bzerror,
- BZFILE* b,
- void* buf,
- int len
- );
-
-BZ_EXTERN void BZ_API(BZ2_bzWriteClose) (
- int* bzerror,
- BZFILE* b,
- int abandon,
- unsigned int* nbytes_in,
- unsigned int* nbytes_out
- );
-
-BZ_EXTERN void BZ_API(BZ2_bzWriteClose64) (
- int* bzerror,
- BZFILE* b,
- int abandon,
- unsigned int* nbytes_in_lo32,
- unsigned int* nbytes_in_hi32,
- unsigned int* nbytes_out_lo32,
- unsigned int* nbytes_out_hi32
- );
-#endif
-
-
-/*-- Utility functions --*/
-
-BZ_EXTERN int BZ_API(BZ2_bzBuffToBuffCompress) (
- char* dest,
- unsigned int* destLen,
- char* source,
- unsigned int sourceLen,
- int blockSize100k,
- int verbosity,
- int workFactor
- );
-
-BZ_EXTERN int BZ_API(BZ2_bzBuffToBuffDecompress) (
- char* dest,
- unsigned int* destLen,
- char* source,
- unsigned int sourceLen,
- int small,
- int verbosity
- );
-
-
-/*--
- Code contributed by Yoshioka Tsuneo (tsuneo at rr.iij4u.or.jp)
- to support better zlib compatibility.
- This code is not _officially_ part of libbzip2 (yet);
- I haven't tested it, documented it, or considered the
- threading-safeness of it.
- If this code breaks, please contact both Yoshioka and me.
---*/
-
-BZ_EXTERN const char * BZ_API(BZ2_bzlibVersion) (
- void
- );
-
-#ifndef BZ_NO_STDIO
-BZ_EXTERN BZFILE * BZ_API(BZ2_bzopen) (
- const char *path,
- const char *mode
- );
-
-BZ_EXTERN BZFILE * BZ_API(BZ2_bzdopen) (
- int fd,
- const char *mode
- );
-
-BZ_EXTERN int BZ_API(BZ2_bzread) (
- BZFILE* b,
- void* buf,
- int len
- );
-
-BZ_EXTERN int BZ_API(BZ2_bzwrite) (
- BZFILE* b,
- void* buf,
- int len
- );
-
-BZ_EXTERN int BZ_API(BZ2_bzflush) (
- BZFILE* b
- );
-
-BZ_EXTERN void BZ_API(BZ2_bzclose) (
- BZFILE* b
- );
-
-BZ_EXTERN const char * BZ_API(BZ2_bzerror) (
- BZFILE *b,
- int *errnum
- );
-#endif
-
-#ifdef __cplusplus
-}
-#endif
-
-#endif
-
-/*-------------------------------------------------------------*/
-/*--- end bzlib.h ---*/
-/*-------------------------------------------------------------*/
diff --git a/third-party/bzip2/bzlib_private.h b/third-party/bzip2/bzlib_private.h
deleted file mode 100644
index 5d0217f..0000000
--- a/third-party/bzip2/bzlib_private.h
+++ /dev/null
@@ -1,509 +0,0 @@
-
-/*-------------------------------------------------------------*/
-/*--- Private header file for the library. ---*/
-/*--- bzlib_private.h ---*/
-/*-------------------------------------------------------------*/
-
-/* ------------------------------------------------------------------
- This file is part of bzip2/libbzip2, a program and library for
- lossless, block-sorting data compression.
-
- bzip2/libbzip2 version 1.0.6 of 6 September 2010
- Copyright (C) 1996-2010 Julian Seward <jseward at bzip.org>
-
- Please read the WARNING, DISCLAIMER and PATENTS sections in the
- README file.
-
- This program is released under the terms of the license contained
- in the file LICENSE.
- ------------------------------------------------------------------ */
-
-
-#ifndef _BZLIB_PRIVATE_H
-#define _BZLIB_PRIVATE_H
-
-#include <stdlib.h>
-
-#ifndef BZ_NO_STDIO
-#include <stdio.h>
-#include <ctype.h>
-#include <string.h>
-#endif
-
-#include "bzlib.h"
-
-
-
-/*-- General stuff. --*/
-
-#define BZ_VERSION "1.0.6, 6-Sept-2010"
-
-typedef char Char;
-typedef unsigned char Bool;
-typedef unsigned char UChar;
-typedef int Int32;
-typedef unsigned int UInt32;
-typedef short Int16;
-typedef unsigned short UInt16;
-
-#define True ((Bool)1)
-#define False ((Bool)0)
-
-#ifndef __GNUC__
-#define __inline__ /* */
-#endif
-
-#ifndef BZ_NO_STDIO
-
-extern void BZ2_bz__AssertH__fail ( int errcode );
-#define AssertH(cond,errcode) \
- { if (!(cond)) BZ2_bz__AssertH__fail ( errcode ); }
-
-#if BZ_DEBUG
-#define AssertD(cond,msg) \
- { if (!(cond)) { \
- fprintf ( stderr, \
- "\n\nlibbzip2(debug build): internal error\n\t%s\n", msg );\
- exit(1); \
- }}
-#else
-#define AssertD(cond,msg) /* */
-#endif
-
-#define VPrintf0(zf) \
- fprintf(stderr,zf)
-#define VPrintf1(zf,za1) \
- fprintf(stderr,zf,za1)
-#define VPrintf2(zf,za1,za2) \
- fprintf(stderr,zf,za1,za2)
-#define VPrintf3(zf,za1,za2,za3) \
- fprintf(stderr,zf,za1,za2,za3)
-#define VPrintf4(zf,za1,za2,za3,za4) \
- fprintf(stderr,zf,za1,za2,za3,za4)
-#define VPrintf5(zf,za1,za2,za3,za4,za5) \
- fprintf(stderr,zf,za1,za2,za3,za4,za5)
-
-#else
-
-extern void bz_internal_error ( int errcode );
-#define AssertH(cond,errcode) \
- { if (!(cond)) bz_internal_error ( errcode ); }
-#define AssertD(cond,msg) do { } while (0)
-#define VPrintf0(zf) do { } while (0)
-#define VPrintf1(zf,za1) do { } while (0)
-#define VPrintf2(zf,za1,za2) do { } while (0)
-#define VPrintf3(zf,za1,za2,za3) do { } while (0)
-#define VPrintf4(zf,za1,za2,za3,za4) do { } while (0)
-#define VPrintf5(zf,za1,za2,za3,za4,za5) do { } while (0)
-
-#endif
-
-
-#define BZALLOC(nnn) (strm->bzalloc)(strm->opaque,(nnn),1)
-#define BZFREE(ppp) (strm->bzfree)(strm->opaque,(ppp))
-
-
-/*-- Header bytes. --*/
-
-#define BZ_HDR_B 0x42 /* 'B' */
-#define BZ_HDR_Z 0x5a /* 'Z' */
-#define BZ_HDR_h 0x68 /* 'h' */
-#define BZ_HDR_0 0x30 /* '0' */
-
-/*-- Constants for the back end. --*/
-
-#define BZ_MAX_ALPHA_SIZE 258
-#define BZ_MAX_CODE_LEN 23
-
-#define BZ_RUNA 0
-#define BZ_RUNB 1
-
-#define BZ_N_GROUPS 6
-#define BZ_G_SIZE 50
-#define BZ_N_ITERS 4
-
-#define BZ_MAX_SELECTORS (2 + (900000 / BZ_G_SIZE))
-
-
-
-/*-- Stuff for randomising repetitive blocks. --*/
-
-extern Int32 BZ2_rNums[512];
-
-#define BZ_RAND_DECLS \
- Int32 rNToGo; \
- Int32 rTPos \
-
-#define BZ_RAND_INIT_MASK \
- s->rNToGo = 0; \
- s->rTPos = 0 \
-
-#define BZ_RAND_MASK ((s->rNToGo == 1) ? 1 : 0)
-
-#define BZ_RAND_UPD_MASK \
- if (s->rNToGo == 0) { \
- s->rNToGo = BZ2_rNums[s->rTPos]; \
- s->rTPos++; \
- if (s->rTPos == 512) s->rTPos = 0; \
- } \
- s->rNToGo--;
-
-
-
-/*-- Stuff for doing CRCs. --*/
-
-extern UInt32 BZ2_crc32Table[256];
-
-#define BZ_INITIALISE_CRC(crcVar) \
-{ \
- crcVar = 0xffffffffL; \
-}
-
-#define BZ_FINALISE_CRC(crcVar) \
-{ \
- crcVar = ~(crcVar); \
-}
-
-#define BZ_UPDATE_CRC(crcVar,cha) \
-{ \
- crcVar = (crcVar << 8) ^ \
- BZ2_crc32Table[(crcVar >> 24) ^ \
- ((UChar)cha)]; \
-}
-
-
-
-/*-- States and modes for compression. --*/
-
-#define BZ_M_IDLE 1
-#define BZ_M_RUNNING 2
-#define BZ_M_FLUSHING 3
-#define BZ_M_FINISHING 4
-
-#define BZ_S_OUTPUT 1
-#define BZ_S_INPUT 2
-
-#define BZ_N_RADIX 2
-#define BZ_N_QSORT 12
-#define BZ_N_SHELL 18
-#define BZ_N_OVERSHOOT (BZ_N_RADIX + BZ_N_QSORT + BZ_N_SHELL + 2)
-
-
-
-
-/*-- Structure holding all the compression-side stuff. --*/
-
-typedef
- struct {
- /* pointer back to the struct bz_stream */
- bz_stream* strm;
-
- /* mode this stream is in, and whether inputting */
- /* or outputting data */
- Int32 mode;
- Int32 state;
-
- /* remembers avail_in when flush/finish requested */
- UInt32 avail_in_expect;
-
- /* for doing the block sorting */
- UInt32* arr1;
- UInt32* arr2;
- UInt32* ftab;
- Int32 origPtr;
-
- /* aliases for arr1 and arr2 */
- UInt32* ptr;
- UChar* block;
- UInt16* mtfv;
- UChar* zbits;
-
- /* for deciding when to use the fallback sorting algorithm */
- Int32 workFactor;
-
- /* run-length-encoding of the input */
- UInt32 state_in_ch;
- Int32 state_in_len;
- BZ_RAND_DECLS;
-
- /* input and output limits and current posns */
- Int32 nblock;
- Int32 nblockMAX;
- Int32 numZ;
- Int32 state_out_pos;
-
- /* map of bytes used in block */
- Int32 nInUse;
- Bool inUse[256];
- UChar unseqToSeq[256];
-
- /* the buffer for bit stream creation */
- UInt32 bsBuff;
- Int32 bsLive;
-
- /* block and combined CRCs */
- UInt32 blockCRC;
- UInt32 combinedCRC;
-
- /* misc administratium */
- Int32 verbosity;
- Int32 blockNo;
- Int32 blockSize100k;
-
- /* stuff for coding the MTF values */
- Int32 nMTF;
- Int32 mtfFreq [BZ_MAX_ALPHA_SIZE];
- UChar selector [BZ_MAX_SELECTORS];
- UChar selectorMtf[BZ_MAX_SELECTORS];
-
- UChar len [BZ_N_GROUPS][BZ_MAX_ALPHA_SIZE];
- Int32 code [BZ_N_GROUPS][BZ_MAX_ALPHA_SIZE];
- Int32 rfreq [BZ_N_GROUPS][BZ_MAX_ALPHA_SIZE];
- /* second dimension: only 3 needed; 4 makes index calculations faster */
- UInt32 len_pack[BZ_MAX_ALPHA_SIZE][4];
-
- }
- EState;
-
-
-
-/*-- externs for compression. --*/
-
-extern void
-BZ2_blockSort ( EState* );
-
-extern void
-BZ2_compressBlock ( EState*, Bool );
-
-extern void
-BZ2_bsInitWrite ( EState* );
-
-extern void
-BZ2_hbAssignCodes ( Int32*, UChar*, Int32, Int32, Int32 );
-
-extern void
-BZ2_hbMakeCodeLengths ( UChar*, Int32*, Int32, Int32 );
-
-
-
-/*-- states for decompression. --*/
-
-#define BZ_X_IDLE 1
-#define BZ_X_OUTPUT 2
-
-#define BZ_X_MAGIC_1 10
-#define BZ_X_MAGIC_2 11
-#define BZ_X_MAGIC_3 12
-#define BZ_X_MAGIC_4 13
-#define BZ_X_BLKHDR_1 14
-#define BZ_X_BLKHDR_2 15
-#define BZ_X_BLKHDR_3 16
-#define BZ_X_BLKHDR_4 17
-#define BZ_X_BLKHDR_5 18
-#define BZ_X_BLKHDR_6 19
-#define BZ_X_BCRC_1 20
-#define BZ_X_BCRC_2 21
-#define BZ_X_BCRC_3 22
-#define BZ_X_BCRC_4 23
-#define BZ_X_RANDBIT 24
-#define BZ_X_ORIGPTR_1 25
-#define BZ_X_ORIGPTR_2 26
-#define BZ_X_ORIGPTR_3 27
-#define BZ_X_MAPPING_1 28
-#define BZ_X_MAPPING_2 29
-#define BZ_X_SELECTOR_1 30
-#define BZ_X_SELECTOR_2 31
-#define BZ_X_SELECTOR_3 32
-#define BZ_X_CODING_1 33
-#define BZ_X_CODING_2 34
-#define BZ_X_CODING_3 35
-#define BZ_X_MTF_1 36
-#define BZ_X_MTF_2 37
-#define BZ_X_MTF_3 38
-#define BZ_X_MTF_4 39
-#define BZ_X_MTF_5 40
-#define BZ_X_MTF_6 41
-#define BZ_X_ENDHDR_2 42
-#define BZ_X_ENDHDR_3 43
-#define BZ_X_ENDHDR_4 44
-#define BZ_X_ENDHDR_5 45
-#define BZ_X_ENDHDR_6 46
-#define BZ_X_CCRC_1 47
-#define BZ_X_CCRC_2 48
-#define BZ_X_CCRC_3 49
-#define BZ_X_CCRC_4 50
-
-
-
-/*-- Constants for the fast MTF decoder. --*/
-
-#define MTFA_SIZE 4096
-#define MTFL_SIZE 16
-
-
-
-/*-- Structure holding all the decompression-side stuff. --*/
-
-typedef
- struct {
- /* pointer back to the struct bz_stream */
- bz_stream* strm;
-
- /* state indicator for this stream */
- Int32 state;
-
- /* for doing the final run-length decoding */
- UChar state_out_ch;
- Int32 state_out_len;
- Bool blockRandomised;
- BZ_RAND_DECLS;
-
- /* the buffer for bit stream reading */
- UInt32 bsBuff;
- Int32 bsLive;
-
- /* misc administratium */
- Int32 blockSize100k;
- Bool smallDecompress;
- Int32 currBlockNo;
- Int32 verbosity;
-
- /* for undoing the Burrows-Wheeler transform */
- Int32 origPtr;
- UInt32 tPos;
- Int32 k0;
- Int32 unzftab[256];
- Int32 nblock_used;
- Int32 cftab[257];
- Int32 cftabCopy[257];
-
- /* for undoing the Burrows-Wheeler transform (FAST) */
- UInt32 *tt;
-
- /* for undoing the Burrows-Wheeler transform (SMALL) */
- UInt16 *ll16;
- UChar *ll4;
-
- /* stored and calculated CRCs */
- UInt32 storedBlockCRC;
- UInt32 storedCombinedCRC;
- UInt32 calculatedBlockCRC;
- UInt32 calculatedCombinedCRC;
-
- /* map of bytes used in block */
- Int32 nInUse;
- Bool inUse[256];
- Bool inUse16[16];
- UChar seqToUnseq[256];
-
- /* for decoding the MTF values */
- UChar mtfa [MTFA_SIZE];
- Int32 mtfbase[256 / MTFL_SIZE];
- UChar selector [BZ_MAX_SELECTORS];
- UChar selectorMtf[BZ_MAX_SELECTORS];
- UChar len [BZ_N_GROUPS][BZ_MAX_ALPHA_SIZE];
-
- Int32 limit [BZ_N_GROUPS][BZ_MAX_ALPHA_SIZE];
- Int32 base [BZ_N_GROUPS][BZ_MAX_ALPHA_SIZE];
- Int32 perm [BZ_N_GROUPS][BZ_MAX_ALPHA_SIZE];
- Int32 minLens[BZ_N_GROUPS];
-
- /* save area for scalars in the main decompress code */
- Int32 save_i;
- Int32 save_j;
- Int32 save_t;
- Int32 save_alphaSize;
- Int32 save_nGroups;
- Int32 save_nSelectors;
- Int32 save_EOB;
- Int32 save_groupNo;
- Int32 save_groupPos;
- Int32 save_nextSym;
- Int32 save_nblockMAX;
- Int32 save_nblock;
- Int32 save_es;
- Int32 save_N;
- Int32 save_curr;
- Int32 save_zt;
- Int32 save_zn;
- Int32 save_zvec;
- Int32 save_zj;
- Int32 save_gSel;
- Int32 save_gMinlen;
- Int32* save_gLimit;
- Int32* save_gBase;
- Int32* save_gPerm;
-
- }
- DState;
-
-
-
-/*-- Macros for decompression. --*/
-
-#define BZ_GET_FAST(cccc) \
- /* c_tPos is unsigned, hence test < 0 is pointless. */ \
- if (s->tPos >= (UInt32)100000 * (UInt32)s->blockSize100k) return True; \
- s->tPos = s->tt[s->tPos]; \
- cccc = (UChar)(s->tPos & 0xff); \
- s->tPos >>= 8;
-
-#define BZ_GET_FAST_C(cccc) \
- /* c_tPos is unsigned, hence test < 0 is pointless. */ \
- if (c_tPos >= (UInt32)100000 * (UInt32)ro_blockSize100k) return True; \
- c_tPos = c_tt[c_tPos]; \
- cccc = (UChar)(c_tPos & 0xff); \
- c_tPos >>= 8;
-
-#define SET_LL4(i,n) \
- { if (((i) & 0x1) == 0) \
- s->ll4[(i) >> 1] = (s->ll4[(i) >> 1] & 0xf0) | (n); else \
- s->ll4[(i) >> 1] = (s->ll4[(i) >> 1] & 0x0f) | ((n) << 4); \
- }
-
-#define GET_LL4(i) \
- ((((UInt32)(s->ll4[(i) >> 1])) >> (((i) << 2) & 0x4)) & 0xF)
-
-#define SET_LL(i,n) \
- { s->ll16[i] = (UInt16)(n & 0x0000ffff); \
- SET_LL4(i, n >> 16); \
- }
-
-#define GET_LL(i) \
- (((UInt32)s->ll16[i]) | (GET_LL4(i) << 16))
-
-#define BZ_GET_SMALL(cccc) \
- /* c_tPos is unsigned, hence test < 0 is pointless. */ \
- if (s->tPos >= (UInt32)100000 * (UInt32)s->blockSize100k) return True; \
- cccc = BZ2_indexIntoF ( s->tPos, s->cftab ); \
- s->tPos = GET_LL(s->tPos);
-
-
-/*-- externs for decompression. --*/
-
-extern Int32
-BZ2_indexIntoF ( Int32, Int32* );
-
-extern Int32
-BZ2_decompress ( DState* );
-
-extern void
-BZ2_hbCreateDecodeTables ( Int32*, Int32*, Int32*, UChar*,
- Int32, Int32, Int32 );
-
-
-#endif
-
-
-/*-- BZ_NO_STDIO seems to make NULL disappear on some platforms. --*/
-
-#ifdef BZ_NO_STDIO
-#ifndef NULL
-#define NULL 0
-#endif
-#endif
-
-
-/*-------------------------------------------------------------*/
-/*--- end bzlib_private.h ---*/
-/*-------------------------------------------------------------*/
diff --git a/third-party/bzip2/bzmore b/third-party/bzip2/bzmore
deleted file mode 100644
index d314043..0000000
--- a/third-party/bzip2/bzmore
+++ /dev/null
@@ -1,61 +0,0 @@
-#!/bin/sh
-
-# Bzmore wrapped for bzip2,
-# adapted from zmore by Philippe Troin <phil at fifi.org> for Debian GNU/Linux.
-
-PATH="/usr/bin:$PATH"; export PATH
-
-prog=`echo $0 | sed 's|.*/||'`
-case "$prog" in
- *less) more=less ;;
- *) more=more ;;
-esac
-
-if test "`echo -n a`" = "-n a"; then
- # looks like a SysV system:
- n1=''; n2='\c'
-else
- n1='-n'; n2=''
-fi
-oldtty=`stty -g 2>/dev/null`
-if stty -cbreak 2>/dev/null; then
- cb='cbreak'; ncb='-cbreak'
-else
- # 'stty min 1' resets eof to ^a on both SunOS and SysV!
- cb='min 1 -icanon'; ncb='icanon eof ^d'
-fi
-if test $? -eq 0 -a -n "$oldtty"; then
- trap 'stty $oldtty 2>/dev/null; exit' 0 2 3 5 10 13 15
-else
- trap 'stty $ncb echo 2>/dev/null; exit' 0 2 3 5 10 13 15
-fi
-
-if test $# = 0; then
- if test -t 0; then
- echo usage: $prog files...
- else
- bzip2 -cdfq | eval $more
- fi
-else
- FIRST=1
- for FILE
- do
- if test $FIRST -eq 0; then
- echo $n1 "--More--(Next file: $FILE)$n2"
- stty $cb -echo 2>/dev/null
- ANS=`dd bs=1 count=1 2>/dev/null`
- stty $ncb echo 2>/dev/null
- echo " "
- if test "$ANS" = 'e' -o "$ANS" = 'q'; then
- exit
- fi
- fi
- if test "$ANS" != 's'; then
- echo "------> $FILE <------"
- bzip2 -cdfq "$FILE" | eval $more
- fi
- if test -t; then
- FIRST=0
- fi
- done
-fi
diff --git a/third-party/bzip2/bzmore.1 b/third-party/bzip2/bzmore.1
deleted file mode 100644
index b437d3b..0000000
--- a/third-party/bzip2/bzmore.1
+++ /dev/null
@@ -1,152 +0,0 @@
-.\"Shamelessly copied from zmore.1 by Philippe Troin <phil at fifi.org>
-.\"for Debian GNU/Linux
-.TH BZMORE 1
-.SH NAME
-bzmore, bzless \- file perusal filter for crt viewing of bzip2 compressed text
-.SH SYNOPSIS
-.B bzmore
-[ name ... ]
-.br
-.B bzless
-[ name ... ]
-.SH NOTE
-In the following description,
-.I bzless
-and
-.I less
-can be used interchangeably with
-.I bzmore
-and
-.I more.
-.SH DESCRIPTION
-.I Bzmore
-is a filter which allows examination of compressed or plain text files
-one screenful at a time on a soft-copy terminal.
-.I bzmore
-works on files compressed with
-.I bzip2
-and also on uncompressed files.
-If a file does not exist,
-.I bzmore
-looks for a file of the same name with the addition of a .bz2 suffix.
-.PP
-.I Bzmore
-normally pauses after each screenful, printing --More--
-at the bottom of the screen.
-If the user then types a carriage return, one more line is displayed.
-If the user hits a space,
-another screenful is displayed. Other possibilities are enumerated later.
-.PP
-.I Bzmore
-looks in the file
-.I /etc/termcap
-to determine terminal characteristics,
-and to determine the default window size.
-On a terminal capable of displaying 24 lines,
-the default window size is 22 lines.
-Other sequences which may be typed when
-.I bzmore
-pauses, and their effects, are as follows (\fIi\fP is an optional integer
-argument, defaulting to 1) :
-.PP
-.IP \fIi\|\fP<space>
-display
-.I i
-more lines, (or another screenful if no argument is given)
-.PP
-.IP ^D
-display 11 more lines (a ``scroll'').
-If
-.I i
-is given, then the scroll size is set to \fIi\|\fP.
-.PP
-.IP d
-same as ^D (control-D)
-.PP
-.IP \fIi\|\fPz
-same as typing a space except that \fIi\|\fP, if present, becomes the new
-window size. Note that the window size reverts back to the default at the
-end of the current file.
-.PP
-.IP \fIi\|\fPs
-skip \fIi\|\fP lines and print a screenful of lines
-.PP
-.IP \fIi\|\fPf
-skip \fIi\fP screenfuls and print a screenful of lines
-.PP
-.IP "q or Q"
-quit reading the current file; go on to the next (if any)
-.PP
-.IP "e or q"
-When the prompt --More--(Next file:
-.IR file )
-is printed, this command causes bzmore to exit.
-.PP
-.IP s
-When the prompt --More--(Next file:
-.IR file )
-is printed, this command causes bzmore to skip the next file and continue.
-.PP
-.IP =
-Display the current line number.
-.PP
-.IP \fIi\|\fP/expr
-search for the \fIi\|\fP-th occurrence of the regular expression \fIexpr.\fP
-If the pattern is not found,
-.I bzmore
-goes on to the next file (if any).
-Otherwise, a screenful is displayed, starting two lines before the place
-where the expression was found.
-The user's erase and kill characters may be used to edit the regular
-expression.
-Erasing back past the first column cancels the search command.
-.PP
-.IP \fIi\|\fPn
-search for the \fIi\|\fP-th occurrence of the last regular expression entered.
-.PP
-.IP !command
-invoke a shell with \fIcommand\|\fP.
-The character `!' in "command" are replaced with the
-previous shell command. The sequence "\\!" is replaced by "!".
-.PP
-.IP ":q or :Q"
-quit reading the current file; go on to the next (if any)
-(same as q or Q).
-.PP
-.IP .
-(dot) repeat the previous command.
-.PP
-The commands take effect immediately, i.e., it is not necessary to
-type a carriage return.
-Up to the time when the command character itself is given,
-the user may hit the line kill character to cancel the numerical
-argument being formed.
-In addition, the user may hit the erase character to redisplay the
---More-- message.
-.PP
-At any time when output is being sent to the terminal, the user can
-hit the quit key (normally control\-\\).
-.I Bzmore
-will stop sending output, and will display the usual --More--
-prompt.
-The user may then enter one of the above commands in the normal manner.
-Unfortunately, some output is lost when this is done, due to the
-fact that any characters waiting in the terminal's output queue
-are flushed when the quit signal occurs.
-.PP
-The terminal is set to
-.I noecho
-mode by this program so that the output can be continuous.
-What you type will thus not show on your terminal, except for the / and !
-commands.
-.PP
-If the standard output is not a teletype, then
-.I bzmore
-acts just like
-.I bzcat,
-except that a header is printed before each file.
-.SH FILES
-.DT
-/etc/termcap Terminal data base
-.SH "SEE ALSO"
-more(1), less(1), bzip2(1), bzdiff(1), bzgrep(1)
diff --git a/third-party/bzip2/compress.c b/third-party/bzip2/compress.c
deleted file mode 100644
index caf7696..0000000
--- a/third-party/bzip2/compress.c
+++ /dev/null
@@ -1,672 +0,0 @@
-
-/*-------------------------------------------------------------*/
-/*--- Compression machinery (not incl block sorting) ---*/
-/*--- compress.c ---*/
-/*-------------------------------------------------------------*/
-
-/* ------------------------------------------------------------------
- This file is part of bzip2/libbzip2, a program and library for
- lossless, block-sorting data compression.
-
- bzip2/libbzip2 version 1.0.6 of 6 September 2010
- Copyright (C) 1996-2010 Julian Seward <jseward at bzip.org>
-
- Please read the WARNING, DISCLAIMER and PATENTS sections in the
- README file.
-
- This program is released under the terms of the license contained
- in the file LICENSE.
- ------------------------------------------------------------------ */
-
-
-/* CHANGES
- 0.9.0 -- original version.
- 0.9.0a/b -- no changes in this file.
- 0.9.0c -- changed setting of nGroups in sendMTFValues()
- so as to do a bit better on small files
-*/
-
-#include "bzlib_private.h"
-
-
-/*---------------------------------------------------*/
-/*--- Bit stream I/O ---*/
-/*---------------------------------------------------*/
-
-/*---------------------------------------------------*/
-void BZ2_bsInitWrite ( EState* s )
-{
- s->bsLive = 0;
- s->bsBuff = 0;
-}
-
-
-/*---------------------------------------------------*/
-static
-void bsFinishWrite ( EState* s )
-{
- while (s->bsLive > 0) {
- s->zbits[s->numZ] = (UChar)(s->bsBuff >> 24);
- s->numZ++;
- s->bsBuff <<= 8;
- s->bsLive -= 8;
- }
-}
-
-
-/*---------------------------------------------------*/
-#define bsNEEDW(nz) \
-{ \
- while (s->bsLive >= 8) { \
- s->zbits[s->numZ] \
- = (UChar)(s->bsBuff >> 24); \
- s->numZ++; \
- s->bsBuff <<= 8; \
- s->bsLive -= 8; \
- } \
-}
-
-
-/*---------------------------------------------------*/
-static
-__inline__
-void bsW ( EState* s, Int32 n, UInt32 v )
-{
- bsNEEDW ( n );
- s->bsBuff |= (v << (32 - s->bsLive - n));
- s->bsLive += n;
-}
-
-
-/*---------------------------------------------------*/
-static
-void bsPutUInt32 ( EState* s, UInt32 u )
-{
- bsW ( s, 8, (u >> 24) & 0xffL );
- bsW ( s, 8, (u >> 16) & 0xffL );
- bsW ( s, 8, (u >> 8) & 0xffL );
- bsW ( s, 8, u & 0xffL );
-}
-
-
-/*---------------------------------------------------*/
-static
-void bsPutUChar ( EState* s, UChar c )
-{
- bsW( s, 8, (UInt32)c );
-}
-
-
-/*---------------------------------------------------*/
-/*--- The back end proper ---*/
-/*---------------------------------------------------*/
-
-/*---------------------------------------------------*/
-static
-void makeMaps_e ( EState* s )
-{
- Int32 i;
- s->nInUse = 0;
- for (i = 0; i < 256; i++)
- if (s->inUse[i]) {
- s->unseqToSeq[i] = s->nInUse;
- s->nInUse++;
- }
-}
-
-
-/*---------------------------------------------------*/
-static
-void generateMTFValues ( EState* s )
-{
- UChar yy[256];
- Int32 i, j;
- Int32 zPend;
- Int32 wr;
- Int32 EOB;
-
- /*
- After sorting (eg, here),
- s->arr1 [ 0 .. s->nblock-1 ] holds sorted order,
- and
- ((UChar*)s->arr2) [ 0 .. s->nblock-1 ]
- holds the original block data.
-
- The first thing to do is generate the MTF values,
- and put them in
- ((UInt16*)s->arr1) [ 0 .. s->nblock-1 ].
- Because there are strictly fewer or equal MTF values
- than block values, ptr values in this area are overwritten
- with MTF values only when they are no longer needed.
-
- The final compressed bitstream is generated into the
- area starting at
- (UChar*) (&((UChar*)s->arr2)[s->nblock])
-
- These storage aliases are set up in bzCompressInit(),
- except for the last one, which is arranged in
- compressBlock().
- */
- UInt32* ptr = s->ptr;
- UChar* block = s->block;
- UInt16* mtfv = s->mtfv;
-
- makeMaps_e ( s );
- EOB = s->nInUse+1;
-
- for (i = 0; i <= EOB; i++) s->mtfFreq[i] = 0;
-
- wr = 0;
- zPend = 0;
- for (i = 0; i < s->nInUse; i++) yy[i] = (UChar) i;
-
- for (i = 0; i < s->nblock; i++) {
- UChar ll_i;
- AssertD ( wr <= i, "generateMTFValues(1)" );
- j = ptr[i]-1; if (j < 0) j += s->nblock;
- ll_i = s->unseqToSeq[block[j]];
- AssertD ( ll_i < s->nInUse, "generateMTFValues(2a)" );
-
- if (yy[0] == ll_i) {
- zPend++;
- } else {
-
- if (zPend > 0) {
- zPend--;
- while (True) {
- if (zPend & 1) {
- mtfv[wr] = BZ_RUNB; wr++;
- s->mtfFreq[BZ_RUNB]++;
- } else {
- mtfv[wr] = BZ_RUNA; wr++;
- s->mtfFreq[BZ_RUNA]++;
- }
- if (zPend < 2) break;
- zPend = (zPend - 2) / 2;
- };
- zPend = 0;
- }
- {
- register UChar rtmp;
- register UChar* ryy_j;
- register UChar rll_i;
- rtmp = yy[1];
- yy[1] = yy[0];
- ryy_j = &(yy[1]);
- rll_i = ll_i;
- while ( rll_i != rtmp ) {
- register UChar rtmp2;
- ryy_j++;
- rtmp2 = rtmp;
- rtmp = *ryy_j;
- *ryy_j = rtmp2;
- };
- yy[0] = rtmp;
- j = ryy_j - &(yy[0]);
- mtfv[wr] = j+1; wr++; s->mtfFreq[j+1]++;
- }
-
- }
- }
-
- if (zPend > 0) {
- zPend--;
- while (True) {
- if (zPend & 1) {
- mtfv[wr] = BZ_RUNB; wr++;
- s->mtfFreq[BZ_RUNB]++;
- } else {
- mtfv[wr] = BZ_RUNA; wr++;
- s->mtfFreq[BZ_RUNA]++;
- }
- if (zPend < 2) break;
- zPend = (zPend - 2) / 2;
- };
- zPend = 0;
- }
-
- mtfv[wr] = EOB; wr++; s->mtfFreq[EOB]++;
-
- s->nMTF = wr;
-}
-
-
-/*---------------------------------------------------*/
-#define BZ_LESSER_ICOST 0
-#define BZ_GREATER_ICOST 15
-
-static
-void sendMTFValues ( EState* s )
-{
- Int32 v, t, i, j, gs, ge, totc, bt, bc, iter;
- Int32 nSelectors, alphaSize, minLen, maxLen, selCtr;
- Int32 nGroups, nBytes;
-
- /*--
- UChar len [BZ_N_GROUPS][BZ_MAX_ALPHA_SIZE];
- is a global since the decoder also needs it.
-
- Int32 code[BZ_N_GROUPS][BZ_MAX_ALPHA_SIZE];
- Int32 rfreq[BZ_N_GROUPS][BZ_MAX_ALPHA_SIZE];
- are also globals only used in this proc.
- Made global to keep stack frame size small.
- --*/
-
-
- UInt16 cost[BZ_N_GROUPS];
- Int32 fave[BZ_N_GROUPS];
-
- UInt16* mtfv = s->mtfv;
-
- if (s->verbosity >= 3)
- VPrintf3( " %d in block, %d after MTF & 1-2 coding, "
- "%d+2 syms in use\n",
- s->nblock, s->nMTF, s->nInUse );
-
- alphaSize = s->nInUse+2;
- for (t = 0; t < BZ_N_GROUPS; t++)
- for (v = 0; v < alphaSize; v++)
- s->len[t][v] = BZ_GREATER_ICOST;
-
- /*--- Decide how many coding tables to use ---*/
- AssertH ( s->nMTF > 0, 3001 );
- if (s->nMTF < 200) nGroups = 2; else
- if (s->nMTF < 600) nGroups = 3; else
- if (s->nMTF < 1200) nGroups = 4; else
- if (s->nMTF < 2400) nGroups = 5; else
- nGroups = 6;
-
- /*--- Generate an initial set of coding tables ---*/
- {
- Int32 nPart, remF, tFreq, aFreq;
-
- nPart = nGroups;
- remF = s->nMTF;
- gs = 0;
- while (nPart > 0) {
- tFreq = remF / nPart;
- ge = gs-1;
- aFreq = 0;
- while (aFreq < tFreq && ge < alphaSize-1) {
- ge++;
- aFreq += s->mtfFreq[ge];
- }
-
- if (ge > gs
- && nPart != nGroups && nPart != 1
- && ((nGroups-nPart) % 2 == 1)) {
- aFreq -= s->mtfFreq[ge];
- ge--;
- }
-
- if (s->verbosity >= 3)
- VPrintf5( " initial group %d, [%d .. %d], "
- "has %d syms (%4.1f%%)\n",
- nPart, gs, ge, aFreq,
- (100.0 * (float)aFreq) / (float)(s->nMTF) );
-
- for (v = 0; v < alphaSize; v++)
- if (v >= gs && v <= ge)
- s->len[nPart-1][v] = BZ_LESSER_ICOST; else
- s->len[nPart-1][v] = BZ_GREATER_ICOST;
-
- nPart--;
- gs = ge+1;
- remF -= aFreq;
- }
- }
-
- /*---
- Iterate up to BZ_N_ITERS times to improve the tables.
- ---*/
- for (iter = 0; iter < BZ_N_ITERS; iter++) {
-
- for (t = 0; t < nGroups; t++) fave[t] = 0;
-
- for (t = 0; t < nGroups; t++)
- for (v = 0; v < alphaSize; v++)
- s->rfreq[t][v] = 0;
-
- /*---
- Set up an auxiliary length table which is used to fast-track
- the common case (nGroups == 6).
- ---*/
- if (nGroups == 6) {
- for (v = 0; v < alphaSize; v++) {
- s->len_pack[v][0] = (s->len[1][v] << 16) | s->len[0][v];
- s->len_pack[v][1] = (s->len[3][v] << 16) | s->len[2][v];
- s->len_pack[v][2] = (s->len[5][v] << 16) | s->len[4][v];
- }
- }
-
- nSelectors = 0;
- totc = 0;
- gs = 0;
- while (True) {
-
- /*--- Set group start & end marks. --*/
- if (gs >= s->nMTF) break;
- ge = gs + BZ_G_SIZE - 1;
- if (ge >= s->nMTF) ge = s->nMTF-1;
-
- /*--
- Calculate the cost of this group as coded
- by each of the coding tables.
- --*/
- for (t = 0; t < nGroups; t++) cost[t] = 0;
-
- if (nGroups == 6 && 50 == ge-gs+1) {
- /*--- fast track the common case ---*/
- register UInt32 cost01, cost23, cost45;
- register UInt16 icv;
- cost01 = cost23 = cost45 = 0;
-
-# define BZ_ITER(nn) \
- icv = mtfv[gs+(nn)]; \
- cost01 += s->len_pack[icv][0]; \
- cost23 += s->len_pack[icv][1]; \
- cost45 += s->len_pack[icv][2]; \
-
- BZ_ITER(0); BZ_ITER(1); BZ_ITER(2); BZ_ITER(3); BZ_ITER(4);
- BZ_ITER(5); BZ_ITER(6); BZ_ITER(7); BZ_ITER(8); BZ_ITER(9);
- BZ_ITER(10); BZ_ITER(11); BZ_ITER(12); BZ_ITER(13); BZ_ITER(14);
- BZ_ITER(15); BZ_ITER(16); BZ_ITER(17); BZ_ITER(18); BZ_ITER(19);
- BZ_ITER(20); BZ_ITER(21); BZ_ITER(22); BZ_ITER(23); BZ_ITER(24);
- BZ_ITER(25); BZ_ITER(26); BZ_ITER(27); BZ_ITER(28); BZ_ITER(29);
- BZ_ITER(30); BZ_ITER(31); BZ_ITER(32); BZ_ITER(33); BZ_ITER(34);
- BZ_ITER(35); BZ_ITER(36); BZ_ITER(37); BZ_ITER(38); BZ_ITER(39);
- BZ_ITER(40); BZ_ITER(41); BZ_ITER(42); BZ_ITER(43); BZ_ITER(44);
- BZ_ITER(45); BZ_ITER(46); BZ_ITER(47); BZ_ITER(48); BZ_ITER(49);
-
-# undef BZ_ITER
-
- cost[0] = cost01 & 0xffff; cost[1] = cost01 >> 16;
- cost[2] = cost23 & 0xffff; cost[3] = cost23 >> 16;
- cost[4] = cost45 & 0xffff; cost[5] = cost45 >> 16;
-
- } else {
- /*--- slow version which correctly handles all situations ---*/
- for (i = gs; i <= ge; i++) {
- UInt16 icv = mtfv[i];
- for (t = 0; t < nGroups; t++) cost[t] += s->len[t][icv];
- }
- }
-
- /*--
- Find the coding table which is best for this group,
- and record its identity in the selector table.
- --*/
- bc = 999999999; bt = -1;
- for (t = 0; t < nGroups; t++)
- if (cost[t] < bc) { bc = cost[t]; bt = t; };
- totc += bc;
- fave[bt]++;
- s->selector[nSelectors] = bt;
- nSelectors++;
-
- /*--
- Increment the symbol frequencies for the selected table.
- --*/
- if (nGroups == 6 && 50 == ge-gs+1) {
- /*--- fast track the common case ---*/
-
-# define BZ_ITUR(nn) s->rfreq[bt][ mtfv[gs+(nn)] ]++
-
- BZ_ITUR(0); BZ_ITUR(1); BZ_ITUR(2); BZ_ITUR(3); BZ_ITUR(4);
- BZ_ITUR(5); BZ_ITUR(6); BZ_ITUR(7); BZ_ITUR(8); BZ_ITUR(9);
- BZ_ITUR(10); BZ_ITUR(11); BZ_ITUR(12); BZ_ITUR(13); BZ_ITUR(14);
- BZ_ITUR(15); BZ_ITUR(16); BZ_ITUR(17); BZ_ITUR(18); BZ_ITUR(19);
- BZ_ITUR(20); BZ_ITUR(21); BZ_ITUR(22); BZ_ITUR(23); BZ_ITUR(24);
- BZ_ITUR(25); BZ_ITUR(26); BZ_ITUR(27); BZ_ITUR(28); BZ_ITUR(29);
- BZ_ITUR(30); BZ_ITUR(31); BZ_ITUR(32); BZ_ITUR(33); BZ_ITUR(34);
- BZ_ITUR(35); BZ_ITUR(36); BZ_ITUR(37); BZ_ITUR(38); BZ_ITUR(39);
- BZ_ITUR(40); BZ_ITUR(41); BZ_ITUR(42); BZ_ITUR(43); BZ_ITUR(44);
- BZ_ITUR(45); BZ_ITUR(46); BZ_ITUR(47); BZ_ITUR(48); BZ_ITUR(49);
-
-# undef BZ_ITUR
-
- } else {
- /*--- slow version which correctly handles all situations ---*/
- for (i = gs; i <= ge; i++)
- s->rfreq[bt][ mtfv[i] ]++;
- }
-
- gs = ge+1;
- }
- if (s->verbosity >= 3) {
- VPrintf2 ( " pass %d: size is %d, grp uses are ",
- iter+1, totc/8 );
- for (t = 0; t < nGroups; t++)
- VPrintf1 ( "%d ", fave[t] );
- VPrintf0 ( "\n" );
- }
-
- /*--
- Recompute the tables based on the accumulated frequencies.
- --*/
- /* maxLen was changed from 20 to 17 in bzip2-1.0.3. See
- comment in huffman.c for details. */
- for (t = 0; t < nGroups; t++)
- BZ2_hbMakeCodeLengths ( &(s->len[t][0]), &(s->rfreq[t][0]),
- alphaSize, 17 /*20*/ );
- }
-
-
- AssertH( nGroups < 8, 3002 );
- AssertH( nSelectors < 32768 &&
- nSelectors <= (2 + (900000 / BZ_G_SIZE)),
- 3003 );
-
-
- /*--- Compute MTF values for the selectors. ---*/
- {
- UChar pos[BZ_N_GROUPS], ll_i, tmp2, tmp;
- for (i = 0; i < nGroups; i++) pos[i] = i;
- for (i = 0; i < nSelectors; i++) {
- ll_i = s->selector[i];
- j = 0;
- tmp = pos[j];
- while ( ll_i != tmp ) {
- j++;
- tmp2 = tmp;
- tmp = pos[j];
- pos[j] = tmp2;
- };
- pos[0] = tmp;
- s->selectorMtf[i] = j;
- }
- };
-
- /*--- Assign actual codes for the tables. --*/
- for (t = 0; t < nGroups; t++) {
- minLen = 32;
- maxLen = 0;
- for (i = 0; i < alphaSize; i++) {
- if (s->len[t][i] > maxLen) maxLen = s->len[t][i];
- if (s->len[t][i] < minLen) minLen = s->len[t][i];
- }
- AssertH ( !(maxLen > 17 /*20*/ ), 3004 );
- AssertH ( !(minLen < 1), 3005 );
- BZ2_hbAssignCodes ( &(s->code[t][0]), &(s->len[t][0]),
- minLen, maxLen, alphaSize );
- }
-
- /*--- Transmit the mapping table. ---*/
- {
- Bool inUse16[16];
- for (i = 0; i < 16; i++) {
- inUse16[i] = False;
- for (j = 0; j < 16; j++)
- if (s->inUse[i * 16 + j]) inUse16[i] = True;
- }
-
- nBytes = s->numZ;
- for (i = 0; i < 16; i++)
- if (inUse16[i]) bsW(s,1,1); else bsW(s,1,0);
-
- for (i = 0; i < 16; i++)
- if (inUse16[i])
- for (j = 0; j < 16; j++) {
- if (s->inUse[i * 16 + j]) bsW(s,1,1); else bsW(s,1,0);
- }
-
- if (s->verbosity >= 3)
- VPrintf1( " bytes: mapping %d, ", s->numZ-nBytes );
- }
-
- /*--- Now the selectors. ---*/
- nBytes = s->numZ;
- bsW ( s, 3, nGroups );
- bsW ( s, 15, nSelectors );
- for (i = 0; i < nSelectors; i++) {
- for (j = 0; j < s->selectorMtf[i]; j++) bsW(s,1,1);
- bsW(s,1,0);
- }
- if (s->verbosity >= 3)
- VPrintf1( "selectors %d, ", s->numZ-nBytes );
-
- /*--- Now the coding tables. ---*/
- nBytes = s->numZ;
-
- for (t = 0; t < nGroups; t++) {
- Int32 curr = s->len[t][0];
- bsW ( s, 5, curr );
- for (i = 0; i < alphaSize; i++) {
- while (curr < s->len[t][i]) { bsW(s,2,2); curr++; /* 10 */ };
- while (curr > s->len[t][i]) { bsW(s,2,3); curr--; /* 11 */ };
- bsW ( s, 1, 0 );
- }
- }
-
- if (s->verbosity >= 3)
- VPrintf1 ( "code lengths %d, ", s->numZ-nBytes );
-
- /*--- And finally, the block data proper ---*/
- nBytes = s->numZ;
- selCtr = 0;
- gs = 0;
- while (True) {
- if (gs >= s->nMTF) break;
- ge = gs + BZ_G_SIZE - 1;
- if (ge >= s->nMTF) ge = s->nMTF-1;
- AssertH ( s->selector[selCtr] < nGroups, 3006 );
-
- if (nGroups == 6 && 50 == ge-gs+1) {
- /*--- fast track the common case ---*/
- UInt16 mtfv_i;
- UChar* s_len_sel_selCtr
- = &(s->len[s->selector[selCtr]][0]);
- Int32* s_code_sel_selCtr
- = &(s->code[s->selector[selCtr]][0]);
-
-# define BZ_ITAH(nn) \
- mtfv_i = mtfv[gs+(nn)]; \
- bsW ( s, \
- s_len_sel_selCtr[mtfv_i], \
- s_code_sel_selCtr[mtfv_i] )
-
- BZ_ITAH(0); BZ_ITAH(1); BZ_ITAH(2); BZ_ITAH(3); BZ_ITAH(4);
- BZ_ITAH(5); BZ_ITAH(6); BZ_ITAH(7); BZ_ITAH(8); BZ_ITAH(9);
- BZ_ITAH(10); BZ_ITAH(11); BZ_ITAH(12); BZ_ITAH(13); BZ_ITAH(14);
- BZ_ITAH(15); BZ_ITAH(16); BZ_ITAH(17); BZ_ITAH(18); BZ_ITAH(19);
- BZ_ITAH(20); BZ_ITAH(21); BZ_ITAH(22); BZ_ITAH(23); BZ_ITAH(24);
- BZ_ITAH(25); BZ_ITAH(26); BZ_ITAH(27); BZ_ITAH(28); BZ_ITAH(29);
- BZ_ITAH(30); BZ_ITAH(31); BZ_ITAH(32); BZ_ITAH(33); BZ_ITAH(34);
- BZ_ITAH(35); BZ_ITAH(36); BZ_ITAH(37); BZ_ITAH(38); BZ_ITAH(39);
- BZ_ITAH(40); BZ_ITAH(41); BZ_ITAH(42); BZ_ITAH(43); BZ_ITAH(44);
- BZ_ITAH(45); BZ_ITAH(46); BZ_ITAH(47); BZ_ITAH(48); BZ_ITAH(49);
-
-# undef BZ_ITAH
-
- } else {
- /*--- slow version which correctly handles all situations ---*/
- for (i = gs; i <= ge; i++) {
- bsW ( s,
- s->len [s->selector[selCtr]] [mtfv[i]],
- s->code [s->selector[selCtr]] [mtfv[i]] );
- }
- }
-
-
- gs = ge+1;
- selCtr++;
- }
- AssertH( selCtr == nSelectors, 3007 );
-
- if (s->verbosity >= 3)
- VPrintf1( "codes %d\n", s->numZ-nBytes );
-}
-
-
-/*---------------------------------------------------*/
-void BZ2_compressBlock ( EState* s, Bool is_last_block )
-{
- if (s->nblock > 0) {
-
- BZ_FINALISE_CRC ( s->blockCRC );
- s->combinedCRC = (s->combinedCRC << 1) | (s->combinedCRC >> 31);
- s->combinedCRC ^= s->blockCRC;
- if (s->blockNo > 1) s->numZ = 0;
-
- if (s->verbosity >= 2)
- VPrintf4( " block %d: crc = 0x%08x, "
- "combined CRC = 0x%08x, size = %d\n",
- s->blockNo, s->blockCRC, s->combinedCRC, s->nblock );
-
- BZ2_blockSort ( s );
- }
-
- s->zbits = (UChar*) (&((UChar*)s->arr2)[s->nblock]);
-
- /*-- If this is the first block, create the stream header. --*/
- if (s->blockNo == 1) {
- BZ2_bsInitWrite ( s );
- bsPutUChar ( s, BZ_HDR_B );
- bsPutUChar ( s, BZ_HDR_Z );
- bsPutUChar ( s, BZ_HDR_h );
- bsPutUChar ( s, (UChar)(BZ_HDR_0 + s->blockSize100k) );
- }
-
- if (s->nblock > 0) {
-
- bsPutUChar ( s, 0x31 ); bsPutUChar ( s, 0x41 );
- bsPutUChar ( s, 0x59 ); bsPutUChar ( s, 0x26 );
- bsPutUChar ( s, 0x53 ); bsPutUChar ( s, 0x59 );
-
- /*-- Now the block's CRC, so it is in a known place. --*/
- bsPutUInt32 ( s, s->blockCRC );
-
- /*--
- Now a single bit indicating (non-)randomisation.
- As of version 0.9.5, we use a better sorting algorithm
- which makes randomisation unnecessary. So always set
- the randomised bit to 'no'. Of course, the decoder
- still needs to be able to handle randomised blocks
- so as to maintain backwards compatibility with
- older versions of bzip2.
- --*/
- bsW(s,1,0);
-
- bsW ( s, 24, s->origPtr );
- generateMTFValues ( s );
- sendMTFValues ( s );
- }
-
-
- /*-- If this is the last block, add the stream trailer. --*/
- if (is_last_block) {
-
- bsPutUChar ( s, 0x17 ); bsPutUChar ( s, 0x72 );
- bsPutUChar ( s, 0x45 ); bsPutUChar ( s, 0x38 );
- bsPutUChar ( s, 0x50 ); bsPutUChar ( s, 0x90 );
- bsPutUInt32 ( s, s->combinedCRC );
- if (s->verbosity >= 2)
- VPrintf1( " final combined CRC = 0x%08x\n ", s->combinedCRC );
- bsFinishWrite ( s );
- }
-}
-
-
-/*-------------------------------------------------------------*/
-/*--- end compress.c ---*/
-/*-------------------------------------------------------------*/
diff --git a/third-party/bzip2/crctable.c b/third-party/bzip2/crctable.c
deleted file mode 100644
index 1fea7e9..0000000
--- a/third-party/bzip2/crctable.c
+++ /dev/null
@@ -1,104 +0,0 @@
-
-/*-------------------------------------------------------------*/
-/*--- Table for doing CRCs ---*/
-/*--- crctable.c ---*/
-/*-------------------------------------------------------------*/
-
-/* ------------------------------------------------------------------
- This file is part of bzip2/libbzip2, a program and library for
- lossless, block-sorting data compression.
-
- bzip2/libbzip2 version 1.0.6 of 6 September 2010
- Copyright (C) 1996-2010 Julian Seward <jseward at bzip.org>
-
- Please read the WARNING, DISCLAIMER and PATENTS sections in the
- README file.
-
- This program is released under the terms of the license contained
- in the file LICENSE.
- ------------------------------------------------------------------ */
-
-
-#include "bzlib_private.h"
-
-/*--
- I think this is an implementation of the AUTODIN-II,
- Ethernet & FDDI 32-bit CRC standard. Vaguely derived
- from code by Rob Warnock, in Section 51 of the
- comp.compression FAQ.
---*/
-
-UInt32 BZ2_crc32Table[256] = {
-
- /*-- Ugly, innit? --*/
-
- 0x00000000L, 0x04c11db7L, 0x09823b6eL, 0x0d4326d9L,
- 0x130476dcL, 0x17c56b6bL, 0x1a864db2L, 0x1e475005L,
- 0x2608edb8L, 0x22c9f00fL, 0x2f8ad6d6L, 0x2b4bcb61L,
- 0x350c9b64L, 0x31cd86d3L, 0x3c8ea00aL, 0x384fbdbdL,
- 0x4c11db70L, 0x48d0c6c7L, 0x4593e01eL, 0x4152fda9L,
- 0x5f15adacL, 0x5bd4b01bL, 0x569796c2L, 0x52568b75L,
- 0x6a1936c8L, 0x6ed82b7fL, 0x639b0da6L, 0x675a1011L,
- 0x791d4014L, 0x7ddc5da3L, 0x709f7b7aL, 0x745e66cdL,
- 0x9823b6e0L, 0x9ce2ab57L, 0x91a18d8eL, 0x95609039L,
- 0x8b27c03cL, 0x8fe6dd8bL, 0x82a5fb52L, 0x8664e6e5L,
- 0xbe2b5b58L, 0xbaea46efL, 0xb7a96036L, 0xb3687d81L,
- 0xad2f2d84L, 0xa9ee3033L, 0xa4ad16eaL, 0xa06c0b5dL,
- 0xd4326d90L, 0xd0f37027L, 0xddb056feL, 0xd9714b49L,
- 0xc7361b4cL, 0xc3f706fbL, 0xceb42022L, 0xca753d95L,
- 0xf23a8028L, 0xf6fb9d9fL, 0xfbb8bb46L, 0xff79a6f1L,
- 0xe13ef6f4L, 0xe5ffeb43L, 0xe8bccd9aL, 0xec7dd02dL,
- 0x34867077L, 0x30476dc0L, 0x3d044b19L, 0x39c556aeL,
- 0x278206abL, 0x23431b1cL, 0x2e003dc5L, 0x2ac12072L,
- 0x128e9dcfL, 0x164f8078L, 0x1b0ca6a1L, 0x1fcdbb16L,
- 0x018aeb13L, 0x054bf6a4L, 0x0808d07dL, 0x0cc9cdcaL,
- 0x7897ab07L, 0x7c56b6b0L, 0x71159069L, 0x75d48ddeL,
- 0x6b93dddbL, 0x6f52c06cL, 0x6211e6b5L, 0x66d0fb02L,
- 0x5e9f46bfL, 0x5a5e5b08L, 0x571d7dd1L, 0x53dc6066L,
- 0x4d9b3063L, 0x495a2dd4L, 0x44190b0dL, 0x40d816baL,
- 0xaca5c697L, 0xa864db20L, 0xa527fdf9L, 0xa1e6e04eL,
- 0xbfa1b04bL, 0xbb60adfcL, 0xb6238b25L, 0xb2e29692L,
- 0x8aad2b2fL, 0x8e6c3698L, 0x832f1041L, 0x87ee0df6L,
- 0x99a95df3L, 0x9d684044L, 0x902b669dL, 0x94ea7b2aL,
- 0xe0b41de7L, 0xe4750050L, 0xe9362689L, 0xedf73b3eL,
- 0xf3b06b3bL, 0xf771768cL, 0xfa325055L, 0xfef34de2L,
- 0xc6bcf05fL, 0xc27dede8L, 0xcf3ecb31L, 0xcbffd686L,
- 0xd5b88683L, 0xd1799b34L, 0xdc3abdedL, 0xd8fba05aL,
- 0x690ce0eeL, 0x6dcdfd59L, 0x608edb80L, 0x644fc637L,
- 0x7a089632L, 0x7ec98b85L, 0x738aad5cL, 0x774bb0ebL,
- 0x4f040d56L, 0x4bc510e1L, 0x46863638L, 0x42472b8fL,
- 0x5c007b8aL, 0x58c1663dL, 0x558240e4L, 0x51435d53L,
- 0x251d3b9eL, 0x21dc2629L, 0x2c9f00f0L, 0x285e1d47L,
- 0x36194d42L, 0x32d850f5L, 0x3f9b762cL, 0x3b5a6b9bL,
- 0x0315d626L, 0x07d4cb91L, 0x0a97ed48L, 0x0e56f0ffL,
- 0x1011a0faL, 0x14d0bd4dL, 0x19939b94L, 0x1d528623L,
- 0xf12f560eL, 0xf5ee4bb9L, 0xf8ad6d60L, 0xfc6c70d7L,
- 0xe22b20d2L, 0xe6ea3d65L, 0xeba91bbcL, 0xef68060bL,
- 0xd727bbb6L, 0xd3e6a601L, 0xdea580d8L, 0xda649d6fL,
- 0xc423cd6aL, 0xc0e2d0ddL, 0xcda1f604L, 0xc960ebb3L,
- 0xbd3e8d7eL, 0xb9ff90c9L, 0xb4bcb610L, 0xb07daba7L,
- 0xae3afba2L, 0xaafbe615L, 0xa7b8c0ccL, 0xa379dd7bL,
- 0x9b3660c6L, 0x9ff77d71L, 0x92b45ba8L, 0x9675461fL,
- 0x8832161aL, 0x8cf30badL, 0x81b02d74L, 0x857130c3L,
- 0x5d8a9099L, 0x594b8d2eL, 0x5408abf7L, 0x50c9b640L,
- 0x4e8ee645L, 0x4a4ffbf2L, 0x470cdd2bL, 0x43cdc09cL,
- 0x7b827d21L, 0x7f436096L, 0x7200464fL, 0x76c15bf8L,
- 0x68860bfdL, 0x6c47164aL, 0x61043093L, 0x65c52d24L,
- 0x119b4be9L, 0x155a565eL, 0x18197087L, 0x1cd86d30L,
- 0x029f3d35L, 0x065e2082L, 0x0b1d065bL, 0x0fdc1becL,
- 0x3793a651L, 0x3352bbe6L, 0x3e119d3fL, 0x3ad08088L,
- 0x2497d08dL, 0x2056cd3aL, 0x2d15ebe3L, 0x29d4f654L,
- 0xc5a92679L, 0xc1683bceL, 0xcc2b1d17L, 0xc8ea00a0L,
- 0xd6ad50a5L, 0xd26c4d12L, 0xdf2f6bcbL, 0xdbee767cL,
- 0xe3a1cbc1L, 0xe760d676L, 0xea23f0afL, 0xeee2ed18L,
- 0xf0a5bd1dL, 0xf464a0aaL, 0xf9278673L, 0xfde69bc4L,
- 0x89b8fd09L, 0x8d79e0beL, 0x803ac667L, 0x84fbdbd0L,
- 0x9abc8bd5L, 0x9e7d9662L, 0x933eb0bbL, 0x97ffad0cL,
- 0xafb010b1L, 0xab710d06L, 0xa6322bdfL, 0xa2f33668L,
- 0xbcb4666dL, 0xb8757bdaL, 0xb5365d03L, 0xb1f740b4L
-};
-
-
-/*-------------------------------------------------------------*/
-/*--- end crctable.c ---*/
-/*-------------------------------------------------------------*/
diff --git a/third-party/bzip2/decompress.c b/third-party/bzip2/decompress.c
deleted file mode 100644
index 311f566..0000000
--- a/third-party/bzip2/decompress.c
+++ /dev/null
@@ -1,646 +0,0 @@
-
-/*-------------------------------------------------------------*/
-/*--- Decompression machinery ---*/
-/*--- decompress.c ---*/
-/*-------------------------------------------------------------*/
-
-/* ------------------------------------------------------------------
- This file is part of bzip2/libbzip2, a program and library for
- lossless, block-sorting data compression.
-
- bzip2/libbzip2 version 1.0.6 of 6 September 2010
- Copyright (C) 1996-2010 Julian Seward <jseward at bzip.org>
-
- Please read the WARNING, DISCLAIMER and PATENTS sections in the
- README file.
-
- This program is released under the terms of the license contained
- in the file LICENSE.
- ------------------------------------------------------------------ */
-
-
-#include "bzlib_private.h"
-
-
-/*---------------------------------------------------*/
-static
-void makeMaps_d ( DState* s )
-{
- Int32 i;
- s->nInUse = 0;
- for (i = 0; i < 256; i++)
- if (s->inUse[i]) {
- s->seqToUnseq[s->nInUse] = i;
- s->nInUse++;
- }
-}
-
-
-/*---------------------------------------------------*/
-#define RETURN(rrr) \
- { retVal = rrr; goto save_state_and_return; };
-
-#define GET_BITS(lll,vvv,nnn) \
- case lll: s->state = lll; \
- while (True) { \
- if (s->bsLive >= nnn) { \
- UInt32 v; \
- v = (s->bsBuff >> \
- (s->bsLive-nnn)) & ((1 << nnn)-1); \
- s->bsLive -= nnn; \
- vvv = v; \
- break; \
- } \
- if (s->strm->avail_in == 0) RETURN(BZ_OK); \
- s->bsBuff \
- = (s->bsBuff << 8) | \
- ((UInt32) \
- (*((UChar*)(s->strm->next_in)))); \
- s->bsLive += 8; \
- s->strm->next_in++; \
- s->strm->avail_in--; \
- s->strm->total_in_lo32++; \
- if (s->strm->total_in_lo32 == 0) \
- s->strm->total_in_hi32++; \
- }
-
-#define GET_UCHAR(lll,uuu) \
- GET_BITS(lll,uuu,8)
-
-#define GET_BIT(lll,uuu) \
- GET_BITS(lll,uuu,1)
-
-/*---------------------------------------------------*/
-#define GET_MTF_VAL(label1,label2,lval) \
-{ \
- if (groupPos == 0) { \
- groupNo++; \
- if (groupNo >= nSelectors) \
- RETURN(BZ_DATA_ERROR); \
- groupPos = BZ_G_SIZE; \
- gSel = s->selector[groupNo]; \
- gMinlen = s->minLens[gSel]; \
- gLimit = &(s->limit[gSel][0]); \
- gPerm = &(s->perm[gSel][0]); \
- gBase = &(s->base[gSel][0]); \
- } \
- groupPos--; \
- zn = gMinlen; \
- GET_BITS(label1, zvec, zn); \
- while (1) { \
- if (zn > 20 /* the longest code */) \
- RETURN(BZ_DATA_ERROR); \
- if (zvec <= gLimit[zn]) break; \
- zn++; \
- GET_BIT(label2, zj); \
- zvec = (zvec << 1) | zj; \
- }; \
- if (zvec - gBase[zn] < 0 \
- || zvec - gBase[zn] >= BZ_MAX_ALPHA_SIZE) \
- RETURN(BZ_DATA_ERROR); \
- lval = gPerm[zvec - gBase[zn]]; \
-}
-
-
-/*---------------------------------------------------*/
-Int32 BZ2_decompress ( DState* s )
-{
- UChar uc;
- Int32 retVal;
- Int32 minLen, maxLen;
- bz_stream* strm = s->strm;
-
- /* stuff that needs to be saved/restored */
- Int32 i;
- Int32 j;
- Int32 t;
- Int32 alphaSize;
- Int32 nGroups;
- Int32 nSelectors;
- Int32 EOB;
- Int32 groupNo;
- Int32 groupPos;
- Int32 nextSym;
- Int32 nblockMAX;
- Int32 nblock;
- Int32 es;
- Int32 N;
- Int32 curr;
- Int32 zt;
- Int32 zn;
- Int32 zvec;
- Int32 zj;
- Int32 gSel;
- Int32 gMinlen;
- Int32* gLimit;
- Int32* gBase;
- Int32* gPerm;
-
- if (s->state == BZ_X_MAGIC_1) {
- /*initialise the save area*/
- s->save_i = 0;
- s->save_j = 0;
- s->save_t = 0;
- s->save_alphaSize = 0;
- s->save_nGroups = 0;
- s->save_nSelectors = 0;
- s->save_EOB = 0;
- s->save_groupNo = 0;
- s->save_groupPos = 0;
- s->save_nextSym = 0;
- s->save_nblockMAX = 0;
- s->save_nblock = 0;
- s->save_es = 0;
- s->save_N = 0;
- s->save_curr = 0;
- s->save_zt = 0;
- s->save_zn = 0;
- s->save_zvec = 0;
- s->save_zj = 0;
- s->save_gSel = 0;
- s->save_gMinlen = 0;
- s->save_gLimit = NULL;
- s->save_gBase = NULL;
- s->save_gPerm = NULL;
- }
-
- /*restore from the save area*/
- i = s->save_i;
- j = s->save_j;
- t = s->save_t;
- alphaSize = s->save_alphaSize;
- nGroups = s->save_nGroups;
- nSelectors = s->save_nSelectors;
- EOB = s->save_EOB;
- groupNo = s->save_groupNo;
- groupPos = s->save_groupPos;
- nextSym = s->save_nextSym;
- nblockMAX = s->save_nblockMAX;
- nblock = s->save_nblock;
- es = s->save_es;
- N = s->save_N;
- curr = s->save_curr;
- zt = s->save_zt;
- zn = s->save_zn;
- zvec = s->save_zvec;
- zj = s->save_zj;
- gSel = s->save_gSel;
- gMinlen = s->save_gMinlen;
- gLimit = s->save_gLimit;
- gBase = s->save_gBase;
- gPerm = s->save_gPerm;
-
- retVal = BZ_OK;
-
- switch (s->state) {
-
- GET_UCHAR(BZ_X_MAGIC_1, uc);
- if (uc != BZ_HDR_B) RETURN(BZ_DATA_ERROR_MAGIC);
-
- GET_UCHAR(BZ_X_MAGIC_2, uc);
- if (uc != BZ_HDR_Z) RETURN(BZ_DATA_ERROR_MAGIC);
-
- GET_UCHAR(BZ_X_MAGIC_3, uc)
- if (uc != BZ_HDR_h) RETURN(BZ_DATA_ERROR_MAGIC);
-
- GET_BITS(BZ_X_MAGIC_4, s->blockSize100k, 8)
- if (s->blockSize100k < (BZ_HDR_0 + 1) ||
- s->blockSize100k > (BZ_HDR_0 + 9)) RETURN(BZ_DATA_ERROR_MAGIC);
- s->blockSize100k -= BZ_HDR_0;
-
- if (s->smallDecompress) {
- s->ll16 = BZALLOC( s->blockSize100k * 100000 * sizeof(UInt16) );
- s->ll4 = BZALLOC(
- ((1 + s->blockSize100k * 100000) >> 1) * sizeof(UChar)
- );
- if (s->ll16 == NULL || s->ll4 == NULL) RETURN(BZ_MEM_ERROR);
- } else {
- s->tt = BZALLOC( s->blockSize100k * 100000 * sizeof(Int32) );
- if (s->tt == NULL) RETURN(BZ_MEM_ERROR);
- }
-
- GET_UCHAR(BZ_X_BLKHDR_1, uc);
-
- if (uc == 0x17) goto endhdr_2;
- if (uc != 0x31) RETURN(BZ_DATA_ERROR);
- GET_UCHAR(BZ_X_BLKHDR_2, uc);
- if (uc != 0x41) RETURN(BZ_DATA_ERROR);
- GET_UCHAR(BZ_X_BLKHDR_3, uc);
- if (uc != 0x59) RETURN(BZ_DATA_ERROR);
- GET_UCHAR(BZ_X_BLKHDR_4, uc);
- if (uc != 0x26) RETURN(BZ_DATA_ERROR);
- GET_UCHAR(BZ_X_BLKHDR_5, uc);
- if (uc != 0x53) RETURN(BZ_DATA_ERROR);
- GET_UCHAR(BZ_X_BLKHDR_6, uc);
- if (uc != 0x59) RETURN(BZ_DATA_ERROR);
-
- s->currBlockNo++;
- if (s->verbosity >= 2)
- VPrintf1 ( "\n [%d: huff+mtf ", s->currBlockNo );
-
- s->storedBlockCRC = 0;
- GET_UCHAR(BZ_X_BCRC_1, uc);
- s->storedBlockCRC = (s->storedBlockCRC << 8) | ((UInt32)uc);
- GET_UCHAR(BZ_X_BCRC_2, uc);
- s->storedBlockCRC = (s->storedBlockCRC << 8) | ((UInt32)uc);
- GET_UCHAR(BZ_X_BCRC_3, uc);
- s->storedBlockCRC = (s->storedBlockCRC << 8) | ((UInt32)uc);
- GET_UCHAR(BZ_X_BCRC_4, uc);
- s->storedBlockCRC = (s->storedBlockCRC << 8) | ((UInt32)uc);
-
- GET_BITS(BZ_X_RANDBIT, s->blockRandomised, 1);
-
- s->origPtr = 0;
- GET_UCHAR(BZ_X_ORIGPTR_1, uc);
- s->origPtr = (s->origPtr << 8) | ((Int32)uc);
- GET_UCHAR(BZ_X_ORIGPTR_2, uc);
- s->origPtr = (s->origPtr << 8) | ((Int32)uc);
- GET_UCHAR(BZ_X_ORIGPTR_3, uc);
- s->origPtr = (s->origPtr << 8) | ((Int32)uc);
-
- if (s->origPtr < 0)
- RETURN(BZ_DATA_ERROR);
- if (s->origPtr > 10 + 100000*s->blockSize100k)
- RETURN(BZ_DATA_ERROR);
-
- /*--- Receive the mapping table ---*/
- for (i = 0; i < 16; i++) {
- GET_BIT(BZ_X_MAPPING_1, uc);
- if (uc == 1)
- s->inUse16[i] = True; else
- s->inUse16[i] = False;
- }
-
- for (i = 0; i < 256; i++) s->inUse[i] = False;
-
- for (i = 0; i < 16; i++)
- if (s->inUse16[i])
- for (j = 0; j < 16; j++) {
- GET_BIT(BZ_X_MAPPING_2, uc);
- if (uc == 1) s->inUse[i * 16 + j] = True;
- }
- makeMaps_d ( s );
- if (s->nInUse == 0) RETURN(BZ_DATA_ERROR);
- alphaSize = s->nInUse+2;
-
- /*--- Now the selectors ---*/
- GET_BITS(BZ_X_SELECTOR_1, nGroups, 3);
- if (nGroups < 2 || nGroups > 6) RETURN(BZ_DATA_ERROR);
- GET_BITS(BZ_X_SELECTOR_2, nSelectors, 15);
- if (nSelectors < 1) RETURN(BZ_DATA_ERROR);
- for (i = 0; i < nSelectors; i++) {
- j = 0;
- while (True) {
- GET_BIT(BZ_X_SELECTOR_3, uc);
- if (uc == 0) break;
- j++;
- if (j >= nGroups) RETURN(BZ_DATA_ERROR);
- }
- s->selectorMtf[i] = j;
- }
-
- /*--- Undo the MTF values for the selectors. ---*/
- {
- UChar pos[BZ_N_GROUPS], tmp, v;
- for (v = 0; v < nGroups; v++) pos[v] = v;
-
- for (i = 0; i < nSelectors; i++) {
- v = s->selectorMtf[i];
- tmp = pos[v];
- while (v > 0) { pos[v] = pos[v-1]; v--; }
- pos[0] = tmp;
- s->selector[i] = tmp;
- }
- }
-
- /*--- Now the coding tables ---*/
- for (t = 0; t < nGroups; t++) {
- GET_BITS(BZ_X_CODING_1, curr, 5);
- for (i = 0; i < alphaSize; i++) {
- while (True) {
- if (curr < 1 || curr > 20) RETURN(BZ_DATA_ERROR);
- GET_BIT(BZ_X_CODING_2, uc);
- if (uc == 0) break;
- GET_BIT(BZ_X_CODING_3, uc);
- if (uc == 0) curr++; else curr--;
- }
- s->len[t][i] = curr;
- }
- }
-
- /*--- Create the Huffman decoding tables ---*/
- for (t = 0; t < nGroups; t++) {
- minLen = 32;
- maxLen = 0;
- for (i = 0; i < alphaSize; i++) {
- if (s->len[t][i] > maxLen) maxLen = s->len[t][i];
- if (s->len[t][i] < minLen) minLen = s->len[t][i];
- }
- BZ2_hbCreateDecodeTables (
- &(s->limit[t][0]),
- &(s->base[t][0]),
- &(s->perm[t][0]),
- &(s->len[t][0]),
- minLen, maxLen, alphaSize
- );
- s->minLens[t] = minLen;
- }
-
- /*--- Now the MTF values ---*/
-
- EOB = s->nInUse+1;
- nblockMAX = 100000 * s->blockSize100k;
- groupNo = -1;
- groupPos = 0;
-
- for (i = 0; i <= 255; i++) s->unzftab[i] = 0;
-
- /*-- MTF init --*/
- {
- Int32 ii, jj, kk;
- kk = MTFA_SIZE-1;
- for (ii = 256 / MTFL_SIZE - 1; ii >= 0; ii--) {
- for (jj = MTFL_SIZE-1; jj >= 0; jj--) {
- s->mtfa[kk] = (UChar)(ii * MTFL_SIZE + jj);
- kk--;
- }
- s->mtfbase[ii] = kk + 1;
- }
- }
- /*-- end MTF init --*/
-
- nblock = 0;
- GET_MTF_VAL(BZ_X_MTF_1, BZ_X_MTF_2, nextSym);
-
- while (True) {
-
- if (nextSym == EOB) break;
-
- if (nextSym == BZ_RUNA || nextSym == BZ_RUNB) {
-
- es = -1;
- N = 1;
- do {
- /* Check that N doesn't get too big, so that es doesn't
- go negative. The maximum value that can be
- RUNA/RUNB encoded is equal to the block size (post
- the initial RLE), viz, 900k, so bounding N at 2
- million should guard against overflow without
- rejecting any legitimate inputs. */
- if (N >= 2*1024*1024) RETURN(BZ_DATA_ERROR);
- if (nextSym == BZ_RUNA) es = es + (0+1) * N; else
- if (nextSym == BZ_RUNB) es = es + (1+1) * N;
- N = N * 2;
- GET_MTF_VAL(BZ_X_MTF_3, BZ_X_MTF_4, nextSym);
- }
- while (nextSym == BZ_RUNA || nextSym == BZ_RUNB);
-
- es++;
- uc = s->seqToUnseq[ s->mtfa[s->mtfbase[0]] ];
- s->unzftab[uc] += es;
-
- if (s->smallDecompress)
- while (es > 0) {
- if (nblock >= nblockMAX) RETURN(BZ_DATA_ERROR);
- s->ll16[nblock] = (UInt16)uc;
- nblock++;
- es--;
- }
- else
- while (es > 0) {
- if (nblock >= nblockMAX) RETURN(BZ_DATA_ERROR);
- s->tt[nblock] = (UInt32)uc;
- nblock++;
- es--;
- };
-
- continue;
-
- } else {
-
- if (nblock >= nblockMAX) RETURN(BZ_DATA_ERROR);
-
- /*-- uc = MTF ( nextSym-1 ) --*/
- {
- Int32 ii, jj, kk, pp, lno, off;
- UInt32 nn;
- nn = (UInt32)(nextSym - 1);
-
- if (nn < MTFL_SIZE) {
- /* avoid general-case expense */
- pp = s->mtfbase[0];
- uc = s->mtfa[pp+nn];
- while (nn > 3) {
- Int32 z = pp+nn;
- s->mtfa[(z) ] = s->mtfa[(z)-1];
- s->mtfa[(z)-1] = s->mtfa[(z)-2];
- s->mtfa[(z)-2] = s->mtfa[(z)-3];
- s->mtfa[(z)-3] = s->mtfa[(z)-4];
- nn -= 4;
- }
- while (nn > 0) {
- s->mtfa[(pp+nn)] = s->mtfa[(pp+nn)-1]; nn--;
- };
- s->mtfa[pp] = uc;
- } else {
- /* general case */
- lno = nn / MTFL_SIZE;
- off = nn % MTFL_SIZE;
- pp = s->mtfbase[lno] + off;
- uc = s->mtfa[pp];
- while (pp > s->mtfbase[lno]) {
- s->mtfa[pp] = s->mtfa[pp-1]; pp--;
- };
- s->mtfbase[lno]++;
- while (lno > 0) {
- s->mtfbase[lno]--;
- s->mtfa[s->mtfbase[lno]]
- = s->mtfa[s->mtfbase[lno-1] + MTFL_SIZE - 1];
- lno--;
- }
- s->mtfbase[0]--;
- s->mtfa[s->mtfbase[0]] = uc;
- if (s->mtfbase[0] == 0) {
- kk = MTFA_SIZE-1;
- for (ii = 256 / MTFL_SIZE-1; ii >= 0; ii--) {
- for (jj = MTFL_SIZE-1; jj >= 0; jj--) {
- s->mtfa[kk] = s->mtfa[s->mtfbase[ii] + jj];
- kk--;
- }
- s->mtfbase[ii] = kk + 1;
- }
- }
- }
- }
- /*-- end uc = MTF ( nextSym-1 ) --*/
-
- s->unzftab[s->seqToUnseq[uc]]++;
- if (s->smallDecompress)
- s->ll16[nblock] = (UInt16)(s->seqToUnseq[uc]); else
- s->tt[nblock] = (UInt32)(s->seqToUnseq[uc]);
- nblock++;
-
- GET_MTF_VAL(BZ_X_MTF_5, BZ_X_MTF_6, nextSym);
- continue;
- }
- }
-
- /* Now we know what nblock is, we can do a better sanity
- check on s->origPtr.
- */
- if (s->origPtr < 0 || s->origPtr >= nblock)
- RETURN(BZ_DATA_ERROR);
-
- /*-- Set up cftab to facilitate generation of T^(-1) --*/
- /* Check: unzftab entries in range. */
- for (i = 0; i <= 255; i++) {
- if (s->unzftab[i] < 0 || s->unzftab[i] > nblock)
- RETURN(BZ_DATA_ERROR);
- }
- /* Actually generate cftab. */
- s->cftab[0] = 0;
- for (i = 1; i <= 256; i++) s->cftab[i] = s->unzftab[i-1];
- for (i = 1; i <= 256; i++) s->cftab[i] += s->cftab[i-1];
- /* Check: cftab entries in range. */
- for (i = 0; i <= 256; i++) {
- if (s->cftab[i] < 0 || s->cftab[i] > nblock) {
- /* s->cftab[i] can legitimately be == nblock */
- RETURN(BZ_DATA_ERROR);
- }
- }
- /* Check: cftab entries non-descending. */
- for (i = 1; i <= 256; i++) {
- if (s->cftab[i-1] > s->cftab[i]) {
- RETURN(BZ_DATA_ERROR);
- }
- }
-
- s->state_out_len = 0;
- s->state_out_ch = 0;
- BZ_INITIALISE_CRC ( s->calculatedBlockCRC );
- s->state = BZ_X_OUTPUT;
- if (s->verbosity >= 2) VPrintf0 ( "rt+rld" );
-
- if (s->smallDecompress) {
-
- /*-- Make a copy of cftab, used in generation of T --*/
- for (i = 0; i <= 256; i++) s->cftabCopy[i] = s->cftab[i];
-
- /*-- compute the T vector --*/
- for (i = 0; i < nblock; i++) {
- uc = (UChar)(s->ll16[i]);
- SET_LL(i, s->cftabCopy[uc]);
- s->cftabCopy[uc]++;
- }
-
- /*-- Compute T^(-1) by pointer reversal on T --*/
- i = s->origPtr;
- j = GET_LL(i);
- do {
- Int32 tmp = GET_LL(j);
- SET_LL(j, i);
- i = j;
- j = tmp;
- }
- while (i != s->origPtr);
-
- s->tPos = s->origPtr;
- s->nblock_used = 0;
- if (s->blockRandomised) {
- BZ_RAND_INIT_MASK;
- BZ_GET_SMALL(s->k0); s->nblock_used++;
- BZ_RAND_UPD_MASK; s->k0 ^= BZ_RAND_MASK;
- } else {
- BZ_GET_SMALL(s->k0); s->nblock_used++;
- }
-
- } else {
-
- /*-- compute the T^(-1) vector --*/
- for (i = 0; i < nblock; i++) {
- uc = (UChar)(s->tt[i] & 0xff);
- s->tt[s->cftab[uc]] |= (i << 8);
- s->cftab[uc]++;
- }
-
- s->tPos = s->tt[s->origPtr] >> 8;
- s->nblock_used = 0;
- if (s->blockRandomised) {
- BZ_RAND_INIT_MASK;
- BZ_GET_FAST(s->k0); s->nblock_used++;
- BZ_RAND_UPD_MASK; s->k0 ^= BZ_RAND_MASK;
- } else {
- BZ_GET_FAST(s->k0); s->nblock_used++;
- }
-
- }
-
- RETURN(BZ_OK);
-
-
-
- endhdr_2:
-
- GET_UCHAR(BZ_X_ENDHDR_2, uc);
- if (uc != 0x72) RETURN(BZ_DATA_ERROR);
- GET_UCHAR(BZ_X_ENDHDR_3, uc);
- if (uc != 0x45) RETURN(BZ_DATA_ERROR);
- GET_UCHAR(BZ_X_ENDHDR_4, uc);
- if (uc != 0x38) RETURN(BZ_DATA_ERROR);
- GET_UCHAR(BZ_X_ENDHDR_5, uc);
- if (uc != 0x50) RETURN(BZ_DATA_ERROR);
- GET_UCHAR(BZ_X_ENDHDR_6, uc);
- if (uc != 0x90) RETURN(BZ_DATA_ERROR);
-
- s->storedCombinedCRC = 0;
- GET_UCHAR(BZ_X_CCRC_1, uc);
- s->storedCombinedCRC = (s->storedCombinedCRC << 8) | ((UInt32)uc);
- GET_UCHAR(BZ_X_CCRC_2, uc);
- s->storedCombinedCRC = (s->storedCombinedCRC << 8) | ((UInt32)uc);
- GET_UCHAR(BZ_X_CCRC_3, uc);
- s->storedCombinedCRC = (s->storedCombinedCRC << 8) | ((UInt32)uc);
- GET_UCHAR(BZ_X_CCRC_4, uc);
- s->storedCombinedCRC = (s->storedCombinedCRC << 8) | ((UInt32)uc);
-
- s->state = BZ_X_IDLE;
- RETURN(BZ_STREAM_END);
-
- default: AssertH ( False, 4001 );
- }
-
- AssertH ( False, 4002 );
-
- save_state_and_return:
-
- s->save_i = i;
- s->save_j = j;
- s->save_t = t;
- s->save_alphaSize = alphaSize;
- s->save_nGroups = nGroups;
- s->save_nSelectors = nSelectors;
- s->save_EOB = EOB;
- s->save_groupNo = groupNo;
- s->save_groupPos = groupPos;
- s->save_nextSym = nextSym;
- s->save_nblockMAX = nblockMAX;
- s->save_nblock = nblock;
- s->save_es = es;
- s->save_N = N;
- s->save_curr = curr;
- s->save_zt = zt;
- s->save_zn = zn;
- s->save_zvec = zvec;
- s->save_zj = zj;
- s->save_gSel = gSel;
- s->save_gMinlen = gMinlen;
- s->save_gLimit = gLimit;
- s->save_gBase = gBase;
- s->save_gPerm = gPerm;
-
- return retVal;
-}
-
-
-/*-------------------------------------------------------------*/
-/*--- end decompress.c ---*/
-/*-------------------------------------------------------------*/
diff --git a/third-party/bzip2/dlltest.c b/third-party/bzip2/dlltest.c
deleted file mode 100644
index 03fa146..0000000
--- a/third-party/bzip2/dlltest.c
+++ /dev/null
@@ -1,175 +0,0 @@
-/*
- minibz2
- libbz2.dll test program.
- by Yoshioka Tsuneo (tsuneo at rr.iij4u.or.jp)
- This file is Public Domain. Welcome any email to me.
-
- usage: minibz2 [-d] [-{1,2,..9}] [[srcfilename] destfilename]
-*/
-
-#define BZ_IMPORT
-#include <stdio.h>
-#include <stdlib.h>
-#include "bzlib.h"
-#ifdef _WIN32
-#include <io.h>
-#endif
-
-
-#ifdef _WIN32
-
-#define BZ2_LIBNAME "libbz2-1.0.2.DLL"
-
-#include <windows.h>
-static int BZ2DLLLoaded = 0;
-static HINSTANCE BZ2DLLhLib;
-int BZ2DLLLoadLibrary(void)
-{
- HINSTANCE hLib;
-
- if(BZ2DLLLoaded==1){return 0;}
- hLib=LoadLibrary(BZ2_LIBNAME);
- if(hLib == NULL){
- fprintf(stderr,"Can't load %s\n",BZ2_LIBNAME);
- return -1;
- }
- BZ2_bzlibVersion=GetProcAddress(hLib,"BZ2_bzlibVersion");
- BZ2_bzopen=GetProcAddress(hLib,"BZ2_bzopen");
- BZ2_bzdopen=GetProcAddress(hLib,"BZ2_bzdopen");
- BZ2_bzread=GetProcAddress(hLib,"BZ2_bzread");
- BZ2_bzwrite=GetProcAddress(hLib,"BZ2_bzwrite");
- BZ2_bzflush=GetProcAddress(hLib,"BZ2_bzflush");
- BZ2_bzclose=GetProcAddress(hLib,"BZ2_bzclose");
- BZ2_bzerror=GetProcAddress(hLib,"BZ2_bzerror");
-
- if (!BZ2_bzlibVersion || !BZ2_bzopen || !BZ2_bzdopen
- || !BZ2_bzread || !BZ2_bzwrite || !BZ2_bzflush
- || !BZ2_bzclose || !BZ2_bzerror) {
- fprintf(stderr,"GetProcAddress failed.\n");
- return -1;
- }
- BZ2DLLLoaded=1;
- BZ2DLLhLib=hLib;
- return 0;
-
-}
-int BZ2DLLFreeLibrary(void)
-{
- if(BZ2DLLLoaded==0){return 0;}
- FreeLibrary(BZ2DLLhLib);
- BZ2DLLLoaded=0;
-}
-#endif /* WIN32 */
-
-void usage(void)
-{
- puts("usage: minibz2 [-d] [-{1,2,..9}] [[srcfilename] destfilename]");
-}
-
-int main(int argc,char *argv[])
-{
- int decompress = 0;
- int level = 9;
- char *fn_r = NULL;
- char *fn_w = NULL;
-
-#ifdef _WIN32
- if(BZ2DLLLoadLibrary()<0){
- fprintf(stderr,"Loading of %s failed. Giving up.\n", BZ2_LIBNAME);
- exit(1);
- }
- printf("Loading of %s succeeded. Library version is %s.\n",
- BZ2_LIBNAME, BZ2_bzlibVersion() );
-#endif
- while(++argv,--argc){
- if(**argv =='-' || **argv=='/'){
- char *p;
-
- for(p=*argv+1;*p;p++){
- if(*p=='d'){
- decompress = 1;
- }else if('1'<=*p && *p<='9'){
- level = *p - '0';
- }else{
- usage();
- exit(1);
- }
- }
- }else{
- break;
- }
- }
- if(argc>=1){
- fn_r = *argv;
- argc--;argv++;
- }else{
- fn_r = NULL;
- }
- if(argc>=1){
- fn_w = *argv;
- argc--;argv++;
- }else{
- fn_w = NULL;
- }
- {
- int len;
- char buff[0x1000];
- char mode[10];
-
- if(decompress){
- BZFILE *BZ2fp_r = NULL;
- FILE *fp_w = NULL;
-
- if(fn_w){
- if((fp_w = fopen(fn_w,"wb"))==NULL){
- printf("can't open [%s]\n",fn_w);
- perror("reason:");
- exit(1);
- }
- }else{
- fp_w = stdout;
- }
- if((fn_r == NULL && (BZ2fp_r = BZ2_bzdopen(fileno(stdin),"rb"))==NULL)
- || (fn_r != NULL && (BZ2fp_r = BZ2_bzopen(fn_r,"rb"))==NULL)){
- printf("can't bz2openstream\n");
- exit(1);
- }
- while((len=BZ2_bzread(BZ2fp_r,buff,0x1000))>0){
- fwrite(buff,1,len,fp_w);
- }
- BZ2_bzclose(BZ2fp_r);
- if(fp_w != stdout) fclose(fp_w);
- }else{
- BZFILE *BZ2fp_w = NULL;
- FILE *fp_r = NULL;
-
- if(fn_r){
- if((fp_r = fopen(fn_r,"rb"))==NULL){
- printf("can't open [%s]\n",fn_r);
- perror("reason:");
- exit(1);
- }
- }else{
- fp_r = stdin;
- }
- mode[0]='w';
- mode[1] = '0' + level;
- mode[2] = '\0';
-
- if((fn_w == NULL && (BZ2fp_w = BZ2_bzdopen(fileno(stdout),mode))==NULL)
- || (fn_w !=NULL && (BZ2fp_w = BZ2_bzopen(fn_w,mode))==NULL)){
- printf("can't bz2openstream\n");
- exit(1);
- }
- while((len=fread(buff,1,0x1000,fp_r))>0){
- BZ2_bzwrite(BZ2fp_w,buff,len);
- }
- BZ2_bzclose(BZ2fp_w);
- if(fp_r!=stdin)fclose(fp_r);
- }
- }
-#ifdef _WIN32
- BZ2DLLFreeLibrary();
-#endif
- return 0;
-}
diff --git a/third-party/bzip2/dlltest.dsp b/third-party/bzip2/dlltest.dsp
deleted file mode 100644
index 4b1615e..0000000
--- a/third-party/bzip2/dlltest.dsp
+++ /dev/null
@@ -1,93 +0,0 @@
-# Microsoft Developer Studio Project File - Name="dlltest" - Package Owner=<4>
-# Microsoft Developer Studio Generated Build File, Format Version 5.00
-# ** �ҏW���Ȃ��ł������� **
-
-# TARGTYPE "Win32 (x86) Console Application" 0x0103
-
-CFG=dlltest - Win32 Debug
-!MESSAGE ����͗L����Ҳ�̧�قł͂���܂���B ������ۼު�Ă�����ނ��邽�߂ɂ� NMAKE ��g�p���Ă��������B
-!MESSAGE [Ҳ�̧�ق̴���߰�] ����ނ�g�p���Ď��s���Ă�������
-!MESSAGE
-!MESSAGE NMAKE /f "dlltest.mak".
-!MESSAGE
-!MESSAGE NMAKE �̎��s���ɍ\����w��ł��܂�
-!MESSAGE ����� ײݏ��ϸۂ̐ݒ���`���܂��B��:
-!MESSAGE
-!MESSAGE NMAKE /f "dlltest.mak" CFG="dlltest - Win32 Debug"
-!MESSAGE
-!MESSAGE �I��”\������� Ӱ��:
-!MESSAGE
-!MESSAGE "dlltest - Win32 Release" ("Win32 (x86) Console Application" �p)
-!MESSAGE "dlltest - Win32 Debug" ("Win32 (x86) Console Application" �p)
-!MESSAGE
-
-# Begin Project
-# PROP Scc_ProjName ""
-# PROP Scc_LocalPath ""
-CPP=cl.exe
-RSC=rc.exe
-
-!IF "$(CFG)" == "dlltest - Win32 Release"
-
-# PROP BASE Use_MFC 0
-# PROP BASE Use_Debug_Libraries 0
-# PROP BASE Output_Dir "Release"
-# PROP BASE Intermediate_Dir "Release"
-# PROP BASE Target_Dir ""
-# PROP Use_MFC 0
-# PROP Use_Debug_Libraries 0
-# PROP Output_Dir "Release"
-# PROP Intermediate_Dir "Release"
-# PROP Ignore_Export_Lib 0
-# PROP Target_Dir ""
-# ADD BASE CPP /nologo /W3 /GX /O2 /D "WIN32" /D "NDEBUG" /D "_CONSOLE" /D "_MBCS" /YX /FD /c
-# ADD CPP /nologo /W3 /GX /O2 /D "WIN32" /D "NDEBUG" /D "_CONSOLE" /D "_MBCS" /YX /FD /c
-# ADD BASE RSC /l 0x411 /d "NDEBUG"
-# ADD RSC /l 0x411 /d "NDEBUG"
-BSC32=bscmake.exe
-# ADD BASE BSC32 /nologo
-# ADD BSC32 /nologo
-LINK32=link.exe
-# ADD BASE LINK32 kernel32.lib user32.lib gdi32.lib winspool.lib comdlg32.lib advapi32.lib shell32.lib ole32.lib oleaut32.lib uuid.lib odbc32.lib odbccp32.lib /nologo /subsystem:console /machine:I386
-# ADD LINK32 kernel32.lib user32.lib gdi32.lib winspool.lib comdlg32.lib advapi32.lib shell32.lib ole32.lib oleaut32.lib uuid.lib odbc32.lib odbccp32.lib /nologo /subsystem:console /machine:I386 /out:"minibz2.exe"
-
-!ELSEIF "$(CFG)" == "dlltest - Win32 Debug"
-
-# PROP BASE Use_MFC 0
-# PROP BASE Use_Debug_Libraries 1
-# PROP BASE Output_Dir "dlltest_"
-# PROP BASE Intermediate_Dir "dlltest_"
-# PROP BASE Target_Dir ""
-# PROP Use_MFC 0
-# PROP Use_Debug_Libraries 1
-# PROP Output_Dir "dlltest_"
-# PROP Intermediate_Dir "dlltest_"
-# PROP Ignore_Export_Lib 0
-# PROP Target_Dir ""
-# ADD BASE CPP /nologo /W3 /Gm /GX /Zi /Od /D "WIN32" /D "_DEBUG" /D "_CONSOLE" /D "_MBCS" /YX /FD /c
-# ADD CPP /nologo /W3 /Gm /GX /Zi /Od /D "WIN32" /D "_DEBUG" /D "_CONSOLE" /D "_MBCS" /YX /FD /c
-# ADD BASE RSC /l 0x411 /d "_DEBUG"
-# ADD RSC /l 0x411 /d "_DEBUG"
-BSC32=bscmake.exe
-# ADD BASE BSC32 /nologo
-# ADD BSC32 /nologo
-LINK32=link.exe
-# ADD BASE LINK32 kernel32.lib user32.lib gdi32.lib winspool.lib comdlg32.lib advapi32.lib shell32.lib ole32.lib oleaut32.lib uuid.lib odbc32.lib odbccp32.lib /nologo /subsystem:console /debug /machine:I386 /pdbtype:sept
-# ADD LINK32 kernel32.lib user32.lib gdi32.lib winspool.lib comdlg32.lib advapi32.lib shell32.lib ole32.lib oleaut32.lib uuid.lib odbc32.lib odbccp32.lib /nologo /subsystem:console /debug /machine:I386 /out:"minibz2.exe" /pdbtype:sept
-
-!ENDIF
-
-# Begin Target
-
-# Name "dlltest - Win32 Release"
-# Name "dlltest - Win32 Debug"
-# Begin Source File
-
-SOURCE=.\bzlib.h
-# End Source File
-# Begin Source File
-
-SOURCE=.\dlltest.c
-# End Source File
-# End Target
-# End Project
diff --git a/third-party/bzip2/entities.xml b/third-party/bzip2/entities.xml
deleted file mode 100644
index 4b28f34..0000000
--- a/third-party/bzip2/entities.xml
+++ /dev/null
@@ -1,9 +0,0 @@
-<!-- misc. strings -->
-<!ENTITY bz-url "http://www.bzip.org">
-<!ENTITY bz-email "jseward at bzip.org">
-<!ENTITY bz-lifespan "1996-2010">
-
-<!ENTITY bz-version "1.0.6">
-<!ENTITY bz-date "6 September 2010">
-
-<!ENTITY manual-title "bzip2 Manual">
diff --git a/third-party/bzip2/format.pl b/third-party/bzip2/format.pl
deleted file mode 100755
index f169fd9..0000000
--- a/third-party/bzip2/format.pl
+++ /dev/null
@@ -1,68 +0,0 @@
-#!/usr/bin/perl -w
-#
-# ------------------------------------------------------------------
-# This file is part of bzip2/libbzip2, a program and library for
-# lossless, block-sorting data compression.
-#
-# bzip2/libbzip2 version 1.0.6 of 6 September 2010
-# Copyright (C) 1996-2010 Julian Seward <jseward at bzip.org>
-#
-# Please read the WARNING, DISCLAIMER and PATENTS sections in the
-# README file.
-#
-# This program is released under the terms of the license contained
-# in the file LICENSE.
-# ------------------------------------------------------------------
-#
-use strict;
-
-# get command line values:
-if ( $#ARGV !=1 ) {
- die "Usage: $0 xml_infile xml_outfile\n";
-}
-
-my $infile = shift;
-# check infile exists
-die "Can't find file \"$infile\""
- unless -f $infile;
-# check we can read infile
-if (! -r $infile) {
- die "Can't read input $infile\n";
-}
-# check we can open infile
-open( INFILE,"<$infile" ) or
- die "Can't input $infile $!";
-
-#my $outfile = 'fmt-manual.xml';
-my $outfile = shift;
-#print "Infile: $infile, Outfile: $outfile\n";
-# check we can write to outfile
-open( OUTFILE,">$outfile" ) or
- die "Can't output $outfile $! for writing";
-
-my ($prev, $curr, $str);
-$prev = ''; $curr = '';
-while ( <INFILE> ) {
-
- print OUTFILE $prev;
- $prev = $curr;
- $curr = $_;
- $str = '';
-
- if ( $prev =~ /<programlisting>$|<screen>$/ ) {
- chomp $prev;
- $curr = join( '', $prev, "<![CDATA[", $curr );
- $prev = '';
- next;
- }
- elsif ( $curr =~ /<\/programlisting>|<\/screen>/ ) {
- chomp $prev;
- $curr = join( '', $prev, "]]>", $curr );
- $prev = '';
- next;
- }
-}
-print OUTFILE $curr;
-close INFILE;
-close OUTFILE;
-exit;
diff --git a/third-party/bzip2/huffman.c b/third-party/bzip2/huffman.c
deleted file mode 100644
index 2283fdb..0000000
--- a/third-party/bzip2/huffman.c
+++ /dev/null
@@ -1,205 +0,0 @@
-
-/*-------------------------------------------------------------*/
-/*--- Huffman coding low-level stuff ---*/
-/*--- huffman.c ---*/
-/*-------------------------------------------------------------*/
-
-/* ------------------------------------------------------------------
- This file is part of bzip2/libbzip2, a program and library for
- lossless, block-sorting data compression.
-
- bzip2/libbzip2 version 1.0.6 of 6 September 2010
- Copyright (C) 1996-2010 Julian Seward <jseward at bzip.org>
-
- Please read the WARNING, DISCLAIMER and PATENTS sections in the
- README file.
-
- This program is released under the terms of the license contained
- in the file LICENSE.
- ------------------------------------------------------------------ */
-
-
-#include "bzlib_private.h"
-
-/*---------------------------------------------------*/
-#define WEIGHTOF(zz0) ((zz0) & 0xffffff00)
-#define DEPTHOF(zz1) ((zz1) & 0x000000ff)
-#define MYMAX(zz2,zz3) ((zz2) > (zz3) ? (zz2) : (zz3))
-
-#define ADDWEIGHTS(zw1,zw2) \
- (WEIGHTOF(zw1)+WEIGHTOF(zw2)) | \
- (1 + MYMAX(DEPTHOF(zw1),DEPTHOF(zw2)))
-
-#define UPHEAP(z) \
-{ \
- Int32 zz, tmp; \
- zz = z; tmp = heap[zz]; \
- while (weight[tmp] < weight[heap[zz >> 1]]) { \
- heap[zz] = heap[zz >> 1]; \
- zz >>= 1; \
- } \
- heap[zz] = tmp; \
-}
-
-#define DOWNHEAP(z) \
-{ \
- Int32 zz, yy, tmp; \
- zz = z; tmp = heap[zz]; \
- while (True) { \
- yy = zz << 1; \
- if (yy > nHeap) break; \
- if (yy < nHeap && \
- weight[heap[yy+1]] < weight[heap[yy]]) \
- yy++; \
- if (weight[tmp] < weight[heap[yy]]) break; \
- heap[zz] = heap[yy]; \
- zz = yy; \
- } \
- heap[zz] = tmp; \
-}
-
-
-/*---------------------------------------------------*/
-void BZ2_hbMakeCodeLengths ( UChar *len,
- Int32 *freq,
- Int32 alphaSize,
- Int32 maxLen )
-{
- /*--
- Nodes and heap entries run from 1. Entry 0
- for both the heap and nodes is a sentinel.
- --*/
- Int32 nNodes, nHeap, n1, n2, i, j, k;
- Bool tooLong;
-
- Int32 heap [ BZ_MAX_ALPHA_SIZE + 2 ];
- Int32 weight [ BZ_MAX_ALPHA_SIZE * 2 ];
- Int32 parent [ BZ_MAX_ALPHA_SIZE * 2 ];
-
- for (i = 0; i < alphaSize; i++)
- weight[i+1] = (freq[i] == 0 ? 1 : freq[i]) << 8;
-
- while (True) {
-
- nNodes = alphaSize;
- nHeap = 0;
-
- heap[0] = 0;
- weight[0] = 0;
- parent[0] = -2;
-
- for (i = 1; i <= alphaSize; i++) {
- parent[i] = -1;
- nHeap++;
- heap[nHeap] = i;
- UPHEAP(nHeap);
- }
-
- AssertH( nHeap < (BZ_MAX_ALPHA_SIZE+2), 2001 );
-
- while (nHeap > 1) {
- n1 = heap[1]; heap[1] = heap[nHeap]; nHeap--; DOWNHEAP(1);
- n2 = heap[1]; heap[1] = heap[nHeap]; nHeap--; DOWNHEAP(1);
- nNodes++;
- parent[n1] = parent[n2] = nNodes;
- weight[nNodes] = ADDWEIGHTS(weight[n1], weight[n2]);
- parent[nNodes] = -1;
- nHeap++;
- heap[nHeap] = nNodes;
- UPHEAP(nHeap);
- }
-
- AssertH( nNodes < (BZ_MAX_ALPHA_SIZE * 2), 2002 );
-
- tooLong = False;
- for (i = 1; i <= alphaSize; i++) {
- j = 0;
- k = i;
- while (parent[k] >= 0) { k = parent[k]; j++; }
- len[i-1] = j;
- if (j > maxLen) tooLong = True;
- }
-
- if (! tooLong) break;
-
- /* 17 Oct 04: keep-going condition for the following loop used
- to be 'i < alphaSize', which missed the last element,
- theoretically leading to the possibility of the compressor
- looping. However, this count-scaling step is only needed if
- one of the generated Huffman code words is longer than
- maxLen, which up to and including version 1.0.2 was 20 bits,
- which is extremely unlikely. In version 1.0.3 maxLen was
- changed to 17 bits, which has minimal effect on compression
- ratio, but does mean this scaling step is used from time to
- time, enough to verify that it works.
-
- This means that bzip2-1.0.3 and later will only produce
- Huffman codes with a maximum length of 17 bits. However, in
- order to preserve backwards compatibility with bitstreams
- produced by versions pre-1.0.3, the decompressor must still
- handle lengths of up to 20. */
-
- for (i = 1; i <= alphaSize; i++) {
- j = weight[i] >> 8;
- j = 1 + (j / 2);
- weight[i] = j << 8;
- }
- }
-}
-
-
-/*---------------------------------------------------*/
-void BZ2_hbAssignCodes ( Int32 *code,
- UChar *length,
- Int32 minLen,
- Int32 maxLen,
- Int32 alphaSize )
-{
- Int32 n, vec, i;
-
- vec = 0;
- for (n = minLen; n <= maxLen; n++) {
- for (i = 0; i < alphaSize; i++)
- if (length[i] == n) { code[i] = vec; vec++; };
- vec <<= 1;
- }
-}
-
-
-/*---------------------------------------------------*/
-void BZ2_hbCreateDecodeTables ( Int32 *limit,
- Int32 *base,
- Int32 *perm,
- UChar *length,
- Int32 minLen,
- Int32 maxLen,
- Int32 alphaSize )
-{
- Int32 pp, i, j, vec;
-
- pp = 0;
- for (i = minLen; i <= maxLen; i++)
- for (j = 0; j < alphaSize; j++)
- if (length[j] == i) { perm[pp] = j; pp++; };
-
- for (i = 0; i < BZ_MAX_CODE_LEN; i++) base[i] = 0;
- for (i = 0; i < alphaSize; i++) base[length[i]+1]++;
-
- for (i = 1; i < BZ_MAX_CODE_LEN; i++) base[i] += base[i-1];
-
- for (i = 0; i < BZ_MAX_CODE_LEN; i++) limit[i] = 0;
- vec = 0;
-
- for (i = minLen; i <= maxLen; i++) {
- vec += (base[i+1] - base[i]);
- limit[i] = vec-1;
- vec <<= 1;
- }
- for (i = minLen + 1; i <= maxLen; i++)
- base[i] = ((limit[i-1] + 1) << 1) - base[i];
-}
-
-
-/*-------------------------------------------------------------*/
-/*--- end huffman.c ---*/
-/*-------------------------------------------------------------*/
diff --git a/third-party/bzip2/libbz2.def b/third-party/bzip2/libbz2.def
deleted file mode 100644
index 2dc0dd8..0000000
--- a/third-party/bzip2/libbz2.def
+++ /dev/null
@@ -1,27 +0,0 @@
-LIBRARY LIBBZ2
-DESCRIPTION "libbzip2: library for data compression"
-EXPORTS
- BZ2_bzCompressInit
- BZ2_bzCompress
- BZ2_bzCompressEnd
- BZ2_bzDecompressInit
- BZ2_bzDecompress
- BZ2_bzDecompressEnd
- BZ2_bzReadOpen
- BZ2_bzReadClose
- BZ2_bzReadGetUnused
- BZ2_bzRead
- BZ2_bzWriteOpen
- BZ2_bzWrite
- BZ2_bzWriteClose
- BZ2_bzWriteClose64
- BZ2_bzBuffToBuffCompress
- BZ2_bzBuffToBuffDecompress
- BZ2_bzlibVersion
- BZ2_bzopen
- BZ2_bzdopen
- BZ2_bzread
- BZ2_bzwrite
- BZ2_bzflush
- BZ2_bzclose
- BZ2_bzerror
diff --git a/third-party/bzip2/libbz2.dsp b/third-party/bzip2/libbz2.dsp
deleted file mode 100644
index a21a20f..0000000
--- a/third-party/bzip2/libbz2.dsp
+++ /dev/null
@@ -1,130 +0,0 @@
-# Microsoft Developer Studio Project File - Name="libbz2" - Package Owner=<4>
-# Microsoft Developer Studio Generated Build File, Format Version 5.00
-# ** �ҏW���Ȃ��ł������� **
-
-# TARGTYPE "Win32 (x86) Dynamic-Link Library" 0x0102
-
-CFG=libbz2 - Win32 Debug
-!MESSAGE ����͗L����Ҳ�̧�قł͂���܂���B ������ۼު�Ă�����ނ��邽�߂ɂ� NMAKE ��g�p���Ă��������B
-!MESSAGE [Ҳ�̧�ق̴���߰�] ����ނ�g�p���Ď��s���Ă�������
-!MESSAGE
-!MESSAGE NMAKE /f "libbz2.mak".
-!MESSAGE
-!MESSAGE NMAKE �̎��s���ɍ\����w��ł��܂�
-!MESSAGE ����� ײݏ��ϸۂ̐ݒ���`���܂��B��:
-!MESSAGE
-!MESSAGE NMAKE /f "libbz2.mak" CFG="libbz2 - Win32 Debug"
-!MESSAGE
-!MESSAGE �I��”\������� Ӱ��:
-!MESSAGE
-!MESSAGE "libbz2 - Win32 Release" ("Win32 (x86) Dynamic-Link Library" �p)
-!MESSAGE "libbz2 - Win32 Debug" ("Win32 (x86) Dynamic-Link Library" �p)
-!MESSAGE
-
-# Begin Project
-# PROP Scc_ProjName ""
-# PROP Scc_LocalPath ""
-CPP=cl.exe
-MTL=midl.exe
-RSC=rc.exe
-
-!IF "$(CFG)" == "libbz2 - Win32 Release"
-
-# PROP BASE Use_MFC 0
-# PROP BASE Use_Debug_Libraries 0
-# PROP BASE Output_Dir "Release"
-# PROP BASE Intermediate_Dir "Release"
-# PROP BASE Target_Dir ""
-# PROP Use_MFC 0
-# PROP Use_Debug_Libraries 0
-# PROP Output_Dir "Release"
-# PROP Intermediate_Dir "Release"
-# PROP Ignore_Export_Lib 0
-# PROP Target_Dir ""
-# ADD BASE CPP /nologo /MT /W3 /GX /O2 /D "WIN32" /D "NDEBUG" /D "_WINDOWS" /YX /FD /c
-# ADD CPP /nologo /MT /W3 /GX /O2 /D "WIN32" /D "NDEBUG" /D "_WINDOWS" /YX /FD /c
-# ADD BASE MTL /nologo /D "NDEBUG" /mktyplib203 /o NUL /win32
-# ADD MTL /nologo /D "NDEBUG" /mktyplib203 /o NUL /win32
-# ADD BASE RSC /l 0x411 /d "NDEBUG"
-# ADD RSC /l 0x411 /d "NDEBUG"
-BSC32=bscmake.exe
-# ADD BASE BSC32 /nologo
-# ADD BSC32 /nologo
-LINK32=link.exe
-# ADD BASE LINK32 kernel32.lib user32.lib gdi32.lib winspool.lib comdlg32.lib advapi32.lib shell32.lib ole32.lib oleaut32.lib uuid.lib odbc32.lib odbccp32.lib /nologo /subsystem:windows /dll /machine:I386
-# ADD LINK32 kernel32.lib user32.lib gdi32.lib winspool.lib comdlg32.lib advapi32.lib shell32.lib ole32.lib oleaut32.lib uuid.lib odbc32.lib odbccp32.lib /nologo /subsystem:windows /dll /machine:I386 /out:"libbz2.dll"
-
-!ELSEIF "$(CFG)" == "libbz2 - Win32 Debug"
-
-# PROP BASE Use_MFC 0
-# PROP BASE Use_Debug_Libraries 1
-# PROP BASE Output_Dir "Debug"
-# PROP BASE Intermediate_Dir "Debug"
-# PROP BASE Target_Dir ""
-# PROP Use_MFC 0
-# PROP Use_Debug_Libraries 1
-# PROP Output_Dir "Debug"
-# PROP Intermediate_Dir "Debug"
-# PROP Ignore_Export_Lib 0
-# PROP Target_Dir ""
-# ADD BASE CPP /nologo /MTd /W3 /Gm /GX /Zi /Od /D "WIN32" /D "_DEBUG" /D "_WINDOWS" /YX /FD /c
-# ADD CPP /nologo /MTd /W3 /Gm /GX /Zi /Od /D "WIN32" /D "_DEBUG" /D "_WINDOWS" /YX /FD /c
-# ADD BASE MTL /nologo /D "_DEBUG" /mktyplib203 /o NUL /win32
-# ADD MTL /nologo /D "_DEBUG" /mktyplib203 /o NUL /win32
-# ADD BASE RSC /l 0x411 /d "_DEBUG"
-# ADD RSC /l 0x411 /d "_DEBUG"
-BSC32=bscmake.exe
-# ADD BASE BSC32 /nologo
-# ADD BSC32 /nologo
-LINK32=link.exe
-# ADD BASE LINK32 kernel32.lib user32.lib gdi32.lib winspool.lib comdlg32.lib advapi32.lib shell32.lib ole32.lib oleaut32.lib uuid.lib odbc32.lib odbccp32.lib /nologo /subsystem:windows /dll /debug /machine:I386 /pdbtype:sept
-# ADD LINK32 kernel32.lib user32.lib gdi32.lib winspool.lib comdlg32.lib advapi32.lib shell32.lib ole32.lib oleaut32.lib uuid.lib odbc32.lib odbccp32.lib /nologo /subsystem:windows /dll /debug /machine:I386 /out:"libbz2.dll" /pdbtype:sept
-
-!ENDIF
-
-# Begin Target
-
-# Name "libbz2 - Win32 Release"
-# Name "libbz2 - Win32 Debug"
-# Begin Source File
-
-SOURCE=.\blocksort.c
-# End Source File
-# Begin Source File
-
-SOURCE=.\bzlib.c
-# End Source File
-# Begin Source File
-
-SOURCE=.\bzlib.h
-# End Source File
-# Begin Source File
-
-SOURCE=.\bzlib_private.h
-# End Source File
-# Begin Source File
-
-SOURCE=.\compress.c
-# End Source File
-# Begin Source File
-
-SOURCE=.\crctable.c
-# End Source File
-# Begin Source File
-
-SOURCE=.\decompress.c
-# End Source File
-# Begin Source File
-
-SOURCE=.\huffman.c
-# End Source File
-# Begin Source File
-
-SOURCE=.\libbz2.def
-# End Source File
-# Begin Source File
-
-SOURCE=.\randtable.c
-# End Source File
-# End Target
-# End Project
diff --git a/third-party/bzip2/makefile.msc b/third-party/bzip2/makefile.msc
deleted file mode 100644
index 799a18a..0000000
--- a/third-party/bzip2/makefile.msc
+++ /dev/null
@@ -1,63 +0,0 @@
-# Makefile for Microsoft Visual C++ 6.0
-# usage: nmake -f makefile.msc
-# K.M. Syring (syring at gsf.de)
-# Fixed up by JRS for bzip2-0.9.5d release.
-
-CC=cl
-CFLAGS= -DWIN32 -MD -Ox -D_FILE_OFFSET_BITS=64 -nologo
-
-OBJS= blocksort.obj \
- huffman.obj \
- crctable.obj \
- randtable.obj \
- compress.obj \
- decompress.obj \
- bzlib.obj
-
-all: lib bzip2 test
-
-bzip2: lib
- $(CC) $(CFLAGS) -o bzip2 bzip2.c libbz2.lib setargv.obj
- $(CC) $(CFLAGS) -o bzip2recover bzip2recover.c
-
-lib: $(OBJS)
- lib /out:libbz2.lib $(OBJS)
-
-test: bzip2
- type words1
- .\\bzip2 -1 < sample1.ref > sample1.rb2
- .\\bzip2 -2 < sample2.ref > sample2.rb2
- .\\bzip2 -3 < sample3.ref > sample3.rb2
- .\\bzip2 -d < sample1.bz2 > sample1.tst
- .\\bzip2 -d < sample2.bz2 > sample2.tst
- .\\bzip2 -ds < sample3.bz2 > sample3.tst
- @echo All six of the fc's should find no differences.
- @echo If fc finds an error on sample3.bz2, this could be
- @echo because WinZip's 'TAR file smart CR/LF conversion'
- @echo is too clever for its own good. Disable this option.
- @echo The correct size for sample3.ref is 120,244. If it
- @echo is 150,251, WinZip has messed it up.
- fc sample1.bz2 sample1.rb2
- fc sample2.bz2 sample2.rb2
- fc sample3.bz2 sample3.rb2
- fc sample1.tst sample1.ref
- fc sample2.tst sample2.ref
- fc sample3.tst sample3.ref
-
-
-
-clean:
- del *.obj
- del libbz2.lib
- del bzip2.exe
- del bzip2recover.exe
- del sample1.rb2
- del sample2.rb2
- del sample3.rb2
- del sample1.tst
- del sample2.tst
- del sample3.tst
-
-.c.obj:
- $(CC) $(CFLAGS) -c $*.c -o $*.obj
-
diff --git a/third-party/bzip2/manual.html b/third-party/bzip2/manual.html
deleted file mode 100644
index f59427f..0000000
--- a/third-party/bzip2/manual.html
+++ /dev/null
@@ -1,2540 +0,0 @@
-<html>
-<head>
-<meta http-equiv="Content-Type" content="text/html; charset=ISO-8859-1">
-<title>bzip2 and libbzip2, version 1.0.6</title>
-<meta name="generator" content="DocBook XSL Stylesheets V1.75.2">
-<style type="text/css" media="screen">/* Colours:
-#74240f dark brown h1, h2, h3, h4
-#336699 medium blue links
-#339999 turquoise link hover colour
-#202020 almost black general text
-#761596 purple md5sum text
-#626262 dark gray pre border
-#eeeeee very light gray pre background
-#f2f2f9 very light blue nav table background
-#3366cc medium blue nav table border
-*/
-
-a, a:link, a:visited, a:active { color: #336699; }
-a:hover { color: #339999; }
-
-body { font: 80%/126% sans-serif; }
-h1, h2, h3, h4 { color: #74240f; }
-
-dt { color: #336699; font-weight: bold }
-dd {
- margin-left: 1.5em;
- padding-bottom: 0.8em;
-}
-
-/* -- ruler -- */
-div.hr_blue {
- height: 3px;
- background:#ffffff url("/images/hr_blue.png") repeat-x; }
-div.hr_blue hr { display:none; }
-
-/* release styles */
-#release p { margin-top: 0.4em; }
-#release .md5sum { color: #761596; }
-
-
-/* ------ styles for docs|manuals|howto ------ */
-/* -- lists -- */
-ul {
- margin: 0px 4px 16px 16px;
- padding: 0px;
- list-style: url("/images/li-blue.png");
-}
-ul li {
- margin-bottom: 10px;
-}
-ul ul {
- list-style-type: none;
- list-style-image: none;
- margin-left: 0px;
-}
-
-/* header / footer nav tables */
-table.nav {
- border: solid 1px #3366cc;
- background: #f2f2f9;
- background-color: #f2f2f9;
- margin-bottom: 0.5em;
-}
-/* don't have underlined links in chunked nav menus */
-table.nav a { text-decoration: none; }
-table.nav a:hover { text-decoration: underline; }
-table.nav td { font-size: 85%; }
-
-code, tt, pre { font-size: 120%; }
-code, tt { color: #761596; }
-
-div.literallayout, pre.programlisting, pre.screen {
- color: #000000;
- padding: 0.5em;
- background: #eeeeee;
- border: 1px solid #626262;
- background-color: #eeeeee;
- margin: 4px 0px 4px 0px;
-}
-</style>
-</head>
-<body bgcolor="white" text="black" link="#0000FF" vlink="#840084" alink="#0000FF"><div lang="en" class="book" title="bzip2 and libbzip2, version 1.0.6">
-<div class="titlepage">
-<div>
-<div><h1 class="title">
-<a name="userman"></a>bzip2 and libbzip2, version 1.0.6</h1></div>
-<div><h2 class="subtitle">A program and library for data compression</h2></div>
-<div><div class="authorgroup"><div class="author">
-<h3 class="author">
-<span class="firstname">Julian</span> <span class="surname">Seward</span>
-</h3>
-<div class="affiliation"><span class="orgname">http://www.bzip.org<br></span></div>
-</div></div></div>
-<div><p class="releaseinfo">Version 1.0.6 of 6 September 2010</p></div>
-<div><p class="copyright">Copyright � 1996-2010 Julian Seward</p></div>
-<div><div class="legalnotice" title="Legal Notice">
-<a name="id537185"></a><p>This program, <code class="computeroutput">bzip2</code>, the
- associated library <code class="computeroutput">libbzip2</code>, and
- all documentation, are copyright � 1996-2010 Julian Seward.
- All rights reserved.</p>
-<p>Redistribution and use in source and binary forms, with
- or without modification, are permitted provided that the
- following conditions are met:</p>
-<div class="itemizedlist"><ul class="itemizedlist" type="bullet">
-<li class="listitem" style="list-style-type: disc"><p>Redistributions of source code must retain the
- above copyright notice, this list of conditions and the
- following disclaimer.</p></li>
-<li class="listitem" style="list-style-type: disc"><p>The origin of this software must not be
- misrepresented; you must not claim that you wrote the original
- software. If you use this software in a product, an
- acknowledgment in the product documentation would be
- appreciated but is not required.</p></li>
-<li class="listitem" style="list-style-type: disc"><p>Altered source versions must be plainly marked
- as such, and must not be misrepresented as being the original
- software.</p></li>
-<li class="listitem" style="list-style-type: disc"><p>The name of the author may not be used to
- endorse or promote products derived from this software without
- specific prior written permission.</p></li>
-</ul></div>
-<p>THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY
- EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
- THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
- PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE
- AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
- EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED
- TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
- DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
- ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
- LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING
- IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF
- THE POSSIBILITY OF SUCH DAMAGE.</p>
-<p>PATENTS: To the best of my knowledge,
- <code class="computeroutput">bzip2</code> and
- <code class="computeroutput">libbzip2</code> do not use any patented
- algorithms. However, I do not have the resources to carry
- out a patent search. Therefore I cannot give any guarantee of
- the above statement.
- </p>
-</div></div>
-</div>
-<hr>
-</div>
-<div class="toc">
-<p><b>Table of Contents</b></p>
-<dl>
-<dt><span class="chapter"><a href="#intro">1. Introduction</a></span></dt>
-<dt><span class="chapter"><a href="#using">2. How to use bzip2</a></span></dt>
-<dd><dl>
-<dt><span class="sect1"><a href="#name">2.1. NAME</a></span></dt>
-<dt><span class="sect1"><a href="#synopsis">2.2. SYNOPSIS</a></span></dt>
-<dt><span class="sect1"><a href="#description">2.3. DESCRIPTION</a></span></dt>
-<dt><span class="sect1"><a href="#options">2.4. OPTIONS</a></span></dt>
-<dt><span class="sect1"><a href="#memory-management">2.5. MEMORY MANAGEMENT</a></span></dt>
-<dt><span class="sect1"><a href="#recovering">2.6. RECOVERING DATA FROM DAMAGED FILES</a></span></dt>
-<dt><span class="sect1"><a href="#performance">2.7. PERFORMANCE NOTES</a></span></dt>
-<dt><span class="sect1"><a href="#caveats">2.8. CAVEATS</a></span></dt>
-<dt><span class="sect1"><a href="#author">2.9. AUTHOR</a></span></dt>
-</dl></dd>
-<dt><span class="chapter"><a href="#libprog">3.
-Programming with <code class="computeroutput">libbzip2</code>
-</a></span></dt>
-<dd><dl>
-<dt><span class="sect1"><a href="#top-level">3.1. Top-level structure</a></span></dt>
-<dd><dl>
-<dt><span class="sect2"><a href="#ll-summary">3.1.1. Low-level summary</a></span></dt>
-<dt><span class="sect2"><a href="#hl-summary">3.1.2. High-level summary</a></span></dt>
-<dt><span class="sect2"><a href="#util-fns-summary">3.1.3. Utility functions summary</a></span></dt>
-</dl></dd>
-<dt><span class="sect1"><a href="#err-handling">3.2. Error handling</a></span></dt>
-<dt><span class="sect1"><a href="#low-level">3.3. Low-level interface</a></span></dt>
-<dd><dl>
-<dt><span class="sect2"><a href="#bzcompress-init">3.3.1. BZ2_bzCompressInit</a></span></dt>
-<dt><span class="sect2"><a href="#bzCompress">3.3.2. BZ2_bzCompress</a></span></dt>
-<dt><span class="sect2"><a href="#bzCompress-end">3.3.3. BZ2_bzCompressEnd</a></span></dt>
-<dt><span class="sect2"><a href="#bzDecompress-init">3.3.4. BZ2_bzDecompressInit</a></span></dt>
-<dt><span class="sect2"><a href="#bzDecompress">3.3.5. BZ2_bzDecompress</a></span></dt>
-<dt><span class="sect2"><a href="#bzDecompress-end">3.3.6. BZ2_bzDecompressEnd</a></span></dt>
-</dl></dd>
-<dt><span class="sect1"><a href="#hl-interface">3.4. High-level interface</a></span></dt>
-<dd><dl>
-<dt><span class="sect2"><a href="#bzreadopen">3.4.1. BZ2_bzReadOpen</a></span></dt>
-<dt><span class="sect2"><a href="#bzread">3.4.2. BZ2_bzRead</a></span></dt>
-<dt><span class="sect2"><a href="#bzreadgetunused">3.4.3. BZ2_bzReadGetUnused</a></span></dt>
-<dt><span class="sect2"><a href="#bzreadclose">3.4.4. BZ2_bzReadClose</a></span></dt>
-<dt><span class="sect2"><a href="#bzwriteopen">3.4.5. BZ2_bzWriteOpen</a></span></dt>
-<dt><span class="sect2"><a href="#bzwrite">3.4.6. BZ2_bzWrite</a></span></dt>
-<dt><span class="sect2"><a href="#bzwriteclose">3.4.7. BZ2_bzWriteClose</a></span></dt>
-<dt><span class="sect2"><a href="#embed">3.4.8. Handling embedded compressed data streams</a></span></dt>
-<dt><span class="sect2"><a href="#std-rdwr">3.4.9. Standard file-reading/writing code</a></span></dt>
-</dl></dd>
-<dt><span class="sect1"><a href="#util-fns">3.5. Utility functions</a></span></dt>
-<dd><dl>
-<dt><span class="sect2"><a href="#bzbufftobuffcompress">3.5.1. BZ2_bzBuffToBuffCompress</a></span></dt>
-<dt><span class="sect2"><a href="#bzbufftobuffdecompress">3.5.2. BZ2_bzBuffToBuffDecompress</a></span></dt>
-</dl></dd>
-<dt><span class="sect1"><a href="#zlib-compat">3.6. zlib compatibility functions</a></span></dt>
-<dt><span class="sect1"><a href="#stdio-free">3.7. Using the library in a stdio-free environment</a></span></dt>
-<dd><dl>
-<dt><span class="sect2"><a href="#stdio-bye">3.7.1. Getting rid of stdio</a></span></dt>
-<dt><span class="sect2"><a href="#critical-error">3.7.2. Critical error handling</a></span></dt>
-</dl></dd>
-<dt><span class="sect1"><a href="#win-dll">3.8. Making a Windows DLL</a></span></dt>
-</dl></dd>
-<dt><span class="chapter"><a href="#misc">4. Miscellanea</a></span></dt>
-<dd><dl>
-<dt><span class="sect1"><a href="#limits">4.1. Limitations of the compressed file format</a></span></dt>
-<dt><span class="sect1"><a href="#port-issues">4.2. Portability issues</a></span></dt>
-<dt><span class="sect1"><a href="#bugs">4.3. Reporting bugs</a></span></dt>
-<dt><span class="sect1"><a href="#package">4.4. Did you get the right package?</a></span></dt>
-<dt><span class="sect1"><a href="#reading">4.5. Further Reading</a></span></dt>
-</dl></dd>
-</dl>
-</div>
-<div class="chapter" title="1.�Introduction">
-<div class="titlepage"><div><div><h2 class="title">
-<a name="intro"></a>1.�Introduction</h2></div></div></div>
-<p><code class="computeroutput">bzip2</code> compresses files
-using the Burrows-Wheeler block-sorting text compression
-algorithm, and Huffman coding. Compression is generally
-considerably better than that achieved by more conventional
-LZ77/LZ78-based compressors, and approaches the performance of
-the PPM family of statistical compressors.</p>
-<p><code class="computeroutput">bzip2</code> is built on top of
-<code class="computeroutput">libbzip2</code>, a flexible library for
-handling compressed data in the
-<code class="computeroutput">bzip2</code> format. This manual
-describes both how to use the program and how to work with the
-library interface. Most of the manual is devoted to this
-library, not the program, which is good news if your interest is
-only in the program.</p>
-<div class="itemizedlist"><ul class="itemizedlist" type="bullet">
-<li class="listitem" style="list-style-type: disc"><p><a class="xref" href="#using" title="2.�How to use bzip2">How to use bzip2</a> describes how to use
- <code class="computeroutput">bzip2</code>; this is the only part
- you need to read if you just want to know how to operate the
- program.</p></li>
-<li class="listitem" style="list-style-type: disc"><p><a class="xref" href="#libprog" title="3.� Programming with libbzip2">Programming with libbzip2</a> describes the
- programming interfaces in detail, and</p></li>
-<li class="listitem" style="list-style-type: disc"><p><a class="xref" href="#misc" title="4.�Miscellanea">Miscellanea</a> records some
- miscellaneous notes which I thought ought to be recorded
- somewhere.</p></li>
-</ul></div>
-</div>
-<div class="chapter" title="2.�How to use bzip2">
-<div class="titlepage"><div><div><h2 class="title">
-<a name="using"></a>2.�How to use bzip2</h2></div></div></div>
-<div class="toc">
-<p><b>Table of Contents</b></p>
-<dl>
-<dt><span class="sect1"><a href="#name">2.1. NAME</a></span></dt>
-<dt><span class="sect1"><a href="#synopsis">2.2. SYNOPSIS</a></span></dt>
-<dt><span class="sect1"><a href="#description">2.3. DESCRIPTION</a></span></dt>
-<dt><span class="sect1"><a href="#options">2.4. OPTIONS</a></span></dt>
-<dt><span class="sect1"><a href="#memory-management">2.5. MEMORY MANAGEMENT</a></span></dt>
-<dt><span class="sect1"><a href="#recovering">2.6. RECOVERING DATA FROM DAMAGED FILES</a></span></dt>
-<dt><span class="sect1"><a href="#performance">2.7. PERFORMANCE NOTES</a></span></dt>
-<dt><span class="sect1"><a href="#caveats">2.8. CAVEATS</a></span></dt>
-<dt><span class="sect1"><a href="#author">2.9. AUTHOR</a></span></dt>
-</dl>
-</div>
-<p>This chapter contains a copy of the
-<code class="computeroutput">bzip2</code> man page, and nothing
-else.</p>
-<div class="sect1" title="2.1.�NAME">
-<div class="titlepage"><div><div><h2 class="title" style="clear: both">
-<a name="name"></a>2.1.�NAME</h2></div></div></div>
-<div class="itemizedlist"><ul class="itemizedlist" type="bullet">
-<li class="listitem" style="list-style-type: disc"><p><code class="computeroutput">bzip2</code>,
- <code class="computeroutput">bunzip2</code> - a block-sorting file
- compressor, v1.0.6</p></li>
-<li class="listitem" style="list-style-type: disc"><p><code class="computeroutput">bzcat</code> -
- decompresses files to stdout</p></li>
-<li class="listitem" style="list-style-type: disc"><p><code class="computeroutput">bzip2recover</code> -
- recovers data from damaged bzip2 files</p></li>
-</ul></div>
-</div>
-<div class="sect1" title="2.2.�SYNOPSIS">
-<div class="titlepage"><div><div><h2 class="title" style="clear: both">
-<a name="synopsis"></a>2.2.�SYNOPSIS</h2></div></div></div>
-<div class="itemizedlist"><ul class="itemizedlist" type="bullet">
-<li class="listitem" style="list-style-type: disc"><p><code class="computeroutput">bzip2</code> [
- -cdfkqstvzVL123456789 ] [ filenames ... ]</p></li>
-<li class="listitem" style="list-style-type: disc"><p><code class="computeroutput">bunzip2</code> [
- -fkvsVL ] [ filenames ... ]</p></li>
-<li class="listitem" style="list-style-type: disc"><p><code class="computeroutput">bzcat</code> [ -s ] [
- filenames ... ]</p></li>
-<li class="listitem" style="list-style-type: disc"><p><code class="computeroutput">bzip2recover</code>
- filename</p></li>
-</ul></div>
-</div>
-<div class="sect1" title="2.3.�DESCRIPTION">
-<div class="titlepage"><div><div><h2 class="title" style="clear: both">
-<a name="description"></a>2.3.�DESCRIPTION</h2></div></div></div>
-<p><code class="computeroutput">bzip2</code> compresses files
-using the Burrows-Wheeler block sorting text compression
-algorithm, and Huffman coding. Compression is generally
-considerably better than that achieved by more conventional
-LZ77/LZ78-based compressors, and approaches the performance of
-the PPM family of statistical compressors.</p>
-<p>The command-line options are deliberately very similar to
-those of GNU <code class="computeroutput">gzip</code>, but they are
-not identical.</p>
-<p><code class="computeroutput">bzip2</code> expects a list of
-file names to accompany the command-line flags. Each file is
-replaced by a compressed version of itself, with the name
-<code class="computeroutput">original_name.bz2</code>. Each
-compressed file has the same modification date, permissions, and,
-when possible, ownership as the corresponding original, so that
-these properties can be correctly restored at decompression time.
-File name handling is naive in the sense that there is no
-mechanism for preserving original file names, permissions,
-ownerships or dates in filesystems which lack these concepts, or
-have serious file name length restrictions, such as
-MS-DOS.</p>
-<p><code class="computeroutput">bzip2</code> and
-<code class="computeroutput">bunzip2</code> will by default not
-overwrite existing files. If you want this to happen, specify
-the <code class="computeroutput">-f</code> flag.</p>
-<p>If no file names are specified,
-<code class="computeroutput">bzip2</code> compresses from standard
-input to standard output. In this case,
-<code class="computeroutput">bzip2</code> will decline to write
-compressed output to a terminal, as this would be entirely
-incomprehensible and therefore pointless.</p>
-<p><code class="computeroutput">bunzip2</code> (or
-<code class="computeroutput">bzip2 -d</code>) decompresses all
-specified files. Files which were not created by
-<code class="computeroutput">bzip2</code> will be detected and
-ignored, and a warning issued.
-<code class="computeroutput">bzip2</code> attempts to guess the
-filename for the decompressed file from that of the compressed
-file as follows:</p>
-<div class="itemizedlist"><ul class="itemizedlist" type="bullet">
-<li class="listitem" style="list-style-type: disc"><p><code class="computeroutput">filename.bz2 </code>
- becomes
- <code class="computeroutput">filename</code></p></li>
-<li class="listitem" style="list-style-type: disc"><p><code class="computeroutput">filename.bz </code>
- becomes
- <code class="computeroutput">filename</code></p></li>
-<li class="listitem" style="list-style-type: disc"><p><code class="computeroutput">filename.tbz2</code>
- becomes
- <code class="computeroutput">filename.tar</code></p></li>
-<li class="listitem" style="list-style-type: disc"><p><code class="computeroutput">filename.tbz </code>
- becomes
- <code class="computeroutput">filename.tar</code></p></li>
-<li class="listitem" style="list-style-type: disc"><p><code class="computeroutput">anyothername </code>
- becomes
- <code class="computeroutput">anyothername.out</code></p></li>
-</ul></div>
-<p>If the file does not end in one of the recognised endings,
-<code class="computeroutput">.bz2</code>,
-<code class="computeroutput">.bz</code>,
-<code class="computeroutput">.tbz2</code> or
-<code class="computeroutput">.tbz</code>,
-<code class="computeroutput">bzip2</code> complains that it cannot
-guess the name of the original file, and uses the original name
-with <code class="computeroutput">.out</code> appended.</p>
-<p>As with compression, supplying no filenames causes
-decompression from standard input to standard output.</p>
-<p><code class="computeroutput">bunzip2</code> will correctly
-decompress a file which is the concatenation of two or more
-compressed files. The result is the concatenation of the
-corresponding uncompressed files. Integrity testing
-(<code class="computeroutput">-t</code>) of concatenated compressed
-files is also supported.</p>
-<p>You can also compress or decompress files to the standard
-output by giving the <code class="computeroutput">-c</code> flag.
-Multiple files may be compressed and decompressed like this. The
-resulting outputs are fed sequentially to stdout. Compression of
-multiple files in this manner generates a stream containing
-multiple compressed file representations. Such a stream can be
-decompressed correctly only by
-<code class="computeroutput">bzip2</code> version 0.9.0 or later.
-Earlier versions of <code class="computeroutput">bzip2</code> will
-stop after decompressing the first file in the stream.</p>
-<p><code class="computeroutput">bzcat</code> (or
-<code class="computeroutput">bzip2 -dc</code>) decompresses all
-specified files to the standard output.</p>
-<p><code class="computeroutput">bzip2</code> will read arguments
-from the environment variables
-<code class="computeroutput">BZIP2</code> and
-<code class="computeroutput">BZIP</code>, in that order, and will
-process them before any arguments read from the command line.
-This gives a convenient way to supply default arguments.</p>
-<p>Compression is always performed, even if the compressed
-file is slightly larger than the original. Files of less than
-about one hundred bytes tend to get larger, since the compression
-mechanism has a constant overhead in the region of 50 bytes.
-Random data (including the output of most file compressors) is
-coded at about 8.05 bits per byte, giving an expansion of around
-0.5%.</p>
-<p>As a self-check for your protection,
-<code class="computeroutput">bzip2</code> uses 32-bit CRCs to make
-sure that the decompressed version of a file is identical to the
-original. This guards against corruption of the compressed data,
-and against undetected bugs in
-<code class="computeroutput">bzip2</code> (hopefully very unlikely).
-The chances of data corruption going undetected is microscopic,
-about one chance in four billion for each file processed. Be
-aware, though, that the check occurs upon decompression, so it
-can only tell you that something is wrong. It can't help you
-recover the original uncompressed data. You can use
-<code class="computeroutput">bzip2recover</code> to try to recover
-data from damaged files.</p>
-<p>Return values: 0 for a normal exit, 1 for environmental
-problems (file not found, invalid flags, I/O errors, etc.), 2
-to indicate a corrupt compressed file, 3 for an internal
-consistency error (eg, bug) which caused
-<code class="computeroutput">bzip2</code> to panic.</p>
-</div>
-<div class="sect1" title="2.4.�OPTIONS">
-<div class="titlepage"><div><div><h2 class="title" style="clear: both">
-<a name="options"></a>2.4.�OPTIONS</h2></div></div></div>
-<div class="variablelist"><dl>
-<dt><span class="term"><code class="computeroutput">-c --stdout</code></span></dt>
-<dd><p>Compress or decompress to standard
- output.</p></dd>
-<dt><span class="term"><code class="computeroutput">-d --decompress</code></span></dt>
-<dd><p>Force decompression.
- <code class="computeroutput">bzip2</code>,
- <code class="computeroutput">bunzip2</code> and
- <code class="computeroutput">bzcat</code> are really the same
- program, and the decision about what actions to take is done on
- the basis of which name is used. This flag overrides that
- mechanism, and forces bzip2 to decompress.</p></dd>
-<dt><span class="term"><code class="computeroutput">-z --compress</code></span></dt>
-<dd><p>The complement to
- <code class="computeroutput">-d</code>: forces compression,
- regardless of the invokation name.</p></dd>
-<dt><span class="term"><code class="computeroutput">-t --test</code></span></dt>
-<dd><p>Check integrity of the specified file(s), but
- don't decompress them. This really performs a trial
- decompression and throws away the result.</p></dd>
-<dt><span class="term"><code class="computeroutput">-f --force</code></span></dt>
-<dd>
-<p>Force overwrite of output files. Normally,
- <code class="computeroutput">bzip2</code> will not overwrite
- existing output files. Also forces
- <code class="computeroutput">bzip2</code> to break hard links to
- files, which it otherwise wouldn't do.</p>
-<p><code class="computeroutput">bzip2</code> normally declines
- to decompress files which don't have the correct magic header
- bytes. If forced (<code class="computeroutput">-f</code>),
- however, it will pass such files through unmodified. This is
- how GNU <code class="computeroutput">gzip</code> behaves.</p>
-</dd>
-<dt><span class="term"><code class="computeroutput">-k --keep</code></span></dt>
-<dd><p>Keep (don't delete) input files during
- compression or decompression.</p></dd>
-<dt><span class="term"><code class="computeroutput">-s --small</code></span></dt>
-<dd>
-<p>Reduce memory usage, for compression,
- decompression and testing. Files are decompressed and tested
- using a modified algorithm which only requires 2.5 bytes per
- block byte. This means any file can be decompressed in 2300k
- of memory, albeit at about half the normal speed.</p>
-<p>During compression, <code class="computeroutput">-s</code>
- selects a block size of 200k, which limits memory use to around
- the same figure, at the expense of your compression ratio. In
- short, if your machine is low on memory (8 megabytes or less),
- use <code class="computeroutput">-s</code> for everything. See
- <a class="xref" href="#memory-management" title="2.5.�MEMORY MANAGEMENT">MEMORY MANAGEMENT</a> below.</p>
-</dd>
-<dt><span class="term"><code class="computeroutput">-q --quiet</code></span></dt>
-<dd><p>Suppress non-essential warning messages.
- Messages pertaining to I/O errors and other critical events
- will not be suppressed.</p></dd>
-<dt><span class="term"><code class="computeroutput">-v --verbose</code></span></dt>
-<dd><p>Verbose mode -- show the compression ratio for
- each file processed. Further
- <code class="computeroutput">-v</code>'s increase the verbosity
- level, spewing out lots of information which is primarily of
- interest for diagnostic purposes.</p></dd>
-<dt><span class="term"><code class="computeroutput">-L --license -V --version</code></span></dt>
-<dd><p>Display the software version, license terms and
- conditions.</p></dd>
-<dt><span class="term"><code class="computeroutput">-1</code> (or
- <code class="computeroutput">--fast</code>) to
- <code class="computeroutput">-9</code> (or
- <code class="computeroutput">-best</code>)</span></dt>
-<dd><p>Set the block size to 100 k, 200 k ... 900 k
- when compressing. Has no effect when decompressing. See <a class="xref" href="#memory-management" title="2.5.�MEMORY MANAGEMENT">MEMORY MANAGEMENT</a> below. The
- <code class="computeroutput">--fast</code> and
- <code class="computeroutput">--best</code> aliases are primarily
- for GNU <code class="computeroutput">gzip</code> compatibility.
- In particular, <code class="computeroutput">--fast</code> doesn't
- make things significantly faster. And
- <code class="computeroutput">--best</code> merely selects the
- default behaviour.</p></dd>
-<dt><span class="term"><code class="computeroutput">--</code></span></dt>
-<dd><p>Treats all subsequent arguments as file names,
- even if they start with a dash. This is so you can handle
- files with names beginning with a dash, for example:
- <code class="computeroutput">bzip2 --
- -myfilename</code>.</p></dd>
-<dt>
-<span class="term"><code class="computeroutput">--repetitive-fast</code>, </span><span class="term"><code class="computeroutput">--repetitive-best</code></span>
-</dt>
-<dd><p>These flags are redundant in versions 0.9.5 and
- above. They provided some coarse control over the behaviour of
- the sorting algorithm in earlier versions, which was sometimes
- useful. 0.9.5 and above have an improved algorithm which
- renders these flags irrelevant.</p></dd>
-</dl></div>
-</div>
-<div class="sect1" title="2.5.�MEMORY MANAGEMENT">
-<div class="titlepage"><div><div><h2 class="title" style="clear: both">
-<a name="memory-management"></a>2.5.�MEMORY MANAGEMENT</h2></div></div></div>
-<p><code class="computeroutput">bzip2</code> compresses large
-files in blocks. The block size affects both the compression
-ratio achieved, and the amount of memory needed for compression
-and decompression. The flags <code class="computeroutput">-1</code>
-through <code class="computeroutput">-9</code> specify the block
-size to be 100,000 bytes through 900,000 bytes (the default)
-respectively. At decompression time, the block size used for
-compression is read from the header of the compressed file, and
-<code class="computeroutput">bunzip2</code> then allocates itself
-just enough memory to decompress the file. Since block sizes are
-stored in compressed files, it follows that the flags
-<code class="computeroutput">-1</code> to
-<code class="computeroutput">-9</code> are irrelevant to and so
-ignored during decompression.</p>
-<p>Compression and decompression requirements, in bytes, can be
-estimated as:</p>
-<pre class="programlisting">Compression: 400k + ( 8 x block size )
-
-Decompression: 100k + ( 4 x block size ), or
- 100k + ( 2.5 x block size )</pre>
-<p>Larger block sizes give rapidly diminishing marginal
-returns. Most of the compression comes from the first two or
-three hundred k of block size, a fact worth bearing in mind when
-using <code class="computeroutput">bzip2</code> on small machines.
-It is also important to appreciate that the decompression memory
-requirement is set at compression time by the choice of block
-size.</p>
-<p>For files compressed with the default 900k block size,
-<code class="computeroutput">bunzip2</code> will require about 3700
-kbytes to decompress. To support decompression of any file on a
-4 megabyte machine, <code class="computeroutput">bunzip2</code> has
-an option to decompress using approximately half this amount of
-memory, about 2300 kbytes. Decompression speed is also halved,
-so you should use this option only where necessary. The relevant
-flag is <code class="computeroutput">-s</code>.</p>
-<p>In general, try and use the largest block size memory
-constraints allow, since that maximises the compression achieved.
-Compression and decompression speed are virtually unaffected by
-block size.</p>
-<p>Another significant point applies to files which fit in a
-single block -- that means most files you'd encounter using a
-large block size. The amount of real memory touched is
-proportional to the size of the file, since the file is smaller
-than a block. For example, compressing a file 20,000 bytes long
-with the flag <code class="computeroutput">-9</code> will cause the
-compressor to allocate around 7600k of memory, but only touch
-400k + 20000 * 8 = 560 kbytes of it. Similarly, the decompressor
-will allocate 3700k but only touch 100k + 20000 * 4 = 180
-kbytes.</p>
-<p>Here is a table which summarises the maximum memory usage
-for different block sizes. Also recorded is the total compressed
-size for 14 files of the Calgary Text Compression Corpus
-totalling 3,141,622 bytes. This column gives some feel for how
-compression varies with block size. These figures tend to
-understate the advantage of larger block sizes for larger files,
-since the Corpus is dominated by smaller files.</p>
-<pre class="programlisting"> Compress Decompress Decompress Corpus
-Flag usage usage -s usage Size
-
- -1 1200k 500k 350k 914704
- -2 2000k 900k 600k 877703
- -3 2800k 1300k 850k 860338
- -4 3600k 1700k 1100k 846899
- -5 4400k 2100k 1350k 845160
- -6 5200k 2500k 1600k 838626
- -7 6100k 2900k 1850k 834096
- -8 6800k 3300k 2100k 828642
- -9 7600k 3700k 2350k 828642</pre>
-</div>
-<div class="sect1" title="2.6.�RECOVERING DATA FROM DAMAGED FILES">
-<div class="titlepage"><div><div><h2 class="title" style="clear: both">
-<a name="recovering"></a>2.6.�RECOVERING DATA FROM DAMAGED FILES</h2></div></div></div>
-<p><code class="computeroutput">bzip2</code> compresses files in
-blocks, usually 900kbytes long. Each block is handled
-independently. If a media or transmission error causes a
-multi-block <code class="computeroutput">.bz2</code> file to become
-damaged, it may be possible to recover data from the undamaged
-blocks in the file.</p>
-<p>The compressed representation of each block is delimited by
-a 48-bit pattern, which makes it possible to find the block
-boundaries with reasonable certainty. Each block also carries
-its own 32-bit CRC, so damaged blocks can be distinguished from
-undamaged ones.</p>
-<p><code class="computeroutput">bzip2recover</code> is a simple
-program whose purpose is to search for blocks in
-<code class="computeroutput">.bz2</code> files, and write each block
-out into its own <code class="computeroutput">.bz2</code> file. You
-can then use <code class="computeroutput">bzip2 -t</code> to test
-the integrity of the resulting files, and decompress those which
-are undamaged.</p>
-<p><code class="computeroutput">bzip2recover</code> takes a
-single argument, the name of the damaged file, and writes a
-number of files <code class="computeroutput">rec0001file.bz2</code>,
-<code class="computeroutput">rec0002file.bz2</code>, etc, containing
-the extracted blocks. The output filenames are designed so that
-the use of wildcards in subsequent processing -- for example,
-<code class="computeroutput">bzip2 -dc rec*file.bz2 >
-recovered_data</code> -- lists the files in the correct
-order.</p>
-<p><code class="computeroutput">bzip2recover</code> should be of
-most use dealing with large <code class="computeroutput">.bz2</code>
-files, as these will contain many blocks. It is clearly futile
-to use it on damaged single-block files, since a damaged block
-cannot be recovered. If you wish to minimise any potential data
-loss through media or transmission errors, you might consider
-compressing with a smaller block size.</p>
-</div>
-<div class="sect1" title="2.7.�PERFORMANCE NOTES">
-<div class="titlepage"><div><div><h2 class="title" style="clear: both">
-<a name="performance"></a>2.7.�PERFORMANCE NOTES</h2></div></div></div>
-<p>The sorting phase of compression gathers together similar
-strings in the file. Because of this, files containing very long
-runs of repeated symbols, like "aabaabaabaab ..." (repeated
-several hundred times) may compress more slowly than normal.
-Versions 0.9.5 and above fare much better than previous versions
-in this respect. The ratio between worst-case and average-case
-compression time is in the region of 10:1. For previous
-versions, this figure was more like 100:1. You can use the
-<code class="computeroutput">-vvvv</code> option to monitor progress
-in great detail, if you want.</p>
-<p>Decompression speed is unaffected by these
-phenomena.</p>
-<p><code class="computeroutput">bzip2</code> usually allocates
-several megabytes of memory to operate in, and then charges all
-over it in a fairly random fashion. This means that performance,
-both for compressing and decompressing, is largely determined by
-the speed at which your machine can service cache misses.
-Because of this, small changes to the code to reduce the miss
-rate have been observed to give disproportionately large
-performance improvements. I imagine
-<code class="computeroutput">bzip2</code> will perform best on
-machines with very large caches.</p>
-</div>
-<div class="sect1" title="2.8.�CAVEATS">
-<div class="titlepage"><div><div><h2 class="title" style="clear: both">
-<a name="caveats"></a>2.8.�CAVEATS</h2></div></div></div>
-<p>I/O error messages are not as helpful as they could be.
-<code class="computeroutput">bzip2</code> tries hard to detect I/O
-errors and exit cleanly, but the details of what the problem is
-sometimes seem rather misleading.</p>
-<p>This manual page pertains to version 1.0.6 of
-<code class="computeroutput">bzip2</code>. Compressed data created by
-this version is entirely forwards and backwards compatible with the
-previous public releases, versions 0.1pl2, 0.9.0 and 0.9.5, 1.0.0,
-1.0.1, 1.0.2 and 1.0.3, but with the following exception: 0.9.0 and
-above can correctly decompress multiple concatenated compressed files.
-0.1pl2 cannot do this; it will stop after decompressing just the first
-file in the stream.</p>
-<p><code class="computeroutput">bzip2recover</code> versions
-prior to 1.0.2 used 32-bit integers to represent bit positions in
-compressed files, so it could not handle compressed files more
-than 512 megabytes long. Versions 1.0.2 and above use 64-bit ints
-on some platforms which support them (GNU supported targets, and
-Windows). To establish whether or not
-<code class="computeroutput">bzip2recover</code> was built with such
-a limitation, run it without arguments. In any event you can
-build yourself an unlimited version if you can recompile it with
-<code class="computeroutput">MaybeUInt64</code> set to be an
-unsigned 64-bit integer.</p>
-</div>
-<div class="sect1" title="2.9.�AUTHOR">
-<div class="titlepage"><div><div><h2 class="title" style="clear: both">
-<a name="author"></a>2.9.�AUTHOR</h2></div></div></div>
-<p>Julian Seward,
-<code class="computeroutput">jseward at bzip.org</code></p>
-<p>The ideas embodied in
-<code class="computeroutput">bzip2</code> are due to (at least) the
-following people: Michael Burrows and David Wheeler (for the
-block sorting transformation), David Wheeler (again, for the
-Huffman coder), Peter Fenwick (for the structured coding model in
-the original <code class="computeroutput">bzip</code>, and many
-refinements), and Alistair Moffat, Radford Neal and Ian Witten
-(for the arithmetic coder in the original
-<code class="computeroutput">bzip</code>). I am much indebted for
-their help, support and advice. See the manual in the source
-distribution for pointers to sources of documentation. Christian
-von Roques encouraged me to look for faster sorting algorithms,
-so as to speed up compression. Bela Lubkin encouraged me to
-improve the worst-case compression performance.
-Donna Robinson XMLised the documentation.
-Many people sent
-patches, helped with portability problems, lent machines, gave
-advice and were generally helpful.</p>
-</div>
-</div>
-<div class="chapter" title="3.� Programming with libbzip2">
-<div class="titlepage"><div><div><h2 class="title">
-<a name="libprog"></a>3.�
-Programming with <code class="computeroutput">libbzip2</code>
-</h2></div></div></div>
-<div class="toc">
-<p><b>Table of Contents</b></p>
-<dl>
-<dt><span class="sect1"><a href="#top-level">3.1. Top-level structure</a></span></dt>
-<dd><dl>
-<dt><span class="sect2"><a href="#ll-summary">3.1.1. Low-level summary</a></span></dt>
-<dt><span class="sect2"><a href="#hl-summary">3.1.2. High-level summary</a></span></dt>
-<dt><span class="sect2"><a href="#util-fns-summary">3.1.3. Utility functions summary</a></span></dt>
-</dl></dd>
-<dt><span class="sect1"><a href="#err-handling">3.2. Error handling</a></span></dt>
-<dt><span class="sect1"><a href="#low-level">3.3. Low-level interface</a></span></dt>
-<dd><dl>
-<dt><span class="sect2"><a href="#bzcompress-init">3.3.1. BZ2_bzCompressInit</a></span></dt>
-<dt><span class="sect2"><a href="#bzCompress">3.3.2. BZ2_bzCompress</a></span></dt>
-<dt><span class="sect2"><a href="#bzCompress-end">3.3.3. BZ2_bzCompressEnd</a></span></dt>
-<dt><span class="sect2"><a href="#bzDecompress-init">3.3.4. BZ2_bzDecompressInit</a></span></dt>
-<dt><span class="sect2"><a href="#bzDecompress">3.3.5. BZ2_bzDecompress</a></span></dt>
-<dt><span class="sect2"><a href="#bzDecompress-end">3.3.6. BZ2_bzDecompressEnd</a></span></dt>
-</dl></dd>
-<dt><span class="sect1"><a href="#hl-interface">3.4. High-level interface</a></span></dt>
-<dd><dl>
-<dt><span class="sect2"><a href="#bzreadopen">3.4.1. BZ2_bzReadOpen</a></span></dt>
-<dt><span class="sect2"><a href="#bzread">3.4.2. BZ2_bzRead</a></span></dt>
-<dt><span class="sect2"><a href="#bzreadgetunused">3.4.3. BZ2_bzReadGetUnused</a></span></dt>
-<dt><span class="sect2"><a href="#bzreadclose">3.4.4. BZ2_bzReadClose</a></span></dt>
-<dt><span class="sect2"><a href="#bzwriteopen">3.4.5. BZ2_bzWriteOpen</a></span></dt>
-<dt><span class="sect2"><a href="#bzwrite">3.4.6. BZ2_bzWrite</a></span></dt>
-<dt><span class="sect2"><a href="#bzwriteclose">3.4.7. BZ2_bzWriteClose</a></span></dt>
-<dt><span class="sect2"><a href="#embed">3.4.8. Handling embedded compressed data streams</a></span></dt>
-<dt><span class="sect2"><a href="#std-rdwr">3.4.9. Standard file-reading/writing code</a></span></dt>
-</dl></dd>
-<dt><span class="sect1"><a href="#util-fns">3.5. Utility functions</a></span></dt>
-<dd><dl>
-<dt><span class="sect2"><a href="#bzbufftobuffcompress">3.5.1. BZ2_bzBuffToBuffCompress</a></span></dt>
-<dt><span class="sect2"><a href="#bzbufftobuffdecompress">3.5.2. BZ2_bzBuffToBuffDecompress</a></span></dt>
-</dl></dd>
-<dt><span class="sect1"><a href="#zlib-compat">3.6. zlib compatibility functions</a></span></dt>
-<dt><span class="sect1"><a href="#stdio-free">3.7. Using the library in a stdio-free environment</a></span></dt>
-<dd><dl>
-<dt><span class="sect2"><a href="#stdio-bye">3.7.1. Getting rid of stdio</a></span></dt>
-<dt><span class="sect2"><a href="#critical-error">3.7.2. Critical error handling</a></span></dt>
-</dl></dd>
-<dt><span class="sect1"><a href="#win-dll">3.8. Making a Windows DLL</a></span></dt>
-</dl>
-</div>
-<p>This chapter describes the programming interface to
-<code class="computeroutput">libbzip2</code>.</p>
-<p>For general background information, particularly about
-memory use and performance aspects, you'd be well advised to read
-<a class="xref" href="#using" title="2.�How to use bzip2">How to use bzip2</a> as well.</p>
-<div class="sect1" title="3.1.�Top-level structure">
-<div class="titlepage"><div><div><h2 class="title" style="clear: both">
-<a name="top-level"></a>3.1.�Top-level structure</h2></div></div></div>
-<p><code class="computeroutput">libbzip2</code> is a flexible
-library for compressing and decompressing data in the
-<code class="computeroutput">bzip2</code> data format. Although
-packaged as a single entity, it helps to regard the library as
-three separate parts: the low level interface, and the high level
-interface, and some utility functions.</p>
-<p>The structure of
-<code class="computeroutput">libbzip2</code>'s interfaces is similar
-to that of Jean-loup Gailly's and Mark Adler's excellent
-<code class="computeroutput">zlib</code> library.</p>
-<p>All externally visible symbols have names beginning
-<code class="computeroutput">BZ2_</code>. This is new in version
-1.0. The intention is to minimise pollution of the namespaces of
-library clients.</p>
-<p>To use any part of the library, you need to
-<code class="computeroutput">#include <bzlib.h></code>
-into your sources.</p>
-<div class="sect2" title="3.1.1.�Low-level summary">
-<div class="titlepage"><div><div><h3 class="title">
-<a name="ll-summary"></a>3.1.1.�Low-level summary</h3></div></div></div>
-<p>This interface provides services for compressing and
-decompressing data in memory. There's no provision for dealing
-with files, streams or any other I/O mechanisms, just straight
-memory-to-memory work. In fact, this part of the library can be
-compiled without inclusion of
-<code class="computeroutput">stdio.h</code>, which may be helpful
-for embedded applications.</p>
-<p>The low-level part of the library has no global variables
-and is therefore thread-safe.</p>
-<p>Six routines make up the low level interface:
-<code class="computeroutput">BZ2_bzCompressInit</code>,
-<code class="computeroutput">BZ2_bzCompress</code>, and
-<code class="computeroutput">BZ2_bzCompressEnd</code> for
-compression, and a corresponding trio
-<code class="computeroutput">BZ2_bzDecompressInit</code>,
-<code class="computeroutput">BZ2_bzDecompress</code> and
-<code class="computeroutput">BZ2_bzDecompressEnd</code> for
-decompression. The <code class="computeroutput">*Init</code>
-functions allocate memory for compression/decompression and do
-other initialisations, whilst the
-<code class="computeroutput">*End</code> functions close down
-operations and release memory.</p>
-<p>The real work is done by
-<code class="computeroutput">BZ2_bzCompress</code> and
-<code class="computeroutput">BZ2_bzDecompress</code>. These
-compress and decompress data from a user-supplied input buffer to
-a user-supplied output buffer. These buffers can be any size;
-arbitrary quantities of data are handled by making repeated calls
-to these functions. This is a flexible mechanism allowing a
-consumer-pull style of activity, or producer-push, or a mixture
-of both.</p>
-</div>
-<div class="sect2" title="3.1.2.�High-level summary">
-<div class="titlepage"><div><div><h3 class="title">
-<a name="hl-summary"></a>3.1.2.�High-level summary</h3></div></div></div>
-<p>This interface provides some handy wrappers around the
-low-level interface to facilitate reading and writing
-<code class="computeroutput">bzip2</code> format files
-(<code class="computeroutput">.bz2</code> files). The routines
-provide hooks to facilitate reading files in which the
-<code class="computeroutput">bzip2</code> data stream is embedded
-within some larger-scale file structure, or where there are
-multiple <code class="computeroutput">bzip2</code> data streams
-concatenated end-to-end.</p>
-<p>For reading files,
-<code class="computeroutput">BZ2_bzReadOpen</code>,
-<code class="computeroutput">BZ2_bzRead</code>,
-<code class="computeroutput">BZ2_bzReadClose</code> and
-<code class="computeroutput">BZ2_bzReadGetUnused</code> are
-supplied. For writing files,
-<code class="computeroutput">BZ2_bzWriteOpen</code>,
-<code class="computeroutput">BZ2_bzWrite</code> and
-<code class="computeroutput">BZ2_bzWriteFinish</code> are
-available.</p>
-<p>As with the low-level library, no global variables are used
-so the library is per se thread-safe. However, if I/O errors
-occur whilst reading or writing the underlying compressed files,
-you may have to consult <code class="computeroutput">errno</code> to
-determine the cause of the error. In that case, you'd need a C
-library which correctly supports
-<code class="computeroutput">errno</code> in a multithreaded
-environment.</p>
-<p>To make the library a little simpler and more portable,
-<code class="computeroutput">BZ2_bzReadOpen</code> and
-<code class="computeroutput">BZ2_bzWriteOpen</code> require you to
-pass them file handles (<code class="computeroutput">FILE*</code>s)
-which have previously been opened for reading or writing
-respectively. That avoids portability problems associated with
-file operations and file attributes, whilst not being much of an
-imposition on the programmer.</p>
-</div>
-<div class="sect2" title="3.1.3.�Utility functions summary">
-<div class="titlepage"><div><div><h3 class="title">
-<a name="util-fns-summary"></a>3.1.3.�Utility functions summary</h3></div></div></div>
-<p>For very simple needs,
-<code class="computeroutput">BZ2_bzBuffToBuffCompress</code> and
-<code class="computeroutput">BZ2_bzBuffToBuffDecompress</code> are
-provided. These compress data in memory from one buffer to
-another buffer in a single function call. You should assess
-whether these functions fulfill your memory-to-memory
-compression/decompression requirements before investing effort in
-understanding the more general but more complex low-level
-interface.</p>
-<p>Yoshioka Tsuneo
-(<code class="computeroutput">tsuneo at rr.iij4u.or.jp</code>) has
-contributed some functions to give better
-<code class="computeroutput">zlib</code> compatibility. These
-functions are <code class="computeroutput">BZ2_bzopen</code>,
-<code class="computeroutput">BZ2_bzread</code>,
-<code class="computeroutput">BZ2_bzwrite</code>,
-<code class="computeroutput">BZ2_bzflush</code>,
-<code class="computeroutput">BZ2_bzclose</code>,
-<code class="computeroutput">BZ2_bzerror</code> and
-<code class="computeroutput">BZ2_bzlibVersion</code>. You may find
-these functions more convenient for simple file reading and
-writing, than those in the high-level interface. These functions
-are not (yet) officially part of the library, and are minimally
-documented here. If they break, you get to keep all the pieces.
-I hope to document them properly when time permits.</p>
-<p>Yoshioka also contributed modifications to allow the
-library to be built as a Windows DLL.</p>
-</div>
-</div>
-<div class="sect1" title="3.2.�Error handling">
-<div class="titlepage"><div><div><h2 class="title" style="clear: both">
-<a name="err-handling"></a>3.2.�Error handling</h2></div></div></div>
-<p>The library is designed to recover cleanly in all
-situations, including the worst-case situation of decompressing
-random data. I'm not 100% sure that it can always do this, so
-you might want to add a signal handler to catch segmentation
-violations during decompression if you are feeling especially
-paranoid. I would be interested in hearing more about the
-robustness of the library to corrupted compressed data.</p>
-<p>Version 1.0.3 more robust in this respect than any
-previous version. Investigations with Valgrind (a tool for detecting
-problems with memory management) indicate
-that, at least for the few files I tested, all single-bit errors
-in the decompressed data are caught properly, with no
-segmentation faults, no uses of uninitialised data, no out of
-range reads or writes, and no infinite looping in the decompressor.
-So it's certainly pretty robust, although
-I wouldn't claim it to be totally bombproof.</p>
-<p>The file <code class="computeroutput">bzlib.h</code> contains
-all definitions needed to use the library. In particular, you
-should definitely not include
-<code class="computeroutput">bzlib_private.h</code>.</p>
-<p>In <code class="computeroutput">bzlib.h</code>, the various
-return values are defined. The following list is not intended as
-an exhaustive description of the circumstances in which a given
-value may be returned -- those descriptions are given later.
-Rather, it is intended to convey the rough meaning of each return
-value. The first five actions are normal and not intended to
-denote an error situation.</p>
-<div class="variablelist"><dl>
-<dt><span class="term"><code class="computeroutput">BZ_OK</code></span></dt>
-<dd><p>The requested action was completed
- successfully.</p></dd>
-<dt><span class="term"><code class="computeroutput">BZ_RUN_OK, BZ_FLUSH_OK,
- BZ_FINISH_OK</code></span></dt>
-<dd><p>In
- <code class="computeroutput">BZ2_bzCompress</code>, the requested
- flush/finish/nothing-special action was completed
- successfully.</p></dd>
-<dt><span class="term"><code class="computeroutput">BZ_STREAM_END</code></span></dt>
-<dd><p>Compression of data was completed, or the
- logical stream end was detected during
- decompression.</p></dd>
-</dl></div>
-<p>The following return values indicate an error of some
-kind.</p>
-<div class="variablelist"><dl>
-<dt><span class="term"><code class="computeroutput">BZ_CONFIG_ERROR</code></span></dt>
-<dd><p>Indicates that the library has been improperly
- compiled on your platform -- a major configuration error.
- Specifically, it means that
- <code class="computeroutput">sizeof(char)</code>,
- <code class="computeroutput">sizeof(short)</code> and
- <code class="computeroutput">sizeof(int)</code> are not 1, 2 and
- 4 respectively, as they should be. Note that the library
- should still work properly on 64-bit platforms which follow
- the LP64 programming model -- that is, where
- <code class="computeroutput">sizeof(long)</code> and
- <code class="computeroutput">sizeof(void*)</code> are 8. Under
- LP64, <code class="computeroutput">sizeof(int)</code> is still 4,
- so <code class="computeroutput">libbzip2</code>, which doesn't
- use the <code class="computeroutput">long</code> type, is
- OK.</p></dd>
-<dt><span class="term"><code class="computeroutput">BZ_SEQUENCE_ERROR</code></span></dt>
-<dd><p>When using the library, it is important to call
- the functions in the correct sequence and with data structures
- (buffers etc) in the correct states.
- <code class="computeroutput">libbzip2</code> checks as much as it
- can to ensure this is happening, and returns
- <code class="computeroutput">BZ_SEQUENCE_ERROR</code> if not.
- Code which complies precisely with the function semantics, as
- detailed below, should never receive this value; such an event
- denotes buggy code which you should
- investigate.</p></dd>
-<dt><span class="term"><code class="computeroutput">BZ_PARAM_ERROR</code></span></dt>
-<dd><p>Returned when a parameter to a function call is
- out of range or otherwise manifestly incorrect. As with
- <code class="computeroutput">BZ_SEQUENCE_ERROR</code>, this
- denotes a bug in the client code. The distinction between
- <code class="computeroutput">BZ_PARAM_ERROR</code> and
- <code class="computeroutput">BZ_SEQUENCE_ERROR</code> is a bit
- hazy, but still worth making.</p></dd>
-<dt><span class="term"><code class="computeroutput">BZ_MEM_ERROR</code></span></dt>
-<dd><p>Returned when a request to allocate memory
- failed. Note that the quantity of memory needed to decompress
- a stream cannot be determined until the stream's header has
- been read. So
- <code class="computeroutput">BZ2_bzDecompress</code> and
- <code class="computeroutput">BZ2_bzRead</code> may return
- <code class="computeroutput">BZ_MEM_ERROR</code> even though some
- of the compressed data has been read. The same is not true
- for compression; once
- <code class="computeroutput">BZ2_bzCompressInit</code> or
- <code class="computeroutput">BZ2_bzWriteOpen</code> have
- successfully completed,
- <code class="computeroutput">BZ_MEM_ERROR</code> cannot
- occur.</p></dd>
-<dt><span class="term"><code class="computeroutput">BZ_DATA_ERROR</code></span></dt>
-<dd><p>Returned when a data integrity error is
- detected during decompression. Most importantly, this means
- when stored and computed CRCs for the data do not match. This
- value is also returned upon detection of any other anomaly in
- the compressed data.</p></dd>
-<dt><span class="term"><code class="computeroutput">BZ_DATA_ERROR_MAGIC</code></span></dt>
-<dd><p>As a special case of
- <code class="computeroutput">BZ_DATA_ERROR</code>, it is
- sometimes useful to know when the compressed stream does not
- start with the correct magic bytes (<code class="computeroutput">'B' 'Z'
- 'h'</code>).</p></dd>
-<dt><span class="term"><code class="computeroutput">BZ_IO_ERROR</code></span></dt>
-<dd><p>Returned by
- <code class="computeroutput">BZ2_bzRead</code> and
- <code class="computeroutput">BZ2_bzWrite</code> when there is an
- error reading or writing in the compressed file, and by
- <code class="computeroutput">BZ2_bzReadOpen</code> and
- <code class="computeroutput">BZ2_bzWriteOpen</code> for attempts
- to use a file for which the error indicator (viz,
- <code class="computeroutput">ferror(f)</code>) is set. On
- receipt of <code class="computeroutput">BZ_IO_ERROR</code>, the
- caller should consult <code class="computeroutput">errno</code>
- and/or <code class="computeroutput">perror</code> to acquire
- operating-system specific information about the
- problem.</p></dd>
-<dt><span class="term"><code class="computeroutput">BZ_UNEXPECTED_EOF</code></span></dt>
-<dd><p>Returned by
- <code class="computeroutput">BZ2_bzRead</code> when the
- compressed file finishes before the logical end of stream is
- detected.</p></dd>
-<dt><span class="term"><code class="computeroutput">BZ_OUTBUFF_FULL</code></span></dt>
-<dd><p>Returned by
- <code class="computeroutput">BZ2_bzBuffToBuffCompress</code> and
- <code class="computeroutput">BZ2_bzBuffToBuffDecompress</code> to
- indicate that the output data will not fit into the output
- buffer provided.</p></dd>
-</dl></div>
-</div>
-<div class="sect1" title="3.3.�Low-level interface">
-<div class="titlepage"><div><div><h2 class="title" style="clear: both">
-<a name="low-level"></a>3.3.�Low-level interface</h2></div></div></div>
-<div class="sect2" title="3.3.1.�BZ2_bzCompressInit">
-<div class="titlepage"><div><div><h3 class="title">
-<a name="bzcompress-init"></a>3.3.1.�BZ2_bzCompressInit</h3></div></div></div>
-<pre class="programlisting">typedef struct {
- char *next_in;
- unsigned int avail_in;
- unsigned int total_in_lo32;
- unsigned int total_in_hi32;
-
- char *next_out;
- unsigned int avail_out;
- unsigned int total_out_lo32;
- unsigned int total_out_hi32;
-
- void *state;
-
- void *(*bzalloc)(void *,int,int);
- void (*bzfree)(void *,void *);
- void *opaque;
-} bz_stream;
-
-int BZ2_bzCompressInit ( bz_stream *strm,
- int blockSize100k,
- int verbosity,
- int workFactor );</pre>
-<p>Prepares for compression. The
-<code class="computeroutput">bz_stream</code> structure holds all
-data pertaining to the compression activity. A
-<code class="computeroutput">bz_stream</code> structure should be
-allocated and initialised prior to the call. The fields of
-<code class="computeroutput">bz_stream</code> comprise the entirety
-of the user-visible data. <code class="computeroutput">state</code>
-is a pointer to the private data structures required for
-compression.</p>
-<p>Custom memory allocators are supported, via fields
-<code class="computeroutput">bzalloc</code>,
-<code class="computeroutput">bzfree</code>, and
-<code class="computeroutput">opaque</code>. The value
-<code class="computeroutput">opaque</code> is passed to as the first
-argument to all calls to <code class="computeroutput">bzalloc</code>
-and <code class="computeroutput">bzfree</code>, but is otherwise
-ignored by the library. The call <code class="computeroutput">bzalloc (
-opaque, n, m )</code> is expected to return a pointer
-<code class="computeroutput">p</code> to <code class="computeroutput">n *
-m</code> bytes of memory, and <code class="computeroutput">bzfree (
-opaque, p )</code> should free that memory.</p>
-<p>If you don't want to use a custom memory allocator, set
-<code class="computeroutput">bzalloc</code>,
-<code class="computeroutput">bzfree</code> and
-<code class="computeroutput">opaque</code> to
-<code class="computeroutput">NULL</code>, and the library will then
-use the standard <code class="computeroutput">malloc</code> /
-<code class="computeroutput">free</code> routines.</p>
-<p>Before calling
-<code class="computeroutput">BZ2_bzCompressInit</code>, fields
-<code class="computeroutput">bzalloc</code>,
-<code class="computeroutput">bzfree</code> and
-<code class="computeroutput">opaque</code> should be filled
-appropriately, as just described. Upon return, the internal
-state will have been allocated and initialised, and
-<code class="computeroutput">total_in_lo32</code>,
-<code class="computeroutput">total_in_hi32</code>,
-<code class="computeroutput">total_out_lo32</code> and
-<code class="computeroutput">total_out_hi32</code> will have been
-set to zero. These four fields are used by the library to inform
-the caller of the total amount of data passed into and out of the
-library, respectively. You should not try to change them. As of
-version 1.0, 64-bit counts are maintained, even on 32-bit
-platforms, using the <code class="computeroutput">_hi32</code>
-fields to store the upper 32 bits of the count. So, for example,
-the total amount of data in is <code class="computeroutput">(total_in_hi32
-<< 32) + total_in_lo32</code>.</p>
-<p>Parameter <code class="computeroutput">blockSize100k</code>
-specifies the block size to be used for compression. It should
-be a value between 1 and 9 inclusive, and the actual block size
-used is 100000 x this figure. 9 gives the best compression but
-takes most memory.</p>
-<p>Parameter <code class="computeroutput">verbosity</code> should
-be set to a number between 0 and 4 inclusive. 0 is silent, and
-greater numbers give increasingly verbose monitoring/debugging
-output. If the library has been compiled with
-<code class="computeroutput">-DBZ_NO_STDIO</code>, no such output
-will appear for any verbosity setting.</p>
-<p>Parameter <code class="computeroutput">workFactor</code>
-controls how the compression phase behaves when presented with
-worst case, highly repetitive, input data. If compression runs
-into difficulties caused by repetitive data, the library switches
-from the standard sorting algorithm to a fallback algorithm. The
-fallback is slower than the standard algorithm by perhaps a
-factor of three, but always behaves reasonably, no matter how bad
-the input.</p>
-<p>Lower values of <code class="computeroutput">workFactor</code>
-reduce the amount of effort the standard algorithm will expend
-before resorting to the fallback. You should set this parameter
-carefully; too low, and many inputs will be handled by the
-fallback algorithm and so compress rather slowly, too high, and
-your average-to-worst case compression times can become very
-large. The default value of 30 gives reasonable behaviour over a
-wide range of circumstances.</p>
-<p>Allowable values range from 0 to 250 inclusive. 0 is a
-special case, equivalent to using the default value of 30.</p>
-<p>Note that the compressed output generated is the same
-regardless of whether or not the fallback algorithm is
-used.</p>
-<p>Be aware also that this parameter may disappear entirely in
-future versions of the library. In principle it should be
-possible to devise a good way to automatically choose which
-algorithm to use. Such a mechanism would render the parameter
-obsolete.</p>
-<p>Possible return values:</p>
-<pre class="programlisting">BZ_CONFIG_ERROR
- if the library has been mis-compiled
-BZ_PARAM_ERROR
- if strm is NULL
- or blockSize < 1 or blockSize > 9
- or verbosity < 0 or verbosity > 4
- or workFactor < 0 or workFactor > 250
-BZ_MEM_ERROR
- if not enough memory is available
-BZ_OK
- otherwise</pre>
-<p>Allowable next actions:</p>
-<pre class="programlisting">BZ2_bzCompress
- if BZ_OK is returned
- no specific action needed in case of error</pre>
-</div>
-<div class="sect2" title="3.3.2.�BZ2_bzCompress">
-<div class="titlepage"><div><div><h3 class="title">
-<a name="bzCompress"></a>3.3.2.�BZ2_bzCompress</h3></div></div></div>
-<pre class="programlisting">int BZ2_bzCompress ( bz_stream *strm, int action );</pre>
-<p>Provides more input and/or output buffer space for the
-library. The caller maintains input and output buffers, and
-calls <code class="computeroutput">BZ2_bzCompress</code> to transfer
-data between them.</p>
-<p>Before each call to
-<code class="computeroutput">BZ2_bzCompress</code>,
-<code class="computeroutput">next_in</code> should point at the data
-to be compressed, and <code class="computeroutput">avail_in</code>
-should indicate how many bytes the library may read.
-<code class="computeroutput">BZ2_bzCompress</code> updates
-<code class="computeroutput">next_in</code>,
-<code class="computeroutput">avail_in</code> and
-<code class="computeroutput">total_in</code> to reflect the number
-of bytes it has read.</p>
-<p>Similarly, <code class="computeroutput">next_out</code> should
-point to a buffer in which the compressed data is to be placed,
-with <code class="computeroutput">avail_out</code> indicating how
-much output space is available.
-<code class="computeroutput">BZ2_bzCompress</code> updates
-<code class="computeroutput">next_out</code>,
-<code class="computeroutput">avail_out</code> and
-<code class="computeroutput">total_out</code> to reflect the number
-of bytes output.</p>
-<p>You may provide and remove as little or as much data as you
-like on each call of
-<code class="computeroutput">BZ2_bzCompress</code>. In the limit,
-it is acceptable to supply and remove data one byte at a time,
-although this would be terribly inefficient. You should always
-ensure that at least one byte of output space is available at
-each call.</p>
-<p>A second purpose of
-<code class="computeroutput">BZ2_bzCompress</code> is to request a
-change of mode of the compressed stream.</p>
-<p>Conceptually, a compressed stream can be in one of four
-states: IDLE, RUNNING, FLUSHING and FINISHING. Before
-initialisation
-(<code class="computeroutput">BZ2_bzCompressInit</code>) and after
-termination (<code class="computeroutput">BZ2_bzCompressEnd</code>),
-a stream is regarded as IDLE.</p>
-<p>Upon initialisation
-(<code class="computeroutput">BZ2_bzCompressInit</code>), the stream
-is placed in the RUNNING state. Subsequent calls to
-<code class="computeroutput">BZ2_bzCompress</code> should pass
-<code class="computeroutput">BZ_RUN</code> as the requested action;
-other actions are illegal and will result in
-<code class="computeroutput">BZ_SEQUENCE_ERROR</code>.</p>
-<p>At some point, the calling program will have provided all
-the input data it wants to. It will then want to finish up -- in
-effect, asking the library to process any data it might have
-buffered internally. In this state,
-<code class="computeroutput">BZ2_bzCompress</code> will no longer
-attempt to read data from
-<code class="computeroutput">next_in</code>, but it will want to
-write data to <code class="computeroutput">next_out</code>. Because
-the output buffer supplied by the user can be arbitrarily small,
-the finishing-up operation cannot necessarily be done with a
-single call of
-<code class="computeroutput">BZ2_bzCompress</code>.</p>
-<p>Instead, the calling program passes
-<code class="computeroutput">BZ_FINISH</code> as an action to
-<code class="computeroutput">BZ2_bzCompress</code>. This changes
-the stream's state to FINISHING. Any remaining input (ie,
-<code class="computeroutput">next_in[0 .. avail_in-1]</code>) is
-compressed and transferred to the output buffer. To do this,
-<code class="computeroutput">BZ2_bzCompress</code> must be called
-repeatedly until all the output has been consumed. At that
-point, <code class="computeroutput">BZ2_bzCompress</code> returns
-<code class="computeroutput">BZ_STREAM_END</code>, and the stream's
-state is set back to IDLE.
-<code class="computeroutput">BZ2_bzCompressEnd</code> should then be
-called.</p>
-<p>Just to make sure the calling program does not cheat, the
-library makes a note of <code class="computeroutput">avail_in</code>
-at the time of the first call to
-<code class="computeroutput">BZ2_bzCompress</code> which has
-<code class="computeroutput">BZ_FINISH</code> as an action (ie, at
-the time the program has announced its intention to not supply
-any more input). By comparing this value with that of
-<code class="computeroutput">avail_in</code> over subsequent calls
-to <code class="computeroutput">BZ2_bzCompress</code>, the library
-can detect any attempts to slip in more data to compress. Any
-calls for which this is detected will return
-<code class="computeroutput">BZ_SEQUENCE_ERROR</code>. This
-indicates a programming mistake which should be corrected.</p>
-<p>Instead of asking to finish, the calling program may ask
-<code class="computeroutput">BZ2_bzCompress</code> to take all the
-remaining input, compress it and terminate the current
-(Burrows-Wheeler) compression block. This could be useful for
-error control purposes. The mechanism is analogous to that for
-finishing: call <code class="computeroutput">BZ2_bzCompress</code>
-with an action of <code class="computeroutput">BZ_FLUSH</code>,
-remove output data, and persist with the
-<code class="computeroutput">BZ_FLUSH</code> action until the value
-<code class="computeroutput">BZ_RUN</code> is returned. As with
-finishing, <code class="computeroutput">BZ2_bzCompress</code>
-detects any attempt to provide more input data once the flush has
-begun.</p>
-<p>Once the flush is complete, the stream returns to the
-normal RUNNING state.</p>
-<p>This all sounds pretty complex, but isn't really. Here's a
-table which shows which actions are allowable in each state, what
-action will be taken, what the next state is, and what the
-non-error return values are. Note that you can't explicitly ask
-what state the stream is in, but nor do you need to -- it can be
-inferred from the values returned by
-<code class="computeroutput">BZ2_bzCompress</code>.</p>
-<pre class="programlisting">IDLE/any
- Illegal. IDLE state only exists after BZ2_bzCompressEnd or
- before BZ2_bzCompressInit.
- Return value = BZ_SEQUENCE_ERROR
-
-RUNNING/BZ_RUN
- Compress from next_in to next_out as much as possible.
- Next state = RUNNING
- Return value = BZ_RUN_OK
-
-RUNNING/BZ_FLUSH
- Remember current value of next_in. Compress from next_in
- to next_out as much as possible, but do not accept any more input.
- Next state = FLUSHING
- Return value = BZ_FLUSH_OK
-
-RUNNING/BZ_FINISH
- Remember current value of next_in. Compress from next_in
- to next_out as much as possible, but do not accept any more input.
- Next state = FINISHING
- Return value = BZ_FINISH_OK
-
-FLUSHING/BZ_FLUSH
- Compress from next_in to next_out as much as possible,
- but do not accept any more input.
- If all the existing input has been used up and all compressed
- output has been removed
- Next state = RUNNING; Return value = BZ_RUN_OK
- else
- Next state = FLUSHING; Return value = BZ_FLUSH_OK
-
-FLUSHING/other
- Illegal.
- Return value = BZ_SEQUENCE_ERROR
-
-FINISHING/BZ_FINISH
- Compress from next_in to next_out as much as possible,
- but to not accept any more input.
- If all the existing input has been used up and all compressed
- output has been removed
- Next state = IDLE; Return value = BZ_STREAM_END
- else
- Next state = FINISHING; Return value = BZ_FINISH_OK
-
-FINISHING/other
- Illegal.
- Return value = BZ_SEQUENCE_ERROR</pre>
-<p>That still looks complicated? Well, fair enough. The
-usual sequence of calls for compressing a load of data is:</p>
-<div class="orderedlist"><ol class="orderedlist" type="1">
-<li class="listitem"><p>Get started with
- <code class="computeroutput">BZ2_bzCompressInit</code>.</p></li>
-<li class="listitem"><p>Shovel data in and shlurp out its compressed form
- using zero or more calls of
- <code class="computeroutput">BZ2_bzCompress</code> with action =
- <code class="computeroutput">BZ_RUN</code>.</p></li>
-<li class="listitem"><p>Finish up. Repeatedly call
- <code class="computeroutput">BZ2_bzCompress</code> with action =
- <code class="computeroutput">BZ_FINISH</code>, copying out the
- compressed output, until
- <code class="computeroutput">BZ_STREAM_END</code> is
- returned.</p></li>
-<li class="listitem"><p>Close up and go home. Call
- <code class="computeroutput">BZ2_bzCompressEnd</code>.</p></li>
-</ol></div>
-<p>If the data you want to compress fits into your input
-buffer all at once, you can skip the calls of
-<code class="computeroutput">BZ2_bzCompress ( ..., BZ_RUN )</code>
-and just do the <code class="computeroutput">BZ2_bzCompress ( ..., BZ_FINISH
-)</code> calls.</p>
-<p>All required memory is allocated by
-<code class="computeroutput">BZ2_bzCompressInit</code>. The
-compression library can accept any data at all (obviously). So
-you shouldn't get any error return values from the
-<code class="computeroutput">BZ2_bzCompress</code> calls. If you
-do, they will be
-<code class="computeroutput">BZ_SEQUENCE_ERROR</code>, and indicate
-a bug in your programming.</p>
-<p>Trivial other possible return values:</p>
-<pre class="programlisting">BZ_PARAM_ERROR
- if strm is NULL, or strm->s is NULL</pre>
-</div>
-<div class="sect2" title="3.3.3.�BZ2_bzCompressEnd">
-<div class="titlepage"><div><div><h3 class="title">
-<a name="bzCompress-end"></a>3.3.3.�BZ2_bzCompressEnd</h3></div></div></div>
-<pre class="programlisting">int BZ2_bzCompressEnd ( bz_stream *strm );</pre>
-<p>Releases all memory associated with a compression
-stream.</p>
-<p>Possible return values:</p>
-<pre class="programlisting">BZ_PARAM_ERROR if strm is NULL or strm->s is NULL
-BZ_OK otherwise</pre>
-</div>
-<div class="sect2" title="3.3.4.�BZ2_bzDecompressInit">
-<div class="titlepage"><div><div><h3 class="title">
-<a name="bzDecompress-init"></a>3.3.4.�BZ2_bzDecompressInit</h3></div></div></div>
-<pre class="programlisting">int BZ2_bzDecompressInit ( bz_stream *strm, int verbosity, int small );</pre>
-<p>Prepares for decompression. As with
-<code class="computeroutput">BZ2_bzCompressInit</code>, a
-<code class="computeroutput">bz_stream</code> record should be
-allocated and initialised before the call. Fields
-<code class="computeroutput">bzalloc</code>,
-<code class="computeroutput">bzfree</code> and
-<code class="computeroutput">opaque</code> should be set if a custom
-memory allocator is required, or made
-<code class="computeroutput">NULL</code> for the normal
-<code class="computeroutput">malloc</code> /
-<code class="computeroutput">free</code> routines. Upon return, the
-internal state will have been initialised, and
-<code class="computeroutput">total_in</code> and
-<code class="computeroutput">total_out</code> will be zero.</p>
-<p>For the meaning of parameter
-<code class="computeroutput">verbosity</code>, see
-<code class="computeroutput">BZ2_bzCompressInit</code>.</p>
-<p>If <code class="computeroutput">small</code> is nonzero, the
-library will use an alternative decompression algorithm which
-uses less memory but at the cost of decompressing more slowly
-(roughly speaking, half the speed, but the maximum memory
-requirement drops to around 2300k). See <a class="xref" href="#using" title="2.�How to use bzip2">How to use bzip2</a>
-for more information on memory management.</p>
-<p>Note that the amount of memory needed to decompress a
-stream cannot be determined until the stream's header has been
-read, so even if
-<code class="computeroutput">BZ2_bzDecompressInit</code> succeeds, a
-subsequent <code class="computeroutput">BZ2_bzDecompress</code>
-could fail with
-<code class="computeroutput">BZ_MEM_ERROR</code>.</p>
-<p>Possible return values:</p>
-<pre class="programlisting">BZ_CONFIG_ERROR
- if the library has been mis-compiled
-BZ_PARAM_ERROR
- if ( small != 0 && small != 1 )
- or (verbosity <; 0 || verbosity > 4)
-BZ_MEM_ERROR
- if insufficient memory is available</pre>
-<p>Allowable next actions:</p>
-<pre class="programlisting">BZ2_bzDecompress
- if BZ_OK was returned
- no specific action required in case of error</pre>
-</div>
-<div class="sect2" title="3.3.5.�BZ2_bzDecompress">
-<div class="titlepage"><div><div><h3 class="title">
-<a name="bzDecompress"></a>3.3.5.�BZ2_bzDecompress</h3></div></div></div>
-<pre class="programlisting">int BZ2_bzDecompress ( bz_stream *strm );</pre>
-<p>Provides more input and/out output buffer space for the
-library. The caller maintains input and output buffers, and uses
-<code class="computeroutput">BZ2_bzDecompress</code> to transfer
-data between them.</p>
-<p>Before each call to
-<code class="computeroutput">BZ2_bzDecompress</code>,
-<code class="computeroutput">next_in</code> should point at the
-compressed data, and <code class="computeroutput">avail_in</code>
-should indicate how many bytes the library may read.
-<code class="computeroutput">BZ2_bzDecompress</code> updates
-<code class="computeroutput">next_in</code>,
-<code class="computeroutput">avail_in</code> and
-<code class="computeroutput">total_in</code> to reflect the number
-of bytes it has read.</p>
-<p>Similarly, <code class="computeroutput">next_out</code> should
-point to a buffer in which the uncompressed output is to be
-placed, with <code class="computeroutput">avail_out</code>
-indicating how much output space is available.
-<code class="computeroutput">BZ2_bzCompress</code> updates
-<code class="computeroutput">next_out</code>,
-<code class="computeroutput">avail_out</code> and
-<code class="computeroutput">total_out</code> to reflect the number
-of bytes output.</p>
-<p>You may provide and remove as little or as much data as you
-like on each call of
-<code class="computeroutput">BZ2_bzDecompress</code>. In the limit,
-it is acceptable to supply and remove data one byte at a time,
-although this would be terribly inefficient. You should always
-ensure that at least one byte of output space is available at
-each call.</p>
-<p>Use of <code class="computeroutput">BZ2_bzDecompress</code> is
-simpler than
-<code class="computeroutput">BZ2_bzCompress</code>.</p>
-<p>You should provide input and remove output as described
-above, and repeatedly call
-<code class="computeroutput">BZ2_bzDecompress</code> until
-<code class="computeroutput">BZ_STREAM_END</code> is returned.
-Appearance of <code class="computeroutput">BZ_STREAM_END</code>
-denotes that <code class="computeroutput">BZ2_bzDecompress</code>
-has detected the logical end of the compressed stream.
-<code class="computeroutput">BZ2_bzDecompress</code> will not
-produce <code class="computeroutput">BZ_STREAM_END</code> until all
-output data has been placed into the output buffer, so once
-<code class="computeroutput">BZ_STREAM_END</code> appears, you are
-guaranteed to have available all the decompressed output, and
-<code class="computeroutput">BZ2_bzDecompressEnd</code> can safely
-be called.</p>
-<p>If case of an error return value, you should call
-<code class="computeroutput">BZ2_bzDecompressEnd</code> to clean up
-and release memory.</p>
-<p>Possible return values:</p>
-<pre class="programlisting">BZ_PARAM_ERROR
- if strm is NULL or strm->s is NULL
- or strm->avail_out < 1
-BZ_DATA_ERROR
- if a data integrity error is detected in the compressed stream
-BZ_DATA_ERROR_MAGIC
- if the compressed stream doesn't begin with the right magic bytes
-BZ_MEM_ERROR
- if there wasn't enough memory available
-BZ_STREAM_END
- if the logical end of the data stream was detected and all
- output in has been consumed, eg s-->avail_out > 0
-BZ_OK
- otherwise</pre>
-<p>Allowable next actions:</p>
-<pre class="programlisting">BZ2_bzDecompress
- if BZ_OK was returned
-BZ2_bzDecompressEnd
- otherwise</pre>
-</div>
-<div class="sect2" title="3.3.6.�BZ2_bzDecompressEnd">
-<div class="titlepage"><div><div><h3 class="title">
-<a name="bzDecompress-end"></a>3.3.6.�BZ2_bzDecompressEnd</h3></div></div></div>
-<pre class="programlisting">int BZ2_bzDecompressEnd ( bz_stream *strm );</pre>
-<p>Releases all memory associated with a decompression
-stream.</p>
-<p>Possible return values:</p>
-<pre class="programlisting">BZ_PARAM_ERROR
- if strm is NULL or strm->s is NULL
-BZ_OK
- otherwise</pre>
-<p>Allowable next actions:</p>
-<pre class="programlisting"> None.</pre>
-</div>
-</div>
-<div class="sect1" title="3.4.�High-level interface">
-<div class="titlepage"><div><div><h2 class="title" style="clear: both">
-<a name="hl-interface"></a>3.4.�High-level interface</h2></div></div></div>
-<p>This interface provides functions for reading and writing
-<code class="computeroutput">bzip2</code> format files. First, some
-general points.</p>
-<div class="itemizedlist"><ul class="itemizedlist" type="bullet">
-<li class="listitem" style="list-style-type: disc"><p>All of the functions take an
- <code class="computeroutput">int*</code> first argument,
- <code class="computeroutput">bzerror</code>. After each call,
- <code class="computeroutput">bzerror</code> should be consulted
- first to determine the outcome of the call. If
- <code class="computeroutput">bzerror</code> is
- <code class="computeroutput">BZ_OK</code>, the call completed
- successfully, and only then should the return value of the
- function (if any) be consulted. If
- <code class="computeroutput">bzerror</code> is
- <code class="computeroutput">BZ_IO_ERROR</code>, there was an
- error reading/writing the underlying compressed file, and you
- should then consult <code class="computeroutput">errno</code> /
- <code class="computeroutput">perror</code> to determine the cause
- of the difficulty. <code class="computeroutput">bzerror</code>
- may also be set to various other values; precise details are
- given on a per-function basis below.</p></li>
-<li class="listitem" style="list-style-type: disc"><p>If <code class="computeroutput">bzerror</code> indicates
- an error (ie, anything except
- <code class="computeroutput">BZ_OK</code> and
- <code class="computeroutput">BZ_STREAM_END</code>), you should
- immediately call
- <code class="computeroutput">BZ2_bzReadClose</code> (or
- <code class="computeroutput">BZ2_bzWriteClose</code>, depending on
- whether you are attempting to read or to write) to free up all
- resources associated with the stream. Once an error has been
- indicated, behaviour of all calls except
- <code class="computeroutput">BZ2_bzReadClose</code>
- (<code class="computeroutput">BZ2_bzWriteClose</code>) is
- undefined. The implication is that (1)
- <code class="computeroutput">bzerror</code> should be checked
- after each call, and (2) if
- <code class="computeroutput">bzerror</code> indicates an error,
- <code class="computeroutput">BZ2_bzReadClose</code>
- (<code class="computeroutput">BZ2_bzWriteClose</code>) should then
- be called to clean up.</p></li>
-<li class="listitem" style="list-style-type: disc"><p>The <code class="computeroutput">FILE*</code> arguments
- passed to <code class="computeroutput">BZ2_bzReadOpen</code> /
- <code class="computeroutput">BZ2_bzWriteOpen</code> should be set
- to binary mode. Most Unix systems will do this by default, but
- other platforms, including Windows and Mac, will not. If you
- omit this, you may encounter problems when moving code to new
- platforms.</p></li>
-<li class="listitem" style="list-style-type: disc"><p>Memory allocation requests are handled by
- <code class="computeroutput">malloc</code> /
- <code class="computeroutput">free</code>. At present there is no
- facility for user-defined memory allocators in the file I/O
- functions (could easily be added, though).</p></li>
-</ul></div>
-<div class="sect2" title="3.4.1.�BZ2_bzReadOpen">
-<div class="titlepage"><div><div><h3 class="title">
-<a name="bzreadopen"></a>3.4.1.�BZ2_bzReadOpen</h3></div></div></div>
-<pre class="programlisting">typedef void BZFILE;
-
-BZFILE *BZ2_bzReadOpen( int *bzerror, FILE *f,
- int verbosity, int small,
- void *unused, int nUnused );</pre>
-<p>Prepare to read compressed data from file handle
-<code class="computeroutput">f</code>.
-<code class="computeroutput">f</code> should refer to a file which
-has been opened for reading, and for which the error indicator
-(<code class="computeroutput">ferror(f)</code>)is not set. If
-<code class="computeroutput">small</code> is 1, the library will try
-to decompress using less memory, at the expense of speed.</p>
-<p>For reasons explained below,
-<code class="computeroutput">BZ2_bzRead</code> will decompress the
-<code class="computeroutput">nUnused</code> bytes starting at
-<code class="computeroutput">unused</code>, before starting to read
-from the file <code class="computeroutput">f</code>. At most
-<code class="computeroutput">BZ_MAX_UNUSED</code> bytes may be
-supplied like this. If this facility is not required, you should
-pass <code class="computeroutput">NULL</code> and
-<code class="computeroutput">0</code> for
-<code class="computeroutput">unused</code> and
-n<code class="computeroutput">Unused</code> respectively.</p>
-<p>For the meaning of parameters
-<code class="computeroutput">small</code> and
-<code class="computeroutput">verbosity</code>, see
-<code class="computeroutput">BZ2_bzDecompressInit</code>.</p>
-<p>The amount of memory needed to decompress a file cannot be
-determined until the file's header has been read. So it is
-possible that <code class="computeroutput">BZ2_bzReadOpen</code>
-returns <code class="computeroutput">BZ_OK</code> but a subsequent
-call of <code class="computeroutput">BZ2_bzRead</code> will return
-<code class="computeroutput">BZ_MEM_ERROR</code>.</p>
-<p>Possible assignments to
-<code class="computeroutput">bzerror</code>:</p>
-<pre class="programlisting">BZ_CONFIG_ERROR
- if the library has been mis-compiled
-BZ_PARAM_ERROR
- if f is NULL
- or small is neither 0 nor 1
- or ( unused == NULL && nUnused != 0 )
- or ( unused != NULL && !(0 <= nUnused <= BZ_MAX_UNUSED) )
-BZ_IO_ERROR
- if ferror(f) is nonzero
-BZ_MEM_ERROR
- if insufficient memory is available
-BZ_OK
- otherwise.</pre>
-<p>Possible return values:</p>
-<pre class="programlisting">Pointer to an abstract BZFILE
- if bzerror is BZ_OK
-NULL
- otherwise</pre>
-<p>Allowable next actions:</p>
-<pre class="programlisting">BZ2_bzRead
- if bzerror is BZ_OK
-BZ2_bzClose
- otherwise</pre>
-</div>
-<div class="sect2" title="3.4.2.�BZ2_bzRead">
-<div class="titlepage"><div><div><h3 class="title">
-<a name="bzread"></a>3.4.2.�BZ2_bzRead</h3></div></div></div>
-<pre class="programlisting">int BZ2_bzRead ( int *bzerror, BZFILE *b, void *buf, int len );</pre>
-<p>Reads up to <code class="computeroutput">len</code>
-(uncompressed) bytes from the compressed file
-<code class="computeroutput">b</code> into the buffer
-<code class="computeroutput">buf</code>. If the read was
-successful, <code class="computeroutput">bzerror</code> is set to
-<code class="computeroutput">BZ_OK</code> and the number of bytes
-read is returned. If the logical end-of-stream was detected,
-<code class="computeroutput">bzerror</code> will be set to
-<code class="computeroutput">BZ_STREAM_END</code>, and the number of
-bytes read is returned. All other
-<code class="computeroutput">bzerror</code> values denote an
-error.</p>
-<p><code class="computeroutput">BZ2_bzRead</code> will supply
-<code class="computeroutput">len</code> bytes, unless the logical
-stream end is detected or an error occurs. Because of this, it
-is possible to detect the stream end by observing when the number
-of bytes returned is less than the number requested.
-Nevertheless, this is regarded as inadvisable; you should instead
-check <code class="computeroutput">bzerror</code> after every call
-and watch out for
-<code class="computeroutput">BZ_STREAM_END</code>.</p>
-<p>Internally, <code class="computeroutput">BZ2_bzRead</code>
-copies data from the compressed file in chunks of size
-<code class="computeroutput">BZ_MAX_UNUSED</code> bytes before
-decompressing it. If the file contains more bytes than strictly
-needed to reach the logical end-of-stream,
-<code class="computeroutput">BZ2_bzRead</code> will almost certainly
-read some of the trailing data before signalling
-<code class="computeroutput">BZ_SEQUENCE_END</code>. To collect the
-read but unused data once
-<code class="computeroutput">BZ_SEQUENCE_END</code> has appeared,
-call <code class="computeroutput">BZ2_bzReadGetUnused</code>
-immediately before
-<code class="computeroutput">BZ2_bzReadClose</code>.</p>
-<p>Possible assignments to
-<code class="computeroutput">bzerror</code>:</p>
-<pre class="programlisting">BZ_PARAM_ERROR
- if b is NULL or buf is NULL or len < 0
-BZ_SEQUENCE_ERROR
- if b was opened with BZ2_bzWriteOpen
-BZ_IO_ERROR
- if there is an error reading from the compressed file
-BZ_UNEXPECTED_EOF
- if the compressed file ended before
- the logical end-of-stream was detected
-BZ_DATA_ERROR
- if a data integrity error was detected in the compressed stream
-BZ_DATA_ERROR_MAGIC
- if the stream does not begin with the requisite header bytes
- (ie, is not a bzip2 data file). This is really
- a special case of BZ_DATA_ERROR.
-BZ_MEM_ERROR
- if insufficient memory was available
-BZ_STREAM_END
- if the logical end of stream was detected.
-BZ_OK
- otherwise.</pre>
-<p>Possible return values:</p>
-<pre class="programlisting">number of bytes read
- if bzerror is BZ_OK or BZ_STREAM_END
-undefined
- otherwise</pre>
-<p>Allowable next actions:</p>
-<pre class="programlisting">collect data from buf, then BZ2_bzRead or BZ2_bzReadClose
- if bzerror is BZ_OK
-collect data from buf, then BZ2_bzReadClose or BZ2_bzReadGetUnused
- if bzerror is BZ_SEQUENCE_END
-BZ2_bzReadClose
- otherwise</pre>
-</div>
-<div class="sect2" title="3.4.3.�BZ2_bzReadGetUnused">
-<div class="titlepage"><div><div><h3 class="title">
-<a name="bzreadgetunused"></a>3.4.3.�BZ2_bzReadGetUnused</h3></div></div></div>
-<pre class="programlisting">void BZ2_bzReadGetUnused( int* bzerror, BZFILE *b,
- void** unused, int* nUnused );</pre>
-<p>Returns data which was read from the compressed file but
-was not needed to get to the logical end-of-stream.
-<code class="computeroutput">*unused</code> is set to the address of
-the data, and <code class="computeroutput">*nUnused</code> to the
-number of bytes. <code class="computeroutput">*nUnused</code> will
-be set to a value between <code class="computeroutput">0</code> and
-<code class="computeroutput">BZ_MAX_UNUSED</code> inclusive.</p>
-<p>This function may only be called once
-<code class="computeroutput">BZ2_bzRead</code> has signalled
-<code class="computeroutput">BZ_STREAM_END</code> but before
-<code class="computeroutput">BZ2_bzReadClose</code>.</p>
-<p>Possible assignments to
-<code class="computeroutput">bzerror</code>:</p>
-<pre class="programlisting">BZ_PARAM_ERROR
- if b is NULL
- or unused is NULL or nUnused is NULL
-BZ_SEQUENCE_ERROR
- if BZ_STREAM_END has not been signalled
- or if b was opened with BZ2_bzWriteOpen
-BZ_OK
- otherwise</pre>
-<p>Allowable next actions:</p>
-<pre class="programlisting">BZ2_bzReadClose</pre>
-</div>
-<div class="sect2" title="3.4.4.�BZ2_bzReadClose">
-<div class="titlepage"><div><div><h3 class="title">
-<a name="bzreadclose"></a>3.4.4.�BZ2_bzReadClose</h3></div></div></div>
-<pre class="programlisting">void BZ2_bzReadClose ( int *bzerror, BZFILE *b );</pre>
-<p>Releases all memory pertaining to the compressed file
-<code class="computeroutput">b</code>.
-<code class="computeroutput">BZ2_bzReadClose</code> does not call
-<code class="computeroutput">fclose</code> on the underlying file
-handle, so you should do that yourself if appropriate.
-<code class="computeroutput">BZ2_bzReadClose</code> should be called
-to clean up after all error situations.</p>
-<p>Possible assignments to
-<code class="computeroutput">bzerror</code>:</p>
-<pre class="programlisting">BZ_SEQUENCE_ERROR
- if b was opened with BZ2_bzOpenWrite
-BZ_OK
- otherwise</pre>
-<p>Allowable next actions:</p>
-<pre class="programlisting">none</pre>
-</div>
-<div class="sect2" title="3.4.5.�BZ2_bzWriteOpen">
-<div class="titlepage"><div><div><h3 class="title">
-<a name="bzwriteopen"></a>3.4.5.�BZ2_bzWriteOpen</h3></div></div></div>
-<pre class="programlisting">BZFILE *BZ2_bzWriteOpen( int *bzerror, FILE *f,
- int blockSize100k, int verbosity,
- int workFactor );</pre>
-<p>Prepare to write compressed data to file handle
-<code class="computeroutput">f</code>.
-<code class="computeroutput">f</code> should refer to a file which
-has been opened for writing, and for which the error indicator
-(<code class="computeroutput">ferror(f)</code>)is not set.</p>
-<p>For the meaning of parameters
-<code class="computeroutput">blockSize100k</code>,
-<code class="computeroutput">verbosity</code> and
-<code class="computeroutput">workFactor</code>, see
-<code class="computeroutput">BZ2_bzCompressInit</code>.</p>
-<p>All required memory is allocated at this stage, so if the
-call completes successfully,
-<code class="computeroutput">BZ_MEM_ERROR</code> cannot be signalled
-by a subsequent call to
-<code class="computeroutput">BZ2_bzWrite</code>.</p>
-<p>Possible assignments to
-<code class="computeroutput">bzerror</code>:</p>
-<pre class="programlisting">BZ_CONFIG_ERROR
- if the library has been mis-compiled
-BZ_PARAM_ERROR
- if f is NULL
- or blockSize100k < 1 or blockSize100k > 9
-BZ_IO_ERROR
- if ferror(f) is nonzero
-BZ_MEM_ERROR
- if insufficient memory is available
-BZ_OK
- otherwise</pre>
-<p>Possible return values:</p>
-<pre class="programlisting">Pointer to an abstract BZFILE
- if bzerror is BZ_OK
-NULL
- otherwise</pre>
-<p>Allowable next actions:</p>
-<pre class="programlisting">BZ2_bzWrite
- if bzerror is BZ_OK
- (you could go directly to BZ2_bzWriteClose, but this would be pretty pointless)
-BZ2_bzWriteClose
- otherwise</pre>
-</div>
-<div class="sect2" title="3.4.6.�BZ2_bzWrite">
-<div class="titlepage"><div><div><h3 class="title">
-<a name="bzwrite"></a>3.4.6.�BZ2_bzWrite</h3></div></div></div>
-<pre class="programlisting">void BZ2_bzWrite ( int *bzerror, BZFILE *b, void *buf, int len );</pre>
-<p>Absorbs <code class="computeroutput">len</code> bytes from the
-buffer <code class="computeroutput">buf</code>, eventually to be
-compressed and written to the file.</p>
-<p>Possible assignments to
-<code class="computeroutput">bzerror</code>:</p>
-<pre class="programlisting">BZ_PARAM_ERROR
- if b is NULL or buf is NULL or len < 0
-BZ_SEQUENCE_ERROR
- if b was opened with BZ2_bzReadOpen
-BZ_IO_ERROR
- if there is an error writing the compressed file.
-BZ_OK
- otherwise</pre>
-</div>
-<div class="sect2" title="3.4.7.�BZ2_bzWriteClose">
-<div class="titlepage"><div><div><h3 class="title">
-<a name="bzwriteclose"></a>3.4.7.�BZ2_bzWriteClose</h3></div></div></div>
-<pre class="programlisting">void BZ2_bzWriteClose( int *bzerror, BZFILE* f,
- int abandon,
- unsigned int* nbytes_in,
- unsigned int* nbytes_out );
-
-void BZ2_bzWriteClose64( int *bzerror, BZFILE* f,
- int abandon,
- unsigned int* nbytes_in_lo32,
- unsigned int* nbytes_in_hi32,
- unsigned int* nbytes_out_lo32,
- unsigned int* nbytes_out_hi32 );</pre>
-<p>Compresses and flushes to the compressed file all data so
-far supplied by <code class="computeroutput">BZ2_bzWrite</code>.
-The logical end-of-stream markers are also written, so subsequent
-calls to <code class="computeroutput">BZ2_bzWrite</code> are
-illegal. All memory associated with the compressed file
-<code class="computeroutput">b</code> is released.
-<code class="computeroutput">fflush</code> is called on the
-compressed file, but it is not
-<code class="computeroutput">fclose</code>'d.</p>
-<p>If <code class="computeroutput">BZ2_bzWriteClose</code> is
-called to clean up after an error, the only action is to release
-the memory. The library records the error codes issued by
-previous calls, so this situation will be detected automatically.
-There is no attempt to complete the compression operation, nor to
-<code class="computeroutput">fflush</code> the compressed file. You
-can force this behaviour to happen even in the case of no error,
-by passing a nonzero value to
-<code class="computeroutput">abandon</code>.</p>
-<p>If <code class="computeroutput">nbytes_in</code> is non-null,
-<code class="computeroutput">*nbytes_in</code> will be set to be the
-total volume of uncompressed data handled. Similarly,
-<code class="computeroutput">nbytes_out</code> will be set to the
-total volume of compressed data written. For compatibility with
-older versions of the library,
-<code class="computeroutput">BZ2_bzWriteClose</code> only yields the
-lower 32 bits of these counts. Use
-<code class="computeroutput">BZ2_bzWriteClose64</code> if you want
-the full 64 bit counts. These two functions are otherwise
-absolutely identical.</p>
-<p>Possible assignments to
-<code class="computeroutput">bzerror</code>:</p>
-<pre class="programlisting">BZ_SEQUENCE_ERROR
- if b was opened with BZ2_bzReadOpen
-BZ_IO_ERROR
- if there is an error writing the compressed file
-BZ_OK
- otherwise</pre>
-</div>
-<div class="sect2" title="3.4.8.�Handling embedded compressed data streams">
-<div class="titlepage"><div><div><h3 class="title">
-<a name="embed"></a>3.4.8.�Handling embedded compressed data streams</h3></div></div></div>
-<p>The high-level library facilitates use of
-<code class="computeroutput">bzip2</code> data streams which form
-some part of a surrounding, larger data stream.</p>
-<div class="itemizedlist"><ul class="itemizedlist" type="bullet">
-<li class="listitem" style="list-style-type: disc"><p>For writing, the library takes an open file handle,
- writes compressed data to it,
- <code class="computeroutput">fflush</code>es it but does not
- <code class="computeroutput">fclose</code> it. The calling
- application can write its own data before and after the
- compressed data stream, using that same file handle.</p></li>
-<li class="listitem" style="list-style-type: disc"><p>Reading is more complex, and the facilities are not as
- general as they could be since generality is hard to reconcile
- with efficiency. <code class="computeroutput">BZ2_bzRead</code>
- reads from the compressed file in blocks of size
- <code class="computeroutput">BZ_MAX_UNUSED</code> bytes, and in
- doing so probably will overshoot the logical end of compressed
- stream. To recover this data once decompression has ended,
- call <code class="computeroutput">BZ2_bzReadGetUnused</code> after
- the last call of <code class="computeroutput">BZ2_bzRead</code>
- (the one returning
- <code class="computeroutput">BZ_STREAM_END</code>) but before
- calling
- <code class="computeroutput">BZ2_bzReadClose</code>.</p></li>
-</ul></div>
-<p>This mechanism makes it easy to decompress multiple
-<code class="computeroutput">bzip2</code> streams placed end-to-end.
-As the end of one stream, when
-<code class="computeroutput">BZ2_bzRead</code> returns
-<code class="computeroutput">BZ_STREAM_END</code>, call
-<code class="computeroutput">BZ2_bzReadGetUnused</code> to collect
-the unused data (copy it into your own buffer somewhere). That
-data forms the start of the next compressed stream. To start
-uncompressing that next stream, call
-<code class="computeroutput">BZ2_bzReadOpen</code> again, feeding in
-the unused data via the <code class="computeroutput">unused</code> /
-<code class="computeroutput">nUnused</code> parameters. Keep doing
-this until <code class="computeroutput">BZ_STREAM_END</code> return
-coincides with the physical end of file
-(<code class="computeroutput">feof(f)</code>). In this situation
-<code class="computeroutput">BZ2_bzReadGetUnused</code> will of
-course return no data.</p>
-<p>This should give some feel for how the high-level interface
-can be used. If you require extra flexibility, you'll have to
-bite the bullet and get to grips with the low-level
-interface.</p>
-</div>
-<div class="sect2" title="3.4.9.�Standard file-reading/writing code">
-<div class="titlepage"><div><div><h3 class="title">
-<a name="std-rdwr"></a>3.4.9.�Standard file-reading/writing code</h3></div></div></div>
-<p>Here's how you'd write data to a compressed file:</p>
-<pre class="programlisting">FILE* f;
-BZFILE* b;
-int nBuf;
-char buf[ /* whatever size you like */ ];
-int bzerror;
-int nWritten;
-
-f = fopen ( "myfile.bz2", "w" );
-if ( !f ) {
- /* handle error */
-}
-b = BZ2_bzWriteOpen( &bzerror, f, 9 );
-if (bzerror != BZ_OK) {
- BZ2_bzWriteClose ( b );
- /* handle error */
-}
-
-while ( /* condition */ ) {
- /* get data to write into buf, and set nBuf appropriately */
- nWritten = BZ2_bzWrite ( &bzerror, b, buf, nBuf );
- if (bzerror == BZ_IO_ERROR) {
- BZ2_bzWriteClose ( &bzerror, b );
- /* handle error */
- }
-}
-
-BZ2_bzWriteClose( &bzerror, b );
-if (bzerror == BZ_IO_ERROR) {
- /* handle error */
-}</pre>
-<p>And to read from a compressed file:</p>
-<pre class="programlisting">FILE* f;
-BZFILE* b;
-int nBuf;
-char buf[ /* whatever size you like */ ];
-int bzerror;
-int nWritten;
-
-f = fopen ( "myfile.bz2", "r" );
-if ( !f ) {
- /* handle error */
-}
-b = BZ2_bzReadOpen ( &bzerror, f, 0, NULL, 0 );
-if ( bzerror != BZ_OK ) {
- BZ2_bzReadClose ( &bzerror, b );
- /* handle error */
-}
-
-bzerror = BZ_OK;
-while ( bzerror == BZ_OK && /* arbitrary other conditions */) {
- nBuf = BZ2_bzRead ( &bzerror, b, buf, /* size of buf */ );
- if ( bzerror == BZ_OK ) {
- /* do something with buf[0 .. nBuf-1] */
- }
-}
-if ( bzerror != BZ_STREAM_END ) {
- BZ2_bzReadClose ( &bzerror, b );
- /* handle error */
-} else {
- BZ2_bzReadClose ( &bzerror, b );
-}</pre>
-</div>
-</div>
-<div class="sect1" title="3.5.�Utility functions">
-<div class="titlepage"><div><div><h2 class="title" style="clear: both">
-<a name="util-fns"></a>3.5.�Utility functions</h2></div></div></div>
-<div class="sect2" title="3.5.1.�BZ2_bzBuffToBuffCompress">
-<div class="titlepage"><div><div><h3 class="title">
-<a name="bzbufftobuffcompress"></a>3.5.1.�BZ2_bzBuffToBuffCompress</h3></div></div></div>
-<pre class="programlisting">int BZ2_bzBuffToBuffCompress( char* dest,
- unsigned int* destLen,
- char* source,
- unsigned int sourceLen,
- int blockSize100k,
- int verbosity,
- int workFactor );</pre>
-<p>Attempts to compress the data in <code class="computeroutput">source[0
-.. sourceLen-1]</code> into the destination buffer,
-<code class="computeroutput">dest[0 .. *destLen-1]</code>. If the
-destination buffer is big enough,
-<code class="computeroutput">*destLen</code> is set to the size of
-the compressed data, and <code class="computeroutput">BZ_OK</code>
-is returned. If the compressed data won't fit,
-<code class="computeroutput">*destLen</code> is unchanged, and
-<code class="computeroutput">BZ_OUTBUFF_FULL</code> is
-returned.</p>
-<p>Compression in this manner is a one-shot event, done with a
-single call to this function. The resulting compressed data is a
-complete <code class="computeroutput">bzip2</code> format data
-stream. There is no mechanism for making additional calls to
-provide extra input data. If you want that kind of mechanism,
-use the low-level interface.</p>
-<p>For the meaning of parameters
-<code class="computeroutput">blockSize100k</code>,
-<code class="computeroutput">verbosity</code> and
-<code class="computeroutput">workFactor</code>, see
-<code class="computeroutput">BZ2_bzCompressInit</code>.</p>
-<p>To guarantee that the compressed data will fit in its
-buffer, allocate an output buffer of size 1% larger than the
-uncompressed data, plus six hundred extra bytes.</p>
-<p><code class="computeroutput">BZ2_bzBuffToBuffDecompress</code>
-will not write data at or beyond
-<code class="computeroutput">dest[*destLen]</code>, even in case of
-buffer overflow.</p>
-<p>Possible return values:</p>
-<pre class="programlisting">BZ_CONFIG_ERROR
- if the library has been mis-compiled
-BZ_PARAM_ERROR
- if dest is NULL or destLen is NULL
- or blockSize100k < 1 or blockSize100k > 9
- or verbosity < 0 or verbosity > 4
- or workFactor < 0 or workFactor > 250
-BZ_MEM_ERROR
- if insufficient memory is available
-BZ_OUTBUFF_FULL
- if the size of the compressed data exceeds *destLen
-BZ_OK
- otherwise</pre>
-</div>
-<div class="sect2" title="3.5.2.�BZ2_bzBuffToBuffDecompress">
-<div class="titlepage"><div><div><h3 class="title">
-<a name="bzbufftobuffdecompress"></a>3.5.2.�BZ2_bzBuffToBuffDecompress</h3></div></div></div>
-<pre class="programlisting">int BZ2_bzBuffToBuffDecompress( char* dest,
- unsigned int* destLen,
- char* source,
- unsigned int sourceLen,
- int small,
- int verbosity );</pre>
-<p>Attempts to decompress the data in <code class="computeroutput">source[0
-.. sourceLen-1]</code> into the destination buffer,
-<code class="computeroutput">dest[0 .. *destLen-1]</code>. If the
-destination buffer is big enough,
-<code class="computeroutput">*destLen</code> is set to the size of
-the uncompressed data, and <code class="computeroutput">BZ_OK</code>
-is returned. If the compressed data won't fit,
-<code class="computeroutput">*destLen</code> is unchanged, and
-<code class="computeroutput">BZ_OUTBUFF_FULL</code> is
-returned.</p>
-<p><code class="computeroutput">source</code> is assumed to hold
-a complete <code class="computeroutput">bzip2</code> format data
-stream.
-<code class="computeroutput">BZ2_bzBuffToBuffDecompress</code> tries
-to decompress the entirety of the stream into the output
-buffer.</p>
-<p>For the meaning of parameters
-<code class="computeroutput">small</code> and
-<code class="computeroutput">verbosity</code>, see
-<code class="computeroutput">BZ2_bzDecompressInit</code>.</p>
-<p>Because the compression ratio of the compressed data cannot
-be known in advance, there is no easy way to guarantee that the
-output buffer will be big enough. You may of course make
-arrangements in your code to record the size of the uncompressed
-data, but such a mechanism is beyond the scope of this
-library.</p>
-<p><code class="computeroutput">BZ2_bzBuffToBuffDecompress</code>
-will not write data at or beyond
-<code class="computeroutput">dest[*destLen]</code>, even in case of
-buffer overflow.</p>
-<p>Possible return values:</p>
-<pre class="programlisting">BZ_CONFIG_ERROR
- if the library has been mis-compiled
-BZ_PARAM_ERROR
- if dest is NULL or destLen is NULL
- or small != 0 && small != 1
- or verbosity < 0 or verbosity > 4
-BZ_MEM_ERROR
- if insufficient memory is available
-BZ_OUTBUFF_FULL
- if the size of the compressed data exceeds *destLen
-BZ_DATA_ERROR
- if a data integrity error was detected in the compressed data
-BZ_DATA_ERROR_MAGIC
- if the compressed data doesn't begin with the right magic bytes
-BZ_UNEXPECTED_EOF
- if the compressed data ends unexpectedly
-BZ_OK
- otherwise</pre>
-</div>
-</div>
-<div class="sect1" title="3.6.�zlib compatibility functions">
-<div class="titlepage"><div><div><h2 class="title" style="clear: both">
-<a name="zlib-compat"></a>3.6.�zlib compatibility functions</h2></div></div></div>
-<p>Yoshioka Tsuneo has contributed some functions to give
-better <code class="computeroutput">zlib</code> compatibility.
-These functions are <code class="computeroutput">BZ2_bzopen</code>,
-<code class="computeroutput">BZ2_bzread</code>,
-<code class="computeroutput">BZ2_bzwrite</code>,
-<code class="computeroutput">BZ2_bzflush</code>,
-<code class="computeroutput">BZ2_bzclose</code>,
-<code class="computeroutput">BZ2_bzerror</code> and
-<code class="computeroutput">BZ2_bzlibVersion</code>. These
-functions are not (yet) officially part of the library. If they
-break, you get to keep all the pieces. Nevertheless, I think
-they work ok.</p>
-<pre class="programlisting">typedef void BZFILE;
-
-const char * BZ2_bzlibVersion ( void );</pre>
-<p>Returns a string indicating the library version.</p>
-<pre class="programlisting">BZFILE * BZ2_bzopen ( const char *path, const char *mode );
-BZFILE * BZ2_bzdopen ( int fd, const char *mode );</pre>
-<p>Opens a <code class="computeroutput">.bz2</code> file for
-reading or writing, using either its name or a pre-existing file
-descriptor. Analogous to <code class="computeroutput">fopen</code>
-and <code class="computeroutput">fdopen</code>.</p>
-<pre class="programlisting">int BZ2_bzread ( BZFILE* b, void* buf, int len );
-int BZ2_bzwrite ( BZFILE* b, void* buf, int len );</pre>
-<p>Reads/writes data from/to a previously opened
-<code class="computeroutput">BZFILE</code>. Analogous to
-<code class="computeroutput">fread</code> and
-<code class="computeroutput">fwrite</code>.</p>
-<pre class="programlisting">int BZ2_bzflush ( BZFILE* b );
-void BZ2_bzclose ( BZFILE* b );</pre>
-<p>Flushes/closes a <code class="computeroutput">BZFILE</code>.
-<code class="computeroutput">BZ2_bzflush</code> doesn't actually do
-anything. Analogous to <code class="computeroutput">fflush</code>
-and <code class="computeroutput">fclose</code>.</p>
-<pre class="programlisting">const char * BZ2_bzerror ( BZFILE *b, int *errnum )</pre>
-<p>Returns a string describing the more recent error status of
-<code class="computeroutput">b</code>, and also sets
-<code class="computeroutput">*errnum</code> to its numerical
-value.</p>
-</div>
-<div class="sect1" title="3.7.�Using the library in a stdio-free environment">
-<div class="titlepage"><div><div><h2 class="title" style="clear: both">
-<a name="stdio-free"></a>3.7.�Using the library in a stdio-free environment</h2></div></div></div>
-<div class="sect2" title="3.7.1.�Getting rid of stdio">
-<div class="titlepage"><div><div><h3 class="title">
-<a name="stdio-bye"></a>3.7.1.�Getting rid of stdio</h3></div></div></div>
-<p>In a deeply embedded application, you might want to use
-just the memory-to-memory functions. You can do this
-conveniently by compiling the library with preprocessor symbol
-<code class="computeroutput">BZ_NO_STDIO</code> defined. Doing this
-gives you a library containing only the following eight
-functions:</p>
-<p><code class="computeroutput">BZ2_bzCompressInit</code>,
-<code class="computeroutput">BZ2_bzCompress</code>,
-<code class="computeroutput">BZ2_bzCompressEnd</code>
-<code class="computeroutput">BZ2_bzDecompressInit</code>,
-<code class="computeroutput">BZ2_bzDecompress</code>,
-<code class="computeroutput">BZ2_bzDecompressEnd</code>
-<code class="computeroutput">BZ2_bzBuffToBuffCompress</code>,
-<code class="computeroutput">BZ2_bzBuffToBuffDecompress</code></p>
-<p>When compiled like this, all functions will ignore
-<code class="computeroutput">verbosity</code> settings.</p>
-</div>
-<div class="sect2" title="3.7.2.�Critical error handling">
-<div class="titlepage"><div><div><h3 class="title">
-<a name="critical-error"></a>3.7.2.�Critical error handling</h3></div></div></div>
-<p><code class="computeroutput">libbzip2</code> contains a number
-of internal assertion checks which should, needless to say, never
-be activated. Nevertheless, if an assertion should fail,
-behaviour depends on whether or not the library was compiled with
-<code class="computeroutput">BZ_NO_STDIO</code> set.</p>
-<p>For a normal compile, an assertion failure yields the
-message:</p>
-<div class="blockquote"><blockquote class="blockquote">
-<p>bzip2/libbzip2: internal error number N.</p>
-<p>This is a bug in bzip2/libbzip2, 1.0.6 of 6 September 2010.
-Please report it to me at: jseward at bzip.org. If this happened
-when you were using some program which uses libbzip2 as a
-component, you should also report this bug to the author(s)
-of that program. Please make an effort to report this bug;
-timely and accurate bug reports eventually lead to higher
-quality software. Thanks. Julian Seward, 6 September 2010.
-</p>
-</blockquote></div>
-<p>where <code class="computeroutput">N</code> is some error code
-number. If <code class="computeroutput">N == 1007</code>, it also
-prints some extra text advising the reader that unreliable memory
-is often associated with internal error 1007. (This is a
-frequently-observed-phenomenon with versions 1.0.0/1.0.1).</p>
-<p><code class="computeroutput">exit(3)</code> is then
-called.</p>
-<p>For a <code class="computeroutput">stdio</code>-free library,
-assertion failures result in a call to a function declared
-as:</p>
-<pre class="programlisting">extern void bz_internal_error ( int errcode );</pre>
-<p>The relevant code is passed as a parameter. You should
-supply such a function.</p>
-<p>In either case, once an assertion failure has occurred, any
-<code class="computeroutput">bz_stream</code> records involved can
-be regarded as invalid. You should not attempt to resume normal
-operation with them.</p>
-<p>You may, of course, change critical error handling to suit
-your needs. As I said above, critical errors indicate bugs in
-the library and should not occur. All "normal" error situations
-are indicated via error return codes from functions, and can be
-recovered from.</p>
-</div>
-</div>
-<div class="sect1" title="3.8.�Making a Windows DLL">
-<div class="titlepage"><div><div><h2 class="title" style="clear: both">
-<a name="win-dll"></a>3.8.�Making a Windows DLL</h2></div></div></div>
-<p>Everything related to Windows has been contributed by
-Yoshioka Tsuneo
-(<code class="computeroutput">tsuneo at rr.iij4u.or.jp</code>), so
-you should send your queries to him (but perhaps Cc: me,
-<code class="computeroutput">jseward at bzip.org</code>).</p>
-<p>My vague understanding of what to do is: using Visual C++
-5.0, open the project file
-<code class="computeroutput">libbz2.dsp</code>, and build. That's
-all.</p>
-<p>If you can't open the project file for some reason, make a
-new one, naming these files:
-<code class="computeroutput">blocksort.c</code>,
-<code class="computeroutput">bzlib.c</code>,
-<code class="computeroutput">compress.c</code>,
-<code class="computeroutput">crctable.c</code>,
-<code class="computeroutput">decompress.c</code>,
-<code class="computeroutput">huffman.c</code>,
-<code class="computeroutput">randtable.c</code> and
-<code class="computeroutput">libbz2.def</code>. You will also need
-to name the header files <code class="computeroutput">bzlib.h</code>
-and <code class="computeroutput">bzlib_private.h</code>.</p>
-<p>If you don't use VC++, you may need to define the
-proprocessor symbol
-<code class="computeroutput">_WIN32</code>.</p>
-<p>Finally, <code class="computeroutput">dlltest.c</code> is a
-sample program using the DLL. It has a project file,
-<code class="computeroutput">dlltest.dsp</code>.</p>
-<p>If you just want a makefile for Visual C, have a look at
-<code class="computeroutput">makefile.msc</code>.</p>
-<p>Be aware that if you compile
-<code class="computeroutput">bzip2</code> itself on Win32, you must
-set <code class="computeroutput">BZ_UNIX</code> to 0 and
-<code class="computeroutput">BZ_LCCWIN32</code> to 1, in the file
-<code class="computeroutput">bzip2.c</code>, before compiling.
-Otherwise the resulting binary won't work correctly.</p>
-<p>I haven't tried any of this stuff myself, but it all looks
-plausible.</p>
-</div>
-</div>
-<div class="chapter" title="4.�Miscellanea">
-<div class="titlepage"><div><div><h2 class="title">
-<a name="misc"></a>4.�Miscellanea</h2></div></div></div>
-<div class="toc">
-<p><b>Table of Contents</b></p>
-<dl>
-<dt><span class="sect1"><a href="#limits">4.1. Limitations of the compressed file format</a></span></dt>
-<dt><span class="sect1"><a href="#port-issues">4.2. Portability issues</a></span></dt>
-<dt><span class="sect1"><a href="#bugs">4.3. Reporting bugs</a></span></dt>
-<dt><span class="sect1"><a href="#package">4.4. Did you get the right package?</a></span></dt>
-<dt><span class="sect1"><a href="#reading">4.5. Further Reading</a></span></dt>
-</dl>
-</div>
-<p>These are just some random thoughts of mine. Your mileage
-may vary.</p>
-<div class="sect1" title="4.1.�Limitations of the compressed file format">
-<div class="titlepage"><div><div><h2 class="title" style="clear: both">
-<a name="limits"></a>4.1.�Limitations of the compressed file format</h2></div></div></div>
-<p><code class="computeroutput">bzip2-1.0.X</code>,
-<code class="computeroutput">0.9.5</code> and
-<code class="computeroutput">0.9.0</code> use exactly the same file
-format as the original version,
-<code class="computeroutput">bzip2-0.1</code>. This decision was
-made in the interests of stability. Creating yet another
-incompatible compressed file format would create further
-confusion and disruption for users.</p>
-<p>Nevertheless, this is not a painless decision. Development
-work since the release of
-<code class="computeroutput">bzip2-0.1</code> in August 1997 has
-shown complexities in the file format which slow down
-decompression and, in retrospect, are unnecessary. These
-are:</p>
-<div class="itemizedlist"><ul class="itemizedlist" type="bullet">
-<li class="listitem" style="list-style-type: disc"><p>The run-length encoder, which is the first of the
- compression transformations, is entirely irrelevant. The
- original purpose was to protect the sorting algorithm from the
- very worst case input: a string of repeated symbols. But
- algorithm steps Q6a and Q6b in the original Burrows-Wheeler
- technical report (SRC-124) show how repeats can be handled
- without difficulty in block sorting.</p></li>
-<li class="listitem" style="list-style-type: disc">
-<p>The randomisation mechanism doesn't really need to be
- there. Udi Manber and Gene Myers published a suffix array
- construction algorithm a few years back, which can be employed
- to sort any block, no matter how repetitive, in O(N log N)
- time. Subsequent work by Kunihiko Sadakane has produced a
- derivative O(N (log N)^2) algorithm which usually outperforms
- the Manber-Myers algorithm.</p>
-<p>I could have changed to Sadakane's algorithm, but I find
- it to be slower than <code class="computeroutput">bzip2</code>'s
- existing algorithm for most inputs, and the randomisation
- mechanism protects adequately against bad cases. I didn't
- think it was a good tradeoff to make. Partly this is due to
- the fact that I was not flooded with email complaints about
- <code class="computeroutput">bzip2-0.1</code>'s performance on
- repetitive data, so perhaps it isn't a problem for real
- inputs.</p>
-<p>Probably the best long-term solution, and the one I have
- incorporated into 0.9.5 and above, is to use the existing
- sorting algorithm initially, and fall back to a O(N (log N)^2)
- algorithm if the standard algorithm gets into
- difficulties.</p>
-</li>
-<li class="listitem" style="list-style-type: disc"><p>The compressed file format was never designed to be
- handled by a library, and I have had to jump though some hoops
- to produce an efficient implementation of decompression. It's
- a bit hairy. Try passing
- <code class="computeroutput">decompress.c</code> through the C
- preprocessor and you'll see what I mean. Much of this
- complexity could have been avoided if the compressed size of
- each block of data was recorded in the data stream.</p></li>
-<li class="listitem" style="list-style-type: disc"><p>An Adler-32 checksum, rather than a CRC32 checksum,
- would be faster to compute.</p></li>
-</ul></div>
-<p>It would be fair to say that the
-<code class="computeroutput">bzip2</code> format was frozen before I
-properly and fully understood the performance consequences of
-doing so.</p>
-<p>Improvements which I was able to incorporate into 0.9.0,
-despite using the same file format, are:</p>
-<div class="itemizedlist"><ul class="itemizedlist" type="bullet">
-<li class="listitem" style="list-style-type: disc"><p>Single array implementation of the inverse BWT. This
- significantly speeds up decompression, presumably because it
- reduces the number of cache misses.</p></li>
-<li class="listitem" style="list-style-type: disc"><p>Faster inverse MTF transform for large MTF values.
- The new implementation is based on the notion of sliding blocks
- of values.</p></li>
-<li class="listitem" style="list-style-type: disc"><p><code class="computeroutput">bzip2-0.9.0</code> now reads
- and writes files with <code class="computeroutput">fread</code>
- and <code class="computeroutput">fwrite</code>; version 0.1 used
- <code class="computeroutput">putc</code> and
- <code class="computeroutput">getc</code>. Duh! Well, you live
- and learn.</p></li>
-</ul></div>
-<p>Further ahead, it would be nice to be able to do random
-access into files. This will require some careful design of
-compressed file formats.</p>
-</div>
-<div class="sect1" title="4.2.�Portability issues">
-<div class="titlepage"><div><div><h2 class="title" style="clear: both">
-<a name="port-issues"></a>4.2.�Portability issues</h2></div></div></div>
-<p>After some consideration, I have decided not to use GNU
-<code class="computeroutput">autoconf</code> to configure 0.9.5 or
-1.0.</p>
-<p><code class="computeroutput">autoconf</code>, admirable and
-wonderful though it is, mainly assists with portability problems
-between Unix-like platforms. But
-<code class="computeroutput">bzip2</code> doesn't have much in the
-way of portability problems on Unix; most of the difficulties
-appear when porting to the Mac, or to Microsoft's operating
-systems. <code class="computeroutput">autoconf</code> doesn't help
-in those cases, and brings in a whole load of new
-complexity.</p>
-<p>Most people should be able to compile the library and
-program under Unix straight out-of-the-box, so to speak,
-especially if you have a version of GNU C available.</p>
-<p>There are a couple of
-<code class="computeroutput">__inline__</code> directives in the
-code. GNU C (<code class="computeroutput">gcc</code>) should be
-able to handle them. If you're not using GNU C, your C compiler
-shouldn't see them at all. If your compiler does, for some
-reason, see them and doesn't like them, just
-<code class="computeroutput">#define</code>
-<code class="computeroutput">__inline__</code> to be
-<code class="computeroutput">/* */</code>. One easy way to do this
-is to compile with the flag
-<code class="computeroutput">-D__inline__=</code>, which should be
-understood by most Unix compilers.</p>
-<p>If you still have difficulties, try compiling with the
-macro <code class="computeroutput">BZ_STRICT_ANSI</code> defined.
-This should enable you to build the library in a strictly ANSI
-compliant environment. Building the program itself like this is
-dangerous and not supported, since you remove
-<code class="computeroutput">bzip2</code>'s checks against
-compressing directories, symbolic links, devices, and other
-not-really-a-file entities. This could cause filesystem
-corruption!</p>
-<p>One other thing: if you create a
-<code class="computeroutput">bzip2</code> binary for public distribution,
-please consider linking it statically (<code class="computeroutput">gcc
--static</code>). This avoids all sorts of library-version
-issues that others may encounter later on.</p>
-<p>If you build <code class="computeroutput">bzip2</code> on
-Win32, you must set <code class="computeroutput">BZ_UNIX</code> to 0
-and <code class="computeroutput">BZ_LCCWIN32</code> to 1, in the
-file <code class="computeroutput">bzip2.c</code>, before compiling.
-Otherwise the resulting binary won't work correctly.</p>
-</div>
-<div class="sect1" title="4.3.�Reporting bugs">
-<div class="titlepage"><div><div><h2 class="title" style="clear: both">
-<a name="bugs"></a>4.3.�Reporting bugs</h2></div></div></div>
-<p>I tried pretty hard to make sure
-<code class="computeroutput">bzip2</code> is bug free, both by
-design and by testing. Hopefully you'll never need to read this
-section for real.</p>
-<p>Nevertheless, if <code class="computeroutput">bzip2</code> dies
-with a segmentation fault, a bus error or an internal assertion
-failure, it will ask you to email me a bug report. Experience from
-years of feedback of bzip2 users indicates that almost all these
-problems can be traced to either compiler bugs or hardware
-problems.</p>
-<div class="itemizedlist"><ul class="itemizedlist" type="bullet">
-<li class="listitem" style="list-style-type: disc">
-<p>Recompile the program with no optimisation, and
- see if it works. And/or try a different compiler. I heard all
- sorts of stories about various flavours of GNU C (and other
- compilers) generating bad code for
- <code class="computeroutput">bzip2</code>, and I've run across two
- such examples myself.</p>
-<p>2.7.X versions of GNU C are known to generate bad code
- from time to time, at high optimisation levels. If you get
- problems, try using the flags
- <code class="computeroutput">-O2</code>
- <code class="computeroutput">-fomit-frame-pointer</code>
- <code class="computeroutput">-fno-strength-reduce</code>. You
- should specifically <span class="emphasis"><em>not</em></span> use
- <code class="computeroutput">-funroll-loops</code>.</p>
-<p>You may notice that the Makefile runs six tests as part
- of the build process. If the program passes all of these, it's
- a pretty good (but not 100%) indication that the compiler has
- done its job correctly.</p>
-</li>
-<li class="listitem" style="list-style-type: disc">
-<p>If <code class="computeroutput">bzip2</code>
- crashes randomly, and the crashes are not repeatable, you may
- have a flaky memory subsystem.
- <code class="computeroutput">bzip2</code> really hammers your
- memory hierarchy, and if it's a bit marginal, you may get these
- problems. Ditto if your disk or I/O subsystem is slowly
- failing. Yup, this really does happen.</p>
-<p>Try using a different machine of the same type, and see
- if you can repeat the problem.</p>
-</li>
-<li class="listitem" style="list-style-type: disc"><p>This isn't really a bug, but ... If
- <code class="computeroutput">bzip2</code> tells you your file is
- corrupted on decompression, and you obtained the file via FTP,
- there is a possibility that you forgot to tell FTP to do a
- binary mode transfer. That absolutely will cause the file to
- be non-decompressible. You'll have to transfer it
- again.</p></li>
-</ul></div>
-<p>If you've incorporated
-<code class="computeroutput">libbzip2</code> into your own program
-and are getting problems, please, please, please, check that the
-parameters you are passing in calls to the library, are correct,
-and in accordance with what the documentation says is allowable.
-I have tried to make the library robust against such problems,
-but I'm sure I haven't succeeded.</p>
-<p>Finally, if the above comments don't help, you'll have to
-send me a bug report. Now, it's just amazing how many people
-will send me a bug report saying something like:</p>
-<pre class="programlisting">bzip2 crashed with segmentation fault on my machine</pre>
-<p>and absolutely nothing else. Needless to say, a such a
-report is <span class="emphasis"><em>totally, utterly, completely and
-comprehensively 100% useless; a waste of your time, my time, and
-net bandwidth</em></span>. With no details at all, there's no way
-I can possibly begin to figure out what the problem is.</p>
-<p>The rules of the game are: facts, facts, facts. Don't omit
-them because "oh, they won't be relevant". At the bare
-minimum:</p>
-<pre class="programlisting">Machine type. Operating system version.
-Exact version of bzip2 (do bzip2 -V).
-Exact version of the compiler used.
-Flags passed to the compiler.</pre>
-<p>However, the most important single thing that will help me
-is the file that you were trying to compress or decompress at the
-time the problem happened. Without that, my ability to do
-anything more than speculate about the cause, is limited.</p>
-</div>
-<div class="sect1" title="4.4.�Did you get the right package?">
-<div class="titlepage"><div><div><h2 class="title" style="clear: both">
-<a name="package"></a>4.4.�Did you get the right package?</h2></div></div></div>
-<p><code class="computeroutput">bzip2</code> is a resource hog.
-It soaks up large amounts of CPU cycles and memory. Also, it
-gives very large latencies. In the worst case, you can feed many
-megabytes of uncompressed data into the library before getting
-any compressed output, so this probably rules out applications
-requiring interactive behaviour.</p>
-<p>These aren't faults of my implementation, I hope, but more
-an intrinsic property of the Burrows-Wheeler transform
-(unfortunately). Maybe this isn't what you want.</p>
-<p>If you want a compressor and/or library which is faster,
-uses less memory but gets pretty good compression, and has
-minimal latency, consider Jean-loup Gailly's and Mark Adler's
-work, <code class="computeroutput">zlib-1.2.1</code> and
-<code class="computeroutput">gzip-1.2.4</code>. Look for them at
-<a class="ulink" href="http://www.zlib.org" target="_top">http://www.zlib.org</a> and
-<a class="ulink" href="http://www.gzip.org" target="_top">http://www.gzip.org</a>
-respectively.</p>
-<p>For something faster and lighter still, you might try Markus F
-X J Oberhumer's <code class="computeroutput">LZO</code> real-time
-compression/decompression library, at
-<a class="ulink" href="http://www.oberhumer.com/opensource" target="_top">http://www.oberhumer.com/opensource</a>.</p>
-</div>
-<div class="sect1" title="4.5.�Further Reading">
-<div class="titlepage"><div><div><h2 class="title" style="clear: both">
-<a name="reading"></a>4.5.�Further Reading</h2></div></div></div>
-<p><code class="computeroutput">bzip2</code> is not research
-work, in the sense that it doesn't present any new ideas.
-Rather, it's an engineering exercise based on existing
-ideas.</p>
-<p>Four documents describe essentially all the ideas behind
-<code class="computeroutput">bzip2</code>:</p>
-<div class="literallayout"><p>Michael�Burrows�and�D.�J.�Wheeler:<br>
-��"A�block-sorting�lossless�data�compression�algorithm"<br>
-���10th�May�1994.�<br>
-���Digital�SRC�Research�Report�124.<br>
-���ftp://ftp.digital.com/pub/DEC/SRC/research-reports/SRC-124.ps.gz<br>
-���If�you�have�trouble�finding�it,�try�searching�at�the<br>
-���New�Zealand�Digital�Library,�http://www.nzdl.org.<br>
-<br>
-Daniel�S.�Hirschberg�and�Debra�A.�LeLewer<br>
-��"Efficient�Decoding�of�Prefix�Codes"<br>
-���Communications�of�the�ACM,�April�1990,�Vol�33,�Number�4.<br>
-���You�might�be�able�to�get�an�electronic�copy�of�this<br>
-���from�the�ACM�Digital�Library.<br>
-<br>
-David�J.�Wheeler<br>
-���Program�bred3.c�and�accompanying�document�bred3.ps.<br>
-���This�contains�the�idea�behind�the�multi-table�Huffman�coding�scheme.<br>
-���ftp://ftp.cl.cam.ac.uk/users/djw3/<br>
-<br>
-Jon�L.�Bentley�and�Robert�Sedgewick<br>
-��"Fast�Algorithms�for�Sorting�and�Searching�Strings"<br>
-���Available�from�Sedgewick's�web�page,<br>
-���www.cs.princeton.edu/~rs<br>
-</p></div>
-<p>The following paper gives valuable additional insights into
-the algorithm, but is not immediately the basis of any code used
-in bzip2.</p>
-<div class="literallayout"><p>Peter�Fenwick:<br>
-���Block�Sorting�Text�Compression<br>
-���Proceedings�of�the�19th�Australasian�Computer�Science�Conference,<br>
-�����Melbourne,�Australia.��Jan�31�-�Feb�2,�1996.<br>
-���ftp://ftp.cs.auckland.ac.nz/pub/peter-f/ACSC96paper.ps</p></div>
-<p>Kunihiko Sadakane's sorting algorithm, mentioned above, is
-available from:</p>
-<div class="literallayout"><p>http://naomi.is.s.u-tokyo.ac.jp/~sada/papers/Sada98b.ps.gz<br>
-</p></div>
-<p>The Manber-Myers suffix array construction algorithm is
-described in a paper available from:</p>
-<div class="literallayout"><p>http://www.cs.arizona.edu/people/gene/PAPERS/suffix.ps<br>
-</p></div>
-<p>Finally, the following papers document some
-investigations I made into the performance of sorting
-and decompression algorithms:</p>
-<div class="literallayout"><p>Julian�Seward<br>
-���On�the�Performance�of�BWT�Sorting�Algorithms<br>
-���Proceedings�of�the�IEEE�Data�Compression�Conference�2000<br>
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-%!PS-AdobeFont-1.0: NimbusRomNo9L-Regu 1.05
-%%CreationDate: Wed Dec 22 1999
-% Copyright (URW)++,Copyright 1999 by (URW)++ Design & Development
-% (URW)++,Copyright 1999 by (URW)++ Design & Development
-% See the file COPYING (GNU General Public License) for license conditions.
-% As a special exception, permission is granted to include this font
-% program in a Postscript or PDF file that consists of a document that
-% contains text to be displayed or printed using this font, regardless
-% of the conditions or license applying to the document itself.
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-/version (1.05) readonly def
-/Notice ((URW)++,Copyright 1999 by (URW)++ Design & Development. See the file COPYING (GNU General Public License) for license conditions. As a special exception, permission is granted to include this font program in a Postscript or PDF file that consists of a document that contains text to be displayed or printed using this font, regardless of the conditions or license applying to the document itself.) readonly def
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-%!PS-AdobeFont-1.0: NimbusMonL-Regu 1.05
-%%CreationDate: Wed Dec 22 1999
-% Copyright (URW)++,Copyright 1999 by (URW)++ Design & Development
-% (URW)++,Copyright 1999 by (URW)++ Design & Development
-% See the file COPYING (GNU General Public License) for license conditions.
-% As a special exception, permission is granted to include this font
-% program in a Postscript or PDF file that consists of a document that
-% contains text to be displayed or printed using this font, regardless
-% of the conditions or license applying to the document itself.
-12 dict begin
-/FontInfo 10 dict dup begin
-/version (1.05) readonly def
-/Notice ((URW)++,Copyright 1999 by (URW)++ Design & Development. See the file COPYING (GNU General Public License) for license conditions. As a special exception, permission is granted to include this font program in a Postscript or PDF file that consists of a document that contains text to be displayed or printed using this font, regardless of the conditions or license applying to the document itself.) readonly def
-/Copyright (Copyright (URW)++,Copyright 1999 by (URW)++ Design & Development) readonly def
-/FullName (Nimbus Mono L Regular) readonly def
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-/UnderlinePosition -100 def
-/UnderlineThickness 50 def
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-/Encoding StandardEncoding def
-currentdict end
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-%Version: 003.002
-%%CreationDate: Mon Jul 13 16:17:00 2009
-%%Creator: David M. Jones
-%Copyright: Copyright (c) 1997, 2009 American Mathematical Society
-%Copyright: (<http://www.ams.org>), with Reserved Font Name CMMI10.
-% This Font Software is licensed under the SIL Open Font License, Version 1.1.
-% This license is in the accompanying file OFL.txt, and is also
-% available with a FAQ at: http://scripts.sil.org/OFL.
-%%EndComments
-FontDirectory/CMMI10 known{/CMMI10 findfont dup/UniqueID known{dup
-/UniqueID get 5087385 eq exch/FontType get 1 eq and}{pop false}ifelse
-{save true}{false}ifelse}{false}ifelse
-11 dict begin
-/FontType 1 def
-/FontMatrix [0.001 0 0 0.001 0 0 ]readonly def
-/FontName /BITXNG+CMMI10 def
-/FontBBox {-32 -250 1048 750 }readonly def
-/UniqueID 5087385 def
-/PaintType 0 def
-/FontInfo 10 dict dup begin
-/version (003.002) readonly def
-/Notice (Copyright \050c\051 1997, 2009 American Mathematical Society \050<http://www.ams.org>\051, with Reserved Font Name CMMI10.) readonly def
-/FullName (CMMI10) readonly def
-/FamilyName (Computer Modern) readonly def
-/Weight (Medium) readonly def
-/ItalicAngle -14.04 def
-/isFixedPitch false def
-/UnderlinePosition -100 def
-/UnderlineThickness 50 def
-/ascent 750 def
-end readonly def
-/Encoding 256 array
-0 1 255 {1 index exch /.notdef put} for
-dup 45 /arrowhookright put
-dup 58 /period put
-readonly def
-currentdict end
-currentfile eexec
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-cleartomark
-%%EndResource
-/F230_0 /BITXNG+CMMI10 1 1
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- /.notdef/.notdef/.notdef/.notdef/.notdef/arrowhookright/.notdef/.notdef
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- /.notdef/.notdef/.notdef/.notdef/.notdef/.notdef/.notdef/.notdef
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- /.notdef/.notdef/.notdef/.notdef/.notdef/.notdef/.notdef/.notdef
- /.notdef/.notdef/.notdef/.notdef/.notdef/.notdef/.notdef/.notdef]
-pdfMakeFont
-%%BeginResource: font ZWXELK+NimbusMonL-Bold
-%!PS-AdobeFont-1.0: NimbusMonL-Bold 1.05
-%%CreationDate: Wed Dec 22 1999
-% Copyright (URW)++,Copyright 1999 by (URW)++ Design & Development
-% (URW)++,Copyright 1999 by (URW)++ Design & Development
-% See the file COPYING (GNU General Public License) for license conditions.
-% As a special exception, permission is granted to include this font
-% program in a Postscript or PDF file that consists of a document that
-% contains text to be displayed or printed using this font, regardless
-% of the conditions or license applying to the document itself.
-12 dict begin
-/FontInfo 10 dict dup begin
-/version (1.05) readonly def
-/Notice ((URW)++,Copyright 1999 by (URW)++ Design & Development. See the file COPYING (GNU General Public License) for license conditions. As a special exception, permission is granted to include this font program in a Postscript or PDF file that consists of a document that contains text to be displayed or printed using this font, regardless of the conditions or license applying to the document itself.) readonly def
-/Copyright (Copyright (URW)++,Copyright 1999 by (URW)++ Design & Development) readonly def
-/FullName (Nimbus Mono L Bold) readonly def
-/FamilyName (Nimbus Mono L) readonly def
-/Weight (Bold) readonly def
-/ItalicAngle 0.0 def
-/isFixedPitch false def
-/UnderlinePosition -100 def
-/UnderlineThickness 50 def
-end readonly def
-/FontName /ZWXELK+NimbusMonL-Bold def
-/PaintType 0 def
-/WMode 0 def
-/FontBBox {-43 -278 681 871} readonly def
-/FontType 1 def
-/FontMatrix [0.001 0.0 0.0 0.001 0.0 0.0] readonly def
-/Encoding StandardEncoding def
-currentdict end
-currentfile eexec
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-/F548_0 /FRBTTO+CMSY10 1 1
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-%%BeginResource: font AMYDOG+NimbusRomNo9L-ReguItal
-%!PS-AdobeFont-1.0: NimbusRomNo9L-ReguItal 1.05
-%%CreationDate: Wed Dec 22 1999
-% Copyright (URW)++,Copyright 1999 by (URW)++ Design & Development
-% (URW)++,Copyright 1999 by (URW)++ Design & Development
-% See the file COPYING (GNU General Public License) for license conditions.
-% As a special exception, permission is granted to include this font
-% program in a Postscript or PDF file that consists of a document that
-% contains text to be displayed or printed using this font, regardless
-% of the conditions or license applying to the document itself.
-12 dict begin
-/FontInfo 10 dict dup begin
-/version (1.05) readonly def
-/Notice ((URW)++,Copyright 1999 by (URW)++ Design & Development. See the file COPYING (GNU General Public License) for license conditions. As a special exception, permission is granted to include this font program in a Postscript or PDF file that consists of a document that contains text to be displayed or printed using this font, regardless of the conditions or license applying to the document itself.) readonly def
-/Copyright (Copyright (URW)++,Copyright 1999 by (URW)++ Design & Development) readonly def
-/FullName (Nimbus Roman No9 L Regular Italic) readonly def
-/FamilyName (Nimbus Roman No9 L) readonly def
-/Weight (Regular) readonly def
-/ItalicAngle -15.5 def
-/isFixedPitch false def
-/UnderlinePosition -100 def
-/UnderlineThickness 50 def
-end readonly def
-/FontName /AMYDOG+NimbusRomNo9L-ReguItal def
-/PaintType 0 def
-/WMode 0 def
-/FontBBox {-169 -270 1010 924} readonly def
-/FontType 1 def
-/FontMatrix [0.001 0.0 0.0 0.001 0.0 0.0] readonly def
-/Encoding StandardEncoding def
-currentdict end
-currentfile eexec
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-(in) 7.7509 Tj
--225 TJm
-(the) 12.1743 Tj
--226 TJm
-(\002le) 12.7322 Tj
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-(format) 26.5603 Tj
--226 TJm
-(which) 24.3486 Tj
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-(slo) 11.6264 Tj
-25 TJm
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--225 TJm
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--226 TJm
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--226 TJm
-(and,) 16.8766 Tj
--231 TJm
-(in) 7.7509 Tj
--226 TJm
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--230 TJm
-(are) 12.1643 Tj
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-(unnecessary) 48.6872 Tj
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--604 TJm
-(These) 23.7907 Tj
--226 TJm
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-/DeviceRGB {} CS
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--287 TJm
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--287 TJm
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--287 TJm
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--288 TJm
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--322 TJm
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-10 TJm
-(as) 8.2988 Tj
--322 TJm
-(to) 7.7509 Tj
--322 TJm
-(protect) 27.6661 Tj
--321 TJm
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--322 TJm
-(sorting) 27.6761 Tj
--322 TJm
-(algorithm) 38.7446 Tj
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--322 TJm
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--322 TJm
-(v) 4.9813 Tj
-15 TJm
-(ery) 12.7222 Tj
--322 TJm
-(w) 7.193 Tj
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--322 TJm
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--321 TJm
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--1052 TJm
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-81.963 385.842 Td
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--229 TJm
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--230 TJm
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--229 TJm
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--230 TJm
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--230 TJm
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--230 TJm
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--229 TJm
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-25 TJm
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--230 TJm
-(technical) 35.965 Tj
--229 TJm
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--230 TJm
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--229 TJm
-(sho) 13.8381 Tj
-25 TJm
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--229 TJm
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-25 TJm
-(w) 7.193 Tj
--230 TJm
-(repeats) 28.2141 Tj
--229 TJm
-(can) 13.8281 Tj
--230 TJm
-(be) 9.4047 Tj
-81.963 373.886 Td
-(handled) 31.5416 Tj
--250 TJm
-(without) 30.4457 Tj
--250 TJm
-(dif) 11.0684 Tj
-25 TJm
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--250 TJm
-(in) 7.7509 Tj
--250 TJm
-(block) 22.1369 Tj
--250 TJm
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-/DeviceRGB {} cs
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-/DeviceRGB {} cs
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-(The) 15.4918 Tj
--315 TJm
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--314 TJm
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--315 TJm
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--314 TJm
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--314 TJm
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-(Udi) 14.9439 Tj
--315 TJm
-(Manber) 30.9837 Tj
--315 TJm
-(and) 14.386 Tj
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--315 TJm
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--315 TJm
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-(array) 20.4632 Tj
--266 TJm
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--266 TJm
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--266 TJm
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--266 TJm
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-25 TJm
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--266 TJm
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--266 TJm
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--269 TJm
-(which) 24.3486 Tj
--266 TJm
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--266 TJm
-(be) 9.4047 Tj
--266 TJm
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--266 TJm
-(to) 7.7509 Tj
--266 TJm
-(sort) 14.9439 Tj
--266 TJm
-(an) 9.4047 Tj
-15 TJm
-(y) 4.9813 Tj
--266 TJm
-(block,) 24.6275 Tj
--270 TJm
-(no) 9.9626 Tj
--266 TJm
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-25 TJm
-(w) 7.193 Tj
--266 TJm
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-25 TJm
-(v) 4.9813 Tj
-15 TJm
-(e,) 6.914 Tj
-81.963 328.058 Td
-(in) 7.7509 Tj
--257 TJm
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--257 TJm
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-(Subsequent) 45.9375 Tj
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-(v) 4.9813 Tj
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-25 TJm
-(v) 4.9813 Tj
-15 TJm
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--257 TJm
-(O\(N) 17.7035 Tj
--257 TJm
-(\(log) 16.0497 Tj
--258 TJm
-(N\)^2\)) 23.4818 Tj
--257 TJm
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-81.963 316.103 Td
-(which) 24.3486 Tj
--250 TJm
-(usually) 28.782 Tj
--250 TJm
-(outperforms) 48.6972 Tj
--250 TJm
-(the) 12.1743 Tj
--250 TJm
-(Manber) 30.9837 Tj
-20 TJm
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--250 TJm
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-/DeviceRGB {} cs
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-(I) 3.3175 Tj
--274 TJm
-(could) 22.1369 Tj
--274 TJm
-(ha) 9.4047 Tj
-20 TJm
-(v) 4.9813 Tj
-15 TJm
-(e) 4.4234 Tj
--274 TJm
-(changed) 33.1954 Tj
--274 TJm
-(to) 7.7509 Tj
--274 TJm
-(Sadakane') 41.4942 Tj
-55 TJm
-(s) 3.8755 Tj
--274 TJm
-(algorithm,) 41.2352 Tj
--280 TJm
-(b) 4.9813 Tj
-20 TJm
-(ut) 7.7509 Tj
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-(I) 3.3175 Tj
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--274 TJm
-(it) 5.5392 Tj
--274 TJm
-(to) 7.7509 Tj
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-(be) 9.4047 Tj
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-(slo) 11.6264 Tj
-25 TJm
-(wer) 14.9339 Tj
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-(than) 17.1556 Tj
-/DeviceRGB {} cs
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-55 TJm
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-(e) 4.4234 Tj
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-18 TJm
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-(as) 8.2988 Tj
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-(a) 4.4234 Tj
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-10 TJm
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-(the) 12.1743 Tj
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-10 TJm
-(act) 11.6164 Tj
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-(that) 14.9439 Tj
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-(I) 3.3175 Tj
--283 TJm
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-10 TJm
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--283 TJm
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--282 TJm
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--282 TJm
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-(') 3.3175 Tj
-55 TJm
-(s) 3.8755 Tj
-81.963 258.32 Td
-(performance) 50.341 Tj
--250 TJm
-(on) 9.9626 Tj
--250 TJm
-(repetiti) 28.224 Tj
-25 TJm
-(v) 4.9813 Tj
-15 TJm
-(e) 4.4234 Tj
--250 TJm
-(data,) 19.0883 Tj
--250 TJm
-(so) 8.8568 Tj
--250 TJm
-(perhaps) 30.9837 Tj
--250 TJm
-(it) 5.5392 Tj
--250 TJm
-(isn') 14.9439 Tj
-18 TJm
-(t) 2.7696 Tj
--250 TJm
-(a) 4.4234 Tj
--250 TJm
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--250 TJm
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--250 TJm
-(real) 14.9339 Tj
--250 TJm
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-/DeviceRGB {} cs
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-81.963 236.402 Td
-(Probably) 35.9749 Tj
--314 TJm
-(the) 12.1743 Tj
--315 TJm
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-(I) 3.3175 Tj
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-20 TJm
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--314 TJm
-(incorporated) 50.351 Tj
--315 TJm
-(into) 15.5018 Tj
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-(0.9.5) 19.9252 Tj
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-(and) 14.386 Tj
--315 TJm
-(abo) 14.386 Tj
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-(the) 12.1743 Tj
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-(e) 4.4234 Tj
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--207 TJm
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-(to) 7.7509 Tj
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-(a) 4.4234 Tj
--207 TJm
-(O\(N) 17.7035 Tj
--206 TJm
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--206 TJm
-(N\)^2\)) 23.4818 Tj
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-(algorithm) 38.7446 Tj
--206 TJm
-(if) 6.0871 Tj
--207 TJm
-(the) 12.1743 Tj
--206 TJm
-(standard) 33.7533 Tj
--206 TJm
-(algorithm) 38.7446 Tj
--206 TJm
-(gets) 16.0497 Tj
--206 TJm
-(into) 15.5018 Tj
--207 TJm
-(dif) 11.0684 Tj
-25 TJm
-(\002culties.) 34.0422 Tj
-/DeviceRGB {} cs
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-(\225) 3.4869 Tj
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-[0 0 0] sc
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-/DeviceRGB {} CS
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diff --git a/third-party/bzip2/manual.xml b/third-party/bzip2/manual.xml
deleted file mode 100644
index a7fbcb3..0000000
--- a/third-party/bzip2/manual.xml
+++ /dev/null
@@ -1,2964 +0,0 @@
-<?xml version="1.0"?> <!-- -*- sgml -*- -->
-<!DOCTYPE book PUBLIC "-//OASIS//DTD DocBook XML V4.2//EN"
- "http://www.oasis-open.org/docbook/xml/4.2/docbookx.dtd"[
-
-<!-- various strings, dates etc. common to all docs -->
-<!ENTITY % common-ents SYSTEM "entities.xml"> %common-ents;
-]>
-
-<book lang="en" id="userman" xreflabel="bzip2 Manual">
-
- <bookinfo>
- <title>bzip2 and libbzip2, version 1.0.6</title>
- <subtitle>A program and library for data compression</subtitle>
- <copyright>
- <year>&bz-lifespan;</year>
- <holder>Julian Seward</holder>
- </copyright>
- <releaseinfo>Version &bz-version; of &bz-date;</releaseinfo>
-
- <authorgroup>
- <author>
- <firstname>Julian</firstname>
- <surname>Seward</surname>
- <affiliation>
- <orgname>&bz-url;</orgname>
- </affiliation>
- </author>
- </authorgroup>
-
- <legalnotice>
-
- <para>This program, <computeroutput>bzip2</computeroutput>, the
- associated library <computeroutput>libbzip2</computeroutput>, and
- all documentation, are copyright © &bz-lifespan; Julian Seward.
- All rights reserved.</para>
-
- <para>Redistribution and use in source and binary forms, with
- or without modification, are permitted provided that the
- following conditions are met:</para>
-
- <itemizedlist mark='bullet'>
-
- <listitem><para>Redistributions of source code must retain the
- above copyright notice, this list of conditions and the
- following disclaimer.</para></listitem>
-
- <listitem><para>The origin of this software must not be
- misrepresented; you must not claim that you wrote the original
- software. If you use this software in a product, an
- acknowledgment in the product documentation would be
- appreciated but is not required.</para></listitem>
-
- <listitem><para>Altered source versions must be plainly marked
- as such, and must not be misrepresented as being the original
- software.</para></listitem>
-
- <listitem><para>The name of the author may not be used to
- endorse or promote products derived from this software without
- specific prior written permission.</para></listitem>
-
- </itemizedlist>
-
- <para>THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY
- EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
- THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
- PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE
- AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
- EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED
- TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
- DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
- ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
- LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING
- IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF
- THE POSSIBILITY OF SUCH DAMAGE.</para>
-
- <para>PATENTS: To the best of my knowledge,
- <computeroutput>bzip2</computeroutput> and
- <computeroutput>libbzip2</computeroutput> do not use any patented
- algorithms. However, I do not have the resources to carry
- out a patent search. Therefore I cannot give any guarantee of
- the above statement.
- </para>
-
-</legalnotice>
-
-</bookinfo>
-
-
-
-<chapter id="intro" xreflabel="Introduction">
-<title>Introduction</title>
-
-<para><computeroutput>bzip2</computeroutput> compresses files
-using the Burrows-Wheeler block-sorting text compression
-algorithm, and Huffman coding. Compression is generally
-considerably better than that achieved by more conventional
-LZ77/LZ78-based compressors, and approaches the performance of
-the PPM family of statistical compressors.</para>
-
-<para><computeroutput>bzip2</computeroutput> is built on top of
-<computeroutput>libbzip2</computeroutput>, a flexible library for
-handling compressed data in the
-<computeroutput>bzip2</computeroutput> format. This manual
-describes both how to use the program and how to work with the
-library interface. Most of the manual is devoted to this
-library, not the program, which is good news if your interest is
-only in the program.</para>
-
-<itemizedlist mark='bullet'>
-
- <listitem><para><xref linkend="using"/> describes how to use
- <computeroutput>bzip2</computeroutput>; this is the only part
- you need to read if you just want to know how to operate the
- program.</para></listitem>
-
- <listitem><para><xref linkend="libprog"/> describes the
- programming interfaces in detail, and</para></listitem>
-
- <listitem><para><xref linkend="misc"/> records some
- miscellaneous notes which I thought ought to be recorded
- somewhere.</para></listitem>
-
-</itemizedlist>
-
-</chapter>
-
-
-<chapter id="using" xreflabel="How to use bzip2">
-<title>How to use bzip2</title>
-
-<para>This chapter contains a copy of the
-<computeroutput>bzip2</computeroutput> man page, and nothing
-else.</para>
-
-<sect1 id="name" xreflabel="NAME">
-<title>NAME</title>
-
-<itemizedlist mark='bullet'>
-
- <listitem><para><computeroutput>bzip2</computeroutput>,
- <computeroutput>bunzip2</computeroutput> - a block-sorting file
- compressor, v1.0.6</para></listitem>
-
- <listitem><para><computeroutput>bzcat</computeroutput> -
- decompresses files to stdout</para></listitem>
-
- <listitem><para><computeroutput>bzip2recover</computeroutput> -
- recovers data from damaged bzip2 files</para></listitem>
-
-</itemizedlist>
-
-</sect1>
-
-
-<sect1 id="synopsis" xreflabel="SYNOPSIS">
-<title>SYNOPSIS</title>
-
-<itemizedlist mark='bullet'>
-
- <listitem><para><computeroutput>bzip2</computeroutput> [
- -cdfkqstvzVL123456789 ] [ filenames ... ]</para></listitem>
-
- <listitem><para><computeroutput>bunzip2</computeroutput> [
- -fkvsVL ] [ filenames ... ]</para></listitem>
-
- <listitem><para><computeroutput>bzcat</computeroutput> [ -s ] [
- filenames ... ]</para></listitem>
-
- <listitem><para><computeroutput>bzip2recover</computeroutput>
- filename</para></listitem>
-
-</itemizedlist>
-
-</sect1>
-
-
-<sect1 id="description" xreflabel="DESCRIPTION">
-<title>DESCRIPTION</title>
-
-<para><computeroutput>bzip2</computeroutput> compresses files
-using the Burrows-Wheeler block sorting text compression
-algorithm, and Huffman coding. Compression is generally
-considerably better than that achieved by more conventional
-LZ77/LZ78-based compressors, and approaches the performance of
-the PPM family of statistical compressors.</para>
-
-<para>The command-line options are deliberately very similar to
-those of GNU <computeroutput>gzip</computeroutput>, but they are
-not identical.</para>
-
-<para><computeroutput>bzip2</computeroutput> expects a list of
-file names to accompany the command-line flags. Each file is
-replaced by a compressed version of itself, with the name
-<computeroutput>original_name.bz2</computeroutput>. Each
-compressed file has the same modification date, permissions, and,
-when possible, ownership as the corresponding original, so that
-these properties can be correctly restored at decompression time.
-File name handling is naive in the sense that there is no
-mechanism for preserving original file names, permissions,
-ownerships or dates in filesystems which lack these concepts, or
-have serious file name length restrictions, such as
-MS-DOS.</para>
-
-<para><computeroutput>bzip2</computeroutput> and
-<computeroutput>bunzip2</computeroutput> will by default not
-overwrite existing files. If you want this to happen, specify
-the <computeroutput>-f</computeroutput> flag.</para>
-
-<para>If no file names are specified,
-<computeroutput>bzip2</computeroutput> compresses from standard
-input to standard output. In this case,
-<computeroutput>bzip2</computeroutput> will decline to write
-compressed output to a terminal, as this would be entirely
-incomprehensible and therefore pointless.</para>
-
-<para><computeroutput>bunzip2</computeroutput> (or
-<computeroutput>bzip2 -d</computeroutput>) decompresses all
-specified files. Files which were not created by
-<computeroutput>bzip2</computeroutput> will be detected and
-ignored, and a warning issued.
-<computeroutput>bzip2</computeroutput> attempts to guess the
-filename for the decompressed file from that of the compressed
-file as follows:</para>
-
-<itemizedlist mark='bullet'>
-
- <listitem><para><computeroutput>filename.bz2 </computeroutput>
- becomes
- <computeroutput>filename</computeroutput></para></listitem>
-
- <listitem><para><computeroutput>filename.bz </computeroutput>
- becomes
- <computeroutput>filename</computeroutput></para></listitem>
-
- <listitem><para><computeroutput>filename.tbz2</computeroutput>
- becomes
- <computeroutput>filename.tar</computeroutput></para></listitem>
-
- <listitem><para><computeroutput>filename.tbz </computeroutput>
- becomes
- <computeroutput>filename.tar</computeroutput></para></listitem>
-
- <listitem><para><computeroutput>anyothername </computeroutput>
- becomes
- <computeroutput>anyothername.out</computeroutput></para></listitem>
-
-</itemizedlist>
-
-<para>If the file does not end in one of the recognised endings,
-<computeroutput>.bz2</computeroutput>,
-<computeroutput>.bz</computeroutput>,
-<computeroutput>.tbz2</computeroutput> or
-<computeroutput>.tbz</computeroutput>,
-<computeroutput>bzip2</computeroutput> complains that it cannot
-guess the name of the original file, and uses the original name
-with <computeroutput>.out</computeroutput> appended.</para>
-
-<para>As with compression, supplying no filenames causes
-decompression from standard input to standard output.</para>
-
-<para><computeroutput>bunzip2</computeroutput> will correctly
-decompress a file which is the concatenation of two or more
-compressed files. The result is the concatenation of the
-corresponding uncompressed files. Integrity testing
-(<computeroutput>-t</computeroutput>) of concatenated compressed
-files is also supported.</para>
-
-<para>You can also compress or decompress files to the standard
-output by giving the <computeroutput>-c</computeroutput> flag.
-Multiple files may be compressed and decompressed like this. The
-resulting outputs are fed sequentially to stdout. Compression of
-multiple files in this manner generates a stream containing
-multiple compressed file representations. Such a stream can be
-decompressed correctly only by
-<computeroutput>bzip2</computeroutput> version 0.9.0 or later.
-Earlier versions of <computeroutput>bzip2</computeroutput> will
-stop after decompressing the first file in the stream.</para>
-
-<para><computeroutput>bzcat</computeroutput> (or
-<computeroutput>bzip2 -dc</computeroutput>) decompresses all
-specified files to the standard output.</para>
-
-<para><computeroutput>bzip2</computeroutput> will read arguments
-from the environment variables
-<computeroutput>BZIP2</computeroutput> and
-<computeroutput>BZIP</computeroutput>, in that order, and will
-process them before any arguments read from the command line.
-This gives a convenient way to supply default arguments.</para>
-
-<para>Compression is always performed, even if the compressed
-file is slightly larger than the original. Files of less than
-about one hundred bytes tend to get larger, since the compression
-mechanism has a constant overhead in the region of 50 bytes.
-Random data (including the output of most file compressors) is
-coded at about 8.05 bits per byte, giving an expansion of around
-0.5%.</para>
-
-<para>As a self-check for your protection,
-<computeroutput>bzip2</computeroutput> uses 32-bit CRCs to make
-sure that the decompressed version of a file is identical to the
-original. This guards against corruption of the compressed data,
-and against undetected bugs in
-<computeroutput>bzip2</computeroutput> (hopefully very unlikely).
-The chances of data corruption going undetected is microscopic,
-about one chance in four billion for each file processed. Be
-aware, though, that the check occurs upon decompression, so it
-can only tell you that something is wrong. It can't help you
-recover the original uncompressed data. You can use
-<computeroutput>bzip2recover</computeroutput> to try to recover
-data from damaged files.</para>
-
-<para>Return values: 0 for a normal exit, 1 for environmental
-problems (file not found, invalid flags, I/O errors, etc.), 2
-to indicate a corrupt compressed file, 3 for an internal
-consistency error (eg, bug) which caused
-<computeroutput>bzip2</computeroutput> to panic.</para>
-
-</sect1>
-
-
-<sect1 id="options" xreflabel="OPTIONS">
-<title>OPTIONS</title>
-
-<variablelist>
-
- <varlistentry>
- <term><computeroutput>-c --stdout</computeroutput></term>
- <listitem><para>Compress or decompress to standard
- output.</para></listitem>
- </varlistentry>
-
- <varlistentry>
- <term><computeroutput>-d --decompress</computeroutput></term>
- <listitem><para>Force decompression.
- <computeroutput>bzip2</computeroutput>,
- <computeroutput>bunzip2</computeroutput> and
- <computeroutput>bzcat</computeroutput> are really the same
- program, and the decision about what actions to take is done on
- the basis of which name is used. This flag overrides that
- mechanism, and forces bzip2 to decompress.</para></listitem>
- </varlistentry>
-
- <varlistentry>
- <term><computeroutput>-z --compress</computeroutput></term>
- <listitem><para>The complement to
- <computeroutput>-d</computeroutput>: forces compression,
- regardless of the invokation name.</para></listitem>
- </varlistentry>
-
- <varlistentry>
- <term><computeroutput>-t --test</computeroutput></term>
- <listitem><para>Check integrity of the specified file(s), but
- don't decompress them. This really performs a trial
- decompression and throws away the result.</para></listitem>
- </varlistentry>
-
- <varlistentry>
- <term><computeroutput>-f --force</computeroutput></term>
- <listitem><para>Force overwrite of output files. Normally,
- <computeroutput>bzip2</computeroutput> will not overwrite
- existing output files. Also forces
- <computeroutput>bzip2</computeroutput> to break hard links to
- files, which it otherwise wouldn't do.</para>
- <para><computeroutput>bzip2</computeroutput> normally declines
- to decompress files which don't have the correct magic header
- bytes. If forced (<computeroutput>-f</computeroutput>),
- however, it will pass such files through unmodified. This is
- how GNU <computeroutput>gzip</computeroutput> behaves.</para>
- </listitem>
- </varlistentry>
-
- <varlistentry>
- <term><computeroutput>-k --keep</computeroutput></term>
- <listitem><para>Keep (don't delete) input files during
- compression or decompression.</para></listitem>
- </varlistentry>
-
- <varlistentry>
- <term><computeroutput>-s --small</computeroutput></term>
- <listitem><para>Reduce memory usage, for compression,
- decompression and testing. Files are decompressed and tested
- using a modified algorithm which only requires 2.5 bytes per
- block byte. This means any file can be decompressed in 2300k
- of memory, albeit at about half the normal speed.</para>
- <para>During compression, <computeroutput>-s</computeroutput>
- selects a block size of 200k, which limits memory use to around
- the same figure, at the expense of your compression ratio. In
- short, if your machine is low on memory (8 megabytes or less),
- use <computeroutput>-s</computeroutput> for everything. See
- <xref linkend="memory-management"/> below.</para></listitem>
- </varlistentry>
-
- <varlistentry>
- <term><computeroutput>-q --quiet</computeroutput></term>
- <listitem><para>Suppress non-essential warning messages.
- Messages pertaining to I/O errors and other critical events
- will not be suppressed.</para></listitem>
- </varlistentry>
-
- <varlistentry>
- <term><computeroutput>-v --verbose</computeroutput></term>
- <listitem><para>Verbose mode -- show the compression ratio for
- each file processed. Further
- <computeroutput>-v</computeroutput>'s increase the verbosity
- level, spewing out lots of information which is primarily of
- interest for diagnostic purposes.</para></listitem>
- </varlistentry>
-
- <varlistentry>
- <term><computeroutput>-L --license -V --version</computeroutput></term>
- <listitem><para>Display the software version, license terms and
- conditions.</para></listitem>
- </varlistentry>
-
- <varlistentry>
- <term><computeroutput>-1</computeroutput> (or
- <computeroutput>--fast</computeroutput>) to
- <computeroutput>-9</computeroutput> (or
- <computeroutput>-best</computeroutput>)</term>
- <listitem><para>Set the block size to 100 k, 200 k ... 900 k
- when compressing. Has no effect when decompressing. See <xref
- linkend="memory-management" /> below. The
- <computeroutput>--fast</computeroutput> and
- <computeroutput>--best</computeroutput> aliases are primarily
- for GNU <computeroutput>gzip</computeroutput> compatibility.
- In particular, <computeroutput>--fast</computeroutput> doesn't
- make things significantly faster. And
- <computeroutput>--best</computeroutput> merely selects the
- default behaviour.</para></listitem>
- </varlistentry>
-
- <varlistentry>
- <term><computeroutput>--</computeroutput></term>
- <listitem><para>Treats all subsequent arguments as file names,
- even if they start with a dash. This is so you can handle
- files with names beginning with a dash, for example:
- <computeroutput>bzip2 --
- -myfilename</computeroutput>.</para></listitem>
- </varlistentry>
-
- <varlistentry>
- <term><computeroutput>--repetitive-fast</computeroutput></term>
- <term><computeroutput>--repetitive-best</computeroutput></term>
- <listitem><para>These flags are redundant in versions 0.9.5 and
- above. They provided some coarse control over the behaviour of
- the sorting algorithm in earlier versions, which was sometimes
- useful. 0.9.5 and above have an improved algorithm which
- renders these flags irrelevant.</para></listitem>
- </varlistentry>
-
-</variablelist>
-
-</sect1>
-
-
-<sect1 id="memory-management" xreflabel="MEMORY MANAGEMENT">
-<title>MEMORY MANAGEMENT</title>
-
-<para><computeroutput>bzip2</computeroutput> compresses large
-files in blocks. The block size affects both the compression
-ratio achieved, and the amount of memory needed for compression
-and decompression. The flags <computeroutput>-1</computeroutput>
-through <computeroutput>-9</computeroutput> specify the block
-size to be 100,000 bytes through 900,000 bytes (the default)
-respectively. At decompression time, the block size used for
-compression is read from the header of the compressed file, and
-<computeroutput>bunzip2</computeroutput> then allocates itself
-just enough memory to decompress the file. Since block sizes are
-stored in compressed files, it follows that the flags
-<computeroutput>-1</computeroutput> to
-<computeroutput>-9</computeroutput> are irrelevant to and so
-ignored during decompression.</para>
-
-<para>Compression and decompression requirements, in bytes, can be
-estimated as:</para>
-<programlisting>
-Compression: 400k + ( 8 x block size )
-
-Decompression: 100k + ( 4 x block size ), or
- 100k + ( 2.5 x block size )
-</programlisting>
-
-<para>Larger block sizes give rapidly diminishing marginal
-returns. Most of the compression comes from the first two or
-three hundred k of block size, a fact worth bearing in mind when
-using <computeroutput>bzip2</computeroutput> on small machines.
-It is also important to appreciate that the decompression memory
-requirement is set at compression time by the choice of block
-size.</para>
-
-<para>For files compressed with the default 900k block size,
-<computeroutput>bunzip2</computeroutput> will require about 3700
-kbytes to decompress. To support decompression of any file on a
-4 megabyte machine, <computeroutput>bunzip2</computeroutput> has
-an option to decompress using approximately half this amount of
-memory, about 2300 kbytes. Decompression speed is also halved,
-so you should use this option only where necessary. The relevant
-flag is <computeroutput>-s</computeroutput>.</para>
-
-<para>In general, try and use the largest block size memory
-constraints allow, since that maximises the compression achieved.
-Compression and decompression speed are virtually unaffected by
-block size.</para>
-
-<para>Another significant point applies to files which fit in a
-single block -- that means most files you'd encounter using a
-large block size. The amount of real memory touched is
-proportional to the size of the file, since the file is smaller
-than a block. For example, compressing a file 20,000 bytes long
-with the flag <computeroutput>-9</computeroutput> will cause the
-compressor to allocate around 7600k of memory, but only touch
-400k + 20000 * 8 = 560 kbytes of it. Similarly, the decompressor
-will allocate 3700k but only touch 100k + 20000 * 4 = 180
-kbytes.</para>
-
-<para>Here is a table which summarises the maximum memory usage
-for different block sizes. Also recorded is the total compressed
-size for 14 files of the Calgary Text Compression Corpus
-totalling 3,141,622 bytes. This column gives some feel for how
-compression varies with block size. These figures tend to
-understate the advantage of larger block sizes for larger files,
-since the Corpus is dominated by smaller files.</para>
-
-<programlisting>
- Compress Decompress Decompress Corpus
-Flag usage usage -s usage Size
-
- -1 1200k 500k 350k 914704
- -2 2000k 900k 600k 877703
- -3 2800k 1300k 850k 860338
- -4 3600k 1700k 1100k 846899
- -5 4400k 2100k 1350k 845160
- -6 5200k 2500k 1600k 838626
- -7 6100k 2900k 1850k 834096
- -8 6800k 3300k 2100k 828642
- -9 7600k 3700k 2350k 828642
-</programlisting>
-
-</sect1>
-
-
-<sect1 id="recovering" xreflabel="RECOVERING DATA FROM DAMAGED FILES">
-<title>RECOVERING DATA FROM DAMAGED FILES</title>
-
-<para><computeroutput>bzip2</computeroutput> compresses files in
-blocks, usually 900kbytes long. Each block is handled
-independently. If a media or transmission error causes a
-multi-block <computeroutput>.bz2</computeroutput> file to become
-damaged, it may be possible to recover data from the undamaged
-blocks in the file.</para>
-
-<para>The compressed representation of each block is delimited by
-a 48-bit pattern, which makes it possible to find the block
-boundaries with reasonable certainty. Each block also carries
-its own 32-bit CRC, so damaged blocks can be distinguished from
-undamaged ones.</para>
-
-<para><computeroutput>bzip2recover</computeroutput> is a simple
-program whose purpose is to search for blocks in
-<computeroutput>.bz2</computeroutput> files, and write each block
-out into its own <computeroutput>.bz2</computeroutput> file. You
-can then use <computeroutput>bzip2 -t</computeroutput> to test
-the integrity of the resulting files, and decompress those which
-are undamaged.</para>
-
-<para><computeroutput>bzip2recover</computeroutput> takes a
-single argument, the name of the damaged file, and writes a
-number of files <computeroutput>rec0001file.bz2</computeroutput>,
-<computeroutput>rec0002file.bz2</computeroutput>, etc, containing
-the extracted blocks. The output filenames are designed so that
-the use of wildcards in subsequent processing -- for example,
-<computeroutput>bzip2 -dc rec*file.bz2 >
-recovered_data</computeroutput> -- lists the files in the correct
-order.</para>
-
-<para><computeroutput>bzip2recover</computeroutput> should be of
-most use dealing with large <computeroutput>.bz2</computeroutput>
-files, as these will contain many blocks. It is clearly futile
-to use it on damaged single-block files, since a damaged block
-cannot be recovered. If you wish to minimise any potential data
-loss through media or transmission errors, you might consider
-compressing with a smaller block size.</para>
-
-</sect1>
-
-
-<sect1 id="performance" xreflabel="PERFORMANCE NOTES">
-<title>PERFORMANCE NOTES</title>
-
-<para>The sorting phase of compression gathers together similar
-strings in the file. Because of this, files containing very long
-runs of repeated symbols, like "aabaabaabaab ..." (repeated
-several hundred times) may compress more slowly than normal.
-Versions 0.9.5 and above fare much better than previous versions
-in this respect. The ratio between worst-case and average-case
-compression time is in the region of 10:1. For previous
-versions, this figure was more like 100:1. You can use the
-<computeroutput>-vvvv</computeroutput> option to monitor progress
-in great detail, if you want.</para>
-
-<para>Decompression speed is unaffected by these
-phenomena.</para>
-
-<para><computeroutput>bzip2</computeroutput> usually allocates
-several megabytes of memory to operate in, and then charges all
-over it in a fairly random fashion. This means that performance,
-both for compressing and decompressing, is largely determined by
-the speed at which your machine can service cache misses.
-Because of this, small changes to the code to reduce the miss
-rate have been observed to give disproportionately large
-performance improvements. I imagine
-<computeroutput>bzip2</computeroutput> will perform best on
-machines with very large caches.</para>
-
-</sect1>
-
-
-
-<sect1 id="caveats" xreflabel="CAVEATS">
-<title>CAVEATS</title>
-
-<para>I/O error messages are not as helpful as they could be.
-<computeroutput>bzip2</computeroutput> tries hard to detect I/O
-errors and exit cleanly, but the details of what the problem is
-sometimes seem rather misleading.</para>
-
-<para>This manual page pertains to version &bz-version; of
-<computeroutput>bzip2</computeroutput>. Compressed data created by
-this version is entirely forwards and backwards compatible with the
-previous public releases, versions 0.1pl2, 0.9.0 and 0.9.5, 1.0.0,
-1.0.1, 1.0.2 and 1.0.3, but with the following exception: 0.9.0 and
-above can correctly decompress multiple concatenated compressed files.
-0.1pl2 cannot do this; it will stop after decompressing just the first
-file in the stream.</para>
-
-<para><computeroutput>bzip2recover</computeroutput> versions
-prior to 1.0.2 used 32-bit integers to represent bit positions in
-compressed files, so it could not handle compressed files more
-than 512 megabytes long. Versions 1.0.2 and above use 64-bit ints
-on some platforms which support them (GNU supported targets, and
-Windows). To establish whether or not
-<computeroutput>bzip2recover</computeroutput> was built with such
-a limitation, run it without arguments. In any event you can
-build yourself an unlimited version if you can recompile it with
-<computeroutput>MaybeUInt64</computeroutput> set to be an
-unsigned 64-bit integer.</para>
-
-</sect1>
-
-
-
-<sect1 id="author" xreflabel="AUTHOR">
-<title>AUTHOR</title>
-
-<para>Julian Seward,
-<computeroutput>&bz-email;</computeroutput></para>
-
-<para>The ideas embodied in
-<computeroutput>bzip2</computeroutput> are due to (at least) the
-following people: Michael Burrows and David Wheeler (for the
-block sorting transformation), David Wheeler (again, for the
-Huffman coder), Peter Fenwick (for the structured coding model in
-the original <computeroutput>bzip</computeroutput>, and many
-refinements), and Alistair Moffat, Radford Neal and Ian Witten
-(for the arithmetic coder in the original
-<computeroutput>bzip</computeroutput>). I am much indebted for
-their help, support and advice. See the manual in the source
-distribution for pointers to sources of documentation. Christian
-von Roques encouraged me to look for faster sorting algorithms,
-so as to speed up compression. Bela Lubkin encouraged me to
-improve the worst-case compression performance.
-Donna Robinson XMLised the documentation.
-Many people sent
-patches, helped with portability problems, lent machines, gave
-advice and were generally helpful.</para>
-
-</sect1>
-
-</chapter>
-
-
-
-<chapter id="libprog" xreflabel="Programming with libbzip2">
-<title>
-Programming with <computeroutput>libbzip2</computeroutput>
-</title>
-
-<para>This chapter describes the programming interface to
-<computeroutput>libbzip2</computeroutput>.</para>
-
-<para>For general background information, particularly about
-memory use and performance aspects, you'd be well advised to read
-<xref linkend="using"/> as well.</para>
-
-
-<sect1 id="top-level" xreflabel="Top-level structure">
-<title>Top-level structure</title>
-
-<para><computeroutput>libbzip2</computeroutput> is a flexible
-library for compressing and decompressing data in the
-<computeroutput>bzip2</computeroutput> data format. Although
-packaged as a single entity, it helps to regard the library as
-three separate parts: the low level interface, and the high level
-interface, and some utility functions.</para>
-
-<para>The structure of
-<computeroutput>libbzip2</computeroutput>'s interfaces is similar
-to that of Jean-loup Gailly's and Mark Adler's excellent
-<computeroutput>zlib</computeroutput> library.</para>
-
-<para>All externally visible symbols have names beginning
-<computeroutput>BZ2_</computeroutput>. This is new in version
-1.0. The intention is to minimise pollution of the namespaces of
-library clients.</para>
-
-<para>To use any part of the library, you need to
-<computeroutput>#include <bzlib.h></computeroutput>
-into your sources.</para>
-
-
-
-<sect2 id="ll-summary" xreflabel="Low-level summary">
-<title>Low-level summary</title>
-
-<para>This interface provides services for compressing and
-decompressing data in memory. There's no provision for dealing
-with files, streams or any other I/O mechanisms, just straight
-memory-to-memory work. In fact, this part of the library can be
-compiled without inclusion of
-<computeroutput>stdio.h</computeroutput>, which may be helpful
-for embedded applications.</para>
-
-<para>The low-level part of the library has no global variables
-and is therefore thread-safe.</para>
-
-<para>Six routines make up the low level interface:
-<computeroutput>BZ2_bzCompressInit</computeroutput>,
-<computeroutput>BZ2_bzCompress</computeroutput>, and
-<computeroutput>BZ2_bzCompressEnd</computeroutput> for
-compression, and a corresponding trio
-<computeroutput>BZ2_bzDecompressInit</computeroutput>,
-<computeroutput>BZ2_bzDecompress</computeroutput> and
-<computeroutput>BZ2_bzDecompressEnd</computeroutput> for
-decompression. The <computeroutput>*Init</computeroutput>
-functions allocate memory for compression/decompression and do
-other initialisations, whilst the
-<computeroutput>*End</computeroutput> functions close down
-operations and release memory.</para>
-
-<para>The real work is done by
-<computeroutput>BZ2_bzCompress</computeroutput> and
-<computeroutput>BZ2_bzDecompress</computeroutput>. These
-compress and decompress data from a user-supplied input buffer to
-a user-supplied output buffer. These buffers can be any size;
-arbitrary quantities of data are handled by making repeated calls
-to these functions. This is a flexible mechanism allowing a
-consumer-pull style of activity, or producer-push, or a mixture
-of both.</para>
-
-</sect2>
-
-
-<sect2 id="hl-summary" xreflabel="High-level summary">
-<title>High-level summary</title>
-
-<para>This interface provides some handy wrappers around the
-low-level interface to facilitate reading and writing
-<computeroutput>bzip2</computeroutput> format files
-(<computeroutput>.bz2</computeroutput> files). The routines
-provide hooks to facilitate reading files in which the
-<computeroutput>bzip2</computeroutput> data stream is embedded
-within some larger-scale file structure, or where there are
-multiple <computeroutput>bzip2</computeroutput> data streams
-concatenated end-to-end.</para>
-
-<para>For reading files,
-<computeroutput>BZ2_bzReadOpen</computeroutput>,
-<computeroutput>BZ2_bzRead</computeroutput>,
-<computeroutput>BZ2_bzReadClose</computeroutput> and
-<computeroutput>BZ2_bzReadGetUnused</computeroutput> are
-supplied. For writing files,
-<computeroutput>BZ2_bzWriteOpen</computeroutput>,
-<computeroutput>BZ2_bzWrite</computeroutput> and
-<computeroutput>BZ2_bzWriteFinish</computeroutput> are
-available.</para>
-
-<para>As with the low-level library, no global variables are used
-so the library is per se thread-safe. However, if I/O errors
-occur whilst reading or writing the underlying compressed files,
-you may have to consult <computeroutput>errno</computeroutput> to
-determine the cause of the error. In that case, you'd need a C
-library which correctly supports
-<computeroutput>errno</computeroutput> in a multithreaded
-environment.</para>
-
-<para>To make the library a little simpler and more portable,
-<computeroutput>BZ2_bzReadOpen</computeroutput> and
-<computeroutput>BZ2_bzWriteOpen</computeroutput> require you to
-pass them file handles (<computeroutput>FILE*</computeroutput>s)
-which have previously been opened for reading or writing
-respectively. That avoids portability problems associated with
-file operations and file attributes, whilst not being much of an
-imposition on the programmer.</para>
-
-</sect2>
-
-
-<sect2 id="util-fns-summary" xreflabel="Utility functions summary">
-<title>Utility functions summary</title>
-
-<para>For very simple needs,
-<computeroutput>BZ2_bzBuffToBuffCompress</computeroutput> and
-<computeroutput>BZ2_bzBuffToBuffDecompress</computeroutput> are
-provided. These compress data in memory from one buffer to
-another buffer in a single function call. You should assess
-whether these functions fulfill your memory-to-memory
-compression/decompression requirements before investing effort in
-understanding the more general but more complex low-level
-interface.</para>
-
-<para>Yoshioka Tsuneo
-(<computeroutput>tsuneo at rr.iij4u.or.jp</computeroutput>) has
-contributed some functions to give better
-<computeroutput>zlib</computeroutput> compatibility. These
-functions are <computeroutput>BZ2_bzopen</computeroutput>,
-<computeroutput>BZ2_bzread</computeroutput>,
-<computeroutput>BZ2_bzwrite</computeroutput>,
-<computeroutput>BZ2_bzflush</computeroutput>,
-<computeroutput>BZ2_bzclose</computeroutput>,
-<computeroutput>BZ2_bzerror</computeroutput> and
-<computeroutput>BZ2_bzlibVersion</computeroutput>. You may find
-these functions more convenient for simple file reading and
-writing, than those in the high-level interface. These functions
-are not (yet) officially part of the library, and are minimally
-documented here. If they break, you get to keep all the pieces.
-I hope to document them properly when time permits.</para>
-
-<para>Yoshioka also contributed modifications to allow the
-library to be built as a Windows DLL.</para>
-
-</sect2>
-
-</sect1>
-
-
-<sect1 id="err-handling" xreflabel="Error handling">
-<title>Error handling</title>
-
-<para>The library is designed to recover cleanly in all
-situations, including the worst-case situation of decompressing
-random data. I'm not 100% sure that it can always do this, so
-you might want to add a signal handler to catch segmentation
-violations during decompression if you are feeling especially
-paranoid. I would be interested in hearing more about the
-robustness of the library to corrupted compressed data.</para>
-
-<para>Version 1.0.3 more robust in this respect than any
-previous version. Investigations with Valgrind (a tool for detecting
-problems with memory management) indicate
-that, at least for the few files I tested, all single-bit errors
-in the decompressed data are caught properly, with no
-segmentation faults, no uses of uninitialised data, no out of
-range reads or writes, and no infinite looping in the decompressor.
-So it's certainly pretty robust, although
-I wouldn't claim it to be totally bombproof.</para>
-
-<para>The file <computeroutput>bzlib.h</computeroutput> contains
-all definitions needed to use the library. In particular, you
-should definitely not include
-<computeroutput>bzlib_private.h</computeroutput>.</para>
-
-<para>In <computeroutput>bzlib.h</computeroutput>, the various
-return values are defined. The following list is not intended as
-an exhaustive description of the circumstances in which a given
-value may be returned -- those descriptions are given later.
-Rather, it is intended to convey the rough meaning of each return
-value. The first five actions are normal and not intended to
-denote an error situation.</para>
-
-<variablelist>
-
- <varlistentry>
- <term><computeroutput>BZ_OK</computeroutput></term>
- <listitem><para>The requested action was completed
- successfully.</para></listitem>
- </varlistentry>
-
- <varlistentry>
- <term><computeroutput>BZ_RUN_OK, BZ_FLUSH_OK,
- BZ_FINISH_OK</computeroutput></term>
- <listitem><para>In
- <computeroutput>BZ2_bzCompress</computeroutput>, the requested
- flush/finish/nothing-special action was completed
- successfully.</para></listitem>
- </varlistentry>
-
- <varlistentry>
- <term><computeroutput>BZ_STREAM_END</computeroutput></term>
- <listitem><para>Compression of data was completed, or the
- logical stream end was detected during
- decompression.</para></listitem>
- </varlistentry>
-
-</variablelist>
-
-<para>The following return values indicate an error of some
-kind.</para>
-
-<variablelist>
-
- <varlistentry>
- <term><computeroutput>BZ_CONFIG_ERROR</computeroutput></term>
- <listitem><para>Indicates that the library has been improperly
- compiled on your platform -- a major configuration error.
- Specifically, it means that
- <computeroutput>sizeof(char)</computeroutput>,
- <computeroutput>sizeof(short)</computeroutput> and
- <computeroutput>sizeof(int)</computeroutput> are not 1, 2 and
- 4 respectively, as they should be. Note that the library
- should still work properly on 64-bit platforms which follow
- the LP64 programming model -- that is, where
- <computeroutput>sizeof(long)</computeroutput> and
- <computeroutput>sizeof(void*)</computeroutput> are 8. Under
- LP64, <computeroutput>sizeof(int)</computeroutput> is still 4,
- so <computeroutput>libbzip2</computeroutput>, which doesn't
- use the <computeroutput>long</computeroutput> type, is
- OK.</para></listitem>
- </varlistentry>
-
- <varlistentry>
- <term><computeroutput>BZ_SEQUENCE_ERROR</computeroutput></term>
- <listitem><para>When using the library, it is important to call
- the functions in the correct sequence and with data structures
- (buffers etc) in the correct states.
- <computeroutput>libbzip2</computeroutput> checks as much as it
- can to ensure this is happening, and returns
- <computeroutput>BZ_SEQUENCE_ERROR</computeroutput> if not.
- Code which complies precisely with the function semantics, as
- detailed below, should never receive this value; such an event
- denotes buggy code which you should
- investigate.</para></listitem>
- </varlistentry>
-
- <varlistentry>
- <term><computeroutput>BZ_PARAM_ERROR</computeroutput></term>
- <listitem><para>Returned when a parameter to a function call is
- out of range or otherwise manifestly incorrect. As with
- <computeroutput>BZ_SEQUENCE_ERROR</computeroutput>, this
- denotes a bug in the client code. The distinction between
- <computeroutput>BZ_PARAM_ERROR</computeroutput> and
- <computeroutput>BZ_SEQUENCE_ERROR</computeroutput> is a bit
- hazy, but still worth making.</para></listitem>
- </varlistentry>
-
- <varlistentry>
- <term><computeroutput>BZ_MEM_ERROR</computeroutput></term>
- <listitem><para>Returned when a request to allocate memory
- failed. Note that the quantity of memory needed to decompress
- a stream cannot be determined until the stream's header has
- been read. So
- <computeroutput>BZ2_bzDecompress</computeroutput> and
- <computeroutput>BZ2_bzRead</computeroutput> may return
- <computeroutput>BZ_MEM_ERROR</computeroutput> even though some
- of the compressed data has been read. The same is not true
- for compression; once
- <computeroutput>BZ2_bzCompressInit</computeroutput> or
- <computeroutput>BZ2_bzWriteOpen</computeroutput> have
- successfully completed,
- <computeroutput>BZ_MEM_ERROR</computeroutput> cannot
- occur.</para></listitem>
- </varlistentry>
-
- <varlistentry>
- <term><computeroutput>BZ_DATA_ERROR</computeroutput></term>
- <listitem><para>Returned when a data integrity error is
- detected during decompression. Most importantly, this means
- when stored and computed CRCs for the data do not match. This
- value is also returned upon detection of any other anomaly in
- the compressed data.</para></listitem>
- </varlistentry>
-
- <varlistentry>
- <term><computeroutput>BZ_DATA_ERROR_MAGIC</computeroutput></term>
- <listitem><para>As a special case of
- <computeroutput>BZ_DATA_ERROR</computeroutput>, it is
- sometimes useful to know when the compressed stream does not
- start with the correct magic bytes (<computeroutput>'B' 'Z'
- 'h'</computeroutput>).</para></listitem>
- </varlistentry>
-
- <varlistentry>
- <term><computeroutput>BZ_IO_ERROR</computeroutput></term>
- <listitem><para>Returned by
- <computeroutput>BZ2_bzRead</computeroutput> and
- <computeroutput>BZ2_bzWrite</computeroutput> when there is an
- error reading or writing in the compressed file, and by
- <computeroutput>BZ2_bzReadOpen</computeroutput> and
- <computeroutput>BZ2_bzWriteOpen</computeroutput> for attempts
- to use a file for which the error indicator (viz,
- <computeroutput>ferror(f)</computeroutput>) is set. On
- receipt of <computeroutput>BZ_IO_ERROR</computeroutput>, the
- caller should consult <computeroutput>errno</computeroutput>
- and/or <computeroutput>perror</computeroutput> to acquire
- operating-system specific information about the
- problem.</para></listitem>
- </varlistentry>
-
- <varlistentry>
- <term><computeroutput>BZ_UNEXPECTED_EOF</computeroutput></term>
- <listitem><para>Returned by
- <computeroutput>BZ2_bzRead</computeroutput> when the
- compressed file finishes before the logical end of stream is
- detected.</para></listitem>
- </varlistentry>
-
- <varlistentry>
- <term><computeroutput>BZ_OUTBUFF_FULL</computeroutput></term>
- <listitem><para>Returned by
- <computeroutput>BZ2_bzBuffToBuffCompress</computeroutput> and
- <computeroutput>BZ2_bzBuffToBuffDecompress</computeroutput> to
- indicate that the output data will not fit into the output
- buffer provided.</para></listitem>
- </varlistentry>
-
-</variablelist>
-
-</sect1>
-
-
-
-<sect1 id="low-level" xreflabel=">Low-level interface">
-<title>Low-level interface</title>
-
-
-<sect2 id="bzcompress-init" xreflabel="BZ2_bzCompressInit">
-<title>BZ2_bzCompressInit</title>
-
-<programlisting>
-typedef struct {
- char *next_in;
- unsigned int avail_in;
- unsigned int total_in_lo32;
- unsigned int total_in_hi32;
-
- char *next_out;
- unsigned int avail_out;
- unsigned int total_out_lo32;
- unsigned int total_out_hi32;
-
- void *state;
-
- void *(*bzalloc)(void *,int,int);
- void (*bzfree)(void *,void *);
- void *opaque;
-} bz_stream;
-
-int BZ2_bzCompressInit ( bz_stream *strm,
- int blockSize100k,
- int verbosity,
- int workFactor );
-</programlisting>
-
-<para>Prepares for compression. The
-<computeroutput>bz_stream</computeroutput> structure holds all
-data pertaining to the compression activity. A
-<computeroutput>bz_stream</computeroutput> structure should be
-allocated and initialised prior to the call. The fields of
-<computeroutput>bz_stream</computeroutput> comprise the entirety
-of the user-visible data. <computeroutput>state</computeroutput>
-is a pointer to the private data structures required for
-compression.</para>
-
-<para>Custom memory allocators are supported, via fields
-<computeroutput>bzalloc</computeroutput>,
-<computeroutput>bzfree</computeroutput>, and
-<computeroutput>opaque</computeroutput>. The value
-<computeroutput>opaque</computeroutput> is passed to as the first
-argument to all calls to <computeroutput>bzalloc</computeroutput>
-and <computeroutput>bzfree</computeroutput>, but is otherwise
-ignored by the library. The call <computeroutput>bzalloc (
-opaque, n, m )</computeroutput> is expected to return a pointer
-<computeroutput>p</computeroutput> to <computeroutput>n *
-m</computeroutput> bytes of memory, and <computeroutput>bzfree (
-opaque, p )</computeroutput> should free that memory.</para>
-
-<para>If you don't want to use a custom memory allocator, set
-<computeroutput>bzalloc</computeroutput>,
-<computeroutput>bzfree</computeroutput> and
-<computeroutput>opaque</computeroutput> to
-<computeroutput>NULL</computeroutput>, and the library will then
-use the standard <computeroutput>malloc</computeroutput> /
-<computeroutput>free</computeroutput> routines.</para>
-
-<para>Before calling
-<computeroutput>BZ2_bzCompressInit</computeroutput>, fields
-<computeroutput>bzalloc</computeroutput>,
-<computeroutput>bzfree</computeroutput> and
-<computeroutput>opaque</computeroutput> should be filled
-appropriately, as just described. Upon return, the internal
-state will have been allocated and initialised, and
-<computeroutput>total_in_lo32</computeroutput>,
-<computeroutput>total_in_hi32</computeroutput>,
-<computeroutput>total_out_lo32</computeroutput> and
-<computeroutput>total_out_hi32</computeroutput> will have been
-set to zero. These four fields are used by the library to inform
-the caller of the total amount of data passed into and out of the
-library, respectively. You should not try to change them. As of
-version 1.0, 64-bit counts are maintained, even on 32-bit
-platforms, using the <computeroutput>_hi32</computeroutput>
-fields to store the upper 32 bits of the count. So, for example,
-the total amount of data in is <computeroutput>(total_in_hi32
-<< 32) + total_in_lo32</computeroutput>.</para>
-
-<para>Parameter <computeroutput>blockSize100k</computeroutput>
-specifies the block size to be used for compression. It should
-be a value between 1 and 9 inclusive, and the actual block size
-used is 100000 x this figure. 9 gives the best compression but
-takes most memory.</para>
-
-<para>Parameter <computeroutput>verbosity</computeroutput> should
-be set to a number between 0 and 4 inclusive. 0 is silent, and
-greater numbers give increasingly verbose monitoring/debugging
-output. If the library has been compiled with
-<computeroutput>-DBZ_NO_STDIO</computeroutput>, no such output
-will appear for any verbosity setting.</para>
-
-<para>Parameter <computeroutput>workFactor</computeroutput>
-controls how the compression phase behaves when presented with
-worst case, highly repetitive, input data. If compression runs
-into difficulties caused by repetitive data, the library switches
-from the standard sorting algorithm to a fallback algorithm. The
-fallback is slower than the standard algorithm by perhaps a
-factor of three, but always behaves reasonably, no matter how bad
-the input.</para>
-
-<para>Lower values of <computeroutput>workFactor</computeroutput>
-reduce the amount of effort the standard algorithm will expend
-before resorting to the fallback. You should set this parameter
-carefully; too low, and many inputs will be handled by the
-fallback algorithm and so compress rather slowly, too high, and
-your average-to-worst case compression times can become very
-large. The default value of 30 gives reasonable behaviour over a
-wide range of circumstances.</para>
-
-<para>Allowable values range from 0 to 250 inclusive. 0 is a
-special case, equivalent to using the default value of 30.</para>
-
-<para>Note that the compressed output generated is the same
-regardless of whether or not the fallback algorithm is
-used.</para>
-
-<para>Be aware also that this parameter may disappear entirely in
-future versions of the library. In principle it should be
-possible to devise a good way to automatically choose which
-algorithm to use. Such a mechanism would render the parameter
-obsolete.</para>
-
-<para>Possible return values:</para>
-
-<programlisting>
-BZ_CONFIG_ERROR
- if the library has been mis-compiled
-BZ_PARAM_ERROR
- if strm is NULL
- or blockSize < 1 or blockSize > 9
- or verbosity < 0 or verbosity > 4
- or workFactor < 0 or workFactor > 250
-BZ_MEM_ERROR
- if not enough memory is available
-BZ_OK
- otherwise
-</programlisting>
-
-<para>Allowable next actions:</para>
-
-<programlisting>
-BZ2_bzCompress
- if BZ_OK is returned
- no specific action needed in case of error
-</programlisting>
-
-</sect2>
-
-
-<sect2 id="bzCompress" xreflabel="BZ2_bzCompress">
-<title>BZ2_bzCompress</title>
-
-<programlisting>
-int BZ2_bzCompress ( bz_stream *strm, int action );
-</programlisting>
-
-<para>Provides more input and/or output buffer space for the
-library. The caller maintains input and output buffers, and
-calls <computeroutput>BZ2_bzCompress</computeroutput> to transfer
-data between them.</para>
-
-<para>Before each call to
-<computeroutput>BZ2_bzCompress</computeroutput>,
-<computeroutput>next_in</computeroutput> should point at the data
-to be compressed, and <computeroutput>avail_in</computeroutput>
-should indicate how many bytes the library may read.
-<computeroutput>BZ2_bzCompress</computeroutput> updates
-<computeroutput>next_in</computeroutput>,
-<computeroutput>avail_in</computeroutput> and
-<computeroutput>total_in</computeroutput> to reflect the number
-of bytes it has read.</para>
-
-<para>Similarly, <computeroutput>next_out</computeroutput> should
-point to a buffer in which the compressed data is to be placed,
-with <computeroutput>avail_out</computeroutput> indicating how
-much output space is available.
-<computeroutput>BZ2_bzCompress</computeroutput> updates
-<computeroutput>next_out</computeroutput>,
-<computeroutput>avail_out</computeroutput> and
-<computeroutput>total_out</computeroutput> to reflect the number
-of bytes output.</para>
-
-<para>You may provide and remove as little or as much data as you
-like on each call of
-<computeroutput>BZ2_bzCompress</computeroutput>. In the limit,
-it is acceptable to supply and remove data one byte at a time,
-although this would be terribly inefficient. You should always
-ensure that at least one byte of output space is available at
-each call.</para>
-
-<para>A second purpose of
-<computeroutput>BZ2_bzCompress</computeroutput> is to request a
-change of mode of the compressed stream.</para>
-
-<para>Conceptually, a compressed stream can be in one of four
-states: IDLE, RUNNING, FLUSHING and FINISHING. Before
-initialisation
-(<computeroutput>BZ2_bzCompressInit</computeroutput>) and after
-termination (<computeroutput>BZ2_bzCompressEnd</computeroutput>),
-a stream is regarded as IDLE.</para>
-
-<para>Upon initialisation
-(<computeroutput>BZ2_bzCompressInit</computeroutput>), the stream
-is placed in the RUNNING state. Subsequent calls to
-<computeroutput>BZ2_bzCompress</computeroutput> should pass
-<computeroutput>BZ_RUN</computeroutput> as the requested action;
-other actions are illegal and will result in
-<computeroutput>BZ_SEQUENCE_ERROR</computeroutput>.</para>
-
-<para>At some point, the calling program will have provided all
-the input data it wants to. It will then want to finish up -- in
-effect, asking the library to process any data it might have
-buffered internally. In this state,
-<computeroutput>BZ2_bzCompress</computeroutput> will no longer
-attempt to read data from
-<computeroutput>next_in</computeroutput>, but it will want to
-write data to <computeroutput>next_out</computeroutput>. Because
-the output buffer supplied by the user can be arbitrarily small,
-the finishing-up operation cannot necessarily be done with a
-single call of
-<computeroutput>BZ2_bzCompress</computeroutput>.</para>
-
-<para>Instead, the calling program passes
-<computeroutput>BZ_FINISH</computeroutput> as an action to
-<computeroutput>BZ2_bzCompress</computeroutput>. This changes
-the stream's state to FINISHING. Any remaining input (ie,
-<computeroutput>next_in[0 .. avail_in-1]</computeroutput>) is
-compressed and transferred to the output buffer. To do this,
-<computeroutput>BZ2_bzCompress</computeroutput> must be called
-repeatedly until all the output has been consumed. At that
-point, <computeroutput>BZ2_bzCompress</computeroutput> returns
-<computeroutput>BZ_STREAM_END</computeroutput>, and the stream's
-state is set back to IDLE.
-<computeroutput>BZ2_bzCompressEnd</computeroutput> should then be
-called.</para>
-
-<para>Just to make sure the calling program does not cheat, the
-library makes a note of <computeroutput>avail_in</computeroutput>
-at the time of the first call to
-<computeroutput>BZ2_bzCompress</computeroutput> which has
-<computeroutput>BZ_FINISH</computeroutput> as an action (ie, at
-the time the program has announced its intention to not supply
-any more input). By comparing this value with that of
-<computeroutput>avail_in</computeroutput> over subsequent calls
-to <computeroutput>BZ2_bzCompress</computeroutput>, the library
-can detect any attempts to slip in more data to compress. Any
-calls for which this is detected will return
-<computeroutput>BZ_SEQUENCE_ERROR</computeroutput>. This
-indicates a programming mistake which should be corrected.</para>
-
-<para>Instead of asking to finish, the calling program may ask
-<computeroutput>BZ2_bzCompress</computeroutput> to take all the
-remaining input, compress it and terminate the current
-(Burrows-Wheeler) compression block. This could be useful for
-error control purposes. The mechanism is analogous to that for
-finishing: call <computeroutput>BZ2_bzCompress</computeroutput>
-with an action of <computeroutput>BZ_FLUSH</computeroutput>,
-remove output data, and persist with the
-<computeroutput>BZ_FLUSH</computeroutput> action until the value
-<computeroutput>BZ_RUN</computeroutput> is returned. As with
-finishing, <computeroutput>BZ2_bzCompress</computeroutput>
-detects any attempt to provide more input data once the flush has
-begun.</para>
-
-<para>Once the flush is complete, the stream returns to the
-normal RUNNING state.</para>
-
-<para>This all sounds pretty complex, but isn't really. Here's a
-table which shows which actions are allowable in each state, what
-action will be taken, what the next state is, and what the
-non-error return values are. Note that you can't explicitly ask
-what state the stream is in, but nor do you need to -- it can be
-inferred from the values returned by
-<computeroutput>BZ2_bzCompress</computeroutput>.</para>
-
-<programlisting>
-IDLE/any
- Illegal. IDLE state only exists after BZ2_bzCompressEnd or
- before BZ2_bzCompressInit.
- Return value = BZ_SEQUENCE_ERROR
-
-RUNNING/BZ_RUN
- Compress from next_in to next_out as much as possible.
- Next state = RUNNING
- Return value = BZ_RUN_OK
-
-RUNNING/BZ_FLUSH
- Remember current value of next_in. Compress from next_in
- to next_out as much as possible, but do not accept any more input.
- Next state = FLUSHING
- Return value = BZ_FLUSH_OK
-
-RUNNING/BZ_FINISH
- Remember current value of next_in. Compress from next_in
- to next_out as much as possible, but do not accept any more input.
- Next state = FINISHING
- Return value = BZ_FINISH_OK
-
-FLUSHING/BZ_FLUSH
- Compress from next_in to next_out as much as possible,
- but do not accept any more input.
- If all the existing input has been used up and all compressed
- output has been removed
- Next state = RUNNING; Return value = BZ_RUN_OK
- else
- Next state = FLUSHING; Return value = BZ_FLUSH_OK
-
-FLUSHING/other
- Illegal.
- Return value = BZ_SEQUENCE_ERROR
-
-FINISHING/BZ_FINISH
- Compress from next_in to next_out as much as possible,
- but to not accept any more input.
- If all the existing input has been used up and all compressed
- output has been removed
- Next state = IDLE; Return value = BZ_STREAM_END
- else
- Next state = FINISHING; Return value = BZ_FINISH_OK
-
-FINISHING/other
- Illegal.
- Return value = BZ_SEQUENCE_ERROR
-</programlisting>
-
-
-<para>That still looks complicated? Well, fair enough. The
-usual sequence of calls for compressing a load of data is:</para>
-
-<orderedlist>
-
- <listitem><para>Get started with
- <computeroutput>BZ2_bzCompressInit</computeroutput>.</para></listitem>
-
- <listitem><para>Shovel data in and shlurp out its compressed form
- using zero or more calls of
- <computeroutput>BZ2_bzCompress</computeroutput> with action =
- <computeroutput>BZ_RUN</computeroutput>.</para></listitem>
-
- <listitem><para>Finish up. Repeatedly call
- <computeroutput>BZ2_bzCompress</computeroutput> with action =
- <computeroutput>BZ_FINISH</computeroutput>, copying out the
- compressed output, until
- <computeroutput>BZ_STREAM_END</computeroutput> is
- returned.</para></listitem> <listitem><para>Close up and go home. Call
- <computeroutput>BZ2_bzCompressEnd</computeroutput>.</para></listitem>
-
-</orderedlist>
-
-<para>If the data you want to compress fits into your input
-buffer all at once, you can skip the calls of
-<computeroutput>BZ2_bzCompress ( ..., BZ_RUN )</computeroutput>
-and just do the <computeroutput>BZ2_bzCompress ( ..., BZ_FINISH
-)</computeroutput> calls.</para>
-
-<para>All required memory is allocated by
-<computeroutput>BZ2_bzCompressInit</computeroutput>. The
-compression library can accept any data at all (obviously). So
-you shouldn't get any error return values from the
-<computeroutput>BZ2_bzCompress</computeroutput> calls. If you
-do, they will be
-<computeroutput>BZ_SEQUENCE_ERROR</computeroutput>, and indicate
-a bug in your programming.</para>
-
-<para>Trivial other possible return values:</para>
-
-<programlisting>
-BZ_PARAM_ERROR
- if strm is NULL, or strm->s is NULL
-</programlisting>
-
-</sect2>
-
-
-<sect2 id="bzCompress-end" xreflabel="BZ2_bzCompressEnd">
-<title>BZ2_bzCompressEnd</title>
-
-<programlisting>
-int BZ2_bzCompressEnd ( bz_stream *strm );
-</programlisting>
-
-<para>Releases all memory associated with a compression
-stream.</para>
-
-<para>Possible return values:</para>
-
-<programlisting>
-BZ_PARAM_ERROR if strm is NULL or strm->s is NULL
-BZ_OK otherwise
-</programlisting>
-
-</sect2>
-
-
-<sect2 id="bzDecompress-init" xreflabel="BZ2_bzDecompressInit">
-<title>BZ2_bzDecompressInit</title>
-
-<programlisting>
-int BZ2_bzDecompressInit ( bz_stream *strm, int verbosity, int small );
-</programlisting>
-
-<para>Prepares for decompression. As with
-<computeroutput>BZ2_bzCompressInit</computeroutput>, a
-<computeroutput>bz_stream</computeroutput> record should be
-allocated and initialised before the call. Fields
-<computeroutput>bzalloc</computeroutput>,
-<computeroutput>bzfree</computeroutput> and
-<computeroutput>opaque</computeroutput> should be set if a custom
-memory allocator is required, or made
-<computeroutput>NULL</computeroutput> for the normal
-<computeroutput>malloc</computeroutput> /
-<computeroutput>free</computeroutput> routines. Upon return, the
-internal state will have been initialised, and
-<computeroutput>total_in</computeroutput> and
-<computeroutput>total_out</computeroutput> will be zero.</para>
-
-<para>For the meaning of parameter
-<computeroutput>verbosity</computeroutput>, see
-<computeroutput>BZ2_bzCompressInit</computeroutput>.</para>
-
-<para>If <computeroutput>small</computeroutput> is nonzero, the
-library will use an alternative decompression algorithm which
-uses less memory but at the cost of decompressing more slowly
-(roughly speaking, half the speed, but the maximum memory
-requirement drops to around 2300k). See <xref linkend="using"/>
-for more information on memory management.</para>
-
-<para>Note that the amount of memory needed to decompress a
-stream cannot be determined until the stream's header has been
-read, so even if
-<computeroutput>BZ2_bzDecompressInit</computeroutput> succeeds, a
-subsequent <computeroutput>BZ2_bzDecompress</computeroutput>
-could fail with
-<computeroutput>BZ_MEM_ERROR</computeroutput>.</para>
-
-<para>Possible return values:</para>
-
-<programlisting>
-BZ_CONFIG_ERROR
- if the library has been mis-compiled
-BZ_PARAM_ERROR
- if ( small != 0 && small != 1 )
- or (verbosity <; 0 || verbosity > 4)
-BZ_MEM_ERROR
- if insufficient memory is available
-</programlisting>
-
-<para>Allowable next actions:</para>
-
-<programlisting>
-BZ2_bzDecompress
- if BZ_OK was returned
- no specific action required in case of error
-</programlisting>
-
-</sect2>
-
-
-<sect2 id="bzDecompress" xreflabel="BZ2_bzDecompress">
-<title>BZ2_bzDecompress</title>
-
-<programlisting>
-int BZ2_bzDecompress ( bz_stream *strm );
-</programlisting>
-
-<para>Provides more input and/out output buffer space for the
-library. The caller maintains input and output buffers, and uses
-<computeroutput>BZ2_bzDecompress</computeroutput> to transfer
-data between them.</para>
-
-<para>Before each call to
-<computeroutput>BZ2_bzDecompress</computeroutput>,
-<computeroutput>next_in</computeroutput> should point at the
-compressed data, and <computeroutput>avail_in</computeroutput>
-should indicate how many bytes the library may read.
-<computeroutput>BZ2_bzDecompress</computeroutput> updates
-<computeroutput>next_in</computeroutput>,
-<computeroutput>avail_in</computeroutput> and
-<computeroutput>total_in</computeroutput> to reflect the number
-of bytes it has read.</para>
-
-<para>Similarly, <computeroutput>next_out</computeroutput> should
-point to a buffer in which the uncompressed output is to be
-placed, with <computeroutput>avail_out</computeroutput>
-indicating how much output space is available.
-<computeroutput>BZ2_bzCompress</computeroutput> updates
-<computeroutput>next_out</computeroutput>,
-<computeroutput>avail_out</computeroutput> and
-<computeroutput>total_out</computeroutput> to reflect the number
-of bytes output.</para>
-
-<para>You may provide and remove as little or as much data as you
-like on each call of
-<computeroutput>BZ2_bzDecompress</computeroutput>. In the limit,
-it is acceptable to supply and remove data one byte at a time,
-although this would be terribly inefficient. You should always
-ensure that at least one byte of output space is available at
-each call.</para>
-
-<para>Use of <computeroutput>BZ2_bzDecompress</computeroutput> is
-simpler than
-<computeroutput>BZ2_bzCompress</computeroutput>.</para>
-
-<para>You should provide input and remove output as described
-above, and repeatedly call
-<computeroutput>BZ2_bzDecompress</computeroutput> until
-<computeroutput>BZ_STREAM_END</computeroutput> is returned.
-Appearance of <computeroutput>BZ_STREAM_END</computeroutput>
-denotes that <computeroutput>BZ2_bzDecompress</computeroutput>
-has detected the logical end of the compressed stream.
-<computeroutput>BZ2_bzDecompress</computeroutput> will not
-produce <computeroutput>BZ_STREAM_END</computeroutput> until all
-output data has been placed into the output buffer, so once
-<computeroutput>BZ_STREAM_END</computeroutput> appears, you are
-guaranteed to have available all the decompressed output, and
-<computeroutput>BZ2_bzDecompressEnd</computeroutput> can safely
-be called.</para>
-
-<para>If case of an error return value, you should call
-<computeroutput>BZ2_bzDecompressEnd</computeroutput> to clean up
-and release memory.</para>
-
-<para>Possible return values:</para>
-
-<programlisting>
-BZ_PARAM_ERROR
- if strm is NULL or strm->s is NULL
- or strm->avail_out < 1
-BZ_DATA_ERROR
- if a data integrity error is detected in the compressed stream
-BZ_DATA_ERROR_MAGIC
- if the compressed stream doesn't begin with the right magic bytes
-BZ_MEM_ERROR
- if there wasn't enough memory available
-BZ_STREAM_END
- if the logical end of the data stream was detected and all
- output in has been consumed, eg s-->avail_out > 0
-BZ_OK
- otherwise
-</programlisting>
-
-<para>Allowable next actions:</para>
-
-<programlisting>
-BZ2_bzDecompress
- if BZ_OK was returned
-BZ2_bzDecompressEnd
- otherwise
-</programlisting>
-
-</sect2>
-
-
-<sect2 id="bzDecompress-end" xreflabel="BZ2_bzDecompressEnd">
-<title>BZ2_bzDecompressEnd</title>
-
-<programlisting>
-int BZ2_bzDecompressEnd ( bz_stream *strm );
-</programlisting>
-
-<para>Releases all memory associated with a decompression
-stream.</para>
-
-<para>Possible return values:</para>
-
-<programlisting>
-BZ_PARAM_ERROR
- if strm is NULL or strm->s is NULL
-BZ_OK
- otherwise
-</programlisting>
-
-<para>Allowable next actions:</para>
-
-<programlisting>
- None.
-</programlisting>
-
-</sect2>
-
-</sect1>
-
-
-<sect1 id="hl-interface" xreflabel="High-level interface">
-<title>High-level interface</title>
-
-<para>This interface provides functions for reading and writing
-<computeroutput>bzip2</computeroutput> format files. First, some
-general points.</para>
-
-<itemizedlist mark='bullet'>
-
- <listitem><para>All of the functions take an
- <computeroutput>int*</computeroutput> first argument,
- <computeroutput>bzerror</computeroutput>. After each call,
- <computeroutput>bzerror</computeroutput> should be consulted
- first to determine the outcome of the call. If
- <computeroutput>bzerror</computeroutput> is
- <computeroutput>BZ_OK</computeroutput>, the call completed
- successfully, and only then should the return value of the
- function (if any) be consulted. If
- <computeroutput>bzerror</computeroutput> is
- <computeroutput>BZ_IO_ERROR</computeroutput>, there was an
- error reading/writing the underlying compressed file, and you
- should then consult <computeroutput>errno</computeroutput> /
- <computeroutput>perror</computeroutput> to determine the cause
- of the difficulty. <computeroutput>bzerror</computeroutput>
- may also be set to various other values; precise details are
- given on a per-function basis below.</para></listitem>
-
- <listitem><para>If <computeroutput>bzerror</computeroutput> indicates
- an error (ie, anything except
- <computeroutput>BZ_OK</computeroutput> and
- <computeroutput>BZ_STREAM_END</computeroutput>), you should
- immediately call
- <computeroutput>BZ2_bzReadClose</computeroutput> (or
- <computeroutput>BZ2_bzWriteClose</computeroutput>, depending on
- whether you are attempting to read or to write) to free up all
- resources associated with the stream. Once an error has been
- indicated, behaviour of all calls except
- <computeroutput>BZ2_bzReadClose</computeroutput>
- (<computeroutput>BZ2_bzWriteClose</computeroutput>) is
- undefined. The implication is that (1)
- <computeroutput>bzerror</computeroutput> should be checked
- after each call, and (2) if
- <computeroutput>bzerror</computeroutput> indicates an error,
- <computeroutput>BZ2_bzReadClose</computeroutput>
- (<computeroutput>BZ2_bzWriteClose</computeroutput>) should then
- be called to clean up.</para></listitem>
-
- <listitem><para>The <computeroutput>FILE*</computeroutput> arguments
- passed to <computeroutput>BZ2_bzReadOpen</computeroutput> /
- <computeroutput>BZ2_bzWriteOpen</computeroutput> should be set
- to binary mode. Most Unix systems will do this by default, but
- other platforms, including Windows and Mac, will not. If you
- omit this, you may encounter problems when moving code to new
- platforms.</para></listitem>
-
- <listitem><para>Memory allocation requests are handled by
- <computeroutput>malloc</computeroutput> /
- <computeroutput>free</computeroutput>. At present there is no
- facility for user-defined memory allocators in the file I/O
- functions (could easily be added, though).</para></listitem>
-
-</itemizedlist>
-
-
-
-<sect2 id="bzreadopen" xreflabel="BZ2_bzReadOpen">
-<title>BZ2_bzReadOpen</title>
-
-<programlisting>
-typedef void BZFILE;
-
-BZFILE *BZ2_bzReadOpen( int *bzerror, FILE *f,
- int verbosity, int small,
- void *unused, int nUnused );
-</programlisting>
-
-<para>Prepare to read compressed data from file handle
-<computeroutput>f</computeroutput>.
-<computeroutput>f</computeroutput> should refer to a file which
-has been opened for reading, and for which the error indicator
-(<computeroutput>ferror(f)</computeroutput>)is not set. If
-<computeroutput>small</computeroutput> is 1, the library will try
-to decompress using less memory, at the expense of speed.</para>
-
-<para>For reasons explained below,
-<computeroutput>BZ2_bzRead</computeroutput> will decompress the
-<computeroutput>nUnused</computeroutput> bytes starting at
-<computeroutput>unused</computeroutput>, before starting to read
-from the file <computeroutput>f</computeroutput>. At most
-<computeroutput>BZ_MAX_UNUSED</computeroutput> bytes may be
-supplied like this. If this facility is not required, you should
-pass <computeroutput>NULL</computeroutput> and
-<computeroutput>0</computeroutput> for
-<computeroutput>unused</computeroutput> and
-n<computeroutput>Unused</computeroutput> respectively.</para>
-
-<para>For the meaning of parameters
-<computeroutput>small</computeroutput> and
-<computeroutput>verbosity</computeroutput>, see
-<computeroutput>BZ2_bzDecompressInit</computeroutput>.</para>
-
-<para>The amount of memory needed to decompress a file cannot be
-determined until the file's header has been read. So it is
-possible that <computeroutput>BZ2_bzReadOpen</computeroutput>
-returns <computeroutput>BZ_OK</computeroutput> but a subsequent
-call of <computeroutput>BZ2_bzRead</computeroutput> will return
-<computeroutput>BZ_MEM_ERROR</computeroutput>.</para>
-
-<para>Possible assignments to
-<computeroutput>bzerror</computeroutput>:</para>
-
-<programlisting>
-BZ_CONFIG_ERROR
- if the library has been mis-compiled
-BZ_PARAM_ERROR
- if f is NULL
- or small is neither 0 nor 1
- or ( unused == NULL && nUnused != 0 )
- or ( unused != NULL && !(0 <= nUnused <= BZ_MAX_UNUSED) )
-BZ_IO_ERROR
- if ferror(f) is nonzero
-BZ_MEM_ERROR
- if insufficient memory is available
-BZ_OK
- otherwise.
-</programlisting>
-
-<para>Possible return values:</para>
-
-<programlisting>
-Pointer to an abstract BZFILE
- if bzerror is BZ_OK
-NULL
- otherwise
-</programlisting>
-
-<para>Allowable next actions:</para>
-
-<programlisting>
-BZ2_bzRead
- if bzerror is BZ_OK
-BZ2_bzClose
- otherwise
-</programlisting>
-
-</sect2>
-
-
-<sect2 id="bzread" xreflabel="BZ2_bzRead">
-<title>BZ2_bzRead</title>
-
-<programlisting>
-int BZ2_bzRead ( int *bzerror, BZFILE *b, void *buf, int len );
-</programlisting>
-
-<para>Reads up to <computeroutput>len</computeroutput>
-(uncompressed) bytes from the compressed file
-<computeroutput>b</computeroutput> into the buffer
-<computeroutput>buf</computeroutput>. If the read was
-successful, <computeroutput>bzerror</computeroutput> is set to
-<computeroutput>BZ_OK</computeroutput> and the number of bytes
-read is returned. If the logical end-of-stream was detected,
-<computeroutput>bzerror</computeroutput> will be set to
-<computeroutput>BZ_STREAM_END</computeroutput>, and the number of
-bytes read is returned. All other
-<computeroutput>bzerror</computeroutput> values denote an
-error.</para>
-
-<para><computeroutput>BZ2_bzRead</computeroutput> will supply
-<computeroutput>len</computeroutput> bytes, unless the logical
-stream end is detected or an error occurs. Because of this, it
-is possible to detect the stream end by observing when the number
-of bytes returned is less than the number requested.
-Nevertheless, this is regarded as inadvisable; you should instead
-check <computeroutput>bzerror</computeroutput> after every call
-and watch out for
-<computeroutput>BZ_STREAM_END</computeroutput>.</para>
-
-<para>Internally, <computeroutput>BZ2_bzRead</computeroutput>
-copies data from the compressed file in chunks of size
-<computeroutput>BZ_MAX_UNUSED</computeroutput> bytes before
-decompressing it. If the file contains more bytes than strictly
-needed to reach the logical end-of-stream,
-<computeroutput>BZ2_bzRead</computeroutput> will almost certainly
-read some of the trailing data before signalling
-<computeroutput>BZ_SEQUENCE_END</computeroutput>. To collect the
-read but unused data once
-<computeroutput>BZ_SEQUENCE_END</computeroutput> has appeared,
-call <computeroutput>BZ2_bzReadGetUnused</computeroutput>
-immediately before
-<computeroutput>BZ2_bzReadClose</computeroutput>.</para>
-
-<para>Possible assignments to
-<computeroutput>bzerror</computeroutput>:</para>
-
-<programlisting>
-BZ_PARAM_ERROR
- if b is NULL or buf is NULL or len < 0
-BZ_SEQUENCE_ERROR
- if b was opened with BZ2_bzWriteOpen
-BZ_IO_ERROR
- if there is an error reading from the compressed file
-BZ_UNEXPECTED_EOF
- if the compressed file ended before
- the logical end-of-stream was detected
-BZ_DATA_ERROR
- if a data integrity error was detected in the compressed stream
-BZ_DATA_ERROR_MAGIC
- if the stream does not begin with the requisite header bytes
- (ie, is not a bzip2 data file). This is really
- a special case of BZ_DATA_ERROR.
-BZ_MEM_ERROR
- if insufficient memory was available
-BZ_STREAM_END
- if the logical end of stream was detected.
-BZ_OK
- otherwise.
-</programlisting>
-
-<para>Possible return values:</para>
-
-<programlisting>
-number of bytes read
- if bzerror is BZ_OK or BZ_STREAM_END
-undefined
- otherwise
-</programlisting>
-
-<para>Allowable next actions:</para>
-
-<programlisting>
-collect data from buf, then BZ2_bzRead or BZ2_bzReadClose
- if bzerror is BZ_OK
-collect data from buf, then BZ2_bzReadClose or BZ2_bzReadGetUnused
- if bzerror is BZ_SEQUENCE_END
-BZ2_bzReadClose
- otherwise
-</programlisting>
-
-</sect2>
-
-
-<sect2 id="bzreadgetunused" xreflabel="BZ2_bzReadGetUnused">
-<title>BZ2_bzReadGetUnused</title>
-
-<programlisting>
-void BZ2_bzReadGetUnused( int* bzerror, BZFILE *b,
- void** unused, int* nUnused );
-</programlisting>
-
-<para>Returns data which was read from the compressed file but
-was not needed to get to the logical end-of-stream.
-<computeroutput>*unused</computeroutput> is set to the address of
-the data, and <computeroutput>*nUnused</computeroutput> to the
-number of bytes. <computeroutput>*nUnused</computeroutput> will
-be set to a value between <computeroutput>0</computeroutput> and
-<computeroutput>BZ_MAX_UNUSED</computeroutput> inclusive.</para>
-
-<para>This function may only be called once
-<computeroutput>BZ2_bzRead</computeroutput> has signalled
-<computeroutput>BZ_STREAM_END</computeroutput> but before
-<computeroutput>BZ2_bzReadClose</computeroutput>.</para>
-
-<para>Possible assignments to
-<computeroutput>bzerror</computeroutput>:</para>
-
-<programlisting>
-BZ_PARAM_ERROR
- if b is NULL
- or unused is NULL or nUnused is NULL
-BZ_SEQUENCE_ERROR
- if BZ_STREAM_END has not been signalled
- or if b was opened with BZ2_bzWriteOpen
-BZ_OK
- otherwise
-</programlisting>
-
-<para>Allowable next actions:</para>
-
-<programlisting>
-BZ2_bzReadClose
-</programlisting>
-
-</sect2>
-
-
-<sect2 id="bzreadclose" xreflabel="BZ2_bzReadClose">
-<title>BZ2_bzReadClose</title>
-
-<programlisting>
-void BZ2_bzReadClose ( int *bzerror, BZFILE *b );
-</programlisting>
-
-<para>Releases all memory pertaining to the compressed file
-<computeroutput>b</computeroutput>.
-<computeroutput>BZ2_bzReadClose</computeroutput> does not call
-<computeroutput>fclose</computeroutput> on the underlying file
-handle, so you should do that yourself if appropriate.
-<computeroutput>BZ2_bzReadClose</computeroutput> should be called
-to clean up after all error situations.</para>
-
-<para>Possible assignments to
-<computeroutput>bzerror</computeroutput>:</para>
-
-<programlisting>
-BZ_SEQUENCE_ERROR
- if b was opened with BZ2_bzOpenWrite
-BZ_OK
- otherwise
-</programlisting>
-
-<para>Allowable next actions:</para>
-
-<programlisting>
-none
-</programlisting>
-
-</sect2>
-
-
-<sect2 id="bzwriteopen" xreflabel="BZ2_bzWriteOpen">
-<title>BZ2_bzWriteOpen</title>
-
-<programlisting>
-BZFILE *BZ2_bzWriteOpen( int *bzerror, FILE *f,
- int blockSize100k, int verbosity,
- int workFactor );
-</programlisting>
-
-<para>Prepare to write compressed data to file handle
-<computeroutput>f</computeroutput>.
-<computeroutput>f</computeroutput> should refer to a file which
-has been opened for writing, and for which the error indicator
-(<computeroutput>ferror(f)</computeroutput>)is not set.</para>
-
-<para>For the meaning of parameters
-<computeroutput>blockSize100k</computeroutput>,
-<computeroutput>verbosity</computeroutput> and
-<computeroutput>workFactor</computeroutput>, see
-<computeroutput>BZ2_bzCompressInit</computeroutput>.</para>
-
-<para>All required memory is allocated at this stage, so if the
-call completes successfully,
-<computeroutput>BZ_MEM_ERROR</computeroutput> cannot be signalled
-by a subsequent call to
-<computeroutput>BZ2_bzWrite</computeroutput>.</para>
-
-<para>Possible assignments to
-<computeroutput>bzerror</computeroutput>:</para>
-
-<programlisting>
-BZ_CONFIG_ERROR
- if the library has been mis-compiled
-BZ_PARAM_ERROR
- if f is NULL
- or blockSize100k < 1 or blockSize100k > 9
-BZ_IO_ERROR
- if ferror(f) is nonzero
-BZ_MEM_ERROR
- if insufficient memory is available
-BZ_OK
- otherwise
-</programlisting>
-
-<para>Possible return values:</para>
-
-<programlisting>
-Pointer to an abstract BZFILE
- if bzerror is BZ_OK
-NULL
- otherwise
-</programlisting>
-
-<para>Allowable next actions:</para>
-
-<programlisting>
-BZ2_bzWrite
- if bzerror is BZ_OK
- (you could go directly to BZ2_bzWriteClose, but this would be pretty pointless)
-BZ2_bzWriteClose
- otherwise
-</programlisting>
-
-</sect2>
-
-
-<sect2 id="bzwrite" xreflabel="BZ2_bzWrite">
-<title>BZ2_bzWrite</title>
-
-<programlisting>
-void BZ2_bzWrite ( int *bzerror, BZFILE *b, void *buf, int len );
-</programlisting>
-
-<para>Absorbs <computeroutput>len</computeroutput> bytes from the
-buffer <computeroutput>buf</computeroutput>, eventually to be
-compressed and written to the file.</para>
-
-<para>Possible assignments to
-<computeroutput>bzerror</computeroutput>:</para>
-
-<programlisting>
-BZ_PARAM_ERROR
- if b is NULL or buf is NULL or len < 0
-BZ_SEQUENCE_ERROR
- if b was opened with BZ2_bzReadOpen
-BZ_IO_ERROR
- if there is an error writing the compressed file.
-BZ_OK
- otherwise
-</programlisting>
-
-</sect2>
-
-
-<sect2 id="bzwriteclose" xreflabel="BZ2_bzWriteClose">
-<title>BZ2_bzWriteClose</title>
-
-<programlisting>
-void BZ2_bzWriteClose( int *bzerror, BZFILE* f,
- int abandon,
- unsigned int* nbytes_in,
- unsigned int* nbytes_out );
-
-void BZ2_bzWriteClose64( int *bzerror, BZFILE* f,
- int abandon,
- unsigned int* nbytes_in_lo32,
- unsigned int* nbytes_in_hi32,
- unsigned int* nbytes_out_lo32,
- unsigned int* nbytes_out_hi32 );
-</programlisting>
-
-<para>Compresses and flushes to the compressed file all data so
-far supplied by <computeroutput>BZ2_bzWrite</computeroutput>.
-The logical end-of-stream markers are also written, so subsequent
-calls to <computeroutput>BZ2_bzWrite</computeroutput> are
-illegal. All memory associated with the compressed file
-<computeroutput>b</computeroutput> is released.
-<computeroutput>fflush</computeroutput> is called on the
-compressed file, but it is not
-<computeroutput>fclose</computeroutput>'d.</para>
-
-<para>If <computeroutput>BZ2_bzWriteClose</computeroutput> is
-called to clean up after an error, the only action is to release
-the memory. The library records the error codes issued by
-previous calls, so this situation will be detected automatically.
-There is no attempt to complete the compression operation, nor to
-<computeroutput>fflush</computeroutput> the compressed file. You
-can force this behaviour to happen even in the case of no error,
-by passing a nonzero value to
-<computeroutput>abandon</computeroutput>.</para>
-
-<para>If <computeroutput>nbytes_in</computeroutput> is non-null,
-<computeroutput>*nbytes_in</computeroutput> will be set to be the
-total volume of uncompressed data handled. Similarly,
-<computeroutput>nbytes_out</computeroutput> will be set to the
-total volume of compressed data written. For compatibility with
-older versions of the library,
-<computeroutput>BZ2_bzWriteClose</computeroutput> only yields the
-lower 32 bits of these counts. Use
-<computeroutput>BZ2_bzWriteClose64</computeroutput> if you want
-the full 64 bit counts. These two functions are otherwise
-absolutely identical.</para>
-
-<para>Possible assignments to
-<computeroutput>bzerror</computeroutput>:</para>
-
-<programlisting>
-BZ_SEQUENCE_ERROR
- if b was opened with BZ2_bzReadOpen
-BZ_IO_ERROR
- if there is an error writing the compressed file
-BZ_OK
- otherwise
-</programlisting>
-
-</sect2>
-
-
-<sect2 id="embed" xreflabel="Handling embedded compressed data streams">
-<title>Handling embedded compressed data streams</title>
-
-<para>The high-level library facilitates use of
-<computeroutput>bzip2</computeroutput> data streams which form
-some part of a surrounding, larger data stream.</para>
-
-<itemizedlist mark='bullet'>
-
- <listitem><para>For writing, the library takes an open file handle,
- writes compressed data to it,
- <computeroutput>fflush</computeroutput>es it but does not
- <computeroutput>fclose</computeroutput> it. The calling
- application can write its own data before and after the
- compressed data stream, using that same file handle.</para></listitem>
-
- <listitem><para>Reading is more complex, and the facilities are not as
- general as they could be since generality is hard to reconcile
- with efficiency. <computeroutput>BZ2_bzRead</computeroutput>
- reads from the compressed file in blocks of size
- <computeroutput>BZ_MAX_UNUSED</computeroutput> bytes, and in
- doing so probably will overshoot the logical end of compressed
- stream. To recover this data once decompression has ended,
- call <computeroutput>BZ2_bzReadGetUnused</computeroutput> after
- the last call of <computeroutput>BZ2_bzRead</computeroutput>
- (the one returning
- <computeroutput>BZ_STREAM_END</computeroutput>) but before
- calling
- <computeroutput>BZ2_bzReadClose</computeroutput>.</para></listitem>
-
-</itemizedlist>
-
-<para>This mechanism makes it easy to decompress multiple
-<computeroutput>bzip2</computeroutput> streams placed end-to-end.
-As the end of one stream, when
-<computeroutput>BZ2_bzRead</computeroutput> returns
-<computeroutput>BZ_STREAM_END</computeroutput>, call
-<computeroutput>BZ2_bzReadGetUnused</computeroutput> to collect
-the unused data (copy it into your own buffer somewhere). That
-data forms the start of the next compressed stream. To start
-uncompressing that next stream, call
-<computeroutput>BZ2_bzReadOpen</computeroutput> again, feeding in
-the unused data via the <computeroutput>unused</computeroutput> /
-<computeroutput>nUnused</computeroutput> parameters. Keep doing
-this until <computeroutput>BZ_STREAM_END</computeroutput> return
-coincides with the physical end of file
-(<computeroutput>feof(f)</computeroutput>). In this situation
-<computeroutput>BZ2_bzReadGetUnused</computeroutput> will of
-course return no data.</para>
-
-<para>This should give some feel for how the high-level interface
-can be used. If you require extra flexibility, you'll have to
-bite the bullet and get to grips with the low-level
-interface.</para>
-
-</sect2>
-
-
-<sect2 id="std-rdwr" xreflabel="Standard file-reading/writing code">
-<title>Standard file-reading/writing code</title>
-
-<para>Here's how you'd write data to a compressed file:</para>
-
-<programlisting>
-FILE* f;
-BZFILE* b;
-int nBuf;
-char buf[ /* whatever size you like */ ];
-int bzerror;
-int nWritten;
-
-f = fopen ( "myfile.bz2", "w" );
-if ( !f ) {
- /* handle error */
-}
-b = BZ2_bzWriteOpen( &bzerror, f, 9 );
-if (bzerror != BZ_OK) {
- BZ2_bzWriteClose ( b );
- /* handle error */
-}
-
-while ( /* condition */ ) {
- /* get data to write into buf, and set nBuf appropriately */
- nWritten = BZ2_bzWrite ( &bzerror, b, buf, nBuf );
- if (bzerror == BZ_IO_ERROR) {
- BZ2_bzWriteClose ( &bzerror, b );
- /* handle error */
- }
-}
-
-BZ2_bzWriteClose( &bzerror, b );
-if (bzerror == BZ_IO_ERROR) {
- /* handle error */
-}
-</programlisting>
-
-<para>And to read from a compressed file:</para>
-
-<programlisting>
-FILE* f;
-BZFILE* b;
-int nBuf;
-char buf[ /* whatever size you like */ ];
-int bzerror;
-int nWritten;
-
-f = fopen ( "myfile.bz2", "r" );
-if ( !f ) {
- /* handle error */
-}
-b = BZ2_bzReadOpen ( &bzerror, f, 0, NULL, 0 );
-if ( bzerror != BZ_OK ) {
- BZ2_bzReadClose ( &bzerror, b );
- /* handle error */
-}
-
-bzerror = BZ_OK;
-while ( bzerror == BZ_OK && /* arbitrary other conditions */) {
- nBuf = BZ2_bzRead ( &bzerror, b, buf, /* size of buf */ );
- if ( bzerror == BZ_OK ) {
- /* do something with buf[0 .. nBuf-1] */
- }
-}
-if ( bzerror != BZ_STREAM_END ) {
- BZ2_bzReadClose ( &bzerror, b );
- /* handle error */
-} else {
- BZ2_bzReadClose ( &bzerror, b );
-}
-</programlisting>
-
-</sect2>
-
-</sect1>
-
-
-<sect1 id="util-fns" xreflabel="Utility functions">
-<title>Utility functions</title>
-
-
-<sect2 id="bzbufftobuffcompress" xreflabel="BZ2_bzBuffToBuffCompress">
-<title>BZ2_bzBuffToBuffCompress</title>
-
-<programlisting>
-int BZ2_bzBuffToBuffCompress( char* dest,
- unsigned int* destLen,
- char* source,
- unsigned int sourceLen,
- int blockSize100k,
- int verbosity,
- int workFactor );
-</programlisting>
-
-<para>Attempts to compress the data in <computeroutput>source[0
-.. sourceLen-1]</computeroutput> into the destination buffer,
-<computeroutput>dest[0 .. *destLen-1]</computeroutput>. If the
-destination buffer is big enough,
-<computeroutput>*destLen</computeroutput> is set to the size of
-the compressed data, and <computeroutput>BZ_OK</computeroutput>
-is returned. If the compressed data won't fit,
-<computeroutput>*destLen</computeroutput> is unchanged, and
-<computeroutput>BZ_OUTBUFF_FULL</computeroutput> is
-returned.</para>
-
-<para>Compression in this manner is a one-shot event, done with a
-single call to this function. The resulting compressed data is a
-complete <computeroutput>bzip2</computeroutput> format data
-stream. There is no mechanism for making additional calls to
-provide extra input data. If you want that kind of mechanism,
-use the low-level interface.</para>
-
-<para>For the meaning of parameters
-<computeroutput>blockSize100k</computeroutput>,
-<computeroutput>verbosity</computeroutput> and
-<computeroutput>workFactor</computeroutput>, see
-<computeroutput>BZ2_bzCompressInit</computeroutput>.</para>
-
-<para>To guarantee that the compressed data will fit in its
-buffer, allocate an output buffer of size 1% larger than the
-uncompressed data, plus six hundred extra bytes.</para>
-
-<para><computeroutput>BZ2_bzBuffToBuffDecompress</computeroutput>
-will not write data at or beyond
-<computeroutput>dest[*destLen]</computeroutput>, even in case of
-buffer overflow.</para>
-
-<para>Possible return values:</para>
-
-<programlisting>
-BZ_CONFIG_ERROR
- if the library has been mis-compiled
-BZ_PARAM_ERROR
- if dest is NULL or destLen is NULL
- or blockSize100k < 1 or blockSize100k > 9
- or verbosity < 0 or verbosity > 4
- or workFactor < 0 or workFactor > 250
-BZ_MEM_ERROR
- if insufficient memory is available
-BZ_OUTBUFF_FULL
- if the size of the compressed data exceeds *destLen
-BZ_OK
- otherwise
-</programlisting>
-
-</sect2>
-
-
-<sect2 id="bzbufftobuffdecompress" xreflabel="BZ2_bzBuffToBuffDecompress">
-<title>BZ2_bzBuffToBuffDecompress</title>
-
-<programlisting>
-int BZ2_bzBuffToBuffDecompress( char* dest,
- unsigned int* destLen,
- char* source,
- unsigned int sourceLen,
- int small,
- int verbosity );
-</programlisting>
-
-<para>Attempts to decompress the data in <computeroutput>source[0
-.. sourceLen-1]</computeroutput> into the destination buffer,
-<computeroutput>dest[0 .. *destLen-1]</computeroutput>. If the
-destination buffer is big enough,
-<computeroutput>*destLen</computeroutput> is set to the size of
-the uncompressed data, and <computeroutput>BZ_OK</computeroutput>
-is returned. If the compressed data won't fit,
-<computeroutput>*destLen</computeroutput> is unchanged, and
-<computeroutput>BZ_OUTBUFF_FULL</computeroutput> is
-returned.</para>
-
-<para><computeroutput>source</computeroutput> is assumed to hold
-a complete <computeroutput>bzip2</computeroutput> format data
-stream.
-<computeroutput>BZ2_bzBuffToBuffDecompress</computeroutput> tries
-to decompress the entirety of the stream into the output
-buffer.</para>
-
-<para>For the meaning of parameters
-<computeroutput>small</computeroutput> and
-<computeroutput>verbosity</computeroutput>, see
-<computeroutput>BZ2_bzDecompressInit</computeroutput>.</para>
-
-<para>Because the compression ratio of the compressed data cannot
-be known in advance, there is no easy way to guarantee that the
-output buffer will be big enough. You may of course make
-arrangements in your code to record the size of the uncompressed
-data, but such a mechanism is beyond the scope of this
-library.</para>
-
-<para><computeroutput>BZ2_bzBuffToBuffDecompress</computeroutput>
-will not write data at or beyond
-<computeroutput>dest[*destLen]</computeroutput>, even in case of
-buffer overflow.</para>
-
-<para>Possible return values:</para>
-
-<programlisting>
-BZ_CONFIG_ERROR
- if the library has been mis-compiled
-BZ_PARAM_ERROR
- if dest is NULL or destLen is NULL
- or small != 0 && small != 1
- or verbosity < 0 or verbosity > 4
-BZ_MEM_ERROR
- if insufficient memory is available
-BZ_OUTBUFF_FULL
- if the size of the compressed data exceeds *destLen
-BZ_DATA_ERROR
- if a data integrity error was detected in the compressed data
-BZ_DATA_ERROR_MAGIC
- if the compressed data doesn't begin with the right magic bytes
-BZ_UNEXPECTED_EOF
- if the compressed data ends unexpectedly
-BZ_OK
- otherwise
-</programlisting>
-
-</sect2>
-
-</sect1>
-
-
-<sect1 id="zlib-compat" xreflabel="zlib compatibility functions">
-<title>zlib compatibility functions</title>
-
-<para>Yoshioka Tsuneo has contributed some functions to give
-better <computeroutput>zlib</computeroutput> compatibility.
-These functions are <computeroutput>BZ2_bzopen</computeroutput>,
-<computeroutput>BZ2_bzread</computeroutput>,
-<computeroutput>BZ2_bzwrite</computeroutput>,
-<computeroutput>BZ2_bzflush</computeroutput>,
-<computeroutput>BZ2_bzclose</computeroutput>,
-<computeroutput>BZ2_bzerror</computeroutput> and
-<computeroutput>BZ2_bzlibVersion</computeroutput>. These
-functions are not (yet) officially part of the library. If they
-break, you get to keep all the pieces. Nevertheless, I think
-they work ok.</para>
-
-<programlisting>
-typedef void BZFILE;
-
-const char * BZ2_bzlibVersion ( void );
-</programlisting>
-
-<para>Returns a string indicating the library version.</para>
-
-<programlisting>
-BZFILE * BZ2_bzopen ( const char *path, const char *mode );
-BZFILE * BZ2_bzdopen ( int fd, const char *mode );
-</programlisting>
-
-<para>Opens a <computeroutput>.bz2</computeroutput> file for
-reading or writing, using either its name or a pre-existing file
-descriptor. Analogous to <computeroutput>fopen</computeroutput>
-and <computeroutput>fdopen</computeroutput>.</para>
-
-<programlisting>
-int BZ2_bzread ( BZFILE* b, void* buf, int len );
-int BZ2_bzwrite ( BZFILE* b, void* buf, int len );
-</programlisting>
-
-<para>Reads/writes data from/to a previously opened
-<computeroutput>BZFILE</computeroutput>. Analogous to
-<computeroutput>fread</computeroutput> and
-<computeroutput>fwrite</computeroutput>.</para>
-
-<programlisting>
-int BZ2_bzflush ( BZFILE* b );
-void BZ2_bzclose ( BZFILE* b );
-</programlisting>
-
-<para>Flushes/closes a <computeroutput>BZFILE</computeroutput>.
-<computeroutput>BZ2_bzflush</computeroutput> doesn't actually do
-anything. Analogous to <computeroutput>fflush</computeroutput>
-and <computeroutput>fclose</computeroutput>.</para>
-
-<programlisting>
-const char * BZ2_bzerror ( BZFILE *b, int *errnum )
-</programlisting>
-
-<para>Returns a string describing the more recent error status of
-<computeroutput>b</computeroutput>, and also sets
-<computeroutput>*errnum</computeroutput> to its numerical
-value.</para>
-
-</sect1>
-
-
-<sect1 id="stdio-free"
- xreflabel="Using the library in a stdio-free environment">
-<title>Using the library in a stdio-free environment</title>
-
-
-<sect2 id="stdio-bye" xreflabel="Getting rid of stdio">
-<title>Getting rid of stdio</title>
-
-<para>In a deeply embedded application, you might want to use
-just the memory-to-memory functions. You can do this
-conveniently by compiling the library with preprocessor symbol
-<computeroutput>BZ_NO_STDIO</computeroutput> defined. Doing this
-gives you a library containing only the following eight
-functions:</para>
-
-<para><computeroutput>BZ2_bzCompressInit</computeroutput>,
-<computeroutput>BZ2_bzCompress</computeroutput>,
-<computeroutput>BZ2_bzCompressEnd</computeroutput>
-<computeroutput>BZ2_bzDecompressInit</computeroutput>,
-<computeroutput>BZ2_bzDecompress</computeroutput>,
-<computeroutput>BZ2_bzDecompressEnd</computeroutput>
-<computeroutput>BZ2_bzBuffToBuffCompress</computeroutput>,
-<computeroutput>BZ2_bzBuffToBuffDecompress</computeroutput></para>
-
-<para>When compiled like this, all functions will ignore
-<computeroutput>verbosity</computeroutput> settings.</para>
-
-</sect2>
-
-
-<sect2 id="critical-error" xreflabel="Critical error handling">
-<title>Critical error handling</title>
-
-<para><computeroutput>libbzip2</computeroutput> contains a number
-of internal assertion checks which should, needless to say, never
-be activated. Nevertheless, if an assertion should fail,
-behaviour depends on whether or not the library was compiled with
-<computeroutput>BZ_NO_STDIO</computeroutput> set.</para>
-
-<para>For a normal compile, an assertion failure yields the
-message:</para>
-
-<blockquote>
-<para>bzip2/libbzip2: internal error number N.</para>
-<para>This is a bug in bzip2/libbzip2, &bz-version; of &bz-date;.
-Please report it to me at: &bz-email;. If this happened
-when you were using some program which uses libbzip2 as a
-component, you should also report this bug to the author(s)
-of that program. Please make an effort to report this bug;
-timely and accurate bug reports eventually lead to higher
-quality software. Thanks. Julian Seward, &bz-date;.
-</para></blockquote>
-
-<para>where <computeroutput>N</computeroutput> is some error code
-number. If <computeroutput>N == 1007</computeroutput>, it also
-prints some extra text advising the reader that unreliable memory
-is often associated with internal error 1007. (This is a
-frequently-observed-phenomenon with versions 1.0.0/1.0.1).</para>
-
-<para><computeroutput>exit(3)</computeroutput> is then
-called.</para>
-
-<para>For a <computeroutput>stdio</computeroutput>-free library,
-assertion failures result in a call to a function declared
-as:</para>
-
-<programlisting>
-extern void bz_internal_error ( int errcode );
-</programlisting>
-
-<para>The relevant code is passed as a parameter. You should
-supply such a function.</para>
-
-<para>In either case, once an assertion failure has occurred, any
-<computeroutput>bz_stream</computeroutput> records involved can
-be regarded as invalid. You should not attempt to resume normal
-operation with them.</para>
-
-<para>You may, of course, change critical error handling to suit
-your needs. As I said above, critical errors indicate bugs in
-the library and should not occur. All "normal" error situations
-are indicated via error return codes from functions, and can be
-recovered from.</para>
-
-</sect2>
-
-</sect1>
-
-
-<sect1 id="win-dll" xreflabel="Making a Windows DLL">
-<title>Making a Windows DLL</title>
-
-<para>Everything related to Windows has been contributed by
-Yoshioka Tsuneo
-(<computeroutput>tsuneo at rr.iij4u.or.jp</computeroutput>), so
-you should send your queries to him (but perhaps Cc: me,
-<computeroutput>&bz-email;</computeroutput>).</para>
-
-<para>My vague understanding of what to do is: using Visual C++
-5.0, open the project file
-<computeroutput>libbz2.dsp</computeroutput>, and build. That's
-all.</para>
-
-<para>If you can't open the project file for some reason, make a
-new one, naming these files:
-<computeroutput>blocksort.c</computeroutput>,
-<computeroutput>bzlib.c</computeroutput>,
-<computeroutput>compress.c</computeroutput>,
-<computeroutput>crctable.c</computeroutput>,
-<computeroutput>decompress.c</computeroutput>,
-<computeroutput>huffman.c</computeroutput>,
-<computeroutput>randtable.c</computeroutput> and
-<computeroutput>libbz2.def</computeroutput>. You will also need
-to name the header files <computeroutput>bzlib.h</computeroutput>
-and <computeroutput>bzlib_private.h</computeroutput>.</para>
-
-<para>If you don't use VC++, you may need to define the
-proprocessor symbol
-<computeroutput>_WIN32</computeroutput>.</para>
-
-<para>Finally, <computeroutput>dlltest.c</computeroutput> is a
-sample program using the DLL. It has a project file,
-<computeroutput>dlltest.dsp</computeroutput>.</para>
-
-<para>If you just want a makefile for Visual C, have a look at
-<computeroutput>makefile.msc</computeroutput>.</para>
-
-<para>Be aware that if you compile
-<computeroutput>bzip2</computeroutput> itself on Win32, you must
-set <computeroutput>BZ_UNIX</computeroutput> to 0 and
-<computeroutput>BZ_LCCWIN32</computeroutput> to 1, in the file
-<computeroutput>bzip2.c</computeroutput>, before compiling.
-Otherwise the resulting binary won't work correctly.</para>
-
-<para>I haven't tried any of this stuff myself, but it all looks
-plausible.</para>
-
-</sect1>
-
-</chapter>
-
-
-
-<chapter id="misc" xreflabel="Miscellanea">
-<title>Miscellanea</title>
-
-<para>These are just some random thoughts of mine. Your mileage
-may vary.</para>
-
-
-<sect1 id="limits" xreflabel="Limitations of the compressed file format">
-<title>Limitations of the compressed file format</title>
-
-<para><computeroutput>bzip2-1.0.X</computeroutput>,
-<computeroutput>0.9.5</computeroutput> and
-<computeroutput>0.9.0</computeroutput> use exactly the same file
-format as the original version,
-<computeroutput>bzip2-0.1</computeroutput>. This decision was
-made in the interests of stability. Creating yet another
-incompatible compressed file format would create further
-confusion and disruption for users.</para>
-
-<para>Nevertheless, this is not a painless decision. Development
-work since the release of
-<computeroutput>bzip2-0.1</computeroutput> in August 1997 has
-shown complexities in the file format which slow down
-decompression and, in retrospect, are unnecessary. These
-are:</para>
-
-<itemizedlist mark='bullet'>
-
- <listitem><para>The run-length encoder, which is the first of the
- compression transformations, is entirely irrelevant. The
- original purpose was to protect the sorting algorithm from the
- very worst case input: a string of repeated symbols. But
- algorithm steps Q6a and Q6b in the original Burrows-Wheeler
- technical report (SRC-124) show how repeats can be handled
- without difficulty in block sorting.</para></listitem>
-
- <listitem><para>The randomisation mechanism doesn't really need to be
- there. Udi Manber and Gene Myers published a suffix array
- construction algorithm a few years back, which can be employed
- to sort any block, no matter how repetitive, in O(N log N)
- time. Subsequent work by Kunihiko Sadakane has produced a
- derivative O(N (log N)^2) algorithm which usually outperforms
- the Manber-Myers algorithm.</para>
-
- <para>I could have changed to Sadakane's algorithm, but I find
- it to be slower than <computeroutput>bzip2</computeroutput>'s
- existing algorithm for most inputs, and the randomisation
- mechanism protects adequately against bad cases. I didn't
- think it was a good tradeoff to make. Partly this is due to
- the fact that I was not flooded with email complaints about
- <computeroutput>bzip2-0.1</computeroutput>'s performance on
- repetitive data, so perhaps it isn't a problem for real
- inputs.</para>
-
- <para>Probably the best long-term solution, and the one I have
- incorporated into 0.9.5 and above, is to use the existing
- sorting algorithm initially, and fall back to a O(N (log N)^2)
- algorithm if the standard algorithm gets into
- difficulties.</para></listitem>
-
- <listitem><para>The compressed file format was never designed to be
- handled by a library, and I have had to jump though some hoops
- to produce an efficient implementation of decompression. It's
- a bit hairy. Try passing
- <computeroutput>decompress.c</computeroutput> through the C
- preprocessor and you'll see what I mean. Much of this
- complexity could have been avoided if the compressed size of
- each block of data was recorded in the data stream.</para></listitem>
-
- <listitem><para>An Adler-32 checksum, rather than a CRC32 checksum,
- would be faster to compute.</para></listitem>
-
-</itemizedlist>
-
-<para>It would be fair to say that the
-<computeroutput>bzip2</computeroutput> format was frozen before I
-properly and fully understood the performance consequences of
-doing so.</para>
-
-<para>Improvements which I was able to incorporate into 0.9.0,
-despite using the same file format, are:</para>
-
-<itemizedlist mark='bullet'>
-
- <listitem><para>Single array implementation of the inverse BWT. This
- significantly speeds up decompression, presumably because it
- reduces the number of cache misses.</para></listitem>
-
- <listitem><para>Faster inverse MTF transform for large MTF values.
- The new implementation is based on the notion of sliding blocks
- of values.</para></listitem>
-
- <listitem><para><computeroutput>bzip2-0.9.0</computeroutput> now reads
- and writes files with <computeroutput>fread</computeroutput>
- and <computeroutput>fwrite</computeroutput>; version 0.1 used
- <computeroutput>putc</computeroutput> and
- <computeroutput>getc</computeroutput>. Duh! Well, you live
- and learn.</para></listitem>
-
-</itemizedlist>
-
-<para>Further ahead, it would be nice to be able to do random
-access into files. This will require some careful design of
-compressed file formats.</para>
-
-</sect1>
-
-
-<sect1 id="port-issues" xreflabel="Portability issues">
-<title>Portability issues</title>
-
-<para>After some consideration, I have decided not to use GNU
-<computeroutput>autoconf</computeroutput> to configure 0.9.5 or
-1.0.</para>
-
-<para><computeroutput>autoconf</computeroutput>, admirable and
-wonderful though it is, mainly assists with portability problems
-between Unix-like platforms. But
-<computeroutput>bzip2</computeroutput> doesn't have much in the
-way of portability problems on Unix; most of the difficulties
-appear when porting to the Mac, or to Microsoft's operating
-systems. <computeroutput>autoconf</computeroutput> doesn't help
-in those cases, and brings in a whole load of new
-complexity.</para>
-
-<para>Most people should be able to compile the library and
-program under Unix straight out-of-the-box, so to speak,
-especially if you have a version of GNU C available.</para>
-
-<para>There are a couple of
-<computeroutput>__inline__</computeroutput> directives in the
-code. GNU C (<computeroutput>gcc</computeroutput>) should be
-able to handle them. If you're not using GNU C, your C compiler
-shouldn't see them at all. If your compiler does, for some
-reason, see them and doesn't like them, just
-<computeroutput>#define</computeroutput>
-<computeroutput>__inline__</computeroutput> to be
-<computeroutput>/* */</computeroutput>. One easy way to do this
-is to compile with the flag
-<computeroutput>-D__inline__=</computeroutput>, which should be
-understood by most Unix compilers.</para>
-
-<para>If you still have difficulties, try compiling with the
-macro <computeroutput>BZ_STRICT_ANSI</computeroutput> defined.
-This should enable you to build the library in a strictly ANSI
-compliant environment. Building the program itself like this is
-dangerous and not supported, since you remove
-<computeroutput>bzip2</computeroutput>'s checks against
-compressing directories, symbolic links, devices, and other
-not-really-a-file entities. This could cause filesystem
-corruption!</para>
-
-<para>One other thing: if you create a
-<computeroutput>bzip2</computeroutput> binary for public distribution,
-please consider linking it statically (<computeroutput>gcc
--static</computeroutput>). This avoids all sorts of library-version
-issues that others may encounter later on.</para>
-
-<para>If you build <computeroutput>bzip2</computeroutput> on
-Win32, you must set <computeroutput>BZ_UNIX</computeroutput> to 0
-and <computeroutput>BZ_LCCWIN32</computeroutput> to 1, in the
-file <computeroutput>bzip2.c</computeroutput>, before compiling.
-Otherwise the resulting binary won't work correctly.</para>
-
-</sect1>
-
-
-<sect1 id="bugs" xreflabel="Reporting bugs">
-<title>Reporting bugs</title>
-
-<para>I tried pretty hard to make sure
-<computeroutput>bzip2</computeroutput> is bug free, both by
-design and by testing. Hopefully you'll never need to read this
-section for real.</para>
-
-<para>Nevertheless, if <computeroutput>bzip2</computeroutput> dies
-with a segmentation fault, a bus error or an internal assertion
-failure, it will ask you to email me a bug report. Experience from
-years of feedback of bzip2 users indicates that almost all these
-problems can be traced to either compiler bugs or hardware
-problems.</para>
-
-<itemizedlist mark='bullet'>
-
- <listitem><para>Recompile the program with no optimisation, and
- see if it works. And/or try a different compiler. I heard all
- sorts of stories about various flavours of GNU C (and other
- compilers) generating bad code for
- <computeroutput>bzip2</computeroutput>, and I've run across two
- such examples myself.</para>
-
- <para>2.7.X versions of GNU C are known to generate bad code
- from time to time, at high optimisation levels. If you get
- problems, try using the flags
- <computeroutput>-O2</computeroutput>
- <computeroutput>-fomit-frame-pointer</computeroutput>
- <computeroutput>-fno-strength-reduce</computeroutput>. You
- should specifically <emphasis>not</emphasis> use
- <computeroutput>-funroll-loops</computeroutput>.</para>
-
- <para>You may notice that the Makefile runs six tests as part
- of the build process. If the program passes all of these, it's
- a pretty good (but not 100%) indication that the compiler has
- done its job correctly.</para></listitem>
-
- <listitem><para>If <computeroutput>bzip2</computeroutput>
- crashes randomly, and the crashes are not repeatable, you may
- have a flaky memory subsystem.
- <computeroutput>bzip2</computeroutput> really hammers your
- memory hierarchy, and if it's a bit marginal, you may get these
- problems. Ditto if your disk or I/O subsystem is slowly
- failing. Yup, this really does happen.</para>
-
- <para>Try using a different machine of the same type, and see
- if you can repeat the problem.</para></listitem>
-
- <listitem><para>This isn't really a bug, but ... If
- <computeroutput>bzip2</computeroutput> tells you your file is
- corrupted on decompression, and you obtained the file via FTP,
- there is a possibility that you forgot to tell FTP to do a
- binary mode transfer. That absolutely will cause the file to
- be non-decompressible. You'll have to transfer it
- again.</para></listitem>
-
-</itemizedlist>
-
-<para>If you've incorporated
-<computeroutput>libbzip2</computeroutput> into your own program
-and are getting problems, please, please, please, check that the
-parameters you are passing in calls to the library, are correct,
-and in accordance with what the documentation says is allowable.
-I have tried to make the library robust against such problems,
-but I'm sure I haven't succeeded.</para>
-
-<para>Finally, if the above comments don't help, you'll have to
-send me a bug report. Now, it's just amazing how many people
-will send me a bug report saying something like:</para>
-
-<programlisting>
-bzip2 crashed with segmentation fault on my machine
-</programlisting>
-
-<para>and absolutely nothing else. Needless to say, a such a
-report is <emphasis>totally, utterly, completely and
-comprehensively 100% useless; a waste of your time, my time, and
-net bandwidth</emphasis>. With no details at all, there's no way
-I can possibly begin to figure out what the problem is.</para>
-
-<para>The rules of the game are: facts, facts, facts. Don't omit
-them because "oh, they won't be relevant". At the bare
-minimum:</para>
-
-<programlisting>
-Machine type. Operating system version.
-Exact version of bzip2 (do bzip2 -V).
-Exact version of the compiler used.
-Flags passed to the compiler.
-</programlisting>
-
-<para>However, the most important single thing that will help me
-is the file that you were trying to compress or decompress at the
-time the problem happened. Without that, my ability to do
-anything more than speculate about the cause, is limited.</para>
-
-</sect1>
-
-
-<sect1 id="package" xreflabel="Did you get the right package?">
-<title>Did you get the right package?</title>
-
-<para><computeroutput>bzip2</computeroutput> is a resource hog.
-It soaks up large amounts of CPU cycles and memory. Also, it
-gives very large latencies. In the worst case, you can feed many
-megabytes of uncompressed data into the library before getting
-any compressed output, so this probably rules out applications
-requiring interactive behaviour.</para>
-
-<para>These aren't faults of my implementation, I hope, but more
-an intrinsic property of the Burrows-Wheeler transform
-(unfortunately). Maybe this isn't what you want.</para>
-
-<para>If you want a compressor and/or library which is faster,
-uses less memory but gets pretty good compression, and has
-minimal latency, consider Jean-loup Gailly's and Mark Adler's
-work, <computeroutput>zlib-1.2.1</computeroutput> and
-<computeroutput>gzip-1.2.4</computeroutput>. Look for them at
-<ulink url="http://www.zlib.org">http://www.zlib.org</ulink> and
-<ulink url="http://www.gzip.org">http://www.gzip.org</ulink>
-respectively.</para>
-
-<para>For something faster and lighter still, you might try Markus F
-X J Oberhumer's <computeroutput>LZO</computeroutput> real-time
-compression/decompression library, at
-<ulink url="http://www.oberhumer.com/opensource">http://www.oberhumer.com/opensource</ulink>.</para>
-
-</sect1>
-
-
-
-<sect1 id="reading" xreflabel="Further Reading">
-<title>Further Reading</title>
-
-<para><computeroutput>bzip2</computeroutput> is not research
-work, in the sense that it doesn't present any new ideas.
-Rather, it's an engineering exercise based on existing
-ideas.</para>
-
-<para>Four documents describe essentially all the ideas behind
-<computeroutput>bzip2</computeroutput>:</para>
-
-<literallayout>Michael Burrows and D. J. Wheeler:
- "A block-sorting lossless data compression algorithm"
- 10th May 1994.
- Digital SRC Research Report 124.
- ftp://ftp.digital.com/pub/DEC/SRC/research-reports/SRC-124.ps.gz
- If you have trouble finding it, try searching at the
- New Zealand Digital Library, http://www.nzdl.org.
-
-Daniel S. Hirschberg and Debra A. LeLewer
- "Efficient Decoding of Prefix Codes"
- Communications of the ACM, April 1990, Vol 33, Number 4.
- You might be able to get an electronic copy of this
- from the ACM Digital Library.
-
-David J. Wheeler
- Program bred3.c and accompanying document bred3.ps.
- This contains the idea behind the multi-table Huffman coding scheme.
- ftp://ftp.cl.cam.ac.uk/users/djw3/
-
-Jon L. Bentley and Robert Sedgewick
- "Fast Algorithms for Sorting and Searching Strings"
- Available from Sedgewick's web page,
- www.cs.princeton.edu/~rs
-</literallayout>
-
-<para>The following paper gives valuable additional insights into
-the algorithm, but is not immediately the basis of any code used
-in bzip2.</para>
-
-<literallayout>Peter Fenwick:
- Block Sorting Text Compression
- Proceedings of the 19th Australasian Computer Science Conference,
- Melbourne, Australia. Jan 31 - Feb 2, 1996.
- ftp://ftp.cs.auckland.ac.nz/pub/peter-f/ACSC96paper.ps</literallayout>
-
-<para>Kunihiko Sadakane's sorting algorithm, mentioned above, is
-available from:</para>
-
-<literallayout>http://naomi.is.s.u-tokyo.ac.jp/~sada/papers/Sada98b.ps.gz
-</literallayout>
-
-<para>The Manber-Myers suffix array construction algorithm is
-described in a paper available from:</para>
-
-<literallayout>http://www.cs.arizona.edu/people/gene/PAPERS/suffix.ps
-</literallayout>
-
-<para>Finally, the following papers document some
-investigations I made into the performance of sorting
-and decompression algorithms:</para>
-
-<literallayout>Julian Seward
- On the Performance of BWT Sorting Algorithms
- Proceedings of the IEEE Data Compression Conference 2000
- Snowbird, Utah. 28-30 March 2000.
-
-Julian Seward
- Space-time Tradeoffs in the Inverse B-W Transform
- Proceedings of the IEEE Data Compression Conference 2001
- Snowbird, Utah. 27-29 March 2001.
-</literallayout>
-
-</sect1>
-
-</chapter>
-
-</book>
diff --git a/third-party/bzip2/mk251.c b/third-party/bzip2/mk251.c
deleted file mode 100644
index c9c36f6..0000000
--- a/third-party/bzip2/mk251.c
+++ /dev/null
@@ -1,31 +0,0 @@
-
-/* Spew out a long sequence of the byte 251. When fed to bzip2
- versions 1.0.0 or 1.0.1, causes it to die with internal error
- 1007 in blocksort.c. This assertion misses an extremely rare
- case, which is fixed in this version (1.0.2) and above.
-*/
-
-/* ------------------------------------------------------------------
- This file is part of bzip2/libbzip2, a program and library for
- lossless, block-sorting data compression.
-
- bzip2/libbzip2 version 1.0.6 of 6 September 2010
- Copyright (C) 1996-2010 Julian Seward <jseward at bzip.org>
-
- Please read the WARNING, DISCLAIMER and PATENTS sections in the
- README file.
-
- This program is released under the terms of the license contained
- in the file LICENSE.
- ------------------------------------------------------------------ */
-
-
-#include <stdio.h>
-
-int main ()
-{
- int i;
- for (i = 0; i < 48500000 ; i++)
- putchar(251);
- return 0;
-}
diff --git a/third-party/bzip2/randtable.c b/third-party/bzip2/randtable.c
deleted file mode 100644
index 6d62459..0000000
--- a/third-party/bzip2/randtable.c
+++ /dev/null
@@ -1,84 +0,0 @@
-
-/*-------------------------------------------------------------*/
-/*--- Table for randomising repetitive blocks ---*/
-/*--- randtable.c ---*/
-/*-------------------------------------------------------------*/
-
-/* ------------------------------------------------------------------
- This file is part of bzip2/libbzip2, a program and library for
- lossless, block-sorting data compression.
-
- bzip2/libbzip2 version 1.0.6 of 6 September 2010
- Copyright (C) 1996-2010 Julian Seward <jseward at bzip.org>
-
- Please read the WARNING, DISCLAIMER and PATENTS sections in the
- README file.
-
- This program is released under the terms of the license contained
- in the file LICENSE.
- ------------------------------------------------------------------ */
-
-
-#include "bzlib_private.h"
-
-
-/*---------------------------------------------*/
-Int32 BZ2_rNums[512] = {
- 619, 720, 127, 481, 931, 816, 813, 233, 566, 247,
- 985, 724, 205, 454, 863, 491, 741, 242, 949, 214,
- 733, 859, 335, 708, 621, 574, 73, 654, 730, 472,
- 419, 436, 278, 496, 867, 210, 399, 680, 480, 51,
- 878, 465, 811, 169, 869, 675, 611, 697, 867, 561,
- 862, 687, 507, 283, 482, 129, 807, 591, 733, 623,
- 150, 238, 59, 379, 684, 877, 625, 169, 643, 105,
- 170, 607, 520, 932, 727, 476, 693, 425, 174, 647,
- 73, 122, 335, 530, 442, 853, 695, 249, 445, 515,
- 909, 545, 703, 919, 874, 474, 882, 500, 594, 612,
- 641, 801, 220, 162, 819, 984, 589, 513, 495, 799,
- 161, 604, 958, 533, 221, 400, 386, 867, 600, 782,
- 382, 596, 414, 171, 516, 375, 682, 485, 911, 276,
- 98, 553, 163, 354, 666, 933, 424, 341, 533, 870,
- 227, 730, 475, 186, 263, 647, 537, 686, 600, 224,
- 469, 68, 770, 919, 190, 373, 294, 822, 808, 206,
- 184, 943, 795, 384, 383, 461, 404, 758, 839, 887,
- 715, 67, 618, 276, 204, 918, 873, 777, 604, 560,
- 951, 160, 578, 722, 79, 804, 96, 409, 713, 940,
- 652, 934, 970, 447, 318, 353, 859, 672, 112, 785,
- 645, 863, 803, 350, 139, 93, 354, 99, 820, 908,
- 609, 772, 154, 274, 580, 184, 79, 626, 630, 742,
- 653, 282, 762, 623, 680, 81, 927, 626, 789, 125,
- 411, 521, 938, 300, 821, 78, 343, 175, 128, 250,
- 170, 774, 972, 275, 999, 639, 495, 78, 352, 126,
- 857, 956, 358, 619, 580, 124, 737, 594, 701, 612,
- 669, 112, 134, 694, 363, 992, 809, 743, 168, 974,
- 944, 375, 748, 52, 600, 747, 642, 182, 862, 81,
- 344, 805, 988, 739, 511, 655, 814, 334, 249, 515,
- 897, 955, 664, 981, 649, 113, 974, 459, 893, 228,
- 433, 837, 553, 268, 926, 240, 102, 654, 459, 51,
- 686, 754, 806, 760, 493, 403, 415, 394, 687, 700,
- 946, 670, 656, 610, 738, 392, 760, 799, 887, 653,
- 978, 321, 576, 617, 626, 502, 894, 679, 243, 440,
- 680, 879, 194, 572, 640, 724, 926, 56, 204, 700,
- 707, 151, 457, 449, 797, 195, 791, 558, 945, 679,
- 297, 59, 87, 824, 713, 663, 412, 693, 342, 606,
- 134, 108, 571, 364, 631, 212, 174, 643, 304, 329,
- 343, 97, 430, 751, 497, 314, 983, 374, 822, 928,
- 140, 206, 73, 263, 980, 736, 876, 478, 430, 305,
- 170, 514, 364, 692, 829, 82, 855, 953, 676, 246,
- 369, 970, 294, 750, 807, 827, 150, 790, 288, 923,
- 804, 378, 215, 828, 592, 281, 565, 555, 710, 82,
- 896, 831, 547, 261, 524, 462, 293, 465, 502, 56,
- 661, 821, 976, 991, 658, 869, 905, 758, 745, 193,
- 768, 550, 608, 933, 378, 286, 215, 979, 792, 961,
- 61, 688, 793, 644, 986, 403, 106, 366, 905, 644,
- 372, 567, 466, 434, 645, 210, 389, 550, 919, 135,
- 780, 773, 635, 389, 707, 100, 626, 958, 165, 504,
- 920, 176, 193, 713, 857, 265, 203, 50, 668, 108,
- 645, 990, 626, 197, 510, 357, 358, 850, 858, 364,
- 936, 638
-};
-
-
-/*-------------------------------------------------------------*/
-/*--- end randtable.c ---*/
-/*-------------------------------------------------------------*/
diff --git a/third-party/bzip2/sample1.bz2 b/third-party/bzip2/sample1.bz2
deleted file mode 100644
index 18dea60..0000000
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diff --git a/third-party/bzip2/sample1.ref b/third-party/bzip2/sample1.ref
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diff --git a/third-party/bzip2/sample2.bz2 b/third-party/bzip2/sample2.bz2
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diff --git a/third-party/bzip2/sample2.ref b/third-party/bzip2/sample2.ref
deleted file mode 100644
index 34af958..0000000
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diff --git a/third-party/bzip2/sample3.bz2 b/third-party/bzip2/sample3.bz2
deleted file mode 100644
index d90cff9..0000000
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diff --git a/third-party/bzip2/sample3.ref b/third-party/bzip2/sample3.ref
deleted file mode 100644
index 775a2f6..0000000
--- a/third-party/bzip2/sample3.ref
+++ /dev/null
@@ -1,30007 +0,0 @@
-This file is exceedingly boring. If you find yourself
-reading it, please (1) take it from me that you can safely
-guess what the rest of the file says, and (2) seek professional
-help.
-
-ps. there are no further sarcastic remarks in this file.
-
-ugh
-ugh
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@@ -1,54 +0,0 @@
-
-/* spew out a thoroughly gigantic file designed so that bzip2
- can compress it reasonably rapidly. This is to help test
- support for large files (> 2GB) in a reasonable amount of time.
- I suggest you use the undocumented --exponential option to
- bzip2 when compressing the resulting file; this saves a bit of
- time. Note: *don't* bother with --exponential when compressing
- Real Files; it'll just waste a lot of CPU time :-)
- (but is otherwise harmless).
-*/
-
-/* ------------------------------------------------------------------
- This file is part of bzip2/libbzip2, a program and library for
- lossless, block-sorting data compression.
-
- bzip2/libbzip2 version 1.0.6 of 6 September 2010
- Copyright (C) 1996-2010 Julian Seward <jseward at bzip.org>
-
- Please read the WARNING, DISCLAIMER and PATENTS sections in the
- README file.
-
- This program is released under the terms of the license contained
- in the file LICENSE.
- ------------------------------------------------------------------ */
-
-
-#define _FILE_OFFSET_BITS 64
-
-#include <stdio.h>
-#include <stdlib.h>
-
-/* The number of megabytes of junk to spew out (roughly) */
-#define MEGABYTES 5000
-
-#define N_BUF 1000000
-char buf[N_BUF];
-
-int main ( int argc, char** argv )
-{
- int ii, kk, p;
- srandom(1);
- setbuffer ( stdout, buf, N_BUF );
- for (kk = 0; kk < MEGABYTES * 515; kk+=3) {
- p = 25+random()%50;
- for (ii = 0; ii < p; ii++)
- printf ( "aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa" );
- for (ii = 0; ii < p-1; ii++)
- printf ( "bbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbb" );
- for (ii = 0; ii < p+1; ii++)
- printf ( "ccccccccccccccccccccccccccccccccccccc" );
- }
- fflush(stdout);
- return 0;
-}
diff --git a/third-party/bzip2/unzcrash.c b/third-party/bzip2/unzcrash.c
deleted file mode 100644
index 7041da5..0000000
--- a/third-party/bzip2/unzcrash.c
+++ /dev/null
@@ -1,141 +0,0 @@
-
-/* A test program written to test robustness to decompression of
- corrupted data. Usage is
- unzcrash filename
- and the program will read the specified file, compress it (in memory),
- and then repeatedly decompress it, each time with a different bit of
- the compressed data inverted, so as to test all possible one-bit errors.
- This should not cause any invalid memory accesses. If it does,
- I want to know about it!
-
- PS. As you can see from the above description, the process is
- incredibly slow. A file of size eg 5KB will cause it to run for
- many hours.
-*/
-
-/* ------------------------------------------------------------------
- This file is part of bzip2/libbzip2, a program and library for
- lossless, block-sorting data compression.
-
- bzip2/libbzip2 version 1.0.6 of 6 September 2010
- Copyright (C) 1996-2010 Julian Seward <jseward at bzip.org>
-
- Please read the WARNING, DISCLAIMER and PATENTS sections in the
- README file.
-
- This program is released under the terms of the license contained
- in the file LICENSE.
- ------------------------------------------------------------------ */
-
-
-#include <stdio.h>
-#include <assert.h>
-#include "bzlib.h"
-
-#define M_BLOCK 1000000
-
-typedef unsigned char uchar;
-
-#define M_BLOCK_OUT (M_BLOCK + 1000000)
-uchar inbuf[M_BLOCK];
-uchar outbuf[M_BLOCK_OUT];
-uchar zbuf[M_BLOCK + 600 + (M_BLOCK / 100)];
-
-int nIn, nOut, nZ;
-
-static char *bzerrorstrings[] = {
- "OK"
- ,"SEQUENCE_ERROR"
- ,"PARAM_ERROR"
- ,"MEM_ERROR"
- ,"DATA_ERROR"
- ,"DATA_ERROR_MAGIC"
- ,"IO_ERROR"
- ,"UNEXPECTED_EOF"
- ,"OUTBUFF_FULL"
- ,"???" /* for future */
- ,"???" /* for future */
- ,"???" /* for future */
- ,"???" /* for future */
- ,"???" /* for future */
- ,"???" /* for future */
-};
-
-void flip_bit ( int bit )
-{
- int byteno = bit / 8;
- int bitno = bit % 8;
- uchar mask = 1 << bitno;
- //fprintf ( stderr, "(byte %d bit %d mask %d)",
- // byteno, bitno, (int)mask );
- zbuf[byteno] ^= mask;
-}
-
-int main ( int argc, char** argv )
-{
- FILE* f;
- int r;
- int bit;
- int i;
-
- if (argc != 2) {
- fprintf ( stderr, "usage: unzcrash filename\n" );
- return 1;
- }
-
- f = fopen ( argv[1], "r" );
- if (!f) {
- fprintf ( stderr, "unzcrash: can't open %s\n", argv[1] );
- return 1;
- }
-
- nIn = fread ( inbuf, 1, M_BLOCK, f );
- fprintf ( stderr, "%d bytes read\n", nIn );
-
- nZ = M_BLOCK;
- r = BZ2_bzBuffToBuffCompress (
- zbuf, &nZ, inbuf, nIn, 9, 0, 30 );
-
- assert (r == BZ_OK);
- fprintf ( stderr, "%d after compression\n", nZ );
-
- for (bit = 0; bit < nZ*8; bit++) {
- fprintf ( stderr, "bit %d ", bit );
- flip_bit ( bit );
- nOut = M_BLOCK_OUT;
- r = BZ2_bzBuffToBuffDecompress (
- outbuf, &nOut, zbuf, nZ, 0, 0 );
- fprintf ( stderr, " %d %s ", r, bzerrorstrings[-r] );
-
- if (r != BZ_OK) {
- fprintf ( stderr, "\n" );
- } else {
- if (nOut != nIn) {
- fprintf(stderr, "nIn/nOut mismatch %d %d\n", nIn, nOut );
- return 1;
- } else {
- for (i = 0; i < nOut; i++)
- if (inbuf[i] != outbuf[i]) {
- fprintf(stderr, "mismatch at %d\n", i );
- return 1;
- }
- if (i == nOut) fprintf(stderr, "really ok!\n" );
- }
- }
-
- flip_bit ( bit );
- }
-
-#if 0
- assert (nOut == nIn);
- for (i = 0; i < nOut; i++) {
- if (inbuf[i] != outbuf[i]) {
- fprintf ( stderr, "difference at %d !\n", i );
- return 1;
- }
- }
-#endif
-
- fprintf ( stderr, "all ok\n" );
- return 0;
-}
diff --git a/third-party/bzip2/words0 b/third-party/bzip2/words0
deleted file mode 100644
index fbf442a..0000000
--- a/third-party/bzip2/words0
+++ /dev/null
@@ -1,9 +0,0 @@
-
-If compilation produces errors, or a large number of warnings,
-please read README.COMPILATION.PROBLEMS -- you might be able to
-adjust the flags in this Makefile to improve matters.
-
-Also in README.COMPILATION.PROBLEMS are some hints that may help
-if your build produces an executable which is unable to correctly
-handle so-called 'large files' -- files of size 2GB or more.
-
diff --git a/third-party/bzip2/words1 b/third-party/bzip2/words1
deleted file mode 100644
index 2e83de9..0000000
--- a/third-party/bzip2/words1
+++ /dev/null
@@ -1,4 +0,0 @@
-
-Doing 6 tests (3 compress, 3 uncompress) ...
-If there's a problem, things might stop at this point.
-
diff --git a/third-party/bzip2/words2 b/third-party/bzip2/words2
deleted file mode 100644
index caddcf4..0000000
--- a/third-party/bzip2/words2
+++ /dev/null
@@ -1,5 +0,0 @@
-
-Checking test results. If any of the four "cmp"s which follow
-report any differences, something is wrong. If you can't easily
-figure out what, please let me know (jseward at bzip.org).
-
diff --git a/third-party/bzip2/words3 b/third-party/bzip2/words3
deleted file mode 100644
index 6972669..0000000
--- a/third-party/bzip2/words3
+++ /dev/null
@@ -1,30 +0,0 @@
-
-If you got this far and the 'cmp's didn't complain, it looks
-like you're in business.
-
-To install in /usr/local/bin, /usr/local/lib, /usr/local/man and
-/usr/local/include, type
-
- make install
-
-To install somewhere else, eg, /xxx/yyy/{bin,lib,man,include}, type
-
- make install PREFIX=/xxx/yyy
-
-If you are (justifiably) paranoid and want to see what 'make install'
-is going to do, you can first do
-
- make -n install or
- make -n install PREFIX=/xxx/yyy respectively.
-
-The -n instructs make to show the commands it would execute, but
-not actually execute them.
-
-Instructions for use are in the preformatted manual page, in the file
-bzip2.txt. For more detailed documentation, read the full manual.
-It is available in Postscript form (manual.ps), PDF form (manual.pdf),
-and HTML form (manual.html).
-
-You can also do "bzip2 --help" to see some helpful information.
-"bzip2 -L" displays the software license.
-
diff --git a/third-party/bzip2/xmlproc.sh b/third-party/bzip2/xmlproc.sh
deleted file mode 100755
index ca284ea..0000000
--- a/third-party/bzip2/xmlproc.sh
+++ /dev/null
@@ -1,114 +0,0 @@
-#!/bin/bash
-# see the README file for usage etc.
-#
-# ------------------------------------------------------------------
-# This file is part of bzip2/libbzip2, a program and library for
-# lossless, block-sorting data compression.
-#
-# bzip2/libbzip2 version 1.0.6 of 6 September 2010
-# Copyright (C) 1996-2010 Julian Seward <jseward at bzip.org>
-#
-# Please read the WARNING, DISCLAIMER and PATENTS sections in the
-# README file.
-#
-# This program is released under the terms of the license contained
-# in the file LICENSE.
-# ----------------------------------------------------------------
-
-
-usage() {
- echo '';
- echo 'Usage: xmlproc.sh -[option] <filename.xml>';
- echo 'Specify a target from:';
- echo '-v verify xml file conforms to dtd';
- echo '-html output in html format (single file)';
- echo '-ps output in postscript format';
- echo '-pdf output in pdf format';
- exit;
-}
-
-if test $# -ne 2; then
- usage
-fi
-# assign the variable for the output type
-action=$1; shift
-# assign the output filename
-xmlfile=$1; shift
-# and check user input it correct
-if !(test -f $xmlfile); then
- echo "No such file: $xmlfile";
- exit;
-fi
-# some other stuff we will use
-OUT=output
-xsl_fo=bz-fo.xsl
-xsl_html=bz-html.xsl
-
-basename=$xmlfile
-basename=${basename//'.xml'/''}
-
-fofile="${basename}.fo"
-htmlfile="${basename}.html"
-pdffile="${basename}.pdf"
-psfile="${basename}.ps"
-xmlfmtfile="${basename}.fmt"
-
-# first process the xmlfile with CDATA tags
-./format.pl $xmlfile $xmlfmtfile
-# so the shell knows where the catalogs live
-export XML_CATALOG_FILES=/etc/xml/catalog
-
-# post-processing tidy up
-cleanup() {
- echo "Cleaning up: $@"
- while [ $# != 0 ]
- do
- arg=$1; shift;
- echo " deleting $arg";
- rm $arg
- done
-}
-
-case $action in
- -v)
- flags='--noout --xinclude --noblanks --postvalid'
- dtd='--dtdvalid http://www.oasis-open.org/docbook/xml/4.2/docbookx.dtd'
- xmllint $flags $dtd $xmlfmtfile 2> $OUT
- egrep 'error' $OUT
- rm $OUT
- ;;
-
- -html)
- echo "Creating $htmlfile ..."
- xsltproc --nonet --xinclude -o $htmlfile $xsl_html $xmlfmtfile
- cleanup $xmlfmtfile
- ;;
-
- -pdf)
- echo "Creating $pdffile ..."
- xsltproc --nonet --xinclude -o $fofile $xsl_fo $xmlfmtfile
- pdfxmltex $fofile >$OUT </dev/null
- pdfxmltex $fofile >$OUT </dev/null
- pdfxmltex $fofile >$OUT </dev/null
- cleanup $OUT $xmlfmtfile *.aux *.fo *.log *.out
- ;;
-
- -ps)
- echo "Creating $psfile ..."
- xsltproc --nonet --xinclude -o $fofile $xsl_fo $xmlfmtfile
- pdfxmltex $fofile >$OUT </dev/null
- pdfxmltex $fofile >$OUT </dev/null
- pdfxmltex $fofile >$OUT </dev/null
- pdftops $pdffile $psfile
- cleanup $OUT $xmlfmtfile $pdffile *.aux *.fo *.log *.out
-# passivetex is broken, so we can't go this route yet.
-# xmltex $fofile >$OUT </dev/null
-# xmltex $fofile >$OUT </dev/null
-# xmltex $fofile >$OUT </dev/null
-# dvips -R -q -o bzip-manual.ps *.dvi
- ;;
-
- *)
- usage
- ;;
-esac
diff --git a/third-party/zlib/.gitignore b/third-party/zlib/.gitignore
deleted file mode 100644
index 676d6e2..0000000
--- a/third-party/zlib/.gitignore
+++ /dev/null
@@ -1,5 +0,0 @@
-libz.so.*
-libz.*dylib
-libz.a
-Makefile
-zconf.h
diff --git a/third-party/zlib/CMakeLists.txt b/third-party/zlib/CMakeLists.txt
deleted file mode 100644
index 0c0247c..0000000
--- a/third-party/zlib/CMakeLists.txt
+++ /dev/null
@@ -1,249 +0,0 @@
-cmake_minimum_required(VERSION 2.4.4)
-set(CMAKE_ALLOW_LOOSE_LOOP_CONSTRUCTS ON)
-
-project(zlib C)
-
-set(VERSION "1.2.8")
-
-option(ASM686 "Enable building i686 assembly implementation")
-option(AMD64 "Enable building amd64 assembly implementation")
-
-set(INSTALL_BIN_DIR "${CMAKE_INSTALL_PREFIX}/bin" CACHE PATH "Installation directory for executables")
-set(INSTALL_LIB_DIR "${CMAKE_INSTALL_PREFIX}/lib" CACHE PATH "Installation directory for libraries")
-set(INSTALL_INC_DIR "${CMAKE_INSTALL_PREFIX}/include" CACHE PATH "Installation directory for headers")
-set(INSTALL_MAN_DIR "${CMAKE_INSTALL_PREFIX}/share/man" CACHE PATH "Installation directory for manual pages")
-set(INSTALL_PKGCONFIG_DIR "${CMAKE_INSTALL_PREFIX}/share/pkgconfig" CACHE PATH "Installation directory for pkgconfig (.pc) files")
-
-include(CheckTypeSize)
-include(CheckFunctionExists)
-include(CheckIncludeFile)
-include(CheckCSourceCompiles)
-enable_testing()
-
-check_include_file(sys/types.h HAVE_SYS_TYPES_H)
-check_include_file(stdint.h HAVE_STDINT_H)
-check_include_file(stddef.h HAVE_STDDEF_H)
-
-#
-# Check to see if we have large file support
-#
-set(CMAKE_REQUIRED_DEFINITIONS -D_LARGEFILE64_SOURCE=1)
-# We add these other definitions here because CheckTypeSize.cmake
-# in CMake 2.4.x does not automatically do so and we want
-# compatibility with CMake 2.4.x.
-if(HAVE_SYS_TYPES_H)
- list(APPEND CMAKE_REQUIRED_DEFINITIONS -DHAVE_SYS_TYPES_H)
-endif()
-if(HAVE_STDINT_H)
- list(APPEND CMAKE_REQUIRED_DEFINITIONS -DHAVE_STDINT_H)
-endif()
-if(HAVE_STDDEF_H)
- list(APPEND CMAKE_REQUIRED_DEFINITIONS -DHAVE_STDDEF_H)
-endif()
-check_type_size(off64_t OFF64_T)
-if(HAVE_OFF64_T)
- add_definitions(-D_LARGEFILE64_SOURCE=1)
-endif()
-set(CMAKE_REQUIRED_DEFINITIONS) # clear variable
-
-#
-# Check for fseeko
-#
-check_function_exists(fseeko HAVE_FSEEKO)
-if(NOT HAVE_FSEEKO)
- add_definitions(-DNO_FSEEKO)
-endif()
-
-#
-# Check for unistd.h
-#
-check_include_file(unistd.h Z_HAVE_UNISTD_H)
-
-if(MSVC)
- set(CMAKE_DEBUG_POSTFIX "d")
- add_definitions(-D_CRT_SECURE_NO_DEPRECATE)
- add_definitions(-D_CRT_NONSTDC_NO_DEPRECATE)
- include_directories(${CMAKE_CURRENT_SOURCE_DIR})
-endif()
-
-if(NOT CMAKE_CURRENT_SOURCE_DIR STREQUAL CMAKE_CURRENT_BINARY_DIR)
- # If we're doing an out of source build and the user has a zconf.h
- # in their source tree...
- if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/zconf.h)
- message(STATUS "Renaming")
- message(STATUS " ${CMAKE_CURRENT_SOURCE_DIR}/zconf.h")
- message(STATUS "to 'zconf.h.included' because this file is included with zlib")
- message(STATUS "but CMake generates it automatically in the build directory.")
- file(RENAME ${CMAKE_CURRENT_SOURCE_DIR}/zconf.h ${CMAKE_CURRENT_SOURCE_DIR}/zconf.h.included)
- endif()
-endif()
-
-set(ZLIB_PC ${CMAKE_CURRENT_BINARY_DIR}/zlib.pc)
-configure_file( ${CMAKE_CURRENT_SOURCE_DIR}/zlib.pc.cmakein
- ${ZLIB_PC} @ONLY)
-configure_file( ${CMAKE_CURRENT_SOURCE_DIR}/zconf.h.cmakein
- ${CMAKE_CURRENT_BINARY_DIR}/zconf.h @ONLY)
-include_directories(${CMAKE_CURRENT_BINARY_DIR} ${CMAKE_SOURCE_DIR})
-
-
-#============================================================================
-# zlib
-#============================================================================
-
-set(ZLIB_PUBLIC_HDRS
- ${CMAKE_CURRENT_BINARY_DIR}/zconf.h
- zlib.h
-)
-set(ZLIB_PRIVATE_HDRS
- crc32.h
- deflate.h
- gzguts.h
- inffast.h
- inffixed.h
- inflate.h
- inftrees.h
- trees.h
- zutil.h
-)
-set(ZLIB_SRCS
- adler32.c
- compress.c
- crc32.c
- deflate.c
- gzclose.c
- gzlib.c
- gzread.c
- gzwrite.c
- inflate.c
- infback.c
- inftrees.c
- inffast.c
- trees.c
- uncompr.c
- zutil.c
-)
-
-if(NOT MINGW)
- set(ZLIB_DLL_SRCS
- win32/zlib1.rc # If present will override custom build rule below.
- )
-endif()
-
-if(CMAKE_COMPILER_IS_GNUCC)
- if(ASM686)
- set(ZLIB_ASMS contrib/asm686/match.S)
- elseif (AMD64)
- set(ZLIB_ASMS contrib/amd64/amd64-match.S)
- endif ()
-
- if(ZLIB_ASMS)
- add_definitions(-DASMV)
- set_source_files_properties(${ZLIB_ASMS} PROPERTIES LANGUAGE C COMPILE_FLAGS -DNO_UNDERLINE)
- endif()
-endif()
-
-if(MSVC)
- if(ASM686)
- ENABLE_LANGUAGE(ASM_MASM)
- set(ZLIB_ASMS
- contrib/masmx86/inffas32.asm
- contrib/masmx86/match686.asm
- )
- elseif (AMD64)
- ENABLE_LANGUAGE(ASM_MASM)
- set(ZLIB_ASMS
- contrib/masmx64/gvmat64.asm
- contrib/masmx64/inffasx64.asm
- )
- endif()
-
- if(ZLIB_ASMS)
- add_definitions(-DASMV -DASMINF)
- endif()
-endif()
-
-# parse the full version number from zlib.h and include in ZLIB_FULL_VERSION
-file(READ ${CMAKE_CURRENT_SOURCE_DIR}/zlib.h _zlib_h_contents)
-string(REGEX REPLACE ".*#define[ \t]+ZLIB_VERSION[ \t]+\"([-0-9A-Za-z.]+)\".*"
- "\\1" ZLIB_FULL_VERSION ${_zlib_h_contents})
-
-if(MINGW)
- # This gets us DLL resource information when compiling on MinGW.
- if(NOT CMAKE_RC_COMPILER)
- set(CMAKE_RC_COMPILER windres.exe)
- endif()
-
- add_custom_command(OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/zlib1rc.obj
- COMMAND ${CMAKE_RC_COMPILER}
- -D GCC_WINDRES
- -I ${CMAKE_CURRENT_SOURCE_DIR}
- -I ${CMAKE_CURRENT_BINARY_DIR}
- -o ${CMAKE_CURRENT_BINARY_DIR}/zlib1rc.obj
- -i ${CMAKE_CURRENT_SOURCE_DIR}/win32/zlib1.rc)
- set(ZLIB_DLL_SRCS ${CMAKE_CURRENT_BINARY_DIR}/zlib1rc.obj)
-endif(MINGW)
-
-add_library(zlib SHARED ${ZLIB_SRCS} ${ZLIB_ASMS} ${ZLIB_DLL_SRCS} ${ZLIB_PUBLIC_HDRS} ${ZLIB_PRIVATE_HDRS})
-add_library(zlibstatic STATIC ${ZLIB_SRCS} ${ZLIB_ASMS} ${ZLIB_PUBLIC_HDRS} ${ZLIB_PRIVATE_HDRS})
-set_target_properties(zlib PROPERTIES DEFINE_SYMBOL ZLIB_DLL)
-set_target_properties(zlib PROPERTIES SOVERSION 1)
-
-if(NOT CYGWIN)
- # This property causes shared libraries on Linux to have the full version
- # encoded into their final filename. We disable this on Cygwin because
- # it causes cygz-${ZLIB_FULL_VERSION}.dll to be created when cygz.dll
- # seems to be the default.
- #
- # This has no effect with MSVC, on that platform the version info for
- # the DLL comes from the resource file win32/zlib1.rc
- set_target_properties(zlib PROPERTIES VERSION ${ZLIB_FULL_VERSION})
-endif()
-
-if(UNIX)
- # On unix-like platforms the library is almost always called libz
- set_target_properties(zlib zlibstatic PROPERTIES OUTPUT_NAME z)
- if(NOT APPLE)
- set_target_properties(zlib PROPERTIES LINK_FLAGS "-Wl,--version-script,\"${CMAKE_CURRENT_SOURCE_DIR}/zlib.map\"")
- endif()
-elseif(BUILD_SHARED_LIBS AND WIN32)
- # Creates zlib1.dll when building shared library version
- set_target_properties(zlib PROPERTIES SUFFIX "1.dll")
-endif()
-
-if(NOT SKIP_INSTALL_LIBRARIES AND NOT SKIP_INSTALL_ALL )
- install(TARGETS zlib zlibstatic
- RUNTIME DESTINATION "${INSTALL_BIN_DIR}"
- ARCHIVE DESTINATION "${INSTALL_LIB_DIR}"
- LIBRARY DESTINATION "${INSTALL_LIB_DIR}" )
-endif()
-if(NOT SKIP_INSTALL_HEADERS AND NOT SKIP_INSTALL_ALL )
- install(FILES ${ZLIB_PUBLIC_HDRS} DESTINATION "${INSTALL_INC_DIR}")
-endif()
-if(NOT SKIP_INSTALL_FILES AND NOT SKIP_INSTALL_ALL )
- install(FILES zlib.3 DESTINATION "${INSTALL_MAN_DIR}/man3")
-endif()
-if(NOT SKIP_INSTALL_FILES AND NOT SKIP_INSTALL_ALL )
- install(FILES ${ZLIB_PC} DESTINATION "${INSTALL_PKGCONFIG_DIR}")
-endif()
-
-#============================================================================
-# Example binaries
-#============================================================================
-
-add_executable(example test/example.c)
-target_link_libraries(example zlib)
-add_test(example example)
-
-add_executable(minigzip test/minigzip.c)
-target_link_libraries(minigzip zlib)
-
-if(HAVE_OFF64_T)
- add_executable(example64 test/example.c)
- target_link_libraries(example64 zlib)
- set_target_properties(example64 PROPERTIES COMPILE_FLAGS "-D_FILE_OFFSET_BITS=64")
- add_test(example64 example64)
-
- add_executable(minigzip64 test/minigzip.c)
- target_link_libraries(minigzip64 zlib)
- set_target_properties(minigzip64 PROPERTIES COMPILE_FLAGS "-D_FILE_OFFSET_BITS=64")
-endif()
diff --git a/third-party/zlib/ChangeLog b/third-party/zlib/ChangeLog
deleted file mode 100644
index f22aaba..0000000
--- a/third-party/zlib/ChangeLog
+++ /dev/null
@@ -1,1472 +0,0 @@
-
- ChangeLog file for zlib
-
-Changes in 1.2.8 (28 Apr 2013)
-- Update contrib/minizip/iowin32.c for Windows RT [Vollant]
-- Do not force Z_CONST for C++
-- Clean up contrib/vstudio [Ro�]
-- Correct spelling error in zlib.h
-- Fix mixed line endings in contrib/vstudio
-
-Changes in 1.2.7.3 (13 Apr 2013)
-- Fix version numbers and DLL names in contrib/vstudio/*/zlib.rc
-
-Changes in 1.2.7.2 (13 Apr 2013)
-- Change check for a four-byte type back to hexadecimal
-- Fix typo in win32/Makefile.msc
-- Add casts in gzwrite.c for pointer differences
-
-Changes in 1.2.7.1 (24 Mar 2013)
-- Replace use of unsafe string functions with snprintf if available
-- Avoid including stddef.h on Windows for Z_SOLO compile [Niessink]
-- Fix gzgetc undefine when Z_PREFIX set [Turk]
-- Eliminate use of mktemp in Makefile (not always available)
-- Fix bug in 'F' mode for gzopen()
-- Add inflateGetDictionary() function
-- Correct comment in deflate.h
-- Use _snprintf for snprintf in Microsoft C
-- On Darwin, only use /usr/bin/libtool if libtool is not Apple
-- Delete "--version" file if created by "ar --version" [Richard G.]
-- Fix configure check for veracity of compiler error return codes
-- Fix CMake compilation of static lib for MSVC2010 x64
-- Remove unused variable in infback9.c
-- Fix argument checks in gzlog_compress() and gzlog_write()
-- Clean up the usage of z_const and respect const usage within zlib
-- Clean up examples/gzlog.[ch] comparisons of different types
-- Avoid shift equal to bits in type (caused endless loop)
-- Fix unintialized value bug in gzputc() introduced by const patches
-- Fix memory allocation error in examples/zran.c [Nor]
-- Fix bug where gzopen(), gzclose() would write an empty file
-- Fix bug in gzclose() when gzwrite() runs out of memory
-- Check for input buffer malloc failure in examples/gzappend.c
-- Add note to contrib/blast to use binary mode in stdio
-- Fix comparisons of differently signed integers in contrib/blast
-- Check for invalid code length codes in contrib/puff
-- Fix serious but very rare decompression bug in inftrees.c
-- Update inflateBack() comments, since inflate() can be faster
-- Use underscored I/O function names for WINAPI_FAMILY
-- Add _tr_flush_bits to the external symbols prefixed by --zprefix
-- Add contrib/vstudio/vc10 pre-build step for static only
-- Quote --version-script argument in CMakeLists.txt
-- Don't specify --version-script on Apple platforms in CMakeLists.txt
-- Fix casting error in contrib/testzlib/testzlib.c
-- Fix types in contrib/minizip to match result of get_crc_table()
-- Simplify contrib/vstudio/vc10 with 'd' suffix
-- Add TOP support to win32/Makefile.msc
-- Suport i686 and amd64 assembler builds in CMakeLists.txt
-- Fix typos in the use of _LARGEFILE64_SOURCE in zconf.h
-- Add vc11 and vc12 build files to contrib/vstudio
-- Add gzvprintf() as an undocumented function in zlib
-- Fix configure for Sun shell
-- Remove runtime check in configure for four-byte integer type
-- Add casts and consts to ease user conversion to C++
-- Add man pages for minizip and miniunzip
-- In Makefile uninstall, don't rm if preceding cd fails
-- Do not return Z_BUF_ERROR if deflateParam() has nothing to write
-
-Changes in 1.2.7 (2 May 2012)
-- Replace use of memmove() with a simple copy for portability
-- Test for existence of strerror
-- Restore gzgetc_ for backward compatibility with 1.2.6
-- Fix build with non-GNU make on Solaris
-- Require gcc 4.0 or later on Mac OS X to use the hidden attribute
-- Include unistd.h for Watcom C
-- Use __WATCOMC__ instead of __WATCOM__
-- Do not use the visibility attribute if NO_VIZ defined
-- Improve the detection of no hidden visibility attribute
-- Avoid using __int64 for gcc or solo compilation
-- Cast to char * in gzprintf to avoid warnings [Zinser]
-- Fix make_vms.com for VAX [Zinser]
-- Don't use library or built-in byte swaps
-- Simplify test and use of gcc hidden attribute
-- Fix bug in gzclose_w() when gzwrite() fails to allocate memory
-- Add "x" (O_EXCL) and "e" (O_CLOEXEC) modes support to gzopen()
-- Fix bug in test/minigzip.c for configure --solo
-- Fix contrib/vstudio project link errors [Mohanathas]
-- Add ability to choose the builder in make_vms.com [Schweda]
-- Add DESTDIR support to mingw32 win32/Makefile.gcc
-- Fix comments in win32/Makefile.gcc for proper usage
-- Allow overriding the default install locations for cmake
-- Generate and install the pkg-config file with cmake
-- Build both a static and a shared version of zlib with cmake
-- Include version symbols for cmake builds
-- If using cmake with MSVC, add the source directory to the includes
-- Remove unneeded EXTRA_CFLAGS from win32/Makefile.gcc [Truta]
-- Move obsolete emx makefile to old [Truta]
-- Allow the use of -Wundef when compiling or using zlib
-- Avoid the use of the -u option with mktemp
-- Improve inflate() documentation on the use of Z_FINISH
-- Recognize clang as gcc
-- Add gzopen_w() in Windows for wide character path names
-- Rename zconf.h in CMakeLists.txt to move it out of the way
-- Add source directory in CMakeLists.txt for building examples
-- Look in build directory for zlib.pc in CMakeLists.txt
-- Remove gzflags from zlibvc.def in vc9 and vc10
-- Fix contrib/minizip compilation in the MinGW environment
-- Update ./configure for Solaris, support --64 [Mooney]
-- Remove -R. from Solaris shared build (possible security issue)
-- Avoid race condition for parallel make (-j) running example
-- Fix type mismatch between get_crc_table() and crc_table
-- Fix parsing of version with "-" in CMakeLists.txt [Snider, Ziegler]
-- Fix the path to zlib.map in CMakeLists.txt
-- Force the native libtool in Mac OS X to avoid GNU libtool [Beebe]
-- Add instructions to win32/Makefile.gcc for shared install [Torri]
-
-Changes in 1.2.6.1 (12 Feb 2012)
-- Avoid the use of the Objective-C reserved name "id"
-- Include io.h in gzguts.h for Microsoft compilers
-- Fix problem with ./configure --prefix and gzgetc macro
-- Include gz_header definition when compiling zlib solo
-- Put gzflags() functionality back in zutil.c
-- Avoid library header include in crc32.c for Z_SOLO
-- Use name in GCC_CLASSIC as C compiler for coverage testing, if set
-- Minor cleanup in contrib/minizip/zip.c [Vollant]
-- Update make_vms.com [Zinser]
-- Remove unnecessary gzgetc_ function
-- Use optimized byte swap operations for Microsoft and GNU [Snyder]
-- Fix minor typo in zlib.h comments [Rzesniowiecki]
-
-Changes in 1.2.6 (29 Jan 2012)
-- Update the Pascal interface in contrib/pascal
-- Fix function numbers for gzgetc_ in zlibvc.def files
-- Fix configure.ac for contrib/minizip [Schiffer]
-- Fix large-entry detection in minizip on 64-bit systems [Schiffer]
-- Have ./configure use the compiler return code for error indication
-- Fix CMakeLists.txt for cross compilation [McClure]
-- Fix contrib/minizip/zip.c for 64-bit architectures [Dalsnes]
-- Fix compilation of contrib/minizip on FreeBSD [Marquez]
-- Correct suggested usages in win32/Makefile.msc [Shachar, Horvath]
-- Include io.h for Turbo C / Borland C on all platforms [Truta]
-- Make version explicit in contrib/minizip/configure.ac [Bosmans]
-- Avoid warning for no encryption in contrib/minizip/zip.c [Vollant]
-- Minor cleanup up contrib/minizip/unzip.c [Vollant]
-- Fix bug when compiling minizip with C++ [Vollant]
-- Protect for long name and extra fields in contrib/minizip [Vollant]
-- Avoid some warnings in contrib/minizip [Vollant]
-- Add -I../.. -L../.. to CFLAGS for minizip and miniunzip
-- Add missing libs to minizip linker command
-- Add support for VPATH builds in contrib/minizip
-- Add an --enable-demos option to contrib/minizip/configure
-- Add the generation of configure.log by ./configure
-- Exit when required parameters not provided to win32/Makefile.gcc
-- Have gzputc return the character written instead of the argument
-- Use the -m option on ldconfig for BSD systems [Tobias]
-- Correct in zlib.map when deflateResetKeep was added
-
-Changes in 1.2.5.3 (15 Jan 2012)
-- Restore gzgetc function for binary compatibility
-- Do not use _lseeki64 under Borland C++ [Truta]
-- Update win32/Makefile.msc to build test/*.c [Truta]
-- Remove old/visualc6 given CMakefile and other alternatives
-- Update AS400 build files and documentation [Monnerat]
-- Update win32/Makefile.gcc to build test/*.c [Truta]
-- Permit stronger flushes after Z_BLOCK flushes
-- Avoid extraneous empty blocks when doing empty flushes
-- Permit Z_NULL arguments to deflatePending
-- Allow deflatePrime() to insert bits in the middle of a stream
-- Remove second empty static block for Z_PARTIAL_FLUSH
-- Write out all of the available bits when using Z_BLOCK
-- Insert the first two strings in the hash table after a flush
-
-Changes in 1.2.5.2 (17 Dec 2011)
-- fix ld error: unable to find version dependency 'ZLIB_1.2.5'
-- use relative symlinks for shared libs
-- Avoid searching past window for Z_RLE strategy
-- Assure that high-water mark initialization is always applied in deflate
-- Add assertions to fill_window() in deflate.c to match comments
-- Update python link in README
-- Correct spelling error in gzread.c
-- Fix bug in gzgets() for a concatenated empty gzip stream
-- Correct error in comment for gz_make()
-- Change gzread() and related to ignore junk after gzip streams
-- Allow gzread() and related to continue after gzclearerr()
-- Allow gzrewind() and gzseek() after a premature end-of-file
-- Simplify gzseek() now that raw after gzip is ignored
-- Change gzgetc() to a macro for speed (~40% speedup in testing)
-- Fix gzclose() to return the actual error last encountered
-- Always add large file support for windows
-- Include zconf.h for windows large file support
-- Include zconf.h.cmakein for windows large file support
-- Update zconf.h.cmakein on make distclean
-- Merge vestigial vsnprintf determination from zutil.h to gzguts.h
-- Clarify how gzopen() appends in zlib.h comments
-- Correct documentation of gzdirect() since junk at end now ignored
-- Add a transparent write mode to gzopen() when 'T' is in the mode
-- Update python link in zlib man page
-- Get inffixed.h and MAKEFIXED result to match
-- Add a ./config --solo option to make zlib subset with no libary use
-- Add undocumented inflateResetKeep() function for CAB file decoding
-- Add --cover option to ./configure for gcc coverage testing
-- Add #define ZLIB_CONST option to use const in the z_stream interface
-- Add comment to gzdopen() in zlib.h to use dup() when using fileno()
-- Note behavior of uncompress() to provide as much data as it can
-- Add files in contrib/minizip to aid in building libminizip
-- Split off AR options in Makefile.in and configure
-- Change ON macro to Z_ARG to avoid application conflicts
-- Facilitate compilation with Borland C++ for pragmas and vsnprintf
-- Include io.h for Turbo C / Borland C++
-- Move example.c and minigzip.c to test/
-- Simplify incomplete code table filling in inflate_table()
-- Remove code from inflate.c and infback.c that is impossible to execute
-- Test the inflate code with full coverage
-- Allow deflateSetDictionary, inflateSetDictionary at any time (in raw)
-- Add deflateResetKeep and fix inflateResetKeep to retain dictionary
-- Fix gzwrite.c to accommodate reduced memory zlib compilation
-- Have inflate() with Z_FINISH avoid the allocation of a window
-- Do not set strm->adler when doing raw inflate
-- Fix gzeof() to behave just like feof() when read is not past end of file
-- Fix bug in gzread.c when end-of-file is reached
-- Avoid use of Z_BUF_ERROR in gz* functions except for premature EOF
-- Document gzread() capability to read concurrently written files
-- Remove hard-coding of resource compiler in CMakeLists.txt [Blammo]
-
-Changes in 1.2.5.1 (10 Sep 2011)
-- Update FAQ entry on shared builds (#13)
-- Avoid symbolic argument to chmod in Makefile.in
-- Fix bug and add consts in contrib/puff [Oberhumer]
-- Update contrib/puff/zeros.raw test file to have all block types
-- Add full coverage test for puff in contrib/puff/Makefile
-- Fix static-only-build install in Makefile.in
-- Fix bug in unzGetCurrentFileInfo() in contrib/minizip [Kuno]
-- Add libz.a dependency to shared in Makefile.in for parallel builds
-- Spell out "number" (instead of "nb") in zlib.h for total_in, total_out
-- Replace $(...) with `...` in configure for non-bash sh [Bowler]
-- Add darwin* to Darwin* and solaris* to SunOS\ 5* in configure [Groffen]
-- Add solaris* to Linux* in configure to allow gcc use [Groffen]
-- Add *bsd* to Linux* case in configure [Bar-Lev]
-- Add inffast.obj to dependencies in win32/Makefile.msc
-- Correct spelling error in deflate.h [Kohler]
-- Change libzdll.a again to libz.dll.a (!) in win32/Makefile.gcc
-- Add test to configure for GNU C looking for gcc in output of $cc -v
-- Add zlib.pc generation to win32/Makefile.gcc [Weigelt]
-- Fix bug in zlib.h for _FILE_OFFSET_BITS set and _LARGEFILE64_SOURCE not
-- Add comment in zlib.h that adler32_combine with len2 < 0 makes no sense
-- Make NO_DIVIDE option in adler32.c much faster (thanks to John Reiser)
-- Make stronger test in zconf.h to include unistd.h for LFS
-- Apply Darwin patches for 64-bit file offsets to contrib/minizip [Slack]
-- Fix zlib.h LFS support when Z_PREFIX used
-- Add updated as400 support (removed from old) [Monnerat]
-- Avoid deflate sensitivity to volatile input data
-- Avoid division in adler32_combine for NO_DIVIDE
-- Clarify the use of Z_FINISH with deflateBound() amount of space
-- Set binary for output file in puff.c
-- Use u4 type for crc_table to avoid conversion warnings
-- Apply casts in zlib.h to avoid conversion warnings
-- Add OF to prototypes for adler32_combine_ and crc32_combine_ [Miller]
-- Improve inflateSync() documentation to note indeterminancy
-- Add deflatePending() function to return the amount of pending output
-- Correct the spelling of "specification" in FAQ [Randers-Pehrson]
-- Add a check in configure for stdarg.h, use for gzprintf()
-- Check that pointers fit in ints when gzprint() compiled old style
-- Add dummy name before $(SHAREDLIBV) in Makefile [Bar-Lev, Bowler]
-- Delete line in configure that adds -L. libz.a to LDFLAGS [Weigelt]
-- Add debug records in assmebler code [Londer]
-- Update RFC references to use http://tools.ietf.org/html/... [Li]
-- Add --archs option, use of libtool to configure for Mac OS X [Borstel]
-
-Changes in 1.2.5 (19 Apr 2010)
-- Disable visibility attribute in win32/Makefile.gcc [Bar-Lev]
-- Default to libdir as sharedlibdir in configure [Nieder]
-- Update copyright dates on modified source files
-- Update trees.c to be able to generate modified trees.h
-- Exit configure for MinGW, suggesting win32/Makefile.gcc
-- Check for NULL path in gz_open [Homurlu]
-
-Changes in 1.2.4.5 (18 Apr 2010)
-- Set sharedlibdir in configure [Torok]
-- Set LDFLAGS in Makefile.in [Bar-Lev]
-- Avoid mkdir objs race condition in Makefile.in [Bowler]
-- Add ZLIB_INTERNAL in front of internal inter-module functions and arrays
-- Define ZLIB_INTERNAL to hide internal functions and arrays for GNU C
-- Don't use hidden attribute when it is a warning generator (e.g. Solaris)
-
-Changes in 1.2.4.4 (18 Apr 2010)
-- Fix CROSS_PREFIX executable testing, CHOST extract, mingw* [Torok]
-- Undefine _LARGEFILE64_SOURCE in zconf.h if it is zero, but not if empty
-- Try to use bash or ksh regardless of functionality of /bin/sh
-- Fix configure incompatibility with NetBSD sh
-- Remove attempt to run under bash or ksh since have better NetBSD fix
-- Fix win32/Makefile.gcc for MinGW [Bar-Lev]
-- Add diagnostic messages when using CROSS_PREFIX in configure
-- Added --sharedlibdir option to configure [Weigelt]
-- Use hidden visibility attribute when available [Frysinger]
-
-Changes in 1.2.4.3 (10 Apr 2010)
-- Only use CROSS_PREFIX in configure for ar and ranlib if they exist
-- Use CROSS_PREFIX for nm [Bar-Lev]
-- Assume _LARGEFILE64_SOURCE defined is equivalent to true
-- Avoid use of undefined symbols in #if with && and ||
-- Make *64 prototypes in gzguts.h consistent with functions
-- Add -shared load option for MinGW in configure [Bowler]
-- Move z_off64_t to public interface, use instead of off64_t
-- Remove ! from shell test in configure (not portable to Solaris)
-- Change +0 macro tests to -0 for possibly increased portability
-
-Changes in 1.2.4.2 (9 Apr 2010)
-- Add consistent carriage returns to readme.txt's in masmx86 and masmx64
-- Really provide prototypes for *64 functions when building without LFS
-- Only define unlink() in minigzip.c if unistd.h not included
-- Update README to point to contrib/vstudio project files
-- Move projects/vc6 to old/ and remove projects/
-- Include stdlib.h in minigzip.c for setmode() definition under WinCE
-- Clean up assembler builds in win32/Makefile.msc [Rowe]
-- Include sys/types.h for Microsoft for off_t definition
-- Fix memory leak on error in gz_open()
-- Symbolize nm as $NM in configure [Weigelt]
-- Use TEST_LDSHARED instead of LDSHARED to link test programs [Weigelt]
-- Add +0 to _FILE_OFFSET_BITS and _LFS64_LARGEFILE in case not defined
-- Fix bug in gzeof() to take into account unused input data
-- Avoid initialization of structures with variables in puff.c
-- Updated win32/README-WIN32.txt [Rowe]
-
-Changes in 1.2.4.1 (28 Mar 2010)
-- Remove the use of [a-z] constructs for sed in configure [gentoo 310225]
-- Remove $(SHAREDLIB) from LIBS in Makefile.in [Creech]
-- Restore "for debugging" comment on sprintf() in gzlib.c
-- Remove fdopen for MVS from gzguts.h
-- Put new README-WIN32.txt in win32 [Rowe]
-- Add check for shell to configure and invoke another shell if needed
-- Fix big fat stinking bug in gzseek() on uncompressed files
-- Remove vestigial F_OPEN64 define in zutil.h
-- Set and check the value of _LARGEFILE_SOURCE and _LARGEFILE64_SOURCE
-- Avoid errors on non-LFS systems when applications define LFS macros
-- Set EXE to ".exe" in configure for MINGW [Kahle]
-- Match crc32() in crc32.c exactly to the prototype in zlib.h [Sherrill]
-- Add prefix for cross-compilation in win32/makefile.gcc [Bar-Lev]
-- Add DLL install in win32/makefile.gcc [Bar-Lev]
-- Allow Linux* or linux* from uname in configure [Bar-Lev]
-- Allow ldconfig to be redefined in configure and Makefile.in [Bar-Lev]
-- Add cross-compilation prefixes to configure [Bar-Lev]
-- Match type exactly in gz_load() invocation in gzread.c
-- Match type exactly of zcalloc() in zutil.c to zlib.h alloc_func
-- Provide prototypes for *64 functions when building zlib without LFS
-- Don't use -lc when linking shared library on MinGW
-- Remove errno.h check in configure and vestigial errno code in zutil.h
-
-Changes in 1.2.4 (14 Mar 2010)
-- Fix VER3 extraction in configure for no fourth subversion
-- Update zlib.3, add docs to Makefile.in to make .pdf out of it
-- Add zlib.3.pdf to distribution
-- Don't set error code in gzerror() if passed pointer is NULL
-- Apply destination directory fixes to CMakeLists.txt [Lowman]
-- Move #cmakedefine's to a new zconf.in.cmakein
-- Restore zconf.h for builds that don't use configure or cmake
-- Add distclean to dummy Makefile for convenience
-- Update and improve INDEX, README, and FAQ
-- Update CMakeLists.txt for the return of zconf.h [Lowman]
-- Update contrib/vstudio/vc9 and vc10 [Vollant]
-- Change libz.dll.a back to libzdll.a in win32/Makefile.gcc
-- Apply license and readme changes to contrib/asm686 [Raiter]
-- Check file name lengths and add -c option in minigzip.c [Li]
-- Update contrib/amd64 and contrib/masmx86/ [Vollant]
-- Avoid use of "eof" parameter in trees.c to not shadow library variable
-- Update make_vms.com for removal of zlibdefs.h [Zinser]
-- Update assembler code and vstudio projects in contrib [Vollant]
-- Remove outdated assembler code contrib/masm686 and contrib/asm586
-- Remove old vc7 and vc8 from contrib/vstudio
-- Update win32/Makefile.msc, add ZLIB_VER_SUBREVISION [Rowe]
-- Fix memory leaks in gzclose_r() and gzclose_w(), file leak in gz_open()
-- Add contrib/gcc_gvmat64 for longest_match and inflate_fast [Vollant]
-- Remove *64 functions from win32/zlib.def (they're not 64-bit yet)
-- Fix bug in void-returning vsprintf() case in gzwrite.c
-- Fix name change from inflate.h in contrib/inflate86/inffas86.c
-- Check if temporary file exists before removing in make_vms.com [Zinser]
-- Fix make install and uninstall for --static option
-- Fix usage of _MSC_VER in gzguts.h and zutil.h [Truta]
-- Update readme.txt in contrib/masmx64 and masmx86 to assemble
-
-Changes in 1.2.3.9 (21 Feb 2010)
-- Expunge gzio.c
-- Move as400 build information to old
-- Fix updates in contrib/minizip and contrib/vstudio
-- Add const to vsnprintf test in configure to avoid warnings [Weigelt]
-- Delete zconf.h (made by configure) [Weigelt]
-- Change zconf.in.h to zconf.h.in per convention [Weigelt]
-- Check for NULL buf in gzgets()
-- Return empty string for gzgets() with len == 1 (like fgets())
-- Fix description of gzgets() in zlib.h for end-of-file, NULL return
-- Update minizip to 1.1 [Vollant]
-- Avoid MSVC loss of data warnings in gzread.c, gzwrite.c
-- Note in zlib.h that gzerror() should be used to distinguish from EOF
-- Remove use of snprintf() from gzlib.c
-- Fix bug in gzseek()
-- Update contrib/vstudio, adding vc9 and vc10 [Kuno, Vollant]
-- Fix zconf.h generation in CMakeLists.txt [Lowman]
-- Improve comments in zconf.h where modified by configure
-
-Changes in 1.2.3.8 (13 Feb 2010)
-- Clean up text files (tabs, trailing whitespace, etc.) [Oberhumer]
-- Use z_off64_t in gz_zero() and gz_skip() to match state->skip
-- Avoid comparison problem when sizeof(int) == sizeof(z_off64_t)
-- Revert to Makefile.in from 1.2.3.6 (live with the clutter)
-- Fix missing error return in gzflush(), add zlib.h note
-- Add *64 functions to zlib.map [Levin]
-- Fix signed/unsigned comparison in gz_comp()
-- Use SFLAGS when testing shared linking in configure
-- Add --64 option to ./configure to use -m64 with gcc
-- Fix ./configure --help to correctly name options
-- Have make fail if a test fails [Levin]
-- Avoid buffer overrun in contrib/masmx64/gvmat64.asm [Simpson]
-- Remove assembler object files from contrib
-
-Changes in 1.2.3.7 (24 Jan 2010)
-- Always gzopen() with O_LARGEFILE if available
-- Fix gzdirect() to work immediately after gzopen() or gzdopen()
-- Make gzdirect() more precise when the state changes while reading
-- Improve zlib.h documentation in many places
-- Catch memory allocation failure in gz_open()
-- Complete close operation if seek forward in gzclose_w() fails
-- Return Z_ERRNO from gzclose_r() if close() fails
-- Return Z_STREAM_ERROR instead of EOF for gzclose() being passed NULL
-- Return zero for gzwrite() errors to match zlib.h description
-- Return -1 on gzputs() error to match zlib.h description
-- Add zconf.in.h to allow recovery from configure modification [Weigelt]
-- Fix static library permissions in Makefile.in [Weigelt]
-- Avoid warnings in configure tests that hide functionality [Weigelt]
-- Add *BSD and DragonFly to Linux case in configure [gentoo 123571]
-- Change libzdll.a to libz.dll.a in win32/Makefile.gcc [gentoo 288212]
-- Avoid access of uninitialized data for first inflateReset2 call [Gomes]
-- Keep object files in subdirectories to reduce the clutter somewhat
-- Remove default Makefile and zlibdefs.h, add dummy Makefile
-- Add new external functions to Z_PREFIX, remove duplicates, z_z_ -> z_
-- Remove zlibdefs.h completely -- modify zconf.h instead
-
-Changes in 1.2.3.6 (17 Jan 2010)
-- Avoid void * arithmetic in gzread.c and gzwrite.c
-- Make compilers happier with const char * for gz_error message
-- Avoid unused parameter warning in inflate.c
-- Avoid signed-unsigned comparison warning in inflate.c
-- Indent #pragma's for traditional C
-- Fix usage of strwinerror() in glib.c, change to gz_strwinerror()
-- Correct email address in configure for system options
-- Update make_vms.com and add make_vms.com to contrib/minizip [Zinser]
-- Update zlib.map [Brown]
-- Fix Makefile.in for Solaris 10 make of example64 and minizip64 [Torok]
-- Apply various fixes to CMakeLists.txt [Lowman]
-- Add checks on len in gzread() and gzwrite()
-- Add error message for no more room for gzungetc()
-- Remove zlib version check in gzwrite()
-- Defer compression of gzprintf() result until need to
-- Use snprintf() in gzdopen() if available
-- Remove USE_MMAP configuration determination (only used by minigzip)
-- Remove examples/pigz.c (available separately)
-- Update examples/gun.c to 1.6
-
-Changes in 1.2.3.5 (8 Jan 2010)
-- Add space after #if in zutil.h for some compilers
-- Fix relatively harmless bug in deflate_fast() [Exarevsky]
-- Fix same problem in deflate_slow()
-- Add $(SHAREDLIBV) to LIBS in Makefile.in [Brown]
-- Add deflate_rle() for faster Z_RLE strategy run-length encoding
-- Add deflate_huff() for faster Z_HUFFMAN_ONLY encoding
-- Change name of "write" variable in inffast.c to avoid library collisions
-- Fix premature EOF from gzread() in gzio.c [Brown]
-- Use zlib header window size if windowBits is 0 in inflateInit2()
-- Remove compressBound() call in deflate.c to avoid linking compress.o
-- Replace use of errno in gz* with functions, support WinCE [Alves]
-- Provide alternative to perror() in minigzip.c for WinCE [Alves]
-- Don't use _vsnprintf on later versions of MSVC [Lowman]
-- Add CMake build script and input file [Lowman]
-- Update contrib/minizip to 1.1 [Svensson, Vollant]
-- Moved nintendods directory from contrib to .
-- Replace gzio.c with a new set of routines with the same functionality
-- Add gzbuffer(), gzoffset(), gzclose_r(), gzclose_w() as part of above
-- Update contrib/minizip to 1.1b
-- Change gzeof() to return 0 on error instead of -1 to agree with zlib.h
-
-Changes in 1.2.3.4 (21 Dec 2009)
-- Use old school .SUFFIXES in Makefile.in for FreeBSD compatibility
-- Update comments in configure and Makefile.in for default --shared
-- Fix test -z's in configure [Marquess]
-- Build examplesh and minigzipsh when not testing
-- Change NULL's to Z_NULL's in deflate.c and in comments in zlib.h
-- Import LDFLAGS from the environment in configure
-- Fix configure to populate SFLAGS with discovered CFLAGS options
-- Adapt make_vms.com to the new Makefile.in [Zinser]
-- Add zlib2ansi script for C++ compilation [Marquess]
-- Add _FILE_OFFSET_BITS=64 test to make test (when applicable)
-- Add AMD64 assembler code for longest match to contrib [Teterin]
-- Include options from $SFLAGS when doing $LDSHARED
-- Simplify 64-bit file support by introducing z_off64_t type
-- Make shared object files in objs directory to work around old Sun cc
-- Use only three-part version number for Darwin shared compiles
-- Add rc option to ar in Makefile.in for when ./configure not run
-- Add -WI,-rpath,. to LDFLAGS for OSF 1 V4*
-- Set LD_LIBRARYN32_PATH for SGI IRIX shared compile
-- Protect against _FILE_OFFSET_BITS being defined when compiling zlib
-- Rename Makefile.in targets allstatic to static and allshared to shared
-- Fix static and shared Makefile.in targets to be independent
-- Correct error return bug in gz_open() by setting state [Brown]
-- Put spaces before ;;'s in configure for better sh compatibility
-- Add pigz.c (parallel implementation of gzip) to examples/
-- Correct constant in crc32.c to UL [Leventhal]
-- Reject negative lengths in crc32_combine()
-- Add inflateReset2() function to work like inflateEnd()/inflateInit2()
-- Include sys/types.h for _LARGEFILE64_SOURCE [Brown]
-- Correct typo in doc/algorithm.txt [Janik]
-- Fix bug in adler32_combine() [Zhu]
-- Catch missing-end-of-block-code error in all inflates and in puff
- Assures that random input to inflate eventually results in an error
-- Added enough.c (calculation of ENOUGH for inftrees.h) to examples/
-- Update ENOUGH and its usage to reflect discovered bounds
-- Fix gzerror() error report on empty input file [Brown]
-- Add ush casts in trees.c to avoid pedantic runtime errors
-- Fix typo in zlib.h uncompress() description [Reiss]
-- Correct inflate() comments with regard to automatic header detection
-- Remove deprecation comment on Z_PARTIAL_FLUSH (it stays)
-- Put new version of gzlog (2.0) in examples with interruption recovery
-- Add puff compile option to permit invalid distance-too-far streams
-- Add puff TEST command options, ability to read piped input
-- Prototype the *64 functions in zlib.h when _FILE_OFFSET_BITS == 64, but
- _LARGEFILE64_SOURCE not defined
-- Fix Z_FULL_FLUSH to truly erase the past by resetting s->strstart
-- Fix deflateSetDictionary() to use all 32K for output consistency
-- Remove extraneous #define MIN_LOOKAHEAD in deflate.c (in deflate.h)
-- Clear bytes after deflate lookahead to avoid use of uninitialized data
-- Change a limit in inftrees.c to be more transparent to Coverity Prevent
-- Update win32/zlib.def with exported symbols from zlib.h
-- Correct spelling errors in zlib.h [Willem, Sobrado]
-- Allow Z_BLOCK for deflate() to force a new block
-- Allow negative bits in inflatePrime() to delete existing bit buffer
-- Add Z_TREES flush option to inflate() to return at end of trees
-- Add inflateMark() to return current state information for random access
-- Add Makefile for NintendoDS to contrib [Costa]
-- Add -w in configure compile tests to avoid spurious warnings [Beucler]
-- Fix typos in zlib.h comments for deflateSetDictionary()
-- Fix EOF detection in transparent gzread() [Maier]
-
-Changes in 1.2.3.3 (2 October 2006)
-- Make --shared the default for configure, add a --static option
-- Add compile option to permit invalid distance-too-far streams
-- Add inflateUndermine() function which is required to enable above
-- Remove use of "this" variable name for C++ compatibility [Marquess]
-- Add testing of shared library in make test, if shared library built
-- Use ftello() and fseeko() if available instead of ftell() and fseek()
-- Provide two versions of all functions that use the z_off_t type for
- binary compatibility -- a normal version and a 64-bit offset version,
- per the Large File Support Extension when _LARGEFILE64_SOURCE is
- defined; use the 64-bit versions by default when _FILE_OFFSET_BITS
- is defined to be 64
-- Add a --uname= option to configure to perhaps help with cross-compiling
-
-Changes in 1.2.3.2 (3 September 2006)
-- Turn off silly Borland warnings [Hay]
-- Use off64_t and define _LARGEFILE64_SOURCE when present
-- Fix missing dependency on inffixed.h in Makefile.in
-- Rig configure --shared to build both shared and static [Teredesai, Truta]
-- Remove zconf.in.h and instead create a new zlibdefs.h file
-- Fix contrib/minizip/unzip.c non-encrypted after encrypted [Vollant]
-- Add treebuild.xml (see http://treebuild.metux.de/) [Weigelt]
-
-Changes in 1.2.3.1 (16 August 2006)
-- Add watcom directory with OpenWatcom make files [Daniel]
-- Remove #undef of FAR in zconf.in.h for MVS [Fedtke]
-- Update make_vms.com [Zinser]
-- Use -fPIC for shared build in configure [Teredesai, Nicholson]
-- Use only major version number for libz.so on IRIX and OSF1 [Reinholdtsen]
-- Use fdopen() (not _fdopen()) for Interix in zutil.h [B�ck]
-- Add some FAQ entries about the contrib directory
-- Update the MVS question in the FAQ
-- Avoid extraneous reads after EOF in gzio.c [Brown]
-- Correct spelling of "successfully" in gzio.c [Randers-Pehrson]
-- Add comments to zlib.h about gzerror() usage [Brown]
-- Set extra flags in gzip header in gzopen() like deflate() does
-- Make configure options more compatible with double-dash conventions
- [Weigelt]
-- Clean up compilation under Solaris SunStudio cc [Rowe, Reinholdtsen]
-- Fix uninstall target in Makefile.in [Truta]
-- Add pkgconfig support [Weigelt]
-- Use $(DESTDIR) macro in Makefile.in [Reinholdtsen, Weigelt]
-- Replace set_data_type() with a more accurate detect_data_type() in
- trees.c, according to the txtvsbin.txt document [Truta]
-- Swap the order of #include <stdio.h> and #include "zlib.h" in
- gzio.c, example.c and minigzip.c [Truta]
-- Shut up annoying VS2005 warnings about standard C deprecation [Rowe,
- Truta] (where?)
-- Fix target "clean" from win32/Makefile.bor [Truta]
-- Create .pdb and .manifest files in win32/makefile.msc [Ziegler, Rowe]
-- Update zlib www home address in win32/DLL_FAQ.txt [Truta]
-- Update contrib/masmx86/inffas32.asm for VS2005 [Vollant, Van Wassenhove]
-- Enable browse info in the "Debug" and "ASM Debug" configurations in
- the Visual C++ 6 project, and set (non-ASM) "Debug" as default [Truta]
-- Add pkgconfig support [Weigelt]
-- Add ZLIB_VER_MAJOR, ZLIB_VER_MINOR and ZLIB_VER_REVISION in zlib.h,
- for use in win32/zlib1.rc [Polushin, Rowe, Truta]
-- Add a document that explains the new text detection scheme to
- doc/txtvsbin.txt [Truta]
-- Add rfc1950.txt, rfc1951.txt and rfc1952.txt to doc/ [Truta]
-- Move algorithm.txt into doc/ [Truta]
-- Synchronize FAQ with website
-- Fix compressBound(), was low for some pathological cases [Fearnley]
-- Take into account wrapper variations in deflateBound()
-- Set examples/zpipe.c input and output to binary mode for Windows
-- Update examples/zlib_how.html with new zpipe.c (also web site)
-- Fix some warnings in examples/gzlog.c and examples/zran.c (it seems
- that gcc became pickier in 4.0)
-- Add zlib.map for Linux: "All symbols from zlib-1.1.4 remain
- un-versioned, the patch adds versioning only for symbols introduced in
- zlib-1.2.0 or later. It also declares as local those symbols which are
- not designed to be exported." [Levin]
-- Update Z_PREFIX list in zconf.in.h, add --zprefix option to configure
-- Do not initialize global static by default in trees.c, add a response
- NO_INIT_GLOBAL_POINTERS to initialize them if needed [Marquess]
-- Don't use strerror() in gzio.c under WinCE [Yakimov]
-- Don't use errno.h in zutil.h under WinCE [Yakimov]
-- Move arguments for AR to its usage to allow replacing ar [Marot]
-- Add HAVE_VISIBILITY_PRAGMA in zconf.in.h for Mozilla [Randers-Pehrson]
-- Improve inflateInit() and inflateInit2() documentation
-- Fix structure size comment in inflate.h
-- Change configure help option from --h* to --help [Santos]
-
-Changes in 1.2.3 (18 July 2005)
-- Apply security vulnerability fixes to contrib/infback9 as well
-- Clean up some text files (carriage returns, trailing space)
-- Update testzlib, vstudio, masmx64, and masmx86 in contrib [Vollant]
-
-Changes in 1.2.2.4 (11 July 2005)
-- Add inflatePrime() function for starting inflation at bit boundary
-- Avoid some Visual C warnings in deflate.c
-- Avoid more silly Visual C warnings in inflate.c and inftrees.c for 64-bit
- compile
-- Fix some spelling errors in comments [Betts]
-- Correct inflateInit2() error return documentation in zlib.h
-- Add zran.c example of compressed data random access to examples
- directory, shows use of inflatePrime()
-- Fix cast for assignments to strm->state in inflate.c and infback.c
-- Fix zlibCompileFlags() in zutil.c to use 1L for long shifts [Oberhumer]
-- Move declarations of gf2 functions to right place in crc32.c [Oberhumer]
-- Add cast in trees.c t avoid a warning [Oberhumer]
-- Avoid some warnings in fitblk.c, gun.c, gzjoin.c in examples [Oberhumer]
-- Update make_vms.com [Zinser]
-- Initialize state->write in inflateReset() since copied in inflate_fast()
-- Be more strict on incomplete code sets in inflate_table() and increase
- ENOUGH and MAXD -- this repairs a possible security vulnerability for
- invalid inflate input. Thanks to Tavis Ormandy and Markus Oberhumer for
- discovering the vulnerability and providing test cases.
-- Add ia64 support to configure for HP-UX [Smith]
-- Add error return to gzread() for format or i/o error [Levin]
-- Use malloc.h for OS/2 [Necasek]
-
-Changes in 1.2.2.3 (27 May 2005)
-- Replace 1U constants in inflate.c and inftrees.c for 64-bit compile
-- Typecast fread() return values in gzio.c [Vollant]
-- Remove trailing space in minigzip.c outmode (VC++ can't deal with it)
-- Fix crc check bug in gzread() after gzungetc() [Heiner]
-- Add the deflateTune() function to adjust internal compression parameters
-- Add a fast gzip decompressor, gun.c, to examples (use of inflateBack)
-- Remove an incorrect assertion in examples/zpipe.c
-- Add C++ wrapper in infback9.h [Donais]
-- Fix bug in inflateCopy() when decoding fixed codes
-- Note in zlib.h how much deflateSetDictionary() actually uses
-- Remove USE_DICT_HEAD in deflate.c (would mess up inflate if used)
-- Add _WIN32_WCE to define WIN32 in zconf.in.h [Spencer]
-- Don't include stderr.h or errno.h for _WIN32_WCE in zutil.h [Spencer]
-- Add gzdirect() function to indicate transparent reads
-- Update contrib/minizip [Vollant]
-- Fix compilation of deflate.c when both ASMV and FASTEST [Oberhumer]
-- Add casts in crc32.c to avoid warnings [Oberhumer]
-- Add contrib/masmx64 [Vollant]
-- Update contrib/asm586, asm686, masmx86, testzlib, vstudio [Vollant]
-
-Changes in 1.2.2.2 (30 December 2004)
-- Replace structure assignments in deflate.c and inflate.c with zmemcpy to
- avoid implicit memcpy calls (portability for no-library compilation)
-- Increase sprintf() buffer size in gzdopen() to allow for large numbers
-- Add INFLATE_STRICT to check distances against zlib header
-- Improve WinCE errno handling and comments [Chang]
-- Remove comment about no gzip header processing in FAQ
-- Add Z_FIXED strategy option to deflateInit2() to force fixed trees
-- Add updated make_vms.com [Coghlan], update README
-- Create a new "examples" directory, move gzappend.c there, add zpipe.c,
- fitblk.c, gzlog.[ch], gzjoin.c, and zlib_how.html.
-- Add FAQ entry and comments in deflate.c on uninitialized memory access
-- Add Solaris 9 make options in configure [Gilbert]
-- Allow strerror() usage in gzio.c for STDC
-- Fix DecompressBuf in contrib/delphi/ZLib.pas [ManChesTer]
-- Update contrib/masmx86/inffas32.asm and gvmat32.asm [Vollant]
-- Use z_off_t for adler32_combine() and crc32_combine() lengths
-- Make adler32() much faster for small len
-- Use OS_CODE in deflate() default gzip header
-
-Changes in 1.2.2.1 (31 October 2004)
-- Allow inflateSetDictionary() call for raw inflate
-- Fix inflate header crc check bug for file names and comments
-- Add deflateSetHeader() and gz_header structure for custom gzip headers
-- Add inflateGetheader() to retrieve gzip headers
-- Add crc32_combine() and adler32_combine() functions
-- Add alloc_func, free_func, in_func, out_func to Z_PREFIX list
-- Use zstreamp consistently in zlib.h (inflate_back functions)
-- Remove GUNZIP condition from definition of inflate_mode in inflate.h
- and in contrib/inflate86/inffast.S [Truta, Anderson]
-- Add support for AMD64 in contrib/inflate86/inffas86.c [Anderson]
-- Update projects/README.projects and projects/visualc6 [Truta]
-- Update win32/DLL_FAQ.txt [Truta]
-- Avoid warning under NO_GZCOMPRESS in gzio.c; fix typo [Truta]
-- Deprecate Z_ASCII; use Z_TEXT instead [Truta]
-- Use a new algorithm for setting strm->data_type in trees.c [Truta]
-- Do not define an exit() prototype in zutil.c unless DEBUG defined
-- Remove prototype of exit() from zutil.c, example.c, minigzip.c [Truta]
-- Add comment in zlib.h for Z_NO_FLUSH parameter to deflate()
-- Fix Darwin build version identification [Peterson]
-
-Changes in 1.2.2 (3 October 2004)
-- Update zlib.h comments on gzip in-memory processing
-- Set adler to 1 in inflateReset() to support Java test suite [Walles]
-- Add contrib/dotzlib [Ravn]
-- Update win32/DLL_FAQ.txt [Truta]
-- Update contrib/minizip [Vollant]
-- Move contrib/visual-basic.txt to old/ [Truta]
-- Fix assembler builds in projects/visualc6/ [Truta]
-
-Changes in 1.2.1.2 (9 September 2004)
-- Update INDEX file
-- Fix trees.c to update strm->data_type (no one ever noticed!)
-- Fix bug in error case in inflate.c, infback.c, and infback9.c [Brown]
-- Add "volatile" to crc table flag declaration (for DYNAMIC_CRC_TABLE)
-- Add limited multitasking protection to DYNAMIC_CRC_TABLE
-- Add NO_vsnprintf for VMS in zutil.h [Mozilla]
-- Don't declare strerror() under VMS [Mozilla]
-- Add comment to DYNAMIC_CRC_TABLE to use get_crc_table() to initialize
-- Update contrib/ada [Anisimkov]
-- Update contrib/minizip [Vollant]
-- Fix configure to not hardcode directories for Darwin [Peterson]
-- Fix gzio.c to not return error on empty files [Brown]
-- Fix indentation; update version in contrib/delphi/ZLib.pas and
- contrib/pascal/zlibpas.pas [Truta]
-- Update mkasm.bat in contrib/masmx86 [Truta]
-- Update contrib/untgz [Truta]
-- Add projects/README.projects [Truta]
-- Add project for MS Visual C++ 6.0 in projects/visualc6 [Cadieux, Truta]
-- Update win32/DLL_FAQ.txt [Truta]
-- Update list of Z_PREFIX symbols in zconf.h [Randers-Pehrson, Truta]
-- Remove an unnecessary assignment to curr in inftrees.c [Truta]
-- Add OS/2 to exe builds in configure [Poltorak]
-- Remove err dummy parameter in zlib.h [Kientzle]
-
-Changes in 1.2.1.1 (9 January 2004)
-- Update email address in README
-- Several FAQ updates
-- Fix a big fat bug in inftrees.c that prevented decoding valid
- dynamic blocks with only literals and no distance codes --
- Thanks to "Hot Emu" for the bug report and sample file
-- Add a note to puff.c on no distance codes case.
-
-Changes in 1.2.1 (17 November 2003)
-- Remove a tab in contrib/gzappend/gzappend.c
-- Update some interfaces in contrib for new zlib functions
-- Update zlib version number in some contrib entries
-- Add Windows CE definition for ptrdiff_t in zutil.h [Mai, Truta]
-- Support shared libraries on Hurd and KFreeBSD [Brown]
-- Fix error in NO_DIVIDE option of adler32.c
-
-Changes in 1.2.0.8 (4 November 2003)
-- Update version in contrib/delphi/ZLib.pas and contrib/pascal/zlibpas.pas
-- Add experimental NO_DIVIDE #define in adler32.c
- - Possibly faster on some processors (let me know if it is)
-- Correct Z_BLOCK to not return on first inflate call if no wrap
-- Fix strm->data_type on inflate() return to correctly indicate EOB
-- Add deflatePrime() function for appending in the middle of a byte
-- Add contrib/gzappend for an example of appending to a stream
-- Update win32/DLL_FAQ.txt [Truta]
-- Delete Turbo C comment in README [Truta]
-- Improve some indentation in zconf.h [Truta]
-- Fix infinite loop on bad input in configure script [Church]
-- Fix gzeof() for concatenated gzip files [Johnson]
-- Add example to contrib/visual-basic.txt [Michael B.]
-- Add -p to mkdir's in Makefile.in [vda]
-- Fix configure to properly detect presence or lack of printf functions
-- Add AS400 support [Monnerat]
-- Add a little Cygwin support [Wilson]
-
-Changes in 1.2.0.7 (21 September 2003)
-- Correct some debug formats in contrib/infback9
-- Cast a type in a debug statement in trees.c
-- Change search and replace delimiter in configure from % to # [Beebe]
-- Update contrib/untgz to 0.2 with various fixes [Truta]
-- Add build support for Amiga [Nikl]
-- Remove some directories in old that have been updated to 1.2
-- Add dylib building for Mac OS X in configure and Makefile.in
-- Remove old distribution stuff from Makefile
-- Update README to point to DLL_FAQ.txt, and add comment on Mac OS X
-- Update links in README
-
-Changes in 1.2.0.6 (13 September 2003)
-- Minor FAQ updates
-- Update contrib/minizip to 1.00 [Vollant]
-- Remove test of gz functions in example.c when GZ_COMPRESS defined [Truta]
-- Update POSTINC comment for 68060 [Nikl]
-- Add contrib/infback9 with deflate64 decoding (unsupported)
-- For MVS define NO_vsnprintf and undefine FAR [van Burik]
-- Add pragma for fdopen on MVS [van Burik]
-
-Changes in 1.2.0.5 (8 September 2003)
-- Add OF to inflateBackEnd() declaration in zlib.h
-- Remember start when using gzdopen in the middle of a file
-- Use internal off_t counters in gz* functions to properly handle seeks
-- Perform more rigorous check for distance-too-far in inffast.c
-- Add Z_BLOCK flush option to return from inflate at block boundary
-- Set strm->data_type on return from inflate
- - Indicate bits unused, if at block boundary, and if in last block
-- Replace size_t with ptrdiff_t in crc32.c, and check for correct size
-- Add condition so old NO_DEFLATE define still works for compatibility
-- FAQ update regarding the Windows DLL [Truta]
-- INDEX update: add qnx entry, remove aix entry [Truta]
-- Install zlib.3 into mandir [Wilson]
-- Move contrib/zlib_dll_FAQ.txt to win32/DLL_FAQ.txt; update [Truta]
-- Adapt the zlib interface to the new DLL convention guidelines [Truta]
-- Introduce ZLIB_WINAPI macro to allow the export of functions using
- the WINAPI calling convention, for Visual Basic [Vollant, Truta]
-- Update msdos and win32 scripts and makefiles [Truta]
-- Export symbols by name, not by ordinal, in win32/zlib.def [Truta]
-- Add contrib/ada [Anisimkov]
-- Move asm files from contrib/vstudio/vc70_32 to contrib/asm386 [Truta]
-- Rename contrib/asm386 to contrib/masmx86 [Truta, Vollant]
-- Add contrib/masm686 [Truta]
-- Fix offsets in contrib/inflate86 and contrib/masmx86/inffas32.asm
- [Truta, Vollant]
-- Update contrib/delphi; rename to contrib/pascal; add example [Truta]
-- Remove contrib/delphi2; add a new contrib/delphi [Truta]
-- Avoid inclusion of the nonstandard <memory.h> in contrib/iostream,
- and fix some method prototypes [Truta]
-- Fix the ZCR_SEED2 constant to avoid warnings in contrib/minizip
- [Truta]
-- Avoid the use of backslash (\) in contrib/minizip [Vollant]
-- Fix file time handling in contrib/untgz; update makefiles [Truta]
-- Update contrib/vstudio/vc70_32 to comply with the new DLL guidelines
- [Vollant]
-- Remove contrib/vstudio/vc15_16 [Vollant]
-- Rename contrib/vstudio/vc70_32 to contrib/vstudio/vc7 [Truta]
-- Update README.contrib [Truta]
-- Invert the assignment order of match_head and s->prev[...] in
- INSERT_STRING [Truta]
-- Compare TOO_FAR with 32767 instead of 32768, to avoid 16-bit warnings
- [Truta]
-- Compare function pointers with 0, not with NULL or Z_NULL [Truta]
-- Fix prototype of syncsearch in inflate.c [Truta]
-- Introduce ASMINF macro to be enabled when using an ASM implementation
- of inflate_fast [Truta]
-- Change NO_DEFLATE to NO_GZCOMPRESS [Truta]
-- Modify test_gzio in example.c to take a single file name as a
- parameter [Truta]
-- Exit the example.c program if gzopen fails [Truta]
-- Add type casts around strlen in example.c [Truta]
-- Remove casting to sizeof in minigzip.c; give a proper type
- to the variable compared with SUFFIX_LEN [Truta]
-- Update definitions of STDC and STDC99 in zconf.h [Truta]
-- Synchronize zconf.h with the new Windows DLL interface [Truta]
-- Use SYS16BIT instead of __32BIT__ to distinguish between
- 16- and 32-bit platforms [Truta]
-- Use far memory allocators in small 16-bit memory models for
- Turbo C [Truta]
-- Add info about the use of ASMV, ASMINF and ZLIB_WINAPI in
- zlibCompileFlags [Truta]
-- Cygwin has vsnprintf [Wilson]
-- In Windows16, OS_CODE is 0, as in MSDOS [Truta]
-- In Cygwin, OS_CODE is 3 (Unix), not 11 (Windows32) [Wilson]
-
-Changes in 1.2.0.4 (10 August 2003)
-- Minor FAQ updates
-- Be more strict when checking inflateInit2's windowBits parameter
-- Change NO_GUNZIP compile option to NO_GZIP to cover deflate as well
-- Add gzip wrapper option to deflateInit2 using windowBits
-- Add updated QNX rule in configure and qnx directory [Bonnefoy]
-- Make inflate distance-too-far checks more rigorous
-- Clean up FAR usage in inflate
-- Add casting to sizeof() in gzio.c and minigzip.c
-
-Changes in 1.2.0.3 (19 July 2003)
-- Fix silly error in gzungetc() implementation [Vollant]
-- Update contrib/minizip and contrib/vstudio [Vollant]
-- Fix printf format in example.c
-- Correct cdecl support in zconf.in.h [Anisimkov]
-- Minor FAQ updates
-
-Changes in 1.2.0.2 (13 July 2003)
-- Add ZLIB_VERNUM in zlib.h for numerical preprocessor comparisons
-- Attempt to avoid warnings in crc32.c for pointer-int conversion
-- Add AIX to configure, remove aix directory [Bakker]
-- Add some casts to minigzip.c
-- Improve checking after insecure sprintf() or vsprintf() calls
-- Remove #elif's from crc32.c
-- Change leave label to inf_leave in inflate.c and infback.c to avoid
- library conflicts
-- Remove inflate gzip decoding by default--only enable gzip decoding by
- special request for stricter backward compatibility
-- Add zlibCompileFlags() function to return compilation information
-- More typecasting in deflate.c to avoid warnings
-- Remove leading underscore from _Capital #defines [Truta]
-- Fix configure to link shared library when testing
-- Add some Windows CE target adjustments [Mai]
-- Remove #define ZLIB_DLL in zconf.h [Vollant]
-- Add zlib.3 [Rodgers]
-- Update RFC URL in deflate.c and algorithm.txt [Mai]
-- Add zlib_dll_FAQ.txt to contrib [Truta]
-- Add UL to some constants [Truta]
-- Update minizip and vstudio [Vollant]
-- Remove vestigial NEED_DUMMY_RETURN from zconf.in.h
-- Expand use of NO_DUMMY_DECL to avoid all dummy structures
-- Added iostream3 to contrib [Schwardt]
-- Replace rewind() with fseek() for WinCE [Truta]
-- Improve setting of zlib format compression level flags
- - Report 0 for huffman and rle strategies and for level == 0 or 1
- - Report 2 only for level == 6
-- Only deal with 64K limit when necessary at compile time [Truta]
-- Allow TOO_FAR check to be turned off at compile time [Truta]
-- Add gzclearerr() function [Souza]
-- Add gzungetc() function
-
-Changes in 1.2.0.1 (17 March 2003)
-- Add Z_RLE strategy for run-length encoding [Truta]
- - When Z_RLE requested, restrict matches to distance one
- - Update zlib.h, minigzip.c, gzopen(), gzdopen() for Z_RLE
-- Correct FASTEST compilation to allow level == 0
-- Clean up what gets compiled for FASTEST
-- Incorporate changes to zconf.in.h [Vollant]
- - Refine detection of Turbo C need for dummy returns
- - Refine ZLIB_DLL compilation
- - Include additional header file on VMS for off_t typedef
-- Try to use _vsnprintf where it supplants vsprintf [Vollant]
-- Add some casts in inffast.c
-- Enchance comments in zlib.h on what happens if gzprintf() tries to
- write more than 4095 bytes before compression
-- Remove unused state from inflateBackEnd()
-- Remove exit(0) from minigzip.c, example.c
-- Get rid of all those darn tabs
-- Add "check" target to Makefile.in that does the same thing as "test"
-- Add "mostlyclean" and "maintainer-clean" targets to Makefile.in
-- Update contrib/inflate86 [Anderson]
-- Update contrib/testzlib, contrib/vstudio, contrib/minizip [Vollant]
-- Add msdos and win32 directories with makefiles [Truta]
-- More additions and improvements to the FAQ
-
-Changes in 1.2.0 (9 March 2003)
-- New and improved inflate code
- - About 20% faster
- - Does not allocate 32K window unless and until needed
- - Automatically detects and decompresses gzip streams
- - Raw inflate no longer needs an extra dummy byte at end
- - Added inflateBack functions using a callback interface--even faster
- than inflate, useful for file utilities (gzip, zip)
- - Added inflateCopy() function to record state for random access on
- externally generated deflate streams (e.g. in gzip files)
- - More readable code (I hope)
-- New and improved crc32()
- - About 50% faster, thanks to suggestions from Rodney Brown
-- Add deflateBound() and compressBound() functions
-- Fix memory leak in deflateInit2()
-- Permit setting dictionary for raw deflate (for parallel deflate)
-- Fix const declaration for gzwrite()
-- Check for some malloc() failures in gzio.c
-- Fix bug in gzopen() on single-byte file 0x1f
-- Fix bug in gzread() on concatenated file with 0x1f at end of buffer
- and next buffer doesn't start with 0x8b
-- Fix uncompress() to return Z_DATA_ERROR on truncated input
-- Free memory at end of example.c
-- Remove MAX #define in trees.c (conflicted with some libraries)
-- Fix static const's in deflate.c, gzio.c, and zutil.[ch]
-- Declare malloc() and free() in gzio.c if STDC not defined
-- Use malloc() instead of calloc() in zutil.c if int big enough
-- Define STDC for AIX
-- Add aix/ with approach for compiling shared library on AIX
-- Add HP-UX support for shared libraries in configure
-- Add OpenUNIX support for shared libraries in configure
-- Use $cc instead of gcc to build shared library
-- Make prefix directory if needed when installing
-- Correct Macintosh avoidance of typedef Byte in zconf.h
-- Correct Turbo C memory allocation when under Linux
-- Use libz.a instead of -lz in Makefile (assure use of compiled library)
-- Update configure to check for snprintf or vsnprintf functions and their
- return value, warn during make if using an insecure function
-- Fix configure problem with compile-time knowledge of HAVE_UNISTD_H that
- is lost when library is used--resolution is to build new zconf.h
-- Documentation improvements (in zlib.h):
- - Document raw deflate and inflate
- - Update RFCs URL
- - Point out that zlib and gzip formats are different
- - Note that Z_BUF_ERROR is not fatal
- - Document string limit for gzprintf() and possible buffer overflow
- - Note requirement on avail_out when flushing
- - Note permitted values of flush parameter of inflate()
-- Add some FAQs (and even answers) to the FAQ
-- Add contrib/inflate86/ for x86 faster inflate
-- Add contrib/blast/ for PKWare Data Compression Library decompression
-- Add contrib/puff/ simple inflate for deflate format description
-
-Changes in 1.1.4 (11 March 2002)
-- ZFREE was repeated on same allocation on some error conditions.
- This creates a security problem described in
- http://www.zlib.org/advisory-2002-03-11.txt
-- Returned incorrect error (Z_MEM_ERROR) on some invalid data
-- Avoid accesses before window for invalid distances with inflate window
- less than 32K.
-- force windowBits > 8 to avoid a bug in the encoder for a window size
- of 256 bytes. (A complete fix will be available in 1.1.5).
-
-Changes in 1.1.3 (9 July 1998)
-- fix "an inflate input buffer bug that shows up on rare but persistent
- occasions" (Mark)
-- fix gzread and gztell for concatenated .gz files (Didier Le Botlan)
-- fix gzseek(..., SEEK_SET) in write mode
-- fix crc check after a gzeek (Frank Faubert)
-- fix miniunzip when the last entry in a zip file is itself a zip file
- (J Lillge)
-- add contrib/asm586 and contrib/asm686 (Brian Raiter)
- See http://www.muppetlabs.com/~breadbox/software/assembly.html
-- add support for Delphi 3 in contrib/delphi (Bob Dellaca)
-- add support for C++Builder 3 and Delphi 3 in contrib/delphi2 (Davide Moretti)
-- do not exit prematurely in untgz if 0 at start of block (Magnus Holmgren)
-- use macro EXTERN instead of extern to support DLL for BeOS (Sander Stoks)
-- added a FAQ file
-
-- Support gzdopen on Mac with Metrowerks (Jason Linhart)
-- Do not redefine Byte on Mac (Brad Pettit & Jason Linhart)
-- define SEEK_END too if SEEK_SET is not defined (Albert Chin-A-Young)
-- avoid some warnings with Borland C (Tom Tanner)
-- fix a problem in contrib/minizip/zip.c for 16-bit MSDOS (Gilles Vollant)
-- emulate utime() for WIN32 in contrib/untgz (Gilles Vollant)
-- allow several arguments to configure (Tim Mooney, Frodo Looijaard)
-- use libdir and includedir in Makefile.in (Tim Mooney)
-- support shared libraries on OSF1 V4 (Tim Mooney)
-- remove so_locations in "make clean" (Tim Mooney)
-- fix maketree.c compilation error (Glenn, Mark)
-- Python interface to zlib now in Python 1.5 (Jeremy Hylton)
-- new Makefile.riscos (Rich Walker)
-- initialize static descriptors in trees.c for embedded targets (Nick Smith)
-- use "foo-gz" in example.c for RISCOS and VMS (Nick Smith)
-- add the OS/2 files in Makefile.in too (Andrew Zabolotny)
-- fix fdopen and halloc macros for Microsoft C 6.0 (Tom Lane)
-- fix maketree.c to allow clean compilation of inffixed.h (Mark)
-- fix parameter check in deflateCopy (Gunther Nikl)
-- cleanup trees.c, use compressed_len only in debug mode (Christian Spieler)
-- Many portability patches by Christian Spieler:
- . zutil.c, zutil.h: added "const" for zmem*
- . Make_vms.com: fixed some typos
- . Make_vms.com: msdos/Makefile.*: removed zutil.h from some dependency lists
- . msdos/Makefile.msc: remove "default rtl link library" info from obj files
- . msdos/Makefile.*: use model-dependent name for the built zlib library
- . msdos/Makefile.emx, nt/Makefile.emx, nt/Makefile.gcc:
- new makefiles, for emx (DOS/OS2), emx&rsxnt and mingw32 (Windows 9x / NT)
-- use define instead of typedef for Bytef also for MSC small/medium (Tom Lane)
-- replace __far with _far for better portability (Christian Spieler, Tom Lane)
-- fix test for errno.h in configure (Tim Newsham)
-
-Changes in 1.1.2 (19 March 98)
-- added contrib/minzip, mini zip and unzip based on zlib (Gilles Vollant)
- See http://www.winimage.com/zLibDll/unzip.html
-- preinitialize the inflate tables for fixed codes, to make the code
- completely thread safe (Mark)
-- some simplifications and slight speed-up to the inflate code (Mark)
-- fix gzeof on non-compressed files (Allan Schrum)
-- add -std1 option in configure for OSF1 to fix gzprintf (Martin Mokrejs)
-- use default value of 4K for Z_BUFSIZE for 16-bit MSDOS (Tim Wegner + Glenn)
-- added os2/Makefile.def and os2/zlib.def (Andrew Zabolotny)
-- add shared lib support for UNIX_SV4.2MP (MATSUURA Takanori)
-- do not wrap extern "C" around system includes (Tom Lane)
-- mention zlib binding for TCL in README (Andreas Kupries)
-- added amiga/Makefile.pup for Amiga powerUP SAS/C PPC (Andreas Kleinert)
-- allow "make install prefix=..." even after configure (Glenn Randers-Pehrson)
-- allow "configure --prefix $HOME" (Tim Mooney)
-- remove warnings in example.c and gzio.c (Glenn Randers-Pehrson)
-- move Makefile.sas to amiga/Makefile.sas
-
-Changes in 1.1.1 (27 Feb 98)
-- fix macros _tr_tally_* in deflate.h for debug mode (Glenn Randers-Pehrson)
-- remove block truncation heuristic which had very marginal effect for zlib
- (smaller lit_bufsize than in gzip 1.2.4) and degraded a little the
- compression ratio on some files. This also allows inlining _tr_tally for
- matches in deflate_slow.
-- added msdos/Makefile.w32 for WIN32 Microsoft Visual C++ (Bob Frazier)
-
-Changes in 1.1.0 (24 Feb 98)
-- do not return STREAM_END prematurely in inflate (John Bowler)
-- revert to the zlib 1.0.8 inflate to avoid the gcc 2.8.0 bug (Jeremy Buhler)
-- compile with -DFASTEST to get compression code optimized for speed only
-- in minigzip, try mmap'ing the input file first (Miguel Albrecht)
-- increase size of I/O buffers in minigzip.c and gzio.c (not a big gain
- on Sun but significant on HP)
-
-- add a pointer to experimental unzip library in README (Gilles Vollant)
-- initialize variable gcc in configure (Chris Herborth)
-
-Changes in 1.0.9 (17 Feb 1998)
-- added gzputs and gzgets functions
-- do not clear eof flag in gzseek (Mark Diekhans)
-- fix gzseek for files in transparent mode (Mark Diekhans)
-- do not assume that vsprintf returns the number of bytes written (Jens Krinke)
-- replace EXPORT with ZEXPORT to avoid conflict with other programs
-- added compress2 in zconf.h, zlib.def, zlib.dnt
-- new asm code from Gilles Vollant in contrib/asm386
-- simplify the inflate code (Mark):
- . Replace ZALLOC's in huft_build() with single ZALLOC in inflate_blocks_new()
- . ZALLOC the length list in inflate_trees_fixed() instead of using stack
- . ZALLOC the value area for huft_build() instead of using stack
- . Simplify Z_FINISH check in inflate()
-
-- Avoid gcc 2.8.0 comparison bug a little differently than zlib 1.0.8
-- in inftrees.c, avoid cc -O bug on HP (Farshid Elahi)
-- in zconf.h move the ZLIB_DLL stuff earlier to avoid problems with
- the declaration of FAR (Gilles VOllant)
-- install libz.so* with mode 755 (executable) instead of 644 (Marc Lehmann)
-- read_buf buf parameter of type Bytef* instead of charf*
-- zmemcpy parameters are of type Bytef*, not charf* (Joseph Strout)
-- do not redeclare unlink in minigzip.c for WIN32 (John Bowler)
-- fix check for presence of directories in "make install" (Ian Willis)
-
-Changes in 1.0.8 (27 Jan 1998)
-- fixed offsets in contrib/asm386/gvmat32.asm (Gilles Vollant)
-- fix gzgetc and gzputc for big endian systems (Markus Oberhumer)
-- added compress2() to allow setting the compression level
-- include sys/types.h to get off_t on some systems (Marc Lehmann & QingLong)
-- use constant arrays for the static trees in trees.c instead of computing
- them at run time (thanks to Ken Raeburn for this suggestion). To create
- trees.h, compile with GEN_TREES_H and run "make test".
-- check return code of example in "make test" and display result
-- pass minigzip command line options to file_compress
-- simplifying code of inflateSync to avoid gcc 2.8 bug
-
-- support CC="gcc -Wall" in configure -s (QingLong)
-- avoid a flush caused by ftell in gzopen for write mode (Ken Raeburn)
-- fix test for shared library support to avoid compiler warnings
-- zlib.lib -> zlib.dll in msdos/zlib.rc (Gilles Vollant)
-- check for TARGET_OS_MAC in addition to MACOS (Brad Pettit)
-- do not use fdopen for Metrowerks on Mac (Brad Pettit))
-- add checks for gzputc and gzputc in example.c
-- avoid warnings in gzio.c and deflate.c (Andreas Kleinert)
-- use const for the CRC table (Ken Raeburn)
-- fixed "make uninstall" for shared libraries
-- use Tracev instead of Trace in infblock.c
-- in example.c use correct compressed length for test_sync
-- suppress +vnocompatwarnings in configure for HPUX (not always supported)
-
-Changes in 1.0.7 (20 Jan 1998)
-- fix gzseek which was broken in write mode
-- return error for gzseek to negative absolute position
-- fix configure for Linux (Chun-Chung Chen)
-- increase stack space for MSC (Tim Wegner)
-- get_crc_table and inflateSyncPoint are EXPORTed (Gilles Vollant)
-- define EXPORTVA for gzprintf (Gilles Vollant)
-- added man page zlib.3 (Rick Rodgers)
-- for contrib/untgz, fix makedir() and improve Makefile
-
-- check gzseek in write mode in example.c
-- allocate extra buffer for seeks only if gzseek is actually called
-- avoid signed/unsigned comparisons (Tim Wegner, Gilles Vollant)
-- add inflateSyncPoint in zconf.h
-- fix list of exported functions in nt/zlib.dnt and mdsos/zlib.def
-
-Changes in 1.0.6 (19 Jan 1998)
-- add functions gzprintf, gzputc, gzgetc, gztell, gzeof, gzseek, gzrewind and
- gzsetparams (thanks to Roland Giersig and Kevin Ruland for some of this code)
-- Fix a deflate bug occurring only with compression level 0 (thanks to
- Andy Buckler for finding this one).
-- In minigzip, pass transparently also the first byte for .Z files.
-- return Z_BUF_ERROR instead of Z_OK if output buffer full in uncompress()
-- check Z_FINISH in inflate (thanks to Marc Schluper)
-- Implement deflateCopy (thanks to Adam Costello)
-- make static libraries by default in configure, add --shared option.
-- move MSDOS or Windows specific files to directory msdos
-- suppress the notion of partial flush to simplify the interface
- (but the symbol Z_PARTIAL_FLUSH is kept for compatibility with 1.0.4)
-- suppress history buffer provided by application to simplify the interface
- (this feature was not implemented anyway in 1.0.4)
-- next_in and avail_in must be initialized before calling inflateInit or
- inflateInit2
-- add EXPORT in all exported functions (for Windows DLL)
-- added Makefile.nt (thanks to Stephen Williams)
-- added the unsupported "contrib" directory:
- contrib/asm386/ by Gilles Vollant <info at winimage.com>
- 386 asm code replacing longest_match().
- contrib/iostream/ by Kevin Ruland <kevin at rodin.wustl.edu>
- A C++ I/O streams interface to the zlib gz* functions
- contrib/iostream2/ by Tyge L�vset <Tyge.Lovset at cmr.no>
- Another C++ I/O streams interface
- contrib/untgz/ by "Pedro A. Aranda Guti\irrez" <paag at tid.es>
- A very simple tar.gz file extractor using zlib
- contrib/visual-basic.txt by Carlos Rios <c_rios at sonda.cl>
- How to use compress(), uncompress() and the gz* functions from VB.
-- pass params -f (filtered data), -h (huffman only), -1 to -9 (compression
- level) in minigzip (thanks to Tom Lane)
-
-- use const for rommable constants in deflate
-- added test for gzseek and gztell in example.c
-- add undocumented function inflateSyncPoint() (hack for Paul Mackerras)
-- add undocumented function zError to convert error code to string
- (for Tim Smithers)
-- Allow compilation of gzio with -DNO_DEFLATE to avoid the compression code.
-- Use default memcpy for Symantec MSDOS compiler.
-- Add EXPORT keyword for check_func (needed for Windows DLL)
-- add current directory to LD_LIBRARY_PATH for "make test"
-- create also a link for libz.so.1
-- added support for FUJITSU UXP/DS (thanks to Toshiaki Nomura)
-- use $(SHAREDLIB) instead of libz.so in Makefile.in (for HPUX)
-- added -soname for Linux in configure (Chun-Chung Chen,
-- assign numbers to the exported functions in zlib.def (for Windows DLL)
-- add advice in zlib.h for best usage of deflateSetDictionary
-- work around compiler bug on Atari (cast Z_NULL in call of s->checkfn)
-- allow compilation with ANSI keywords only enabled for TurboC in large model
-- avoid "versionString"[0] (Borland bug)
-- add NEED_DUMMY_RETURN for Borland
-- use variable z_verbose for tracing in debug mode (L. Peter Deutsch).
-- allow compilation with CC
-- defined STDC for OS/2 (David Charlap)
-- limit external names to 8 chars for MVS (Thomas Lund)
-- in minigzip.c, use static buffers only for 16-bit systems
-- fix suffix check for "minigzip -d foo.gz"
-- do not return an error for the 2nd of two consecutive gzflush() (Felix Lee)
-- use _fdopen instead of fdopen for MSC >= 6.0 (Thomas Fanslau)
-- added makelcc.bat for lcc-win32 (Tom St Denis)
-- in Makefile.dj2, use copy and del instead of install and rm (Frank Donahoe)
-- Avoid expanded $Id$. Use "rcs -kb" or "cvs admin -kb" to avoid Id expansion.
-- check for unistd.h in configure (for off_t)
-- remove useless check parameter in inflate_blocks_free
-- avoid useless assignment of s->check to itself in inflate_blocks_new
-- do not flush twice in gzclose (thanks to Ken Raeburn)
-- rename FOPEN as F_OPEN to avoid clash with /usr/include/sys/file.h
-- use NO_ERRNO_H instead of enumeration of operating systems with errno.h
-- work around buggy fclose on pipes for HP/UX
-- support zlib DLL with BORLAND C++ 5.0 (thanks to Glenn Randers-Pehrson)
-- fix configure if CC is already equal to gcc
-
-Changes in 1.0.5 (3 Jan 98)
-- Fix inflate to terminate gracefully when fed corrupted or invalid data
-- Use const for rommable constants in inflate
-- Eliminate memory leaks on error conditions in inflate
-- Removed some vestigial code in inflate
-- Update web address in README
-
-Changes in 1.0.4 (24 Jul 96)
-- In very rare conditions, deflate(s, Z_FINISH) could fail to produce an EOF
- bit, so the decompressor could decompress all the correct data but went
- on to attempt decompressing extra garbage data. This affected minigzip too.
-- zlibVersion and gzerror return const char* (needed for DLL)
-- port to RISCOS (no fdopen, no multiple dots, no unlink, no fileno)
-- use z_error only for DEBUG (avoid problem with DLLs)
-
-Changes in 1.0.3 (2 Jul 96)
-- use z_streamp instead of z_stream *, which is now a far pointer in MSDOS
- small and medium models; this makes the library incompatible with previous
- versions for these models. (No effect in large model or on other systems.)
-- return OK instead of BUF_ERROR if previous deflate call returned with
- avail_out as zero but there is nothing to do
-- added memcmp for non STDC compilers
-- define NO_DUMMY_DECL for more Mac compilers (.h files merged incorrectly)
-- define __32BIT__ if __386__ or i386 is defined (pb. with Watcom and SCO)
-- better check for 16-bit mode MSC (avoids problem with Symantec)
-
-Changes in 1.0.2 (23 May 96)
-- added Windows DLL support
-- added a function zlibVersion (for the DLL support)
-- fixed declarations using Bytef in infutil.c (pb with MSDOS medium model)
-- Bytef is define's instead of typedef'd only for Borland C
-- avoid reading uninitialized memory in example.c
-- mention in README that the zlib format is now RFC1950
-- updated Makefile.dj2
-- added algorithm.doc
-
-Changes in 1.0.1 (20 May 96) [1.0 skipped to avoid confusion]
-- fix array overlay in deflate.c which sometimes caused bad compressed data
-- fix inflate bug with empty stored block
-- fix MSDOS medium model which was broken in 0.99
-- fix deflateParams() which could generated bad compressed data.
-- Bytef is define'd instead of typedef'ed (work around Borland bug)
-- added an INDEX file
-- new makefiles for DJGPP (Makefile.dj2), 32-bit Borland (Makefile.b32),
- Watcom (Makefile.wat), Amiga SAS/C (Makefile.sas)
-- speed up adler32 for modern machines without auto-increment
-- added -ansi for IRIX in configure
-- static_init_done in trees.c is an int
-- define unlink as delete for VMS
-- fix configure for QNX
-- add configure branch for SCO and HPUX
-- avoid many warnings (unused variables, dead assignments, etc...)
-- no fdopen for BeOS
-- fix the Watcom fix for 32 bit mode (define FAR as empty)
-- removed redefinition of Byte for MKWERKS
-- work around an MWKERKS bug (incorrect merge of all .h files)
-
-Changes in 0.99 (27 Jan 96)
-- allow preset dictionary shared between compressor and decompressor
-- allow compression level 0 (no compression)
-- add deflateParams in zlib.h: allow dynamic change of compression level
- and compression strategy.
-- test large buffers and deflateParams in example.c
-- add optional "configure" to build zlib as a shared library
-- suppress Makefile.qnx, use configure instead
-- fixed deflate for 64-bit systems (detected on Cray)
-- fixed inflate_blocks for 64-bit systems (detected on Alpha)
-- declare Z_DEFLATED in zlib.h (possible parameter for deflateInit2)
-- always return Z_BUF_ERROR when deflate() has nothing to do
-- deflateInit and inflateInit are now macros to allow version checking
-- prefix all global functions and types with z_ with -DZ_PREFIX
-- make falloc completely reentrant (inftrees.c)
-- fixed very unlikely race condition in ct_static_init
-- free in reverse order of allocation to help memory manager
-- use zlib-1.0/* instead of zlib/* inside the tar.gz
-- make zlib warning-free with "gcc -O3 -Wall -Wwrite-strings -Wpointer-arith
- -Wconversion -Wstrict-prototypes -Wmissing-prototypes"
-- allow gzread on concatenated .gz files
-- deflateEnd now returns Z_DATA_ERROR if it was premature
-- deflate is finally (?) fully deterministic (no matches beyond end of input)
-- Document Z_SYNC_FLUSH
-- add uninstall in Makefile
-- Check for __cpluplus in zlib.h
-- Better test in ct_align for partial flush
-- avoid harmless warnings for Borland C++
-- initialize hash_head in deflate.c
-- avoid warning on fdopen (gzio.c) for HP cc -Aa
-- include stdlib.h for STDC compilers
-- include errno.h for Cray
-- ignore error if ranlib doesn't exist
-- call ranlib twice for NeXTSTEP
-- use exec_prefix instead of prefix for libz.a
-- renamed ct_* as _tr_* to avoid conflict with applications
-- clear z->msg in inflateInit2 before any error return
-- initialize opaque in example.c, gzio.c, deflate.c and inflate.c
-- fixed typo in zconf.h (_GNUC__ => __GNUC__)
-- check for WIN32 in zconf.h and zutil.c (avoid farmalloc in 32-bit mode)
-- fix typo in Make_vms.com (f$trnlnm -> f$getsyi)
-- in fcalloc, normalize pointer if size > 65520 bytes
-- don't use special fcalloc for 32 bit Borland C++
-- use STDC instead of __GO32__ to avoid redeclaring exit, calloc, etc...
-- use Z_BINARY instead of BINARY
-- document that gzclose after gzdopen will close the file
-- allow "a" as mode in gzopen.
-- fix error checking in gzread
-- allow skipping .gz extra-field on pipes
-- added reference to Perl interface in README
-- put the crc table in FAR data (I dislike more and more the medium model :)
-- added get_crc_table
-- added a dimension to all arrays (Borland C can't count).
-- workaround Borland C bug in declaration of inflate_codes_new & inflate_fast
-- guard against multiple inclusion of *.h (for precompiled header on Mac)
-- Watcom C pretends to be Microsoft C small model even in 32 bit mode.
-- don't use unsized arrays to avoid silly warnings by Visual C++:
- warning C4746: 'inflate_mask' : unsized array treated as '__far'
- (what's wrong with far data in far model?).
-- define enum out of inflate_blocks_state to allow compilation with C++
-
-Changes in 0.95 (16 Aug 95)
-- fix MSDOS small and medium model (now easier to adapt to any compiler)
-- inlined send_bits
-- fix the final (:-) bug for deflate with flush (output was correct but
- not completely flushed in rare occasions).
-- default window size is same for compression and decompression
- (it's now sufficient to set MAX_WBITS in zconf.h).
-- voidp -> voidpf and voidnp -> voidp (for consistency with other
- typedefs and because voidnp was not near in large model).
-
-Changes in 0.94 (13 Aug 95)
-- support MSDOS medium model
-- fix deflate with flush (could sometimes generate bad output)
-- fix deflateReset (zlib header was incorrectly suppressed)
-- added support for VMS
-- allow a compression level in gzopen()
-- gzflush now calls fflush
-- For deflate with flush, flush even if no more input is provided.
-- rename libgz.a as libz.a
-- avoid complex expression in infcodes.c triggering Turbo C bug
-- work around a problem with gcc on Alpha (in INSERT_STRING)
-- don't use inline functions (problem with some gcc versions)
-- allow renaming of Byte, uInt, etc... with #define.
-- avoid warning about (unused) pointer before start of array in deflate.c
-- avoid various warnings in gzio.c, example.c, infblock.c, adler32.c, zutil.c
-- avoid reserved word 'new' in trees.c
-
-Changes in 0.93 (25 June 95)
-- temporarily disable inline functions
-- make deflate deterministic
-- give enough lookahead for PARTIAL_FLUSH
-- Set binary mode for stdin/stdout in minigzip.c for OS/2
-- don't even use signed char in inflate (not portable enough)
-- fix inflate memory leak for segmented architectures
-
-Changes in 0.92 (3 May 95)
-- don't assume that char is signed (problem on SGI)
-- Clear bit buffer when starting a stored block
-- no memcpy on Pyramid
-- suppressed inftest.c
-- optimized fill_window, put longest_match inline for gcc
-- optimized inflate on stored blocks.
-- untabify all sources to simplify patches
-
-Changes in 0.91 (2 May 95)
-- Default MEM_LEVEL is 8 (not 9 for Unix) as documented in zlib.h
-- Document the memory requirements in zconf.h
-- added "make install"
-- fix sync search logic in inflateSync
-- deflate(Z_FULL_FLUSH) now works even if output buffer too short
-- after inflateSync, don't scare people with just "lo world"
-- added support for DJGPP
-
-Changes in 0.9 (1 May 95)
-- don't assume that zalloc clears the allocated memory (the TurboC bug
- was Mark's bug after all :)
-- let again gzread copy uncompressed data unchanged (was working in 0.71)
-- deflate(Z_FULL_FLUSH), inflateReset and inflateSync are now fully implemented
-- added a test of inflateSync in example.c
-- moved MAX_WBITS to zconf.h because users might want to change that.
-- document explicitly that zalloc(64K) on MSDOS must return a normalized
- pointer (zero offset)
-- added Makefiles for Microsoft C, Turbo C, Borland C++
-- faster crc32()
-
-Changes in 0.8 (29 April 95)
-- added fast inflate (inffast.c)
-- deflate(Z_FINISH) now returns Z_STREAM_END when done. Warning: this
- is incompatible with previous versions of zlib which returned Z_OK.
-- work around a TurboC compiler bug (bad code for b << 0, see infutil.h)
- (actually that was not a compiler bug, see 0.81 above)
-- gzread no longer reads one extra byte in certain cases
-- In gzio destroy(), don't reference a freed structure
-- avoid many warnings for MSDOS
-- avoid the ERROR symbol which is used by MS Windows
-
-Changes in 0.71 (14 April 95)
-- Fixed more MSDOS compilation problems :( There is still a bug with
- TurboC large model.
-
-Changes in 0.7 (14 April 95)
-- Added full inflate support.
-- Simplified the crc32() interface. The pre- and post-conditioning
- (one's complement) is now done inside crc32(). WARNING: this is
- incompatible with previous versions; see zlib.h for the new usage.
-
-Changes in 0.61 (12 April 95)
-- workaround for a bug in TurboC. example and minigzip now work on MSDOS.
-
-Changes in 0.6 (11 April 95)
-- added minigzip.c
-- added gzdopen to reopen a file descriptor as gzFile
-- added transparent reading of non-gziped files in gzread.
-- fixed bug in gzread (don't read crc as data)
-- fixed bug in destroy (gzio.c) (don't return Z_STREAM_END for gzclose).
-- don't allocate big arrays in the stack (for MSDOS)
-- fix some MSDOS compilation problems
-
-Changes in 0.5:
-- do real compression in deflate.c. Z_PARTIAL_FLUSH is supported but
- not yet Z_FULL_FLUSH.
-- support decompression but only in a single step (forced Z_FINISH)
-- added opaque object for zalloc and zfree.
-- added deflateReset and inflateReset
-- added a variable zlib_version for consistency checking.
-- renamed the 'filter' parameter of deflateInit2 as 'strategy'.
- Added Z_FILTERED and Z_HUFFMAN_ONLY constants.
-
-Changes in 0.4:
-- avoid "zip" everywhere, use zlib instead of ziplib.
-- suppress Z_BLOCK_FLUSH, interpret Z_PARTIAL_FLUSH as block flush
- if compression method == 8.
-- added adler32 and crc32
-- renamed deflateOptions as deflateInit2, call one or the other but not both
-- added the method parameter for deflateInit2.
-- added inflateInit2
-- simplied considerably deflateInit and inflateInit by not supporting
- user-provided history buffer. This is supported only in deflateInit2
- and inflateInit2.
-
-Changes in 0.3:
-- prefix all macro names with Z_
-- use Z_FINISH instead of deflateEnd to finish compression.
-- added Z_HUFFMAN_ONLY
-- added gzerror()
diff --git a/third-party/zlib/FAQ b/third-party/zlib/FAQ
deleted file mode 100644
index 99b7cf9..0000000
--- a/third-party/zlib/FAQ
+++ /dev/null
@@ -1,368 +0,0 @@
-
- Frequently Asked Questions about zlib
-
-
-If your question is not there, please check the zlib home page
-http://zlib.net/ which may have more recent information.
-The lastest zlib FAQ is at http://zlib.net/zlib_faq.html
-
-
- 1. Is zlib Y2K-compliant?
-
- Yes. zlib doesn't handle dates.
-
- 2. Where can I get a Windows DLL version?
-
- The zlib sources can be compiled without change to produce a DLL. See the
- file win32/DLL_FAQ.txt in the zlib distribution. Pointers to the
- precompiled DLL are found in the zlib web site at http://zlib.net/ .
-
- 3. Where can I get a Visual Basic interface to zlib?
-
- See
- * http://marknelson.us/1997/01/01/zlib-engine/
- * win32/DLL_FAQ.txt in the zlib distribution
-
- 4. compress() returns Z_BUF_ERROR.
-
- Make sure that before the call of compress(), the length of the compressed
- buffer is equal to the available size of the compressed buffer and not
- zero. For Visual Basic, check that this parameter is passed by reference
- ("as any"), not by value ("as long").
-
- 5. deflate() or inflate() returns Z_BUF_ERROR.
-
- Before making the call, make sure that avail_in and avail_out are not zero.
- When setting the parameter flush equal to Z_FINISH, also make sure that
- avail_out is big enough to allow processing all pending input. Note that a
- Z_BUF_ERROR is not fatal--another call to deflate() or inflate() can be
- made with more input or output space. A Z_BUF_ERROR may in fact be
- unavoidable depending on how the functions are used, since it is not
- possible to tell whether or not there is more output pending when
- strm.avail_out returns with zero. See http://zlib.net/zlib_how.html for a
- heavily annotated example.
-
- 6. Where's the zlib documentation (man pages, etc.)?
-
- It's in zlib.h . Examples of zlib usage are in the files test/example.c
- and test/minigzip.c, with more in examples/ .
-
- 7. Why don't you use GNU autoconf or libtool or ...?
-
- Because we would like to keep zlib as a very small and simple package.
- zlib is rather portable and doesn't need much configuration.
-
- 8. I found a bug in zlib.
-
- Most of the time, such problems are due to an incorrect usage of zlib.
- Please try to reproduce the problem with a small program and send the
- corresponding source to us at zlib at gzip.org . Do not send multi-megabyte
- data files without prior agreement.
-
- 9. Why do I get "undefined reference to gzputc"?
-
- If "make test" produces something like
-
- example.o(.text+0x154): undefined reference to `gzputc'
-
- check that you don't have old files libz.* in /usr/lib, /usr/local/lib or
- /usr/X11R6/lib. Remove any old versions, then do "make install".
-
-10. I need a Delphi interface to zlib.
-
- See the contrib/delphi directory in the zlib distribution.
-
-11. Can zlib handle .zip archives?
-
- Not by itself, no. See the directory contrib/minizip in the zlib
- distribution.
-
-12. Can zlib handle .Z files?
-
- No, sorry. You have to spawn an uncompress or gunzip subprocess, or adapt
- the code of uncompress on your own.
-
-13. How can I make a Unix shared library?
-
- By default a shared (and a static) library is built for Unix. So:
-
- make distclean
- ./configure
- make
-
-14. How do I install a shared zlib library on Unix?
-
- After the above, then:
-
- make install
-
- However, many flavors of Unix come with a shared zlib already installed.
- Before going to the trouble of compiling a shared version of zlib and
- trying to install it, you may want to check if it's already there! If you
- can #include <zlib.h>, it's there. The -lz option will probably link to
- it. You can check the version at the top of zlib.h or with the
- ZLIB_VERSION symbol defined in zlib.h .
-
-15. I have a question about OttoPDF.
-
- We are not the authors of OttoPDF. The real author is on the OttoPDF web
- site: Joel Hainley, jhainley at myndkryme.com.
-
-16. Can zlib decode Flate data in an Adobe PDF file?
-
- Yes. See http://www.pdflib.com/ . To modify PDF forms, see
- http://sourceforge.net/projects/acroformtool/ .
-
-17. Why am I getting this "register_frame_info not found" error on Solaris?
-
- After installing zlib 1.1.4 on Solaris 2.6, running applications using zlib
- generates an error such as:
-
- ld.so.1: rpm: fatal: relocation error: file /usr/local/lib/libz.so:
- symbol __register_frame_info: referenced symbol not found
-
- The symbol __register_frame_info is not part of zlib, it is generated by
- the C compiler (cc or gcc). You must recompile applications using zlib
- which have this problem. This problem is specific to Solaris. See
- http://www.sunfreeware.com for Solaris versions of zlib and applications
- using zlib.
-
-18. Why does gzip give an error on a file I make with compress/deflate?
-
- The compress and deflate functions produce data in the zlib format, which
- is different and incompatible with the gzip format. The gz* functions in
- zlib on the other hand use the gzip format. Both the zlib and gzip formats
- use the same compressed data format internally, but have different headers
- and trailers around the compressed data.
-
-19. Ok, so why are there two different formats?
-
- The gzip format was designed to retain the directory information about a
- single file, such as the name and last modification date. The zlib format
- on the other hand was designed for in-memory and communication channel
- applications, and has a much more compact header and trailer and uses a
- faster integrity check than gzip.
-
-20. Well that's nice, but how do I make a gzip file in memory?
-
- You can request that deflate write the gzip format instead of the zlib
- format using deflateInit2(). You can also request that inflate decode the
- gzip format using inflateInit2(). Read zlib.h for more details.
-
-21. Is zlib thread-safe?
-
- Yes. However any library routines that zlib uses and any application-
- provided memory allocation routines must also be thread-safe. zlib's gz*
- functions use stdio library routines, and most of zlib's functions use the
- library memory allocation routines by default. zlib's *Init* functions
- allow for the application to provide custom memory allocation routines.
-
- Of course, you should only operate on any given zlib or gzip stream from a
- single thread at a time.
-
-22. Can I use zlib in my commercial application?
-
- Yes. Please read the license in zlib.h.
-
-23. Is zlib under the GNU license?
-
- No. Please read the license in zlib.h.
-
-24. The license says that altered source versions must be "plainly marked". So
- what exactly do I need to do to meet that requirement?
-
- You need to change the ZLIB_VERSION and ZLIB_VERNUM #defines in zlib.h. In
- particular, the final version number needs to be changed to "f", and an
- identification string should be appended to ZLIB_VERSION. Version numbers
- x.x.x.f are reserved for modifications to zlib by others than the zlib
- maintainers. For example, if the version of the base zlib you are altering
- is "1.2.3.4", then in zlib.h you should change ZLIB_VERNUM to 0x123f, and
- ZLIB_VERSION to something like "1.2.3.f-zachary-mods-v3". You can also
- update the version strings in deflate.c and inftrees.c.
-
- For altered source distributions, you should also note the origin and
- nature of the changes in zlib.h, as well as in ChangeLog and README, along
- with the dates of the alterations. The origin should include at least your
- name (or your company's name), and an email address to contact for help or
- issues with the library.
-
- Note that distributing a compiled zlib library along with zlib.h and
- zconf.h is also a source distribution, and so you should change
- ZLIB_VERSION and ZLIB_VERNUM and note the origin and nature of the changes
- in zlib.h as you would for a full source distribution.
-
-25. Will zlib work on a big-endian or little-endian architecture, and can I
- exchange compressed data between them?
-
- Yes and yes.
-
-26. Will zlib work on a 64-bit machine?
-
- Yes. It has been tested on 64-bit machines, and has no dependence on any
- data types being limited to 32-bits in length. If you have any
- difficulties, please provide a complete problem report to zlib at gzip.org
-
-27. Will zlib decompress data from the PKWare Data Compression Library?
-
- No. The PKWare DCL uses a completely different compressed data format than
- does PKZIP and zlib. However, you can look in zlib's contrib/blast
- directory for a possible solution to your problem.
-
-28. Can I access data randomly in a compressed stream?
-
- No, not without some preparation. If when compressing you periodically use
- Z_FULL_FLUSH, carefully write all the pending data at those points, and
- keep an index of those locations, then you can start decompression at those
- points. You have to be careful to not use Z_FULL_FLUSH too often, since it
- can significantly degrade compression. Alternatively, you can scan a
- deflate stream once to generate an index, and then use that index for
- random access. See examples/zran.c .
-
-29. Does zlib work on MVS, OS/390, CICS, etc.?
-
- It has in the past, but we have not heard of any recent evidence. There
- were working ports of zlib 1.1.4 to MVS, but those links no longer work.
- If you know of recent, successful applications of zlib on these operating
- systems, please let us know. Thanks.
-
-30. Is there some simpler, easier to read version of inflate I can look at to
- understand the deflate format?
-
- First off, you should read RFC 1951. Second, yes. Look in zlib's
- contrib/puff directory.
-
-31. Does zlib infringe on any patents?
-
- As far as we know, no. In fact, that was originally the whole point behind
- zlib. Look here for some more information:
-
- http://www.gzip.org/#faq11
-
-32. Can zlib work with greater than 4 GB of data?
-
- Yes. inflate() and deflate() will process any amount of data correctly.
- Each call of inflate() or deflate() is limited to input and output chunks
- of the maximum value that can be stored in the compiler's "unsigned int"
- type, but there is no limit to the number of chunks. Note however that the
- strm.total_in and strm_total_out counters may be limited to 4 GB. These
- counters are provided as a convenience and are not used internally by
- inflate() or deflate(). The application can easily set up its own counters
- updated after each call of inflate() or deflate() to count beyond 4 GB.
- compress() and uncompress() may be limited to 4 GB, since they operate in a
- single call. gzseek() and gztell() may be limited to 4 GB depending on how
- zlib is compiled. See the zlibCompileFlags() function in zlib.h.
-
- The word "may" appears several times above since there is a 4 GB limit only
- if the compiler's "long" type is 32 bits. If the compiler's "long" type is
- 64 bits, then the limit is 16 exabytes.
-
-33. Does zlib have any security vulnerabilities?
-
- The only one that we are aware of is potentially in gzprintf(). If zlib is
- compiled to use sprintf() or vsprintf(), then there is no protection
- against a buffer overflow of an 8K string space (or other value as set by
- gzbuffer()), other than the caller of gzprintf() assuring that the output
- will not exceed 8K. On the other hand, if zlib is compiled to use
- snprintf() or vsnprintf(), which should normally be the case, then there is
- no vulnerability. The ./configure script will display warnings if an
- insecure variation of sprintf() will be used by gzprintf(). Also the
- zlibCompileFlags() function will return information on what variant of
- sprintf() is used by gzprintf().
-
- If you don't have snprintf() or vsnprintf() and would like one, you can
- find a portable implementation here:
-
- http://www.ijs.si/software/snprintf/
-
- Note that you should be using the most recent version of zlib. Versions
- 1.1.3 and before were subject to a double-free vulnerability, and versions
- 1.2.1 and 1.2.2 were subject to an access exception when decompressing
- invalid compressed data.
-
-34. Is there a Java version of zlib?
-
- Probably what you want is to use zlib in Java. zlib is already included
- as part of the Java SDK in the java.util.zip package. If you really want
- a version of zlib written in the Java language, look on the zlib home
- page for links: http://zlib.net/ .
-
-35. I get this or that compiler or source-code scanner warning when I crank it
- up to maximally-pedantic. Can't you guys write proper code?
-
- Many years ago, we gave up attempting to avoid warnings on every compiler
- in the universe. It just got to be a waste of time, and some compilers
- were downright silly as well as contradicted each other. So now, we simply
- make sure that the code always works.
-
-36. Valgrind (or some similar memory access checker) says that deflate is
- performing a conditional jump that depends on an uninitialized value.
- Isn't that a bug?
-
- No. That is intentional for performance reasons, and the output of deflate
- is not affected. This only started showing up recently since zlib 1.2.x
- uses malloc() by default for allocations, whereas earlier versions used
- calloc(), which zeros out the allocated memory. Even though the code was
- correct, versions 1.2.4 and later was changed to not stimulate these
- checkers.
-
-37. Will zlib read the (insert any ancient or arcane format here) compressed
- data format?
-
- Probably not. Look in the comp.compression FAQ for pointers to various
- formats and associated software.
-
-38. How can I encrypt/decrypt zip files with zlib?
-
- zlib doesn't support encryption. The original PKZIP encryption is very
- weak and can be broken with freely available programs. To get strong
- encryption, use GnuPG, http://www.gnupg.org/ , which already includes zlib
- compression. For PKZIP compatible "encryption", look at
- http://www.info-zip.org/
-
-39. What's the difference between the "gzip" and "deflate" HTTP 1.1 encodings?
-
- "gzip" is the gzip format, and "deflate" is the zlib format. They should
- probably have called the second one "zlib" instead to avoid confusion with
- the raw deflate compressed data format. While the HTTP 1.1 RFC 2616
- correctly points to the zlib specification in RFC 1950 for the "deflate"
- transfer encoding, there have been reports of servers and browsers that
- incorrectly produce or expect raw deflate data per the deflate
- specification in RFC 1951, most notably Microsoft. So even though the
- "deflate" transfer encoding using the zlib format would be the more
- efficient approach (and in fact exactly what the zlib format was designed
- for), using the "gzip" transfer encoding is probably more reliable due to
- an unfortunate choice of name on the part of the HTTP 1.1 authors.
-
- Bottom line: use the gzip format for HTTP 1.1 encoding.
-
-40. Does zlib support the new "Deflate64" format introduced by PKWare?
-
- No. PKWare has apparently decided to keep that format proprietary, since
- they have not documented it as they have previous compression formats. In
- any case, the compression improvements are so modest compared to other more
- modern approaches, that it's not worth the effort to implement.
-
-41. I'm having a problem with the zip functions in zlib, can you help?
-
- There are no zip functions in zlib. You are probably using minizip by
- Giles Vollant, which is found in the contrib directory of zlib. It is not
- part of zlib. In fact none of the stuff in contrib is part of zlib. The
- files in there are not supported by the zlib authors. You need to contact
- the authors of the respective contribution for help.
-
-42. The match.asm code in contrib is under the GNU General Public License.
- Since it's part of zlib, doesn't that mean that all of zlib falls under the
- GNU GPL?
-
- No. The files in contrib are not part of zlib. They were contributed by
- other authors and are provided as a convenience to the user within the zlib
- distribution. Each item in contrib has its own license.
-
-43. Is zlib subject to export controls? What is its ECCN?
-
- zlib is not subject to export controls, and so is classified as EAR99.
-
-44. Can you please sign these lengthy legal documents and fax them back to us
- so that we can use your software in our product?
-
- No. Go away. Shoo.
diff --git a/third-party/zlib/INDEX b/third-party/zlib/INDEX
deleted file mode 100644
index 2ba0641..0000000
--- a/third-party/zlib/INDEX
+++ /dev/null
@@ -1,68 +0,0 @@
-CMakeLists.txt cmake build file
-ChangeLog history of changes
-FAQ Frequently Asked Questions about zlib
-INDEX this file
-Makefile dummy Makefile that tells you to ./configure
-Makefile.in template for Unix Makefile
-README guess what
-configure configure script for Unix
-make_vms.com makefile for VMS
-test/example.c zlib usages examples for build testing
-test/minigzip.c minimal gzip-like functionality for build testing
-test/infcover.c inf*.c code coverage for build coverage testing
-treebuild.xml XML description of source file dependencies
-zconf.h.cmakein zconf.h template for cmake
-zconf.h.in zconf.h template for configure
-zlib.3 Man page for zlib
-zlib.3.pdf Man page in PDF format
-zlib.map Linux symbol information
-zlib.pc.in Template for pkg-config descriptor
-zlib.pc.cmakein zlib.pc template for cmake
-zlib2ansi perl script to convert source files for C++ compilation
-
-amiga/ makefiles for Amiga SAS C
-as400/ makefiles for AS/400
-doc/ documentation for formats and algorithms
-msdos/ makefiles for MSDOS
-nintendods/ makefile for Nintendo DS
-old/ makefiles for various architectures and zlib documentation
- files that have not yet been updated for zlib 1.2.x
-qnx/ makefiles for QNX
-watcom/ makefiles for OpenWatcom
-win32/ makefiles for Windows
-
- zlib public header files (required for library use):
-zconf.h
-zlib.h
-
- private source files used to build the zlib library:
-adler32.c
-compress.c
-crc32.c
-crc32.h
-deflate.c
-deflate.h
-gzclose.c
-gzguts.h
-gzlib.c
-gzread.c
-gzwrite.c
-infback.c
-inffast.c
-inffast.h
-inffixed.h
-inflate.c
-inflate.h
-inftrees.c
-inftrees.h
-trees.c
-trees.h
-uncompr.c
-zutil.c
-zutil.h
-
- source files for sample programs
-See examples/README.examples
-
- unsupported contributions by third parties
-See contrib/README.contrib
diff --git a/third-party/zlib/Makefile.in b/third-party/zlib/Makefile.in
deleted file mode 100644
index c61aa30..0000000
--- a/third-party/zlib/Makefile.in
+++ /dev/null
@@ -1,288 +0,0 @@
-# Makefile for zlib
-# Copyright (C) 1995-2013 Jean-loup Gailly, Mark Adler
-# For conditions of distribution and use, see copyright notice in zlib.h
-
-# To compile and test, type:
-# ./configure; make test
-# Normally configure builds both a static and a shared library.
-# If you want to build just a static library, use: ./configure --static
-
-# To use the asm code, type:
-# cp contrib/asm?86/match.S ./match.S
-# make LOC=-DASMV OBJA=match.o
-
-# To install /usr/local/lib/libz.* and /usr/local/include/zlib.h, type:
-# make install
-# To install in $HOME instead of /usr/local, use:
-# make install prefix=$HOME
-
-CC=cc
-
-CFLAGS=-O
-#CFLAGS=-O -DMAX_WBITS=14 -DMAX_MEM_LEVEL=7
-#CFLAGS=-g -DDEBUG
-#CFLAGS=-O3 -Wall -Wwrite-strings -Wpointer-arith -Wconversion \
-# -Wstrict-prototypes -Wmissing-prototypes
-
-SFLAGS=-O
-LDFLAGS=
-TEST_LDFLAGS=-L. libz.a
-LDSHARED=$(CC)
-CPP=$(CC) -E
-
-STATICLIB=libz.a
-SHAREDLIB=libz.so
-SHAREDLIBV=libz.so.1.2.8
-SHAREDLIBM=libz.so.1
-LIBS=$(STATICLIB) $(SHAREDLIBV)
-
-AR=ar
-ARFLAGS=rc
-RANLIB=ranlib
-LDCONFIG=ldconfig
-LDSHAREDLIBC=-lc
-TAR=tar
-SHELL=/bin/sh
-EXE=
-
-prefix = /usr/local
-exec_prefix = ${prefix}
-libdir = ${exec_prefix}/lib
-sharedlibdir = ${libdir}
-includedir = ${prefix}/include
-mandir = ${prefix}/share/man
-man3dir = ${mandir}/man3
-pkgconfigdir = ${libdir}/pkgconfig
-
-OBJZ = adler32.o crc32.o deflate.o infback.o inffast.o inflate.o inftrees.o trees.o zutil.o
-OBJG = compress.o uncompr.o gzclose.o gzlib.o gzread.o gzwrite.o
-OBJC = $(OBJZ) $(OBJG)
-
-PIC_OBJZ = adler32.lo crc32.lo deflate.lo infback.lo inffast.lo inflate.lo inftrees.lo trees.lo zutil.lo
-PIC_OBJG = compress.lo uncompr.lo gzclose.lo gzlib.lo gzread.lo gzwrite.lo
-PIC_OBJC = $(PIC_OBJZ) $(PIC_OBJG)
-
-# to use the asm code: make OBJA=match.o, PIC_OBJA=match.lo
-OBJA =
-PIC_OBJA =
-
-OBJS = $(OBJC) $(OBJA)
-
-PIC_OBJS = $(PIC_OBJC) $(PIC_OBJA)
-
-all: static shared
-
-static: example$(EXE) minigzip$(EXE)
-
-shared: examplesh$(EXE) minigzipsh$(EXE)
-
-all64: example64$(EXE) minigzip64$(EXE)
-
-check: test
-
-test: all teststatic testshared
-
-teststatic: static
- @TMPST=tmpst_$$; \
- if echo hello world | ./minigzip | ./minigzip -d && ./example $$TMPST ; then \
- echo ' *** zlib test OK ***'; \
- else \
- echo ' *** zlib test FAILED ***'; false; \
- fi; \
- rm -f $$TMPST
-
-testshared: shared
- @LD_LIBRARY_PATH=`pwd`:$(LD_LIBRARY_PATH) ; export LD_LIBRARY_PATH; \
- LD_LIBRARYN32_PATH=`pwd`:$(LD_LIBRARYN32_PATH) ; export LD_LIBRARYN32_PATH; \
- DYLD_LIBRARY_PATH=`pwd`:$(DYLD_LIBRARY_PATH) ; export DYLD_LIBRARY_PATH; \
- SHLIB_PATH=`pwd`:$(SHLIB_PATH) ; export SHLIB_PATH; \
- TMPSH=tmpsh_$$; \
- if echo hello world | ./minigzipsh | ./minigzipsh -d && ./examplesh $$TMPSH; then \
- echo ' *** zlib shared test OK ***'; \
- else \
- echo ' *** zlib shared test FAILED ***'; false; \
- fi; \
- rm -f $$TMPSH
-
-test64: all64
- @TMP64=tmp64_$$; \
- if echo hello world | ./minigzip64 | ./minigzip64 -d && ./example64 $$TMP64; then \
- echo ' *** zlib 64-bit test OK ***'; \
- else \
- echo ' *** zlib 64-bit test FAILED ***'; false; \
- fi; \
- rm -f $$TMP64
-
-infcover.o: test/infcover.c zlib.h zconf.h
- $(CC) $(CFLAGS) -I. -c -o $@ test/infcover.c
-
-infcover: infcover.o libz.a
- $(CC) $(CFLAGS) -o $@ infcover.o libz.a
-
-cover: infcover
- rm -f *.gcda
- ./infcover
- gcov inf*.c
-
-libz.a: $(OBJS)
- $(AR) $(ARFLAGS) $@ $(OBJS)
- -@ ($(RANLIB) $@ || true) >/dev/null 2>&1
-
-match.o: match.S
- $(CPP) match.S > _match.s
- $(CC) -c _match.s
- mv _match.o match.o
- rm -f _match.s
-
-match.lo: match.S
- $(CPP) match.S > _match.s
- $(CC) -c -fPIC _match.s
- mv _match.o match.lo
- rm -f _match.s
-
-example.o: test/example.c zlib.h zconf.h
- $(CC) $(CFLAGS) -I. -c -o $@ test/example.c
-
-minigzip.o: test/minigzip.c zlib.h zconf.h
- $(CC) $(CFLAGS) -I. -c -o $@ test/minigzip.c
-
-example64.o: test/example.c zlib.h zconf.h
- $(CC) $(CFLAGS) -I. -D_FILE_OFFSET_BITS=64 -c -o $@ test/example.c
-
-minigzip64.o: test/minigzip.c zlib.h zconf.h
- $(CC) $(CFLAGS) -I. -D_FILE_OFFSET_BITS=64 -c -o $@ test/minigzip.c
-
-.SUFFIXES: .lo
-
-.c.lo:
- - at mkdir objs 2>/dev/null || test -d objs
- $(CC) $(SFLAGS) -DPIC -c -o objs/$*.o $<
- - at mv objs/$*.o $@
-
-placebo $(SHAREDLIBV): $(PIC_OBJS) libz.a
- $(LDSHARED) $(SFLAGS) -o $@ $(PIC_OBJS) $(LDSHAREDLIBC) $(LDFLAGS)
- rm -f $(SHAREDLIB) $(SHAREDLIBM)
- ln -s $@ $(SHAREDLIB)
- ln -s $@ $(SHAREDLIBM)
- - at rmdir objs
-
-example$(EXE): example.o $(STATICLIB)
- $(CC) $(CFLAGS) -o $@ example.o $(TEST_LDFLAGS)
-
-minigzip$(EXE): minigzip.o $(STATICLIB)
- $(CC) $(CFLAGS) -o $@ minigzip.o $(TEST_LDFLAGS)
-
-examplesh$(EXE): example.o $(SHAREDLIBV)
- $(CC) $(CFLAGS) -o $@ example.o -L. $(SHAREDLIBV)
-
-minigzipsh$(EXE): minigzip.o $(SHAREDLIBV)
- $(CC) $(CFLAGS) -o $@ minigzip.o -L. $(SHAREDLIBV)
-
-example64$(EXE): example64.o $(STATICLIB)
- $(CC) $(CFLAGS) -o $@ example64.o $(TEST_LDFLAGS)
-
-minigzip64$(EXE): minigzip64.o $(STATICLIB)
- $(CC) $(CFLAGS) -o $@ minigzip64.o $(TEST_LDFLAGS)
-
-install-libs: $(LIBS)
- - at if [ ! -d $(DESTDIR)$(exec_prefix) ]; then mkdir -p $(DESTDIR)$(exec_prefix); fi
- - at if [ ! -d $(DESTDIR)$(libdir) ]; then mkdir -p $(DESTDIR)$(libdir); fi
- - at if [ ! -d $(DESTDIR)$(sharedlibdir) ]; then mkdir -p $(DESTDIR)$(sharedlibdir); fi
- - at if [ ! -d $(DESTDIR)$(man3dir) ]; then mkdir -p $(DESTDIR)$(man3dir); fi
- - at if [ ! -d $(DESTDIR)$(pkgconfigdir) ]; then mkdir -p $(DESTDIR)$(pkgconfigdir); fi
- cp $(STATICLIB) $(DESTDIR)$(libdir)
- chmod 644 $(DESTDIR)$(libdir)/$(STATICLIB)
- -@($(RANLIB) $(DESTDIR)$(libdir)/libz.a || true) >/dev/null 2>&1
- - at if test -n "$(SHAREDLIBV)"; then \
- cp $(SHAREDLIBV) $(DESTDIR)$(sharedlibdir); \
- echo "cp $(SHAREDLIBV) $(DESTDIR)$(sharedlibdir)"; \
- chmod 755 $(DESTDIR)$(sharedlibdir)/$(SHAREDLIBV); \
- echo "chmod 755 $(DESTDIR)$(sharedlibdir)/$(SHAREDLIBV)"; \
- rm -f $(DESTDIR)$(sharedlibdir)/$(SHAREDLIB) $(DESTDIR)$(sharedlibdir)/$(SHAREDLIBM); \
- ln -s $(SHAREDLIBV) $(DESTDIR)$(sharedlibdir)/$(SHAREDLIB); \
- ln -s $(SHAREDLIBV) $(DESTDIR)$(sharedlibdir)/$(SHAREDLIBM); \
- ($(LDCONFIG) || true) >/dev/null 2>&1; \
- fi
- cp zlib.3 $(DESTDIR)$(man3dir)
- chmod 644 $(DESTDIR)$(man3dir)/zlib.3
- cp zlib.pc $(DESTDIR)$(pkgconfigdir)
- chmod 644 $(DESTDIR)$(pkgconfigdir)/zlib.pc
-# The ranlib in install is needed on NeXTSTEP which checks file times
-# ldconfig is for Linux
-
-install: install-libs
- - at if [ ! -d $(DESTDIR)$(includedir) ]; then mkdir -p $(DESTDIR)$(includedir); fi
- cp zlib.h zconf.h $(DESTDIR)$(includedir)
- chmod 644 $(DESTDIR)$(includedir)/zlib.h $(DESTDIR)$(includedir)/zconf.h
-
-uninstall:
- cd $(DESTDIR)$(includedir) && rm -f zlib.h zconf.h
- cd $(DESTDIR)$(libdir) && rm -f libz.a; \
- if test -n "$(SHAREDLIBV)" -a -f $(SHAREDLIBV); then \
- rm -f $(SHAREDLIBV) $(SHAREDLIB) $(SHAREDLIBM); \
- fi
- cd $(DESTDIR)$(man3dir) && rm -f zlib.3
- cd $(DESTDIR)$(pkgconfigdir) && rm -f zlib.pc
-
-docs: zlib.3.pdf
-
-zlib.3.pdf: zlib.3
- groff -mandoc -f H -T ps zlib.3 | ps2pdf - zlib.3.pdf
-
-zconf.h.cmakein: zconf.h.in
- -@ TEMPFILE=zconfh_$$; \
- echo "/#define ZCONF_H/ a\\\\\n#cmakedefine Z_PREFIX\\\\\n#cmakedefine Z_HAVE_UNISTD_H\n" >> $$TEMPFILE &&\
- sed -f $$TEMPFILE zconf.h.in > zconf.h.cmakein &&\
- touch -r zconf.h.in zconf.h.cmakein &&\
- rm $$TEMPFILE
-
-zconf: zconf.h.in
- cp -p zconf.h.in zconf.h
-
-mostlyclean: clean
-clean:
- rm -f *.o *.lo *~ \
- example$(EXE) minigzip$(EXE) examplesh$(EXE) minigzipsh$(EXE) \
- example64$(EXE) minigzip64$(EXE) \
- infcover \
- libz.* foo.gz so_locations \
- _match.s maketree contrib/infback9/*.o
- rm -rf objs
- rm -f *.gcda *.gcno *.gcov
- rm -f contrib/infback9/*.gcda contrib/infback9/*.gcno contrib/infback9/*.gcov
-
-maintainer-clean: distclean
-distclean: clean zconf zconf.h.cmakein docs
- rm -f Makefile zlib.pc configure.log
- - at rm -f .DS_Store
- - at printf 'all:\n\t- at echo "Please use ./configure first. Thank you."\n' > Makefile
- - at printf '\ndistclean:\n\tmake -f Makefile.in distclean\n' >> Makefile
- - at touch -r Makefile.in Makefile
-
-tags:
- etags *.[ch]
-
-depend:
- makedepend -- $(CFLAGS) -- *.[ch]
-
-# DO NOT DELETE THIS LINE -- make depend depends on it.
-
-adler32.o zutil.o: zutil.h zlib.h zconf.h
-gzclose.o gzlib.o gzread.o gzwrite.o: zlib.h zconf.h gzguts.h
-compress.o example.o minigzip.o uncompr.o: zlib.h zconf.h
-crc32.o: zutil.h zlib.h zconf.h crc32.h
-deflate.o: deflate.h zutil.h zlib.h zconf.h
-infback.o inflate.o: zutil.h zlib.h zconf.h inftrees.h inflate.h inffast.h inffixed.h
-inffast.o: zutil.h zlib.h zconf.h inftrees.h inflate.h inffast.h
-inftrees.o: zutil.h zlib.h zconf.h inftrees.h
-trees.o: deflate.h zutil.h zlib.h zconf.h trees.h
-
-adler32.lo zutil.lo: zutil.h zlib.h zconf.h
-gzclose.lo gzlib.lo gzread.lo gzwrite.lo: zlib.h zconf.h gzguts.h
-compress.lo example.lo minigzip.lo uncompr.lo: zlib.h zconf.h
-crc32.lo: zutil.h zlib.h zconf.h crc32.h
-deflate.lo: deflate.h zutil.h zlib.h zconf.h
-infback.lo inflate.lo: zutil.h zlib.h zconf.h inftrees.h inflate.h inffast.h inffixed.h
-inffast.lo: zutil.h zlib.h zconf.h inftrees.h inflate.h inffast.h
-inftrees.lo: zutil.h zlib.h zconf.h inftrees.h
-trees.lo: deflate.h zutil.h zlib.h zconf.h trees.h
diff --git a/third-party/zlib/Makefile.pic b/third-party/zlib/Makefile.pic
deleted file mode 100644
index 1d4d914..0000000
--- a/third-party/zlib/Makefile.pic
+++ /dev/null
@@ -1,3 +0,0 @@
-include Makefile
-
-PIC: $(PIC_OBJS)
diff --git a/third-party/zlib/README b/third-party/zlib/README
deleted file mode 100644
index 5ca9d12..0000000
--- a/third-party/zlib/README
+++ /dev/null
@@ -1,115 +0,0 @@
-ZLIB DATA COMPRESSION LIBRARY
-
-zlib 1.2.8 is a general purpose data compression library. All the code is
-thread safe. The data format used by the zlib library is described by RFCs
-(Request for Comments) 1950 to 1952 in the files
-http://tools.ietf.org/html/rfc1950 (zlib format), rfc1951 (deflate format) and
-rfc1952 (gzip format).
-
-All functions of the compression library are documented in the file zlib.h
-(volunteer to write man pages welcome, contact zlib at gzip.org). A usage example
-of the library is given in the file test/example.c which also tests that
-the library is working correctly. Another example is given in the file
-test/minigzip.c. The compression library itself is composed of all source
-files in the root directory.
-
-To compile all files and run the test program, follow the instructions given at
-the top of Makefile.in. In short "./configure; make test", and if that goes
-well, "make install" should work for most flavors of Unix. For Windows, use
-one of the special makefiles in win32/ or contrib/vstudio/ . For VMS, use
-make_vms.com.
-
-Questions about zlib should be sent to <zlib at gzip.org>, or to Gilles Vollant
-<info at winimage.com> for the Windows DLL version. The zlib home page is
-http://zlib.net/ . Before reporting a problem, please check this site to
-verify that you have the latest version of zlib; otherwise get the latest
-version and check whether the problem still exists or not.
-
-PLEASE read the zlib FAQ http://zlib.net/zlib_faq.html before asking for help.
-
-Mark Nelson <markn at ieee.org> wrote an article about zlib for the Jan. 1997
-issue of Dr. Dobb's Journal; a copy of the article is available at
-http://marknelson.us/1997/01/01/zlib-engine/ .
-
-The changes made in version 1.2.8 are documented in the file ChangeLog.
-
-Unsupported third party contributions are provided in directory contrib/ .
-
-zlib is available in Java using the java.util.zip package, documented at
-http://java.sun.com/developer/technicalArticles/Programming/compression/ .
-
-A Perl interface to zlib written by Paul Marquess <pmqs at cpan.org> is available
-at CPAN (Comprehensive Perl Archive Network) sites, including
-http://search.cpan.org/~pmqs/IO-Compress-Zlib/ .
-
-A Python interface to zlib written by A.M. Kuchling <amk at amk.ca> is
-available in Python 1.5 and later versions, see
-http://docs.python.org/library/zlib.html .
-
-zlib is built into tcl: http://wiki.tcl.tk/4610 .
-
-An experimental package to read and write files in .zip format, written on top
-of zlib by Gilles Vollant <info at winimage.com>, is available in the
-contrib/minizip directory of zlib.
-
-
-Notes for some targets:
-
-- For Windows DLL versions, please see win32/DLL_FAQ.txt
-
-- For 64-bit Irix, deflate.c must be compiled without any optimization. With
- -O, one libpng test fails. The test works in 32 bit mode (with the -n32
- compiler flag). The compiler bug has been reported to SGI.
-
-- zlib doesn't work with gcc 2.6.3 on a DEC 3000/300LX under OSF/1 2.1 it works
- when compiled with cc.
-
-- On Digital Unix 4.0D (formely OSF/1) on AlphaServer, the cc option -std1 is
- necessary to get gzprintf working correctly. This is done by configure.
-
-- zlib doesn't work on HP-UX 9.05 with some versions of /bin/cc. It works with
- other compilers. Use "make test" to check your compiler.
-
-- gzdopen is not supported on RISCOS or BEOS.
-
-- For PalmOs, see http://palmzlib.sourceforge.net/
-
-
-Acknowledgments:
-
- The deflate format used by zlib was defined by Phil Katz. The deflate and
- zlib specifications were written by L. Peter Deutsch. Thanks to all the
- people who reported problems and suggested various improvements in zlib; they
- are too numerous to cite here.
-
-Copyright notice:
-
- (C) 1995-2013 Jean-loup Gailly and Mark Adler
-
- This software is provided 'as-is', without any express or implied
- warranty. In no event will the authors be held liable for any damages
- arising from the use of this software.
-
- Permission is granted to anyone to use this software for any purpose,
- including commercial applications, and to alter it and redistribute it
- freely, subject to the following restrictions:
-
- 1. The origin of this software must not be misrepresented; you must not
- claim that you wrote the original software. If you use this software
- in a product, an acknowledgment in the product documentation would be
- appreciated but is not required.
- 2. Altered source versions must be plainly marked as such, and must not be
- misrepresented as being the original software.
- 3. This notice may not be removed or altered from any source distribution.
-
- Jean-loup Gailly Mark Adler
- jloup at gzip.org madler at alumni.caltech.edu
-
-If you use the zlib library in a product, we would appreciate *not* receiving
-lengthy legal documents to sign. The sources are provided for free but without
-warranty of any kind. The library has been entirely written by Jean-loup
-Gailly and Mark Adler; it does not include third-party code.
-
-If you redistribute modified sources, we would appreciate that you include in
-the file ChangeLog history information documenting your changes. Please read
-the FAQ for more information on the distribution of modified source versions.
diff --git a/third-party/zlib/adler32.c b/third-party/zlib/adler32.c
deleted file mode 100644
index a868f07..0000000
--- a/third-party/zlib/adler32.c
+++ /dev/null
@@ -1,179 +0,0 @@
-/* adler32.c -- compute the Adler-32 checksum of a data stream
- * Copyright (C) 1995-2011 Mark Adler
- * For conditions of distribution and use, see copyright notice in zlib.h
- */
-
-/* @(#) $Id$ */
-
-#include "zutil.h"
-
-#define local static
-
-local uLong adler32_combine_ OF((uLong adler1, uLong adler2, z_off64_t len2));
-
-#define BASE 65521 /* largest prime smaller than 65536 */
-#define NMAX 5552
-/* NMAX is the largest n such that 255n(n+1)/2 + (n+1)(BASE-1) <= 2^32-1 */
-
-#define DO1(buf,i) {adler += (buf)[i]; sum2 += adler;}
-#define DO2(buf,i) DO1(buf,i); DO1(buf,i+1);
-#define DO4(buf,i) DO2(buf,i); DO2(buf,i+2);
-#define DO8(buf,i) DO4(buf,i); DO4(buf,i+4);
-#define DO16(buf) DO8(buf,0); DO8(buf,8);
-
-/* use NO_DIVIDE if your processor does not do division in hardware --
- try it both ways to see which is faster */
-#ifdef NO_DIVIDE
-/* note that this assumes BASE is 65521, where 65536 % 65521 == 15
- (thank you to John Reiser for pointing this out) */
-# define CHOP(a) \
- do { \
- unsigned long tmp = a >> 16; \
- a &= 0xffffUL; \
- a += (tmp << 4) - tmp; \
- } while (0)
-# define MOD28(a) \
- do { \
- CHOP(a); \
- if (a >= BASE) a -= BASE; \
- } while (0)
-# define MOD(a) \
- do { \
- CHOP(a); \
- MOD28(a); \
- } while (0)
-# define MOD63(a) \
- do { /* this assumes a is not negative */ \
- z_off64_t tmp = a >> 32; \
- a &= 0xffffffffL; \
- a += (tmp << 8) - (tmp << 5) + tmp; \
- tmp = a >> 16; \
- a &= 0xffffL; \
- a += (tmp << 4) - tmp; \
- tmp = a >> 16; \
- a &= 0xffffL; \
- a += (tmp << 4) - tmp; \
- if (a >= BASE) a -= BASE; \
- } while (0)
-#else
-# define MOD(a) a %= BASE
-# define MOD28(a) a %= BASE
-# define MOD63(a) a %= BASE
-#endif
-
-/* ========================================================================= */
-uLong ZEXPORT adler32(adler, buf, len)
- uLong adler;
- const Bytef *buf;
- uInt len;
-{
- unsigned long sum2;
- unsigned n;
-
- /* split Adler-32 into component sums */
- sum2 = (adler >> 16) & 0xffff;
- adler &= 0xffff;
-
- /* in case user likes doing a byte at a time, keep it fast */
- if (len == 1) {
- adler += buf[0];
- if (adler >= BASE)
- adler -= BASE;
- sum2 += adler;
- if (sum2 >= BASE)
- sum2 -= BASE;
- return adler | (sum2 << 16);
- }
-
- /* initial Adler-32 value (deferred check for len == 1 speed) */
- if (buf == Z_NULL)
- return 1L;
-
- /* in case short lengths are provided, keep it somewhat fast */
- if (len < 16) {
- while (len--) {
- adler += *buf++;
- sum2 += adler;
- }
- if (adler >= BASE)
- adler -= BASE;
- MOD28(sum2); /* only added so many BASE's */
- return adler | (sum2 << 16);
- }
-
- /* do length NMAX blocks -- requires just one modulo operation */
- while (len >= NMAX) {
- len -= NMAX;
- n = NMAX / 16; /* NMAX is divisible by 16 */
- do {
- DO16(buf); /* 16 sums unrolled */
- buf += 16;
- } while (--n);
- MOD(adler);
- MOD(sum2);
- }
-
- /* do remaining bytes (less than NMAX, still just one modulo) */
- if (len) { /* avoid modulos if none remaining */
- while (len >= 16) {
- len -= 16;
- DO16(buf);
- buf += 16;
- }
- while (len--) {
- adler += *buf++;
- sum2 += adler;
- }
- MOD(adler);
- MOD(sum2);
- }
-
- /* return recombined sums */
- return adler | (sum2 << 16);
-}
-
-/* ========================================================================= */
-local uLong adler32_combine_(adler1, adler2, len2)
- uLong adler1;
- uLong adler2;
- z_off64_t len2;
-{
- unsigned long sum1;
- unsigned long sum2;
- unsigned rem;
-
- /* for negative len, return invalid adler32 as a clue for debugging */
- if (len2 < 0)
- return 0xffffffffUL;
-
- /* the derivation of this formula is left as an exercise for the reader */
- MOD63(len2); /* assumes len2 >= 0 */
- rem = (unsigned)len2;
- sum1 = adler1 & 0xffff;
- sum2 = rem * sum1;
- MOD(sum2);
- sum1 += (adler2 & 0xffff) + BASE - 1;
- sum2 += ((adler1 >> 16) & 0xffff) + ((adler2 >> 16) & 0xffff) + BASE - rem;
- if (sum1 >= BASE) sum1 -= BASE;
- if (sum1 >= BASE) sum1 -= BASE;
- if (sum2 >= (BASE << 1)) sum2 -= (BASE << 1);
- if (sum2 >= BASE) sum2 -= BASE;
- return sum1 | (sum2 << 16);
-}
-
-/* ========================================================================= */
-uLong ZEXPORT adler32_combine(adler1, adler2, len2)
- uLong adler1;
- uLong adler2;
- z_off_t len2;
-{
- return adler32_combine_(adler1, adler2, len2);
-}
-
-uLong ZEXPORT adler32_combine64(adler1, adler2, len2)
- uLong adler1;
- uLong adler2;
- z_off64_t len2;
-{
- return adler32_combine_(adler1, adler2, len2);
-}
diff --git a/third-party/zlib/amiga/Makefile.pup b/third-party/zlib/amiga/Makefile.pup
deleted file mode 100644
index 8940c12..0000000
--- a/third-party/zlib/amiga/Makefile.pup
+++ /dev/null
@@ -1,69 +0,0 @@
-# Amiga powerUP (TM) Makefile
-# makefile for libpng and SAS C V6.58/7.00 PPC compiler
-# Copyright (C) 1998 by Andreas R. Kleinert
-
-LIBNAME = libzip.a
-
-CC = scppc
-CFLAGS = NOSTKCHK NOSINT OPTIMIZE OPTGO OPTPEEP OPTINLOCAL OPTINL \
- OPTLOOP OPTRDEP=8 OPTDEP=8 OPTCOMP=8 NOVER
-AR = ppc-amigaos-ar cr
-RANLIB = ppc-amigaos-ranlib
-LD = ppc-amigaos-ld -r
-LDFLAGS = -o
-LDLIBS = LIB:scppc.a LIB:end.o
-RM = delete quiet
-
-OBJS = adler32.o compress.o crc32.o gzclose.o gzlib.o gzread.o gzwrite.o \
- uncompr.o deflate.o trees.o zutil.o inflate.o infback.o inftrees.o inffast.o
-
-TEST_OBJS = example.o minigzip.o
-
-all: example minigzip
-
-check: test
-test: all
- example
- echo hello world | minigzip | minigzip -d
-
-$(LIBNAME): $(OBJS)
- $(AR) $@ $(OBJS)
- -$(RANLIB) $@
-
-example: example.o $(LIBNAME)
- $(LD) $(LDFLAGS) $@ LIB:c_ppc.o $@.o $(LIBNAME) $(LDLIBS)
-
-minigzip: minigzip.o $(LIBNAME)
- $(LD) $(LDFLAGS) $@ LIB:c_ppc.o $@.o $(LIBNAME) $(LDLIBS)
-
-mostlyclean: clean
-clean:
- $(RM) *.o example minigzip $(LIBNAME) foo.gz
-
-zip:
- zip -ul9 zlib README ChangeLog Makefile Make????.??? Makefile.?? \
- descrip.mms *.[ch]
-
-tgz:
- cd ..; tar cfz zlib/zlib.tgz zlib/README zlib/ChangeLog zlib/Makefile \
- zlib/Make????.??? zlib/Makefile.?? zlib/descrip.mms zlib/*.[ch]
-
-# DO NOT DELETE THIS LINE -- make depend depends on it.
-
-adler32.o: zlib.h zconf.h
-compress.o: zlib.h zconf.h
-crc32.o: crc32.h zlib.h zconf.h
-deflate.o: deflate.h zutil.h zlib.h zconf.h
-example.o: zlib.h zconf.h
-gzclose.o: zlib.h zconf.h gzguts.h
-gzlib.o: zlib.h zconf.h gzguts.h
-gzread.o: zlib.h zconf.h gzguts.h
-gzwrite.o: zlib.h zconf.h gzguts.h
-inffast.o: zutil.h zlib.h zconf.h inftrees.h inflate.h inffast.h
-inflate.o: zutil.h zlib.h zconf.h inftrees.h inflate.h inffast.h
-infback.o: zutil.h zlib.h zconf.h inftrees.h inflate.h inffast.h
-inftrees.o: zutil.h zlib.h zconf.h inftrees.h
-minigzip.o: zlib.h zconf.h
-trees.o: deflate.h zutil.h zlib.h zconf.h trees.h
-uncompr.o: zlib.h zconf.h
-zutil.o: zutil.h zlib.h zconf.h
diff --git a/third-party/zlib/amiga/Makefile.sas b/third-party/zlib/amiga/Makefile.sas
deleted file mode 100644
index 749e291..0000000
--- a/third-party/zlib/amiga/Makefile.sas
+++ /dev/null
@@ -1,68 +0,0 @@
-# SMakefile for zlib
-# Modified from the standard UNIX Makefile Copyright Jean-loup Gailly
-# Osma Ahvenlampi <Osma.Ahvenlampi at hut.fi>
-# Amiga, SAS/C 6.56 & Smake
-
-CC=sc
-CFLAGS=OPT
-#CFLAGS=OPT CPU=68030
-#CFLAGS=DEBUG=LINE
-LDFLAGS=LIB z.lib
-
-SCOPTIONS=OPTSCHED OPTINLINE OPTALIAS OPTTIME OPTINLOCAL STRMERGE \
- NOICONS PARMS=BOTH NOSTACKCHECK UTILLIB NOVERSION ERRORREXX \
- DEF=POSTINC
-
-OBJS = adler32.o compress.o crc32.o gzclose.o gzlib.o gzread.o gzwrite.o \
- uncompr.o deflate.o trees.o zutil.o inflate.o infback.o inftrees.o inffast.o
-
-TEST_OBJS = example.o minigzip.o
-
-all: SCOPTIONS example minigzip
-
-check: test
-test: all
- example
- echo hello world | minigzip | minigzip -d
-
-install: z.lib
- copy clone zlib.h zconf.h INCLUDE:
- copy clone z.lib LIB:
-
-z.lib: $(OBJS)
- oml z.lib r $(OBJS)
-
-example: example.o z.lib
- $(CC) $(CFLAGS) LINK TO $@ example.o $(LDFLAGS)
-
-minigzip: minigzip.o z.lib
- $(CC) $(CFLAGS) LINK TO $@ minigzip.o $(LDFLAGS)
-
-mostlyclean: clean
-clean:
- -delete force quiet example minigzip *.o z.lib foo.gz *.lnk SCOPTIONS
-
-SCOPTIONS: Makefile.sas
- copy to $@ <from <
-$(SCOPTIONS)
-<
-
-# DO NOT DELETE THIS LINE -- make depend depends on it.
-
-adler32.o: zlib.h zconf.h
-compress.o: zlib.h zconf.h
-crc32.o: crc32.h zlib.h zconf.h
-deflate.o: deflate.h zutil.h zlib.h zconf.h
-example.o: zlib.h zconf.h
-gzclose.o: zlib.h zconf.h gzguts.h
-gzlib.o: zlib.h zconf.h gzguts.h
-gzread.o: zlib.h zconf.h gzguts.h
-gzwrite.o: zlib.h zconf.h gzguts.h
-inffast.o: zutil.h zlib.h zconf.h inftrees.h inflate.h inffast.h
-inflate.o: zutil.h zlib.h zconf.h inftrees.h inflate.h inffast.h
-infback.o: zutil.h zlib.h zconf.h inftrees.h inflate.h inffast.h
-inftrees.o: zutil.h zlib.h zconf.h inftrees.h
-minigzip.o: zlib.h zconf.h
-trees.o: deflate.h zutil.h zlib.h zconf.h trees.h
-uncompr.o: zlib.h zconf.h
-zutil.o: zutil.h zlib.h zconf.h
diff --git a/third-party/zlib/as400/bndsrc b/third-party/zlib/as400/bndsrc
deleted file mode 100644
index 98814fd..0000000
--- a/third-party/zlib/as400/bndsrc
+++ /dev/null
@@ -1,215 +0,0 @@
-STRPGMEXP PGMLVL(*CURRENT) SIGNATURE('ZLIB')
-
-/*@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@*/
-/* Version 1.1.3 entry points. */
-/*@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@*/
-
-/********************************************************************/
-/* *MODULE ADLER32 ZLIB 01/02/01 00:15:09 */
-/********************************************************************/
-
- EXPORT SYMBOL("adler32")
-
-/********************************************************************/
-/* *MODULE COMPRESS ZLIB 01/02/01 00:15:09 */
-/********************************************************************/
-
- EXPORT SYMBOL("compress")
- EXPORT SYMBOL("compress2")
-
-/********************************************************************/
-/* *MODULE CRC32 ZLIB 01/02/01 00:15:09 */
-/********************************************************************/
-
- EXPORT SYMBOL("crc32")
- EXPORT SYMBOL("get_crc_table")
-
-/********************************************************************/
-/* *MODULE DEFLATE ZLIB 01/02/01 00:15:09 */
-/********************************************************************/
-
- EXPORT SYMBOL("deflate")
- EXPORT SYMBOL("deflateEnd")
- EXPORT SYMBOL("deflateSetDictionary")
- EXPORT SYMBOL("deflateCopy")
- EXPORT SYMBOL("deflateReset")
- EXPORT SYMBOL("deflateParams")
- EXPORT SYMBOL("deflatePrime")
- EXPORT SYMBOL("deflateInit_")
- EXPORT SYMBOL("deflateInit2_")
-
-/********************************************************************/
-/* *MODULE GZIO ZLIB 01/02/01 00:15:09 */
-/********************************************************************/
-
- EXPORT SYMBOL("gzopen")
- EXPORT SYMBOL("gzdopen")
- EXPORT SYMBOL("gzsetparams")
- EXPORT SYMBOL("gzread")
- EXPORT SYMBOL("gzwrite")
- EXPORT SYMBOL("gzprintf")
- EXPORT SYMBOL("gzputs")
- EXPORT SYMBOL("gzgets")
- EXPORT SYMBOL("gzputc")
- EXPORT SYMBOL("gzgetc")
- EXPORT SYMBOL("gzflush")
- EXPORT SYMBOL("gzseek")
- EXPORT SYMBOL("gzrewind")
- EXPORT SYMBOL("gztell")
- EXPORT SYMBOL("gzeof")
- EXPORT SYMBOL("gzclose")
- EXPORT SYMBOL("gzerror")
-
-/********************************************************************/
-/* *MODULE INFLATE ZLIB 01/02/01 00:15:09 */
-/********************************************************************/
-
- EXPORT SYMBOL("inflate")
- EXPORT SYMBOL("inflateEnd")
- EXPORT SYMBOL("inflateSetDictionary")
- EXPORT SYMBOL("inflateSync")
- EXPORT SYMBOL("inflateReset")
- EXPORT SYMBOL("inflateInit_")
- EXPORT SYMBOL("inflateInit2_")
- EXPORT SYMBOL("inflateSyncPoint")
-
-/********************************************************************/
-/* *MODULE UNCOMPR ZLIB 01/02/01 00:15:09 */
-/********************************************************************/
-
- EXPORT SYMBOL("uncompress")
-
-/********************************************************************/
-/* *MODULE ZUTIL ZLIB 01/02/01 00:15:09 */
-/********************************************************************/
-
- EXPORT SYMBOL("zlibVersion")
- EXPORT SYMBOL("zError")
-
-/*@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@*/
-/* Version 1.2.1 additional entry points. */
-/*@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@*/
-
-/********************************************************************/
-/* *MODULE COMPRESS ZLIB 01/02/01 00:15:09 */
-/********************************************************************/
-
- EXPORT SYMBOL("compressBound")
-
-/********************************************************************/
-/* *MODULE DEFLATE ZLIB 01/02/01 00:15:09 */
-/********************************************************************/
-
- EXPORT SYMBOL("deflateBound")
-
-/********************************************************************/
-/* *MODULE GZIO ZLIB 01/02/01 00:15:09 */
-/********************************************************************/
-
- EXPORT SYMBOL("gzungetc")
- EXPORT SYMBOL("gzclearerr")
-
-/********************************************************************/
-/* *MODULE INFBACK ZLIB 01/02/01 00:15:09 */
-/********************************************************************/
-
- EXPORT SYMBOL("inflateBack")
- EXPORT SYMBOL("inflateBackEnd")
- EXPORT SYMBOL("inflateBackInit_")
-
-/********************************************************************/
-/* *MODULE INFLATE ZLIB 01/02/01 00:15:09 */
-/********************************************************************/
-
- EXPORT SYMBOL("inflateCopy")
-
-/********************************************************************/
-/* *MODULE ZUTIL ZLIB 01/02/01 00:15:09 */
-/********************************************************************/
-
- EXPORT SYMBOL("zlibCompileFlags")
-
-/*@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@*/
-/* Version 1.2.5 additional entry points. */
-/*@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@*/
-
-/********************************************************************/
-/* *MODULE ADLER32 ZLIB 01/02/01 00:15:09 */
-/********************************************************************/
-
- EXPORT SYMBOL("adler32_combine")
- EXPORT SYMBOL("adler32_combine64")
-
-/********************************************************************/
-/* *MODULE CRC32 ZLIB 01/02/01 00:15:09 */
-/********************************************************************/
-
- EXPORT SYMBOL("crc32_combine")
- EXPORT SYMBOL("crc32_combine64")
-
-/********************************************************************/
-/* *MODULE GZLIB ZLIB 01/02/01 00:15:09 */
-/********************************************************************/
-
- EXPORT SYMBOL("gzbuffer")
- EXPORT SYMBOL("gzoffset")
- EXPORT SYMBOL("gzoffset64")
- EXPORT SYMBOL("gzopen64")
- EXPORT SYMBOL("gzseek64")
- EXPORT SYMBOL("gztell64")
-
-/********************************************************************/
-/* *MODULE GZREAD ZLIB 01/02/01 00:15:09 */
-/********************************************************************/
-
- EXPORT SYMBOL("gzclose_r")
-
-/********************************************************************/
-/* *MODULE GZWRITE ZLIB 01/02/01 00:15:09 */
-/********************************************************************/
-
- EXPORT SYMBOL("gzclose_w")
-
-/********************************************************************/
-/* *MODULE INFLATE ZLIB 01/02/01 00:15:09 */
-/********************************************************************/
-
- EXPORT SYMBOL("inflateMark")
- EXPORT SYMBOL("inflatePrime")
- EXPORT SYMBOL("inflateReset2")
- EXPORT SYMBOL("inflateUndermine")
-
-/*@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@*/
-/* Version 1.2.6 additional entry points. */
-/*@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@*/
-
-/********************************************************************/
-/* *MODULE DEFLATE ZLIB 01/02/01 00:15:09 */
-/********************************************************************/
-
- EXPORT SYMBOL("deflateResetKeep")
- EXPORT SYMBOL("deflatePending")
-
-/********************************************************************/
-/* *MODULE GZWRITE ZLIB 01/02/01 00:15:09 */
-/********************************************************************/
-
- EXPORT SYMBOL("gzgetc_")
-
-/********************************************************************/
-/* *MODULE INFLATE ZLIB 01/02/01 00:15:09 */
-/********************************************************************/
-
- EXPORT SYMBOL("inflateResetKeep")
-
-/*@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@*/
-/* Version 1.2.8 additional entry points. */
-/*@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@*/
-
-/********************************************************************/
-/* *MODULE INFLATE ZLIB 01/02/01 00:15:09 */
-/********************************************************************/
-
- EXPORT SYMBOL("inflateGetDictionary")
-
-ENDPGMEXP
diff --git a/third-party/zlib/as400/compile.clp b/third-party/zlib/as400/compile.clp
deleted file mode 100644
index e3f47c6..0000000
--- a/third-party/zlib/as400/compile.clp
+++ /dev/null
@@ -1,110 +0,0 @@
-/******************************************************************************/
-/* */
-/* ZLIB */
-/* */
-/* Compile sources into modules and link them into a service program. */
-/* */
-/******************************************************************************/
-
- PGM
-
-/* Configuration adjustable parameters. */
-
- DCL VAR(&SRCLIB) TYPE(*CHAR) LEN(10) +
- VALUE('ZLIB') /* Source library. */
- DCL VAR(&SRCFILE) TYPE(*CHAR) LEN(10) +
- VALUE('SOURCES') /* Source member file. */
- DCL VAR(&CTLFILE) TYPE(*CHAR) LEN(10) +
- VALUE('TOOLS') /* Control member file. */
-
- DCL VAR(&MODLIB) TYPE(*CHAR) LEN(10) +
- VALUE('ZLIB') /* Module library. */
-
- DCL VAR(&SRVLIB) TYPE(*CHAR) LEN(10) +
- VALUE('LGPL') /* Service program library. */
-
- DCL VAR(&CFLAGS) TYPE(*CHAR) +
- VALUE('OPTIMIZE(40)') /* Compile options. */
-
- DCL VAR(&TGTRLS) TYPE(*CHAR) +
- VALUE('V5R3M0') /* Target release. */
-
-
-/* Working storage. */
-
- DCL VAR(&CMDLEN) TYPE(*DEC) LEN(15 5) VALUE(300) /* Command length. */
- DCL VAR(&CMD) TYPE(*CHAR) LEN(512)
- DCL VAR(&FIXDCMD) TYPE(*CHAR) LEN(512)
-
-
-/* Compile sources into modules. */
-
- CHGVAR VAR(&FIXDCMD) VALUE('CRTCMOD' *BCAT &CFLAGS *BCAT +
- 'SYSIFCOPT(*IFS64IO)' *BCAT +
- 'DEFINE(''_LARGEFILE64_SOURCE''' *BCAT +
- '''_LFS64_LARGEFILE=1'') TGTRLS(' *TCAT &TGTRLS *TCAT +
- ') SRCFILE(' *TCAT &SRCLIB *TCAT '/' *TCAT +
- &SRCFILE *TCAT ') MODULE(' *TCAT &MODLIB *TCAT '/')
-
-
- CHGVAR VAR(&CMD) VALUE(&FIXDCMD *TCAT 'ADLER32)')
- CALL PGM(QCMDEXC) PARM(&CMD &CMDLEN)
-
- CHGVAR VAR(&CMD) VALUE(&FIXDCMD *TCAT 'COMPRESS)')
- CALL PGM(QCMDEXC) PARM(&CMD &CMDLEN)
-
- CHGVAR VAR(&CMD) VALUE(&FIXDCMD *TCAT 'CRC32)')
- CALL PGM(QCMDEXC) PARM(&CMD &CMDLEN)
-
- CHGVAR VAR(&CMD) VALUE(&FIXDCMD *TCAT 'DEFLATE)')
- CALL PGM(QCMDEXC) PARM(&CMD &CMDLEN)
-
- CHGVAR VAR(&CMD) VALUE(&FIXDCMD *TCAT 'GZCLOSE)')
- CALL PGM(QCMDEXC) PARM(&CMD &CMDLEN)
-
- CHGVAR VAR(&CMD) VALUE(&FIXDCMD *TCAT 'GZLIB)')
- CALL PGM(QCMDEXC) PARM(&CMD &CMDLEN)
-
- CHGVAR VAR(&CMD) VALUE(&FIXDCMD *TCAT 'GZREAD)')
- CALL PGM(QCMDEXC) PARM(&CMD &CMDLEN)
-
- CHGVAR VAR(&CMD) VALUE(&FIXDCMD *TCAT 'GZWRITE)')
- CALL PGM(QCMDEXC) PARM(&CMD &CMDLEN)
-
- CHGVAR VAR(&CMD) VALUE(&FIXDCMD *TCAT 'INFBACK)')
- CALL PGM(QCMDEXC) PARM(&CMD &CMDLEN)
-
- CHGVAR VAR(&CMD) VALUE(&FIXDCMD *TCAT 'INFFAST)')
- CALL PGM(QCMDEXC) PARM(&CMD &CMDLEN)
-
- CHGVAR VAR(&CMD) VALUE(&FIXDCMD *TCAT 'INFLATE)')
- CALL PGM(QCMDEXC) PARM(&CMD &CMDLEN)
-
- CHGVAR VAR(&CMD) VALUE(&FIXDCMD *TCAT 'INFTREES)')
- CALL PGM(QCMDEXC) PARM(&CMD &CMDLEN)
-
- CHGVAR VAR(&CMD) VALUE(&FIXDCMD *TCAT 'TREES)')
- CALL PGM(QCMDEXC) PARM(&CMD &CMDLEN)
-
- CHGVAR VAR(&CMD) VALUE(&FIXDCMD *TCAT 'UNCOMPR)')
- CALL PGM(QCMDEXC) PARM(&CMD &CMDLEN)
-
- CHGVAR VAR(&CMD) VALUE(&FIXDCMD *TCAT 'ZUTIL)')
- CALL PGM(QCMDEXC) PARM(&CMD &CMDLEN)
-
-
-/* Link modules into a service program. */
-
- CRTSRVPGM SRVPGM(&SRVLIB/ZLIB) +
- MODULE(&MODLIB/ADLER32 &MODLIB/COMPRESS +
- &MODLIB/CRC32 &MODLIB/DEFLATE +
- &MODLIB/GZCLOSE &MODLIB/GZLIB +
- &MODLIB/GZREAD &MODLIB/GZWRITE +
- &MODLIB/INFBACK &MODLIB/INFFAST +
- &MODLIB/INFLATE &MODLIB/INFTREES +
- &MODLIB/TREES &MODLIB/UNCOMPR +
- &MODLIB/ZUTIL) +
- SRCFILE(&SRCLIB/&CTLFILE) SRCMBR(BNDSRC) +
- TEXT('ZLIB 1.2.8') TGTRLS(&TGTRLS)
-
- ENDPGM
diff --git a/third-party/zlib/as400/readme.txt b/third-party/zlib/as400/readme.txt
deleted file mode 100644
index 7b5d93b..0000000
--- a/third-party/zlib/as400/readme.txt
+++ /dev/null
@@ -1,115 +0,0 @@
- ZLIB version 1.2.8 for AS400 installation instructions
-
-I) From an AS400 *SAVF file:
-
-1) Unpacking archive to an AS400 save file
-
-On the AS400:
-
-_ Create the ZLIB AS400 library:
-
- CRTLIB LIB(ZLIB) TYPE(*PROD) TEXT('ZLIB compression API library')
-
-_ Create a work save file, for example:
-
- CRTSAVF FILE(ZLIB/ZLIBSAVF)
-
-On a PC connected to the target AS400:
-
-_ Unpack the save file image to a PC file "ZLIBSAVF"
-_ Upload this file into the save file on the AS400, for example
- using ftp in BINARY mode.
-
-
-2) Populating the ZLIB AS400 source library
-
-On the AS400:
-
-_ Extract the saved objects into the ZLIB AS400 library using:
-
-RSTOBJ OBJ(*ALL) SAVLIB(ZLIB) DEV(*SAVF) SAVF(ZLIB/ZLIBSAVF) RSTLIB(ZLIB)
-
-
-3) Customize installation:
-
-_ Edit CL member ZLIB/TOOLS(COMPILE) and change parameters if needed,
- according to the comments.
-
-_ Compile this member with:
-
- CRTCLPGM PGM(ZLIB/COMPILE) SRCFILE(ZLIB/TOOLS) SRCMBR(COMPILE)
-
-
-4) Compile and generate the service program:
-
-_ This can now be done by executing:
-
- CALL PGM(ZLIB/COMPILE)
-
-
-
-II) From the original source distribution:
-
-1) On the AS400, create the source library:
-
- CRTLIB LIB(ZLIB) TYPE(*PROD) TEXT('ZLIB compression API library')
-
-2) Create the source files:
-
- CRTSRCPF FILE(ZLIB/SOURCES) RCDLEN(112) TEXT('ZLIB library modules')
- CRTSRCPF FILE(ZLIB/H) RCDLEN(112) TEXT('ZLIB library includes')
- CRTSRCPF FILE(ZLIB/TOOLS) RCDLEN(112) TEXT('ZLIB library control utilities')
-
-3) From the machine hosting the distribution files, upload them (with
- FTP in text mode, for example) according to the following table:
-
- Original AS400 AS400 AS400 AS400
- file file member type description
- SOURCES Original ZLIB C subprogram sources
- adler32.c ADLER32 C ZLIB - Compute the Adler-32 checksum of a dta strm
- compress.c COMPRESS C ZLIB - Compress a memory buffer
- crc32.c CRC32 C ZLIB - Compute the CRC-32 of a data stream
- deflate.c DEFLATE C ZLIB - Compress data using the deflation algorithm
- gzclose.c GZCLOSE C ZLIB - Close .gz files
- gzlib.c GZLIB C ZLIB - Miscellaneous .gz files IO support
- gzread.c GZREAD C ZLIB - Read .gz files
- gzwrite.c GZWRITE C ZLIB - Write .gz files
- infback.c INFBACK C ZLIB - Inflate using a callback interface
- inffast.c INFFAST C ZLIB - Fast proc. literals & length/distance pairs
- inflate.c INFLATE C ZLIB - Interface to inflate modules
- inftrees.c INFTREES C ZLIB - Generate Huffman trees for efficient decode
- trees.c TREES C ZLIB - Output deflated data using Huffman coding
- uncompr.c UNCOMPR C ZLIB - Decompress a memory buffer
- zutil.c ZUTIL C ZLIB - Target dependent utility functions
- H Original ZLIB C and ILE/RPG include files
- crc32.h CRC32 C ZLIB - CRC32 tables
- deflate.h DEFLATE C ZLIB - Internal compression state
- gzguts.h GZGUTS C ZLIB - Definitions for the gzclose module
- inffast.h INFFAST C ZLIB - Header to use inffast.c
- inffixed.h INFFIXED C ZLIB - Table for decoding fixed codes
- inflate.h INFLATE C ZLIB - Internal inflate state definitions
- inftrees.h INFTREES C ZLIB - Header to use inftrees.c
- trees.h TREES C ZLIB - Created automatically with -DGEN_TREES_H
- zconf.h ZCONF C ZLIB - Compression library configuration
- zlib.h ZLIB C ZLIB - Compression library C user interface
- as400/zlib.inc ZLIB.INC RPGLE ZLIB - Compression library ILE RPG user interface
- zutil.h ZUTIL C ZLIB - Internal interface and configuration
- TOOLS Building source software & AS/400 README
- as400/bndsrc BNDSRC Entry point exportation list
- as400/compile.clp COMPILE CLP Compile sources & generate service program
- as400/readme.txt README TXT Installation instructions
-
-4) Continue as in I)3).
-
-
-
-
-Notes: For AS400 ILE RPG programmers, a /copy member defining the ZLIB
- API prototypes for ILE RPG can be found in ZLIB/H(ZLIB.INC).
- Please read comments in this member for more information.
-
- Remember that most foreign textual data are ASCII coded: this
- implementation does not handle conversion from/to ASCII, so
- text data code conversions must be done explicitely.
-
- Mainly for the reason above, always open zipped files in binary mode.
diff --git a/third-party/zlib/as400/zlib.inc b/third-party/zlib/as400/zlib.inc
deleted file mode 100644
index 7341a6d..0000000
--- a/third-party/zlib/as400/zlib.inc
+++ /dev/null
@@ -1,451 +0,0 @@
- * ZLIB.INC - Interface to the general purpose compression library
- *
- * ILE RPG400 version by Patrick Monnerat, DATASPHERE.
- * Version 1.2.8
- *
- *
- * WARNING:
- * Procedures inflateInit(), inflateInit2(), deflateInit(),
- * deflateInit2() and inflateBackInit() need to be called with
- * two additional arguments:
- * the package version string and the stream control structure.
- * size. This is needed because RPG lacks some macro feature.
- * Call these procedures as:
- * inflateInit(...: ZLIB_VERSION: %size(z_stream))
- *
- /if not defined(ZLIB_H_)
- /define ZLIB_H_
- *
- **************************************************************************
- * Constants
- **************************************************************************
- *
- * Versioning information.
- *
- D ZLIB_VERSION C '1.2.8'
- D ZLIB_VERNUM C X'1280'
- D ZLIB_VER_MAJOR C 1
- D ZLIB_VER_MINOR C 2
- D ZLIB_VER_REVISION...
- D C 8
- D ZLIB_VER_SUBREVISION...
- D C 0
- *
- * Other equates.
- *
- D Z_NO_FLUSH C 0
- D Z_PARTIAL_FLUSH...
- D C 1
- D Z_SYNC_FLUSH C 2
- D Z_FULL_FLUSH C 3
- D Z_FINISH C 4
- D Z_BLOCK C 5
- D Z_TREES C 6
- *
- D Z_OK C 0
- D Z_STREAM_END C 1
- D Z_NEED_DICT C 2
- D Z_ERRNO C -1
- D Z_STREAM_ERROR C -2
- D Z_DATA_ERROR C -3
- D Z_MEM_ERROR C -4
- D Z_BUF_ERROR C -5
- DZ_VERSION_ERROR C -6
- *
- D Z_NO_COMPRESSION...
- D C 0
- D Z_BEST_SPEED C 1
- D Z_BEST_COMPRESSION...
- D C 9
- D Z_DEFAULT_COMPRESSION...
- D C -1
- *
- D Z_FILTERED C 1
- D Z_HUFFMAN_ONLY C 2
- D Z_RLE C 3
- D Z_DEFAULT_STRATEGY...
- D C 0
- *
- D Z_BINARY C 0
- D Z_ASCII C 1
- D Z_UNKNOWN C 2
- *
- D Z_DEFLATED C 8
- *
- D Z_NULL C 0
- *
- **************************************************************************
- * Types
- **************************************************************************
- *
- D z_streamp S * Stream struct ptr
- D gzFile S * File pointer
- D z_off_t S 10i 0 Stream offsets
- D z_off64_t S 20i 0 Stream offsets
- *
- **************************************************************************
- * Structures
- **************************************************************************
- *
- * The GZIP encode/decode stream support structure.
- *
- D z_stream DS align based(z_streamp)
- D zs_next_in * Next input byte
- D zs_avail_in 10U 0 Byte cnt at next_in
- D zs_total_in 10U 0 Total bytes read
- D zs_next_out * Output buffer ptr
- D zs_avail_out 10U 0 Room left @ next_out
- D zs_total_out 10U 0 Total bytes written
- D zs_msg * Last errmsg or null
- D zs_state * Internal state
- D zs_zalloc * procptr Int. state allocator
- D zs_free * procptr Int. state dealloc.
- D zs_opaque * Private alloc. data
- D zs_data_type 10i 0 ASC/BIN best guess
- D zs_adler 10u 0 Uncompr. adler32 val
- D 10U 0 Reserved
- D 10U 0 Ptr. alignment
- *
- **************************************************************************
- * Utility function prototypes
- **************************************************************************
- *
- D compress PR 10I 0 extproc('compress')
- D dest 65535 options(*varsize) Destination buffer
- D destLen 10U 0 Destination length
- D source 65535 const options(*varsize) Source buffer
- D sourceLen 10u 0 value Source length
- *
- D compress2 PR 10I 0 extproc('compress2')
- D dest 65535 options(*varsize) Destination buffer
- D destLen 10U 0 Destination length
- D source 65535 const options(*varsize) Source buffer
- D sourceLen 10U 0 value Source length
- D level 10I 0 value Compression level
- *
- D compressBound PR 10U 0 extproc('compressBound')
- D sourceLen 10U 0 value
- *
- D uncompress PR 10I 0 extproc('uncompress')
- D dest 65535 options(*varsize) Destination buffer
- D destLen 10U 0 Destination length
- D source 65535 const options(*varsize) Source buffer
- D sourceLen 10U 0 value Source length
- *
- /if not defined(LARGE_FILES)
- D gzopen PR extproc('gzopen')
- D like(gzFile)
- D path * value options(*string) File pathname
- D mode * value options(*string) Open mode
- /else
- D gzopen PR extproc('gzopen64')
- D like(gzFile)
- D path * value options(*string) File pathname
- D mode * value options(*string) Open mode
- *
- D gzopen64 PR extproc('gzopen64')
- D like(gzFile)
- D path * value options(*string) File pathname
- D mode * value options(*string) Open mode
- /endif
- *
- D gzdopen PR extproc('gzdopen')
- D like(gzFile)
- D fd 10I 0 value File descriptor
- D mode * value options(*string) Open mode
- *
- D gzbuffer PR 10I 0 extproc('gzbuffer')
- D file value like(gzFile) File pointer
- D size 10U 0 value
- *
- D gzsetparams PR 10I 0 extproc('gzsetparams')
- D file value like(gzFile) File pointer
- D level 10I 0 value
- D strategy 10I 0 value
- *
- D gzread PR 10I 0 extproc('gzread')
- D file value like(gzFile) File pointer
- D buf 65535 options(*varsize) Buffer
- D len 10u 0 value Buffer length
- *
- D gzwrite PR 10I 0 extproc('gzwrite')
- D file value like(gzFile) File pointer
- D buf 65535 const options(*varsize) Buffer
- D len 10u 0 value Buffer length
- *
- D gzputs PR 10I 0 extproc('gzputs')
- D file value like(gzFile) File pointer
- D s * value options(*string) String to output
- *
- D gzgets PR * extproc('gzgets')
- D file value like(gzFile) File pointer
- D buf 65535 options(*varsize) Read buffer
- D len 10i 0 value Buffer length
- *
- D gzputc PR 10i 0 extproc('gzputc')
- D file value like(gzFile) File pointer
- D c 10I 0 value Character to write
- *
- D gzgetc PR 10i 0 extproc('gzgetc')
- D file value like(gzFile) File pointer
- *
- D gzgetc_ PR 10i 0 extproc('gzgetc_')
- D file value like(gzFile) File pointer
- *
- D gzungetc PR 10i 0 extproc('gzungetc')
- D c 10I 0 value Character to push
- D file value like(gzFile) File pointer
- *
- D gzflush PR 10i 0 extproc('gzflush')
- D file value like(gzFile) File pointer
- D flush 10I 0 value Type of flush
- *
- /if not defined(LARGE_FILES)
- D gzseek PR extproc('gzseek')
- D like(z_off_t)
- D file value like(gzFile) File pointer
- D offset value like(z_off_t) Offset
- D whence 10i 0 value Origin
- /else
- D gzseek PR extproc('gzseek64')
- D like(z_off_t)
- D file value like(gzFile) File pointer
- D offset value like(z_off_t) Offset
- D whence 10i 0 value Origin
- *
- D gzseek64 PR extproc('gzseek64')
- D like(z_off64_t)
- D file value like(gzFile) File pointer
- D offset value like(z_off64_t) Offset
- D whence 10i 0 value Origin
- /endif
- *
- D gzrewind PR 10i 0 extproc('gzrewind')
- D file value like(gzFile) File pointer
- *
- /if not defined(LARGE_FILES)
- D gztell PR extproc('gztell')
- D like(z_off_t)
- D file value like(gzFile) File pointer
- /else
- D gztell PR extproc('gztell64')
- D like(z_off_t)
- D file value like(gzFile) File pointer
- *
- D gztell64 PR extproc('gztell64')
- D like(z_off64_t)
- D file value like(gzFile) File pointer
- /endif
- *
- /if not defined(LARGE_FILES)
- D gzoffset PR extproc('gzoffset')
- D like(z_off_t)
- D file value like(gzFile) File pointer
- /else
- D gzoffset PR extproc('gzoffset64')
- D like(z_off_t)
- D file value like(gzFile) File pointer
- *
- D gzoffset64 PR extproc('gzoffset64')
- D like(z_off64_t)
- D file value like(gzFile) File pointer
- /endif
- *
- D gzeof PR 10i 0 extproc('gzeof')
- D file value like(gzFile) File pointer
- *
- D gzclose_r PR 10i 0 extproc('gzclose_r')
- D file value like(gzFile) File pointer
- *
- D gzclose_w PR 10i 0 extproc('gzclose_w')
- D file value like(gzFile) File pointer
- *
- D gzclose PR 10i 0 extproc('gzclose')
- D file value like(gzFile) File pointer
- *
- D gzerror PR * extproc('gzerror') Error string
- D file value like(gzFile) File pointer
- D errnum 10I 0 Error code
- *
- D gzclearerr PR extproc('gzclearerr')
- D file value like(gzFile) File pointer
- *
- **************************************************************************
- * Basic function prototypes
- **************************************************************************
- *
- D zlibVersion PR * extproc('zlibVersion') Version string
- *
- D deflateInit PR 10I 0 extproc('deflateInit_') Init. compression
- D strm like(z_stream) Compression stream
- D level 10I 0 value Compression level
- D version * value options(*string) Version string
- D stream_size 10i 0 value Stream struct. size
- *
- D deflate PR 10I 0 extproc('deflate') Compress data
- D strm like(z_stream) Compression stream
- D flush 10I 0 value Flush type required
- *
- D deflateEnd PR 10I 0 extproc('deflateEnd') Termin. compression
- D strm like(z_stream) Compression stream
- *
- D inflateInit PR 10I 0 extproc('inflateInit_') Init. expansion
- D strm like(z_stream) Expansion stream
- D version * value options(*string) Version string
- D stream_size 10i 0 value Stream struct. size
- *
- D inflate PR 10I 0 extproc('inflate') Expand data
- D strm like(z_stream) Expansion stream
- D flush 10I 0 value Flush type required
- *
- D inflateEnd PR 10I 0 extproc('inflateEnd') Termin. expansion
- D strm like(z_stream) Expansion stream
- *
- **************************************************************************
- * Advanced function prototypes
- **************************************************************************
- *
- D deflateInit2 PR 10I 0 extproc('deflateInit2_') Init. compression
- D strm like(z_stream) Compression stream
- D level 10I 0 value Compression level
- D method 10I 0 value Compression method
- D windowBits 10I 0 value log2(window size)
- D memLevel 10I 0 value Mem/cmpress tradeoff
- D strategy 10I 0 value Compression stategy
- D version * value options(*string) Version string
- D stream_size 10i 0 value Stream struct. size
- *
- D deflateSetDictionary...
- D PR 10I 0 extproc('deflateSetDictionary') Init. dictionary
- D strm like(z_stream) Compression stream
- D dictionary 65535 const options(*varsize) Dictionary bytes
- D dictLength 10U 0 value Dictionary length
- *
- D deflateCopy PR 10I 0 extproc('deflateCopy') Compress strm 2 strm
- D dest like(z_stream) Destination stream
- D source like(z_stream) Source stream
- *
- D deflateReset PR 10I 0 extproc('deflateReset') End and init. stream
- D strm like(z_stream) Compression stream
- *
- D deflateParams PR 10I 0 extproc('deflateParams') Change level & strat
- D strm like(z_stream) Compression stream
- D level 10I 0 value Compression level
- D strategy 10I 0 value Compression stategy
- *
- D deflateBound PR 10U 0 extproc('deflateBound') Change level & strat
- D strm like(z_stream) Compression stream
- D sourcelen 10U 0 value Compression level
- *
- D deflatePending PR 10I 0 extproc('deflatePending') Change level & strat
- D strm like(z_stream) Compression stream
- D pending 10U 0 Pending bytes
- D bits 10I 0 Pending bits
- *
- D deflatePrime PR 10I 0 extproc('deflatePrime') Change level & strat
- D strm like(z_stream) Compression stream
- D bits 10I 0 value # of bits to insert
- D value 10I 0 value Bits to insert
- *
- D inflateInit2 PR 10I 0 extproc('inflateInit2_') Init. expansion
- D strm like(z_stream) Expansion stream
- D windowBits 10I 0 value log2(window size)
- D version * value options(*string) Version string
- D stream_size 10i 0 value Stream struct. size
- *
- D inflateSetDictionary...
- D PR 10I 0 extproc('inflateSetDictionary') Init. dictionary
- D strm like(z_stream) Expansion stream
- D dictionary 65535 const options(*varsize) Dictionary bytes
- D dictLength 10U 0 value Dictionary length
- *
- D inflateGetDictionary...
- D PR 10I 0 extproc('inflateGetDictionary') Get dictionary
- D strm like(z_stream) Expansion stream
- D dictionary 65535 options(*varsize) Dictionary bytes
- D dictLength 10U 0 Dictionary length
- *
- D inflateSync PR 10I 0 extproc('inflateSync') Sync. expansion
- D strm like(z_stream) Expansion stream
- *
- D inflateCopy PR 10I 0 extproc('inflateCopy')
- D dest like(z_stream) Destination stream
- D source like(z_stream) Source stream
- *
- D inflateReset PR 10I 0 extproc('inflateReset') End and init. stream
- D strm like(z_stream) Expansion stream
- *
- D inflateReset2 PR 10I 0 extproc('inflateReset2') End and init. stream
- D strm like(z_stream) Expansion stream
- D windowBits 10I 0 value Log2(buffer size)
- *
- D inflatePrime PR 10I 0 extproc('inflatePrime') Insert bits
- D strm like(z_stream) Expansion stream
- D bits 10I 0 value Bit count
- D value 10I 0 value Bits to insert
- *
- D inflateMark PR 10I 0 extproc('inflateMark') Get inflate info
- D strm like(z_stream) Expansion stream
- *
- D inflateBackInit...
- D PR 10I 0 extproc('inflateBackInit_')
- D strm like(z_stream) Expansion stream
- D windowBits 10I 0 value Log2(buffer size)
- D window 65535 options(*varsize) Buffer
- D version * value options(*string) Version string
- D stream_size 10i 0 value Stream struct. size
- *
- D inflateBack PR 10I 0 extproc('inflateBack')
- D strm like(z_stream) Expansion stream
- D in * value procptr Input function
- D in_desc * value Input descriptor
- D out * value procptr Output function
- D out_desc * value Output descriptor
- *
- D inflateBackEnd PR 10I 0 extproc('inflateBackEnd')
- D strm like(z_stream) Expansion stream
- *
- D zlibCompileFlags...
- D PR 10U 0 extproc('zlibCompileFlags')
- *
- **************************************************************************
- * Checksum function prototypes
- **************************************************************************
- *
- D adler32 PR 10U 0 extproc('adler32') New checksum
- D adler 10U 0 value Old checksum
- D buf 65535 const options(*varsize) Bytes to accumulate
- D len 10U 0 value Buffer length
- *
- D crc32 PR 10U 0 extproc('crc32') New checksum
- D crc 10U 0 value Old checksum
- D buf 65535 const options(*varsize) Bytes to accumulate
- D len 10U 0 value Buffer length
- *
- **************************************************************************
- * Miscellaneous function prototypes
- **************************************************************************
- *
- D zError PR * extproc('zError') Error string
- D err 10I 0 value Error code
- *
- D inflateSyncPoint...
- D PR 10I 0 extproc('inflateSyncPoint')
- D strm like(z_stream) Expansion stream
- *
- D get_crc_table PR * extproc('get_crc_table') Ptr to ulongs
- *
- D inflateUndermine...
- D PR 10I 0 extproc('inflateUndermine')
- D strm like(z_stream) Expansion stream
- D arg 10I 0 value Error code
- *
- D inflateResetKeep...
- D PR 10I 0 extproc('inflateResetKeep') End and init. stream
- D strm like(z_stream) Expansion stream
- *
- D deflateResetKeep...
- D PR 10I 0 extproc('deflateResetKeep') End and init. stream
- D strm like(z_stream) Expansion stream
- *
- /endif
diff --git a/third-party/zlib/compress.c b/third-party/zlib/compress.c
deleted file mode 100644
index 6e97626..0000000
--- a/third-party/zlib/compress.c
+++ /dev/null
@@ -1,80 +0,0 @@
-/* compress.c -- compress a memory buffer
- * Copyright (C) 1995-2005 Jean-loup Gailly.
- * For conditions of distribution and use, see copyright notice in zlib.h
- */
-
-/* @(#) $Id$ */
-
-#define ZLIB_INTERNAL
-#include "zlib.h"
-
-/* ===========================================================================
- Compresses the source buffer into the destination buffer. The level
- parameter has the same meaning as in deflateInit. sourceLen is the byte
- length of the source buffer. Upon entry, destLen is the total size of the
- destination buffer, which must be at least 0.1% larger than sourceLen plus
- 12 bytes. Upon exit, destLen is the actual size of the compressed buffer.
-
- compress2 returns Z_OK if success, Z_MEM_ERROR if there was not enough
- memory, Z_BUF_ERROR if there was not enough room in the output buffer,
- Z_STREAM_ERROR if the level parameter is invalid.
-*/
-int ZEXPORT compress2 (dest, destLen, source, sourceLen, level)
- Bytef *dest;
- uLongf *destLen;
- const Bytef *source;
- uLong sourceLen;
- int level;
-{
- z_stream stream;
- int err;
-
- stream.next_in = (z_const Bytef *)source;
- stream.avail_in = (uInt)sourceLen;
-#ifdef MAXSEG_64K
- /* Check for source > 64K on 16-bit machine: */
- if ((uLong)stream.avail_in != sourceLen) return Z_BUF_ERROR;
-#endif
- stream.next_out = dest;
- stream.avail_out = (uInt)*destLen;
- if ((uLong)stream.avail_out != *destLen) return Z_BUF_ERROR;
-
- stream.zalloc = (alloc_func)0;
- stream.zfree = (free_func)0;
- stream.opaque = (voidpf)0;
-
- err = deflateInit(&stream, level);
- if (err != Z_OK) return err;
-
- err = deflate(&stream, Z_FINISH);
- if (err != Z_STREAM_END) {
- deflateEnd(&stream);
- return err == Z_OK ? Z_BUF_ERROR : err;
- }
- *destLen = stream.total_out;
-
- err = deflateEnd(&stream);
- return err;
-}
-
-/* ===========================================================================
- */
-int ZEXPORT compress (dest, destLen, source, sourceLen)
- Bytef *dest;
- uLongf *destLen;
- const Bytef *source;
- uLong sourceLen;
-{
- return compress2(dest, destLen, source, sourceLen, Z_DEFAULT_COMPRESSION);
-}
-
-/* ===========================================================================
- If the default memLevel or windowBits for deflateInit() is changed, then
- this function needs to be updated.
- */
-uLong ZEXPORT compressBound (sourceLen)
- uLong sourceLen;
-{
- return sourceLen + (sourceLen >> 12) + (sourceLen >> 14) +
- (sourceLen >> 25) + 13;
-}
diff --git a/third-party/zlib/configure b/third-party/zlib/configure
deleted file mode 100755
index b77a8a8..0000000
--- a/third-party/zlib/configure
+++ /dev/null
@@ -1,831 +0,0 @@
-#!/bin/sh
-# configure script for zlib.
-#
-# Normally configure builds both a static and a shared library.
-# If you want to build just a static library, use: ./configure --static
-#
-# To impose specific compiler or flags or install directory, use for example:
-# prefix=$HOME CC=cc CFLAGS="-O4" ./configure
-# or for csh/tcsh users:
-# (setenv prefix $HOME; setenv CC cc; setenv CFLAGS "-O4"; ./configure)
-
-# Incorrect settings of CC or CFLAGS may prevent creating a shared library.
-# If you have problems, try without defining CC and CFLAGS before reporting
-# an error.
-
-# start off configure.log
-echo -------------------- >> configure.log
-echo $0 $* >> configure.log
-date >> configure.log
-
-# set command prefix for cross-compilation
-if [ -n "${CHOST}" ]; then
- uname="`echo "${CHOST}" | sed -e 's/^[^-]*-\([^-]*\)$/\1/' -e 's/^[^-]*-[^-]*-\([^-]*\)$/\1/' -e 's/^[^-]*-[^-]*-\([^-]*\)-.*$/\1/'`"
- CROSS_PREFIX="${CHOST}-"
-fi
-
-# destination name for static library
-STATICLIB=libz.a
-
-# extract zlib version numbers from zlib.h
-VER=`sed -n -e '/VERSION "/s/.*"\(.*\)".*/\1/p' < zlib.h`
-VER3=`sed -n -e '/VERSION "/s/.*"\([0-9]*\\.[0-9]*\\.[0-9]*\).*/\1/p' < zlib.h`
-VER2=`sed -n -e '/VERSION "/s/.*"\([0-9]*\\.[0-9]*\)\\..*/\1/p' < zlib.h`
-VER1=`sed -n -e '/VERSION "/s/.*"\([0-9]*\)\\..*/\1/p' < zlib.h`
-
-# establish commands for library building
-if "${CROSS_PREFIX}ar" --version >/dev/null 2>/dev/null || test $? -lt 126; then
- AR=${AR-"${CROSS_PREFIX}ar"}
- test -n "${CROSS_PREFIX}" && echo Using ${AR} | tee -a configure.log
-else
- AR=${AR-"ar"}
- test -n "${CROSS_PREFIX}" && echo Using ${AR} | tee -a configure.log
-fi
-ARFLAGS=${ARFLAGS-"rc"}
-if "${CROSS_PREFIX}ranlib" --version >/dev/null 2>/dev/null || test $? -lt 126; then
- RANLIB=${RANLIB-"${CROSS_PREFIX}ranlib"}
- test -n "${CROSS_PREFIX}" && echo Using ${RANLIB} | tee -a configure.log
-else
- RANLIB=${RANLIB-"ranlib"}
-fi
-if "${CROSS_PREFIX}nm" --version >/dev/null 2>/dev/null || test $? -lt 126; then
- NM=${NM-"${CROSS_PREFIX}nm"}
- test -n "${CROSS_PREFIX}" && echo Using ${NM} | tee -a configure.log
-else
- NM=${NM-"nm"}
-fi
-
-# set defaults before processing command line options
-LDCONFIG=${LDCONFIG-"ldconfig"}
-LDSHAREDLIBC="${LDSHAREDLIBC--lc}"
-ARCHS=
-prefix=${prefix-/usr/local}
-exec_prefix=${exec_prefix-'${prefix}'}
-libdir=${libdir-'${exec_prefix}/lib'}
-sharedlibdir=${sharedlibdir-'${libdir}'}
-includedir=${includedir-'${prefix}/include'}
-mandir=${mandir-'${prefix}/share/man'}
-shared_ext='.so'
-shared=1
-solo=0
-cover=0
-zprefix=0
-zconst=0
-build64=0
-gcc=0
-old_cc="$CC"
-old_cflags="$CFLAGS"
-OBJC='$(OBJZ) $(OBJG)'
-PIC_OBJC='$(PIC_OBJZ) $(PIC_OBJG)'
-
-# leave this script, optionally in a bad way
-leave()
-{
- if test "$*" != "0"; then
- echo "** $0 aborting." | tee -a configure.log
- fi
- rm -f $test.[co] $test $test$shared_ext $test.gcno ./--version
- echo -------------------- >> configure.log
- echo >> configure.log
- echo >> configure.log
- exit $1
-}
-
-# process command line options
-while test $# -ge 1
-do
-case "$1" in
- -h* | --help)
- echo 'usage:' | tee -a configure.log
- echo ' configure [--const] [--zprefix] [--prefix=PREFIX] [--eprefix=EXPREFIX]' | tee -a configure.log
- echo ' [--static] [--64] [--libdir=LIBDIR] [--sharedlibdir=LIBDIR]' | tee -a configure.log
- echo ' [--includedir=INCLUDEDIR] [--archs="-arch i386 -arch x86_64"]' | tee -a configure.log
- exit 0 ;;
- -p*=* | --prefix=*) prefix=`echo $1 | sed 's/.*=//'`; shift ;;
- -e*=* | --eprefix=*) exec_prefix=`echo $1 | sed 's/.*=//'`; shift ;;
- -l*=* | --libdir=*) libdir=`echo $1 | sed 's/.*=//'`; shift ;;
- --sharedlibdir=*) sharedlibdir=`echo $1 | sed 's/.*=//'`; shift ;;
- -i*=* | --includedir=*) includedir=`echo $1 | sed 's/.*=//'`;shift ;;
- -u*=* | --uname=*) uname=`echo $1 | sed 's/.*=//'`;shift ;;
- -p* | --prefix) prefix="$2"; shift; shift ;;
- -e* | --eprefix) exec_prefix="$2"; shift; shift ;;
- -l* | --libdir) libdir="$2"; shift; shift ;;
- -i* | --includedir) includedir="$2"; shift; shift ;;
- -s* | --shared | --enable-shared) shared=1; shift ;;
- -t | --static) shared=0; shift ;;
- --solo) solo=1; shift ;;
- --cover) cover=1; shift ;;
- -z* | --zprefix) zprefix=1; shift ;;
- -6* | --64) build64=1; shift ;;
- -a*=* | --archs=*) ARCHS=`echo $1 | sed 's/.*=//'`; shift ;;
- --sysconfdir=*) echo "ignored option: --sysconfdir" | tee -a configure.log; shift ;;
- --localstatedir=*) echo "ignored option: --localstatedir" | tee -a configure.log; shift ;;
- -c* | --const) zconst=1; shift ;;
- *)
- echo "unknown option: $1" | tee -a configure.log
- echo "$0 --help for help" | tee -a configure.log
- leave 1;;
- esac
-done
-
-# temporary file name
-test=ztest$$
-
-# put arguments in log, also put test file in log if used in arguments
-show()
-{
- case "$*" in
- *$test.c*)
- echo === $test.c === >> configure.log
- cat $test.c >> configure.log
- echo === >> configure.log;;
- esac
- echo $* >> configure.log
-}
-
-# check for gcc vs. cc and set compile and link flags based on the system identified by uname
-cat > $test.c <<EOF
-extern int getchar();
-int hello() {return getchar();}
-EOF
-
-test -z "$CC" && echo Checking for ${CROSS_PREFIX}gcc... | tee -a configure.log
-cc=${CC-${CROSS_PREFIX}gcc}
-cflags=${CFLAGS-"-O3"}
-# to force the asm version use: CFLAGS="-O3 -DASMV" ./configure
-case "$cc" in
- *gcc*) gcc=1 ;;
- *clang*) gcc=1 ;;
-esac
-case `$cc -v 2>&1` in
- *gcc*) gcc=1 ;;
-esac
-
-show $cc -c $test.c
-if test "$gcc" -eq 1 && ($cc -c $test.c) >> configure.log 2>&1; then
- echo ... using gcc >> configure.log
- CC="$cc"
- CFLAGS="${CFLAGS--O3} ${ARCHS}"
- SFLAGS="${CFLAGS--O3} -fPIC"
- LDFLAGS="${LDFLAGS} ${ARCHS}"
- if test $build64 -eq 1; then
- CFLAGS="${CFLAGS} -m64"
- SFLAGS="${SFLAGS} -m64"
- fi
- if test "${ZLIBGCCWARN}" = "YES"; then
- if test "$zconst" -eq 1; then
- CFLAGS="${CFLAGS} -Wall -Wextra -Wcast-qual -pedantic -DZLIB_CONST"
- else
- CFLAGS="${CFLAGS} -Wall -Wextra -pedantic"
- fi
- fi
- if test -z "$uname"; then
- uname=`(uname -s || echo unknown) 2>/dev/null`
- fi
- case "$uname" in
- Linux* | linux* | GNU | GNU/* | solaris*)
- LDSHARED=${LDSHARED-"$cc -shared -Wl,-soname,libz.so.1,--version-script,zlib.map"} ;;
- *BSD | *bsd* | DragonFly)
- LDSHARED=${LDSHARED-"$cc -shared -Wl,-soname,libz.so.1,--version-script,zlib.map"}
- LDCONFIG="ldconfig -m" ;;
- CYGWIN* | Cygwin* | cygwin* | OS/2*)
- EXE='.exe' ;;
- MINGW* | mingw*)
-# temporary bypass
- rm -f $test.[co] $test $test$shared_ext
- echo "Please use win32/Makefile.gcc instead." | tee -a configure.log
- leave 1
- LDSHARED=${LDSHARED-"$cc -shared"}
- LDSHAREDLIBC=""
- EXE='.exe' ;;
- QNX*) # This is for QNX6. I suppose that the QNX rule below is for QNX2,QNX4
- # (alain.bonnefoy at icbt.com)
- LDSHARED=${LDSHARED-"$cc -shared -Wl,-hlibz.so.1"} ;;
- HP-UX*)
- LDSHARED=${LDSHARED-"$cc -shared $SFLAGS"}
- case `(uname -m || echo unknown) 2>/dev/null` in
- ia64)
- shared_ext='.so'
- SHAREDLIB='libz.so' ;;
- *)
- shared_ext='.sl'
- SHAREDLIB='libz.sl' ;;
- esac ;;
- Darwin* | darwin*)
- shared_ext='.dylib'
- SHAREDLIB=libz$shared_ext
- SHAREDLIBV=libz.$VER$shared_ext
- SHAREDLIBM=libz.$VER1$shared_ext
- LDSHARED=${LDSHARED-"$cc -dynamiclib -install_name $libdir/$SHAREDLIBM -compatibility_version $VER1 -current_version $VER3"}
- if libtool -V 2>&1 | grep Apple > /dev/null; then
- AR="libtool"
- else
- AR="/usr/bin/libtool"
- fi
- ARFLAGS="-o" ;;
- *) LDSHARED=${LDSHARED-"$cc -shared"} ;;
- esac
-else
- # find system name and corresponding cc options
- CC=${CC-cc}
- gcc=0
- echo ... using $CC >> configure.log
- if test -z "$uname"; then
- uname=`(uname -sr || echo unknown) 2>/dev/null`
- fi
- case "$uname" in
- HP-UX*) SFLAGS=${CFLAGS-"-O +z"}
- CFLAGS=${CFLAGS-"-O"}
-# LDSHARED=${LDSHARED-"ld -b +vnocompatwarnings"}
- LDSHARED=${LDSHARED-"ld -b"}
- case `(uname -m || echo unknown) 2>/dev/null` in
- ia64)
- shared_ext='.so'
- SHAREDLIB='libz.so' ;;
- *)
- shared_ext='.sl'
- SHAREDLIB='libz.sl' ;;
- esac ;;
- IRIX*) SFLAGS=${CFLAGS-"-ansi -O2 -rpath ."}
- CFLAGS=${CFLAGS-"-ansi -O2"}
- LDSHARED=${LDSHARED-"cc -shared -Wl,-soname,libz.so.1"} ;;
- OSF1\ V4*) SFLAGS=${CFLAGS-"-O -std1"}
- CFLAGS=${CFLAGS-"-O -std1"}
- LDFLAGS="${LDFLAGS} -Wl,-rpath,."
- LDSHARED=${LDSHARED-"cc -shared -Wl,-soname,libz.so -Wl,-msym -Wl,-rpath,$(libdir) -Wl,-set_version,${VER}:1.0"} ;;
- OSF1*) SFLAGS=${CFLAGS-"-O -std1"}
- CFLAGS=${CFLAGS-"-O -std1"}
- LDSHARED=${LDSHARED-"cc -shared -Wl,-soname,libz.so.1"} ;;
- QNX*) SFLAGS=${CFLAGS-"-4 -O"}
- CFLAGS=${CFLAGS-"-4 -O"}
- LDSHARED=${LDSHARED-"cc"}
- RANLIB=${RANLIB-"true"}
- AR="cc"
- ARFLAGS="-A" ;;
- SCO_SV\ 3.2*) SFLAGS=${CFLAGS-"-O3 -dy -KPIC "}
- CFLAGS=${CFLAGS-"-O3"}
- LDSHARED=${LDSHARED-"cc -dy -KPIC -G"} ;;
- SunOS\ 5* | solaris*)
- LDSHARED=${LDSHARED-"cc -G -h libz$shared_ext.$VER1"}
- SFLAGS=${CFLAGS-"-fast -KPIC"}
- CFLAGS=${CFLAGS-"-fast"}
- if test $build64 -eq 1; then
- # old versions of SunPRO/Workshop/Studio don't support -m64,
- # but newer ones do. Check for it.
- flag64=`$CC -flags | egrep -- '^-m64'`
- if test x"$flag64" != x"" ; then
- CFLAGS="${CFLAGS} -m64"
- SFLAGS="${SFLAGS} -m64"
- else
- case `(uname -m || echo unknown) 2>/dev/null` in
- i86*)
- SFLAGS="$SFLAGS -xarch=amd64"
- CFLAGS="$CFLAGS -xarch=amd64" ;;
- *)
- SFLAGS="$SFLAGS -xarch=v9"
- CFLAGS="$CFLAGS -xarch=v9" ;;
- esac
- fi
- fi
- ;;
- SunOS\ 4*) SFLAGS=${CFLAGS-"-O2 -PIC"}
- CFLAGS=${CFLAGS-"-O2"}
- LDSHARED=${LDSHARED-"ld"} ;;
- SunStudio\ 9*) SFLAGS=${CFLAGS-"-fast -xcode=pic32 -xtarget=ultra3 -xarch=v9b"}
- CFLAGS=${CFLAGS-"-fast -xtarget=ultra3 -xarch=v9b"}
- LDSHARED=${LDSHARED-"cc -xarch=v9b"} ;;
- UNIX_System_V\ 4.2.0)
- SFLAGS=${CFLAGS-"-KPIC -O"}
- CFLAGS=${CFLAGS-"-O"}
- LDSHARED=${LDSHARED-"cc -G"} ;;
- UNIX_SV\ 4.2MP)
- SFLAGS=${CFLAGS-"-Kconform_pic -O"}
- CFLAGS=${CFLAGS-"-O"}
- LDSHARED=${LDSHARED-"cc -G"} ;;
- OpenUNIX\ 5)
- SFLAGS=${CFLAGS-"-KPIC -O"}
- CFLAGS=${CFLAGS-"-O"}
- LDSHARED=${LDSHARED-"cc -G"} ;;
- AIX*) # Courtesy of dbakker at arrayasolutions.com
- SFLAGS=${CFLAGS-"-O -qmaxmem=8192"}
- CFLAGS=${CFLAGS-"-O -qmaxmem=8192"}
- LDSHARED=${LDSHARED-"xlc -G"} ;;
- # send working options for other systems to zlib at gzip.org
- *) SFLAGS=${CFLAGS-"-O"}
- CFLAGS=${CFLAGS-"-O"}
- LDSHARED=${LDSHARED-"cc -shared"} ;;
- esac
-fi
-
-# destination names for shared library if not defined above
-SHAREDLIB=${SHAREDLIB-"libz$shared_ext"}
-SHAREDLIBV=${SHAREDLIBV-"libz$shared_ext.$VER"}
-SHAREDLIBM=${SHAREDLIBM-"libz$shared_ext.$VER1"}
-
-echo >> configure.log
-
-# define functions for testing compiler and library characteristics and logging the results
-
-cat > $test.c <<EOF
-#error error
-EOF
-if ($CC -c $CFLAGS $test.c) 2>/dev/null; then
- try()
- {
- show $*
- test "`( $* ) 2>&1 | tee -a configure.log`" = ""
- }
- echo - using any output from compiler to indicate an error >> configure.log
-else
-try()
-{
- show $*
- ( $* ) >> configure.log 2>&1
- ret=$?
- if test $ret -ne 0; then
- echo "(exit code "$ret")" >> configure.log
- fi
- return $ret
-}
-fi
-
-tryboth()
-{
- show $*
- got=`( $* ) 2>&1`
- ret=$?
- printf %s "$got" >> configure.log
- if test $ret -ne 0; then
- return $ret
- fi
- test "$got" = ""
-}
-
-cat > $test.c << EOF
-int foo() { return 0; }
-EOF
-echo "Checking for obsessive-compulsive compiler options..." >> configure.log
-if try $CC -c $CFLAGS $test.c; then
- :
-else
- echo "Compiler error reporting is too harsh for $0 (perhaps remove -Werror)." | tee -a configure.log
- leave 1
-fi
-
-echo >> configure.log
-
-# see if shared library build supported
-cat > $test.c <<EOF
-extern int getchar();
-int hello() {return getchar();}
-EOF
-if test $shared -eq 1; then
- echo Checking for shared library support... | tee -a configure.log
- # we must test in two steps (cc then ld), required at least on SunOS 4.x
- if try $CC -w -c $SFLAGS $test.c &&
- try $LDSHARED $SFLAGS -o $test$shared_ext $test.o; then
- echo Building shared library $SHAREDLIBV with $CC. | tee -a configure.log
- elif test -z "$old_cc" -a -z "$old_cflags"; then
- echo No shared library support. | tee -a configure.log
- shared=0;
- else
- echo 'No shared library support; try without defining CC and CFLAGS' | tee -a configure.log
- shared=0;
- fi
-fi
-if test $shared -eq 0; then
- LDSHARED="$CC"
- ALL="static"
- TEST="all teststatic"
- SHAREDLIB=""
- SHAREDLIBV=""
- SHAREDLIBM=""
- echo Building static library $STATICLIB version $VER with $CC. | tee -a configure.log
-else
- ALL="static shared"
- TEST="all teststatic testshared"
-fi
-
-# check for underscores in external names for use by assembler code
-CPP=${CPP-"$CC -E"}
-case $CFLAGS in
- *ASMV*)
- echo >> configure.log
- show "$NM $test.o | grep _hello"
- if test "`$NM $test.o | grep _hello | tee -a configure.log`" = ""; then
- CPP="$CPP -DNO_UNDERLINE"
- echo Checking for underline in external names... No. | tee -a configure.log
- else
- echo Checking for underline in external names... Yes. | tee -a configure.log
- fi ;;
-esac
-
-echo >> configure.log
-
-# check for large file support, and if none, check for fseeko()
-cat > $test.c <<EOF
-#include <sys/types.h>
-off64_t dummy = 0;
-EOF
-if try $CC -c $CFLAGS -D_LARGEFILE64_SOURCE=1 $test.c; then
- CFLAGS="${CFLAGS} -D_LARGEFILE64_SOURCE=1"
- SFLAGS="${SFLAGS} -D_LARGEFILE64_SOURCE=1"
- ALL="${ALL} all64"
- TEST="${TEST} test64"
- echo "Checking for off64_t... Yes." | tee -a configure.log
- echo "Checking for fseeko... Yes." | tee -a configure.log
-else
- echo "Checking for off64_t... No." | tee -a configure.log
- echo >> configure.log
- cat > $test.c <<EOF
-#include <stdio.h>
-int main(void) {
- fseeko(NULL, 0, 0);
- return 0;
-}
-EOF
- if try $CC $CFLAGS -o $test $test.c; then
- echo "Checking for fseeko... Yes." | tee -a configure.log
- else
- CFLAGS="${CFLAGS} -DNO_FSEEKO"
- SFLAGS="${SFLAGS} -DNO_FSEEKO"
- echo "Checking for fseeko... No." | tee -a configure.log
- fi
-fi
-
-echo >> configure.log
-
-# check for strerror() for use by gz* functions
-cat > $test.c <<EOF
-#include <string.h>
-#include <errno.h>
-int main() { return strlen(strerror(errno)); }
-EOF
-if try $CC $CFLAGS -o $test $test.c; then
- echo "Checking for strerror... Yes." | tee -a configure.log
-else
- CFLAGS="${CFLAGS} -DNO_STRERROR"
- SFLAGS="${SFLAGS} -DNO_STRERROR"
- echo "Checking for strerror... No." | tee -a configure.log
-fi
-
-# copy clean zconf.h for subsequent edits
-cp -p zconf.h.in zconf.h
-
-echo >> configure.log
-
-# check for unistd.h and save result in zconf.h
-cat > $test.c <<EOF
-#include <unistd.h>
-int main() { return 0; }
-EOF
-if try $CC -c $CFLAGS $test.c; then
- sed < zconf.h "/^#ifdef HAVE_UNISTD_H.* may be/s/def HAVE_UNISTD_H\(.*\) may be/ 1\1 was/" > zconf.temp.h
- mv zconf.temp.h zconf.h
- echo "Checking for unistd.h... Yes." | tee -a configure.log
-else
- echo "Checking for unistd.h... No." | tee -a configure.log
-fi
-
-echo >> configure.log
-
-# check for stdarg.h and save result in zconf.h
-cat > $test.c <<EOF
-#include <stdarg.h>
-int main() { return 0; }
-EOF
-if try $CC -c $CFLAGS $test.c; then
- sed < zconf.h "/^#ifdef HAVE_STDARG_H.* may be/s/def HAVE_STDARG_H\(.*\) may be/ 1\1 was/" > zconf.temp.h
- mv zconf.temp.h zconf.h
- echo "Checking for stdarg.h... Yes." | tee -a configure.log
-else
- echo "Checking for stdarg.h... No." | tee -a configure.log
-fi
-
-# if the z_ prefix was requested, save that in zconf.h
-if test $zprefix -eq 1; then
- sed < zconf.h "/#ifdef Z_PREFIX.* may be/s/def Z_PREFIX\(.*\) may be/ 1\1 was/" > zconf.temp.h
- mv zconf.temp.h zconf.h
- echo >> configure.log
- echo "Using z_ prefix on all symbols." | tee -a configure.log
-fi
-
-# if --solo compilation was requested, save that in zconf.h and remove gz stuff from object lists
-if test $solo -eq 1; then
- sed '/#define ZCONF_H/a\
-#define Z_SOLO
-
-' < zconf.h > zconf.temp.h
- mv zconf.temp.h zconf.h
-OBJC='$(OBJZ)'
-PIC_OBJC='$(PIC_OBJZ)'
-fi
-
-# if code coverage testing was requested, use older gcc if defined, e.g. "gcc-4.2" on Mac OS X
-if test $cover -eq 1; then
- CFLAGS="${CFLAGS} -fprofile-arcs -ftest-coverage"
- if test -n "$GCC_CLASSIC"; then
- CC=$GCC_CLASSIC
- fi
-fi
-
-echo >> configure.log
-
-# conduct a series of tests to resolve eight possible cases of using "vs" or "s" printf functions
-# (using stdarg or not), with or without "n" (proving size of buffer), and with or without a
-# return value. The most secure result is vsnprintf() with a return value. snprintf() with a
-# return value is secure as well, but then gzprintf() will be limited to 20 arguments.
-cat > $test.c <<EOF
-#include <stdio.h>
-#include <stdarg.h>
-#include "zconf.h"
-int main()
-{
-#ifndef STDC
- choke me
-#endif
- return 0;
-}
-EOF
-if try $CC -c $CFLAGS $test.c; then
- echo "Checking whether to use vs[n]printf() or s[n]printf()... using vs[n]printf()." | tee -a configure.log
-
- echo >> configure.log
- cat > $test.c <<EOF
-#include <stdio.h>
-#include <stdarg.h>
-int mytest(const char *fmt, ...)
-{
- char buf[20];
- va_list ap;
- va_start(ap, fmt);
- vsnprintf(buf, sizeof(buf), fmt, ap);
- va_end(ap);
- return 0;
-}
-int main()
-{
- return (mytest("Hello%d\n", 1));
-}
-EOF
- if try $CC $CFLAGS -o $test $test.c; then
- echo "Checking for vsnprintf() in stdio.h... Yes." | tee -a configure.log
-
- echo >> configure.log
- cat >$test.c <<EOF
-#include <stdio.h>
-#include <stdarg.h>
-int mytest(const char *fmt, ...)
-{
- int n;
- char buf[20];
- va_list ap;
- va_start(ap, fmt);
- n = vsnprintf(buf, sizeof(buf), fmt, ap);
- va_end(ap);
- return n;
-}
-int main()
-{
- return (mytest("Hello%d\n", 1));
-}
-EOF
-
- if try $CC -c $CFLAGS $test.c; then
- echo "Checking for return value of vsnprintf()... Yes." | tee -a configure.log
- else
- CFLAGS="$CFLAGS -DHAS_vsnprintf_void"
- SFLAGS="$SFLAGS -DHAS_vsnprintf_void"
- echo "Checking for return value of vsnprintf()... No." | tee -a configure.log
- echo " WARNING: apparently vsnprintf() does not return a value. zlib" | tee -a configure.log
- echo " can build but will be open to possible string-format security" | tee -a configure.log
- echo " vulnerabilities." | tee -a configure.log
- fi
- else
- CFLAGS="$CFLAGS -DNO_vsnprintf"
- SFLAGS="$SFLAGS -DNO_vsnprintf"
- echo "Checking for vsnprintf() in stdio.h... No." | tee -a configure.log
- echo " WARNING: vsnprintf() not found, falling back to vsprintf(). zlib" | tee -a configure.log
- echo " can build but will be open to possible buffer-overflow security" | tee -a configure.log
- echo " vulnerabilities." | tee -a configure.log
-
- echo >> configure.log
- cat >$test.c <<EOF
-#include <stdio.h>
-#include <stdarg.h>
-int mytest(const char *fmt, ...)
-{
- int n;
- char buf[20];
- va_list ap;
- va_start(ap, fmt);
- n = vsprintf(buf, fmt, ap);
- va_end(ap);
- return n;
-}
-int main()
-{
- return (mytest("Hello%d\n", 1));
-}
-EOF
-
- if try $CC -c $CFLAGS $test.c; then
- echo "Checking for return value of vsprintf()... Yes." | tee -a configure.log
- else
- CFLAGS="$CFLAGS -DHAS_vsprintf_void"
- SFLAGS="$SFLAGS -DHAS_vsprintf_void"
- echo "Checking for return value of vsprintf()... No." | tee -a configure.log
- echo " WARNING: apparently vsprintf() does not return a value. zlib" | tee -a configure.log
- echo " can build but will be open to possible string-format security" | tee -a configure.log
- echo " vulnerabilities." | tee -a configure.log
- fi
- fi
-else
- echo "Checking whether to use vs[n]printf() or s[n]printf()... using s[n]printf()." | tee -a configure.log
-
- echo >> configure.log
- cat >$test.c <<EOF
-#include <stdio.h>
-int mytest()
-{
- char buf[20];
- snprintf(buf, sizeof(buf), "%s", "foo");
- return 0;
-}
-int main()
-{
- return (mytest());
-}
-EOF
-
- if try $CC $CFLAGS -o $test $test.c; then
- echo "Checking for snprintf() in stdio.h... Yes." | tee -a configure.log
-
- echo >> configure.log
- cat >$test.c <<EOF
-#include <stdio.h>
-int mytest()
-{
- char buf[20];
- return snprintf(buf, sizeof(buf), "%s", "foo");
-}
-int main()
-{
- return (mytest());
-}
-EOF
-
- if try $CC -c $CFLAGS $test.c; then
- echo "Checking for return value of snprintf()... Yes." | tee -a configure.log
- else
- CFLAGS="$CFLAGS -DHAS_snprintf_void"
- SFLAGS="$SFLAGS -DHAS_snprintf_void"
- echo "Checking for return value of snprintf()... No." | tee -a configure.log
- echo " WARNING: apparently snprintf() does not return a value. zlib" | tee -a configure.log
- echo " can build but will be open to possible string-format security" | tee -a configure.log
- echo " vulnerabilities." | tee -a configure.log
- fi
- else
- CFLAGS="$CFLAGS -DNO_snprintf"
- SFLAGS="$SFLAGS -DNO_snprintf"
- echo "Checking for snprintf() in stdio.h... No." | tee -a configure.log
- echo " WARNING: snprintf() not found, falling back to sprintf(). zlib" | tee -a configure.log
- echo " can build but will be open to possible buffer-overflow security" | tee -a configure.log
- echo " vulnerabilities." | tee -a configure.log
-
- echo >> configure.log
- cat >$test.c <<EOF
-#include <stdio.h>
-int mytest()
-{
- char buf[20];
- return sprintf(buf, "%s", "foo");
-}
-int main()
-{
- return (mytest());
-}
-EOF
-
- if try $CC -c $CFLAGS $test.c; then
- echo "Checking for return value of sprintf()... Yes." | tee -a configure.log
- else
- CFLAGS="$CFLAGS -DHAS_sprintf_void"
- SFLAGS="$SFLAGS -DHAS_sprintf_void"
- echo "Checking for return value of sprintf()... No." | tee -a configure.log
- echo " WARNING: apparently sprintf() does not return a value. zlib" | tee -a configure.log
- echo " can build but will be open to possible string-format security" | tee -a configure.log
- echo " vulnerabilities." | tee -a configure.log
- fi
- fi
-fi
-
-# see if we can hide zlib internal symbols that are linked between separate source files
-if test "$gcc" -eq 1; then
- echo >> configure.log
- cat > $test.c <<EOF
-#define ZLIB_INTERNAL __attribute__((visibility ("hidden")))
-int ZLIB_INTERNAL foo;
-int main()
-{
- return 0;
-}
-EOF
- if tryboth $CC -c $CFLAGS $test.c; then
- CFLAGS="$CFLAGS -DHAVE_HIDDEN"
- SFLAGS="$SFLAGS -DHAVE_HIDDEN"
- echo "Checking for attribute(visibility) support... Yes." | tee -a configure.log
- else
- echo "Checking for attribute(visibility) support... No." | tee -a configure.log
- fi
-fi
-
-# show the results in the log
-echo >> configure.log
-echo ALL = $ALL >> configure.log
-echo AR = $AR >> configure.log
-echo ARFLAGS = $ARFLAGS >> configure.log
-echo CC = $CC >> configure.log
-echo CFLAGS = $CFLAGS >> configure.log
-echo CPP = $CPP >> configure.log
-echo EXE = $EXE >> configure.log
-echo LDCONFIG = $LDCONFIG >> configure.log
-echo LDFLAGS = $LDFLAGS >> configure.log
-echo LDSHARED = $LDSHARED >> configure.log
-echo LDSHAREDLIBC = $LDSHAREDLIBC >> configure.log
-echo OBJC = $OBJC >> configure.log
-echo PIC_OBJC = $PIC_OBJC >> configure.log
-echo RANLIB = $RANLIB >> configure.log
-echo SFLAGS = $SFLAGS >> configure.log
-echo SHAREDLIB = $SHAREDLIB >> configure.log
-echo SHAREDLIBM = $SHAREDLIBM >> configure.log
-echo SHAREDLIBV = $SHAREDLIBV >> configure.log
-echo STATICLIB = $STATICLIB >> configure.log
-echo TEST = $TEST >> configure.log
-echo VER = $VER >> configure.log
-echo Z_U4 = $Z_U4 >> configure.log
-echo exec_prefix = $exec_prefix >> configure.log
-echo includedir = $includedir >> configure.log
-echo libdir = $libdir >> configure.log
-echo mandir = $mandir >> configure.log
-echo prefix = $prefix >> configure.log
-echo sharedlibdir = $sharedlibdir >> configure.log
-echo uname = $uname >> configure.log
-
-# udpate Makefile with the configure results
-sed < Makefile.in "
-/^CC *=/s#=.*#=$CC#
-/^CFLAGS *=/s#=.*#=$CFLAGS#
-/^SFLAGS *=/s#=.*#=$SFLAGS#
-/^LDFLAGS *=/s#=.*#=$LDFLAGS#
-/^LDSHARED *=/s#=.*#=$LDSHARED#
-/^CPP *=/s#=.*#=$CPP#
-/^STATICLIB *=/s#=.*#=$STATICLIB#
-/^SHAREDLIB *=/s#=.*#=$SHAREDLIB#
-/^SHAREDLIBV *=/s#=.*#=$SHAREDLIBV#
-/^SHAREDLIBM *=/s#=.*#=$SHAREDLIBM#
-/^AR *=/s#=.*#=$AR#
-/^ARFLAGS *=/s#=.*#=$ARFLAGS#
-/^RANLIB *=/s#=.*#=$RANLIB#
-/^LDCONFIG *=/s#=.*#=$LDCONFIG#
-/^LDSHAREDLIBC *=/s#=.*#=$LDSHAREDLIBC#
-/^EXE *=/s#=.*#=$EXE#
-/^prefix *=/s#=.*#=$prefix#
-/^exec_prefix *=/s#=.*#=$exec_prefix#
-/^libdir *=/s#=.*#=$libdir#
-/^sharedlibdir *=/s#=.*#=$sharedlibdir#
-/^includedir *=/s#=.*#=$includedir#
-/^mandir *=/s#=.*#=$mandir#
-/^OBJC *=/s#=.*#= $OBJC#
-/^PIC_OBJC *=/s#=.*#= $PIC_OBJC#
-/^all: */s#:.*#: $ALL#
-/^test: */s#:.*#: $TEST#
-" > Makefile
-
-# create zlib.pc with the configure results
-sed < zlib.pc.in "
-/^CC *=/s#=.*#=$CC#
-/^CFLAGS *=/s#=.*#=$CFLAGS#
-/^CPP *=/s#=.*#=$CPP#
-/^LDSHARED *=/s#=.*#=$LDSHARED#
-/^STATICLIB *=/s#=.*#=$STATICLIB#
-/^SHAREDLIB *=/s#=.*#=$SHAREDLIB#
-/^SHAREDLIBV *=/s#=.*#=$SHAREDLIBV#
-/^SHAREDLIBM *=/s#=.*#=$SHAREDLIBM#
-/^AR *=/s#=.*#=$AR#
-/^ARFLAGS *=/s#=.*#=$ARFLAGS#
-/^RANLIB *=/s#=.*#=$RANLIB#
-/^EXE *=/s#=.*#=$EXE#
-/^prefix *=/s#=.*#=$prefix#
-/^exec_prefix *=/s#=.*#=$exec_prefix#
-/^libdir *=/s#=.*#=$libdir#
-/^sharedlibdir *=/s#=.*#=$sharedlibdir#
-/^includedir *=/s#=.*#=$includedir#
-/^mandir *=/s#=.*#=$mandir#
-/^LDFLAGS *=/s#=.*#=$LDFLAGS#
-" | sed -e "
-s/\@VERSION\@/$VER/g;
-" > zlib.pc
-
-# done
-leave 0
diff --git a/third-party/zlib/contrib/README.contrib b/third-party/zlib/contrib/README.contrib
deleted file mode 100644
index c66349b..0000000
--- a/third-party/zlib/contrib/README.contrib
+++ /dev/null
@@ -1,78 +0,0 @@
-All files under this contrib directory are UNSUPPORTED. There were
-provided by users of zlib and were not tested by the authors of zlib.
-Use at your own risk. Please contact the authors of the contributions
-for help about these, not the zlib authors. Thanks.
-
-
-ada/ by Dmitriy Anisimkov <anisimkov at yahoo.com>
- Support for Ada
- See http://zlib-ada.sourceforge.net/
-
-amd64/ by Mikhail Teterin <mi at ALDAN.algebra.com>
- asm code for AMD64
- See patch at http://www.freebsd.org/cgi/query-pr.cgi?pr=bin/96393
-
-asm686/ by Brian Raiter <breadbox at muppetlabs.com>
- asm code for Pentium and PPro/PII, using the AT&T (GNU as) syntax
- See http://www.muppetlabs.com/~breadbox/software/assembly.html
-
-blast/ by Mark Adler <madler at alumni.caltech.edu>
- Decompressor for output of PKWare Data Compression Library (DCL)
-
-delphi/ by Cosmin Truta <cosmint at cs.ubbcluj.ro>
- Support for Delphi and C++ Builder
-
-dotzlib/ by Henrik Ravn <henrik at ravn.com>
- Support for Microsoft .Net and Visual C++ .Net
-
-gcc_gvmat64/by Gilles Vollant <info at winimage.com>
- GCC Version of x86 64-bit (AMD64 and Intel EM64t) code for x64
- assembler to replace longest_match() and inflate_fast()
-
-infback9/ by Mark Adler <madler at alumni.caltech.edu>
- Unsupported diffs to infback to decode the deflate64 format
-
-inflate86/ by Chris Anderson <christop at charm.net>
- Tuned x86 gcc asm code to replace inflate_fast()
-
-iostream/ by Kevin Ruland <kevin at rodin.wustl.edu>
- A C++ I/O streams interface to the zlib gz* functions
-
-iostream2/ by Tyge L�vset <Tyge.Lovset at cmr.no>
- Another C++ I/O streams interface
-
-iostream3/ by Ludwig Schwardt <schwardt at sun.ac.za>
- and Kevin Ruland <kevin at rodin.wustl.edu>
- Yet another C++ I/O streams interface
-
-masmx64/ by Gilles Vollant <info at winimage.com>
- x86 64-bit (AMD64 and Intel EM64t) code for x64 assembler to
- replace longest_match() and inflate_fast(), also masm x86
- 64-bits translation of Chris Anderson inflate_fast()
-
-masmx86/ by Gilles Vollant <info at winimage.com>
- x86 asm code to replace longest_match() and inflate_fast(),
- for Visual C++ and MASM (32 bits).
- Based on Brian Raiter (asm686) and Chris Anderson (inflate86)
-
-minizip/ by Gilles Vollant <info at winimage.com>
- Mini zip and unzip based on zlib
- Includes Zip64 support by Mathias Svensson <mathias at result42.com>
- See http://www.winimage.com/zLibDll/unzip.html
-
-pascal/ by Bob Dellaca <bobdl at xtra.co.nz> et al.
- Support for Pascal
-
-puff/ by Mark Adler <madler at alumni.caltech.edu>
- Small, low memory usage inflate. Also serves to provide an
- unambiguous description of the deflate format.
-
-testzlib/ by Gilles Vollant <info at winimage.com>
- Example of the use of zlib
-
-untgz/ by Pedro A. Aranda Gutierrez <paag at tid.es>
- A very simple tar.gz file extractor using zlib
-
-vstudio/ by Gilles Vollant <info at winimage.com>
- Building a minizip-enhanced zlib with Microsoft Visual Studio
- Includes vc11 from kreuzerkrieg and vc12 from davispuh
diff --git a/third-party/zlib/contrib/ada/buffer_demo.adb b/third-party/zlib/contrib/ada/buffer_demo.adb
deleted file mode 100644
index 46b8638..0000000
--- a/third-party/zlib/contrib/ada/buffer_demo.adb
+++ /dev/null
@@ -1,106 +0,0 @@
-----------------------------------------------------------------
--- ZLib for Ada thick binding. --
--- --
--- Copyright (C) 2002-2004 Dmitriy Anisimkov --
--- --
--- Open source license information is in the zlib.ads file. --
-----------------------------------------------------------------
---
--- $Id: buffer_demo.adb,v 1.3 2004/09/06 06:55:35 vagul Exp $
-
--- This demo program provided by Dr Steve Sangwine <sjs at essex.ac.uk>
---
--- Demonstration of a problem with Zlib-Ada (already fixed) when a buffer
--- of exactly the correct size is used for decompressed data, and the last
--- few bytes passed in to Zlib are checksum bytes.
-
--- This program compresses a string of text, and then decompresses the
--- compressed text into a buffer of the same size as the original text.
-
-with Ada.Streams; use Ada.Streams;
-with Ada.Text_IO;
-
-with ZLib; use ZLib;
-
-procedure Buffer_Demo is
- EOL : Character renames ASCII.LF;
- Text : constant String
- := "Four score and seven years ago our fathers brought forth," & EOL &
- "upon this continent, a new nation, conceived in liberty," & EOL &
- "and dedicated to the proposition that `all men are created equal'.";
-
- Source : Stream_Element_Array (1 .. Text'Length);
- for Source'Address use Text'Address;
-
-begin
- Ada.Text_IO.Put (Text);
- Ada.Text_IO.New_Line;
- Ada.Text_IO.Put_Line
- ("Uncompressed size : " & Positive'Image (Text'Length) & " bytes");
-
- declare
- Compressed_Data : Stream_Element_Array (1 .. Text'Length);
- L : Stream_Element_Offset;
- begin
- Compress : declare
- Compressor : Filter_Type;
- I : Stream_Element_Offset;
- begin
- Deflate_Init (Compressor);
-
- -- Compress the whole of T at once.
-
- Translate (Compressor, Source, I, Compressed_Data, L, Finish);
- pragma Assert (I = Source'Last);
-
- Close (Compressor);
-
- Ada.Text_IO.Put_Line
- ("Compressed size : "
- & Stream_Element_Offset'Image (L) & " bytes");
- end Compress;
-
- -- Now we decompress the data, passing short blocks of data to Zlib
- -- (because this demonstrates the problem - the last block passed will
- -- contain checksum information and there will be no output, only a
- -- check inside Zlib that the checksum is correct).
-
- Decompress : declare
- Decompressor : Filter_Type;
-
- Uncompressed_Data : Stream_Element_Array (1 .. Text'Length);
-
- Block_Size : constant := 4;
- -- This makes sure that the last block contains
- -- only Adler checksum data.
-
- P : Stream_Element_Offset := Compressed_Data'First - 1;
- O : Stream_Element_Offset;
- begin
- Inflate_Init (Decompressor);
-
- loop
- Translate
- (Decompressor,
- Compressed_Data
- (P + 1 .. Stream_Element_Offset'Min (P + Block_Size, L)),
- P,
- Uncompressed_Data
- (Total_Out (Decompressor) + 1 .. Uncompressed_Data'Last),
- O,
- No_Flush);
-
- Ada.Text_IO.Put_Line
- ("Total in : " & Count'Image (Total_In (Decompressor)) &
- ", out : " & Count'Image (Total_Out (Decompressor)));
-
- exit when P = L;
- end loop;
-
- Ada.Text_IO.New_Line;
- Ada.Text_IO.Put_Line
- ("Decompressed text matches original text : "
- & Boolean'Image (Uncompressed_Data = Source));
- end Decompress;
- end;
-end Buffer_Demo;
diff --git a/third-party/zlib/contrib/ada/mtest.adb b/third-party/zlib/contrib/ada/mtest.adb
deleted file mode 100644
index c4dfd08..0000000
--- a/third-party/zlib/contrib/ada/mtest.adb
+++ /dev/null
@@ -1,156 +0,0 @@
-----------------------------------------------------------------
--- ZLib for Ada thick binding. --
--- --
--- Copyright (C) 2002-2003 Dmitriy Anisimkov --
--- --
--- Open source license information is in the zlib.ads file. --
-----------------------------------------------------------------
--- Continuous test for ZLib multithreading. If the test would fail
--- we should provide thread safe allocation routines for the Z_Stream.
---
--- $Id: mtest.adb,v 1.4 2004/07/23 07:49:54 vagul Exp $
-
-with ZLib;
-with Ada.Streams;
-with Ada.Numerics.Discrete_Random;
-with Ada.Text_IO;
-with Ada.Exceptions;
-with Ada.Task_Identification;
-
-procedure MTest is
- use Ada.Streams;
- use ZLib;
-
- Stop : Boolean := False;
-
- pragma Atomic (Stop);
-
- subtype Visible_Symbols is Stream_Element range 16#20# .. 16#7E#;
-
- package Random_Elements is
- new Ada.Numerics.Discrete_Random (Visible_Symbols);
-
- task type Test_Task;
-
- task body Test_Task is
- Buffer : Stream_Element_Array (1 .. 100_000);
- Gen : Random_Elements.Generator;
-
- Buffer_First : Stream_Element_Offset;
- Compare_First : Stream_Element_Offset;
-
- Deflate : Filter_Type;
- Inflate : Filter_Type;
-
- procedure Further (Item : in Stream_Element_Array);
-
- procedure Read_Buffer
- (Item : out Ada.Streams.Stream_Element_Array;
- Last : out Ada.Streams.Stream_Element_Offset);
-
- -------------
- -- Further --
- -------------
-
- procedure Further (Item : in Stream_Element_Array) is
-
- procedure Compare (Item : in Stream_Element_Array);
-
- -------------
- -- Compare --
- -------------
-
- procedure Compare (Item : in Stream_Element_Array) is
- Next_First : Stream_Element_Offset := Compare_First + Item'Length;
- begin
- if Buffer (Compare_First .. Next_First - 1) /= Item then
- raise Program_Error;
- end if;
-
- Compare_First := Next_First;
- end Compare;
-
- procedure Compare_Write is new ZLib.Write (Write => Compare);
- begin
- Compare_Write (Inflate, Item, No_Flush);
- end Further;
-
- -----------------
- -- Read_Buffer --
- -----------------
-
- procedure Read_Buffer
- (Item : out Ada.Streams.Stream_Element_Array;
- Last : out Ada.Streams.Stream_Element_Offset)
- is
- Buff_Diff : Stream_Element_Offset := Buffer'Last - Buffer_First;
- Next_First : Stream_Element_Offset;
- begin
- if Item'Length <= Buff_Diff then
- Last := Item'Last;
-
- Next_First := Buffer_First + Item'Length;
-
- Item := Buffer (Buffer_First .. Next_First - 1);
-
- Buffer_First := Next_First;
- else
- Last := Item'First + Buff_Diff;
- Item (Item'First .. Last) := Buffer (Buffer_First .. Buffer'Last);
- Buffer_First := Buffer'Last + 1;
- end if;
- end Read_Buffer;
-
- procedure Translate is new Generic_Translate
- (Data_In => Read_Buffer,
- Data_Out => Further);
-
- begin
- Random_Elements.Reset (Gen);
-
- Buffer := (others => 20);
-
- Main : loop
- for J in Buffer'Range loop
- Buffer (J) := Random_Elements.Random (Gen);
-
- Deflate_Init (Deflate);
- Inflate_Init (Inflate);
-
- Buffer_First := Buffer'First;
- Compare_First := Buffer'First;
-
- Translate (Deflate);
-
- if Compare_First /= Buffer'Last + 1 then
- raise Program_Error;
- end if;
-
- Ada.Text_IO.Put_Line
- (Ada.Task_Identification.Image
- (Ada.Task_Identification.Current_Task)
- & Stream_Element_Offset'Image (J)
- & ZLib.Count'Image (Total_Out (Deflate)));
-
- Close (Deflate);
- Close (Inflate);
-
- exit Main when Stop;
- end loop;
- end loop Main;
- exception
- when E : others =>
- Ada.Text_IO.Put_Line (Ada.Exceptions.Exception_Information (E));
- Stop := True;
- end Test_Task;
-
- Test : array (1 .. 4) of Test_Task;
-
- pragma Unreferenced (Test);
-
- Dummy : Character;
-
-begin
- Ada.Text_IO.Get_Immediate (Dummy);
- Stop := True;
-end MTest;
diff --git a/third-party/zlib/contrib/ada/read.adb b/third-party/zlib/contrib/ada/read.adb
deleted file mode 100644
index 1f2efbf..0000000
--- a/third-party/zlib/contrib/ada/read.adb
+++ /dev/null
@@ -1,156 +0,0 @@
-----------------------------------------------------------------
--- ZLib for Ada thick binding. --
--- --
--- Copyright (C) 2002-2003 Dmitriy Anisimkov --
--- --
--- Open source license information is in the zlib.ads file. --
-----------------------------------------------------------------
-
--- $Id: read.adb,v 1.8 2004/05/31 10:53:40 vagul Exp $
-
--- Test/demo program for the generic read interface.
-
-with Ada.Numerics.Discrete_Random;
-with Ada.Streams;
-with Ada.Text_IO;
-
-with ZLib;
-
-procedure Read is
-
- use Ada.Streams;
-
- ------------------------------------
- -- Test configuration parameters --
- ------------------------------------
-
- File_Size : Stream_Element_Offset := 100_000;
-
- Continuous : constant Boolean := False;
- -- If this constant is True, the test would be repeated again and again,
- -- with increment File_Size for every iteration.
-
- Header : constant ZLib.Header_Type := ZLib.Default;
- -- Do not use Header other than Default in ZLib versions 1.1.4 and older.
-
- Init_Random : constant := 8;
- -- We are using the same random sequence, in case of we catch bug,
- -- so we would be able to reproduce it.
-
- -- End --
-
- Pack_Size : Stream_Element_Offset;
- Offset : Stream_Element_Offset;
-
- Filter : ZLib.Filter_Type;
-
- subtype Visible_Symbols
- is Stream_Element range 16#20# .. 16#7E#;
-
- package Random_Elements is new
- Ada.Numerics.Discrete_Random (Visible_Symbols);
-
- Gen : Random_Elements.Generator;
- Period : constant Stream_Element_Offset := 200;
- -- Period constant variable for random generator not to be very random.
- -- Bigger period, harder random.
-
- Read_Buffer : Stream_Element_Array (1 .. 2048);
- Read_First : Stream_Element_Offset;
- Read_Last : Stream_Element_Offset;
-
- procedure Reset;
-
- procedure Read
- (Item : out Stream_Element_Array;
- Last : out Stream_Element_Offset);
- -- this procedure is for generic instantiation of
- -- ZLib.Read
- -- reading data from the File_In.
-
- procedure Read is new ZLib.Read
- (Read,
- Read_Buffer,
- Rest_First => Read_First,
- Rest_Last => Read_Last);
-
- ----------
- -- Read --
- ----------
-
- procedure Read
- (Item : out Stream_Element_Array;
- Last : out Stream_Element_Offset) is
- begin
- Last := Stream_Element_Offset'Min
- (Item'Last,
- Item'First + File_Size - Offset);
-
- for J in Item'First .. Last loop
- if J < Item'First + Period then
- Item (J) := Random_Elements.Random (Gen);
- else
- Item (J) := Item (J - Period);
- end if;
-
- Offset := Offset + 1;
- end loop;
- end Read;
-
- -----------
- -- Reset --
- -----------
-
- procedure Reset is
- begin
- Random_Elements.Reset (Gen, Init_Random);
- Pack_Size := 0;
- Offset := 1;
- Read_First := Read_Buffer'Last + 1;
- Read_Last := Read_Buffer'Last;
- end Reset;
-
-begin
- Ada.Text_IO.Put_Line ("ZLib " & ZLib.Version);
-
- loop
- for Level in ZLib.Compression_Level'Range loop
-
- Ada.Text_IO.Put ("Level ="
- & ZLib.Compression_Level'Image (Level));
-
- -- Deflate using generic instantiation.
-
- ZLib.Deflate_Init
- (Filter,
- Level,
- Header => Header);
-
- Reset;
-
- Ada.Text_IO.Put
- (Stream_Element_Offset'Image (File_Size) & " ->");
-
- loop
- declare
- Buffer : Stream_Element_Array (1 .. 1024);
- Last : Stream_Element_Offset;
- begin
- Read (Filter, Buffer, Last);
-
- Pack_Size := Pack_Size + Last - Buffer'First + 1;
-
- exit when Last < Buffer'Last;
- end;
- end loop;
-
- Ada.Text_IO.Put_Line (Stream_Element_Offset'Image (Pack_Size));
-
- ZLib.Close (Filter);
- end loop;
-
- exit when not Continuous;
-
- File_Size := File_Size + 1;
- end loop;
-end Read;
diff --git a/third-party/zlib/contrib/ada/readme.txt b/third-party/zlib/contrib/ada/readme.txt
deleted file mode 100644
index ce4d2ca..0000000
--- a/third-party/zlib/contrib/ada/readme.txt
+++ /dev/null
@@ -1,65 +0,0 @@
- ZLib for Ada thick binding (ZLib.Ada)
- Release 1.3
-
-ZLib.Ada is a thick binding interface to the popular ZLib data
-compression library, available at http://www.gzip.org/zlib/.
-It provides Ada-style access to the ZLib C library.
-
-
- Here are the main changes since ZLib.Ada 1.2:
-
-- Attension: ZLib.Read generic routine have a initialization requirement
- for Read_Last parameter now. It is a bit incompartible with previous version,
- but extends functionality, we could use new parameters Allow_Read_Some and
- Flush now.
-
-- Added Is_Open routines to ZLib and ZLib.Streams packages.
-
-- Add pragma Assert to check Stream_Element is 8 bit.
-
-- Fix extraction to buffer with exact known decompressed size. Error reported by
- Steve Sangwine.
-
-- Fix definition of ULong (changed to unsigned_long), fix regression on 64 bits
- computers. Patch provided by Pascal Obry.
-
-- Add Status_Error exception definition.
-
-- Add pragma Assertion that Ada.Streams.Stream_Element size is 8 bit.
-
-
- How to build ZLib.Ada under GNAT
-
-You should have the ZLib library already build on your computer, before
-building ZLib.Ada. Make the directory of ZLib.Ada sources current and
-issue the command:
-
- gnatmake test -largs -L<directory where libz.a is> -lz
-
-Or use the GNAT project file build for GNAT 3.15 or later:
-
- gnatmake -Pzlib.gpr -L<directory where libz.a is>
-
-
- How to build ZLib.Ada under Aonix ObjectAda for Win32 7.2.2
-
-1. Make a project with all *.ads and *.adb files from the distribution.
-2. Build the libz.a library from the ZLib C sources.
-3. Rename libz.a to z.lib.
-4. Add the library z.lib to the project.
-5. Add the libc.lib library from the ObjectAda distribution to the project.
-6. Build the executable using test.adb as a main procedure.
-
-
- How to use ZLib.Ada
-
-The source files test.adb and read.adb are small demo programs that show
-the main functionality of ZLib.Ada.
-
-The routines from the package specifications are commented.
-
-
-Homepage: http://zlib-ada.sourceforge.net/
-Author: Dmitriy Anisimkov <anisimkov at yahoo.com>
-
-Contributors: Pascal Obry <pascal at obry.org>, Steve Sangwine <sjs at essex.ac.uk>
diff --git a/third-party/zlib/contrib/ada/test.adb b/third-party/zlib/contrib/ada/test.adb
deleted file mode 100644
index 90773ac..0000000
--- a/third-party/zlib/contrib/ada/test.adb
+++ /dev/null
@@ -1,463 +0,0 @@
-----------------------------------------------------------------
--- ZLib for Ada thick binding. --
--- --
--- Copyright (C) 2002-2003 Dmitriy Anisimkov --
--- --
--- Open source license information is in the zlib.ads file. --
-----------------------------------------------------------------
-
--- $Id: test.adb,v 1.17 2003/08/12 12:13:30 vagul Exp $
-
--- The program has a few aims.
--- 1. Test ZLib.Ada95 thick binding functionality.
--- 2. Show the example of use main functionality of the ZLib.Ada95 binding.
--- 3. Build this program automatically compile all ZLib.Ada95 packages under
--- GNAT Ada95 compiler.
-
-with ZLib.Streams;
-with Ada.Streams.Stream_IO;
-with Ada.Numerics.Discrete_Random;
-
-with Ada.Text_IO;
-
-with Ada.Calendar;
-
-procedure Test is
-
- use Ada.Streams;
- use Stream_IO;
-
- ------------------------------------
- -- Test configuration parameters --
- ------------------------------------
-
- File_Size : Count := 100_000;
- Continuous : constant Boolean := False;
-
- Header : constant ZLib.Header_Type := ZLib.Default;
- -- ZLib.None;
- -- ZLib.Auto;
- -- ZLib.GZip;
- -- Do not use Header other then Default in ZLib versions 1.1.4
- -- and older.
-
- Strategy : constant ZLib.Strategy_Type := ZLib.Default_Strategy;
- Init_Random : constant := 10;
-
- -- End --
-
- In_File_Name : constant String := "testzlib.in";
- -- Name of the input file
-
- Z_File_Name : constant String := "testzlib.zlb";
- -- Name of the compressed file.
-
- Out_File_Name : constant String := "testzlib.out";
- -- Name of the decompressed file.
-
- File_In : File_Type;
- File_Out : File_Type;
- File_Back : File_Type;
- File_Z : ZLib.Streams.Stream_Type;
-
- Filter : ZLib.Filter_Type;
-
- Time_Stamp : Ada.Calendar.Time;
-
- procedure Generate_File;
- -- Generate file of spetsified size with some random data.
- -- The random data is repeatable, for the good compression.
-
- procedure Compare_Streams
- (Left, Right : in out Root_Stream_Type'Class);
- -- The procedure compearing data in 2 streams.
- -- It is for compare data before and after compression/decompression.
-
- procedure Compare_Files (Left, Right : String);
- -- Compare files. Based on the Compare_Streams.
-
- procedure Copy_Streams
- (Source, Target : in out Root_Stream_Type'Class;
- Buffer_Size : in Stream_Element_Offset := 1024);
- -- Copying data from one stream to another. It is for test stream
- -- interface of the library.
-
- procedure Data_In
- (Item : out Stream_Element_Array;
- Last : out Stream_Element_Offset);
- -- this procedure is for generic instantiation of
- -- ZLib.Generic_Translate.
- -- reading data from the File_In.
-
- procedure Data_Out (Item : in Stream_Element_Array);
- -- this procedure is for generic instantiation of
- -- ZLib.Generic_Translate.
- -- writing data to the File_Out.
-
- procedure Stamp;
- -- Store the timestamp to the local variable.
-
- procedure Print_Statistic (Msg : String; Data_Size : ZLib.Count);
- -- Print the time statistic with the message.
-
- procedure Translate is new ZLib.Generic_Translate
- (Data_In => Data_In,
- Data_Out => Data_Out);
- -- This procedure is moving data from File_In to File_Out
- -- with compression or decompression, depend on initialization of
- -- Filter parameter.
-
- -------------------
- -- Compare_Files --
- -------------------
-
- procedure Compare_Files (Left, Right : String) is
- Left_File, Right_File : File_Type;
- begin
- Open (Left_File, In_File, Left);
- Open (Right_File, In_File, Right);
- Compare_Streams (Stream (Left_File).all, Stream (Right_File).all);
- Close (Left_File);
- Close (Right_File);
- end Compare_Files;
-
- ---------------------
- -- Compare_Streams --
- ---------------------
-
- procedure Compare_Streams
- (Left, Right : in out Ada.Streams.Root_Stream_Type'Class)
- is
- Left_Buffer, Right_Buffer : Stream_Element_Array (0 .. 16#FFF#);
- Left_Last, Right_Last : Stream_Element_Offset;
- begin
- loop
- Read (Left, Left_Buffer, Left_Last);
- Read (Right, Right_Buffer, Right_Last);
-
- if Left_Last /= Right_Last then
- Ada.Text_IO.Put_Line ("Compare error :"
- & Stream_Element_Offset'Image (Left_Last)
- & " /= "
- & Stream_Element_Offset'Image (Right_Last));
-
- raise Constraint_Error;
-
- elsif Left_Buffer (0 .. Left_Last)
- /= Right_Buffer (0 .. Right_Last)
- then
- Ada.Text_IO.Put_Line ("ERROR: IN and OUT files is not equal.");
- raise Constraint_Error;
-
- end if;
-
- exit when Left_Last < Left_Buffer'Last;
- end loop;
- end Compare_Streams;
-
- ------------------
- -- Copy_Streams --
- ------------------
-
- procedure Copy_Streams
- (Source, Target : in out Ada.Streams.Root_Stream_Type'Class;
- Buffer_Size : in Stream_Element_Offset := 1024)
- is
- Buffer : Stream_Element_Array (1 .. Buffer_Size);
- Last : Stream_Element_Offset;
- begin
- loop
- Read (Source, Buffer, Last);
- Write (Target, Buffer (1 .. Last));
-
- exit when Last < Buffer'Last;
- end loop;
- end Copy_Streams;
-
- -------------
- -- Data_In --
- -------------
-
- procedure Data_In
- (Item : out Stream_Element_Array;
- Last : out Stream_Element_Offset) is
- begin
- Read (File_In, Item, Last);
- end Data_In;
-
- --------------
- -- Data_Out --
- --------------
-
- procedure Data_Out (Item : in Stream_Element_Array) is
- begin
- Write (File_Out, Item);
- end Data_Out;
-
- -------------------
- -- Generate_File --
- -------------------
-
- procedure Generate_File is
- subtype Visible_Symbols is Stream_Element range 16#20# .. 16#7E#;
-
- package Random_Elements is
- new Ada.Numerics.Discrete_Random (Visible_Symbols);
-
- Gen : Random_Elements.Generator;
- Buffer : Stream_Element_Array := (1 .. 77 => 16#20#) & 10;
-
- Buffer_Count : constant Count := File_Size / Buffer'Length;
- -- Number of same buffers in the packet.
-
- Density : constant Count := 30; -- from 0 to Buffer'Length - 2;
-
- procedure Fill_Buffer (J, D : in Count);
- -- Change the part of the buffer.
-
- -----------------
- -- Fill_Buffer --
- -----------------
-
- procedure Fill_Buffer (J, D : in Count) is
- begin
- for K in 0 .. D loop
- Buffer
- (Stream_Element_Offset ((J + K) mod (Buffer'Length - 1) + 1))
- := Random_Elements.Random (Gen);
-
- end loop;
- end Fill_Buffer;
-
- begin
- Random_Elements.Reset (Gen, Init_Random);
-
- Create (File_In, Out_File, In_File_Name);
-
- Fill_Buffer (1, Buffer'Length - 2);
-
- for J in 1 .. Buffer_Count loop
- Write (File_In, Buffer);
-
- Fill_Buffer (J, Density);
- end loop;
-
- -- fill remain size.
-
- Write
- (File_In,
- Buffer
- (1 .. Stream_Element_Offset
- (File_Size - Buffer'Length * Buffer_Count)));
-
- Flush (File_In);
- Close (File_In);
- end Generate_File;
-
- ---------------------
- -- Print_Statistic --
- ---------------------
-
- procedure Print_Statistic (Msg : String; Data_Size : ZLib.Count) is
- use Ada.Calendar;
- use Ada.Text_IO;
-
- package Count_IO is new Integer_IO (ZLib.Count);
-
- Curr_Dur : Duration := Clock - Time_Stamp;
- begin
- Put (Msg);
-
- Set_Col (20);
- Ada.Text_IO.Put ("size =");
-
- Count_IO.Put
- (Data_Size,
- Width => Stream_IO.Count'Image (File_Size)'Length);
-
- Put_Line (" duration =" & Duration'Image (Curr_Dur));
- end Print_Statistic;
-
- -----------
- -- Stamp --
- -----------
-
- procedure Stamp is
- begin
- Time_Stamp := Ada.Calendar.Clock;
- end Stamp;
-
-begin
- Ada.Text_IO.Put_Line ("ZLib " & ZLib.Version);
-
- loop
- Generate_File;
-
- for Level in ZLib.Compression_Level'Range loop
-
- Ada.Text_IO.Put_Line ("Level ="
- & ZLib.Compression_Level'Image (Level));
-
- -- Test generic interface.
- Open (File_In, In_File, In_File_Name);
- Create (File_Out, Out_File, Z_File_Name);
-
- Stamp;
-
- -- Deflate using generic instantiation.
-
- ZLib.Deflate_Init
- (Filter => Filter,
- Level => Level,
- Strategy => Strategy,
- Header => Header);
-
- Translate (Filter);
- Print_Statistic ("Generic compress", ZLib.Total_Out (Filter));
- ZLib.Close (Filter);
-
- Close (File_In);
- Close (File_Out);
-
- Open (File_In, In_File, Z_File_Name);
- Create (File_Out, Out_File, Out_File_Name);
-
- Stamp;
-
- -- Inflate using generic instantiation.
-
- ZLib.Inflate_Init (Filter, Header => Header);
-
- Translate (Filter);
- Print_Statistic ("Generic decompress", ZLib.Total_Out (Filter));
-
- ZLib.Close (Filter);
-
- Close (File_In);
- Close (File_Out);
-
- Compare_Files (In_File_Name, Out_File_Name);
-
- -- Test stream interface.
-
- -- Compress to the back stream.
-
- Open (File_In, In_File, In_File_Name);
- Create (File_Back, Out_File, Z_File_Name);
-
- Stamp;
-
- ZLib.Streams.Create
- (Stream => File_Z,
- Mode => ZLib.Streams.Out_Stream,
- Back => ZLib.Streams.Stream_Access
- (Stream (File_Back)),
- Back_Compressed => True,
- Level => Level,
- Strategy => Strategy,
- Header => Header);
-
- Copy_Streams
- (Source => Stream (File_In).all,
- Target => File_Z);
-
- -- Flushing internal buffers to the back stream.
-
- ZLib.Streams.Flush (File_Z, ZLib.Finish);
-
- Print_Statistic ("Write compress",
- ZLib.Streams.Write_Total_Out (File_Z));
-
- ZLib.Streams.Close (File_Z);
-
- Close (File_In);
- Close (File_Back);
-
- -- Compare reading from original file and from
- -- decompression stream.
-
- Open (File_In, In_File, In_File_Name);
- Open (File_Back, In_File, Z_File_Name);
-
- ZLib.Streams.Create
- (Stream => File_Z,
- Mode => ZLib.Streams.In_Stream,
- Back => ZLib.Streams.Stream_Access
- (Stream (File_Back)),
- Back_Compressed => True,
- Header => Header);
-
- Stamp;
- Compare_Streams (Stream (File_In).all, File_Z);
-
- Print_Statistic ("Read decompress",
- ZLib.Streams.Read_Total_Out (File_Z));
-
- ZLib.Streams.Close (File_Z);
- Close (File_In);
- Close (File_Back);
-
- -- Compress by reading from compression stream.
-
- Open (File_Back, In_File, In_File_Name);
- Create (File_Out, Out_File, Z_File_Name);
-
- ZLib.Streams.Create
- (Stream => File_Z,
- Mode => ZLib.Streams.In_Stream,
- Back => ZLib.Streams.Stream_Access
- (Stream (File_Back)),
- Back_Compressed => False,
- Level => Level,
- Strategy => Strategy,
- Header => Header);
-
- Stamp;
- Copy_Streams
- (Source => File_Z,
- Target => Stream (File_Out).all);
-
- Print_Statistic ("Read compress",
- ZLib.Streams.Read_Total_Out (File_Z));
-
- ZLib.Streams.Close (File_Z);
-
- Close (File_Out);
- Close (File_Back);
-
- -- Decompress to decompression stream.
-
- Open (File_In, In_File, Z_File_Name);
- Create (File_Back, Out_File, Out_File_Name);
-
- ZLib.Streams.Create
- (Stream => File_Z,
- Mode => ZLib.Streams.Out_Stream,
- Back => ZLib.Streams.Stream_Access
- (Stream (File_Back)),
- Back_Compressed => False,
- Header => Header);
-
- Stamp;
-
- Copy_Streams
- (Source => Stream (File_In).all,
- Target => File_Z);
-
- Print_Statistic ("Write decompress",
- ZLib.Streams.Write_Total_Out (File_Z));
-
- ZLib.Streams.Close (File_Z);
- Close (File_In);
- Close (File_Back);
-
- Compare_Files (In_File_Name, Out_File_Name);
- end loop;
-
- Ada.Text_IO.Put_Line (Count'Image (File_Size) & " Ok.");
-
- exit when not Continuous;
-
- File_Size := File_Size + 1;
- end loop;
-end Test;
diff --git a/third-party/zlib/contrib/ada/zlib-streams.adb b/third-party/zlib/contrib/ada/zlib-streams.adb
deleted file mode 100644
index b6497ba..0000000
--- a/third-party/zlib/contrib/ada/zlib-streams.adb
+++ /dev/null
@@ -1,225 +0,0 @@
-----------------------------------------------------------------
--- ZLib for Ada thick binding. --
--- --
--- Copyright (C) 2002-2003 Dmitriy Anisimkov --
--- --
--- Open source license information is in the zlib.ads file. --
-----------------------------------------------------------------
-
--- $Id: zlib-streams.adb,v 1.10 2004/05/31 10:53:40 vagul Exp $
-
-with Ada.Unchecked_Deallocation;
-
-package body ZLib.Streams is
-
- -----------
- -- Close --
- -----------
-
- procedure Close (Stream : in out Stream_Type) is
- procedure Free is new Ada.Unchecked_Deallocation
- (Stream_Element_Array, Buffer_Access);
- begin
- if Stream.Mode = Out_Stream or Stream.Mode = Duplex then
- -- We should flush the data written by the writer.
-
- Flush (Stream, Finish);
-
- Close (Stream.Writer);
- end if;
-
- if Stream.Mode = In_Stream or Stream.Mode = Duplex then
- Close (Stream.Reader);
- Free (Stream.Buffer);
- end if;
- end Close;
-
- ------------
- -- Create --
- ------------
-
- procedure Create
- (Stream : out Stream_Type;
- Mode : in Stream_Mode;
- Back : in Stream_Access;
- Back_Compressed : in Boolean;
- Level : in Compression_Level := Default_Compression;
- Strategy : in Strategy_Type := Default_Strategy;
- Header : in Header_Type := Default;
- Read_Buffer_Size : in Ada.Streams.Stream_Element_Offset
- := Default_Buffer_Size;
- Write_Buffer_Size : in Ada.Streams.Stream_Element_Offset
- := Default_Buffer_Size)
- is
-
- subtype Buffer_Subtype is Stream_Element_Array (1 .. Read_Buffer_Size);
-
- procedure Init_Filter
- (Filter : in out Filter_Type;
- Compress : in Boolean);
-
- -----------------
- -- Init_Filter --
- -----------------
-
- procedure Init_Filter
- (Filter : in out Filter_Type;
- Compress : in Boolean) is
- begin
- if Compress then
- Deflate_Init
- (Filter, Level, Strategy, Header => Header);
- else
- Inflate_Init (Filter, Header => Header);
- end if;
- end Init_Filter;
-
- begin
- Stream.Back := Back;
- Stream.Mode := Mode;
-
- if Mode = Out_Stream or Mode = Duplex then
- Init_Filter (Stream.Writer, Back_Compressed);
- Stream.Buffer_Size := Write_Buffer_Size;
- else
- Stream.Buffer_Size := 0;
- end if;
-
- if Mode = In_Stream or Mode = Duplex then
- Init_Filter (Stream.Reader, not Back_Compressed);
-
- Stream.Buffer := new Buffer_Subtype;
- Stream.Rest_First := Stream.Buffer'Last + 1;
- Stream.Rest_Last := Stream.Buffer'Last;
- end if;
- end Create;
-
- -----------
- -- Flush --
- -----------
-
- procedure Flush
- (Stream : in out Stream_Type;
- Mode : in Flush_Mode := Sync_Flush)
- is
- Buffer : Stream_Element_Array (1 .. Stream.Buffer_Size);
- Last : Stream_Element_Offset;
- begin
- loop
- Flush (Stream.Writer, Buffer, Last, Mode);
-
- Ada.Streams.Write (Stream.Back.all, Buffer (1 .. Last));
-
- exit when Last < Buffer'Last;
- end loop;
- end Flush;
-
- -------------
- -- Is_Open --
- -------------
-
- function Is_Open (Stream : Stream_Type) return Boolean is
- begin
- return Is_Open (Stream.Reader) or else Is_Open (Stream.Writer);
- end Is_Open;
-
- ----------
- -- Read --
- ----------
-
- procedure Read
- (Stream : in out Stream_Type;
- Item : out Stream_Element_Array;
- Last : out Stream_Element_Offset)
- is
-
- procedure Read
- (Item : out Stream_Element_Array;
- Last : out Stream_Element_Offset);
-
- ----------
- -- Read --
- ----------
-
- procedure Read
- (Item : out Stream_Element_Array;
- Last : out Stream_Element_Offset) is
- begin
- Ada.Streams.Read (Stream.Back.all, Item, Last);
- end Read;
-
- procedure Read is new ZLib.Read
- (Read => Read,
- Buffer => Stream.Buffer.all,
- Rest_First => Stream.Rest_First,
- Rest_Last => Stream.Rest_Last);
-
- begin
- Read (Stream.Reader, Item, Last);
- end Read;
-
- -------------------
- -- Read_Total_In --
- -------------------
-
- function Read_Total_In (Stream : in Stream_Type) return Count is
- begin
- return Total_In (Stream.Reader);
- end Read_Total_In;
-
- --------------------
- -- Read_Total_Out --
- --------------------
-
- function Read_Total_Out (Stream : in Stream_Type) return Count is
- begin
- return Total_Out (Stream.Reader);
- end Read_Total_Out;
-
- -----------
- -- Write --
- -----------
-
- procedure Write
- (Stream : in out Stream_Type;
- Item : in Stream_Element_Array)
- is
-
- procedure Write (Item : in Stream_Element_Array);
-
- -----------
- -- Write --
- -----------
-
- procedure Write (Item : in Stream_Element_Array) is
- begin
- Ada.Streams.Write (Stream.Back.all, Item);
- end Write;
-
- procedure Write is new ZLib.Write
- (Write => Write,
- Buffer_Size => Stream.Buffer_Size);
-
- begin
- Write (Stream.Writer, Item, No_Flush);
- end Write;
-
- --------------------
- -- Write_Total_In --
- --------------------
-
- function Write_Total_In (Stream : in Stream_Type) return Count is
- begin
- return Total_In (Stream.Writer);
- end Write_Total_In;
-
- ---------------------
- -- Write_Total_Out --
- ---------------------
-
- function Write_Total_Out (Stream : in Stream_Type) return Count is
- begin
- return Total_Out (Stream.Writer);
- end Write_Total_Out;
-
-end ZLib.Streams;
diff --git a/third-party/zlib/contrib/ada/zlib-streams.ads b/third-party/zlib/contrib/ada/zlib-streams.ads
deleted file mode 100644
index f0193c6..0000000
--- a/third-party/zlib/contrib/ada/zlib-streams.ads
+++ /dev/null
@@ -1,114 +0,0 @@
-----------------------------------------------------------------
--- ZLib for Ada thick binding. --
--- --
--- Copyright (C) 2002-2003 Dmitriy Anisimkov --
--- --
--- Open source license information is in the zlib.ads file. --
-----------------------------------------------------------------
-
--- $Id: zlib-streams.ads,v 1.12 2004/05/31 10:53:40 vagul Exp $
-
-package ZLib.Streams is
-
- type Stream_Mode is (In_Stream, Out_Stream, Duplex);
-
- type Stream_Access is access all Ada.Streams.Root_Stream_Type'Class;
-
- type Stream_Type is
- new Ada.Streams.Root_Stream_Type with private;
-
- procedure Read
- (Stream : in out Stream_Type;
- Item : out Ada.Streams.Stream_Element_Array;
- Last : out Ada.Streams.Stream_Element_Offset);
-
- procedure Write
- (Stream : in out Stream_Type;
- Item : in Ada.Streams.Stream_Element_Array);
-
- procedure Flush
- (Stream : in out Stream_Type;
- Mode : in Flush_Mode := Sync_Flush);
- -- Flush the written data to the back stream,
- -- all data placed to the compressor is flushing to the Back stream.
- -- Should not be used untill necessary, becouse it is decreasing
- -- compression.
-
- function Read_Total_In (Stream : in Stream_Type) return Count;
- pragma Inline (Read_Total_In);
- -- Return total number of bytes read from back stream so far.
-
- function Read_Total_Out (Stream : in Stream_Type) return Count;
- pragma Inline (Read_Total_Out);
- -- Return total number of bytes read so far.
-
- function Write_Total_In (Stream : in Stream_Type) return Count;
- pragma Inline (Write_Total_In);
- -- Return total number of bytes written so far.
-
- function Write_Total_Out (Stream : in Stream_Type) return Count;
- pragma Inline (Write_Total_Out);
- -- Return total number of bytes written to the back stream.
-
- procedure Create
- (Stream : out Stream_Type;
- Mode : in Stream_Mode;
- Back : in Stream_Access;
- Back_Compressed : in Boolean;
- Level : in Compression_Level := Default_Compression;
- Strategy : in Strategy_Type := Default_Strategy;
- Header : in Header_Type := Default;
- Read_Buffer_Size : in Ada.Streams.Stream_Element_Offset
- := Default_Buffer_Size;
- Write_Buffer_Size : in Ada.Streams.Stream_Element_Offset
- := Default_Buffer_Size);
- -- Create the Comression/Decompression stream.
- -- If mode is In_Stream then Write operation is disabled.
- -- If mode is Out_Stream then Read operation is disabled.
-
- -- If Back_Compressed is true then
- -- Data written to the Stream is compressing to the Back stream
- -- and data read from the Stream is decompressed data from the Back stream.
-
- -- If Back_Compressed is false then
- -- Data written to the Stream is decompressing to the Back stream
- -- and data read from the Stream is compressed data from the Back stream.
-
- -- !!! When the Need_Header is False ZLib-Ada is using undocumented
- -- ZLib 1.1.4 functionality to do not create/wait for ZLib headers.
-
- function Is_Open (Stream : Stream_Type) return Boolean;
-
- procedure Close (Stream : in out Stream_Type);
-
-private
-
- use Ada.Streams;
-
- type Buffer_Access is access all Stream_Element_Array;
-
- type Stream_Type
- is new Root_Stream_Type with
- record
- Mode : Stream_Mode;
-
- Buffer : Buffer_Access;
- Rest_First : Stream_Element_Offset;
- Rest_Last : Stream_Element_Offset;
- -- Buffer for Read operation.
- -- We need to have this buffer in the record
- -- becouse not all read data from back stream
- -- could be processed during the read operation.
-
- Buffer_Size : Stream_Element_Offset;
- -- Buffer size for write operation.
- -- We do not need to have this buffer
- -- in the record becouse all data could be
- -- processed in the write operation.
-
- Back : Stream_Access;
- Reader : Filter_Type;
- Writer : Filter_Type;
- end record;
-
-end ZLib.Streams;
diff --git a/third-party/zlib/contrib/ada/zlib-thin.adb b/third-party/zlib/contrib/ada/zlib-thin.adb
deleted file mode 100644
index 0ca4a71..0000000
--- a/third-party/zlib/contrib/ada/zlib-thin.adb
+++ /dev/null
@@ -1,141 +0,0 @@
-----------------------------------------------------------------
--- ZLib for Ada thick binding. --
--- --
--- Copyright (C) 2002-2003 Dmitriy Anisimkov --
--- --
--- Open source license information is in the zlib.ads file. --
-----------------------------------------------------------------
-
--- $Id: zlib-thin.adb,v 1.8 2003/12/14 18:27:31 vagul Exp $
-
-package body ZLib.Thin is
-
- ZLIB_VERSION : constant Chars_Ptr := zlibVersion;
-
- Z_Stream_Size : constant Int := Z_Stream'Size / System.Storage_Unit;
-
- --------------
- -- Avail_In --
- --------------
-
- function Avail_In (Strm : in Z_Stream) return UInt is
- begin
- return Strm.Avail_In;
- end Avail_In;
-
- ---------------
- -- Avail_Out --
- ---------------
-
- function Avail_Out (Strm : in Z_Stream) return UInt is
- begin
- return Strm.Avail_Out;
- end Avail_Out;
-
- ------------------
- -- Deflate_Init --
- ------------------
-
- function Deflate_Init
- (strm : Z_Streamp;
- level : Int;
- method : Int;
- windowBits : Int;
- memLevel : Int;
- strategy : Int)
- return Int is
- begin
- return deflateInit2
- (strm,
- level,
- method,
- windowBits,
- memLevel,
- strategy,
- ZLIB_VERSION,
- Z_Stream_Size);
- end Deflate_Init;
-
- ------------------
- -- Inflate_Init --
- ------------------
-
- function Inflate_Init (strm : Z_Streamp; windowBits : Int) return Int is
- begin
- return inflateInit2 (strm, windowBits, ZLIB_VERSION, Z_Stream_Size);
- end Inflate_Init;
-
- ------------------------
- -- Last_Error_Message --
- ------------------------
-
- function Last_Error_Message (Strm : in Z_Stream) return String is
- use Interfaces.C.Strings;
- begin
- if Strm.msg = Null_Ptr then
- return "";
- else
- return Value (Strm.msg);
- end if;
- end Last_Error_Message;
-
- ------------
- -- Set_In --
- ------------
-
- procedure Set_In
- (Strm : in out Z_Stream;
- Buffer : in Voidp;
- Size : in UInt) is
- begin
- Strm.Next_In := Buffer;
- Strm.Avail_In := Size;
- end Set_In;
-
- ------------------
- -- Set_Mem_Func --
- ------------------
-
- procedure Set_Mem_Func
- (Strm : in out Z_Stream;
- Opaque : in Voidp;
- Alloc : in alloc_func;
- Free : in free_func) is
- begin
- Strm.opaque := Opaque;
- Strm.zalloc := Alloc;
- Strm.zfree := Free;
- end Set_Mem_Func;
-
- -------------
- -- Set_Out --
- -------------
-
- procedure Set_Out
- (Strm : in out Z_Stream;
- Buffer : in Voidp;
- Size : in UInt) is
- begin
- Strm.Next_Out := Buffer;
- Strm.Avail_Out := Size;
- end Set_Out;
-
- --------------
- -- Total_In --
- --------------
-
- function Total_In (Strm : in Z_Stream) return ULong is
- begin
- return Strm.Total_In;
- end Total_In;
-
- ---------------
- -- Total_Out --
- ---------------
-
- function Total_Out (Strm : in Z_Stream) return ULong is
- begin
- return Strm.Total_Out;
- end Total_Out;
-
-end ZLib.Thin;
diff --git a/third-party/zlib/contrib/ada/zlib-thin.ads b/third-party/zlib/contrib/ada/zlib-thin.ads
deleted file mode 100644
index d4407eb..0000000
--- a/third-party/zlib/contrib/ada/zlib-thin.ads
+++ /dev/null
@@ -1,450 +0,0 @@
-----------------------------------------------------------------
--- ZLib for Ada thick binding. --
--- --
--- Copyright (C) 2002-2003 Dmitriy Anisimkov --
--- --
--- Open source license information is in the zlib.ads file. --
-----------------------------------------------------------------
-
--- $Id: zlib-thin.ads,v 1.11 2004/07/23 06:33:11 vagul Exp $
-
-with Interfaces.C.Strings;
-
-with System;
-
-private package ZLib.Thin is
-
- -- From zconf.h
-
- MAX_MEM_LEVEL : constant := 9; -- zconf.h:105
- -- zconf.h:105
- MAX_WBITS : constant := 15; -- zconf.h:115
- -- 32K LZ77 window
- -- zconf.h:115
- SEEK_SET : constant := 8#0000#; -- zconf.h:244
- -- Seek from beginning of file.
- -- zconf.h:244
- SEEK_CUR : constant := 1; -- zconf.h:245
- -- Seek from current position.
- -- zconf.h:245
- SEEK_END : constant := 2; -- zconf.h:246
- -- Set file pointer to EOF plus "offset"
- -- zconf.h:246
-
- type Byte is new Interfaces.C.unsigned_char; -- 8 bits
- -- zconf.h:214
- type UInt is new Interfaces.C.unsigned; -- 16 bits or more
- -- zconf.h:216
- type Int is new Interfaces.C.int;
-
- type ULong is new Interfaces.C.unsigned_long; -- 32 bits or more
- -- zconf.h:217
- subtype Chars_Ptr is Interfaces.C.Strings.chars_ptr;
-
- type ULong_Access is access ULong;
- type Int_Access is access Int;
-
- subtype Voidp is System.Address; -- zconf.h:232
-
- subtype Byte_Access is Voidp;
-
- Nul : constant Voidp := System.Null_Address;
- -- end from zconf
-
- Z_NO_FLUSH : constant := 8#0000#; -- zlib.h:125
- -- zlib.h:125
- Z_PARTIAL_FLUSH : constant := 1; -- zlib.h:126
- -- will be removed, use
- -- Z_SYNC_FLUSH instead
- -- zlib.h:126
- Z_SYNC_FLUSH : constant := 2; -- zlib.h:127
- -- zlib.h:127
- Z_FULL_FLUSH : constant := 3; -- zlib.h:128
- -- zlib.h:128
- Z_FINISH : constant := 4; -- zlib.h:129
- -- zlib.h:129
- Z_OK : constant := 8#0000#; -- zlib.h:132
- -- zlib.h:132
- Z_STREAM_END : constant := 1; -- zlib.h:133
- -- zlib.h:133
- Z_NEED_DICT : constant := 2; -- zlib.h:134
- -- zlib.h:134
- Z_ERRNO : constant := -1; -- zlib.h:135
- -- zlib.h:135
- Z_STREAM_ERROR : constant := -2; -- zlib.h:136
- -- zlib.h:136
- Z_DATA_ERROR : constant := -3; -- zlib.h:137
- -- zlib.h:137
- Z_MEM_ERROR : constant := -4; -- zlib.h:138
- -- zlib.h:138
- Z_BUF_ERROR : constant := -5; -- zlib.h:139
- -- zlib.h:139
- Z_VERSION_ERROR : constant := -6; -- zlib.h:140
- -- zlib.h:140
- Z_NO_COMPRESSION : constant := 8#0000#; -- zlib.h:145
- -- zlib.h:145
- Z_BEST_SPEED : constant := 1; -- zlib.h:146
- -- zlib.h:146
- Z_BEST_COMPRESSION : constant := 9; -- zlib.h:147
- -- zlib.h:147
- Z_DEFAULT_COMPRESSION : constant := -1; -- zlib.h:148
- -- zlib.h:148
- Z_FILTERED : constant := 1; -- zlib.h:151
- -- zlib.h:151
- Z_HUFFMAN_ONLY : constant := 2; -- zlib.h:152
- -- zlib.h:152
- Z_DEFAULT_STRATEGY : constant := 8#0000#; -- zlib.h:153
- -- zlib.h:153
- Z_BINARY : constant := 8#0000#; -- zlib.h:156
- -- zlib.h:156
- Z_ASCII : constant := 1; -- zlib.h:157
- -- zlib.h:157
- Z_UNKNOWN : constant := 2; -- zlib.h:158
- -- zlib.h:158
- Z_DEFLATED : constant := 8; -- zlib.h:161
- -- zlib.h:161
- Z_NULL : constant := 8#0000#; -- zlib.h:164
- -- for initializing zalloc, zfree, opaque
- -- zlib.h:164
- type gzFile is new Voidp; -- zlib.h:646
-
- type Z_Stream is private;
-
- type Z_Streamp is access all Z_Stream; -- zlib.h:89
-
- type alloc_func is access function
- (Opaque : Voidp;
- Items : UInt;
- Size : UInt)
- return Voidp; -- zlib.h:63
-
- type free_func is access procedure (opaque : Voidp; address : Voidp);
-
- function zlibVersion return Chars_Ptr;
-
- function Deflate (strm : Z_Streamp; flush : Int) return Int;
-
- function DeflateEnd (strm : Z_Streamp) return Int;
-
- function Inflate (strm : Z_Streamp; flush : Int) return Int;
-
- function InflateEnd (strm : Z_Streamp) return Int;
-
- function deflateSetDictionary
- (strm : Z_Streamp;
- dictionary : Byte_Access;
- dictLength : UInt)
- return Int;
-
- function deflateCopy (dest : Z_Streamp; source : Z_Streamp) return Int;
- -- zlib.h:478
-
- function deflateReset (strm : Z_Streamp) return Int; -- zlib.h:495
-
- function deflateParams
- (strm : Z_Streamp;
- level : Int;
- strategy : Int)
- return Int; -- zlib.h:506
-
- function inflateSetDictionary
- (strm : Z_Streamp;
- dictionary : Byte_Access;
- dictLength : UInt)
- return Int; -- zlib.h:548
-
- function inflateSync (strm : Z_Streamp) return Int; -- zlib.h:565
-
- function inflateReset (strm : Z_Streamp) return Int; -- zlib.h:580
-
- function compress
- (dest : Byte_Access;
- destLen : ULong_Access;
- source : Byte_Access;
- sourceLen : ULong)
- return Int; -- zlib.h:601
-
- function compress2
- (dest : Byte_Access;
- destLen : ULong_Access;
- source : Byte_Access;
- sourceLen : ULong;
- level : Int)
- return Int; -- zlib.h:615
-
- function uncompress
- (dest : Byte_Access;
- destLen : ULong_Access;
- source : Byte_Access;
- sourceLen : ULong)
- return Int;
-
- function gzopen (path : Chars_Ptr; mode : Chars_Ptr) return gzFile;
-
- function gzdopen (fd : Int; mode : Chars_Ptr) return gzFile;
-
- function gzsetparams
- (file : gzFile;
- level : Int;
- strategy : Int)
- return Int;
-
- function gzread
- (file : gzFile;
- buf : Voidp;
- len : UInt)
- return Int;
-
- function gzwrite
- (file : in gzFile;
- buf : in Voidp;
- len : in UInt)
- return Int;
-
- function gzprintf (file : in gzFile; format : in Chars_Ptr) return Int;
-
- function gzputs (file : in gzFile; s : in Chars_Ptr) return Int;
-
- function gzgets
- (file : gzFile;
- buf : Chars_Ptr;
- len : Int)
- return Chars_Ptr;
-
- function gzputc (file : gzFile; char : Int) return Int;
-
- function gzgetc (file : gzFile) return Int;
-
- function gzflush (file : gzFile; flush : Int) return Int;
-
- function gzseek
- (file : gzFile;
- offset : Int;
- whence : Int)
- return Int;
-
- function gzrewind (file : gzFile) return Int;
-
- function gztell (file : gzFile) return Int;
-
- function gzeof (file : gzFile) return Int;
-
- function gzclose (file : gzFile) return Int;
-
- function gzerror (file : gzFile; errnum : Int_Access) return Chars_Ptr;
-
- function adler32
- (adler : ULong;
- buf : Byte_Access;
- len : UInt)
- return ULong;
-
- function crc32
- (crc : ULong;
- buf : Byte_Access;
- len : UInt)
- return ULong;
-
- function deflateInit
- (strm : Z_Streamp;
- level : Int;
- version : Chars_Ptr;
- stream_size : Int)
- return Int;
-
- function deflateInit2
- (strm : Z_Streamp;
- level : Int;
- method : Int;
- windowBits : Int;
- memLevel : Int;
- strategy : Int;
- version : Chars_Ptr;
- stream_size : Int)
- return Int;
-
- function Deflate_Init
- (strm : Z_Streamp;
- level : Int;
- method : Int;
- windowBits : Int;
- memLevel : Int;
- strategy : Int)
- return Int;
- pragma Inline (Deflate_Init);
-
- function inflateInit
- (strm : Z_Streamp;
- version : Chars_Ptr;
- stream_size : Int)
- return Int;
-
- function inflateInit2
- (strm : in Z_Streamp;
- windowBits : in Int;
- version : in Chars_Ptr;
- stream_size : in Int)
- return Int;
-
- function inflateBackInit
- (strm : in Z_Streamp;
- windowBits : in Int;
- window : in Byte_Access;
- version : in Chars_Ptr;
- stream_size : in Int)
- return Int;
- -- Size of window have to be 2**windowBits.
-
- function Inflate_Init (strm : Z_Streamp; windowBits : Int) return Int;
- pragma Inline (Inflate_Init);
-
- function zError (err : Int) return Chars_Ptr;
-
- function inflateSyncPoint (z : Z_Streamp) return Int;
-
- function get_crc_table return ULong_Access;
-
- -- Interface to the available fields of the z_stream structure.
- -- The application must update next_in and avail_in when avail_in has
- -- dropped to zero. It must update next_out and avail_out when avail_out
- -- has dropped to zero. The application must initialize zalloc, zfree and
- -- opaque before calling the init function.
-
- procedure Set_In
- (Strm : in out Z_Stream;
- Buffer : in Voidp;
- Size : in UInt);
- pragma Inline (Set_In);
-
- procedure Set_Out
- (Strm : in out Z_Stream;
- Buffer : in Voidp;
- Size : in UInt);
- pragma Inline (Set_Out);
-
- procedure Set_Mem_Func
- (Strm : in out Z_Stream;
- Opaque : in Voidp;
- Alloc : in alloc_func;
- Free : in free_func);
- pragma Inline (Set_Mem_Func);
-
- function Last_Error_Message (Strm : in Z_Stream) return String;
- pragma Inline (Last_Error_Message);
-
- function Avail_Out (Strm : in Z_Stream) return UInt;
- pragma Inline (Avail_Out);
-
- function Avail_In (Strm : in Z_Stream) return UInt;
- pragma Inline (Avail_In);
-
- function Total_In (Strm : in Z_Stream) return ULong;
- pragma Inline (Total_In);
-
- function Total_Out (Strm : in Z_Stream) return ULong;
- pragma Inline (Total_Out);
-
- function inflateCopy
- (dest : in Z_Streamp;
- Source : in Z_Streamp)
- return Int;
-
- function compressBound (Source_Len : in ULong) return ULong;
-
- function deflateBound
- (Strm : in Z_Streamp;
- Source_Len : in ULong)
- return ULong;
-
- function gzungetc (C : in Int; File : in gzFile) return Int;
-
- function zlibCompileFlags return ULong;
-
-private
-
- type Z_Stream is record -- zlib.h:68
- Next_In : Voidp := Nul; -- next input byte
- Avail_In : UInt := 0; -- number of bytes available at next_in
- Total_In : ULong := 0; -- total nb of input bytes read so far
- Next_Out : Voidp := Nul; -- next output byte should be put there
- Avail_Out : UInt := 0; -- remaining free space at next_out
- Total_Out : ULong := 0; -- total nb of bytes output so far
- msg : Chars_Ptr; -- last error message, NULL if no error
- state : Voidp; -- not visible by applications
- zalloc : alloc_func := null; -- used to allocate the internal state
- zfree : free_func := null; -- used to free the internal state
- opaque : Voidp; -- private data object passed to
- -- zalloc and zfree
- data_type : Int; -- best guess about the data type:
- -- ascii or binary
- adler : ULong; -- adler32 value of the uncompressed
- -- data
- reserved : ULong; -- reserved for future use
- end record;
-
- pragma Convention (C, Z_Stream);
-
- pragma Import (C, zlibVersion, "zlibVersion");
- pragma Import (C, Deflate, "deflate");
- pragma Import (C, DeflateEnd, "deflateEnd");
- pragma Import (C, Inflate, "inflate");
- pragma Import (C, InflateEnd, "inflateEnd");
- pragma Import (C, deflateSetDictionary, "deflateSetDictionary");
- pragma Import (C, deflateCopy, "deflateCopy");
- pragma Import (C, deflateReset, "deflateReset");
- pragma Import (C, deflateParams, "deflateParams");
- pragma Import (C, inflateSetDictionary, "inflateSetDictionary");
- pragma Import (C, inflateSync, "inflateSync");
- pragma Import (C, inflateReset, "inflateReset");
- pragma Import (C, compress, "compress");
- pragma Import (C, compress2, "compress2");
- pragma Import (C, uncompress, "uncompress");
- pragma Import (C, gzopen, "gzopen");
- pragma Import (C, gzdopen, "gzdopen");
- pragma Import (C, gzsetparams, "gzsetparams");
- pragma Import (C, gzread, "gzread");
- pragma Import (C, gzwrite, "gzwrite");
- pragma Import (C, gzprintf, "gzprintf");
- pragma Import (C, gzputs, "gzputs");
- pragma Import (C, gzgets, "gzgets");
- pragma Import (C, gzputc, "gzputc");
- pragma Import (C, gzgetc, "gzgetc");
- pragma Import (C, gzflush, "gzflush");
- pragma Import (C, gzseek, "gzseek");
- pragma Import (C, gzrewind, "gzrewind");
- pragma Import (C, gztell, "gztell");
- pragma Import (C, gzeof, "gzeof");
- pragma Import (C, gzclose, "gzclose");
- pragma Import (C, gzerror, "gzerror");
- pragma Import (C, adler32, "adler32");
- pragma Import (C, crc32, "crc32");
- pragma Import (C, deflateInit, "deflateInit_");
- pragma Import (C, inflateInit, "inflateInit_");
- pragma Import (C, deflateInit2, "deflateInit2_");
- pragma Import (C, inflateInit2, "inflateInit2_");
- pragma Import (C, zError, "zError");
- pragma Import (C, inflateSyncPoint, "inflateSyncPoint");
- pragma Import (C, get_crc_table, "get_crc_table");
-
- -- since zlib 1.2.0:
-
- pragma Import (C, inflateCopy, "inflateCopy");
- pragma Import (C, compressBound, "compressBound");
- pragma Import (C, deflateBound, "deflateBound");
- pragma Import (C, gzungetc, "gzungetc");
- pragma Import (C, zlibCompileFlags, "zlibCompileFlags");
-
- pragma Import (C, inflateBackInit, "inflateBackInit_");
-
- -- I stopped binding the inflateBack routines, becouse realize that
- -- it does not support zlib and gzip headers for now, and have no
- -- symmetric deflateBack routines.
- -- ZLib-Ada is symmetric regarding deflate/inflate data transformation
- -- and has a similar generic callback interface for the
- -- deflate/inflate transformation based on the regular Deflate/Inflate
- -- routines.
-
- -- pragma Import (C, inflateBack, "inflateBack");
- -- pragma Import (C, inflateBackEnd, "inflateBackEnd");
-
-end ZLib.Thin;
diff --git a/third-party/zlib/contrib/ada/zlib.adb b/third-party/zlib/contrib/ada/zlib.adb
deleted file mode 100644
index 8b6fd68..0000000
--- a/third-party/zlib/contrib/ada/zlib.adb
+++ /dev/null
@@ -1,701 +0,0 @@
-----------------------------------------------------------------
--- ZLib for Ada thick binding. --
--- --
--- Copyright (C) 2002-2004 Dmitriy Anisimkov --
--- --
--- Open source license information is in the zlib.ads file. --
-----------------------------------------------------------------
-
--- $Id: zlib.adb,v 1.31 2004/09/06 06:53:19 vagul Exp $
-
-with Ada.Exceptions;
-with Ada.Unchecked_Conversion;
-with Ada.Unchecked_Deallocation;
-
-with Interfaces.C.Strings;
-
-with ZLib.Thin;
-
-package body ZLib is
-
- use type Thin.Int;
-
- type Z_Stream is new Thin.Z_Stream;
-
- type Return_Code_Enum is
- (OK,
- STREAM_END,
- NEED_DICT,
- ERRNO,
- STREAM_ERROR,
- DATA_ERROR,
- MEM_ERROR,
- BUF_ERROR,
- VERSION_ERROR);
-
- type Flate_Step_Function is access
- function (Strm : in Thin.Z_Streamp; Flush : in Thin.Int) return Thin.Int;
- pragma Convention (C, Flate_Step_Function);
-
- type Flate_End_Function is access
- function (Ctrm : in Thin.Z_Streamp) return Thin.Int;
- pragma Convention (C, Flate_End_Function);
-
- type Flate_Type is record
- Step : Flate_Step_Function;
- Done : Flate_End_Function;
- end record;
-
- subtype Footer_Array is Stream_Element_Array (1 .. 8);
-
- Simple_GZip_Header : constant Stream_Element_Array (1 .. 10)
- := (16#1f#, 16#8b#, -- Magic header
- 16#08#, -- Z_DEFLATED
- 16#00#, -- Flags
- 16#00#, 16#00#, 16#00#, 16#00#, -- Time
- 16#00#, -- XFlags
- 16#03# -- OS code
- );
- -- The simplest gzip header is not for informational, but just for
- -- gzip format compatibility.
- -- Note that some code below is using assumption
- -- Simple_GZip_Header'Last > Footer_Array'Last, so do not make
- -- Simple_GZip_Header'Last <= Footer_Array'Last.
-
- Return_Code : constant array (Thin.Int range <>) of Return_Code_Enum
- := (0 => OK,
- 1 => STREAM_END,
- 2 => NEED_DICT,
- -1 => ERRNO,
- -2 => STREAM_ERROR,
- -3 => DATA_ERROR,
- -4 => MEM_ERROR,
- -5 => BUF_ERROR,
- -6 => VERSION_ERROR);
-
- Flate : constant array (Boolean) of Flate_Type
- := (True => (Step => Thin.Deflate'Access,
- Done => Thin.DeflateEnd'Access),
- False => (Step => Thin.Inflate'Access,
- Done => Thin.InflateEnd'Access));
-
- Flush_Finish : constant array (Boolean) of Flush_Mode
- := (True => Finish, False => No_Flush);
-
- procedure Raise_Error (Stream : in Z_Stream);
- pragma Inline (Raise_Error);
-
- procedure Raise_Error (Message : in String);
- pragma Inline (Raise_Error);
-
- procedure Check_Error (Stream : in Z_Stream; Code : in Thin.Int);
-
- procedure Free is new Ada.Unchecked_Deallocation
- (Z_Stream, Z_Stream_Access);
-
- function To_Thin_Access is new Ada.Unchecked_Conversion
- (Z_Stream_Access, Thin.Z_Streamp);
-
- procedure Translate_GZip
- (Filter : in out Filter_Type;
- In_Data : in Ada.Streams.Stream_Element_Array;
- In_Last : out Ada.Streams.Stream_Element_Offset;
- Out_Data : out Ada.Streams.Stream_Element_Array;
- Out_Last : out Ada.Streams.Stream_Element_Offset;
- Flush : in Flush_Mode);
- -- Separate translate routine for make gzip header.
-
- procedure Translate_Auto
- (Filter : in out Filter_Type;
- In_Data : in Ada.Streams.Stream_Element_Array;
- In_Last : out Ada.Streams.Stream_Element_Offset;
- Out_Data : out Ada.Streams.Stream_Element_Array;
- Out_Last : out Ada.Streams.Stream_Element_Offset;
- Flush : in Flush_Mode);
- -- translate routine without additional headers.
-
- -----------------
- -- Check_Error --
- -----------------
-
- procedure Check_Error (Stream : in Z_Stream; Code : in Thin.Int) is
- use type Thin.Int;
- begin
- if Code /= Thin.Z_OK then
- Raise_Error
- (Return_Code_Enum'Image (Return_Code (Code))
- & ": " & Last_Error_Message (Stream));
- end if;
- end Check_Error;
-
- -----------
- -- Close --
- -----------
-
- procedure Close
- (Filter : in out Filter_Type;
- Ignore_Error : in Boolean := False)
- is
- Code : Thin.Int;
- begin
- if not Ignore_Error and then not Is_Open (Filter) then
- raise Status_Error;
- end if;
-
- Code := Flate (Filter.Compression).Done (To_Thin_Access (Filter.Strm));
-
- if Ignore_Error or else Code = Thin.Z_OK then
- Free (Filter.Strm);
- else
- declare
- Error_Message : constant String
- := Last_Error_Message (Filter.Strm.all);
- begin
- Free (Filter.Strm);
- Ada.Exceptions.Raise_Exception
- (ZLib_Error'Identity,
- Return_Code_Enum'Image (Return_Code (Code))
- & ": " & Error_Message);
- end;
- end if;
- end Close;
-
- -----------
- -- CRC32 --
- -----------
-
- function CRC32
- (CRC : in Unsigned_32;
- Data : in Ada.Streams.Stream_Element_Array)
- return Unsigned_32
- is
- use Thin;
- begin
- return Unsigned_32 (crc32 (ULong (CRC),
- Data'Address,
- Data'Length));
- end CRC32;
-
- procedure CRC32
- (CRC : in out Unsigned_32;
- Data : in Ada.Streams.Stream_Element_Array) is
- begin
- CRC := CRC32 (CRC, Data);
- end CRC32;
-
- ------------------
- -- Deflate_Init --
- ------------------
-
- procedure Deflate_Init
- (Filter : in out Filter_Type;
- Level : in Compression_Level := Default_Compression;
- Strategy : in Strategy_Type := Default_Strategy;
- Method : in Compression_Method := Deflated;
- Window_Bits : in Window_Bits_Type := Default_Window_Bits;
- Memory_Level : in Memory_Level_Type := Default_Memory_Level;
- Header : in Header_Type := Default)
- is
- use type Thin.Int;
- Win_Bits : Thin.Int := Thin.Int (Window_Bits);
- begin
- if Is_Open (Filter) then
- raise Status_Error;
- end if;
-
- -- We allow ZLib to make header only in case of default header type.
- -- Otherwise we would either do header by ourselfs, or do not do
- -- header at all.
-
- if Header = None or else Header = GZip then
- Win_Bits := -Win_Bits;
- end if;
-
- -- For the GZip CRC calculation and make headers.
-
- if Header = GZip then
- Filter.CRC := 0;
- Filter.Offset := Simple_GZip_Header'First;
- else
- Filter.Offset := Simple_GZip_Header'Last + 1;
- end if;
-
- Filter.Strm := new Z_Stream;
- Filter.Compression := True;
- Filter.Stream_End := False;
- Filter.Header := Header;
-
- if Thin.Deflate_Init
- (To_Thin_Access (Filter.Strm),
- Level => Thin.Int (Level),
- method => Thin.Int (Method),
- windowBits => Win_Bits,
- memLevel => Thin.Int (Memory_Level),
- strategy => Thin.Int (Strategy)) /= Thin.Z_OK
- then
- Raise_Error (Filter.Strm.all);
- end if;
- end Deflate_Init;
-
- -----------
- -- Flush --
- -----------
-
- procedure Flush
- (Filter : in out Filter_Type;
- Out_Data : out Ada.Streams.Stream_Element_Array;
- Out_Last : out Ada.Streams.Stream_Element_Offset;
- Flush : in Flush_Mode)
- is
- No_Data : Stream_Element_Array := (1 .. 0 => 0);
- Last : Stream_Element_Offset;
- begin
- Translate (Filter, No_Data, Last, Out_Data, Out_Last, Flush);
- end Flush;
-
- -----------------------
- -- Generic_Translate --
- -----------------------
-
- procedure Generic_Translate
- (Filter : in out ZLib.Filter_Type;
- In_Buffer_Size : in Integer := Default_Buffer_Size;
- Out_Buffer_Size : in Integer := Default_Buffer_Size)
- is
- In_Buffer : Stream_Element_Array
- (1 .. Stream_Element_Offset (In_Buffer_Size));
- Out_Buffer : Stream_Element_Array
- (1 .. Stream_Element_Offset (Out_Buffer_Size));
- Last : Stream_Element_Offset;
- In_Last : Stream_Element_Offset;
- In_First : Stream_Element_Offset;
- Out_Last : Stream_Element_Offset;
- begin
- Main : loop
- Data_In (In_Buffer, Last);
-
- In_First := In_Buffer'First;
-
- loop
- Translate
- (Filter => Filter,
- In_Data => In_Buffer (In_First .. Last),
- In_Last => In_Last,
- Out_Data => Out_Buffer,
- Out_Last => Out_Last,
- Flush => Flush_Finish (Last < In_Buffer'First));
-
- if Out_Buffer'First <= Out_Last then
- Data_Out (Out_Buffer (Out_Buffer'First .. Out_Last));
- end if;
-
- exit Main when Stream_End (Filter);
-
- -- The end of in buffer.
-
- exit when In_Last = Last;
-
- In_First := In_Last + 1;
- end loop;
- end loop Main;
-
- end Generic_Translate;
-
- ------------------
- -- Inflate_Init --
- ------------------
-
- procedure Inflate_Init
- (Filter : in out Filter_Type;
- Window_Bits : in Window_Bits_Type := Default_Window_Bits;
- Header : in Header_Type := Default)
- is
- use type Thin.Int;
- Win_Bits : Thin.Int := Thin.Int (Window_Bits);
-
- procedure Check_Version;
- -- Check the latest header types compatibility.
-
- procedure Check_Version is
- begin
- if Version <= "1.1.4" then
- Raise_Error
- ("Inflate header type " & Header_Type'Image (Header)
- & " incompatible with ZLib version " & Version);
- end if;
- end Check_Version;
-
- begin
- if Is_Open (Filter) then
- raise Status_Error;
- end if;
-
- case Header is
- when None =>
- Check_Version;
-
- -- Inflate data without headers determined
- -- by negative Win_Bits.
-
- Win_Bits := -Win_Bits;
- when GZip =>
- Check_Version;
-
- -- Inflate gzip data defined by flag 16.
-
- Win_Bits := Win_Bits + 16;
- when Auto =>
- Check_Version;
-
- -- Inflate with automatic detection
- -- of gzip or native header defined by flag 32.
-
- Win_Bits := Win_Bits + 32;
- when Default => null;
- end case;
-
- Filter.Strm := new Z_Stream;
- Filter.Compression := False;
- Filter.Stream_End := False;
- Filter.Header := Header;
-
- if Thin.Inflate_Init
- (To_Thin_Access (Filter.Strm), Win_Bits) /= Thin.Z_OK
- then
- Raise_Error (Filter.Strm.all);
- end if;
- end Inflate_Init;
-
- -------------
- -- Is_Open --
- -------------
-
- function Is_Open (Filter : in Filter_Type) return Boolean is
- begin
- return Filter.Strm /= null;
- end Is_Open;
-
- -----------------
- -- Raise_Error --
- -----------------
-
- procedure Raise_Error (Message : in String) is
- begin
- Ada.Exceptions.Raise_Exception (ZLib_Error'Identity, Message);
- end Raise_Error;
-
- procedure Raise_Error (Stream : in Z_Stream) is
- begin
- Raise_Error (Last_Error_Message (Stream));
- end Raise_Error;
-
- ----------
- -- Read --
- ----------
-
- procedure Read
- (Filter : in out Filter_Type;
- Item : out Ada.Streams.Stream_Element_Array;
- Last : out Ada.Streams.Stream_Element_Offset;
- Flush : in Flush_Mode := No_Flush)
- is
- In_Last : Stream_Element_Offset;
- Item_First : Ada.Streams.Stream_Element_Offset := Item'First;
- V_Flush : Flush_Mode := Flush;
-
- begin
- pragma Assert (Rest_First in Buffer'First .. Buffer'Last + 1);
- pragma Assert (Rest_Last in Buffer'First - 1 .. Buffer'Last);
-
- loop
- if Rest_Last = Buffer'First - 1 then
- V_Flush := Finish;
-
- elsif Rest_First > Rest_Last then
- Read (Buffer, Rest_Last);
- Rest_First := Buffer'First;
-
- if Rest_Last < Buffer'First then
- V_Flush := Finish;
- end if;
- end if;
-
- Translate
- (Filter => Filter,
- In_Data => Buffer (Rest_First .. Rest_Last),
- In_Last => In_Last,
- Out_Data => Item (Item_First .. Item'Last),
- Out_Last => Last,
- Flush => V_Flush);
-
- Rest_First := In_Last + 1;
-
- exit when Stream_End (Filter)
- or else Last = Item'Last
- or else (Last >= Item'First and then Allow_Read_Some);
-
- Item_First := Last + 1;
- end loop;
- end Read;
-
- ----------------
- -- Stream_End --
- ----------------
-
- function Stream_End (Filter : in Filter_Type) return Boolean is
- begin
- if Filter.Header = GZip and Filter.Compression then
- return Filter.Stream_End
- and then Filter.Offset = Footer_Array'Last + 1;
- else
- return Filter.Stream_End;
- end if;
- end Stream_End;
-
- --------------
- -- Total_In --
- --------------
-
- function Total_In (Filter : in Filter_Type) return Count is
- begin
- return Count (Thin.Total_In (To_Thin_Access (Filter.Strm).all));
- end Total_In;
-
- ---------------
- -- Total_Out --
- ---------------
-
- function Total_Out (Filter : in Filter_Type) return Count is
- begin
- return Count (Thin.Total_Out (To_Thin_Access (Filter.Strm).all));
- end Total_Out;
-
- ---------------
- -- Translate --
- ---------------
-
- procedure Translate
- (Filter : in out Filter_Type;
- In_Data : in Ada.Streams.Stream_Element_Array;
- In_Last : out Ada.Streams.Stream_Element_Offset;
- Out_Data : out Ada.Streams.Stream_Element_Array;
- Out_Last : out Ada.Streams.Stream_Element_Offset;
- Flush : in Flush_Mode) is
- begin
- if Filter.Header = GZip and then Filter.Compression then
- Translate_GZip
- (Filter => Filter,
- In_Data => In_Data,
- In_Last => In_Last,
- Out_Data => Out_Data,
- Out_Last => Out_Last,
- Flush => Flush);
- else
- Translate_Auto
- (Filter => Filter,
- In_Data => In_Data,
- In_Last => In_Last,
- Out_Data => Out_Data,
- Out_Last => Out_Last,
- Flush => Flush);
- end if;
- end Translate;
-
- --------------------
- -- Translate_Auto --
- --------------------
-
- procedure Translate_Auto
- (Filter : in out Filter_Type;
- In_Data : in Ada.Streams.Stream_Element_Array;
- In_Last : out Ada.Streams.Stream_Element_Offset;
- Out_Data : out Ada.Streams.Stream_Element_Array;
- Out_Last : out Ada.Streams.Stream_Element_Offset;
- Flush : in Flush_Mode)
- is
- use type Thin.Int;
- Code : Thin.Int;
-
- begin
- if not Is_Open (Filter) then
- raise Status_Error;
- end if;
-
- if Out_Data'Length = 0 and then In_Data'Length = 0 then
- raise Constraint_Error;
- end if;
-
- Set_Out (Filter.Strm.all, Out_Data'Address, Out_Data'Length);
- Set_In (Filter.Strm.all, In_Data'Address, In_Data'Length);
-
- Code := Flate (Filter.Compression).Step
- (To_Thin_Access (Filter.Strm),
- Thin.Int (Flush));
-
- if Code = Thin.Z_STREAM_END then
- Filter.Stream_End := True;
- else
- Check_Error (Filter.Strm.all, Code);
- end if;
-
- In_Last := In_Data'Last
- - Stream_Element_Offset (Avail_In (Filter.Strm.all));
- Out_Last := Out_Data'Last
- - Stream_Element_Offset (Avail_Out (Filter.Strm.all));
- end Translate_Auto;
-
- --------------------
- -- Translate_GZip --
- --------------------
-
- procedure Translate_GZip
- (Filter : in out Filter_Type;
- In_Data : in Ada.Streams.Stream_Element_Array;
- In_Last : out Ada.Streams.Stream_Element_Offset;
- Out_Data : out Ada.Streams.Stream_Element_Array;
- Out_Last : out Ada.Streams.Stream_Element_Offset;
- Flush : in Flush_Mode)
- is
- Out_First : Stream_Element_Offset;
-
- procedure Add_Data (Data : in Stream_Element_Array);
- -- Add data to stream from the Filter.Offset till necessary,
- -- used for add gzip headr/footer.
-
- procedure Put_32
- (Item : in out Stream_Element_Array;
- Data : in Unsigned_32);
- pragma Inline (Put_32);
-
- --------------
- -- Add_Data --
- --------------
-
- procedure Add_Data (Data : in Stream_Element_Array) is
- Data_First : Stream_Element_Offset renames Filter.Offset;
- Data_Last : Stream_Element_Offset;
- Data_Len : Stream_Element_Offset; -- -1
- Out_Len : Stream_Element_Offset; -- -1
- begin
- Out_First := Out_Last + 1;
-
- if Data_First > Data'Last then
- return;
- end if;
-
- Data_Len := Data'Last - Data_First;
- Out_Len := Out_Data'Last - Out_First;
-
- if Data_Len <= Out_Len then
- Out_Last := Out_First + Data_Len;
- Data_Last := Data'Last;
- else
- Out_Last := Out_Data'Last;
- Data_Last := Data_First + Out_Len;
- end if;
-
- Out_Data (Out_First .. Out_Last) := Data (Data_First .. Data_Last);
-
- Data_First := Data_Last + 1;
- Out_First := Out_Last + 1;
- end Add_Data;
-
- ------------
- -- Put_32 --
- ------------
-
- procedure Put_32
- (Item : in out Stream_Element_Array;
- Data : in Unsigned_32)
- is
- D : Unsigned_32 := Data;
- begin
- for J in Item'First .. Item'First + 3 loop
- Item (J) := Stream_Element (D and 16#FF#);
- D := Shift_Right (D, 8);
- end loop;
- end Put_32;
-
- begin
- Out_Last := Out_Data'First - 1;
-
- if not Filter.Stream_End then
- Add_Data (Simple_GZip_Header);
-
- Translate_Auto
- (Filter => Filter,
- In_Data => In_Data,
- In_Last => In_Last,
- Out_Data => Out_Data (Out_First .. Out_Data'Last),
- Out_Last => Out_Last,
- Flush => Flush);
-
- CRC32 (Filter.CRC, In_Data (In_Data'First .. In_Last));
- end if;
-
- if Filter.Stream_End and then Out_Last <= Out_Data'Last then
- -- This detection method would work only when
- -- Simple_GZip_Header'Last > Footer_Array'Last
-
- if Filter.Offset = Simple_GZip_Header'Last + 1 then
- Filter.Offset := Footer_Array'First;
- end if;
-
- declare
- Footer : Footer_Array;
- begin
- Put_32 (Footer, Filter.CRC);
- Put_32 (Footer (Footer'First + 4 .. Footer'Last),
- Unsigned_32 (Total_In (Filter)));
- Add_Data (Footer);
- end;
- end if;
- end Translate_GZip;
-
- -------------
- -- Version --
- -------------
-
- function Version return String is
- begin
- return Interfaces.C.Strings.Value (Thin.zlibVersion);
- end Version;
-
- -----------
- -- Write --
- -----------
-
- procedure Write
- (Filter : in out Filter_Type;
- Item : in Ada.Streams.Stream_Element_Array;
- Flush : in Flush_Mode := No_Flush)
- is
- Buffer : Stream_Element_Array (1 .. Buffer_Size);
- In_Last : Stream_Element_Offset;
- Out_Last : Stream_Element_Offset;
- In_First : Stream_Element_Offset := Item'First;
- begin
- if Item'Length = 0 and Flush = No_Flush then
- return;
- end if;
-
- loop
- Translate
- (Filter => Filter,
- In_Data => Item (In_First .. Item'Last),
- In_Last => In_Last,
- Out_Data => Buffer,
- Out_Last => Out_Last,
- Flush => Flush);
-
- if Out_Last >= Buffer'First then
- Write (Buffer (1 .. Out_Last));
- end if;
-
- exit when In_Last = Item'Last or Stream_End (Filter);
-
- In_First := In_Last + 1;
- end loop;
- end Write;
-
-end ZLib;
diff --git a/third-party/zlib/contrib/ada/zlib.ads b/third-party/zlib/contrib/ada/zlib.ads
deleted file mode 100644
index 79ffc40..0000000
--- a/third-party/zlib/contrib/ada/zlib.ads
+++ /dev/null
@@ -1,328 +0,0 @@
-------------------------------------------------------------------------------
--- ZLib for Ada thick binding. --
--- --
--- Copyright (C) 2002-2004 Dmitriy Anisimkov --
--- --
--- This library is free software; you can redistribute it and/or modify --
--- it under the terms of the GNU General Public License as published by --
--- the Free Software Foundation; either version 2 of the License, or (at --
--- your option) any later version. --
--- --
--- This library is distributed in the hope that it will be useful, but --
--- WITHOUT ANY WARRANTY; without even the implied warranty of --
--- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU --
--- General Public License for more details. --
--- --
--- You should have received a copy of the GNU General Public License --
--- along with this library; if not, write to the Free Software Foundation, --
--- Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. --
--- --
--- As a special exception, if other files instantiate generics from this --
--- unit, or you link this unit with other files to produce an executable, --
--- this unit does not by itself cause the resulting executable to be --
--- covered by the GNU General Public License. This exception does not --
--- however invalidate any other reasons why the executable file might be --
--- covered by the GNU Public License. --
-------------------------------------------------------------------------------
-
--- $Id: zlib.ads,v 1.26 2004/09/06 06:53:19 vagul Exp $
-
-with Ada.Streams;
-
-with Interfaces;
-
-package ZLib is
-
- ZLib_Error : exception;
- Status_Error : exception;
-
- type Compression_Level is new Integer range -1 .. 9;
-
- type Flush_Mode is private;
-
- type Compression_Method is private;
-
- type Window_Bits_Type is new Integer range 8 .. 15;
-
- type Memory_Level_Type is new Integer range 1 .. 9;
-
- type Unsigned_32 is new Interfaces.Unsigned_32;
-
- type Strategy_Type is private;
-
- type Header_Type is (None, Auto, Default, GZip);
- -- Header type usage have a some limitation for inflate.
- -- See comment for Inflate_Init.
-
- subtype Count is Ada.Streams.Stream_Element_Count;
-
- Default_Memory_Level : constant Memory_Level_Type := 8;
- Default_Window_Bits : constant Window_Bits_Type := 15;
-
- ----------------------------------
- -- Compression method constants --
- ----------------------------------
-
- Deflated : constant Compression_Method;
- -- Only one method allowed in this ZLib version
-
- ---------------------------------
- -- Compression level constants --
- ---------------------------------
-
- No_Compression : constant Compression_Level := 0;
- Best_Speed : constant Compression_Level := 1;
- Best_Compression : constant Compression_Level := 9;
- Default_Compression : constant Compression_Level := -1;
-
- --------------------------
- -- Flush mode constants --
- --------------------------
-
- No_Flush : constant Flush_Mode;
- -- Regular way for compression, no flush
-
- Partial_Flush : constant Flush_Mode;
- -- Will be removed, use Z_SYNC_FLUSH instead
-
- Sync_Flush : constant Flush_Mode;
- -- All pending output is flushed to the output buffer and the output
- -- is aligned on a byte boundary, so that the decompressor can get all
- -- input data available so far. (In particular avail_in is zero after the
- -- call if enough output space has been provided before the call.)
- -- Flushing may degrade compression for some compression algorithms and so
- -- it should be used only when necessary.
-
- Block_Flush : constant Flush_Mode;
- -- Z_BLOCK requests that inflate() stop
- -- if and when it get to the next deflate block boundary. When decoding the
- -- zlib or gzip format, this will cause inflate() to return immediately
- -- after the header and before the first block. When doing a raw inflate,
- -- inflate() will go ahead and process the first block, and will return
- -- when it gets to the end of that block, or when it runs out of data.
-
- Full_Flush : constant Flush_Mode;
- -- All output is flushed as with SYNC_FLUSH, and the compression state
- -- is reset so that decompression can restart from this point if previous
- -- compressed data has been damaged or if random access is desired. Using
- -- Full_Flush too often can seriously degrade the compression.
-
- Finish : constant Flush_Mode;
- -- Just for tell the compressor that input data is complete.
-
- ------------------------------------
- -- Compression strategy constants --
- ------------------------------------
-
- -- RLE stategy could be used only in version 1.2.0 and later.
-
- Filtered : constant Strategy_Type;
- Huffman_Only : constant Strategy_Type;
- RLE : constant Strategy_Type;
- Default_Strategy : constant Strategy_Type;
-
- Default_Buffer_Size : constant := 4096;
-
- type Filter_Type is tagged limited private;
- -- The filter is for compression and for decompression.
- -- The usage of the type is depend of its initialization.
-
- function Version return String;
- pragma Inline (Version);
- -- Return string representation of the ZLib version.
-
- procedure Deflate_Init
- (Filter : in out Filter_Type;
- Level : in Compression_Level := Default_Compression;
- Strategy : in Strategy_Type := Default_Strategy;
- Method : in Compression_Method := Deflated;
- Window_Bits : in Window_Bits_Type := Default_Window_Bits;
- Memory_Level : in Memory_Level_Type := Default_Memory_Level;
- Header : in Header_Type := Default);
- -- Compressor initialization.
- -- When Header parameter is Auto or Default, then default zlib header
- -- would be provided for compressed data.
- -- When Header is GZip, then gzip header would be set instead of
- -- default header.
- -- When Header is None, no header would be set for compressed data.
-
- procedure Inflate_Init
- (Filter : in out Filter_Type;
- Window_Bits : in Window_Bits_Type := Default_Window_Bits;
- Header : in Header_Type := Default);
- -- Decompressor initialization.
- -- Default header type mean that ZLib default header is expecting in the
- -- input compressed stream.
- -- Header type None mean that no header is expecting in the input stream.
- -- GZip header type mean that GZip header is expecting in the
- -- input compressed stream.
- -- Auto header type mean that header type (GZip or Native) would be
- -- detected automatically in the input stream.
- -- Note that header types parameter values None, GZip and Auto are
- -- supported for inflate routine only in ZLib versions 1.2.0.2 and later.
- -- Deflate_Init is supporting all header types.
-
- function Is_Open (Filter : in Filter_Type) return Boolean;
- pragma Inline (Is_Open);
- -- Is the filter opened for compression or decompression.
-
- procedure Close
- (Filter : in out Filter_Type;
- Ignore_Error : in Boolean := False);
- -- Closing the compression or decompressor.
- -- If stream is closing before the complete and Ignore_Error is False,
- -- The exception would be raised.
-
- generic
- with procedure Data_In
- (Item : out Ada.Streams.Stream_Element_Array;
- Last : out Ada.Streams.Stream_Element_Offset);
- with procedure Data_Out
- (Item : in Ada.Streams.Stream_Element_Array);
- procedure Generic_Translate
- (Filter : in out Filter_Type;
- In_Buffer_Size : in Integer := Default_Buffer_Size;
- Out_Buffer_Size : in Integer := Default_Buffer_Size);
- -- Compress/decompress data fetch from Data_In routine and pass the result
- -- to the Data_Out routine. User should provide Data_In and Data_Out
- -- for compression/decompression data flow.
- -- Compression or decompression depend on Filter initialization.
-
- function Total_In (Filter : in Filter_Type) return Count;
- pragma Inline (Total_In);
- -- Returns total number of input bytes read so far
-
- function Total_Out (Filter : in Filter_Type) return Count;
- pragma Inline (Total_Out);
- -- Returns total number of bytes output so far
-
- function CRC32
- (CRC : in Unsigned_32;
- Data : in Ada.Streams.Stream_Element_Array)
- return Unsigned_32;
- pragma Inline (CRC32);
- -- Compute CRC32, it could be necessary for make gzip format
-
- procedure CRC32
- (CRC : in out Unsigned_32;
- Data : in Ada.Streams.Stream_Element_Array);
- pragma Inline (CRC32);
- -- Compute CRC32, it could be necessary for make gzip format
-
- -------------------------------------------------
- -- Below is more complex low level routines. --
- -------------------------------------------------
-
- procedure Translate
- (Filter : in out Filter_Type;
- In_Data : in Ada.Streams.Stream_Element_Array;
- In_Last : out Ada.Streams.Stream_Element_Offset;
- Out_Data : out Ada.Streams.Stream_Element_Array;
- Out_Last : out Ada.Streams.Stream_Element_Offset;
- Flush : in Flush_Mode);
- -- Compress/decompress the In_Data buffer and place the result into
- -- Out_Data. In_Last is the index of last element from In_Data accepted by
- -- the Filter. Out_Last is the last element of the received data from
- -- Filter. To tell the filter that incoming data are complete put the
- -- Flush parameter to Finish.
-
- function Stream_End (Filter : in Filter_Type) return Boolean;
- pragma Inline (Stream_End);
- -- Return the true when the stream is complete.
-
- procedure Flush
- (Filter : in out Filter_Type;
- Out_Data : out Ada.Streams.Stream_Element_Array;
- Out_Last : out Ada.Streams.Stream_Element_Offset;
- Flush : in Flush_Mode);
- pragma Inline (Flush);
- -- Flushing the data from the compressor.
-
- generic
- with procedure Write
- (Item : in Ada.Streams.Stream_Element_Array);
- -- User should provide this routine for accept
- -- compressed/decompressed data.
-
- Buffer_Size : in Ada.Streams.Stream_Element_Offset
- := Default_Buffer_Size;
- -- Buffer size for Write user routine.
-
- procedure Write
- (Filter : in out Filter_Type;
- Item : in Ada.Streams.Stream_Element_Array;
- Flush : in Flush_Mode := No_Flush);
- -- Compress/Decompress data from Item to the generic parameter procedure
- -- Write. Output buffer size could be set in Buffer_Size generic parameter.
-
- generic
- with procedure Read
- (Item : out Ada.Streams.Stream_Element_Array;
- Last : out Ada.Streams.Stream_Element_Offset);
- -- User should provide data for compression/decompression
- -- thru this routine.
-
- Buffer : in out Ada.Streams.Stream_Element_Array;
- -- Buffer for keep remaining data from the previous
- -- back read.
-
- Rest_First, Rest_Last : in out Ada.Streams.Stream_Element_Offset;
- -- Rest_First have to be initialized to Buffer'Last + 1
- -- Rest_Last have to be initialized to Buffer'Last
- -- before usage.
-
- Allow_Read_Some : in Boolean := False;
- -- Is it allowed to return Last < Item'Last before end of data.
-
- procedure Read
- (Filter : in out Filter_Type;
- Item : out Ada.Streams.Stream_Element_Array;
- Last : out Ada.Streams.Stream_Element_Offset;
- Flush : in Flush_Mode := No_Flush);
- -- Compress/Decompress data from generic parameter procedure Read to the
- -- Item. User should provide Buffer and initialized Rest_First, Rest_Last
- -- indicators. If Allow_Read_Some is True, Read routines could return
- -- Last < Item'Last only at end of stream.
-
-private
-
- use Ada.Streams;
-
- pragma Assert (Ada.Streams.Stream_Element'Size = 8);
- pragma Assert (Ada.Streams.Stream_Element'Modulus = 2**8);
-
- type Flush_Mode is new Integer range 0 .. 5;
-
- type Compression_Method is new Integer range 8 .. 8;
-
- type Strategy_Type is new Integer range 0 .. 3;
-
- No_Flush : constant Flush_Mode := 0;
- Partial_Flush : constant Flush_Mode := 1;
- Sync_Flush : constant Flush_Mode := 2;
- Full_Flush : constant Flush_Mode := 3;
- Finish : constant Flush_Mode := 4;
- Block_Flush : constant Flush_Mode := 5;
-
- Filtered : constant Strategy_Type := 1;
- Huffman_Only : constant Strategy_Type := 2;
- RLE : constant Strategy_Type := 3;
- Default_Strategy : constant Strategy_Type := 0;
-
- Deflated : constant Compression_Method := 8;
-
- type Z_Stream;
-
- type Z_Stream_Access is access all Z_Stream;
-
- type Filter_Type is tagged limited record
- Strm : Z_Stream_Access;
- Compression : Boolean;
- Stream_End : Boolean;
- Header : Header_Type;
- CRC : Unsigned_32;
- Offset : Stream_Element_Offset;
- -- Offset for gzip header/footer output.
- end record;
-
-end ZLib;
diff --git a/third-party/zlib/contrib/ada/zlib.gpr b/third-party/zlib/contrib/ada/zlib.gpr
deleted file mode 100644
index 296b22a..0000000
--- a/third-party/zlib/contrib/ada/zlib.gpr
+++ /dev/null
@@ -1,20 +0,0 @@
-project Zlib is
-
- for Languages use ("Ada");
- for Source_Dirs use (".");
- for Object_Dir use ".";
- for Main use ("test.adb", "mtest.adb", "read.adb", "buffer_demo");
-
- package Compiler is
- for Default_Switches ("ada") use ("-gnatwcfilopru", "-gnatVcdfimorst", "-gnatyabcefhiklmnoprst");
- end Compiler;
-
- package Linker is
- for Default_Switches ("ada") use ("-lz");
- end Linker;
-
- package Builder is
- for Default_Switches ("ada") use ("-s", "-gnatQ");
- end Builder;
-
-end Zlib;
diff --git a/third-party/zlib/contrib/amd64/amd64-match.S b/third-party/zlib/contrib/amd64/amd64-match.S
deleted file mode 100644
index 81d4a1c..0000000
--- a/third-party/zlib/contrib/amd64/amd64-match.S
+++ /dev/null
@@ -1,452 +0,0 @@
-/*
- * match.S -- optimized version of longest_match()
- * based on the similar work by Gilles Vollant, and Brian Raiter, written 1998
- *
- * This is free software; you can redistribute it and/or modify it
- * under the terms of the BSD License. Use by owners of Che Guevarra
- * parafernalia is prohibited, where possible, and highly discouraged
- * elsewhere.
- */
-
-#ifndef NO_UNDERLINE
-# define match_init _match_init
-# define longest_match _longest_match
-#endif
-
-#define scanend ebx
-#define scanendw bx
-#define chainlenwmask edx /* high word: current chain len low word: s->wmask */
-#define curmatch rsi
-#define curmatchd esi
-#define windowbestlen r8
-#define scanalign r9
-#define scanalignd r9d
-#define window r10
-#define bestlen r11
-#define bestlend r11d
-#define scanstart r12d
-#define scanstartw r12w
-#define scan r13
-#define nicematch r14d
-#define limit r15
-#define limitd r15d
-#define prev rcx
-
-/*
- * The 258 is a "magic number, not a parameter -- changing it
- * breaks the hell loose
- */
-#define MAX_MATCH (258)
-#define MIN_MATCH (3)
-#define MIN_LOOKAHEAD (MAX_MATCH + MIN_MATCH + 1)
-#define MAX_MATCH_8 ((MAX_MATCH + 7) & ~7)
-
-/* stack frame offsets */
-#define LocalVarsSize (112)
-#define _chainlenwmask ( 8-LocalVarsSize)(%rsp)
-#define _windowbestlen (16-LocalVarsSize)(%rsp)
-#define save_r14 (24-LocalVarsSize)(%rsp)
-#define save_rsi (32-LocalVarsSize)(%rsp)
-#define save_rbx (40-LocalVarsSize)(%rsp)
-#define save_r12 (56-LocalVarsSize)(%rsp)
-#define save_r13 (64-LocalVarsSize)(%rsp)
-#define save_r15 (80-LocalVarsSize)(%rsp)
-
-
-.globl match_init, longest_match
-
-/*
- * On AMD64 the first argument of a function (in our case -- the pointer to
- * deflate_state structure) is passed in %rdi, hence our offsets below are
- * all off of that.
- */
-
-/* you can check the structure offset by running
-
-#include <stdlib.h>
-#include <stdio.h>
-#include "deflate.h"
-
-void print_depl()
-{
-deflate_state ds;
-deflate_state *s=&ds;
-printf("size pointer=%u\n",(int)sizeof(void*));
-
-printf("#define dsWSize (%3u)(%%rdi)\n",(int)(((char*)&(s->w_size))-((char*)s)));
-printf("#define dsWMask (%3u)(%%rdi)\n",(int)(((char*)&(s->w_mask))-((char*)s)));
-printf("#define dsWindow (%3u)(%%rdi)\n",(int)(((char*)&(s->window))-((char*)s)));
-printf("#define dsPrev (%3u)(%%rdi)\n",(int)(((char*)&(s->prev))-((char*)s)));
-printf("#define dsMatchLen (%3u)(%%rdi)\n",(int)(((char*)&(s->match_length))-((char*)s)));
-printf("#define dsPrevMatch (%3u)(%%rdi)\n",(int)(((char*)&(s->prev_match))-((char*)s)));
-printf("#define dsStrStart (%3u)(%%rdi)\n",(int)(((char*)&(s->strstart))-((char*)s)));
-printf("#define dsMatchStart (%3u)(%%rdi)\n",(int)(((char*)&(s->match_start))-((char*)s)));
-printf("#define dsLookahead (%3u)(%%rdi)\n",(int)(((char*)&(s->lookahead))-((char*)s)));
-printf("#define dsPrevLen (%3u)(%%rdi)\n",(int)(((char*)&(s->prev_length))-((char*)s)));
-printf("#define dsMaxChainLen (%3u)(%%rdi)\n",(int)(((char*)&(s->max_chain_length))-((char*)s)));
-printf("#define dsGoodMatch (%3u)(%%rdi)\n",(int)(((char*)&(s->good_match))-((char*)s)));
-printf("#define dsNiceMatch (%3u)(%%rdi)\n",(int)(((char*)&(s->nice_match))-((char*)s)));
-}
-
-*/
-
-
-/*
- to compile for XCode 3.2 on MacOSX x86_64
- - run "gcc -g -c -DXCODE_MAC_X64_STRUCTURE amd64-match.S"
- */
-
-
-#ifndef CURRENT_LINX_XCODE_MAC_X64_STRUCTURE
-#define dsWSize ( 68)(%rdi)
-#define dsWMask ( 76)(%rdi)
-#define dsWindow ( 80)(%rdi)
-#define dsPrev ( 96)(%rdi)
-#define dsMatchLen (144)(%rdi)
-#define dsPrevMatch (148)(%rdi)
-#define dsStrStart (156)(%rdi)
-#define dsMatchStart (160)(%rdi)
-#define dsLookahead (164)(%rdi)
-#define dsPrevLen (168)(%rdi)
-#define dsMaxChainLen (172)(%rdi)
-#define dsGoodMatch (188)(%rdi)
-#define dsNiceMatch (192)(%rdi)
-
-#else
-
-#ifndef STRUCT_OFFSET
-# define STRUCT_OFFSET (0)
-#endif
-
-
-#define dsWSize ( 56 + STRUCT_OFFSET)(%rdi)
-#define dsWMask ( 64 + STRUCT_OFFSET)(%rdi)
-#define dsWindow ( 72 + STRUCT_OFFSET)(%rdi)
-#define dsPrev ( 88 + STRUCT_OFFSET)(%rdi)
-#define dsMatchLen (136 + STRUCT_OFFSET)(%rdi)
-#define dsPrevMatch (140 + STRUCT_OFFSET)(%rdi)
-#define dsStrStart (148 + STRUCT_OFFSET)(%rdi)
-#define dsMatchStart (152 + STRUCT_OFFSET)(%rdi)
-#define dsLookahead (156 + STRUCT_OFFSET)(%rdi)
-#define dsPrevLen (160 + STRUCT_OFFSET)(%rdi)
-#define dsMaxChainLen (164 + STRUCT_OFFSET)(%rdi)
-#define dsGoodMatch (180 + STRUCT_OFFSET)(%rdi)
-#define dsNiceMatch (184 + STRUCT_OFFSET)(%rdi)
-
-#endif
-
-
-
-
-.text
-
-/* uInt longest_match(deflate_state *deflatestate, IPos curmatch) */
-
-longest_match:
-/*
- * Retrieve the function arguments. %curmatch will hold cur_match
- * throughout the entire function (passed via rsi on amd64).
- * rdi will hold the pointer to the deflate_state (first arg on amd64)
- */
- mov %rsi, save_rsi
- mov %rbx, save_rbx
- mov %r12, save_r12
- mov %r13, save_r13
- mov %r14, save_r14
- mov %r15, save_r15
-
-/* uInt wmask = s->w_mask; */
-/* unsigned chain_length = s->max_chain_length; */
-/* if (s->prev_length >= s->good_match) { */
-/* chain_length >>= 2; */
-/* } */
-
- movl dsPrevLen, %eax
- movl dsGoodMatch, %ebx
- cmpl %ebx, %eax
- movl dsWMask, %eax
- movl dsMaxChainLen, %chainlenwmask
- jl LastMatchGood
- shrl $2, %chainlenwmask
-LastMatchGood:
-
-/* chainlen is decremented once beforehand so that the function can */
-/* use the sign flag instead of the zero flag for the exit test. */
-/* It is then shifted into the high word, to make room for the wmask */
-/* value, which it will always accompany. */
-
- decl %chainlenwmask
- shll $16, %chainlenwmask
- orl %eax, %chainlenwmask
-
-/* if ((uInt)nice_match > s->lookahead) nice_match = s->lookahead; */
-
- movl dsNiceMatch, %eax
- movl dsLookahead, %ebx
- cmpl %eax, %ebx
- jl LookaheadLess
- movl %eax, %ebx
-LookaheadLess: movl %ebx, %nicematch
-
-/* register Bytef *scan = s->window + s->strstart; */
-
- mov dsWindow, %window
- movl dsStrStart, %limitd
- lea (%limit, %window), %scan
-
-/* Determine how many bytes the scan ptr is off from being */
-/* dword-aligned. */
-
- mov %scan, %scanalign
- negl %scanalignd
- andl $3, %scanalignd
-
-/* IPos limit = s->strstart > (IPos)MAX_DIST(s) ? */
-/* s->strstart - (IPos)MAX_DIST(s) : NIL; */
-
- movl dsWSize, %eax
- subl $MIN_LOOKAHEAD, %eax
- xorl %ecx, %ecx
- subl %eax, %limitd
- cmovng %ecx, %limitd
-
-/* int best_len = s->prev_length; */
-
- movl dsPrevLen, %bestlend
-
-/* Store the sum of s->window + best_len in %windowbestlen locally, and in memory. */
-
- lea (%window, %bestlen), %windowbestlen
- mov %windowbestlen, _windowbestlen
-
-/* register ush scan_start = *(ushf*)scan; */
-/* register ush scan_end = *(ushf*)(scan+best_len-1); */
-/* Posf *prev = s->prev; */
-
- movzwl (%scan), %scanstart
- movzwl -1(%scan, %bestlen), %scanend
- mov dsPrev, %prev
-
-/* Jump into the main loop. */
-
- movl %chainlenwmask, _chainlenwmask
- jmp LoopEntry
-
-.balign 16
-
-/* do {
- * match = s->window + cur_match;
- * if (*(ushf*)(match+best_len-1) != scan_end ||
- * *(ushf*)match != scan_start) continue;
- * [...]
- * } while ((cur_match = prev[cur_match & wmask]) > limit
- * && --chain_length != 0);
- *
- * Here is the inner loop of the function. The function will spend the
- * majority of its time in this loop, and majority of that time will
- * be spent in the first ten instructions.
- */
-LookupLoop:
- andl %chainlenwmask, %curmatchd
- movzwl (%prev, %curmatch, 2), %curmatchd
- cmpl %limitd, %curmatchd
- jbe LeaveNow
- subl $0x00010000, %chainlenwmask
- js LeaveNow
-LoopEntry: cmpw -1(%windowbestlen, %curmatch), %scanendw
- jne LookupLoop
- cmpw %scanstartw, (%window, %curmatch)
- jne LookupLoop
-
-/* Store the current value of chainlen. */
- movl %chainlenwmask, _chainlenwmask
-
-/* %scan is the string under scrutiny, and %prev to the string we */
-/* are hoping to match it up with. In actuality, %esi and %edi are */
-/* both pointed (MAX_MATCH_8 - scanalign) bytes ahead, and %edx is */
-/* initialized to -(MAX_MATCH_8 - scanalign). */
-
- mov $(-MAX_MATCH_8), %rdx
- lea (%curmatch, %window), %windowbestlen
- lea MAX_MATCH_8(%windowbestlen, %scanalign), %windowbestlen
- lea MAX_MATCH_8(%scan, %scanalign), %prev
-
-/* the prefetching below makes very little difference... */
- prefetcht1 (%windowbestlen, %rdx)
- prefetcht1 (%prev, %rdx)
-
-/*
- * Test the strings for equality, 8 bytes at a time. At the end,
- * adjust %rdx so that it is offset to the exact byte that mismatched.
- *
- * It should be confessed that this loop usually does not represent
- * much of the total running time. Replacing it with a more
- * straightforward "rep cmpsb" would not drastically degrade
- * performance -- unrolling it, for example, makes no difference.
- */
-
-#undef USE_SSE /* works, but is 6-7% slower, than non-SSE... */
-
-LoopCmps:
-#ifdef USE_SSE
- /* Preload the SSE registers */
- movdqu (%windowbestlen, %rdx), %xmm1
- movdqu (%prev, %rdx), %xmm2
- pcmpeqb %xmm2, %xmm1
- movdqu 16(%windowbestlen, %rdx), %xmm3
- movdqu 16(%prev, %rdx), %xmm4
- pcmpeqb %xmm4, %xmm3
- movdqu 32(%windowbestlen, %rdx), %xmm5
- movdqu 32(%prev, %rdx), %xmm6
- pcmpeqb %xmm6, %xmm5
- movdqu 48(%windowbestlen, %rdx), %xmm7
- movdqu 48(%prev, %rdx), %xmm8
- pcmpeqb %xmm8, %xmm7
-
- /* Check the comparisions' results */
- pmovmskb %xmm1, %rax
- notw %ax
- bsfw %ax, %ax
- jnz LeaveLoopCmps
-
- /* this is the only iteration of the loop with a possibility of having
- incremented rdx by 0x108 (each loop iteration add 16*4 = 0x40
- and (0x40*4)+8=0x108 */
- add $8, %rdx
- jz LenMaximum
- add $8, %rdx
-
-
- pmovmskb %xmm3, %rax
- notw %ax
- bsfw %ax, %ax
- jnz LeaveLoopCmps
-
-
- add $16, %rdx
-
-
- pmovmskb %xmm5, %rax
- notw %ax
- bsfw %ax, %ax
- jnz LeaveLoopCmps
-
- add $16, %rdx
-
-
- pmovmskb %xmm7, %rax
- notw %ax
- bsfw %ax, %ax
- jnz LeaveLoopCmps
-
- add $16, %rdx
-
- jmp LoopCmps
-LeaveLoopCmps: add %rax, %rdx
-#else
- mov (%windowbestlen, %rdx), %rax
- xor (%prev, %rdx), %rax
- jnz LeaveLoopCmps
-
- mov 8(%windowbestlen, %rdx), %rax
- xor 8(%prev, %rdx), %rax
- jnz LeaveLoopCmps8
-
- mov 16(%windowbestlen, %rdx), %rax
- xor 16(%prev, %rdx), %rax
- jnz LeaveLoopCmps16
-
- add $24, %rdx
- jnz LoopCmps
- jmp LenMaximum
-# if 0
-/*
- * This three-liner is tantalizingly simple, but bsf is a slow instruction,
- * and the complicated alternative down below is quite a bit faster. Sad...
- */
-
-LeaveLoopCmps: bsf %rax, %rax /* find the first non-zero bit */
- shrl $3, %eax /* divide by 8 to get the byte */
- add %rax, %rdx
-# else
-LeaveLoopCmps16:
- add $8, %rdx
-LeaveLoopCmps8:
- add $8, %rdx
-LeaveLoopCmps: testl $0xFFFFFFFF, %eax /* Check the first 4 bytes */
- jnz Check16
- add $4, %rdx
- shr $32, %rax
-Check16: testw $0xFFFF, %ax
- jnz LenLower
- add $2, %rdx
- shrl $16, %eax
-LenLower: subb $1, %al
- adc $0, %rdx
-# endif
-#endif
-
-/* Calculate the length of the match. If it is longer than MAX_MATCH, */
-/* then automatically accept it as the best possible match and leave. */
-
- lea (%prev, %rdx), %rax
- sub %scan, %rax
- cmpl $MAX_MATCH, %eax
- jge LenMaximum
-
-/* If the length of the match is not longer than the best match we */
-/* have so far, then forget it and return to the lookup loop. */
-
- cmpl %bestlend, %eax
- jg LongerMatch
- mov _windowbestlen, %windowbestlen
- mov dsPrev, %prev
- movl _chainlenwmask, %edx
- jmp LookupLoop
-
-/* s->match_start = cur_match; */
-/* best_len = len; */
-/* if (len >= nice_match) break; */
-/* scan_end = *(ushf*)(scan+best_len-1); */
-
-LongerMatch:
- movl %eax, %bestlend
- movl %curmatchd, dsMatchStart
- cmpl %nicematch, %eax
- jge LeaveNow
-
- lea (%window, %bestlen), %windowbestlen
- mov %windowbestlen, _windowbestlen
-
- movzwl -1(%scan, %rax), %scanend
- mov dsPrev, %prev
- movl _chainlenwmask, %chainlenwmask
- jmp LookupLoop
-
-/* Accept the current string, with the maximum possible length. */
-
-LenMaximum:
- movl $MAX_MATCH, %bestlend
- movl %curmatchd, dsMatchStart
-
-/* if ((uInt)best_len <= s->lookahead) return (uInt)best_len; */
-/* return s->lookahead; */
-
-LeaveNow:
- movl dsLookahead, %eax
- cmpl %eax, %bestlend
- cmovngl %bestlend, %eax
-LookaheadRet:
-
-/* Restore the registers and return from whence we came. */
-
- mov save_rsi, %rsi
- mov save_rbx, %rbx
- mov save_r12, %r12
- mov save_r13, %r13
- mov save_r14, %r14
- mov save_r15, %r15
-
- ret
-
-match_init: ret
diff --git a/third-party/zlib/contrib/asm686/README.686 b/third-party/zlib/contrib/asm686/README.686
deleted file mode 100644
index a0bf3be..0000000
--- a/third-party/zlib/contrib/asm686/README.686
+++ /dev/null
@@ -1,51 +0,0 @@
-This is a patched version of zlib, modified to use
-Pentium-Pro-optimized assembly code in the deflation algorithm. The
-files changed/added by this patch are:
-
-README.686
-match.S
-
-The speedup that this patch provides varies, depending on whether the
-compiler used to build the original version of zlib falls afoul of the
-PPro's speed traps. My own tests show a speedup of around 10-20% at
-the default compression level, and 20-30% using -9, against a version
-compiled using gcc 2.7.2.3. Your mileage may vary.
-
-Note that this code has been tailored for the PPro/PII in particular,
-and will not perform particuarly well on a Pentium.
-
-If you are using an assembler other than GNU as, you will have to
-translate match.S to use your assembler's syntax. (Have fun.)
-
-Brian Raiter
-breadbox at muppetlabs.com
-April, 1998
-
-
-Added for zlib 1.1.3:
-
-The patches come from
-http://www.muppetlabs.com/~breadbox/software/assembly.html
-
-To compile zlib with this asm file, copy match.S to the zlib directory
-then do:
-
-CFLAGS="-O3 -DASMV" ./configure
-make OBJA=match.o
-
-
-Update:
-
-I've been ignoring these assembly routines for years, believing that
-gcc's generated code had caught up with it sometime around gcc 2.95
-and the major rearchitecting of the Pentium 4. However, I recently
-learned that, despite what I believed, this code still has some life
-in it. On the Pentium 4 and AMD64 chips, it continues to run about 8%
-faster than the code produced by gcc 4.1.
-
-In acknowledgement of its continuing usefulness, I've altered the
-license to match that of the rest of zlib. Share and Enjoy!
-
-Brian Raiter
-breadbox at muppetlabs.com
-April, 2007
diff --git a/third-party/zlib/contrib/asm686/match.S b/third-party/zlib/contrib/asm686/match.S
deleted file mode 100644
index fa42109..0000000
--- a/third-party/zlib/contrib/asm686/match.S
+++ /dev/null
@@ -1,357 +0,0 @@
-/* match.S -- x86 assembly version of the zlib longest_match() function.
- * Optimized for the Intel 686 chips (PPro and later).
- *
- * Copyright (C) 1998, 2007 Brian Raiter <breadbox at muppetlabs.com>
- *
- * This software is provided 'as-is', without any express or implied
- * warranty. In no event will the author be held liable for any damages
- * arising from the use of this software.
- *
- * Permission is granted to anyone to use this software for any purpose,
- * including commercial applications, and to alter it and redistribute it
- * freely, subject to the following restrictions:
- *
- * 1. The origin of this software must not be misrepresented; you must not
- * claim that you wrote the original software. If you use this software
- * in a product, an acknowledgment in the product documentation would be
- * appreciated but is not required.
- * 2. Altered source versions must be plainly marked as such, and must not be
- * misrepresented as being the original software.
- * 3. This notice may not be removed or altered from any source distribution.
- */
-
-#ifndef NO_UNDERLINE
-#define match_init _match_init
-#define longest_match _longest_match
-#endif
-
-#define MAX_MATCH (258)
-#define MIN_MATCH (3)
-#define MIN_LOOKAHEAD (MAX_MATCH + MIN_MATCH + 1)
-#define MAX_MATCH_8 ((MAX_MATCH + 7) & ~7)
-
-/* stack frame offsets */
-
-#define chainlenwmask 0 /* high word: current chain len */
- /* low word: s->wmask */
-#define window 4 /* local copy of s->window */
-#define windowbestlen 8 /* s->window + bestlen */
-#define scanstart 16 /* first two bytes of string */
-#define scanend 12 /* last two bytes of string */
-#define scanalign 20 /* dword-misalignment of string */
-#define nicematch 24 /* a good enough match size */
-#define bestlen 28 /* size of best match so far */
-#define scan 32 /* ptr to string wanting match */
-
-#define LocalVarsSize (36)
-/* saved ebx 36 */
-/* saved edi 40 */
-/* saved esi 44 */
-/* saved ebp 48 */
-/* return address 52 */
-#define deflatestate 56 /* the function arguments */
-#define curmatch 60
-
-/* All the +zlib1222add offsets are due to the addition of fields
- * in zlib in the deflate_state structure since the asm code was first written
- * (if you compile with zlib 1.0.4 or older, use "zlib1222add equ (-4)").
- * (if you compile with zlib between 1.0.5 and 1.2.2.1, use "zlib1222add equ 0").
- * if you compile with zlib 1.2.2.2 or later , use "zlib1222add equ 8").
- */
-
-#define zlib1222add (8)
-
-#define dsWSize (36+zlib1222add)
-#define dsWMask (44+zlib1222add)
-#define dsWindow (48+zlib1222add)
-#define dsPrev (56+zlib1222add)
-#define dsMatchLen (88+zlib1222add)
-#define dsPrevMatch (92+zlib1222add)
-#define dsStrStart (100+zlib1222add)
-#define dsMatchStart (104+zlib1222add)
-#define dsLookahead (108+zlib1222add)
-#define dsPrevLen (112+zlib1222add)
-#define dsMaxChainLen (116+zlib1222add)
-#define dsGoodMatch (132+zlib1222add)
-#define dsNiceMatch (136+zlib1222add)
-
-
-.file "match.S"
-
-.globl match_init, longest_match
-
-.text
-
-/* uInt longest_match(deflate_state *deflatestate, IPos curmatch) */
-.cfi_sections .debug_frame
-
-longest_match:
-
-.cfi_startproc
-/* Save registers that the compiler may be using, and adjust %esp to */
-/* make room for our stack frame. */
-
- pushl %ebp
- .cfi_def_cfa_offset 8
- .cfi_offset ebp, -8
- pushl %edi
- .cfi_def_cfa_offset 12
- pushl %esi
- .cfi_def_cfa_offset 16
- pushl %ebx
- .cfi_def_cfa_offset 20
- subl $LocalVarsSize, %esp
- .cfi_def_cfa_offset LocalVarsSize+20
-
-/* Retrieve the function arguments. %ecx will hold cur_match */
-/* throughout the entire function. %edx will hold the pointer to the */
-/* deflate_state structure during the function's setup (before */
-/* entering the main loop). */
-
- movl deflatestate(%esp), %edx
- movl curmatch(%esp), %ecx
-
-/* uInt wmask = s->w_mask; */
-/* unsigned chain_length = s->max_chain_length; */
-/* if (s->prev_length >= s->good_match) { */
-/* chain_length >>= 2; */
-/* } */
-
- movl dsPrevLen(%edx), %eax
- movl dsGoodMatch(%edx), %ebx
- cmpl %ebx, %eax
- movl dsWMask(%edx), %eax
- movl dsMaxChainLen(%edx), %ebx
- jl LastMatchGood
- shrl $2, %ebx
-LastMatchGood:
-
-/* chainlen is decremented once beforehand so that the function can */
-/* use the sign flag instead of the zero flag for the exit test. */
-/* It is then shifted into the high word, to make room for the wmask */
-/* value, which it will always accompany. */
-
- decl %ebx
- shll $16, %ebx
- orl %eax, %ebx
- movl %ebx, chainlenwmask(%esp)
-
-/* if ((uInt)nice_match > s->lookahead) nice_match = s->lookahead; */
-
- movl dsNiceMatch(%edx), %eax
- movl dsLookahead(%edx), %ebx
- cmpl %eax, %ebx
- jl LookaheadLess
- movl %eax, %ebx
-LookaheadLess: movl %ebx, nicematch(%esp)
-
-/* register Bytef *scan = s->window + s->strstart; */
-
- movl dsWindow(%edx), %esi
- movl %esi, window(%esp)
- movl dsStrStart(%edx), %ebp
- lea (%esi,%ebp), %edi
- movl %edi, scan(%esp)
-
-/* Determine how many bytes the scan ptr is off from being */
-/* dword-aligned. */
-
- movl %edi, %eax
- negl %eax
- andl $3, %eax
- movl %eax, scanalign(%esp)
-
-/* IPos limit = s->strstart > (IPos)MAX_DIST(s) ? */
-/* s->strstart - (IPos)MAX_DIST(s) : NIL; */
-
- movl dsWSize(%edx), %eax
- subl $MIN_LOOKAHEAD, %eax
- subl %eax, %ebp
- jg LimitPositive
- xorl %ebp, %ebp
-LimitPositive:
-
-/* int best_len = s->prev_length; */
-
- movl dsPrevLen(%edx), %eax
- movl %eax, bestlen(%esp)
-
-/* Store the sum of s->window + best_len in %esi locally, and in %esi. */
-
- addl %eax, %esi
- movl %esi, windowbestlen(%esp)
-
-/* register ush scan_start = *(ushf*)scan; */
-/* register ush scan_end = *(ushf*)(scan+best_len-1); */
-/* Posf *prev = s->prev; */
-
- movzwl (%edi), %ebx
- movl %ebx, scanstart(%esp)
- movzwl -1(%edi,%eax), %ebx
- movl %ebx, scanend(%esp)
- movl dsPrev(%edx), %edi
-
-/* Jump into the main loop. */
-
- movl chainlenwmask(%esp), %edx
- jmp LoopEntry
-
-.balign 16
-
-/* do {
- * match = s->window + cur_match;
- * if (*(ushf*)(match+best_len-1) != scan_end ||
- * *(ushf*)match != scan_start) continue;
- * [...]
- * } while ((cur_match = prev[cur_match & wmask]) > limit
- * && --chain_length != 0);
- *
- * Here is the inner loop of the function. The function will spend the
- * majority of its time in this loop, and majority of that time will
- * be spent in the first ten instructions.
- *
- * Within this loop:
- * %ebx = scanend
- * %ecx = curmatch
- * %edx = chainlenwmask - i.e., ((chainlen << 16) | wmask)
- * %esi = windowbestlen - i.e., (window + bestlen)
- * %edi = prev
- * %ebp = limit
- */
-LookupLoop:
- andl %edx, %ecx
- movzwl (%edi,%ecx,2), %ecx
- cmpl %ebp, %ecx
- jbe LeaveNow
- subl $0x00010000, %edx
- js LeaveNow
-LoopEntry: movzwl -1(%esi,%ecx), %eax
- cmpl %ebx, %eax
- jnz LookupLoop
- movl window(%esp), %eax
- movzwl (%eax,%ecx), %eax
- cmpl scanstart(%esp), %eax
- jnz LookupLoop
-
-/* Store the current value of chainlen. */
-
- movl %edx, chainlenwmask(%esp)
-
-/* Point %edi to the string under scrutiny, and %esi to the string we */
-/* are hoping to match it up with. In actuality, %esi and %edi are */
-/* both pointed (MAX_MATCH_8 - scanalign) bytes ahead, and %edx is */
-/* initialized to -(MAX_MATCH_8 - scanalign). */
-
- movl window(%esp), %esi
- movl scan(%esp), %edi
- addl %ecx, %esi
- movl scanalign(%esp), %eax
- movl $(-MAX_MATCH_8), %edx
- lea MAX_MATCH_8(%edi,%eax), %edi
- lea MAX_MATCH_8(%esi,%eax), %esi
-
-/* Test the strings for equality, 8 bytes at a time. At the end,
- * adjust %edx so that it is offset to the exact byte that mismatched.
- *
- * We already know at this point that the first three bytes of the
- * strings match each other, and they can be safely passed over before
- * starting the compare loop. So what this code does is skip over 0-3
- * bytes, as much as necessary in order to dword-align the %edi
- * pointer. (%esi will still be misaligned three times out of four.)
- *
- * It should be confessed that this loop usually does not represent
- * much of the total running time. Replacing it with a more
- * straightforward "rep cmpsb" would not drastically degrade
- * performance.
- */
-LoopCmps:
- movl (%esi,%edx), %eax
- xorl (%edi,%edx), %eax
- jnz LeaveLoopCmps
- movl 4(%esi,%edx), %eax
- xorl 4(%edi,%edx), %eax
- jnz LeaveLoopCmps4
- addl $8, %edx
- jnz LoopCmps
- jmp LenMaximum
-LeaveLoopCmps4: addl $4, %edx
-LeaveLoopCmps: testl $0x0000FFFF, %eax
- jnz LenLower
- addl $2, %edx
- shrl $16, %eax
-LenLower: subb $1, %al
- adcl $0, %edx
-
-/* Calculate the length of the match. If it is longer than MAX_MATCH, */
-/* then automatically accept it as the best possible match and leave. */
-
- lea (%edi,%edx), %eax
- movl scan(%esp), %edi
- subl %edi, %eax
- cmpl $MAX_MATCH, %eax
- jge LenMaximum
-
-/* If the length of the match is not longer than the best match we */
-/* have so far, then forget it and return to the lookup loop. */
-
- movl deflatestate(%esp), %edx
- movl bestlen(%esp), %ebx
- cmpl %ebx, %eax
- jg LongerMatch
- movl windowbestlen(%esp), %esi
- movl dsPrev(%edx), %edi
- movl scanend(%esp), %ebx
- movl chainlenwmask(%esp), %edx
- jmp LookupLoop
-
-/* s->match_start = cur_match; */
-/* best_len = len; */
-/* if (len >= nice_match) break; */
-/* scan_end = *(ushf*)(scan+best_len-1); */
-
-LongerMatch: movl nicematch(%esp), %ebx
- movl %eax, bestlen(%esp)
- movl %ecx, dsMatchStart(%edx)
- cmpl %ebx, %eax
- jge LeaveNow
- movl window(%esp), %esi
- addl %eax, %esi
- movl %esi, windowbestlen(%esp)
- movzwl -1(%edi,%eax), %ebx
- movl dsPrev(%edx), %edi
- movl %ebx, scanend(%esp)
- movl chainlenwmask(%esp), %edx
- jmp LookupLoop
-
-/* Accept the current string, with the maximum possible length. */
-
-LenMaximum: movl deflatestate(%esp), %edx
- movl $MAX_MATCH, bestlen(%esp)
- movl %ecx, dsMatchStart(%edx)
-
-/* if ((uInt)best_len <= s->lookahead) return (uInt)best_len; */
-/* return s->lookahead; */
-
-LeaveNow:
- movl deflatestate(%esp), %edx
- movl bestlen(%esp), %ebx
- movl dsLookahead(%edx), %eax
- cmpl %eax, %ebx
- jg LookaheadRet
- movl %ebx, %eax
-LookaheadRet:
-
-/* Restore the stack and return from whence we came. */
-
- addl $LocalVarsSize, %esp
- .cfi_def_cfa_offset 20
- popl %ebx
- .cfi_def_cfa_offset 16
- popl %esi
- .cfi_def_cfa_offset 12
- popl %edi
- .cfi_def_cfa_offset 8
- popl %ebp
- .cfi_def_cfa_offset 4
-.cfi_endproc
-match_init: ret
diff --git a/third-party/zlib/contrib/blast/Makefile b/third-party/zlib/contrib/blast/Makefile
deleted file mode 100644
index 9be80ba..0000000
--- a/third-party/zlib/contrib/blast/Makefile
+++ /dev/null
@@ -1,8 +0,0 @@
-blast: blast.c blast.h
- cc -DTEST -o blast blast.c
-
-test: blast
- blast < test.pk | cmp - test.txt
-
-clean:
- rm -f blast blast.o
diff --git a/third-party/zlib/contrib/blast/README b/third-party/zlib/contrib/blast/README
deleted file mode 100644
index e3a60b3..0000000
--- a/third-party/zlib/contrib/blast/README
+++ /dev/null
@@ -1,4 +0,0 @@
-Read blast.h for purpose and usage.
-
-Mark Adler
-madler at alumni.caltech.edu
diff --git a/third-party/zlib/contrib/blast/blast.c b/third-party/zlib/contrib/blast/blast.c
deleted file mode 100644
index 69ef0fe..0000000
--- a/third-party/zlib/contrib/blast/blast.c
+++ /dev/null
@@ -1,446 +0,0 @@
-/* blast.c
- * Copyright (C) 2003, 2012 Mark Adler
- * For conditions of distribution and use, see copyright notice in blast.h
- * version 1.2, 24 Oct 2012
- *
- * blast.c decompresses data compressed by the PKWare Compression Library.
- * This function provides functionality similar to the explode() function of
- * the PKWare library, hence the name "blast".
- *
- * This decompressor is based on the excellent format description provided by
- * Ben Rudiak-Gould in comp.compression on August 13, 2001. Interestingly, the
- * example Ben provided in the post is incorrect. The distance 110001 should
- * instead be 111000. When corrected, the example byte stream becomes:
- *
- * 00 04 82 24 25 8f 80 7f
- *
- * which decompresses to "AIAIAIAIAIAIA" (without the quotes).
- */
-
-/*
- * Change history:
- *
- * 1.0 12 Feb 2003 - First version
- * 1.1 16 Feb 2003 - Fixed distance check for > 4 GB uncompressed data
- * 1.2 24 Oct 2012 - Add note about using binary mode in stdio
- * - Fix comparisons of differently signed integers
- */
-
-#include <setjmp.h> /* for setjmp(), longjmp(), and jmp_buf */
-#include "blast.h" /* prototype for blast() */
-
-#define local static /* for local function definitions */
-#define MAXBITS 13 /* maximum code length */
-#define MAXWIN 4096 /* maximum window size */
-
-/* input and output state */
-struct state {
- /* input state */
- blast_in infun; /* input function provided by user */
- void *inhow; /* opaque information passed to infun() */
- unsigned char *in; /* next input location */
- unsigned left; /* available input at in */
- int bitbuf; /* bit buffer */
- int bitcnt; /* number of bits in bit buffer */
-
- /* input limit error return state for bits() and decode() */
- jmp_buf env;
-
- /* output state */
- blast_out outfun; /* output function provided by user */
- void *outhow; /* opaque information passed to outfun() */
- unsigned next; /* index of next write location in out[] */
- int first; /* true to check distances (for first 4K) */
- unsigned char out[MAXWIN]; /* output buffer and sliding window */
-};
-
-/*
- * Return need bits from the input stream. This always leaves less than
- * eight bits in the buffer. bits() works properly for need == 0.
- *
- * Format notes:
- *
- * - Bits are stored in bytes from the least significant bit to the most
- * significant bit. Therefore bits are dropped from the bottom of the bit
- * buffer, using shift right, and new bytes are appended to the top of the
- * bit buffer, using shift left.
- */
-local int bits(struct state *s, int need)
-{
- int val; /* bit accumulator */
-
- /* load at least need bits into val */
- val = s->bitbuf;
- while (s->bitcnt < need) {
- if (s->left == 0) {
- s->left = s->infun(s->inhow, &(s->in));
- if (s->left == 0) longjmp(s->env, 1); /* out of input */
- }
- val |= (int)(*(s->in)++) << s->bitcnt; /* load eight bits */
- s->left--;
- s->bitcnt += 8;
- }
-
- /* drop need bits and update buffer, always zero to seven bits left */
- s->bitbuf = val >> need;
- s->bitcnt -= need;
-
- /* return need bits, zeroing the bits above that */
- return val & ((1 << need) - 1);
-}
-
-/*
- * Huffman code decoding tables. count[1..MAXBITS] is the number of symbols of
- * each length, which for a canonical code are stepped through in order.
- * symbol[] are the symbol values in canonical order, where the number of
- * entries is the sum of the counts in count[]. The decoding process can be
- * seen in the function decode() below.
- */
-struct huffman {
- short *count; /* number of symbols of each length */
- short *symbol; /* canonically ordered symbols */
-};
-
-/*
- * Decode a code from the stream s using huffman table h. Return the symbol or
- * a negative value if there is an error. If all of the lengths are zero, i.e.
- * an empty code, or if the code is incomplete and an invalid code is received,
- * then -9 is returned after reading MAXBITS bits.
- *
- * Format notes:
- *
- * - The codes as stored in the compressed data are bit-reversed relative to
- * a simple integer ordering of codes of the same lengths. Hence below the
- * bits are pulled from the compressed data one at a time and used to
- * build the code value reversed from what is in the stream in order to
- * permit simple integer comparisons for decoding.
- *
- * - The first code for the shortest length is all ones. Subsequent codes of
- * the same length are simply integer decrements of the previous code. When
- * moving up a length, a one bit is appended to the code. For a complete
- * code, the last code of the longest length will be all zeros. To support
- * this ordering, the bits pulled during decoding are inverted to apply the
- * more "natural" ordering starting with all zeros and incrementing.
- */
-local int decode(struct state *s, struct huffman *h)
-{
- int len; /* current number of bits in code */
- int code; /* len bits being decoded */
- int first; /* first code of length len */
- int count; /* number of codes of length len */
- int index; /* index of first code of length len in symbol table */
- int bitbuf; /* bits from stream */
- int left; /* bits left in next or left to process */
- short *next; /* next number of codes */
-
- bitbuf = s->bitbuf;
- left = s->bitcnt;
- code = first = index = 0;
- len = 1;
- next = h->count + 1;
- while (1) {
- while (left--) {
- code |= (bitbuf & 1) ^ 1; /* invert code */
- bitbuf >>= 1;
- count = *next++;
- if (code < first + count) { /* if length len, return symbol */
- s->bitbuf = bitbuf;
- s->bitcnt = (s->bitcnt - len) & 7;
- return h->symbol[index + (code - first)];
- }
- index += count; /* else update for next length */
- first += count;
- first <<= 1;
- code <<= 1;
- len++;
- }
- left = (MAXBITS+1) - len;
- if (left == 0) break;
- if (s->left == 0) {
- s->left = s->infun(s->inhow, &(s->in));
- if (s->left == 0) longjmp(s->env, 1); /* out of input */
- }
- bitbuf = *(s->in)++;
- s->left--;
- if (left > 8) left = 8;
- }
- return -9; /* ran out of codes */
-}
-
-/*
- * Given a list of repeated code lengths rep[0..n-1], where each byte is a
- * count (high four bits + 1) and a code length (low four bits), generate the
- * list of code lengths. This compaction reduces the size of the object code.
- * Then given the list of code lengths length[0..n-1] representing a canonical
- * Huffman code for n symbols, construct the tables required to decode those
- * codes. Those tables are the number of codes of each length, and the symbols
- * sorted by length, retaining their original order within each length. The
- * return value is zero for a complete code set, negative for an over-
- * subscribed code set, and positive for an incomplete code set. The tables
- * can be used if the return value is zero or positive, but they cannot be used
- * if the return value is negative. If the return value is zero, it is not
- * possible for decode() using that table to return an error--any stream of
- * enough bits will resolve to a symbol. If the return value is positive, then
- * it is possible for decode() using that table to return an error for received
- * codes past the end of the incomplete lengths.
- */
-local int construct(struct huffman *h, const unsigned char *rep, int n)
-{
- int symbol; /* current symbol when stepping through length[] */
- int len; /* current length when stepping through h->count[] */
- int left; /* number of possible codes left of current length */
- short offs[MAXBITS+1]; /* offsets in symbol table for each length */
- short length[256]; /* code lengths */
-
- /* convert compact repeat counts into symbol bit length list */
- symbol = 0;
- do {
- len = *rep++;
- left = (len >> 4) + 1;
- len &= 15;
- do {
- length[symbol++] = len;
- } while (--left);
- } while (--n);
- n = symbol;
-
- /* count number of codes of each length */
- for (len = 0; len <= MAXBITS; len++)
- h->count[len] = 0;
- for (symbol = 0; symbol < n; symbol++)
- (h->count[length[symbol]])++; /* assumes lengths are within bounds */
- if (h->count[0] == n) /* no codes! */
- return 0; /* complete, but decode() will fail */
-
- /* check for an over-subscribed or incomplete set of lengths */
- left = 1; /* one possible code of zero length */
- for (len = 1; len <= MAXBITS; len++) {
- left <<= 1; /* one more bit, double codes left */
- left -= h->count[len]; /* deduct count from possible codes */
- if (left < 0) return left; /* over-subscribed--return negative */
- } /* left > 0 means incomplete */
-
- /* generate offsets into symbol table for each length for sorting */
- offs[1] = 0;
- for (len = 1; len < MAXBITS; len++)
- offs[len + 1] = offs[len] + h->count[len];
-
- /*
- * put symbols in table sorted by length, by symbol order within each
- * length
- */
- for (symbol = 0; symbol < n; symbol++)
- if (length[symbol] != 0)
- h->symbol[offs[length[symbol]]++] = symbol;
-
- /* return zero for complete set, positive for incomplete set */
- return left;
-}
-
-/*
- * Decode PKWare Compression Library stream.
- *
- * Format notes:
- *
- * - First byte is 0 if literals are uncoded or 1 if they are coded. Second
- * byte is 4, 5, or 6 for the number of extra bits in the distance code.
- * This is the base-2 logarithm of the dictionary size minus six.
- *
- * - Compressed data is a combination of literals and length/distance pairs
- * terminated by an end code. Literals are either Huffman coded or
- * uncoded bytes. A length/distance pair is a coded length followed by a
- * coded distance to represent a string that occurs earlier in the
- * uncompressed data that occurs again at the current location.
- *
- * - A bit preceding a literal or length/distance pair indicates which comes
- * next, 0 for literals, 1 for length/distance.
- *
- * - If literals are uncoded, then the next eight bits are the literal, in the
- * normal bit order in th stream, i.e. no bit-reversal is needed. Similarly,
- * no bit reversal is needed for either the length extra bits or the distance
- * extra bits.
- *
- * - Literal bytes are simply written to the output. A length/distance pair is
- * an instruction to copy previously uncompressed bytes to the output. The
- * copy is from distance bytes back in the output stream, copying for length
- * bytes.
- *
- * - Distances pointing before the beginning of the output data are not
- * permitted.
- *
- * - Overlapped copies, where the length is greater than the distance, are
- * allowed and common. For example, a distance of one and a length of 518
- * simply copies the last byte 518 times. A distance of four and a length of
- * twelve copies the last four bytes three times. A simple forward copy
- * ignoring whether the length is greater than the distance or not implements
- * this correctly.
- */
-local int decomp(struct state *s)
-{
- int lit; /* true if literals are coded */
- int dict; /* log2(dictionary size) - 6 */
- int symbol; /* decoded symbol, extra bits for distance */
- int len; /* length for copy */
- unsigned dist; /* distance for copy */
- int copy; /* copy counter */
- unsigned char *from, *to; /* copy pointers */
- static int virgin = 1; /* build tables once */
- static short litcnt[MAXBITS+1], litsym[256]; /* litcode memory */
- static short lencnt[MAXBITS+1], lensym[16]; /* lencode memory */
- static short distcnt[MAXBITS+1], distsym[64]; /* distcode memory */
- static struct huffman litcode = {litcnt, litsym}; /* length code */
- static struct huffman lencode = {lencnt, lensym}; /* length code */
- static struct huffman distcode = {distcnt, distsym};/* distance code */
- /* bit lengths of literal codes */
- static const unsigned char litlen[] = {
- 11, 124, 8, 7, 28, 7, 188, 13, 76, 4, 10, 8, 12, 10, 12, 10, 8, 23, 8,
- 9, 7, 6, 7, 8, 7, 6, 55, 8, 23, 24, 12, 11, 7, 9, 11, 12, 6, 7, 22, 5,
- 7, 24, 6, 11, 9, 6, 7, 22, 7, 11, 38, 7, 9, 8, 25, 11, 8, 11, 9, 12,
- 8, 12, 5, 38, 5, 38, 5, 11, 7, 5, 6, 21, 6, 10, 53, 8, 7, 24, 10, 27,
- 44, 253, 253, 253, 252, 252, 252, 13, 12, 45, 12, 45, 12, 61, 12, 45,
- 44, 173};
- /* bit lengths of length codes 0..15 */
- static const unsigned char lenlen[] = {2, 35, 36, 53, 38, 23};
- /* bit lengths of distance codes 0..63 */
- static const unsigned char distlen[] = {2, 20, 53, 230, 247, 151, 248};
- static const short base[16] = { /* base for length codes */
- 3, 2, 4, 5, 6, 7, 8, 9, 10, 12, 16, 24, 40, 72, 136, 264};
- static const char extra[16] = { /* extra bits for length codes */
- 0, 0, 0, 0, 0, 0, 0, 0, 1, 2, 3, 4, 5, 6, 7, 8};
-
- /* set up decoding tables (once--might not be thread-safe) */
- if (virgin) {
- construct(&litcode, litlen, sizeof(litlen));
- construct(&lencode, lenlen, sizeof(lenlen));
- construct(&distcode, distlen, sizeof(distlen));
- virgin = 0;
- }
-
- /* read header */
- lit = bits(s, 8);
- if (lit > 1) return -1;
- dict = bits(s, 8);
- if (dict < 4 || dict > 6) return -2;
-
- /* decode literals and length/distance pairs */
- do {
- if (bits(s, 1)) {
- /* get length */
- symbol = decode(s, &lencode);
- len = base[symbol] + bits(s, extra[symbol]);
- if (len == 519) break; /* end code */
-
- /* get distance */
- symbol = len == 2 ? 2 : dict;
- dist = decode(s, &distcode) << symbol;
- dist += bits(s, symbol);
- dist++;
- if (s->first && dist > s->next)
- return -3; /* distance too far back */
-
- /* copy length bytes from distance bytes back */
- do {
- to = s->out + s->next;
- from = to - dist;
- copy = MAXWIN;
- if (s->next < dist) {
- from += copy;
- copy = dist;
- }
- copy -= s->next;
- if (copy > len) copy = len;
- len -= copy;
- s->next += copy;
- do {
- *to++ = *from++;
- } while (--copy);
- if (s->next == MAXWIN) {
- if (s->outfun(s->outhow, s->out, s->next)) return 1;
- s->next = 0;
- s->first = 0;
- }
- } while (len != 0);
- }
- else {
- /* get literal and write it */
- symbol = lit ? decode(s, &litcode) : bits(s, 8);
- s->out[s->next++] = symbol;
- if (s->next == MAXWIN) {
- if (s->outfun(s->outhow, s->out, s->next)) return 1;
- s->next = 0;
- s->first = 0;
- }
- }
- } while (1);
- return 0;
-}
-
-/* See comments in blast.h */
-int blast(blast_in infun, void *inhow, blast_out outfun, void *outhow)
-{
- struct state s; /* input/output state */
- int err; /* return value */
-
- /* initialize input state */
- s.infun = infun;
- s.inhow = inhow;
- s.left = 0;
- s.bitbuf = 0;
- s.bitcnt = 0;
-
- /* initialize output state */
- s.outfun = outfun;
- s.outhow = outhow;
- s.next = 0;
- s.first = 1;
-
- /* return if bits() or decode() tries to read past available input */
- if (setjmp(s.env) != 0) /* if came back here via longjmp(), */
- err = 2; /* then skip decomp(), return error */
- else
- err = decomp(&s); /* decompress */
-
- /* write any leftover output and update the error code if needed */
- if (err != 1 && s.next && s.outfun(s.outhow, s.out, s.next) && err == 0)
- err = 1;
- return err;
-}
-
-#ifdef TEST
-/* Example of how to use blast() */
-#include <stdio.h>
-#include <stdlib.h>
-
-#define CHUNK 16384
-
-local unsigned inf(void *how, unsigned char **buf)
-{
- static unsigned char hold[CHUNK];
-
- *buf = hold;
- return fread(hold, 1, CHUNK, (FILE *)how);
-}
-
-local int outf(void *how, unsigned char *buf, unsigned len)
-{
- return fwrite(buf, 1, len, (FILE *)how) != len;
-}
-
-/* Decompress a PKWare Compression Library stream from stdin to stdout */
-int main(void)
-{
- int ret, n;
-
- /* decompress to stdout */
- ret = blast(inf, stdin, outf, stdout);
- if (ret != 0) fprintf(stderr, "blast error: %d\n", ret);
-
- /* see if there are any leftover bytes */
- n = 0;
- while (getchar() != EOF) n++;
- if (n) fprintf(stderr, "blast warning: %d unused bytes of input\n", n);
-
- /* return blast() error code */
- return ret;
-}
-#endif
diff --git a/third-party/zlib/contrib/blast/blast.h b/third-party/zlib/contrib/blast/blast.h
deleted file mode 100644
index 658cfd3..0000000
--- a/third-party/zlib/contrib/blast/blast.h
+++ /dev/null
@@ -1,75 +0,0 @@
-/* blast.h -- interface for blast.c
- Copyright (C) 2003, 2012 Mark Adler
- version 1.2, 24 Oct 2012
-
- This software is provided 'as-is', without any express or implied
- warranty. In no event will the author be held liable for any damages
- arising from the use of this software.
-
- Permission is granted to anyone to use this software for any purpose,
- including commercial applications, and to alter it and redistribute it
- freely, subject to the following restrictions:
-
- 1. The origin of this software must not be misrepresented; you must not
- claim that you wrote the original software. If you use this software
- in a product, an acknowledgment in the product documentation would be
- appreciated but is not required.
- 2. Altered source versions must be plainly marked as such, and must not be
- misrepresented as being the original software.
- 3. This notice may not be removed or altered from any source distribution.
-
- Mark Adler madler at alumni.caltech.edu
- */
-
-
-/*
- * blast() decompresses the PKWare Data Compression Library (DCL) compressed
- * format. It provides the same functionality as the explode() function in
- * that library. (Note: PKWare overused the "implode" verb, and the format
- * used by their library implode() function is completely different and
- * incompatible with the implode compression method supported by PKZIP.)
- *
- * The binary mode for stdio functions should be used to assure that the
- * compressed data is not corrupted when read or written. For example:
- * fopen(..., "rb") and fopen(..., "wb").
- */
-
-
-typedef unsigned (*blast_in)(void *how, unsigned char **buf);
-typedef int (*blast_out)(void *how, unsigned char *buf, unsigned len);
-/* Definitions for input/output functions passed to blast(). See below for
- * what the provided functions need to do.
- */
-
-
-int blast(blast_in infun, void *inhow, blast_out outfun, void *outhow);
-/* Decompress input to output using the provided infun() and outfun() calls.
- * On success, the return value of blast() is zero. If there is an error in
- * the source data, i.e. it is not in the proper format, then a negative value
- * is returned. If there is not enough input available or there is not enough
- * output space, then a positive error is returned.
- *
- * The input function is invoked: len = infun(how, &buf), where buf is set by
- * infun() to point to the input buffer, and infun() returns the number of
- * available bytes there. If infun() returns zero, then blast() returns with
- * an input error. (blast() only asks for input if it needs it.) inhow is for
- * use by the application to pass an input descriptor to infun(), if desired.
- *
- * The output function is invoked: err = outfun(how, buf, len), where the bytes
- * to be written are buf[0..len-1]. If err is not zero, then blast() returns
- * with an output error. outfun() is always called with len <= 4096. outhow
- * is for use by the application to pass an output descriptor to outfun(), if
- * desired.
- *
- * The return codes are:
- *
- * 2: ran out of input before completing decompression
- * 1: output error before completing decompression
- * 0: successful decompression
- * -1: literal flag not zero or one
- * -2: dictionary size not in 4..6
- * -3: distance is too far back
- *
- * At the bottom of blast.c is an example program that uses blast() that can be
- * compiled to produce a command-line decompression filter by defining TEST.
- */
diff --git a/third-party/zlib/contrib/blast/test.pk b/third-party/zlib/contrib/blast/test.pk
deleted file mode 100644
index be10b2b..0000000
Binary files a/third-party/zlib/contrib/blast/test.pk and /dev/null differ
diff --git a/third-party/zlib/contrib/blast/test.txt b/third-party/zlib/contrib/blast/test.txt
deleted file mode 100644
index bfdf1c5..0000000
--- a/third-party/zlib/contrib/blast/test.txt
+++ /dev/null
@@ -1 +0,0 @@
-AIAIAIAIAIAIA
\ No newline at end of file
diff --git a/third-party/zlib/contrib/delphi/ZLib.pas b/third-party/zlib/contrib/delphi/ZLib.pas
deleted file mode 100644
index a579974..0000000
--- a/third-party/zlib/contrib/delphi/ZLib.pas
+++ /dev/null
@@ -1,557 +0,0 @@
-{*******************************************************}
-{ }
-{ Borland Delphi Supplemental Components }
-{ ZLIB Data Compression Interface Unit }
-{ }
-{ Copyright (c) 1997,99 Borland Corporation }
-{ }
-{*******************************************************}
-
-{ Updated for zlib 1.2.x by Cosmin Truta <cosmint at cs.ubbcluj.ro> }
-
-unit ZLib;
-
-interface
-
-uses SysUtils, Classes;
-
-type
- TAlloc = function (AppData: Pointer; Items, Size: Integer): Pointer; cdecl;
- TFree = procedure (AppData, Block: Pointer); cdecl;
-
- // Internal structure. Ignore.
- TZStreamRec = packed record
- next_in: PChar; // next input byte
- avail_in: Integer; // number of bytes available at next_in
- total_in: Longint; // total nb of input bytes read so far
-
- next_out: PChar; // next output byte should be put here
- avail_out: Integer; // remaining free space at next_out
- total_out: Longint; // total nb of bytes output so far
-
- msg: PChar; // last error message, NULL if no error
- internal: Pointer; // not visible by applications
-
- zalloc: TAlloc; // used to allocate the internal state
- zfree: TFree; // used to free the internal state
- AppData: Pointer; // private data object passed to zalloc and zfree
-
- data_type: Integer; // best guess about the data type: ascii or binary
- adler: Longint; // adler32 value of the uncompressed data
- reserved: Longint; // reserved for future use
- end;
-
- // Abstract ancestor class
- TCustomZlibStream = class(TStream)
- private
- FStrm: TStream;
- FStrmPos: Integer;
- FOnProgress: TNotifyEvent;
- FZRec: TZStreamRec;
- FBuffer: array [Word] of Char;
- protected
- procedure Progress(Sender: TObject); dynamic;
- property OnProgress: TNotifyEvent read FOnProgress write FOnProgress;
- constructor Create(Strm: TStream);
- end;
-
-{ TCompressionStream compresses data on the fly as data is written to it, and
- stores the compressed data to another stream.
-
- TCompressionStream is write-only and strictly sequential. Reading from the
- stream will raise an exception. Using Seek to move the stream pointer
- will raise an exception.
-
- Output data is cached internally, written to the output stream only when
- the internal output buffer is full. All pending output data is flushed
- when the stream is destroyed.
-
- The Position property returns the number of uncompressed bytes of
- data that have been written to the stream so far.
-
- CompressionRate returns the on-the-fly percentage by which the original
- data has been compressed: (1 - (CompressedBytes / UncompressedBytes)) * 100
- If raw data size = 100 and compressed data size = 25, the CompressionRate
- is 75%
-
- The OnProgress event is called each time the output buffer is filled and
- written to the output stream. This is useful for updating a progress
- indicator when you are writing a large chunk of data to the compression
- stream in a single call.}
-
-
- TCompressionLevel = (clNone, clFastest, clDefault, clMax);
-
- TCompressionStream = class(TCustomZlibStream)
- private
- function GetCompressionRate: Single;
- public
- constructor Create(CompressionLevel: TCompressionLevel; Dest: TStream);
- destructor Destroy; override;
- function Read(var Buffer; Count: Longint): Longint; override;
- function Write(const Buffer; Count: Longint): Longint; override;
- function Seek(Offset: Longint; Origin: Word): Longint; override;
- property CompressionRate: Single read GetCompressionRate;
- property OnProgress;
- end;
-
-{ TDecompressionStream decompresses data on the fly as data is read from it.
-
- Compressed data comes from a separate source stream. TDecompressionStream
- is read-only and unidirectional; you can seek forward in the stream, but not
- backwards. The special case of setting the stream position to zero is
- allowed. Seeking forward decompresses data until the requested position in
- the uncompressed data has been reached. Seeking backwards, seeking relative
- to the end of the stream, requesting the size of the stream, and writing to
- the stream will raise an exception.
-
- The Position property returns the number of bytes of uncompressed data that
- have been read from the stream so far.
-
- The OnProgress event is called each time the internal input buffer of
- compressed data is exhausted and the next block is read from the input stream.
- This is useful for updating a progress indicator when you are reading a
- large chunk of data from the decompression stream in a single call.}
-
- TDecompressionStream = class(TCustomZlibStream)
- public
- constructor Create(Source: TStream);
- destructor Destroy; override;
- function Read(var Buffer; Count: Longint): Longint; override;
- function Write(const Buffer; Count: Longint): Longint; override;
- function Seek(Offset: Longint; Origin: Word): Longint; override;
- property OnProgress;
- end;
-
-
-
-{ CompressBuf compresses data, buffer to buffer, in one call.
- In: InBuf = ptr to compressed data
- InBytes = number of bytes in InBuf
- Out: OutBuf = ptr to newly allocated buffer containing decompressed data
- OutBytes = number of bytes in OutBuf }
-procedure CompressBuf(const InBuf: Pointer; InBytes: Integer;
- out OutBuf: Pointer; out OutBytes: Integer);
-
-
-{ DecompressBuf decompresses data, buffer to buffer, in one call.
- In: InBuf = ptr to compressed data
- InBytes = number of bytes in InBuf
- OutEstimate = zero, or est. size of the decompressed data
- Out: OutBuf = ptr to newly allocated buffer containing decompressed data
- OutBytes = number of bytes in OutBuf }
-procedure DecompressBuf(const InBuf: Pointer; InBytes: Integer;
- OutEstimate: Integer; out OutBuf: Pointer; out OutBytes: Integer);
-
-{ DecompressToUserBuf decompresses data, buffer to buffer, in one call.
- In: InBuf = ptr to compressed data
- InBytes = number of bytes in InBuf
- Out: OutBuf = ptr to user-allocated buffer to contain decompressed data
- BufSize = number of bytes in OutBuf }
-procedure DecompressToUserBuf(const InBuf: Pointer; InBytes: Integer;
- const OutBuf: Pointer; BufSize: Integer);
-
-const
- zlib_version = '1.2.8';
-
-type
- EZlibError = class(Exception);
- ECompressionError = class(EZlibError);
- EDecompressionError = class(EZlibError);
-
-implementation
-
-uses ZLibConst;
-
-const
- Z_NO_FLUSH = 0;
- Z_PARTIAL_FLUSH = 1;
- Z_SYNC_FLUSH = 2;
- Z_FULL_FLUSH = 3;
- Z_FINISH = 4;
-
- Z_OK = 0;
- Z_STREAM_END = 1;
- Z_NEED_DICT = 2;
- Z_ERRNO = (-1);
- Z_STREAM_ERROR = (-2);
- Z_DATA_ERROR = (-3);
- Z_MEM_ERROR = (-4);
- Z_BUF_ERROR = (-5);
- Z_VERSION_ERROR = (-6);
-
- Z_NO_COMPRESSION = 0;
- Z_BEST_SPEED = 1;
- Z_BEST_COMPRESSION = 9;
- Z_DEFAULT_COMPRESSION = (-1);
-
- Z_FILTERED = 1;
- Z_HUFFMAN_ONLY = 2;
- Z_RLE = 3;
- Z_DEFAULT_STRATEGY = 0;
-
- Z_BINARY = 0;
- Z_ASCII = 1;
- Z_UNKNOWN = 2;
-
- Z_DEFLATED = 8;
-
-
-{$L adler32.obj}
-{$L compress.obj}
-{$L crc32.obj}
-{$L deflate.obj}
-{$L infback.obj}
-{$L inffast.obj}
-{$L inflate.obj}
-{$L inftrees.obj}
-{$L trees.obj}
-{$L uncompr.obj}
-{$L zutil.obj}
-
-procedure adler32; external;
-procedure compressBound; external;
-procedure crc32; external;
-procedure deflateInit2_; external;
-procedure deflateParams; external;
-
-function _malloc(Size: Integer): Pointer; cdecl;
-begin
- Result := AllocMem(Size);
-end;
-
-procedure _free(Block: Pointer); cdecl;
-begin
- FreeMem(Block);
-end;
-
-procedure _memset(P: Pointer; B: Byte; count: Integer); cdecl;
-begin
- FillChar(P^, count, B);
-end;
-
-procedure _memcpy(dest, source: Pointer; count: Integer); cdecl;
-begin
- Move(source^, dest^, count);
-end;
-
-
-
-// deflate compresses data
-function deflateInit_(var strm: TZStreamRec; level: Integer; version: PChar;
- recsize: Integer): Integer; external;
-function deflate(var strm: TZStreamRec; flush: Integer): Integer; external;
-function deflateEnd(var strm: TZStreamRec): Integer; external;
-
-// inflate decompresses data
-function inflateInit_(var strm: TZStreamRec; version: PChar;
- recsize: Integer): Integer; external;
-function inflate(var strm: TZStreamRec; flush: Integer): Integer; external;
-function inflateEnd(var strm: TZStreamRec): Integer; external;
-function inflateReset(var strm: TZStreamRec): Integer; external;
-
-
-function zlibAllocMem(AppData: Pointer; Items, Size: Integer): Pointer; cdecl;
-begin
-// GetMem(Result, Items*Size);
- Result := AllocMem(Items * Size);
-end;
-
-procedure zlibFreeMem(AppData, Block: Pointer); cdecl;
-begin
- FreeMem(Block);
-end;
-
-{function zlibCheck(code: Integer): Integer;
-begin
- Result := code;
- if code < 0 then
- raise EZlibError.Create('error'); //!!
-end;}
-
-function CCheck(code: Integer): Integer;
-begin
- Result := code;
- if code < 0 then
- raise ECompressionError.Create('error'); //!!
-end;
-
-function DCheck(code: Integer): Integer;
-begin
- Result := code;
- if code < 0 then
- raise EDecompressionError.Create('error'); //!!
-end;
-
-procedure CompressBuf(const InBuf: Pointer; InBytes: Integer;
- out OutBuf: Pointer; out OutBytes: Integer);
-var
- strm: TZStreamRec;
- P: Pointer;
-begin
- FillChar(strm, sizeof(strm), 0);
- strm.zalloc := zlibAllocMem;
- strm.zfree := zlibFreeMem;
- OutBytes := ((InBytes + (InBytes div 10) + 12) + 255) and not 255;
- GetMem(OutBuf, OutBytes);
- try
- strm.next_in := InBuf;
- strm.avail_in := InBytes;
- strm.next_out := OutBuf;
- strm.avail_out := OutBytes;
- CCheck(deflateInit_(strm, Z_BEST_COMPRESSION, zlib_version, sizeof(strm)));
- try
- while CCheck(deflate(strm, Z_FINISH)) <> Z_STREAM_END do
- begin
- P := OutBuf;
- Inc(OutBytes, 256);
- ReallocMem(OutBuf, OutBytes);
- strm.next_out := PChar(Integer(OutBuf) + (Integer(strm.next_out) - Integer(P)));
- strm.avail_out := 256;
- end;
- finally
- CCheck(deflateEnd(strm));
- end;
- ReallocMem(OutBuf, strm.total_out);
- OutBytes := strm.total_out;
- except
- FreeMem(OutBuf);
- raise
- end;
-end;
-
-
-procedure DecompressBuf(const InBuf: Pointer; InBytes: Integer;
- OutEstimate: Integer; out OutBuf: Pointer; out OutBytes: Integer);
-var
- strm: TZStreamRec;
- P: Pointer;
- BufInc: Integer;
-begin
- FillChar(strm, sizeof(strm), 0);
- strm.zalloc := zlibAllocMem;
- strm.zfree := zlibFreeMem;
- BufInc := (InBytes + 255) and not 255;
- if OutEstimate = 0 then
- OutBytes := BufInc
- else
- OutBytes := OutEstimate;
- GetMem(OutBuf, OutBytes);
- try
- strm.next_in := InBuf;
- strm.avail_in := InBytes;
- strm.next_out := OutBuf;
- strm.avail_out := OutBytes;
- DCheck(inflateInit_(strm, zlib_version, sizeof(strm)));
- try
- while DCheck(inflate(strm, Z_NO_FLUSH)) <> Z_STREAM_END do
- begin
- P := OutBuf;
- Inc(OutBytes, BufInc);
- ReallocMem(OutBuf, OutBytes);
- strm.next_out := PChar(Integer(OutBuf) + (Integer(strm.next_out) - Integer(P)));
- strm.avail_out := BufInc;
- end;
- finally
- DCheck(inflateEnd(strm));
- end;
- ReallocMem(OutBuf, strm.total_out);
- OutBytes := strm.total_out;
- except
- FreeMem(OutBuf);
- raise
- end;
-end;
-
-procedure DecompressToUserBuf(const InBuf: Pointer; InBytes: Integer;
- const OutBuf: Pointer; BufSize: Integer);
-var
- strm: TZStreamRec;
-begin
- FillChar(strm, sizeof(strm), 0);
- strm.zalloc := zlibAllocMem;
- strm.zfree := zlibFreeMem;
- strm.next_in := InBuf;
- strm.avail_in := InBytes;
- strm.next_out := OutBuf;
- strm.avail_out := BufSize;
- DCheck(inflateInit_(strm, zlib_version, sizeof(strm)));
- try
- if DCheck(inflate(strm, Z_FINISH)) <> Z_STREAM_END then
- raise EZlibError.CreateRes(@sTargetBufferTooSmall);
- finally
- DCheck(inflateEnd(strm));
- end;
-end;
-
-// TCustomZlibStream
-
-constructor TCustomZLibStream.Create(Strm: TStream);
-begin
- inherited Create;
- FStrm := Strm;
- FStrmPos := Strm.Position;
- FZRec.zalloc := zlibAllocMem;
- FZRec.zfree := zlibFreeMem;
-end;
-
-procedure TCustomZLibStream.Progress(Sender: TObject);
-begin
- if Assigned(FOnProgress) then FOnProgress(Sender);
-end;
-
-
-// TCompressionStream
-
-constructor TCompressionStream.Create(CompressionLevel: TCompressionLevel;
- Dest: TStream);
-const
- Levels: array [TCompressionLevel] of ShortInt =
- (Z_NO_COMPRESSION, Z_BEST_SPEED, Z_DEFAULT_COMPRESSION, Z_BEST_COMPRESSION);
-begin
- inherited Create(Dest);
- FZRec.next_out := FBuffer;
- FZRec.avail_out := sizeof(FBuffer);
- CCheck(deflateInit_(FZRec, Levels[CompressionLevel], zlib_version, sizeof(FZRec)));
-end;
-
-destructor TCompressionStream.Destroy;
-begin
- FZRec.next_in := nil;
- FZRec.avail_in := 0;
- try
- if FStrm.Position <> FStrmPos then FStrm.Position := FStrmPos;
- while (CCheck(deflate(FZRec, Z_FINISH)) <> Z_STREAM_END)
- and (FZRec.avail_out = 0) do
- begin
- FStrm.WriteBuffer(FBuffer, sizeof(FBuffer));
- FZRec.next_out := FBuffer;
- FZRec.avail_out := sizeof(FBuffer);
- end;
- if FZRec.avail_out < sizeof(FBuffer) then
- FStrm.WriteBuffer(FBuffer, sizeof(FBuffer) - FZRec.avail_out);
- finally
- deflateEnd(FZRec);
- end;
- inherited Destroy;
-end;
-
-function TCompressionStream.Read(var Buffer; Count: Longint): Longint;
-begin
- raise ECompressionError.CreateRes(@sInvalidStreamOp);
-end;
-
-function TCompressionStream.Write(const Buffer; Count: Longint): Longint;
-begin
- FZRec.next_in := @Buffer;
- FZRec.avail_in := Count;
- if FStrm.Position <> FStrmPos then FStrm.Position := FStrmPos;
- while (FZRec.avail_in > 0) do
- begin
- CCheck(deflate(FZRec, 0));
- if FZRec.avail_out = 0 then
- begin
- FStrm.WriteBuffer(FBuffer, sizeof(FBuffer));
- FZRec.next_out := FBuffer;
- FZRec.avail_out := sizeof(FBuffer);
- FStrmPos := FStrm.Position;
- Progress(Self);
- end;
- end;
- Result := Count;
-end;
-
-function TCompressionStream.Seek(Offset: Longint; Origin: Word): Longint;
-begin
- if (Offset = 0) and (Origin = soFromCurrent) then
- Result := FZRec.total_in
- else
- raise ECompressionError.CreateRes(@sInvalidStreamOp);
-end;
-
-function TCompressionStream.GetCompressionRate: Single;
-begin
- if FZRec.total_in = 0 then
- Result := 0
- else
- Result := (1.0 - (FZRec.total_out / FZRec.total_in)) * 100.0;
-end;
-
-
-// TDecompressionStream
-
-constructor TDecompressionStream.Create(Source: TStream);
-begin
- inherited Create(Source);
- FZRec.next_in := FBuffer;
- FZRec.avail_in := 0;
- DCheck(inflateInit_(FZRec, zlib_version, sizeof(FZRec)));
-end;
-
-destructor TDecompressionStream.Destroy;
-begin
- FStrm.Seek(-FZRec.avail_in, 1);
- inflateEnd(FZRec);
- inherited Destroy;
-end;
-
-function TDecompressionStream.Read(var Buffer; Count: Longint): Longint;
-begin
- FZRec.next_out := @Buffer;
- FZRec.avail_out := Count;
- if FStrm.Position <> FStrmPos then FStrm.Position := FStrmPos;
- while (FZRec.avail_out > 0) do
- begin
- if FZRec.avail_in = 0 then
- begin
- FZRec.avail_in := FStrm.Read(FBuffer, sizeof(FBuffer));
- if FZRec.avail_in = 0 then
- begin
- Result := Count - FZRec.avail_out;
- Exit;
- end;
- FZRec.next_in := FBuffer;
- FStrmPos := FStrm.Position;
- Progress(Self);
- end;
- CCheck(inflate(FZRec, 0));
- end;
- Result := Count;
-end;
-
-function TDecompressionStream.Write(const Buffer; Count: Longint): Longint;
-begin
- raise EDecompressionError.CreateRes(@sInvalidStreamOp);
-end;
-
-function TDecompressionStream.Seek(Offset: Longint; Origin: Word): Longint;
-var
- I: Integer;
- Buf: array [0..4095] of Char;
-begin
- if (Offset = 0) and (Origin = soFromBeginning) then
- begin
- DCheck(inflateReset(FZRec));
- FZRec.next_in := FBuffer;
- FZRec.avail_in := 0;
- FStrm.Position := 0;
- FStrmPos := 0;
- end
- else if ( (Offset >= 0) and (Origin = soFromCurrent)) or
- ( ((Offset - FZRec.total_out) > 0) and (Origin = soFromBeginning)) then
- begin
- if Origin = soFromBeginning then Dec(Offset, FZRec.total_out);
- if Offset > 0 then
- begin
- for I := 1 to Offset div sizeof(Buf) do
- ReadBuffer(Buf, sizeof(Buf));
- ReadBuffer(Buf, Offset mod sizeof(Buf));
- end;
- end
- else
- raise EDecompressionError.CreateRes(@sInvalidStreamOp);
- Result := FZRec.total_out;
-end;
-
-
-end.
diff --git a/third-party/zlib/contrib/delphi/ZLibConst.pas b/third-party/zlib/contrib/delphi/ZLibConst.pas
deleted file mode 100644
index cdfe136..0000000
--- a/third-party/zlib/contrib/delphi/ZLibConst.pas
+++ /dev/null
@@ -1,11 +0,0 @@
-unit ZLibConst;
-
-interface
-
-resourcestring
- sTargetBufferTooSmall = 'ZLib error: target buffer may be too small';
- sInvalidStreamOp = 'Invalid stream operation';
-
-implementation
-
-end.
diff --git a/third-party/zlib/contrib/delphi/readme.txt b/third-party/zlib/contrib/delphi/readme.txt
deleted file mode 100644
index 2dc9a8b..0000000
--- a/third-party/zlib/contrib/delphi/readme.txt
+++ /dev/null
@@ -1,76 +0,0 @@
-
-Overview
-========
-
-This directory contains an update to the ZLib interface unit,
-distributed by Borland as a Delphi supplemental component.
-
-The original ZLib unit is Copyright (c) 1997,99 Borland Corp.,
-and is based on zlib version 1.0.4. There are a series of bugs
-and security problems associated with that old zlib version, and
-we recommend the users to update their ZLib unit.
-
-
-Summary of modifications
-========================
-
-- Improved makefile, adapted to zlib version 1.2.1.
-
-- Some field types from TZStreamRec are changed from Integer to
- Longint, for consistency with the zlib.h header, and for 64-bit
- readiness.
-
-- The zlib_version constant is updated.
-
-- The new Z_RLE strategy has its corresponding symbolic constant.
-
-- The allocation and deallocation functions and function types
- (TAlloc, TFree, zlibAllocMem and zlibFreeMem) are now cdecl,
- and _malloc and _free are added as C RTL stubs. As a result,
- the original C sources of zlib can be compiled out of the box,
- and linked to the ZLib unit.
-
-
-Suggestions for improvements
-============================
-
-Currently, the ZLib unit provides only a limited wrapper around
-the zlib library, and much of the original zlib functionality is
-missing. Handling compressed file formats like ZIP/GZIP or PNG
-cannot be implemented without having this functionality.
-Applications that handle these formats are either using their own,
-duplicated code, or not using the ZLib unit at all.
-
-Here are a few suggestions:
-
-- Checksum class wrappers around adler32() and crc32(), similar
- to the Java classes that implement the java.util.zip.Checksum
- interface.
-
-- The ability to read and write raw deflate streams, without the
- zlib stream header and trailer. Raw deflate streams are used
- in the ZIP file format.
-
-- The ability to read and write gzip streams, used in the GZIP
- file format, and normally produced by the gzip program.
-
-- The ability to select a different compression strategy, useful
- to PNG and MNG image compression, and to multimedia compression
- in general. Besides the compression level
-
- TCompressionLevel = (clNone, clFastest, clDefault, clMax);
-
- which, in fact, could have used the 'z' prefix and avoided
- TColor-like symbols
-
- TCompressionLevel = (zcNone, zcFastest, zcDefault, zcMax);
-
- there could be a compression strategy
-
- TCompressionStrategy = (zsDefault, zsFiltered, zsHuffmanOnly, zsRle);
-
-- ZIP and GZIP stream handling via TStreams.
-
-
---
-Cosmin Truta <cosmint at cs.ubbcluj.ro>
diff --git a/third-party/zlib/contrib/delphi/zlibd32.mak b/third-party/zlib/contrib/delphi/zlibd32.mak
deleted file mode 100644
index 9bb00b7..0000000
--- a/third-party/zlib/contrib/delphi/zlibd32.mak
+++ /dev/null
@@ -1,99 +0,0 @@
-# Makefile for zlib
-# For use with Delphi and C++ Builder under Win32
-# Updated for zlib 1.2.x by Cosmin Truta
-
-# ------------ Borland C++ ------------
-
-# This project uses the Delphi (fastcall/register) calling convention:
-LOC = -DZEXPORT=__fastcall -DZEXPORTVA=__cdecl
-
-CC = bcc32
-LD = bcc32
-AR = tlib
-# do not use "-pr" in CFLAGS
-CFLAGS = -a -d -k- -O2 $(LOC)
-LDFLAGS =
-
-
-# variables
-ZLIB_LIB = zlib.lib
-
-OBJ1 = adler32.obj compress.obj crc32.obj deflate.obj gzclose.obj gzlib.obj gzread.obj
-OBJ2 = gzwrite.obj infback.obj inffast.obj inflate.obj inftrees.obj trees.obj uncompr.obj zutil.obj
-OBJP1 = +adler32.obj+compress.obj+crc32.obj+deflate.obj+gzclose.obj+gzlib.obj+gzread.obj
-OBJP2 = +gzwrite.obj+infback.obj+inffast.obj+inflate.obj+inftrees.obj+trees.obj+uncompr.obj+zutil.obj
-
-
-# targets
-all: $(ZLIB_LIB) example.exe minigzip.exe
-
-.c.obj:
- $(CC) -c $(CFLAGS) $*.c
-
-adler32.obj: adler32.c zlib.h zconf.h
-
-compress.obj: compress.c zlib.h zconf.h
-
-crc32.obj: crc32.c zlib.h zconf.h crc32.h
-
-deflate.obj: deflate.c deflate.h zutil.h zlib.h zconf.h
-
-gzclose.obj: gzclose.c zlib.h zconf.h gzguts.h
-
-gzlib.obj: gzlib.c zlib.h zconf.h gzguts.h
-
-gzread.obj: gzread.c zlib.h zconf.h gzguts.h
-
-gzwrite.obj: gzwrite.c zlib.h zconf.h gzguts.h
-
-infback.obj: infback.c zutil.h zlib.h zconf.h inftrees.h inflate.h \
- inffast.h inffixed.h
-
-inffast.obj: inffast.c zutil.h zlib.h zconf.h inftrees.h inflate.h \
- inffast.h
-
-inflate.obj: inflate.c zutil.h zlib.h zconf.h inftrees.h inflate.h \
- inffast.h inffixed.h
-
-inftrees.obj: inftrees.c zutil.h zlib.h zconf.h inftrees.h
-
-trees.obj: trees.c zutil.h zlib.h zconf.h deflate.h trees.h
-
-uncompr.obj: uncompr.c zlib.h zconf.h
-
-zutil.obj: zutil.c zutil.h zlib.h zconf.h
-
-example.obj: test/example.c zlib.h zconf.h
-
-minigzip.obj: test/minigzip.c zlib.h zconf.h
-
-
-# For the sake of the old Borland make,
-# the command line is cut to fit in the MS-DOS 128 byte limit:
-$(ZLIB_LIB): $(OBJ1) $(OBJ2)
- -del $(ZLIB_LIB)
- $(AR) $(ZLIB_LIB) $(OBJP1)
- $(AR) $(ZLIB_LIB) $(OBJP2)
-
-
-# testing
-test: example.exe minigzip.exe
- example
- echo hello world | minigzip | minigzip -d
-
-example.exe: example.obj $(ZLIB_LIB)
- $(LD) $(LDFLAGS) example.obj $(ZLIB_LIB)
-
-minigzip.exe: minigzip.obj $(ZLIB_LIB)
- $(LD) $(LDFLAGS) minigzip.obj $(ZLIB_LIB)
-
-
-# cleanup
-clean:
- -del *.obj
- -del *.exe
- -del *.lib
- -del *.tds
- -del zlib.bak
- -del foo.gz
-
diff --git a/third-party/zlib/contrib/dotzlib/DotZLib.build b/third-party/zlib/contrib/dotzlib/DotZLib.build
deleted file mode 100644
index 7f90d6b..0000000
--- a/third-party/zlib/contrib/dotzlib/DotZLib.build
+++ /dev/null
@@ -1,33 +0,0 @@
-<?xml version="1.0" encoding="utf-8" ?>
-<project name="DotZLib" default="build" basedir="./DotZLib">
- <description>A .Net wrapper library around ZLib1.dll</description>
-
- <property name="nunit.location" value="c:/program files/NUnit V2.1/bin" />
- <property name="build.root" value="bin" />
-
- <property name="debug" value="true" />
- <property name="nunit" value="true" />
-
- <property name="build.folder" value="${build.root}/debug/" if="${debug}" />
- <property name="build.folder" value="${build.root}/release/" unless="${debug}" />
-
- <target name="clean" description="Remove all generated files">
- <delete dir="${build.root}" failonerror="false" />
- </target>
-
- <target name="build" description="compiles the source code">
-
- <mkdir dir="${build.folder}" />
- <csc target="library" output="${build.folder}DotZLib.dll" debug="${debug}">
- <references basedir="${nunit.location}">
- <includes if="${nunit}" name="nunit.framework.dll" />
- </references>
- <sources>
- <includes name="*.cs" />
- <excludes name="UnitTests.cs" unless="${nunit}" />
- </sources>
- <arg value="/d:nunit" if="${nunit}" />
- </csc>
- </target>
-
-</project>
\ No newline at end of file
diff --git a/third-party/zlib/contrib/dotzlib/DotZLib.chm b/third-party/zlib/contrib/dotzlib/DotZLib.chm
deleted file mode 100644
index f214a44..0000000
Binary files a/third-party/zlib/contrib/dotzlib/DotZLib.chm and /dev/null differ
diff --git a/third-party/zlib/contrib/dotzlib/DotZLib.sln b/third-party/zlib/contrib/dotzlib/DotZLib.sln
deleted file mode 100644
index ac45ca0..0000000
--- a/third-party/zlib/contrib/dotzlib/DotZLib.sln
+++ /dev/null
@@ -1,21 +0,0 @@
-Microsoft Visual Studio Solution File, Format Version 8.00
-Project("{FAE04EC0-301F-11D3-BF4B-00C04F79EFBC}") = "DotZLib", "DotZLib\DotZLib.csproj", "{BB1EE0B1-1808-46CB-B786-949D91117FC5}"
- ProjectSection(ProjectDependencies) = postProject
- EndProjectSection
-EndProject
-Global
- GlobalSection(SolutionConfiguration) = preSolution
- Debug = Debug
- Release = Release
- EndGlobalSection
- GlobalSection(ProjectConfiguration) = postSolution
- {BB1EE0B1-1808-46CB-B786-949D91117FC5}.Debug.ActiveCfg = Debug|.NET
- {BB1EE0B1-1808-46CB-B786-949D91117FC5}.Debug.Build.0 = Debug|.NET
- {BB1EE0B1-1808-46CB-B786-949D91117FC5}.Release.ActiveCfg = Release|.NET
- {BB1EE0B1-1808-46CB-B786-949D91117FC5}.Release.Build.0 = Release|.NET
- EndGlobalSection
- GlobalSection(ExtensibilityGlobals) = postSolution
- EndGlobalSection
- GlobalSection(ExtensibilityAddIns) = postSolution
- EndGlobalSection
-EndGlobal
diff --git a/third-party/zlib/contrib/dotzlib/DotZLib/AssemblyInfo.cs b/third-party/zlib/contrib/dotzlib/DotZLib/AssemblyInfo.cs
deleted file mode 100644
index 0491bfc..0000000
--- a/third-party/zlib/contrib/dotzlib/DotZLib/AssemblyInfo.cs
+++ /dev/null
@@ -1,58 +0,0 @@
-using System.Reflection;
-using System.Runtime.CompilerServices;
-
-//
-// General Information about an assembly is controlled through the following
-// set of attributes. Change these attribute values to modify the information
-// associated with an assembly.
-//
-[assembly: AssemblyTitle("DotZLib")]
-[assembly: AssemblyDescription(".Net bindings for ZLib compression dll 1.2.x")]
-[assembly: AssemblyConfiguration("")]
-[assembly: AssemblyCompany("Henrik Ravn")]
-[assembly: AssemblyProduct("")]
-[assembly: AssemblyCopyright("(c) 2004 by Henrik Ravn")]
-[assembly: AssemblyTrademark("")]
-[assembly: AssemblyCulture("")]
-
-//
-// Version information for an assembly consists of the following four values:
-//
-// Major Version
-// Minor Version
-// Build Number
-// Revision
-//
-// You can specify all the values or you can default the Revision and Build Numbers
-// by using the '*' as shown below:
-
-[assembly: AssemblyVersion("1.0.*")]
-
-//
-// In order to sign your assembly you must specify a key to use. Refer to the
-// Microsoft .NET Framework documentation for more information on assembly signing.
-//
-// Use the attributes below to control which key is used for signing.
-//
-// Notes:
-// (*) If no key is specified, the assembly is not signed.
-// (*) KeyName refers to a key that has been installed in the Crypto Service
-// Provider (CSP) on your machine. KeyFile refers to a file which contains
-// a key.
-// (*) If the KeyFile and the KeyName values are both specified, the
-// following processing occurs:
-// (1) If the KeyName can be found in the CSP, that key is used.
-// (2) If the KeyName does not exist and the KeyFile does exist, the key
-// in the KeyFile is installed into the CSP and used.
-// (*) In order to create a KeyFile, you can use the sn.exe (Strong Name) utility.
-// When specifying the KeyFile, the location of the KeyFile should be
-// relative to the project output directory which is
-// %Project Directory%\obj\<configuration>. For example, if your KeyFile is
-// located in the project directory, you would specify the AssemblyKeyFile
-// attribute as [assembly: AssemblyKeyFile("..\\..\\mykey.snk")]
-// (*) Delay Signing is an advanced option - see the Microsoft .NET Framework
-// documentation for more information on this.
-//
-[assembly: AssemblyDelaySign(false)]
-[assembly: AssemblyKeyFile("")]
-[assembly: AssemblyKeyName("")]
diff --git a/third-party/zlib/contrib/dotzlib/DotZLib/ChecksumImpl.cs b/third-party/zlib/contrib/dotzlib/DotZLib/ChecksumImpl.cs
deleted file mode 100644
index 788b2fc..0000000
--- a/third-party/zlib/contrib/dotzlib/DotZLib/ChecksumImpl.cs
+++ /dev/null
@@ -1,202 +0,0 @@
-//
-// � Copyright Henrik Ravn 2004
-//
-// Use, modification and distribution are subject to the Boost Software License, Version 1.0.
-// (See accompanying file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
-//
-
-using System;
-using System.Runtime.InteropServices;
-using System.Text;
-
-
-namespace DotZLib
-{
- #region ChecksumGeneratorBase
- /// <summary>
- /// Implements the common functionality needed for all <see cref="ChecksumGenerator"/>s
- /// </summary>
- /// <example></example>
- public abstract class ChecksumGeneratorBase : ChecksumGenerator
- {
- /// <summary>
- /// The value of the current checksum
- /// </summary>
- protected uint _current;
-
- /// <summary>
- /// Initializes a new instance of the checksum generator base - the current checksum is
- /// set to zero
- /// </summary>
- public ChecksumGeneratorBase()
- {
- _current = 0;
- }
-
- /// <summary>
- /// Initializes a new instance of the checksum generator basewith a specified value
- /// </summary>
- /// <param name="initialValue">The value to set the current checksum to</param>
- public ChecksumGeneratorBase(uint initialValue)
- {
- _current = initialValue;
- }
-
- /// <summary>
- /// Resets the current checksum to zero
- /// </summary>
- public void Reset() { _current = 0; }
-
- /// <summary>
- /// Gets the current checksum value
- /// </summary>
- public uint Value { get { return _current; } }
-
- /// <summary>
- /// Updates the current checksum with part of an array of bytes
- /// </summary>
- /// <param name="data">The data to update the checksum with</param>
- /// <param name="offset">Where in <c>data</c> to start updating</param>
- /// <param name="count">The number of bytes from <c>data</c> to use</param>
- /// <exception cref="ArgumentException">The sum of offset and count is larger than the length of <c>data</c></exception>
- /// <exception cref="NullReferenceException"><c>data</c> is a null reference</exception>
- /// <exception cref="ArgumentOutOfRangeException">Offset or count is negative.</exception>
- /// <remarks>All the other <c>Update</c> methods are implmeneted in terms of this one.
- /// This is therefore the only method a derived class has to implement</remarks>
- public abstract void Update(byte[] data, int offset, int count);
-
- /// <summary>
- /// Updates the current checksum with an array of bytes.
- /// </summary>
- /// <param name="data">The data to update the checksum with</param>
- public void Update(byte[] data)
- {
- Update(data, 0, data.Length);
- }
-
- /// <summary>
- /// Updates the current checksum with the data from a string
- /// </summary>
- /// <param name="data">The string to update the checksum with</param>
- /// <remarks>The characters in the string are converted by the UTF-8 encoding</remarks>
- public void Update(string data)
- {
- Update(Encoding.UTF8.GetBytes(data));
- }
-
- /// <summary>
- /// Updates the current checksum with the data from a string, using a specific encoding
- /// </summary>
- /// <param name="data">The string to update the checksum with</param>
- /// <param name="encoding">The encoding to use</param>
- public void Update(string data, Encoding encoding)
- {
- Update(encoding.GetBytes(data));
- }
-
- }
- #endregion
-
- #region CRC32
- /// <summary>
- /// Implements a CRC32 checksum generator
- /// </summary>
- public sealed class CRC32Checksum : ChecksumGeneratorBase
- {
- #region DLL imports
-
- [DllImport("ZLIB1.dll", CallingConvention=CallingConvention.Cdecl)]
- private static extern uint crc32(uint crc, int data, uint length);
-
- #endregion
-
- /// <summary>
- /// Initializes a new instance of the CRC32 checksum generator
- /// </summary>
- public CRC32Checksum() : base() {}
-
- /// <summary>
- /// Initializes a new instance of the CRC32 checksum generator with a specified value
- /// </summary>
- /// <param name="initialValue">The value to set the current checksum to</param>
- public CRC32Checksum(uint initialValue) : base(initialValue) {}
-
- /// <summary>
- /// Updates the current checksum with part of an array of bytes
- /// </summary>
- /// <param name="data">The data to update the checksum with</param>
- /// <param name="offset">Where in <c>data</c> to start updating</param>
- /// <param name="count">The number of bytes from <c>data</c> to use</param>
- /// <exception cref="ArgumentException">The sum of offset and count is larger than the length of <c>data</c></exception>
- /// <exception cref="NullReferenceException"><c>data</c> is a null reference</exception>
- /// <exception cref="ArgumentOutOfRangeException">Offset or count is negative.</exception>
- public override void Update(byte[] data, int offset, int count)
- {
- if (offset < 0 || count < 0) throw new ArgumentOutOfRangeException();
- if ((offset+count) > data.Length) throw new ArgumentException();
- GCHandle hData = GCHandle.Alloc(data, GCHandleType.Pinned);
- try
- {
- _current = crc32(_current, hData.AddrOfPinnedObject().ToInt32()+offset, (uint)count);
- }
- finally
- {
- hData.Free();
- }
- }
-
- }
- #endregion
-
- #region Adler
- /// <summary>
- /// Implements a checksum generator that computes the Adler checksum on data
- /// </summary>
- public sealed class AdlerChecksum : ChecksumGeneratorBase
- {
- #region DLL imports
-
- [DllImport("ZLIB1.dll", CallingConvention=CallingConvention.Cdecl)]
- private static extern uint adler32(uint adler, int data, uint length);
-
- #endregion
-
- /// <summary>
- /// Initializes a new instance of the Adler checksum generator
- /// </summary>
- public AdlerChecksum() : base() {}
-
- /// <summary>
- /// Initializes a new instance of the Adler checksum generator with a specified value
- /// </summary>
- /// <param name="initialValue">The value to set the current checksum to</param>
- public AdlerChecksum(uint initialValue) : base(initialValue) {}
-
- /// <summary>
- /// Updates the current checksum with part of an array of bytes
- /// </summary>
- /// <param name="data">The data to update the checksum with</param>
- /// <param name="offset">Where in <c>data</c> to start updating</param>
- /// <param name="count">The number of bytes from <c>data</c> to use</param>
- /// <exception cref="ArgumentException">The sum of offset and count is larger than the length of <c>data</c></exception>
- /// <exception cref="NullReferenceException"><c>data</c> is a null reference</exception>
- /// <exception cref="ArgumentOutOfRangeException">Offset or count is negative.</exception>
- public override void Update(byte[] data, int offset, int count)
- {
- if (offset < 0 || count < 0) throw new ArgumentOutOfRangeException();
- if ((offset+count) > data.Length) throw new ArgumentException();
- GCHandle hData = GCHandle.Alloc(data, GCHandleType.Pinned);
- try
- {
- _current = adler32(_current, hData.AddrOfPinnedObject().ToInt32()+offset, (uint)count);
- }
- finally
- {
- hData.Free();
- }
- }
-
- }
- #endregion
-
-}
\ No newline at end of file
diff --git a/third-party/zlib/contrib/dotzlib/DotZLib/CircularBuffer.cs b/third-party/zlib/contrib/dotzlib/DotZLib/CircularBuffer.cs
deleted file mode 100644
index c1cab3a..0000000
--- a/third-party/zlib/contrib/dotzlib/DotZLib/CircularBuffer.cs
+++ /dev/null
@@ -1,83 +0,0 @@
-//
-// � Copyright Henrik Ravn 2004
-//
-// Use, modification and distribution are subject to the Boost Software License, Version 1.0.
-// (See accompanying file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
-//
-
-using System;
-using System.Diagnostics;
-
-namespace DotZLib
-{
-
- /// <summary>
- /// This class implements a circular buffer
- /// </summary>
- internal class CircularBuffer
- {
- #region Private data
- private int _capacity;
- private int _head;
- private int _tail;
- private int _size;
- private byte[] _buffer;
- #endregion
-
- public CircularBuffer(int capacity)
- {
- Debug.Assert( capacity > 0 );
- _buffer = new byte[capacity];
- _capacity = capacity;
- _head = 0;
- _tail = 0;
- _size = 0;
- }
-
- public int Size { get { return _size; } }
-
- public int Put(byte[] source, int offset, int count)
- {
- Debug.Assert( count > 0 );
- int trueCount = Math.Min(count, _capacity - Size);
- for (int i = 0; i < trueCount; ++i)
- _buffer[(_tail+i) % _capacity] = source[offset+i];
- _tail += trueCount;
- _tail %= _capacity;
- _size += trueCount;
- return trueCount;
- }
-
- public bool Put(byte b)
- {
- if (Size == _capacity) // no room
- return false;
- _buffer[_tail++] = b;
- _tail %= _capacity;
- ++_size;
- return true;
- }
-
- public int Get(byte[] destination, int offset, int count)
- {
- int trueCount = Math.Min(count,Size);
- for (int i = 0; i < trueCount; ++i)
- destination[offset + i] = _buffer[(_head+i) % _capacity];
- _head += trueCount;
- _head %= _capacity;
- _size -= trueCount;
- return trueCount;
- }
-
- public int Get()
- {
- if (Size == 0)
- return -1;
-
- int result = (int)_buffer[_head++ % _capacity];
- --_size;
- return result;
- }
-
- }
-}
diff --git a/third-party/zlib/contrib/dotzlib/DotZLib/CodecBase.cs b/third-party/zlib/contrib/dotzlib/DotZLib/CodecBase.cs
deleted file mode 100644
index 42e6da3..0000000
--- a/third-party/zlib/contrib/dotzlib/DotZLib/CodecBase.cs
+++ /dev/null
@@ -1,198 +0,0 @@
-//
-// � Copyright Henrik Ravn 2004
-//
-// Use, modification and distribution are subject to the Boost Software License, Version 1.0.
-// (See accompanying file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
-//
-
-using System;
-using System.Runtime.InteropServices;
-
-namespace DotZLib
-{
- /// <summary>
- /// Implements the common functionality needed for all <see cref="Codec"/>s
- /// </summary>
- public abstract class CodecBase : Codec, IDisposable
- {
-
- #region Data members
-
- /// <summary>
- /// Instance of the internal zlib buffer structure that is
- /// passed to all functions in the zlib dll
- /// </summary>
- internal ZStream _ztream = new ZStream();
-
- /// <summary>
- /// True if the object instance has been disposed, false otherwise
- /// </summary>
- protected bool _isDisposed = false;
-
- /// <summary>
- /// The size of the internal buffers
- /// </summary>
- protected const int kBufferSize = 16384;
-
- private byte[] _outBuffer = new byte[kBufferSize];
- private byte[] _inBuffer = new byte[kBufferSize];
-
- private GCHandle _hInput;
- private GCHandle _hOutput;
-
- private uint _checksum = 0;
-
- #endregion
-
- /// <summary>
- /// Initializes a new instance of the <c>CodeBase</c> class.
- /// </summary>
- public CodecBase()
- {
- try
- {
- _hInput = GCHandle.Alloc(_inBuffer, GCHandleType.Pinned);
- _hOutput = GCHandle.Alloc(_outBuffer, GCHandleType.Pinned);
- }
- catch (Exception)
- {
- CleanUp(false);
- throw;
- }
- }
-
-
- #region Codec Members
-
- /// <summary>
- /// Occurs when more processed data are available.
- /// </summary>
- public event DataAvailableHandler DataAvailable;
-
- /// <summary>
- /// Fires the <see cref="DataAvailable"/> event
- /// </summary>
- protected void OnDataAvailable()
- {
- if (_ztream.total_out > 0)
- {
- if (DataAvailable != null)
- DataAvailable( _outBuffer, 0, (int)_ztream.total_out);
- resetOutput();
- }
- }
-
- /// <summary>
- /// Adds more data to the codec to be processed.
- /// </summary>
- /// <param name="data">Byte array containing the data to be added to the codec</param>
- /// <remarks>Adding data may, or may not, raise the <c>DataAvailable</c> event</remarks>
- public void Add(byte[] data)
- {
- Add(data,0,data.Length);
- }
-
- /// <summary>
- /// Adds more data to the codec to be processed.
- /// </summary>
- /// <param name="data">Byte array containing the data to be added to the codec</param>
- /// <param name="offset">The index of the first byte to add from <c>data</c></param>
- /// <param name="count">The number of bytes to add</param>
- /// <remarks>Adding data may, or may not, raise the <c>DataAvailable</c> event</remarks>
- /// <remarks>This must be implemented by a derived class</remarks>
- public abstract void Add(byte[] data, int offset, int count);
-
- /// <summary>
- /// Finishes up any pending data that needs to be processed and handled.
- /// </summary>
- /// <remarks>This must be implemented by a derived class</remarks>
- public abstract void Finish();
-
- /// <summary>
- /// Gets the checksum of the data that has been added so far
- /// </summary>
- public uint Checksum { get { return _checksum; } }
-
- #endregion
-
- #region Destructor & IDisposable stuff
-
- /// <summary>
- /// Destroys this instance
- /// </summary>
- ~CodecBase()
- {
- CleanUp(false);
- }
-
- /// <summary>
- /// Releases any unmanaged resources and calls the <see cref="CleanUp()"/> method of the derived class
- /// </summary>
- public void Dispose()
- {
- CleanUp(true);
- }
-
- /// <summary>
- /// Performs any codec specific cleanup
- /// </summary>
- /// <remarks>This must be implemented by a derived class</remarks>
- protected abstract void CleanUp();
-
- // performs the release of the handles and calls the dereived CleanUp()
- private void CleanUp(bool isDisposing)
- {
- if (!_isDisposed)
- {
- CleanUp();
- if (_hInput.IsAllocated)
- _hInput.Free();
- if (_hOutput.IsAllocated)
- _hOutput.Free();
-
- _isDisposed = true;
- }
- }
-
-
- #endregion
-
- #region Helper methods
-
- /// <summary>
- /// Copies a number of bytes to the internal codec buffer - ready for proccesing
- /// </summary>
- /// <param name="data">The byte array that contains the data to copy</param>
- /// <param name="startIndex">The index of the first byte to copy</param>
- /// <param name="count">The number of bytes to copy from <c>data</c></param>
- protected void copyInput(byte[] data, int startIndex, int count)
- {
- Array.Copy(data, startIndex, _inBuffer,0, count);
- _ztream.next_in = _hInput.AddrOfPinnedObject();
- _ztream.total_in = 0;
- _ztream.avail_in = (uint)count;
-
- }
-
- /// <summary>
- /// Resets the internal output buffers to a known state - ready for processing
- /// </summary>
- protected void resetOutput()
- {
- _ztream.total_out = 0;
- _ztream.avail_out = kBufferSize;
- _ztream.next_out = _hOutput.AddrOfPinnedObject();
- }
-
- /// <summary>
- /// Updates the running checksum property
- /// </summary>
- /// <param name="newSum">The new checksum value</param>
- protected void setChecksum(uint newSum)
- {
- _checksum = newSum;
- }
- #endregion
-
- }
-}
diff --git a/third-party/zlib/contrib/dotzlib/DotZLib/Deflater.cs b/third-party/zlib/contrib/dotzlib/DotZLib/Deflater.cs
deleted file mode 100644
index c247792..0000000
--- a/third-party/zlib/contrib/dotzlib/DotZLib/Deflater.cs
+++ /dev/null
@@ -1,106 +0,0 @@
-//
-// � Copyright Henrik Ravn 2004
-//
-// Use, modification and distribution are subject to the Boost Software License, Version 1.0.
-// (See accompanying file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
-//
-
-using System;
-using System.Diagnostics;
-using System.Runtime.InteropServices;
-
-namespace DotZLib
-{
-
- /// <summary>
- /// Implements a data compressor, using the deflate algorithm in the ZLib dll
- /// </summary>
- public sealed class Deflater : CodecBase
- {
- #region Dll imports
- [DllImport("ZLIB1.dll", CallingConvention=CallingConvention.Cdecl, CharSet=CharSet.Ansi)]
- private static extern int deflateInit_(ref ZStream sz, int level, string vs, int size);
-
- [DllImport("ZLIB1.dll", CallingConvention=CallingConvention.Cdecl)]
- private static extern int deflate(ref ZStream sz, int flush);
-
- [DllImport("ZLIB1.dll", CallingConvention=CallingConvention.Cdecl)]
- private static extern int deflateReset(ref ZStream sz);
-
- [DllImport("ZLIB1.dll", CallingConvention=CallingConvention.Cdecl)]
- private static extern int deflateEnd(ref ZStream sz);
- #endregion
-
- /// <summary>
- /// Constructs an new instance of the <c>Deflater</c>
- /// </summary>
- /// <param name="level">The compression level to use for this <c>Deflater</c></param>
- public Deflater(CompressLevel level) : base()
- {
- int retval = deflateInit_(ref _ztream, (int)level, Info.Version, Marshal.SizeOf(_ztream));
- if (retval != 0)
- throw new ZLibException(retval, "Could not initialize deflater");
-
- resetOutput();
- }
-
- /// <summary>
- /// Adds more data to the codec to be processed.
- /// </summary>
- /// <param name="data">Byte array containing the data to be added to the codec</param>
- /// <param name="offset">The index of the first byte to add from <c>data</c></param>
- /// <param name="count">The number of bytes to add</param>
- /// <remarks>Adding data may, or may not, raise the <c>DataAvailable</c> event</remarks>
- public override void Add(byte[] data, int offset, int count)
- {
- if (data == null) throw new ArgumentNullException();
- if (offset < 0 || count < 0) throw new ArgumentOutOfRangeException();
- if ((offset+count) > data.Length) throw new ArgumentException();
-
- int total = count;
- int inputIndex = offset;
- int err = 0;
-
- while (err >= 0 && inputIndex < total)
- {
- copyInput(data, inputIndex, Math.Min(total - inputIndex, kBufferSize));
- while (err >= 0 && _ztream.avail_in > 0)
- {
- err = deflate(ref _ztream, (int)FlushTypes.None);
- if (err == 0)
- while (_ztream.avail_out == 0)
- {
- OnDataAvailable();
- err = deflate(ref _ztream, (int)FlushTypes.None);
- }
- inputIndex += (int)_ztream.total_in;
- }
- }
- setChecksum( _ztream.adler );
- }
-
-
- /// <summary>
- /// Finishes up any pending data that needs to be processed and handled.
- /// </summary>
- public override void Finish()
- {
- int err;
- do
- {
- err = deflate(ref _ztream, (int)FlushTypes.Finish);
- OnDataAvailable();
- }
- while (err == 0);
- setChecksum( _ztream.adler );
- deflateReset(ref _ztream);
- resetOutput();
- }
-
- /// <summary>
- /// Closes the internal zlib deflate stream
- /// </summary>
- protected override void CleanUp() { deflateEnd(ref _ztream); }
-
- }
-}
diff --git a/third-party/zlib/contrib/dotzlib/DotZLib/DotZLib.cs b/third-party/zlib/contrib/dotzlib/DotZLib/DotZLib.cs
deleted file mode 100644
index be184b4..0000000
--- a/third-party/zlib/contrib/dotzlib/DotZLib/DotZLib.cs
+++ /dev/null
@@ -1,288 +0,0 @@
-//
-// � Copyright Henrik Ravn 2004
-//
-// Use, modification and distribution are subject to the Boost Software License, Version 1.0.
-// (See accompanying file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
-//
-
-using System;
-using System.IO;
-using System.Runtime.InteropServices;
-using System.Text;
-
-
-namespace DotZLib
-{
-
- #region Internal types
-
- /// <summary>
- /// Defines constants for the various flush types used with zlib
- /// </summary>
- internal enum FlushTypes
- {
- None, Partial, Sync, Full, Finish, Block
- }
-
- #region ZStream structure
- // internal mapping of the zlib zstream structure for marshalling
- [StructLayoutAttribute(LayoutKind.Sequential, Pack=4, Size=0, CharSet=CharSet.Ansi)]
- internal struct ZStream
- {
- public IntPtr next_in;
- public uint avail_in;
- public uint total_in;
-
- public IntPtr next_out;
- public uint avail_out;
- public uint total_out;
-
- [MarshalAs(UnmanagedType.LPStr)]
- string msg;
- uint state;
-
- uint zalloc;
- uint zfree;
- uint opaque;
-
- int data_type;
- public uint adler;
- uint reserved;
- }
-
- #endregion
-
- #endregion
-
- #region Public enums
- /// <summary>
- /// Defines constants for the available compression levels in zlib
- /// </summary>
- public enum CompressLevel : int
- {
- /// <summary>
- /// The default compression level with a reasonable compromise between compression and speed
- /// </summary>
- Default = -1,
- /// <summary>
- /// No compression at all. The data are passed straight through.
- /// </summary>
- None = 0,
- /// <summary>
- /// The maximum compression rate available.
- /// </summary>
- Best = 9,
- /// <summary>
- /// The fastest available compression level.
- /// </summary>
- Fastest = 1
- }
- #endregion
-
- #region Exception classes
- /// <summary>
- /// The exception that is thrown when an error occurs on the zlib dll
- /// </summary>
- public class ZLibException : ApplicationException
- {
- /// <summary>
- /// Initializes a new instance of the <see cref="ZLibException"/> class with a specified
- /// error message and error code
- /// </summary>
- /// <param name="errorCode">The zlib error code that caused the exception</param>
- /// <param name="msg">A message that (hopefully) describes the error</param>
- public ZLibException(int errorCode, string msg) : base(String.Format("ZLib error {0} {1}", errorCode, msg))
- {
- }
-
- /// <summary>
- /// Initializes a new instance of the <see cref="ZLibException"/> class with a specified
- /// error code
- /// </summary>
- /// <param name="errorCode">The zlib error code that caused the exception</param>
- public ZLibException(int errorCode) : base(String.Format("ZLib error {0}", errorCode))
- {
- }
- }
- #endregion
-
- #region Interfaces
-
- /// <summary>
- /// Declares methods and properties that enables a running checksum to be calculated
- /// </summary>
- public interface ChecksumGenerator
- {
- /// <summary>
- /// Gets the current value of the checksum
- /// </summary>
- uint Value { get; }
-
- /// <summary>
- /// Clears the current checksum to 0
- /// </summary>
- void Reset();
-
- /// <summary>
- /// Updates the current checksum with an array of bytes
- /// </summary>
- /// <param name="data">The data to update the checksum with</param>
- void Update(byte[] data);
-
- /// <summary>
- /// Updates the current checksum with part of an array of bytes
- /// </summary>
- /// <param name="data">The data to update the checksum with</param>
- /// <param name="offset">Where in <c>data</c> to start updating</param>
- /// <param name="count">The number of bytes from <c>data</c> to use</param>
- /// <exception cref="ArgumentException">The sum of offset and count is larger than the length of <c>data</c></exception>
- /// <exception cref="ArgumentNullException"><c>data</c> is a null reference</exception>
- /// <exception cref="ArgumentOutOfRangeException">Offset or count is negative.</exception>
- void Update(byte[] data, int offset, int count);
-
- /// <summary>
- /// Updates the current checksum with the data from a string
- /// </summary>
- /// <param name="data">The string to update the checksum with</param>
- /// <remarks>The characters in the string are converted by the UTF-8 encoding</remarks>
- void Update(string data);
-
- /// <summary>
- /// Updates the current checksum with the data from a string, using a specific encoding
- /// </summary>
- /// <param name="data">The string to update the checksum with</param>
- /// <param name="encoding">The encoding to use</param>
- void Update(string data, Encoding encoding);
- }
-
-
- /// <summary>
- /// Represents the method that will be called from a codec when new data
- /// are available.
- /// </summary>
- /// <paramref name="data">The byte array containing the processed data</paramref>
- /// <paramref name="startIndex">The index of the first processed byte in <c>data</c></paramref>
- /// <paramref name="count">The number of processed bytes available</paramref>
- /// <remarks>On return from this method, the data may be overwritten, so grab it while you can.
- /// You cannot assume that startIndex will be zero.
- /// </remarks>
- public delegate void DataAvailableHandler(byte[] data, int startIndex, int count);
-
- /// <summary>
- /// Declares methods and events for implementing compressors/decompressors
- /// </summary>
- public interface Codec
- {
- /// <summary>
- /// Occurs when more processed data are available.
- /// </summary>
- event DataAvailableHandler DataAvailable;
-
- /// <summary>
- /// Adds more data to the codec to be processed.
- /// </summary>
- /// <param name="data">Byte array containing the data to be added to the codec</param>
- /// <remarks>Adding data may, or may not, raise the <c>DataAvailable</c> event</remarks>
- void Add(byte[] data);
-
- /// <summary>
- /// Adds more data to the codec to be processed.
- /// </summary>
- /// <param name="data">Byte array containing the data to be added to the codec</param>
- /// <param name="offset">The index of the first byte to add from <c>data</c></param>
- /// <param name="count">The number of bytes to add</param>
- /// <remarks>Adding data may, or may not, raise the <c>DataAvailable</c> event</remarks>
- void Add(byte[] data, int offset, int count);
-
- /// <summary>
- /// Finishes up any pending data that needs to be processed and handled.
- /// </summary>
- void Finish();
-
- /// <summary>
- /// Gets the checksum of the data that has been added so far
- /// </summary>
- uint Checksum { get; }
-
-
- }
-
- #endregion
-
- #region Classes
- /// <summary>
- /// Encapsulates general information about the ZLib library
- /// </summary>
- public class Info
- {
- #region DLL imports
- [DllImport("ZLIB1.dll", CallingConvention=CallingConvention.Cdecl)]
- private static extern uint zlibCompileFlags();
-
- [DllImport("ZLIB1.dll", CallingConvention=CallingConvention.Cdecl)]
- private static extern string zlibVersion();
- #endregion
-
- #region Private stuff
- private uint _flags;
-
- // helper function that unpacks a bitsize mask
- private static int bitSize(uint bits)
- {
- switch (bits)
- {
- case 0: return 16;
- case 1: return 32;
- case 2: return 64;
- }
- return -1;
- }
- #endregion
-
- /// <summary>
- /// Constructs an instance of the <c>Info</c> class.
- /// </summary>
- public Info()
- {
- _flags = zlibCompileFlags();
- }
-
- /// <summary>
- /// True if the library is compiled with debug info
- /// </summary>
- public bool HasDebugInfo { get { return 0 != (_flags & 0x100); } }
-
- /// <summary>
- /// True if the library is compiled with assembly optimizations
- /// </summary>
- public bool UsesAssemblyCode { get { return 0 != (_flags & 0x200); } }
-
- /// <summary>
- /// Gets the size of the unsigned int that was compiled into Zlib
- /// </summary>
- public int SizeOfUInt { get { return bitSize(_flags & 3); } }
-
- /// <summary>
- /// Gets the size of the unsigned long that was compiled into Zlib
- /// </summary>
- public int SizeOfULong { get { return bitSize((_flags >> 2) & 3); } }
-
- /// <summary>
- /// Gets the size of the pointers that were compiled into Zlib
- /// </summary>
- public int SizeOfPointer { get { return bitSize((_flags >> 4) & 3); } }
-
- /// <summary>
- /// Gets the size of the z_off_t type that was compiled into Zlib
- /// </summary>
- public int SizeOfOffset { get { return bitSize((_flags >> 6) & 3); } }
-
- /// <summary>
- /// Gets the version of ZLib as a string, e.g. "1.2.1"
- /// </summary>
- public static string Version { get { return zlibVersion(); } }
- }
-
- #endregion
-
-}
diff --git a/third-party/zlib/contrib/dotzlib/DotZLib/DotZLib.csproj b/third-party/zlib/contrib/dotzlib/DotZLib/DotZLib.csproj
deleted file mode 100644
index 71eeb85..0000000
--- a/third-party/zlib/contrib/dotzlib/DotZLib/DotZLib.csproj
+++ /dev/null
@@ -1,141 +0,0 @@
-<VisualStudioProject>
- <CSHARP
- ProjectType = "Local"
- ProductVersion = "7.10.3077"
- SchemaVersion = "2.0"
- ProjectGuid = "{BB1EE0B1-1808-46CB-B786-949D91117FC5}"
- >
- <Build>
- <Settings
- ApplicationIcon = ""
- AssemblyKeyContainerName = ""
- AssemblyName = "DotZLib"
- AssemblyOriginatorKeyFile = ""
- DefaultClientScript = "JScript"
- DefaultHTMLPageLayout = "Grid"
- DefaultTargetSchema = "IE50"
- DelaySign = "false"
- OutputType = "Library"
- PreBuildEvent = ""
- PostBuildEvent = ""
- RootNamespace = "DotZLib"
- RunPostBuildEvent = "OnBuildSuccess"
- StartupObject = ""
- >
- <Config
- Name = "Debug"
- AllowUnsafeBlocks = "false"
- BaseAddress = "285212672"
- CheckForOverflowUnderflow = "false"
- ConfigurationOverrideFile = ""
- DefineConstants = "DEBUG;TRACE"
- DocumentationFile = "docs\DotZLib.xml"
- DebugSymbols = "true"
- FileAlignment = "4096"
- IncrementalBuild = "false"
- NoStdLib = "false"
- NoWarn = "1591"
- Optimize = "false"
- OutputPath = "bin\Debug\"
- RegisterForComInterop = "false"
- RemoveIntegerChecks = "false"
- TreatWarningsAsErrors = "false"
- WarningLevel = "4"
- />
- <Config
- Name = "Release"
- AllowUnsafeBlocks = "false"
- BaseAddress = "285212672"
- CheckForOverflowUnderflow = "false"
- ConfigurationOverrideFile = ""
- DefineConstants = "TRACE"
- DocumentationFile = "docs\DotZLib.xml"
- DebugSymbols = "false"
- FileAlignment = "4096"
- IncrementalBuild = "false"
- NoStdLib = "false"
- NoWarn = ""
- Optimize = "true"
- OutputPath = "bin\Release\"
- RegisterForComInterop = "false"
- RemoveIntegerChecks = "false"
- TreatWarningsAsErrors = "false"
- WarningLevel = "4"
- />
- </Settings>
- <References>
- <Reference
- Name = "System"
- AssemblyName = "System"
- HintPath = "C:\WINNT\Microsoft.NET\Framework\v1.1.4322\System.dll"
- />
- <Reference
- Name = "System.Data"
- AssemblyName = "System.Data"
- HintPath = "C:\WINNT\Microsoft.NET\Framework\v1.1.4322\System.Data.dll"
- />
- <Reference
- Name = "System.XML"
- AssemblyName = "System.Xml"
- HintPath = "C:\WINNT\Microsoft.NET\Framework\v1.1.4322\System.XML.dll"
- />
- <Reference
- Name = "nunit.framework"
- AssemblyName = "nunit.framework"
- HintPath = "E:\apps\NUnit V2.1\\bin\nunit.framework.dll"
- AssemblyFolderKey = "hklm\dn\nunit.framework"
- />
- </References>
- </Build>
- <Files>
- <Include>
- <File
- RelPath = "AssemblyInfo.cs"
- SubType = "Code"
- BuildAction = "Compile"
- />
- <File
- RelPath = "ChecksumImpl.cs"
- SubType = "Code"
- BuildAction = "Compile"
- />
- <File
- RelPath = "CircularBuffer.cs"
- SubType = "Code"
- BuildAction = "Compile"
- />
- <File
- RelPath = "CodecBase.cs"
- SubType = "Code"
- BuildAction = "Compile"
- />
- <File
- RelPath = "Deflater.cs"
- SubType = "Code"
- BuildAction = "Compile"
- />
- <File
- RelPath = "DotZLib.cs"
- SubType = "Code"
- BuildAction = "Compile"
- />
- <File
- RelPath = "GZipStream.cs"
- SubType = "Code"
- BuildAction = "Compile"
- />
- <File
- RelPath = "Inflater.cs"
- SubType = "Code"
- BuildAction = "Compile"
- />
- <File
- RelPath = "UnitTests.cs"
- SubType = "Code"
- BuildAction = "Compile"
- />
- </Include>
- </Files>
- </CSHARP>
-</VisualStudioProject>
-
diff --git a/third-party/zlib/contrib/dotzlib/DotZLib/GZipStream.cs b/third-party/zlib/contrib/dotzlib/DotZLib/GZipStream.cs
deleted file mode 100644
index b161300..0000000
--- a/third-party/zlib/contrib/dotzlib/DotZLib/GZipStream.cs
+++ /dev/null
@@ -1,301 +0,0 @@
-//
-// � Copyright Henrik Ravn 2004
-//
-// Use, modification and distribution are subject to the Boost Software License, Version 1.0.
-// (See accompanying file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
-//
-
-using System;
-using System.IO;
-using System.Runtime.InteropServices;
-
-namespace DotZLib
-{
- /// <summary>
- /// Implements a compressed <see cref="Stream"/>, in GZip (.gz) format.
- /// </summary>
- public class GZipStream : Stream, IDisposable
- {
- #region Dll Imports
- [DllImport("ZLIB1.dll", CallingConvention=CallingConvention.Cdecl, CharSet=CharSet.Ansi)]
- private static extern IntPtr gzopen(string name, string mode);
-
- [DllImport("ZLIB1.dll", CallingConvention=CallingConvention.Cdecl)]
- private static extern int gzclose(IntPtr gzFile);
-
- [DllImport("ZLIB1.dll", CallingConvention=CallingConvention.Cdecl)]
- private static extern int gzwrite(IntPtr gzFile, int data, int length);
-
- [DllImport("ZLIB1.dll", CallingConvention=CallingConvention.Cdecl)]
- private static extern int gzread(IntPtr gzFile, int data, int length);
-
- [DllImport("ZLIB1.dll", CallingConvention=CallingConvention.Cdecl)]
- private static extern int gzgetc(IntPtr gzFile);
-
- [DllImport("ZLIB1.dll", CallingConvention=CallingConvention.Cdecl)]
- private static extern int gzputc(IntPtr gzFile, int c);
-
- #endregion
-
- #region Private data
- private IntPtr _gzFile;
- private bool _isDisposed = false;
- private bool _isWriting;
- #endregion
-
- #region Constructors
- /// <summary>
- /// Creates a new file as a writeable GZipStream
- /// </summary>
- /// <param name="fileName">The name of the compressed file to create</param>
- /// <param name="level">The compression level to use when adding data</param>
- /// <exception cref="ZLibException">If an error occurred in the internal zlib function</exception>
- public GZipStream(string fileName, CompressLevel level)
- {
- _isWriting = true;
- _gzFile = gzopen(fileName, String.Format("wb{0}", (int)level));
- if (_gzFile == IntPtr.Zero)
- throw new ZLibException(-1, "Could not open " + fileName);
- }
-
- /// <summary>
- /// Opens an existing file as a readable GZipStream
- /// </summary>
- /// <param name="fileName">The name of the file to open</param>
- /// <exception cref="ZLibException">If an error occurred in the internal zlib function</exception>
- public GZipStream(string fileName)
- {
- _isWriting = false;
- _gzFile = gzopen(fileName, "rb");
- if (_gzFile == IntPtr.Zero)
- throw new ZLibException(-1, "Could not open " + fileName);
-
- }
- #endregion
-
- #region Access properties
- /// <summary>
- /// Returns true of this stream can be read from, false otherwise
- /// </summary>
- public override bool CanRead
- {
- get
- {
- return !_isWriting;
- }
- }
-
-
- /// <summary>
- /// Returns false.
- /// </summary>
- public override bool CanSeek
- {
- get
- {
- return false;
- }
- }
-
- /// <summary>
- /// Returns true if this tsream is writeable, false otherwise
- /// </summary>
- public override bool CanWrite
- {
- get
- {
- return _isWriting;
- }
- }
- #endregion
-
- #region Destructor & IDispose stuff
-
- /// <summary>
- /// Destroys this instance
- /// </summary>
- ~GZipStream()
- {
- cleanUp(false);
- }
-
- /// <summary>
- /// Closes the external file handle
- /// </summary>
- public void Dispose()
- {
- cleanUp(true);
- }
-
- // Does the actual closing of the file handle.
- private void cleanUp(bool isDisposing)
- {
- if (!_isDisposed)
- {
- gzclose(_gzFile);
- _isDisposed = true;
- }
- }
- #endregion
-
- #region Basic reading and writing
- /// <summary>
- /// Attempts to read a number of bytes from the stream.
- /// </summary>
- /// <param name="buffer">The destination data buffer</param>
- /// <param name="offset">The index of the first destination byte in <c>buffer</c></param>
- /// <param name="count">The number of bytes requested</param>
- /// <returns>The number of bytes read</returns>
- /// <exception cref="ArgumentNullException">If <c>buffer</c> is null</exception>
- /// <exception cref="ArgumentOutOfRangeException">If <c>count</c> or <c>offset</c> are negative</exception>
- /// <exception cref="ArgumentException">If <c>offset</c> + <c>count</c> is > buffer.Length</exception>
- /// <exception cref="NotSupportedException">If this stream is not readable.</exception>
- /// <exception cref="ObjectDisposedException">If this stream has been disposed.</exception>
- public override int Read(byte[] buffer, int offset, int count)
- {
- if (!CanRead) throw new NotSupportedException();
- if (buffer == null) throw new ArgumentNullException();
- if (offset < 0 || count < 0) throw new ArgumentOutOfRangeException();
- if ((offset+count) > buffer.Length) throw new ArgumentException();
- if (_isDisposed) throw new ObjectDisposedException("GZipStream");
-
- GCHandle h = GCHandle.Alloc(buffer, GCHandleType.Pinned);
- int result;
- try
- {
- result = gzread(_gzFile, h.AddrOfPinnedObject().ToInt32() + offset, count);
- if (result < 0)
- throw new IOException();
- }
- finally
- {
- h.Free();
- }
- return result;
- }
-
- /// <summary>
- /// Attempts to read a single byte from the stream.
- /// </summary>
- /// <returns>The byte that was read, or -1 in case of error or End-Of-File</returns>
- public override int ReadByte()
- {
- if (!CanRead) throw new NotSupportedException();
- if (_isDisposed) throw new ObjectDisposedException("GZipStream");
- return gzgetc(_gzFile);
- }
-
- /// <summary>
- /// Writes a number of bytes to the stream
- /// </summary>
- /// <param name="buffer"></param>
- /// <param name="offset"></param>
- /// <param name="count"></param>
- /// <exception cref="ArgumentNullException">If <c>buffer</c> is null</exception>
- /// <exception cref="ArgumentOutOfRangeException">If <c>count</c> or <c>offset</c> are negative</exception>
- /// <exception cref="ArgumentException">If <c>offset</c> + <c>count</c> is > buffer.Length</exception>
- /// <exception cref="NotSupportedException">If this stream is not writeable.</exception>
- /// <exception cref="ObjectDisposedException">If this stream has been disposed.</exception>
- public override void Write(byte[] buffer, int offset, int count)
- {
- if (!CanWrite) throw new NotSupportedException();
- if (buffer == null) throw new ArgumentNullException();
- if (offset < 0 || count < 0) throw new ArgumentOutOfRangeException();
- if ((offset+count) > buffer.Length) throw new ArgumentException();
- if (_isDisposed) throw new ObjectDisposedException("GZipStream");
-
- GCHandle h = GCHandle.Alloc(buffer, GCHandleType.Pinned);
- try
- {
- int result = gzwrite(_gzFile, h.AddrOfPinnedObject().ToInt32() + offset, count);
- if (result < 0)
- throw new IOException();
- }
- finally
- {
- h.Free();
- }
- }
-
- /// <summary>
- /// Writes a single byte to the stream
- /// </summary>
- /// <param name="value">The byte to add to the stream.</param>
- /// <exception cref="NotSupportedException">If this stream is not writeable.</exception>
- /// <exception cref="ObjectDisposedException">If this stream has been disposed.</exception>
- public override void WriteByte(byte value)
- {
- if (!CanWrite) throw new NotSupportedException();
- if (_isDisposed) throw new ObjectDisposedException("GZipStream");
-
- int result = gzputc(_gzFile, (int)value);
- if (result < 0)
- throw new IOException();
- }
- #endregion
-
- #region Position & length stuff
- /// <summary>
- /// Not supported.
- /// </summary>
- /// <param name="value"></param>
- /// <exception cref="NotSupportedException">Always thrown</exception>
- public override void SetLength(long value)
- {
- throw new NotSupportedException();
- }
-
- /// <summary>
- /// Not suppported.
- /// </summary>
- /// <param name="offset"></param>
- /// <param name="origin"></param>
- /// <returns></returns>
- /// <exception cref="NotSupportedException">Always thrown</exception>
- public override long Seek(long offset, SeekOrigin origin)
- {
- throw new NotSupportedException();
- }
-
- /// <summary>
- /// Flushes the <c>GZipStream</c>.
- /// </summary>
- /// <remarks>In this implementation, this method does nothing. This is because excessive
- /// flushing may degrade the achievable compression rates.</remarks>
- public override void Flush()
- {
- // left empty on purpose
- }
-
- /// <summary>
- /// Gets/sets the current position in the <c>GZipStream</c>. Not suppported.
- /// </summary>
- /// <remarks>In this implementation this property is not supported</remarks>
- /// <exception cref="NotSupportedException">Always thrown</exception>
- public override long Position
- {
- get
- {
- throw new NotSupportedException();
- }
- set
- {
- throw new NotSupportedException();
- }
- }
-
- /// <summary>
- /// Gets the size of the stream. Not suppported.
- /// </summary>
- /// <remarks>In this implementation this property is not supported</remarks>
- /// <exception cref="NotSupportedException">Always thrown</exception>
- public override long Length
- {
- get
- {
- throw new NotSupportedException();
- }
- }
- #endregion
- }
-}
diff --git a/third-party/zlib/contrib/dotzlib/DotZLib/Inflater.cs b/third-party/zlib/contrib/dotzlib/DotZLib/Inflater.cs
deleted file mode 100644
index 8ed5451..0000000
--- a/third-party/zlib/contrib/dotzlib/DotZLib/Inflater.cs
+++ /dev/null
@@ -1,105 +0,0 @@
-//
-// � Copyright Henrik Ravn 2004
-//
-// Use, modification and distribution are subject to the Boost Software License, Version 1.0.
-// (See accompanying file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
-//
-
-using System;
-using System.Diagnostics;
-using System.Runtime.InteropServices;
-
-namespace DotZLib
-{
-
- /// <summary>
- /// Implements a data decompressor, using the inflate algorithm in the ZLib dll
- /// </summary>
- public class Inflater : CodecBase
- {
- #region Dll imports
- [DllImport("ZLIB1.dll", CallingConvention=CallingConvention.Cdecl, CharSet=CharSet.Ansi)]
- private static extern int inflateInit_(ref ZStream sz, string vs, int size);
-
- [DllImport("ZLIB1.dll", CallingConvention=CallingConvention.Cdecl)]
- private static extern int inflate(ref ZStream sz, int flush);
-
- [DllImport("ZLIB1.dll", CallingConvention=CallingConvention.Cdecl)]
- private static extern int inflateReset(ref ZStream sz);
-
- [DllImport("ZLIB1.dll", CallingConvention=CallingConvention.Cdecl)]
- private static extern int inflateEnd(ref ZStream sz);
- #endregion
-
- /// <summary>
- /// Constructs an new instance of the <c>Inflater</c>
- /// </summary>
- public Inflater() : base()
- {
- int retval = inflateInit_(ref _ztream, Info.Version, Marshal.SizeOf(_ztream));
- if (retval != 0)
- throw new ZLibException(retval, "Could not initialize inflater");
-
- resetOutput();
- }
-
-
- /// <summary>
- /// Adds more data to the codec to be processed.
- /// </summary>
- /// <param name="data">Byte array containing the data to be added to the codec</param>
- /// <param name="offset">The index of the first byte to add from <c>data</c></param>
- /// <param name="count">The number of bytes to add</param>
- /// <remarks>Adding data may, or may not, raise the <c>DataAvailable</c> event</remarks>
- public override void Add(byte[] data, int offset, int count)
- {
- if (data == null) throw new ArgumentNullException();
- if (offset < 0 || count < 0) throw new ArgumentOutOfRangeException();
- if ((offset+count) > data.Length) throw new ArgumentException();
-
- int total = count;
- int inputIndex = offset;
- int err = 0;
-
- while (err >= 0 && inputIndex < total)
- {
- copyInput(data, inputIndex, Math.Min(total - inputIndex, kBufferSize));
- err = inflate(ref _ztream, (int)FlushTypes.None);
- if (err == 0)
- while (_ztream.avail_out == 0)
- {
- OnDataAvailable();
- err = inflate(ref _ztream, (int)FlushTypes.None);
- }
-
- inputIndex += (int)_ztream.total_in;
- }
- setChecksum( _ztream.adler );
- }
-
-
- /// <summary>
- /// Finishes up any pending data that needs to be processed and handled.
- /// </summary>
- public override void Finish()
- {
- int err;
- do
- {
- err = inflate(ref _ztream, (int)FlushTypes.Finish);
- OnDataAvailable();
- }
- while (err == 0);
- setChecksum( _ztream.adler );
- inflateReset(ref _ztream);
- resetOutput();
- }
-
- /// <summary>
- /// Closes the internal zlib inflate stream
- /// </summary>
- protected override void CleanUp() { inflateEnd(ref _ztream); }
-
-
- }
-}
diff --git a/third-party/zlib/contrib/dotzlib/DotZLib/UnitTests.cs b/third-party/zlib/contrib/dotzlib/DotZLib/UnitTests.cs
deleted file mode 100644
index b273d54..0000000
--- a/third-party/zlib/contrib/dotzlib/DotZLib/UnitTests.cs
+++ /dev/null
@@ -1,274 +0,0 @@
-//
-// © Copyright Henrik Ravn 2004
-//
-// Use, modification and distribution are subject to the Boost Software License, Version 1.0.
-// (See accompanying file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
-//
-
-using System;
-using System.Collections;
-using System.IO;
-
-// uncomment the define below to include unit tests
-//#define nunit
-#if nunit
-using NUnit.Framework;
-
-// Unit tests for the DotZLib class library
-// ----------------------------------------
-//
-// Use this with NUnit 2 from http://www.nunit.org
-//
-
-namespace DotZLibTests
-{
- using DotZLib;
-
- // helper methods
- internal class Utils
- {
- public static bool byteArrEqual( byte[] lhs, byte[] rhs )
- {
- if (lhs.Length != rhs.Length)
- return false;
- for (int i = lhs.Length-1; i >= 0; --i)
- if (lhs[i] != rhs[i])
- return false;
- return true;
- }
-
- }
-
-
- [TestFixture]
- public class CircBufferTests
- {
- #region Circular buffer tests
- [Test]
- public void SinglePutGet()
- {
- CircularBuffer buf = new CircularBuffer(10);
- Assert.AreEqual( 0, buf.Size );
- Assert.AreEqual( -1, buf.Get() );
-
- Assert.IsTrue(buf.Put( 1 ));
- Assert.AreEqual( 1, buf.Size );
- Assert.AreEqual( 1, buf.Get() );
- Assert.AreEqual( 0, buf.Size );
- Assert.AreEqual( -1, buf.Get() );
- }
-
- [Test]
- public void BlockPutGet()
- {
- CircularBuffer buf = new CircularBuffer(10);
- byte[] arr = {1,2,3,4,5,6,7,8,9,10};
- Assert.AreEqual( 10, buf.Put(arr,0,10) );
- Assert.AreEqual( 10, buf.Size );
- Assert.IsFalse( buf.Put(11) );
- Assert.AreEqual( 1, buf.Get() );
- Assert.IsTrue( buf.Put(11) );
-
- byte[] arr2 = (byte[])arr.Clone();
- Assert.AreEqual( 9, buf.Get(arr2,1,9) );
- Assert.IsTrue( Utils.byteArrEqual(arr,arr2) );
- }
-
- #endregion
- }
-
- [TestFixture]
- public class ChecksumTests
- {
- #region CRC32 Tests
- [Test]
- public void CRC32_Null()
- {
- CRC32Checksum crc32 = new CRC32Checksum();
- Assert.AreEqual( 0, crc32.Value );
-
- crc32 = new CRC32Checksum(1);
- Assert.AreEqual( 1, crc32.Value );
-
- crc32 = new CRC32Checksum(556);
- Assert.AreEqual( 556, crc32.Value );
- }
-
- [Test]
- public void CRC32_Data()
- {
- CRC32Checksum crc32 = new CRC32Checksum();
- byte[] data = { 1,2,3,4,5,6,7 };
- crc32.Update(data);
- Assert.AreEqual( 0x70e46888, crc32.Value );
-
- crc32 = new CRC32Checksum();
- crc32.Update("penguin");
- Assert.AreEqual( 0x0e5c1a120, crc32.Value );
-
- crc32 = new CRC32Checksum(1);
- crc32.Update("penguin");
- Assert.AreEqual(0x43b6aa94, crc32.Value);
-
- }
- #endregion
-
- #region Adler tests
-
- [Test]
- public void Adler_Null()
- {
- AdlerChecksum adler = new AdlerChecksum();
- Assert.AreEqual(0, adler.Value);
-
- adler = new AdlerChecksum(1);
- Assert.AreEqual( 1, adler.Value );
-
- adler = new AdlerChecksum(556);
- Assert.AreEqual( 556, adler.Value );
- }
-
- [Test]
- public void Adler_Data()
- {
- AdlerChecksum adler = new AdlerChecksum(1);
- byte[] data = { 1,2,3,4,5,6,7 };
- adler.Update(data);
- Assert.AreEqual( 0x5b001d, adler.Value );
-
- adler = new AdlerChecksum();
- adler.Update("penguin");
- Assert.AreEqual(0x0bcf02f6, adler.Value );
-
- adler = new AdlerChecksum(1);
- adler.Update("penguin");
- Assert.AreEqual(0x0bd602f7, adler.Value);
-
- }
- #endregion
- }
-
- [TestFixture]
- public class InfoTests
- {
- #region Info tests
- [Test]
- public void Info_Version()
- {
- Info info = new Info();
- Assert.AreEqual("1.2.8", Info.Version);
- Assert.AreEqual(32, info.SizeOfUInt);
- Assert.AreEqual(32, info.SizeOfULong);
- Assert.AreEqual(32, info.SizeOfPointer);
- Assert.AreEqual(32, info.SizeOfOffset);
- }
- #endregion
- }
-
- [TestFixture]
- public class DeflateInflateTests
- {
- #region Deflate tests
- [Test]
- public void Deflate_Init()
- {
- using (Deflater def = new Deflater(CompressLevel.Default))
- {
- }
- }
-
- private ArrayList compressedData = new ArrayList();
- private uint adler1;
-
- private ArrayList uncompressedData = new ArrayList();
- private uint adler2;
-
- public void CDataAvail(byte[] data, int startIndex, int count)
- {
- for (int i = 0; i < count; ++i)
- compressedData.Add(data[i+startIndex]);
- }
-
- [Test]
- public void Deflate_Compress()
- {
- compressedData.Clear();
-
- byte[] testData = new byte[35000];
- for (int i = 0; i < testData.Length; ++i)
- testData[i] = 5;
-
- using (Deflater def = new Deflater((CompressLevel)5))
- {
- def.DataAvailable += new DataAvailableHandler(CDataAvail);
- def.Add(testData);
- def.Finish();
- adler1 = def.Checksum;
- }
- }
- #endregion
-
- #region Inflate tests
- [Test]
- public void Inflate_Init()
- {
- using (Inflater inf = new Inflater())
- {
- }
- }
-
- private void DDataAvail(byte[] data, int startIndex, int count)
- {
- for (int i = 0; i < count; ++i)
- uncompressedData.Add(data[i+startIndex]);
- }
-
- [Test]
- public void Inflate_Expand()
- {
- uncompressedData.Clear();
-
- using (Inflater inf = new Inflater())
- {
- inf.DataAvailable += new DataAvailableHandler(DDataAvail);
- inf.Add((byte[])compressedData.ToArray(typeof(byte)));
- inf.Finish();
- adler2 = inf.Checksum;
- }
- Assert.AreEqual( adler1, adler2 );
- }
- #endregion
- }
-
- [TestFixture]
- public class GZipStreamTests
- {
- #region GZipStream test
- [Test]
- public void GZipStream_WriteRead()
- {
- using (GZipStream gzOut = new GZipStream("gzstream.gz", CompressLevel.Best))
- {
- BinaryWriter writer = new BinaryWriter(gzOut);
- writer.Write("hi there");
- writer.Write(Math.PI);
- writer.Write(42);
- }
-
- using (GZipStream gzIn = new GZipStream("gzstream.gz"))
- {
- BinaryReader reader = new BinaryReader(gzIn);
- string s = reader.ReadString();
- Assert.AreEqual("hi there",s);
- double d = reader.ReadDouble();
- Assert.AreEqual(Math.PI, d);
- int i = reader.ReadInt32();
- Assert.AreEqual(42,i);
- }
-
- }
- #endregion
- }
-}
-
-#endif
diff --git a/third-party/zlib/contrib/dotzlib/LICENSE_1_0.txt b/third-party/zlib/contrib/dotzlib/LICENSE_1_0.txt
deleted file mode 100644
index 30aac2c..0000000
--- a/third-party/zlib/contrib/dotzlib/LICENSE_1_0.txt
+++ /dev/null
@@ -1,23 +0,0 @@
-Boost Software License - Version 1.0 - August 17th, 2003
-
-Permission is hereby granted, free of charge, to any person or organization
-obtaining a copy of the software and accompanying documentation covered by
-this license (the "Software") to use, reproduce, display, distribute,
-execute, and transmit the Software, and to prepare derivative works of the
-Software, and to permit third-parties to whom the Software is furnished to
-do so, all subject to the following:
-
-The copyright notices in the Software and this entire statement, including
-the above license grant, this restriction and the following disclaimer,
-must be included in all copies of the Software, in whole or in part, and
-all derivative works of the Software, unless such copies or derivative
-works are solely in the form of machine-executable object code generated by
-a source language processor.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-FITNESS FOR A PARTICULAR PURPOSE, TITLE AND NON-INFRINGEMENT. IN NO EVENT
-SHALL THE COPYRIGHT HOLDERS OR ANYONE DISTRIBUTING THE SOFTWARE BE LIABLE
-FOR ANY DAMAGES OR OTHER LIABILITY, WHETHER IN CONTRACT, TORT OR OTHERWISE,
-ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
-DEALINGS IN THE SOFTWARE.
\ No newline at end of file
diff --git a/third-party/zlib/contrib/dotzlib/readme.txt b/third-party/zlib/contrib/dotzlib/readme.txt
deleted file mode 100644
index b239572..0000000
--- a/third-party/zlib/contrib/dotzlib/readme.txt
+++ /dev/null
@@ -1,58 +0,0 @@
-This directory contains a .Net wrapper class library for the ZLib1.dll
-
-The wrapper includes support for inflating/deflating memory buffers,
-.Net streaming wrappers for the gz streams part of zlib, and wrappers
-for the checksum parts of zlib. See DotZLib/UnitTests.cs for examples.
-
-Directory structure:
---------------------
-
-LICENSE_1_0.txt - License file.
-readme.txt - This file.
-DotZLib.chm - Class library documentation
-DotZLib.build - NAnt build file
-DotZLib.sln - Microsoft Visual Studio 2003 solution file
-
-DotZLib\*.cs - Source files for the class library
-
-Unit tests:
------------
-The file DotZLib/UnitTests.cs contains unit tests for use with NUnit 2.1 or higher.
-To include unit tests in the build, define nunit before building.
-
-
-Build instructions:
--------------------
-
-1. Using Visual Studio.Net 2003:
- Open DotZLib.sln in VS.Net and build from there. Output file (DotZLib.dll)
- will be found ./DotZLib/bin/release or ./DotZLib/bin/debug, depending on
- you are building the release or debug version of the library. Check
- DotZLib/UnitTests.cs for instructions on how to include unit tests in the
- build.
-
-2. Using NAnt:
- Open a command prompt with access to the build environment and run nant
- in the same directory as the DotZLib.build file.
- You can define 2 properties on the nant command-line to control the build:
- debug={true|false} to toggle between release/debug builds (default=true).
- nunit={true|false} to include or esclude unit tests (default=true).
- Also the target clean will remove binaries.
- Output file (DotZLib.dll) will be found in either ./DotZLib/bin/release
- or ./DotZLib/bin/debug, depending on whether you are building the release
- or debug version of the library.
-
- Examples:
- nant -D:debug=false -D:nunit=false
- will build a release mode version of the library without unit tests.
- nant
- will build a debug version of the library with unit tests
- nant clean
- will remove all previously built files.
-
-
----------------------------------
-Copyright (c) Henrik Ravn 2004
-
-Use, modification and distribution are subject to the Boost Software License, Version 1.0.
-(See accompanying file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
diff --git a/third-party/zlib/contrib/gcc_gvmat64/gvmat64.S b/third-party/zlib/contrib/gcc_gvmat64/gvmat64.S
deleted file mode 100644
index dd858dd..0000000
--- a/third-party/zlib/contrib/gcc_gvmat64/gvmat64.S
+++ /dev/null
@@ -1,574 +0,0 @@
-/*
-;uInt longest_match_x64(
-; deflate_state *s,
-; IPos cur_match); // current match
-
-; gvmat64.S -- Asm portion of the optimized longest_match for 32 bits x86_64
-; (AMD64 on Athlon 64, Opteron, Phenom
-; and Intel EM64T on Pentium 4 with EM64T, Pentium D, Core 2 Duo, Core I5/I7)
-; this file is translation from gvmat64.asm to GCC 4.x (for Linux, Mac XCode)
-; Copyright (C) 1995-2010 Jean-loup Gailly, Brian Raiter and Gilles Vollant.
-;
-; File written by Gilles Vollant, by converting to assembly the longest_match
-; from Jean-loup Gailly in deflate.c of zLib and infoZip zip.
-; and by taking inspiration on asm686 with masm, optimised assembly code
-; from Brian Raiter, written 1998
-;
-; This software is provided 'as-is', without any express or implied
-; warranty. In no event will the authors be held liable for any damages
-; arising from the use of this software.
-;
-; Permission is granted to anyone to use this software for any purpose,
-; including commercial applications, and to alter it and redistribute it
-; freely, subject to the following restrictions:
-;
-; 1. The origin of this software must not be misrepresented; you must not
-; claim that you wrote the original software. If you use this software
-; in a product, an acknowledgment in the product documentation would be
-; appreciated but is not required.
-; 2. Altered source versions must be plainly marked as such, and must not be
-; misrepresented as being the original software
-; 3. This notice may not be removed or altered from any source distribution.
-;
-; http://www.zlib.net
-; http://www.winimage.com/zLibDll
-; http://www.muppetlabs.com/~breadbox/software/assembly.html
-;
-; to compile this file for zLib, I use option:
-; gcc -c -arch x86_64 gvmat64.S
-
-
-;uInt longest_match(s, cur_match)
-; deflate_state *s;
-; IPos cur_match; // current match /
-;
-; with XCode for Mac, I had strange error with some jump on intel syntax
-; this is why BEFORE_JMP and AFTER_JMP are used
- */
-
-
-#define BEFORE_JMP .att_syntax
-#define AFTER_JMP .intel_syntax noprefix
-
-#ifndef NO_UNDERLINE
-# define match_init _match_init
-# define longest_match _longest_match
-#endif
-
-.intel_syntax noprefix
-
-.globl match_init, longest_match
-.text
-longest_match:
-
-
-
-#define LocalVarsSize 96
-/*
-; register used : rax,rbx,rcx,rdx,rsi,rdi,r8,r9,r10,r11,r12
-; free register : r14,r15
-; register can be saved : rsp
-*/
-
-#define chainlenwmask (rsp + 8 - LocalVarsSize)
-#define nicematch (rsp + 16 - LocalVarsSize)
-
-#define save_rdi (rsp + 24 - LocalVarsSize)
-#define save_rsi (rsp + 32 - LocalVarsSize)
-#define save_rbx (rsp + 40 - LocalVarsSize)
-#define save_rbp (rsp + 48 - LocalVarsSize)
-#define save_r12 (rsp + 56 - LocalVarsSize)
-#define save_r13 (rsp + 64 - LocalVarsSize)
-#define save_r14 (rsp + 72 - LocalVarsSize)
-#define save_r15 (rsp + 80 - LocalVarsSize)
-
-
-/*
-; all the +4 offsets are due to the addition of pending_buf_size (in zlib
-; in the deflate_state structure since the asm code was first written
-; (if you compile with zlib 1.0.4 or older, remove the +4).
-; Note : these value are good with a 8 bytes boundary pack structure
-*/
-
-#define MAX_MATCH 258
-#define MIN_MATCH 3
-#define MIN_LOOKAHEAD (MAX_MATCH+MIN_MATCH+1)
-
-/*
-;;; Offsets for fields in the deflate_state structure. These numbers
-;;; are calculated from the definition of deflate_state, with the
-;;; assumption that the compiler will dword-align the fields. (Thus,
-;;; changing the definition of deflate_state could easily cause this
-;;; program to crash horribly, without so much as a warning at
-;;; compile time. Sigh.)
-
-; all the +zlib1222add offsets are due to the addition of fields
-; in zlib in the deflate_state structure since the asm code was first written
-; (if you compile with zlib 1.0.4 or older, use "zlib1222add equ (-4)").
-; (if you compile with zlib between 1.0.5 and 1.2.2.1, use "zlib1222add equ 0").
-; if you compile with zlib 1.2.2.2 or later , use "zlib1222add equ 8").
-*/
-
-
-
-/* you can check the structure offset by running
-
-#include <stdlib.h>
-#include <stdio.h>
-#include "deflate.h"
-
-void print_depl()
-{
-deflate_state ds;
-deflate_state *s=&ds;
-printf("size pointer=%u\n",(int)sizeof(void*));
-
-printf("#define dsWSize %u\n",(int)(((char*)&(s->w_size))-((char*)s)));
-printf("#define dsWMask %u\n",(int)(((char*)&(s->w_mask))-((char*)s)));
-printf("#define dsWindow %u\n",(int)(((char*)&(s->window))-((char*)s)));
-printf("#define dsPrev %u\n",(int)(((char*)&(s->prev))-((char*)s)));
-printf("#define dsMatchLen %u\n",(int)(((char*)&(s->match_length))-((char*)s)));
-printf("#define dsPrevMatch %u\n",(int)(((char*)&(s->prev_match))-((char*)s)));
-printf("#define dsStrStart %u\n",(int)(((char*)&(s->strstart))-((char*)s)));
-printf("#define dsMatchStart %u\n",(int)(((char*)&(s->match_start))-((char*)s)));
-printf("#define dsLookahead %u\n",(int)(((char*)&(s->lookahead))-((char*)s)));
-printf("#define dsPrevLen %u\n",(int)(((char*)&(s->prev_length))-((char*)s)));
-printf("#define dsMaxChainLen %u\n",(int)(((char*)&(s->max_chain_length))-((char*)s)));
-printf("#define dsGoodMatch %u\n",(int)(((char*)&(s->good_match))-((char*)s)));
-printf("#define dsNiceMatch %u\n",(int)(((char*)&(s->nice_match))-((char*)s)));
-}
-*/
-
-#define dsWSize 68
-#define dsWMask 76
-#define dsWindow 80
-#define dsPrev 96
-#define dsMatchLen 144
-#define dsPrevMatch 148
-#define dsStrStart 156
-#define dsMatchStart 160
-#define dsLookahead 164
-#define dsPrevLen 168
-#define dsMaxChainLen 172
-#define dsGoodMatch 188
-#define dsNiceMatch 192
-
-#define window_size [ rcx + dsWSize]
-#define WMask [ rcx + dsWMask]
-#define window_ad [ rcx + dsWindow]
-#define prev_ad [ rcx + dsPrev]
-#define strstart [ rcx + dsStrStart]
-#define match_start [ rcx + dsMatchStart]
-#define Lookahead [ rcx + dsLookahead] //; 0ffffffffh on infozip
-#define prev_length [ rcx + dsPrevLen]
-#define max_chain_length [ rcx + dsMaxChainLen]
-#define good_match [ rcx + dsGoodMatch]
-#define nice_match [ rcx + dsNiceMatch]
-
-/*
-; windows:
-; parameter 1 in rcx(deflate state s), param 2 in rdx (cur match)
-
-; see http://weblogs.asp.net/oldnewthing/archive/2004/01/14/58579.aspx and
-; http://msdn.microsoft.com/library/en-us/kmarch/hh/kmarch/64bitAMD_8e951dd2-ee77-4728-8702-55ce4b5dd24a.xml.asp
-;
-; All registers must be preserved across the call, except for
-; rax, rcx, rdx, r8, r9, r10, and r11, which are scratch.
-
-;
-; gcc on macosx-linux:
-; see http://www.x86-64.org/documentation/abi-0.99.pdf
-; param 1 in rdi, param 2 in rsi
-; rbx, rsp, rbp, r12 to r15 must be preserved
-
-;;; Save registers that the compiler may be using, and adjust esp to
-;;; make room for our stack frame.
-
-
-;;; Retrieve the function arguments. r8d will hold cur_match
-;;; throughout the entire function. edx will hold the pointer to the
-;;; deflate_state structure during the function's setup (before
-;;; entering the main loop.
-
-; ms: parameter 1 in rcx (deflate_state* s), param 2 in edx -> r8 (cur match)
-; mac: param 1 in rdi, param 2 rsi
-; this clear high 32 bits of r8, which can be garbage in both r8 and rdx
-*/
- mov [save_rbx],rbx
- mov [save_rbp],rbp
-
-
- mov rcx,rdi
-
- mov r8d,esi
-
-
- mov [save_r12],r12
- mov [save_r13],r13
- mov [save_r14],r14
- mov [save_r15],r15
-
-
-//;;; uInt wmask = s->w_mask;
-//;;; unsigned chain_length = s->max_chain_length;
-//;;; if (s->prev_length >= s->good_match) {
-//;;; chain_length >>= 2;
-//;;; }
-
-
- mov edi, prev_length
- mov esi, good_match
- mov eax, WMask
- mov ebx, max_chain_length
- cmp edi, esi
- jl LastMatchGood
- shr ebx, 2
-LastMatchGood:
-
-//;;; chainlen is decremented once beforehand so that the function can
-//;;; use the sign flag instead of the zero flag for the exit test.
-//;;; It is then shifted into the high word, to make room for the wmask
-//;;; value, which it will always accompany.
-
- dec ebx
- shl ebx, 16
- or ebx, eax
-
-//;;; on zlib only
-//;;; if ((uInt)nice_match > s->lookahead) nice_match = s->lookahead;
-
-
-
- mov eax, nice_match
- mov [chainlenwmask], ebx
- mov r10d, Lookahead
- cmp r10d, eax
- cmovnl r10d, eax
- mov [nicematch],r10d
-
-
-
-//;;; register Bytef *scan = s->window + s->strstart;
- mov r10, window_ad
- mov ebp, strstart
- lea r13, [r10 + rbp]
-
-//;;; Determine how many bytes the scan ptr is off from being
-//;;; dword-aligned.
-
- mov r9,r13
- neg r13
- and r13,3
-
-//;;; IPos limit = s->strstart > (IPos)MAX_DIST(s) ?
-//;;; s->strstart - (IPos)MAX_DIST(s) : NIL;
-
-
- mov eax, window_size
- sub eax, MIN_LOOKAHEAD
-
-
- xor edi,edi
- sub ebp, eax
-
- mov r11d, prev_length
-
- cmovng ebp,edi
-
-//;;; int best_len = s->prev_length;
-
-
-//;;; Store the sum of s->window + best_len in esi locally, and in esi.
-
- lea rsi,[r10+r11]
-
-//;;; register ush scan_start = *(ushf*)scan;
-//;;; register ush scan_end = *(ushf*)(scan+best_len-1);
-//;;; Posf *prev = s->prev;
-
- movzx r12d,word ptr [r9]
- movzx ebx, word ptr [r9 + r11 - 1]
-
- mov rdi, prev_ad
-
-//;;; Jump into the main loop.
-
- mov edx, [chainlenwmask]
-
- cmp bx,word ptr [rsi + r8 - 1]
- jz LookupLoopIsZero
-
-
-
-LookupLoop1:
- and r8d, edx
-
- movzx r8d, word ptr [rdi + r8*2]
- cmp r8d, ebp
- jbe LeaveNow
-
-
-
- sub edx, 0x00010000
- BEFORE_JMP
- js LeaveNow
- AFTER_JMP
-
-LoopEntry1:
- cmp bx,word ptr [rsi + r8 - 1]
- BEFORE_JMP
- jz LookupLoopIsZero
- AFTER_JMP
-
-LookupLoop2:
- and r8d, edx
-
- movzx r8d, word ptr [rdi + r8*2]
- cmp r8d, ebp
- BEFORE_JMP
- jbe LeaveNow
- AFTER_JMP
- sub edx, 0x00010000
- BEFORE_JMP
- js LeaveNow
- AFTER_JMP
-
-LoopEntry2:
- cmp bx,word ptr [rsi + r8 - 1]
- BEFORE_JMP
- jz LookupLoopIsZero
- AFTER_JMP
-
-LookupLoop4:
- and r8d, edx
-
- movzx r8d, word ptr [rdi + r8*2]
- cmp r8d, ebp
- BEFORE_JMP
- jbe LeaveNow
- AFTER_JMP
- sub edx, 0x00010000
- BEFORE_JMP
- js LeaveNow
- AFTER_JMP
-
-LoopEntry4:
-
- cmp bx,word ptr [rsi + r8 - 1]
- BEFORE_JMP
- jnz LookupLoop1
- jmp LookupLoopIsZero
- AFTER_JMP
-/*
-;;; do {
-;;; match = s->window + cur_match;
-;;; if (*(ushf*)(match+best_len-1) != scan_end ||
-;;; *(ushf*)match != scan_start) continue;
-;;; [...]
-;;; } while ((cur_match = prev[cur_match & wmask]) > limit
-;;; && --chain_length != 0);
-;;;
-;;; Here is the inner loop of the function. The function will spend the
-;;; majority of its time in this loop, and majority of that time will
-;;; be spent in the first ten instructions.
-;;;
-;;; Within this loop:
-;;; ebx = scanend
-;;; r8d = curmatch
-;;; edx = chainlenwmask - i.e., ((chainlen << 16) | wmask)
-;;; esi = windowbestlen - i.e., (window + bestlen)
-;;; edi = prev
-;;; ebp = limit
-*/
-.balign 16
-LookupLoop:
- and r8d, edx
-
- movzx r8d, word ptr [rdi + r8*2]
- cmp r8d, ebp
- BEFORE_JMP
- jbe LeaveNow
- AFTER_JMP
- sub edx, 0x00010000
- BEFORE_JMP
- js LeaveNow
- AFTER_JMP
-
-LoopEntry:
-
- cmp bx,word ptr [rsi + r8 - 1]
- BEFORE_JMP
- jnz LookupLoop1
- AFTER_JMP
-LookupLoopIsZero:
- cmp r12w, word ptr [r10 + r8]
- BEFORE_JMP
- jnz LookupLoop1
- AFTER_JMP
-
-
-//;;; Store the current value of chainlen.
- mov [chainlenwmask], edx
-/*
-;;; Point edi to the string under scrutiny, and esi to the string we
-;;; are hoping to match it up with. In actuality, esi and edi are
-;;; both pointed (MAX_MATCH_8 - scanalign) bytes ahead, and edx is
-;;; initialized to -(MAX_MATCH_8 - scanalign).
-*/
- lea rsi,[r8+r10]
- mov rdx, 0xfffffffffffffef8 //; -(MAX_MATCH_8)
- lea rsi, [rsi + r13 + 0x0108] //;MAX_MATCH_8]
- lea rdi, [r9 + r13 + 0x0108] //;MAX_MATCH_8]
-
- prefetcht1 [rsi+rdx]
- prefetcht1 [rdi+rdx]
-
-/*
-;;; Test the strings for equality, 8 bytes at a time. At the end,
-;;; adjust rdx so that it is offset to the exact byte that mismatched.
-;;;
-;;; We already know at this point that the first three bytes of the
-;;; strings match each other, and they can be safely passed over before
-;;; starting the compare loop. So what this code does is skip over 0-3
-;;; bytes, as much as necessary in order to dword-align the edi
-;;; pointer. (rsi will still be misaligned three times out of four.)
-;;;
-;;; It should be confessed that this loop usually does not represent
-;;; much of the total running time. Replacing it with a more
-;;; straightforward "rep cmpsb" would not drastically degrade
-;;; performance.
-*/
-
-LoopCmps:
- mov rax, [rsi + rdx]
- xor rax, [rdi + rdx]
- jnz LeaveLoopCmps
-
- mov rax, [rsi + rdx + 8]
- xor rax, [rdi + rdx + 8]
- jnz LeaveLoopCmps8
-
-
- mov rax, [rsi + rdx + 8+8]
- xor rax, [rdi + rdx + 8+8]
- jnz LeaveLoopCmps16
-
- add rdx,8+8+8
-
- BEFORE_JMP
- jnz LoopCmps
- jmp LenMaximum
- AFTER_JMP
-
-LeaveLoopCmps16: add rdx,8
-LeaveLoopCmps8: add rdx,8
-LeaveLoopCmps:
-
- test eax, 0x0000FFFF
- jnz LenLower
-
- test eax,0xffffffff
-
- jnz LenLower32
-
- add rdx,4
- shr rax,32
- or ax,ax
- BEFORE_JMP
- jnz LenLower
- AFTER_JMP
-
-LenLower32:
- shr eax,16
- add rdx,2
-
-LenLower:
- sub al, 1
- adc rdx, 0
-//;;; Calculate the length of the match. If it is longer than MAX_MATCH,
-//;;; then automatically accept it as the best possible match and leave.
-
- lea rax, [rdi + rdx]
- sub rax, r9
- cmp eax, MAX_MATCH
- BEFORE_JMP
- jge LenMaximum
- AFTER_JMP
-/*
-;;; If the length of the match is not longer than the best match we
-;;; have so far, then forget it and return to the lookup loop.
-;///////////////////////////////////
-*/
- cmp eax, r11d
- jg LongerMatch
-
- lea rsi,[r10+r11]
-
- mov rdi, prev_ad
- mov edx, [chainlenwmask]
- BEFORE_JMP
- jmp LookupLoop
- AFTER_JMP
-/*
-;;; s->match_start = cur_match;
-;;; best_len = len;
-;;; if (len >= nice_match) break;
-;;; scan_end = *(ushf*)(scan+best_len-1);
-*/
-LongerMatch:
- mov r11d, eax
- mov match_start, r8d
- cmp eax, [nicematch]
- BEFORE_JMP
- jge LeaveNow
- AFTER_JMP
-
- lea rsi,[r10+rax]
-
- movzx ebx, word ptr [r9 + rax - 1]
- mov rdi, prev_ad
- mov edx, [chainlenwmask]
- BEFORE_JMP
- jmp LookupLoop
- AFTER_JMP
-
-//;;; Accept the current string, with the maximum possible length.
-
-LenMaximum:
- mov r11d,MAX_MATCH
- mov match_start, r8d
-
-//;;; if ((uInt)best_len <= s->lookahead) return (uInt)best_len;
-//;;; return s->lookahead;
-
-LeaveNow:
- mov eax, Lookahead
- cmp r11d, eax
- cmovng eax, r11d
-
-
-
-//;;; Restore the stack and return from whence we came.
-
-
-// mov rsi,[save_rsi]
-// mov rdi,[save_rdi]
- mov rbx,[save_rbx]
- mov rbp,[save_rbp]
- mov r12,[save_r12]
- mov r13,[save_r13]
- mov r14,[save_r14]
- mov r15,[save_r15]
-
-
- ret 0
-//; please don't remove this string !
-//; Your can freely use gvmat64 in any free or commercial app
-//; but it is far better don't remove the string in the binary!
- // db 0dh,0ah,"asm686 with masm, optimised assembly code from Brian Raiter, written 1998, converted to amd 64 by Gilles Vollant 2005",0dh,0ah,0
-
-
-match_init:
- ret 0
-
-
diff --git a/third-party/zlib/contrib/infback9/README b/third-party/zlib/contrib/infback9/README
deleted file mode 100644
index e75ed13..0000000
--- a/third-party/zlib/contrib/infback9/README
+++ /dev/null
@@ -1 +0,0 @@
-See infback9.h for what this is and how to use it.
diff --git a/third-party/zlib/contrib/infback9/infback9.c b/third-party/zlib/contrib/infback9/infback9.c
deleted file mode 100644
index 05fb3e3..0000000
--- a/third-party/zlib/contrib/infback9/infback9.c
+++ /dev/null
@@ -1,615 +0,0 @@
-/* infback9.c -- inflate deflate64 data using a call-back interface
- * Copyright (C) 1995-2008 Mark Adler
- * For conditions of distribution and use, see copyright notice in zlib.h
- */
-
-#include "zutil.h"
-#include "infback9.h"
-#include "inftree9.h"
-#include "inflate9.h"
-
-#define WSIZE 65536UL
-
-/*
- strm provides memory allocation functions in zalloc and zfree, or
- Z_NULL to use the library memory allocation functions.
-
- window is a user-supplied window and output buffer that is 64K bytes.
- */
-int ZEXPORT inflateBack9Init_(strm, window, version, stream_size)
-z_stream FAR *strm;
-unsigned char FAR *window;
-const char *version;
-int stream_size;
-{
- struct inflate_state FAR *state;
-
- if (version == Z_NULL || version[0] != ZLIB_VERSION[0] ||
- stream_size != (int)(sizeof(z_stream)))
- return Z_VERSION_ERROR;
- if (strm == Z_NULL || window == Z_NULL)
- return Z_STREAM_ERROR;
- strm->msg = Z_NULL; /* in case we return an error */
- if (strm->zalloc == (alloc_func)0) {
- strm->zalloc = zcalloc;
- strm->opaque = (voidpf)0;
- }
- if (strm->zfree == (free_func)0) strm->zfree = zcfree;
- state = (struct inflate_state FAR *)ZALLOC(strm, 1,
- sizeof(struct inflate_state));
- if (state == Z_NULL) return Z_MEM_ERROR;
- Tracev((stderr, "inflate: allocated\n"));
- strm->state = (voidpf)state;
- state->window = window;
- return Z_OK;
-}
-
-/*
- Build and output length and distance decoding tables for fixed code
- decoding.
- */
-#ifdef MAKEFIXED
-#include <stdio.h>
-
-void makefixed9(void)
-{
- unsigned sym, bits, low, size;
- code *next, *lenfix, *distfix;
- struct inflate_state state;
- code fixed[544];
-
- /* literal/length table */
- sym = 0;
- while (sym < 144) state.lens[sym++] = 8;
- while (sym < 256) state.lens[sym++] = 9;
- while (sym < 280) state.lens[sym++] = 7;
- while (sym < 288) state.lens[sym++] = 8;
- next = fixed;
- lenfix = next;
- bits = 9;
- inflate_table9(LENS, state.lens, 288, &(next), &(bits), state.work);
-
- /* distance table */
- sym = 0;
- while (sym < 32) state.lens[sym++] = 5;
- distfix = next;
- bits = 5;
- inflate_table9(DISTS, state.lens, 32, &(next), &(bits), state.work);
-
- /* write tables */
- puts(" /* inffix9.h -- table for decoding deflate64 fixed codes");
- puts(" * Generated automatically by makefixed9().");
- puts(" */");
- puts("");
- puts(" /* WARNING: this file should *not* be used by applications.");
- puts(" It is part of the implementation of this library and is");
- puts(" subject to change. Applications should only use zlib.h.");
- puts(" */");
- puts("");
- size = 1U << 9;
- printf(" static const code lenfix[%u] = {", size);
- low = 0;
- for (;;) {
- if ((low % 6) == 0) printf("\n ");
- printf("{%u,%u,%d}", lenfix[low].op, lenfix[low].bits,
- lenfix[low].val);
- if (++low == size) break;
- putchar(',');
- }
- puts("\n };");
- size = 1U << 5;
- printf("\n static const code distfix[%u] = {", size);
- low = 0;
- for (;;) {
- if ((low % 5) == 0) printf("\n ");
- printf("{%u,%u,%d}", distfix[low].op, distfix[low].bits,
- distfix[low].val);
- if (++low == size) break;
- putchar(',');
- }
- puts("\n };");
-}
-#endif /* MAKEFIXED */
-
-/* Macros for inflateBack(): */
-
-/* Clear the input bit accumulator */
-#define INITBITS() \
- do { \
- hold = 0; \
- bits = 0; \
- } while (0)
-
-/* Assure that some input is available. If input is requested, but denied,
- then return a Z_BUF_ERROR from inflateBack(). */
-#define PULL() \
- do { \
- if (have == 0) { \
- have = in(in_desc, &next); \
- if (have == 0) { \
- next = Z_NULL; \
- ret = Z_BUF_ERROR; \
- goto inf_leave; \
- } \
- } \
- } while (0)
-
-/* Get a byte of input into the bit accumulator, or return from inflateBack()
- with an error if there is no input available. */
-#define PULLBYTE() \
- do { \
- PULL(); \
- have--; \
- hold += (unsigned long)(*next++) << bits; \
- bits += 8; \
- } while (0)
-
-/* Assure that there are at least n bits in the bit accumulator. If there is
- not enough available input to do that, then return from inflateBack() with
- an error. */
-#define NEEDBITS(n) \
- do { \
- while (bits < (unsigned)(n)) \
- PULLBYTE(); \
- } while (0)
-
-/* Return the low n bits of the bit accumulator (n <= 16) */
-#define BITS(n) \
- ((unsigned)hold & ((1U << (n)) - 1))
-
-/* Remove n bits from the bit accumulator */
-#define DROPBITS(n) \
- do { \
- hold >>= (n); \
- bits -= (unsigned)(n); \
- } while (0)
-
-/* Remove zero to seven bits as needed to go to a byte boundary */
-#define BYTEBITS() \
- do { \
- hold >>= bits & 7; \
- bits -= bits & 7; \
- } while (0)
-
-/* Assure that some output space is available, by writing out the window
- if it's full. If the write fails, return from inflateBack() with a
- Z_BUF_ERROR. */
-#define ROOM() \
- do { \
- if (left == 0) { \
- put = window; \
- left = WSIZE; \
- wrap = 1; \
- if (out(out_desc, put, (unsigned)left)) { \
- ret = Z_BUF_ERROR; \
- goto inf_leave; \
- } \
- } \
- } while (0)
-
-/*
- strm provides the memory allocation functions and window buffer on input,
- and provides information on the unused input on return. For Z_DATA_ERROR
- returns, strm will also provide an error message.
-
- in() and out() are the call-back input and output functions. When
- inflateBack() needs more input, it calls in(). When inflateBack() has
- filled the window with output, or when it completes with data in the
- window, it calls out() to write out the data. The application must not
- change the provided input until in() is called again or inflateBack()
- returns. The application must not change the window/output buffer until
- inflateBack() returns.
-
- in() and out() are called with a descriptor parameter provided in the
- inflateBack() call. This parameter can be a structure that provides the
- information required to do the read or write, as well as accumulated
- information on the input and output such as totals and check values.
-
- in() should return zero on failure. out() should return non-zero on
- failure. If either in() or out() fails, than inflateBack() returns a
- Z_BUF_ERROR. strm->next_in can be checked for Z_NULL to see whether it
- was in() or out() that caused in the error. Otherwise, inflateBack()
- returns Z_STREAM_END on success, Z_DATA_ERROR for an deflate format
- error, or Z_MEM_ERROR if it could not allocate memory for the state.
- inflateBack() can also return Z_STREAM_ERROR if the input parameters
- are not correct, i.e. strm is Z_NULL or the state was not initialized.
- */
-int ZEXPORT inflateBack9(strm, in, in_desc, out, out_desc)
-z_stream FAR *strm;
-in_func in;
-void FAR *in_desc;
-out_func out;
-void FAR *out_desc;
-{
- struct inflate_state FAR *state;
- z_const unsigned char FAR *next; /* next input */
- unsigned char FAR *put; /* next output */
- unsigned have; /* available input */
- unsigned long left; /* available output */
- inflate_mode mode; /* current inflate mode */
- int lastblock; /* true if processing last block */
- int wrap; /* true if the window has wrapped */
- unsigned char FAR *window; /* allocated sliding window, if needed */
- unsigned long hold; /* bit buffer */
- unsigned bits; /* bits in bit buffer */
- unsigned extra; /* extra bits needed */
- unsigned long length; /* literal or length of data to copy */
- unsigned long offset; /* distance back to copy string from */
- unsigned long copy; /* number of stored or match bytes to copy */
- unsigned char FAR *from; /* where to copy match bytes from */
- code const FAR *lencode; /* starting table for length/literal codes */
- code const FAR *distcode; /* starting table for distance codes */
- unsigned lenbits; /* index bits for lencode */
- unsigned distbits; /* index bits for distcode */
- code here; /* current decoding table entry */
- code last; /* parent table entry */
- unsigned len; /* length to copy for repeats, bits to drop */
- int ret; /* return code */
- static const unsigned short order[19] = /* permutation of code lengths */
- {16, 17, 18, 0, 8, 7, 9, 6, 10, 5, 11, 4, 12, 3, 13, 2, 14, 1, 15};
-#include "inffix9.h"
-
- /* Check that the strm exists and that the state was initialized */
- if (strm == Z_NULL || strm->state == Z_NULL)
- return Z_STREAM_ERROR;
- state = (struct inflate_state FAR *)strm->state;
-
- /* Reset the state */
- strm->msg = Z_NULL;
- mode = TYPE;
- lastblock = 0;
- wrap = 0;
- window = state->window;
- next = strm->next_in;
- have = next != Z_NULL ? strm->avail_in : 0;
- hold = 0;
- bits = 0;
- put = window;
- left = WSIZE;
- lencode = Z_NULL;
- distcode = Z_NULL;
-
- /* Inflate until end of block marked as last */
- for (;;)
- switch (mode) {
- case TYPE:
- /* determine and dispatch block type */
- if (lastblock) {
- BYTEBITS();
- mode = DONE;
- break;
- }
- NEEDBITS(3);
- lastblock = BITS(1);
- DROPBITS(1);
- switch (BITS(2)) {
- case 0: /* stored block */
- Tracev((stderr, "inflate: stored block%s\n",
- lastblock ? " (last)" : ""));
- mode = STORED;
- break;
- case 1: /* fixed block */
- lencode = lenfix;
- lenbits = 9;
- distcode = distfix;
- distbits = 5;
- Tracev((stderr, "inflate: fixed codes block%s\n",
- lastblock ? " (last)" : ""));
- mode = LEN; /* decode codes */
- break;
- case 2: /* dynamic block */
- Tracev((stderr, "inflate: dynamic codes block%s\n",
- lastblock ? " (last)" : ""));
- mode = TABLE;
- break;
- case 3:
- strm->msg = (char *)"invalid block type";
- mode = BAD;
- }
- DROPBITS(2);
- break;
-
- case STORED:
- /* get and verify stored block length */
- BYTEBITS(); /* go to byte boundary */
- NEEDBITS(32);
- if ((hold & 0xffff) != ((hold >> 16) ^ 0xffff)) {
- strm->msg = (char *)"invalid stored block lengths";
- mode = BAD;
- break;
- }
- length = (unsigned)hold & 0xffff;
- Tracev((stderr, "inflate: stored length %lu\n",
- length));
- INITBITS();
-
- /* copy stored block from input to output */
- while (length != 0) {
- copy = length;
- PULL();
- ROOM();
- if (copy > have) copy = have;
- if (copy > left) copy = left;
- zmemcpy(put, next, copy);
- have -= copy;
- next += copy;
- left -= copy;
- put += copy;
- length -= copy;
- }
- Tracev((stderr, "inflate: stored end\n"));
- mode = TYPE;
- break;
-
- case TABLE:
- /* get dynamic table entries descriptor */
- NEEDBITS(14);
- state->nlen = BITS(5) + 257;
- DROPBITS(5);
- state->ndist = BITS(5) + 1;
- DROPBITS(5);
- state->ncode = BITS(4) + 4;
- DROPBITS(4);
- if (state->nlen > 286) {
- strm->msg = (char *)"too many length symbols";
- mode = BAD;
- break;
- }
- Tracev((stderr, "inflate: table sizes ok\n"));
-
- /* get code length code lengths (not a typo) */
- state->have = 0;
- while (state->have < state->ncode) {
- NEEDBITS(3);
- state->lens[order[state->have++]] = (unsigned short)BITS(3);
- DROPBITS(3);
- }
- while (state->have < 19)
- state->lens[order[state->have++]] = 0;
- state->next = state->codes;
- lencode = (code const FAR *)(state->next);
- lenbits = 7;
- ret = inflate_table9(CODES, state->lens, 19, &(state->next),
- &(lenbits), state->work);
- if (ret) {
- strm->msg = (char *)"invalid code lengths set";
- mode = BAD;
- break;
- }
- Tracev((stderr, "inflate: code lengths ok\n"));
-
- /* get length and distance code code lengths */
- state->have = 0;
- while (state->have < state->nlen + state->ndist) {
- for (;;) {
- here = lencode[BITS(lenbits)];
- if ((unsigned)(here.bits) <= bits) break;
- PULLBYTE();
- }
- if (here.val < 16) {
- NEEDBITS(here.bits);
- DROPBITS(here.bits);
- state->lens[state->have++] = here.val;
- }
- else {
- if (here.val == 16) {
- NEEDBITS(here.bits + 2);
- DROPBITS(here.bits);
- if (state->have == 0) {
- strm->msg = (char *)"invalid bit length repeat";
- mode = BAD;
- break;
- }
- len = (unsigned)(state->lens[state->have - 1]);
- copy = 3 + BITS(2);
- DROPBITS(2);
- }
- else if (here.val == 17) {
- NEEDBITS(here.bits + 3);
- DROPBITS(here.bits);
- len = 0;
- copy = 3 + BITS(3);
- DROPBITS(3);
- }
- else {
- NEEDBITS(here.bits + 7);
- DROPBITS(here.bits);
- len = 0;
- copy = 11 + BITS(7);
- DROPBITS(7);
- }
- if (state->have + copy > state->nlen + state->ndist) {
- strm->msg = (char *)"invalid bit length repeat";
- mode = BAD;
- break;
- }
- while (copy--)
- state->lens[state->have++] = (unsigned short)len;
- }
- }
-
- /* handle error breaks in while */
- if (mode == BAD) break;
-
- /* check for end-of-block code (better have one) */
- if (state->lens[256] == 0) {
- strm->msg = (char *)"invalid code -- missing end-of-block";
- mode = BAD;
- break;
- }
-
- /* build code tables -- note: do not change the lenbits or distbits
- values here (9 and 6) without reading the comments in inftree9.h
- concerning the ENOUGH constants, which depend on those values */
- state->next = state->codes;
- lencode = (code const FAR *)(state->next);
- lenbits = 9;
- ret = inflate_table9(LENS, state->lens, state->nlen,
- &(state->next), &(lenbits), state->work);
- if (ret) {
- strm->msg = (char *)"invalid literal/lengths set";
- mode = BAD;
- break;
- }
- distcode = (code const FAR *)(state->next);
- distbits = 6;
- ret = inflate_table9(DISTS, state->lens + state->nlen,
- state->ndist, &(state->next), &(distbits),
- state->work);
- if (ret) {
- strm->msg = (char *)"invalid distances set";
- mode = BAD;
- break;
- }
- Tracev((stderr, "inflate: codes ok\n"));
- mode = LEN;
-
- case LEN:
- /* get a literal, length, or end-of-block code */
- for (;;) {
- here = lencode[BITS(lenbits)];
- if ((unsigned)(here.bits) <= bits) break;
- PULLBYTE();
- }
- if (here.op && (here.op & 0xf0) == 0) {
- last = here;
- for (;;) {
- here = lencode[last.val +
- (BITS(last.bits + last.op) >> last.bits)];
- if ((unsigned)(last.bits + here.bits) <= bits) break;
- PULLBYTE();
- }
- DROPBITS(last.bits);
- }
- DROPBITS(here.bits);
- length = (unsigned)here.val;
-
- /* process literal */
- if (here.op == 0) {
- Tracevv((stderr, here.val >= 0x20 && here.val < 0x7f ?
- "inflate: literal '%c'\n" :
- "inflate: literal 0x%02x\n", here.val));
- ROOM();
- *put++ = (unsigned char)(length);
- left--;
- mode = LEN;
- break;
- }
-
- /* process end of block */
- if (here.op & 32) {
- Tracevv((stderr, "inflate: end of block\n"));
- mode = TYPE;
- break;
- }
-
- /* invalid code */
- if (here.op & 64) {
- strm->msg = (char *)"invalid literal/length code";
- mode = BAD;
- break;
- }
-
- /* length code -- get extra bits, if any */
- extra = (unsigned)(here.op) & 31;
- if (extra != 0) {
- NEEDBITS(extra);
- length += BITS(extra);
- DROPBITS(extra);
- }
- Tracevv((stderr, "inflate: length %lu\n", length));
-
- /* get distance code */
- for (;;) {
- here = distcode[BITS(distbits)];
- if ((unsigned)(here.bits) <= bits) break;
- PULLBYTE();
- }
- if ((here.op & 0xf0) == 0) {
- last = here;
- for (;;) {
- here = distcode[last.val +
- (BITS(last.bits + last.op) >> last.bits)];
- if ((unsigned)(last.bits + here.bits) <= bits) break;
- PULLBYTE();
- }
- DROPBITS(last.bits);
- }
- DROPBITS(here.bits);
- if (here.op & 64) {
- strm->msg = (char *)"invalid distance code";
- mode = BAD;
- break;
- }
- offset = (unsigned)here.val;
-
- /* get distance extra bits, if any */
- extra = (unsigned)(here.op) & 15;
- if (extra != 0) {
- NEEDBITS(extra);
- offset += BITS(extra);
- DROPBITS(extra);
- }
- if (offset > WSIZE - (wrap ? 0: left)) {
- strm->msg = (char *)"invalid distance too far back";
- mode = BAD;
- break;
- }
- Tracevv((stderr, "inflate: distance %lu\n", offset));
-
- /* copy match from window to output */
- do {
- ROOM();
- copy = WSIZE - offset;
- if (copy < left) {
- from = put + copy;
- copy = left - copy;
- }
- else {
- from = put - offset;
- copy = left;
- }
- if (copy > length) copy = length;
- length -= copy;
- left -= copy;
- do {
- *put++ = *from++;
- } while (--copy);
- } while (length != 0);
- break;
-
- case DONE:
- /* inflate stream terminated properly -- write leftover output */
- ret = Z_STREAM_END;
- if (left < WSIZE) {
- if (out(out_desc, window, (unsigned)(WSIZE - left)))
- ret = Z_BUF_ERROR;
- }
- goto inf_leave;
-
- case BAD:
- ret = Z_DATA_ERROR;
- goto inf_leave;
-
- default: /* can't happen, but makes compilers happy */
- ret = Z_STREAM_ERROR;
- goto inf_leave;
- }
-
- /* Return unused input */
- inf_leave:
- strm->next_in = next;
- strm->avail_in = have;
- return ret;
-}
-
-int ZEXPORT inflateBack9End(strm)
-z_stream FAR *strm;
-{
- if (strm == Z_NULL || strm->state == Z_NULL || strm->zfree == (free_func)0)
- return Z_STREAM_ERROR;
- ZFREE(strm, strm->state);
- strm->state = Z_NULL;
- Tracev((stderr, "inflate: end\n"));
- return Z_OK;
-}
diff --git a/third-party/zlib/contrib/infback9/infback9.h b/third-party/zlib/contrib/infback9/infback9.h
deleted file mode 100644
index 1073c0a..0000000
--- a/third-party/zlib/contrib/infback9/infback9.h
+++ /dev/null
@@ -1,37 +0,0 @@
-/* infback9.h -- header for using inflateBack9 functions
- * Copyright (C) 2003 Mark Adler
- * For conditions of distribution and use, see copyright notice in zlib.h
- */
-
-/*
- * This header file and associated patches provide a decoder for PKWare's
- * undocumented deflate64 compression method (method 9). Use with infback9.c,
- * inftree9.h, inftree9.c, and inffix9.h. These patches are not supported.
- * This should be compiled with zlib, since it uses zutil.h and zutil.o.
- * This code has not yet been tested on 16-bit architectures. See the
- * comments in zlib.h for inflateBack() usage. These functions are used
- * identically, except that there is no windowBits parameter, and a 64K
- * window must be provided. Also if int's are 16 bits, then a zero for
- * the third parameter of the "out" function actually means 65536UL.
- * zlib.h must be included before this header file.
- */
-
-#ifdef __cplusplus
-extern "C" {
-#endif
-
-ZEXTERN int ZEXPORT inflateBack9 OF((z_stream FAR *strm,
- in_func in, void FAR *in_desc,
- out_func out, void FAR *out_desc));
-ZEXTERN int ZEXPORT inflateBack9End OF((z_stream FAR *strm));
-ZEXTERN int ZEXPORT inflateBack9Init_ OF((z_stream FAR *strm,
- unsigned char FAR *window,
- const char *version,
- int stream_size));
-#define inflateBack9Init(strm, window) \
- inflateBack9Init_((strm), (window), \
- ZLIB_VERSION, sizeof(z_stream))
-
-#ifdef __cplusplus
-}
-#endif
diff --git a/third-party/zlib/contrib/infback9/inffix9.h b/third-party/zlib/contrib/infback9/inffix9.h
deleted file mode 100644
index ee5671d..0000000
--- a/third-party/zlib/contrib/infback9/inffix9.h
+++ /dev/null
@@ -1,107 +0,0 @@
- /* inffix9.h -- table for decoding deflate64 fixed codes
- * Generated automatically by makefixed9().
- */
-
- /* WARNING: this file should *not* be used by applications.
- It is part of the implementation of this library and is
- subject to change. Applications should only use zlib.h.
- */
-
- static const code lenfix[512] = {
- {96,7,0},{0,8,80},{0,8,16},{132,8,115},{130,7,31},{0,8,112},
- {0,8,48},{0,9,192},{128,7,10},{0,8,96},{0,8,32},{0,9,160},
- {0,8,0},{0,8,128},{0,8,64},{0,9,224},{128,7,6},{0,8,88},
- {0,8,24},{0,9,144},{131,7,59},{0,8,120},{0,8,56},{0,9,208},
- {129,7,17},{0,8,104},{0,8,40},{0,9,176},{0,8,8},{0,8,136},
- {0,8,72},{0,9,240},{128,7,4},{0,8,84},{0,8,20},{133,8,227},
- {131,7,43},{0,8,116},{0,8,52},{0,9,200},{129,7,13},{0,8,100},
- {0,8,36},{0,9,168},{0,8,4},{0,8,132},{0,8,68},{0,9,232},
- {128,7,8},{0,8,92},{0,8,28},{0,9,152},{132,7,83},{0,8,124},
- {0,8,60},{0,9,216},{130,7,23},{0,8,108},{0,8,44},{0,9,184},
- {0,8,12},{0,8,140},{0,8,76},{0,9,248},{128,7,3},{0,8,82},
- {0,8,18},{133,8,163},{131,7,35},{0,8,114},{0,8,50},{0,9,196},
- {129,7,11},{0,8,98},{0,8,34},{0,9,164},{0,8,2},{0,8,130},
- {0,8,66},{0,9,228},{128,7,7},{0,8,90},{0,8,26},{0,9,148},
- {132,7,67},{0,8,122},{0,8,58},{0,9,212},{130,7,19},{0,8,106},
- {0,8,42},{0,9,180},{0,8,10},{0,8,138},{0,8,74},{0,9,244},
- {128,7,5},{0,8,86},{0,8,22},{65,8,0},{131,7,51},{0,8,118},
- {0,8,54},{0,9,204},{129,7,15},{0,8,102},{0,8,38},{0,9,172},
- {0,8,6},{0,8,134},{0,8,70},{0,9,236},{128,7,9},{0,8,94},
- {0,8,30},{0,9,156},{132,7,99},{0,8,126},{0,8,62},{0,9,220},
- {130,7,27},{0,8,110},{0,8,46},{0,9,188},{0,8,14},{0,8,142},
- {0,8,78},{0,9,252},{96,7,0},{0,8,81},{0,8,17},{133,8,131},
- {130,7,31},{0,8,113},{0,8,49},{0,9,194},{128,7,10},{0,8,97},
- {0,8,33},{0,9,162},{0,8,1},{0,8,129},{0,8,65},{0,9,226},
- {128,7,6},{0,8,89},{0,8,25},{0,9,146},{131,7,59},{0,8,121},
- {0,8,57},{0,9,210},{129,7,17},{0,8,105},{0,8,41},{0,9,178},
- {0,8,9},{0,8,137},{0,8,73},{0,9,242},{128,7,4},{0,8,85},
- {0,8,21},{144,8,3},{131,7,43},{0,8,117},{0,8,53},{0,9,202},
- {129,7,13},{0,8,101},{0,8,37},{0,9,170},{0,8,5},{0,8,133},
- {0,8,69},{0,9,234},{128,7,8},{0,8,93},{0,8,29},{0,9,154},
- {132,7,83},{0,8,125},{0,8,61},{0,9,218},{130,7,23},{0,8,109},
- {0,8,45},{0,9,186},{0,8,13},{0,8,141},{0,8,77},{0,9,250},
- {128,7,3},{0,8,83},{0,8,19},{133,8,195},{131,7,35},{0,8,115},
- {0,8,51},{0,9,198},{129,7,11},{0,8,99},{0,8,35},{0,9,166},
- {0,8,3},{0,8,131},{0,8,67},{0,9,230},{128,7,7},{0,8,91},
- {0,8,27},{0,9,150},{132,7,67},{0,8,123},{0,8,59},{0,9,214},
- {130,7,19},{0,8,107},{0,8,43},{0,9,182},{0,8,11},{0,8,139},
- {0,8,75},{0,9,246},{128,7,5},{0,8,87},{0,8,23},{77,8,0},
- {131,7,51},{0,8,119},{0,8,55},{0,9,206},{129,7,15},{0,8,103},
- {0,8,39},{0,9,174},{0,8,7},{0,8,135},{0,8,71},{0,9,238},
- {128,7,9},{0,8,95},{0,8,31},{0,9,158},{132,7,99},{0,8,127},
- {0,8,63},{0,9,222},{130,7,27},{0,8,111},{0,8,47},{0,9,190},
- {0,8,15},{0,8,143},{0,8,79},{0,9,254},{96,7,0},{0,8,80},
- {0,8,16},{132,8,115},{130,7,31},{0,8,112},{0,8,48},{0,9,193},
- {128,7,10},{0,8,96},{0,8,32},{0,9,161},{0,8,0},{0,8,128},
- {0,8,64},{0,9,225},{128,7,6},{0,8,88},{0,8,24},{0,9,145},
- {131,7,59},{0,8,120},{0,8,56},{0,9,209},{129,7,17},{0,8,104},
- {0,8,40},{0,9,177},{0,8,8},{0,8,136},{0,8,72},{0,9,241},
- {128,7,4},{0,8,84},{0,8,20},{133,8,227},{131,7,43},{0,8,116},
- {0,8,52},{0,9,201},{129,7,13},{0,8,100},{0,8,36},{0,9,169},
- {0,8,4},{0,8,132},{0,8,68},{0,9,233},{128,7,8},{0,8,92},
- {0,8,28},{0,9,153},{132,7,83},{0,8,124},{0,8,60},{0,9,217},
- {130,7,23},{0,8,108},{0,8,44},{0,9,185},{0,8,12},{0,8,140},
- {0,8,76},{0,9,249},{128,7,3},{0,8,82},{0,8,18},{133,8,163},
- {131,7,35},{0,8,114},{0,8,50},{0,9,197},{129,7,11},{0,8,98},
- {0,8,34},{0,9,165},{0,8,2},{0,8,130},{0,8,66},{0,9,229},
- {128,7,7},{0,8,90},{0,8,26},{0,9,149},{132,7,67},{0,8,122},
- {0,8,58},{0,9,213},{130,7,19},{0,8,106},{0,8,42},{0,9,181},
- {0,8,10},{0,8,138},{0,8,74},{0,9,245},{128,7,5},{0,8,86},
- {0,8,22},{65,8,0},{131,7,51},{0,8,118},{0,8,54},{0,9,205},
- {129,7,15},{0,8,102},{0,8,38},{0,9,173},{0,8,6},{0,8,134},
- {0,8,70},{0,9,237},{128,7,9},{0,8,94},{0,8,30},{0,9,157},
- {132,7,99},{0,8,126},{0,8,62},{0,9,221},{130,7,27},{0,8,110},
- {0,8,46},{0,9,189},{0,8,14},{0,8,142},{0,8,78},{0,9,253},
- {96,7,0},{0,8,81},{0,8,17},{133,8,131},{130,7,31},{0,8,113},
- {0,8,49},{0,9,195},{128,7,10},{0,8,97},{0,8,33},{0,9,163},
- {0,8,1},{0,8,129},{0,8,65},{0,9,227},{128,7,6},{0,8,89},
- {0,8,25},{0,9,147},{131,7,59},{0,8,121},{0,8,57},{0,9,211},
- {129,7,17},{0,8,105},{0,8,41},{0,9,179},{0,8,9},{0,8,137},
- {0,8,73},{0,9,243},{128,7,4},{0,8,85},{0,8,21},{144,8,3},
- {131,7,43},{0,8,117},{0,8,53},{0,9,203},{129,7,13},{0,8,101},
- {0,8,37},{0,9,171},{0,8,5},{0,8,133},{0,8,69},{0,9,235},
- {128,7,8},{0,8,93},{0,8,29},{0,9,155},{132,7,83},{0,8,125},
- {0,8,61},{0,9,219},{130,7,23},{0,8,109},{0,8,45},{0,9,187},
- {0,8,13},{0,8,141},{0,8,77},{0,9,251},{128,7,3},{0,8,83},
- {0,8,19},{133,8,195},{131,7,35},{0,8,115},{0,8,51},{0,9,199},
- {129,7,11},{0,8,99},{0,8,35},{0,9,167},{0,8,3},{0,8,131},
- {0,8,67},{0,9,231},{128,7,7},{0,8,91},{0,8,27},{0,9,151},
- {132,7,67},{0,8,123},{0,8,59},{0,9,215},{130,7,19},{0,8,107},
- {0,8,43},{0,9,183},{0,8,11},{0,8,139},{0,8,75},{0,9,247},
- {128,7,5},{0,8,87},{0,8,23},{77,8,0},{131,7,51},{0,8,119},
- {0,8,55},{0,9,207},{129,7,15},{0,8,103},{0,8,39},{0,9,175},
- {0,8,7},{0,8,135},{0,8,71},{0,9,239},{128,7,9},{0,8,95},
- {0,8,31},{0,9,159},{132,7,99},{0,8,127},{0,8,63},{0,9,223},
- {130,7,27},{0,8,111},{0,8,47},{0,9,191},{0,8,15},{0,8,143},
- {0,8,79},{0,9,255}
- };
-
- static const code distfix[32] = {
- {128,5,1},{135,5,257},{131,5,17},{139,5,4097},{129,5,5},
- {137,5,1025},{133,5,65},{141,5,16385},{128,5,3},{136,5,513},
- {132,5,33},{140,5,8193},{130,5,9},{138,5,2049},{134,5,129},
- {142,5,32769},{128,5,2},{135,5,385},{131,5,25},{139,5,6145},
- {129,5,7},{137,5,1537},{133,5,97},{141,5,24577},{128,5,4},
- {136,5,769},{132,5,49},{140,5,12289},{130,5,13},{138,5,3073},
- {134,5,193},{142,5,49153}
- };
diff --git a/third-party/zlib/contrib/infback9/inflate9.h b/third-party/zlib/contrib/infback9/inflate9.h
deleted file mode 100644
index ee9a793..0000000
--- a/third-party/zlib/contrib/infback9/inflate9.h
+++ /dev/null
@@ -1,47 +0,0 @@
-/* inflate9.h -- internal inflate state definition
- * Copyright (C) 1995-2003 Mark Adler
- * For conditions of distribution and use, see copyright notice in zlib.h
- */
-
-/* WARNING: this file should *not* be used by applications. It is
- part of the implementation of the compression library and is
- subject to change. Applications should only use zlib.h.
- */
-
-/* Possible inflate modes between inflate() calls */
-typedef enum {
- TYPE, /* i: waiting for type bits, including last-flag bit */
- STORED, /* i: waiting for stored size (length and complement) */
- TABLE, /* i: waiting for dynamic block table lengths */
- LEN, /* i: waiting for length/lit code */
- DONE, /* finished check, done -- remain here until reset */
- BAD /* got a data error -- remain here until reset */
-} inflate_mode;
-
-/*
- State transitions between above modes -
-
- (most modes can go to the BAD mode -- not shown for clarity)
-
- Read deflate blocks:
- TYPE -> STORED or TABLE or LEN or DONE
- STORED -> TYPE
- TABLE -> LENLENS -> CODELENS -> LEN
- Read deflate codes:
- LEN -> LEN or TYPE
- */
-
-/* state maintained between inflate() calls. Approximately 7K bytes. */
-struct inflate_state {
- /* sliding window */
- unsigned char FAR *window; /* allocated sliding window, if needed */
- /* dynamic table building */
- unsigned ncode; /* number of code length code lengths */
- unsigned nlen; /* number of length code lengths */
- unsigned ndist; /* number of distance code lengths */
- unsigned have; /* number of code lengths in lens[] */
- code FAR *next; /* next available space in codes[] */
- unsigned short lens[320]; /* temporary storage for code lengths */
- unsigned short work[288]; /* work area for code table building */
- code codes[ENOUGH]; /* space for code tables */
-};
diff --git a/third-party/zlib/contrib/infback9/inftree9.c b/third-party/zlib/contrib/infback9/inftree9.c
deleted file mode 100644
index 4a73ad2..0000000
--- a/third-party/zlib/contrib/infback9/inftree9.c
+++ /dev/null
@@ -1,324 +0,0 @@
-/* inftree9.c -- generate Huffman trees for efficient decoding
- * Copyright (C) 1995-2013 Mark Adler
- * For conditions of distribution and use, see copyright notice in zlib.h
- */
-
-#include "zutil.h"
-#include "inftree9.h"
-
-#define MAXBITS 15
-
-const char inflate9_copyright[] =
- " inflate9 1.2.8 Copyright 1995-2013 Mark Adler ";
-/*
- If you use the zlib library in a product, an acknowledgment is welcome
- in the documentation of your product. If for some reason you cannot
- include such an acknowledgment, I would appreciate that you keep this
- copyright string in the executable of your product.
- */
-
-/*
- Build a set of tables to decode the provided canonical Huffman code.
- The code lengths are lens[0..codes-1]. The result starts at *table,
- whose indices are 0..2^bits-1. work is a writable array of at least
- lens shorts, which is used as a work area. type is the type of code
- to be generated, CODES, LENS, or DISTS. On return, zero is success,
- -1 is an invalid code, and +1 means that ENOUGH isn't enough. table
- on return points to the next available entry's address. bits is the
- requested root table index bits, and on return it is the actual root
- table index bits. It will differ if the request is greater than the
- longest code or if it is less than the shortest code.
- */
-int inflate_table9(type, lens, codes, table, bits, work)
-codetype type;
-unsigned short FAR *lens;
-unsigned codes;
-code FAR * FAR *table;
-unsigned FAR *bits;
-unsigned short FAR *work;
-{
- unsigned len; /* a code's length in bits */
- unsigned sym; /* index of code symbols */
- unsigned min, max; /* minimum and maximum code lengths */
- unsigned root; /* number of index bits for root table */
- unsigned curr; /* number of index bits for current table */
- unsigned drop; /* code bits to drop for sub-table */
- int left; /* number of prefix codes available */
- unsigned used; /* code entries in table used */
- unsigned huff; /* Huffman code */
- unsigned incr; /* for incrementing code, index */
- unsigned fill; /* index for replicating entries */
- unsigned low; /* low bits for current root entry */
- unsigned mask; /* mask for low root bits */
- code this; /* table entry for duplication */
- code FAR *next; /* next available space in table */
- const unsigned short FAR *base; /* base value table to use */
- const unsigned short FAR *extra; /* extra bits table to use */
- int end; /* use base and extra for symbol > end */
- unsigned short count[MAXBITS+1]; /* number of codes of each length */
- unsigned short offs[MAXBITS+1]; /* offsets in table for each length */
- static const unsigned short lbase[31] = { /* Length codes 257..285 base */
- 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 15, 17,
- 19, 23, 27, 31, 35, 43, 51, 59, 67, 83, 99, 115,
- 131, 163, 195, 227, 3, 0, 0};
- static const unsigned short lext[31] = { /* Length codes 257..285 extra */
- 128, 128, 128, 128, 128, 128, 128, 128, 129, 129, 129, 129,
- 130, 130, 130, 130, 131, 131, 131, 131, 132, 132, 132, 132,
- 133, 133, 133, 133, 144, 72, 78};
- static const unsigned short dbase[32] = { /* Distance codes 0..31 base */
- 1, 2, 3, 4, 5, 7, 9, 13, 17, 25, 33, 49,
- 65, 97, 129, 193, 257, 385, 513, 769, 1025, 1537, 2049, 3073,
- 4097, 6145, 8193, 12289, 16385, 24577, 32769, 49153};
- static const unsigned short dext[32] = { /* Distance codes 0..31 extra */
- 128, 128, 128, 128, 129, 129, 130, 130, 131, 131, 132, 132,
- 133, 133, 134, 134, 135, 135, 136, 136, 137, 137, 138, 138,
- 139, 139, 140, 140, 141, 141, 142, 142};
-
- /*
- Process a set of code lengths to create a canonical Huffman code. The
- code lengths are lens[0..codes-1]. Each length corresponds to the
- symbols 0..codes-1. The Huffman code is generated by first sorting the
- symbols by length from short to long, and retaining the symbol order
- for codes with equal lengths. Then the code starts with all zero bits
- for the first code of the shortest length, and the codes are integer
- increments for the same length, and zeros are appended as the length
- increases. For the deflate format, these bits are stored backwards
- from their more natural integer increment ordering, and so when the
- decoding tables are built in the large loop below, the integer codes
- are incremented backwards.
-
- This routine assumes, but does not check, that all of the entries in
- lens[] are in the range 0..MAXBITS. The caller must assure this.
- 1..MAXBITS is interpreted as that code length. zero means that that
- symbol does not occur in this code.
-
- The codes are sorted by computing a count of codes for each length,
- creating from that a table of starting indices for each length in the
- sorted table, and then entering the symbols in order in the sorted
- table. The sorted table is work[], with that space being provided by
- the caller.
-
- The length counts are used for other purposes as well, i.e. finding
- the minimum and maximum length codes, determining if there are any
- codes at all, checking for a valid set of lengths, and looking ahead
- at length counts to determine sub-table sizes when building the
- decoding tables.
- */
-
- /* accumulate lengths for codes (assumes lens[] all in 0..MAXBITS) */
- for (len = 0; len <= MAXBITS; len++)
- count[len] = 0;
- for (sym = 0; sym < codes; sym++)
- count[lens[sym]]++;
-
- /* bound code lengths, force root to be within code lengths */
- root = *bits;
- for (max = MAXBITS; max >= 1; max--)
- if (count[max] != 0) break;
- if (root > max) root = max;
- if (max == 0) return -1; /* no codes! */
- for (min = 1; min <= MAXBITS; min++)
- if (count[min] != 0) break;
- if (root < min) root = min;
-
- /* check for an over-subscribed or incomplete set of lengths */
- left = 1;
- for (len = 1; len <= MAXBITS; len++) {
- left <<= 1;
- left -= count[len];
- if (left < 0) return -1; /* over-subscribed */
- }
- if (left > 0 && (type == CODES || max != 1))
- return -1; /* incomplete set */
-
- /* generate offsets into symbol table for each length for sorting */
- offs[1] = 0;
- for (len = 1; len < MAXBITS; len++)
- offs[len + 1] = offs[len] + count[len];
-
- /* sort symbols by length, by symbol order within each length */
- for (sym = 0; sym < codes; sym++)
- if (lens[sym] != 0) work[offs[lens[sym]]++] = (unsigned short)sym;
-
- /*
- Create and fill in decoding tables. In this loop, the table being
- filled is at next and has curr index bits. The code being used is huff
- with length len. That code is converted to an index by dropping drop
- bits off of the bottom. For codes where len is less than drop + curr,
- those top drop + curr - len bits are incremented through all values to
- fill the table with replicated entries.
-
- root is the number of index bits for the root table. When len exceeds
- root, sub-tables are created pointed to by the root entry with an index
- of the low root bits of huff. This is saved in low to check for when a
- new sub-table should be started. drop is zero when the root table is
- being filled, and drop is root when sub-tables are being filled.
-
- When a new sub-table is needed, it is necessary to look ahead in the
- code lengths to determine what size sub-table is needed. The length
- counts are used for this, and so count[] is decremented as codes are
- entered in the tables.
-
- used keeps track of how many table entries have been allocated from the
- provided *table space. It is checked for LENS and DIST tables against
- the constants ENOUGH_LENS and ENOUGH_DISTS to guard against changes in
- the initial root table size constants. See the comments in inftree9.h
- for more information.
-
- sym increments through all symbols, and the loop terminates when
- all codes of length max, i.e. all codes, have been processed. This
- routine permits incomplete codes, so another loop after this one fills
- in the rest of the decoding tables with invalid code markers.
- */
-
- /* set up for code type */
- switch (type) {
- case CODES:
- base = extra = work; /* dummy value--not used */
- end = 19;
- break;
- case LENS:
- base = lbase;
- base -= 257;
- extra = lext;
- extra -= 257;
- end = 256;
- break;
- default: /* DISTS */
- base = dbase;
- extra = dext;
- end = -1;
- }
-
- /* initialize state for loop */
- huff = 0; /* starting code */
- sym = 0; /* starting code symbol */
- len = min; /* starting code length */
- next = *table; /* current table to fill in */
- curr = root; /* current table index bits */
- drop = 0; /* current bits to drop from code for index */
- low = (unsigned)(-1); /* trigger new sub-table when len > root */
- used = 1U << root; /* use root table entries */
- mask = used - 1; /* mask for comparing low */
-
- /* check available table space */
- if ((type == LENS && used >= ENOUGH_LENS) ||
- (type == DISTS && used >= ENOUGH_DISTS))
- return 1;
-
- /* process all codes and make table entries */
- for (;;) {
- /* create table entry */
- this.bits = (unsigned char)(len - drop);
- if ((int)(work[sym]) < end) {
- this.op = (unsigned char)0;
- this.val = work[sym];
- }
- else if ((int)(work[sym]) > end) {
- this.op = (unsigned char)(extra[work[sym]]);
- this.val = base[work[sym]];
- }
- else {
- this.op = (unsigned char)(32 + 64); /* end of block */
- this.val = 0;
- }
-
- /* replicate for those indices with low len bits equal to huff */
- incr = 1U << (len - drop);
- fill = 1U << curr;
- do {
- fill -= incr;
- next[(huff >> drop) + fill] = this;
- } while (fill != 0);
-
- /* backwards increment the len-bit code huff */
- incr = 1U << (len - 1);
- while (huff & incr)
- incr >>= 1;
- if (incr != 0) {
- huff &= incr - 1;
- huff += incr;
- }
- else
- huff = 0;
-
- /* go to next symbol, update count, len */
- sym++;
- if (--(count[len]) == 0) {
- if (len == max) break;
- len = lens[work[sym]];
- }
-
- /* create new sub-table if needed */
- if (len > root && (huff & mask) != low) {
- /* if first time, transition to sub-tables */
- if (drop == 0)
- drop = root;
-
- /* increment past last table */
- next += 1U << curr;
-
- /* determine length of next table */
- curr = len - drop;
- left = (int)(1 << curr);
- while (curr + drop < max) {
- left -= count[curr + drop];
- if (left <= 0) break;
- curr++;
- left <<= 1;
- }
-
- /* check for enough space */
- used += 1U << curr;
- if ((type == LENS && used >= ENOUGH_LENS) ||
- (type == DISTS && used >= ENOUGH_DISTS))
- return 1;
-
- /* point entry in root table to sub-table */
- low = huff & mask;
- (*table)[low].op = (unsigned char)curr;
- (*table)[low].bits = (unsigned char)root;
- (*table)[low].val = (unsigned short)(next - *table);
- }
- }
-
- /*
- Fill in rest of table for incomplete codes. This loop is similar to the
- loop above in incrementing huff for table indices. It is assumed that
- len is equal to curr + drop, so there is no loop needed to increment
- through high index bits. When the current sub-table is filled, the loop
- drops back to the root table to fill in any remaining entries there.
- */
- this.op = (unsigned char)64; /* invalid code marker */
- this.bits = (unsigned char)(len - drop);
- this.val = (unsigned short)0;
- while (huff != 0) {
- /* when done with sub-table, drop back to root table */
- if (drop != 0 && (huff & mask) != low) {
- drop = 0;
- len = root;
- next = *table;
- curr = root;
- this.bits = (unsigned char)len;
- }
-
- /* put invalid code marker in table */
- next[huff >> drop] = this;
-
- /* backwards increment the len-bit code huff */
- incr = 1U << (len - 1);
- while (huff & incr)
- incr >>= 1;
- if (incr != 0) {
- huff &= incr - 1;
- huff += incr;
- }
- else
- huff = 0;
- }
-
- /* set return parameters */
- *table += used;
- *bits = root;
- return 0;
-}
diff --git a/third-party/zlib/contrib/infback9/inftree9.h b/third-party/zlib/contrib/infback9/inftree9.h
deleted file mode 100644
index 5ab21f0..0000000
--- a/third-party/zlib/contrib/infback9/inftree9.h
+++ /dev/null
@@ -1,61 +0,0 @@
-/* inftree9.h -- header to use inftree9.c
- * Copyright (C) 1995-2008 Mark Adler
- * For conditions of distribution and use, see copyright notice in zlib.h
- */
-
-/* WARNING: this file should *not* be used by applications. It is
- part of the implementation of the compression library and is
- subject to change. Applications should only use zlib.h.
- */
-
-/* Structure for decoding tables. Each entry provides either the
- information needed to do the operation requested by the code that
- indexed that table entry, or it provides a pointer to another
- table that indexes more bits of the code. op indicates whether
- the entry is a pointer to another table, a literal, a length or
- distance, an end-of-block, or an invalid code. For a table
- pointer, the low four bits of op is the number of index bits of
- that table. For a length or distance, the low four bits of op
- is the number of extra bits to get after the code. bits is
- the number of bits in this code or part of the code to drop off
- of the bit buffer. val is the actual byte to output in the case
- of a literal, the base length or distance, or the offset from
- the current table to the next table. Each entry is four bytes. */
-typedef struct {
- unsigned char op; /* operation, extra bits, table bits */
- unsigned char bits; /* bits in this part of the code */
- unsigned short val; /* offset in table or code value */
-} code;
-
-/* op values as set by inflate_table():
- 00000000 - literal
- 0000tttt - table link, tttt != 0 is the number of table index bits
- 100eeeee - length or distance, eeee is the number of extra bits
- 01100000 - end of block
- 01000000 - invalid code
- */
-
-/* Maximum size of the dynamic table. The maximum number of code structures is
- 1446, which is the sum of 852 for literal/length codes and 594 for distance
- codes. These values were found by exhaustive searches using the program
- examples/enough.c found in the zlib distribtution. The arguments to that
- program are the number of symbols, the initial root table size, and the
- maximum bit length of a code. "enough 286 9 15" for literal/length codes
- returns returns 852, and "enough 32 6 15" for distance codes returns 594.
- The initial root table size (9 or 6) is found in the fifth argument of the
- inflate_table() calls in infback9.c. If the root table size is changed,
- then these maximum sizes would be need to be recalculated and updated. */
-#define ENOUGH_LENS 852
-#define ENOUGH_DISTS 594
-#define ENOUGH (ENOUGH_LENS+ENOUGH_DISTS)
-
-/* Type of code to build for inflate_table9() */
-typedef enum {
- CODES,
- LENS,
- DISTS
-} codetype;
-
-extern int inflate_table9 OF((codetype type, unsigned short FAR *lens,
- unsigned codes, code FAR * FAR *table,
- unsigned FAR *bits, unsigned short FAR *work));
diff --git a/third-party/zlib/contrib/inflate86/inffas86.c b/third-party/zlib/contrib/inflate86/inffas86.c
deleted file mode 100644
index 7292f67..0000000
--- a/third-party/zlib/contrib/inflate86/inffas86.c
+++ /dev/null
@@ -1,1157 +0,0 @@
-/* inffas86.c is a hand tuned assembler version of
- *
- * inffast.c -- fast decoding
- * Copyright (C) 1995-2003 Mark Adler
- * For conditions of distribution and use, see copyright notice in zlib.h
- *
- * Copyright (C) 2003 Chris Anderson <christop at charm.net>
- * Please use the copyright conditions above.
- *
- * Dec-29-2003 -- I added AMD64 inflate asm support. This version is also
- * slightly quicker on x86 systems because, instead of using rep movsb to copy
- * data, it uses rep movsw, which moves data in 2-byte chunks instead of single
- * bytes. I've tested the AMD64 code on a Fedora Core 1 + the x86_64 updates
- * from http://fedora.linux.duke.edu/fc1_x86_64
- * which is running on an Athlon 64 3000+ / Gigabyte GA-K8VT800M system with
- * 1GB ram. The 64-bit version is about 4% faster than the 32-bit version,
- * when decompressing mozilla-source-1.3.tar.gz.
- *
- * Mar-13-2003 -- Most of this is derived from inffast.S which is derived from
- * the gcc -S output of zlib-1.2.0/inffast.c. Zlib-1.2.0 is in beta release at
- * the moment. I have successfully compiled and tested this code with gcc2.96,
- * gcc3.2, icc5.0, msvc6.0. It is very close to the speed of inffast.S
- * compiled with gcc -DNO_MMX, but inffast.S is still faster on the P3 with MMX
- * enabled. I will attempt to merge the MMX code into this version. Newer
- * versions of this and inffast.S can be found at
- * http://www.eetbeetee.com/zlib/ and http://www.charm.net/~christop/zlib/
- */
-
-#include "zutil.h"
-#include "inftrees.h"
-#include "inflate.h"
-#include "inffast.h"
-
-/* Mark Adler's comments from inffast.c: */
-
-/*
- Decode literal, length, and distance codes and write out the resulting
- literal and match bytes until either not enough input or output is
- available, an end-of-block is encountered, or a data error is encountered.
- When large enough input and output buffers are supplied to inflate(), for
- example, a 16K input buffer and a 64K output buffer, more than 95% of the
- inflate execution time is spent in this routine.
-
- Entry assumptions:
-
- state->mode == LEN
- strm->avail_in >= 6
- strm->avail_out >= 258
- start >= strm->avail_out
- state->bits < 8
-
- On return, state->mode is one of:
-
- LEN -- ran out of enough output space or enough available input
- TYPE -- reached end of block code, inflate() to interpret next block
- BAD -- error in block data
-
- Notes:
-
- - The maximum input bits used by a length/distance pair is 15 bits for the
- length code, 5 bits for the length extra, 15 bits for the distance code,
- and 13 bits for the distance extra. This totals 48 bits, or six bytes.
- Therefore if strm->avail_in >= 6, then there is enough input to avoid
- checking for available input while decoding.
-
- - The maximum bytes that a single length/distance pair can output is 258
- bytes, which is the maximum length that can be coded. inflate_fast()
- requires strm->avail_out >= 258 for each loop to avoid checking for
- output space.
- */
-void inflate_fast(strm, start)
-z_streamp strm;
-unsigned start; /* inflate()'s starting value for strm->avail_out */
-{
- struct inflate_state FAR *state;
- struct inffast_ar {
-/* 64 32 x86 x86_64 */
-/* ar offset register */
-/* 0 0 */ void *esp; /* esp save */
-/* 8 4 */ void *ebp; /* ebp save */
-/* 16 8 */ unsigned char FAR *in; /* esi rsi local strm->next_in */
-/* 24 12 */ unsigned char FAR *last; /* r9 while in < last */
-/* 32 16 */ unsigned char FAR *out; /* edi rdi local strm->next_out */
-/* 40 20 */ unsigned char FAR *beg; /* inflate()'s init next_out */
-/* 48 24 */ unsigned char FAR *end; /* r10 while out < end */
-/* 56 28 */ unsigned char FAR *window;/* size of window, wsize!=0 */
-/* 64 32 */ code const FAR *lcode; /* ebp rbp local strm->lencode */
-/* 72 36 */ code const FAR *dcode; /* r11 local strm->distcode */
-/* 80 40 */ unsigned long hold; /* edx rdx local strm->hold */
-/* 88 44 */ unsigned bits; /* ebx rbx local strm->bits */
-/* 92 48 */ unsigned wsize; /* window size */
-/* 96 52 */ unsigned write; /* window write index */
-/*100 56 */ unsigned lmask; /* r12 mask for lcode */
-/*104 60 */ unsigned dmask; /* r13 mask for dcode */
-/*108 64 */ unsigned len; /* r14 match length */
-/*112 68 */ unsigned dist; /* r15 match distance */
-/*116 72 */ unsigned status; /* set when state chng*/
- } ar;
-
-#if defined( __GNUC__ ) && defined( __amd64__ ) && ! defined( __i386 )
-#define PAD_AVAIL_IN 6
-#define PAD_AVAIL_OUT 258
-#else
-#define PAD_AVAIL_IN 5
-#define PAD_AVAIL_OUT 257
-#endif
-
- /* copy state to local variables */
- state = (struct inflate_state FAR *)strm->state;
- ar.in = strm->next_in;
- ar.last = ar.in + (strm->avail_in - PAD_AVAIL_IN);
- ar.out = strm->next_out;
- ar.beg = ar.out - (start - strm->avail_out);
- ar.end = ar.out + (strm->avail_out - PAD_AVAIL_OUT);
- ar.wsize = state->wsize;
- ar.write = state->wnext;
- ar.window = state->window;
- ar.hold = state->hold;
- ar.bits = state->bits;
- ar.lcode = state->lencode;
- ar.dcode = state->distcode;
- ar.lmask = (1U << state->lenbits) - 1;
- ar.dmask = (1U << state->distbits) - 1;
-
- /* decode literals and length/distances until end-of-block or not enough
- input data or output space */
-
- /* align in on 1/2 hold size boundary */
- while (((unsigned long)(void *)ar.in & (sizeof(ar.hold) / 2 - 1)) != 0) {
- ar.hold += (unsigned long)*ar.in++ << ar.bits;
- ar.bits += 8;
- }
-
-#if defined( __GNUC__ ) && defined( __amd64__ ) && ! defined( __i386 )
- __asm__ __volatile__ (
-" leaq %0, %%rax\n"
-" movq %%rbp, 8(%%rax)\n" /* save regs rbp and rsp */
-" movq %%rsp, (%%rax)\n"
-" movq %%rax, %%rsp\n" /* make rsp point to &ar */
-" movq 16(%%rsp), %%rsi\n" /* rsi = in */
-" movq 32(%%rsp), %%rdi\n" /* rdi = out */
-" movq 24(%%rsp), %%r9\n" /* r9 = last */
-" movq 48(%%rsp), %%r10\n" /* r10 = end */
-" movq 64(%%rsp), %%rbp\n" /* rbp = lcode */
-" movq 72(%%rsp), %%r11\n" /* r11 = dcode */
-" movq 80(%%rsp), %%rdx\n" /* rdx = hold */
-" movl 88(%%rsp), %%ebx\n" /* ebx = bits */
-" movl 100(%%rsp), %%r12d\n" /* r12d = lmask */
-" movl 104(%%rsp), %%r13d\n" /* r13d = dmask */
- /* r14d = len */
- /* r15d = dist */
-" cld\n"
-" cmpq %%rdi, %%r10\n"
-" je .L_one_time\n" /* if only one decode left */
-" cmpq %%rsi, %%r9\n"
-" je .L_one_time\n"
-" jmp .L_do_loop\n"
-
-".L_one_time:\n"
-" movq %%r12, %%r8\n" /* r8 = lmask */
-" cmpb $32, %%bl\n"
-" ja .L_get_length_code_one_time\n"
-
-" lodsl\n" /* eax = *(uint *)in++ */
-" movb %%bl, %%cl\n" /* cl = bits, needs it for shifting */
-" addb $32, %%bl\n" /* bits += 32 */
-" shlq %%cl, %%rax\n"
-" orq %%rax, %%rdx\n" /* hold |= *((uint *)in)++ << bits */
-" jmp .L_get_length_code_one_time\n"
-
-".align 32,0x90\n"
-".L_while_test:\n"
-" cmpq %%rdi, %%r10\n"
-" jbe .L_break_loop\n"
-" cmpq %%rsi, %%r9\n"
-" jbe .L_break_loop\n"
-
-".L_do_loop:\n"
-" movq %%r12, %%r8\n" /* r8 = lmask */
-" cmpb $32, %%bl\n"
-" ja .L_get_length_code\n" /* if (32 < bits) */
-
-" lodsl\n" /* eax = *(uint *)in++ */
-" movb %%bl, %%cl\n" /* cl = bits, needs it for shifting */
-" addb $32, %%bl\n" /* bits += 32 */
-" shlq %%cl, %%rax\n"
-" orq %%rax, %%rdx\n" /* hold |= *((uint *)in)++ << bits */
-
-".L_get_length_code:\n"
-" andq %%rdx, %%r8\n" /* r8 &= hold */
-" movl (%%rbp,%%r8,4), %%eax\n" /* eax = lcode[hold & lmask] */
-
-" movb %%ah, %%cl\n" /* cl = this.bits */
-" subb %%ah, %%bl\n" /* bits -= this.bits */
-" shrq %%cl, %%rdx\n" /* hold >>= this.bits */
-
-" testb %%al, %%al\n"
-" jnz .L_test_for_length_base\n" /* if (op != 0) 45.7% */
-
-" movq %%r12, %%r8\n" /* r8 = lmask */
-" shrl $16, %%eax\n" /* output this.val char */
-" stosb\n"
-
-".L_get_length_code_one_time:\n"
-" andq %%rdx, %%r8\n" /* r8 &= hold */
-" movl (%%rbp,%%r8,4), %%eax\n" /* eax = lcode[hold & lmask] */
-
-".L_dolen:\n"
-" movb %%ah, %%cl\n" /* cl = this.bits */
-" subb %%ah, %%bl\n" /* bits -= this.bits */
-" shrq %%cl, %%rdx\n" /* hold >>= this.bits */
-
-" testb %%al, %%al\n"
-" jnz .L_test_for_length_base\n" /* if (op != 0) 45.7% */
-
-" shrl $16, %%eax\n" /* output this.val char */
-" stosb\n"
-" jmp .L_while_test\n"
-
-".align 32,0x90\n"
-".L_test_for_length_base:\n"
-" movl %%eax, %%r14d\n" /* len = this */
-" shrl $16, %%r14d\n" /* len = this.val */
-" movb %%al, %%cl\n"
-
-" testb $16, %%al\n"
-" jz .L_test_for_second_level_length\n" /* if ((op & 16) == 0) 8% */
-" andb $15, %%cl\n" /* op &= 15 */
-" jz .L_decode_distance\n" /* if (!op) */
-
-".L_add_bits_to_len:\n"
-" subb %%cl, %%bl\n"
-" xorl %%eax, %%eax\n"
-" incl %%eax\n"
-" shll %%cl, %%eax\n"
-" decl %%eax\n"
-" andl %%edx, %%eax\n" /* eax &= hold */
-" shrq %%cl, %%rdx\n"
-" addl %%eax, %%r14d\n" /* len += hold & mask[op] */
-
-".L_decode_distance:\n"
-" movq %%r13, %%r8\n" /* r8 = dmask */
-" cmpb $32, %%bl\n"
-" ja .L_get_distance_code\n" /* if (32 < bits) */
-
-" lodsl\n" /* eax = *(uint *)in++ */
-" movb %%bl, %%cl\n" /* cl = bits, needs it for shifting */
-" addb $32, %%bl\n" /* bits += 32 */
-" shlq %%cl, %%rax\n"
-" orq %%rax, %%rdx\n" /* hold |= *((uint *)in)++ << bits */
-
-".L_get_distance_code:\n"
-" andq %%rdx, %%r8\n" /* r8 &= hold */
-" movl (%%r11,%%r8,4), %%eax\n" /* eax = dcode[hold & dmask] */
-
-".L_dodist:\n"
-" movl %%eax, %%r15d\n" /* dist = this */
-" shrl $16, %%r15d\n" /* dist = this.val */
-" movb %%ah, %%cl\n"
-" subb %%ah, %%bl\n" /* bits -= this.bits */
-" shrq %%cl, %%rdx\n" /* hold >>= this.bits */
-" movb %%al, %%cl\n" /* cl = this.op */
-
-" testb $16, %%al\n" /* if ((op & 16) == 0) */
-" jz .L_test_for_second_level_dist\n"
-" andb $15, %%cl\n" /* op &= 15 */
-" jz .L_check_dist_one\n"
-
-".L_add_bits_to_dist:\n"
-" subb %%cl, %%bl\n"
-" xorl %%eax, %%eax\n"
-" incl %%eax\n"
-" shll %%cl, %%eax\n"
-" decl %%eax\n" /* (1 << op) - 1 */
-" andl %%edx, %%eax\n" /* eax &= hold */
-" shrq %%cl, %%rdx\n"
-" addl %%eax, %%r15d\n" /* dist += hold & ((1 << op) - 1) */
-
-".L_check_window:\n"
-" movq %%rsi, %%r8\n" /* save in so from can use it's reg */
-" movq %%rdi, %%rax\n"
-" subq 40(%%rsp), %%rax\n" /* nbytes = out - beg */
-
-" cmpl %%r15d, %%eax\n"
-" jb .L_clip_window\n" /* if (dist > nbytes) 4.2% */
-
-" movl %%r14d, %%ecx\n" /* ecx = len */
-" movq %%rdi, %%rsi\n"
-" subq %%r15, %%rsi\n" /* from = out - dist */
-
-" sarl %%ecx\n"
-" jnc .L_copy_two\n" /* if len % 2 == 0 */
-
-" rep movsw\n"
-" movb (%%rsi), %%al\n"
-" movb %%al, (%%rdi)\n"
-" incq %%rdi\n"
-
-" movq %%r8, %%rsi\n" /* move in back to %rsi, toss from */
-" jmp .L_while_test\n"
-
-".L_copy_two:\n"
-" rep movsw\n"
-" movq %%r8, %%rsi\n" /* move in back to %rsi, toss from */
-" jmp .L_while_test\n"
-
-".align 32,0x90\n"
-".L_check_dist_one:\n"
-" cmpl $1, %%r15d\n" /* if dist 1, is a memset */
-" jne .L_check_window\n"
-" cmpq %%rdi, 40(%%rsp)\n" /* if out == beg, outside window */
-" je .L_check_window\n"
-
-" movl %%r14d, %%ecx\n" /* ecx = len */
-" movb -1(%%rdi), %%al\n"
-" movb %%al, %%ah\n"
-
-" sarl %%ecx\n"
-" jnc .L_set_two\n"
-" movb %%al, (%%rdi)\n"
-" incq %%rdi\n"
-
-".L_set_two:\n"
-" rep stosw\n"
-" jmp .L_while_test\n"
-
-".align 32,0x90\n"
-".L_test_for_second_level_length:\n"
-" testb $64, %%al\n"
-" jnz .L_test_for_end_of_block\n" /* if ((op & 64) != 0) */
-
-" xorl %%eax, %%eax\n"
-" incl %%eax\n"
-" shll %%cl, %%eax\n"
-" decl %%eax\n"
-" andl %%edx, %%eax\n" /* eax &= hold */
-" addl %%r14d, %%eax\n" /* eax += len */
-" movl (%%rbp,%%rax,4), %%eax\n" /* eax = lcode[val+(hold&mask[op])]*/
-" jmp .L_dolen\n"
-
-".align 32,0x90\n"
-".L_test_for_second_level_dist:\n"
-" testb $64, %%al\n"
-" jnz .L_invalid_distance_code\n" /* if ((op & 64) != 0) */
-
-" xorl %%eax, %%eax\n"
-" incl %%eax\n"
-" shll %%cl, %%eax\n"
-" decl %%eax\n"
-" andl %%edx, %%eax\n" /* eax &= hold */
-" addl %%r15d, %%eax\n" /* eax += dist */
-" movl (%%r11,%%rax,4), %%eax\n" /* eax = dcode[val+(hold&mask[op])]*/
-" jmp .L_dodist\n"
-
-".align 32,0x90\n"
-".L_clip_window:\n"
-" movl %%eax, %%ecx\n" /* ecx = nbytes */
-" movl 92(%%rsp), %%eax\n" /* eax = wsize, prepare for dist cmp */
-" negl %%ecx\n" /* nbytes = -nbytes */
-
-" cmpl %%r15d, %%eax\n"
-" jb .L_invalid_distance_too_far\n" /* if (dist > wsize) */
-
-" addl %%r15d, %%ecx\n" /* nbytes = dist - nbytes */
-" cmpl $0, 96(%%rsp)\n"
-" jne .L_wrap_around_window\n" /* if (write != 0) */
-
-" movq 56(%%rsp), %%rsi\n" /* from = window */
-" subl %%ecx, %%eax\n" /* eax -= nbytes */
-" addq %%rax, %%rsi\n" /* from += wsize - nbytes */
-
-" movl %%r14d, %%eax\n" /* eax = len */
-" cmpl %%ecx, %%r14d\n"
-" jbe .L_do_copy\n" /* if (nbytes >= len) */
-
-" subl %%ecx, %%eax\n" /* eax -= nbytes */
-" rep movsb\n"
-" movq %%rdi, %%rsi\n"
-" subq %%r15, %%rsi\n" /* from = &out[ -dist ] */
-" jmp .L_do_copy\n"
-
-".align 32,0x90\n"
-".L_wrap_around_window:\n"
-" movl 96(%%rsp), %%eax\n" /* eax = write */
-" cmpl %%eax, %%ecx\n"
-" jbe .L_contiguous_in_window\n" /* if (write >= nbytes) */
-
-" movl 92(%%rsp), %%esi\n" /* from = wsize */
-" addq 56(%%rsp), %%rsi\n" /* from += window */
-" addq %%rax, %%rsi\n" /* from += write */
-" subq %%rcx, %%rsi\n" /* from -= nbytes */
-" subl %%eax, %%ecx\n" /* nbytes -= write */
-
-" movl %%r14d, %%eax\n" /* eax = len */
-" cmpl %%ecx, %%eax\n"
-" jbe .L_do_copy\n" /* if (nbytes >= len) */
-
-" subl %%ecx, %%eax\n" /* len -= nbytes */
-" rep movsb\n"
-" movq 56(%%rsp), %%rsi\n" /* from = window */
-" movl 96(%%rsp), %%ecx\n" /* nbytes = write */
-" cmpl %%ecx, %%eax\n"
-" jbe .L_do_copy\n" /* if (nbytes >= len) */
-
-" subl %%ecx, %%eax\n" /* len -= nbytes */
-" rep movsb\n"
-" movq %%rdi, %%rsi\n"
-" subq %%r15, %%rsi\n" /* from = out - dist */
-" jmp .L_do_copy\n"
-
-".align 32,0x90\n"
-".L_contiguous_in_window:\n"
-" movq 56(%%rsp), %%rsi\n" /* rsi = window */
-" addq %%rax, %%rsi\n"
-" subq %%rcx, %%rsi\n" /* from += write - nbytes */
-
-" movl %%r14d, %%eax\n" /* eax = len */
-" cmpl %%ecx, %%eax\n"
-" jbe .L_do_copy\n" /* if (nbytes >= len) */
-
-" subl %%ecx, %%eax\n" /* len -= nbytes */
-" rep movsb\n"
-" movq %%rdi, %%rsi\n"
-" subq %%r15, %%rsi\n" /* from = out - dist */
-" jmp .L_do_copy\n" /* if (nbytes >= len) */
-
-".align 32,0x90\n"
-".L_do_copy:\n"
-" movl %%eax, %%ecx\n" /* ecx = len */
-" rep movsb\n"
-
-" movq %%r8, %%rsi\n" /* move in back to %esi, toss from */
-" jmp .L_while_test\n"
-
-".L_test_for_end_of_block:\n"
-" testb $32, %%al\n"
-" jz .L_invalid_literal_length_code\n"
-" movl $1, 116(%%rsp)\n"
-" jmp .L_break_loop_with_status\n"
-
-".L_invalid_literal_length_code:\n"
-" movl $2, 116(%%rsp)\n"
-" jmp .L_break_loop_with_status\n"
-
-".L_invalid_distance_code:\n"
-" movl $3, 116(%%rsp)\n"
-" jmp .L_break_loop_with_status\n"
-
-".L_invalid_distance_too_far:\n"
-" movl $4, 116(%%rsp)\n"
-" jmp .L_break_loop_with_status\n"
-
-".L_break_loop:\n"
-" movl $0, 116(%%rsp)\n"
-
-".L_break_loop_with_status:\n"
-/* put in, out, bits, and hold back into ar and pop esp */
-" movq %%rsi, 16(%%rsp)\n" /* in */
-" movq %%rdi, 32(%%rsp)\n" /* out */
-" movl %%ebx, 88(%%rsp)\n" /* bits */
-" movq %%rdx, 80(%%rsp)\n" /* hold */
-" movq (%%rsp), %%rax\n" /* restore rbp and rsp */
-" movq 8(%%rsp), %%rbp\n"
-" movq %%rax, %%rsp\n"
- :
- : "m" (ar)
- : "memory", "%rax", "%rbx", "%rcx", "%rdx", "%rsi", "%rdi",
- "%r8", "%r9", "%r10", "%r11", "%r12", "%r13", "%r14", "%r15"
- );
-#elif ( defined( __GNUC__ ) || defined( __ICC ) ) && defined( __i386 )
- __asm__ __volatile__ (
-" leal %0, %%eax\n"
-" movl %%esp, (%%eax)\n" /* save esp, ebp */
-" movl %%ebp, 4(%%eax)\n"
-" movl %%eax, %%esp\n"
-" movl 8(%%esp), %%esi\n" /* esi = in */
-" movl 16(%%esp), %%edi\n" /* edi = out */
-" movl 40(%%esp), %%edx\n" /* edx = hold */
-" movl 44(%%esp), %%ebx\n" /* ebx = bits */
-" movl 32(%%esp), %%ebp\n" /* ebp = lcode */
-
-" cld\n"
-" jmp .L_do_loop\n"
-
-".align 32,0x90\n"
-".L_while_test:\n"
-" cmpl %%edi, 24(%%esp)\n" /* out < end */
-" jbe .L_break_loop\n"
-" cmpl %%esi, 12(%%esp)\n" /* in < last */
-" jbe .L_break_loop\n"
-
-".L_do_loop:\n"
-" cmpb $15, %%bl\n"
-" ja .L_get_length_code\n" /* if (15 < bits) */
-
-" xorl %%eax, %%eax\n"
-" lodsw\n" /* al = *(ushort *)in++ */
-" movb %%bl, %%cl\n" /* cl = bits, needs it for shifting */
-" addb $16, %%bl\n" /* bits += 16 */
-" shll %%cl, %%eax\n"
-" orl %%eax, %%edx\n" /* hold |= *((ushort *)in)++ << bits */
-
-".L_get_length_code:\n"
-" movl 56(%%esp), %%eax\n" /* eax = lmask */
-" andl %%edx, %%eax\n" /* eax &= hold */
-" movl (%%ebp,%%eax,4), %%eax\n" /* eax = lcode[hold & lmask] */
-
-".L_dolen:\n"
-" movb %%ah, %%cl\n" /* cl = this.bits */
-" subb %%ah, %%bl\n" /* bits -= this.bits */
-" shrl %%cl, %%edx\n" /* hold >>= this.bits */
-
-" testb %%al, %%al\n"
-" jnz .L_test_for_length_base\n" /* if (op != 0) 45.7% */
-
-" shrl $16, %%eax\n" /* output this.val char */
-" stosb\n"
-" jmp .L_while_test\n"
-
-".align 32,0x90\n"
-".L_test_for_length_base:\n"
-" movl %%eax, %%ecx\n" /* len = this */
-" shrl $16, %%ecx\n" /* len = this.val */
-" movl %%ecx, 64(%%esp)\n" /* save len */
-" movb %%al, %%cl\n"
-
-" testb $16, %%al\n"
-" jz .L_test_for_second_level_length\n" /* if ((op & 16) == 0) 8% */
-" andb $15, %%cl\n" /* op &= 15 */
-" jz .L_decode_distance\n" /* if (!op) */
-" cmpb %%cl, %%bl\n"
-" jae .L_add_bits_to_len\n" /* if (op <= bits) */
-
-" movb %%cl, %%ch\n" /* stash op in ch, freeing cl */
-" xorl %%eax, %%eax\n"
-" lodsw\n" /* al = *(ushort *)in++ */
-" movb %%bl, %%cl\n" /* cl = bits, needs it for shifting */
-" addb $16, %%bl\n" /* bits += 16 */
-" shll %%cl, %%eax\n"
-" orl %%eax, %%edx\n" /* hold |= *((ushort *)in)++ << bits */
-" movb %%ch, %%cl\n" /* move op back to ecx */
-
-".L_add_bits_to_len:\n"
-" subb %%cl, %%bl\n"
-" xorl %%eax, %%eax\n"
-" incl %%eax\n"
-" shll %%cl, %%eax\n"
-" decl %%eax\n"
-" andl %%edx, %%eax\n" /* eax &= hold */
-" shrl %%cl, %%edx\n"
-" addl %%eax, 64(%%esp)\n" /* len += hold & mask[op] */
-
-".L_decode_distance:\n"
-" cmpb $15, %%bl\n"
-" ja .L_get_distance_code\n" /* if (15 < bits) */
-
-" xorl %%eax, %%eax\n"
-" lodsw\n" /* al = *(ushort *)in++ */
-" movb %%bl, %%cl\n" /* cl = bits, needs it for shifting */
-" addb $16, %%bl\n" /* bits += 16 */
-" shll %%cl, %%eax\n"
-" orl %%eax, %%edx\n" /* hold |= *((ushort *)in)++ << bits */
-
-".L_get_distance_code:\n"
-" movl 60(%%esp), %%eax\n" /* eax = dmask */
-" movl 36(%%esp), %%ecx\n" /* ecx = dcode */
-" andl %%edx, %%eax\n" /* eax &= hold */
-" movl (%%ecx,%%eax,4), %%eax\n"/* eax = dcode[hold & dmask] */
-
-".L_dodist:\n"
-" movl %%eax, %%ebp\n" /* dist = this */
-" shrl $16, %%ebp\n" /* dist = this.val */
-" movb %%ah, %%cl\n"
-" subb %%ah, %%bl\n" /* bits -= this.bits */
-" shrl %%cl, %%edx\n" /* hold >>= this.bits */
-" movb %%al, %%cl\n" /* cl = this.op */
-
-" testb $16, %%al\n" /* if ((op & 16) == 0) */
-" jz .L_test_for_second_level_dist\n"
-" andb $15, %%cl\n" /* op &= 15 */
-" jz .L_check_dist_one\n"
-" cmpb %%cl, %%bl\n"
-" jae .L_add_bits_to_dist\n" /* if (op <= bits) 97.6% */
-
-" movb %%cl, %%ch\n" /* stash op in ch, freeing cl */
-" xorl %%eax, %%eax\n"
-" lodsw\n" /* al = *(ushort *)in++ */
-" movb %%bl, %%cl\n" /* cl = bits, needs it for shifting */
-" addb $16, %%bl\n" /* bits += 16 */
-" shll %%cl, %%eax\n"
-" orl %%eax, %%edx\n" /* hold |= *((ushort *)in)++ << bits */
-" movb %%ch, %%cl\n" /* move op back to ecx */
-
-".L_add_bits_to_dist:\n"
-" subb %%cl, %%bl\n"
-" xorl %%eax, %%eax\n"
-" incl %%eax\n"
-" shll %%cl, %%eax\n"
-" decl %%eax\n" /* (1 << op) - 1 */
-" andl %%edx, %%eax\n" /* eax &= hold */
-" shrl %%cl, %%edx\n"
-" addl %%eax, %%ebp\n" /* dist += hold & ((1 << op) - 1) */
-
-".L_check_window:\n"
-" movl %%esi, 8(%%esp)\n" /* save in so from can use it's reg */
-" movl %%edi, %%eax\n"
-" subl 20(%%esp), %%eax\n" /* nbytes = out - beg */
-
-" cmpl %%ebp, %%eax\n"
-" jb .L_clip_window\n" /* if (dist > nbytes) 4.2% */
-
-" movl 64(%%esp), %%ecx\n" /* ecx = len */
-" movl %%edi, %%esi\n"
-" subl %%ebp, %%esi\n" /* from = out - dist */
-
-" sarl %%ecx\n"
-" jnc .L_copy_two\n" /* if len % 2 == 0 */
-
-" rep movsw\n"
-" movb (%%esi), %%al\n"
-" movb %%al, (%%edi)\n"
-" incl %%edi\n"
-
-" movl 8(%%esp), %%esi\n" /* move in back to %esi, toss from */
-" movl 32(%%esp), %%ebp\n" /* ebp = lcode */
-" jmp .L_while_test\n"
-
-".L_copy_two:\n"
-" rep movsw\n"
-" movl 8(%%esp), %%esi\n" /* move in back to %esi, toss from */
-" movl 32(%%esp), %%ebp\n" /* ebp = lcode */
-" jmp .L_while_test\n"
-
-".align 32,0x90\n"
-".L_check_dist_one:\n"
-" cmpl $1, %%ebp\n" /* if dist 1, is a memset */
-" jne .L_check_window\n"
-" cmpl %%edi, 20(%%esp)\n"
-" je .L_check_window\n" /* out == beg, if outside window */
-
-" movl 64(%%esp), %%ecx\n" /* ecx = len */
-" movb -1(%%edi), %%al\n"
-" movb %%al, %%ah\n"
-
-" sarl %%ecx\n"
-" jnc .L_set_two\n"
-" movb %%al, (%%edi)\n"
-" incl %%edi\n"
-
-".L_set_two:\n"
-" rep stosw\n"
-" movl 32(%%esp), %%ebp\n" /* ebp = lcode */
-" jmp .L_while_test\n"
-
-".align 32,0x90\n"
-".L_test_for_second_level_length:\n"
-" testb $64, %%al\n"
-" jnz .L_test_for_end_of_block\n" /* if ((op & 64) != 0) */
-
-" xorl %%eax, %%eax\n"
-" incl %%eax\n"
-" shll %%cl, %%eax\n"
-" decl %%eax\n"
-" andl %%edx, %%eax\n" /* eax &= hold */
-" addl 64(%%esp), %%eax\n" /* eax += len */
-" movl (%%ebp,%%eax,4), %%eax\n" /* eax = lcode[val+(hold&mask[op])]*/
-" jmp .L_dolen\n"
-
-".align 32,0x90\n"
-".L_test_for_second_level_dist:\n"
-" testb $64, %%al\n"
-" jnz .L_invalid_distance_code\n" /* if ((op & 64) != 0) */
-
-" xorl %%eax, %%eax\n"
-" incl %%eax\n"
-" shll %%cl, %%eax\n"
-" decl %%eax\n"
-" andl %%edx, %%eax\n" /* eax &= hold */
-" addl %%ebp, %%eax\n" /* eax += dist */
-" movl 36(%%esp), %%ecx\n" /* ecx = dcode */
-" movl (%%ecx,%%eax,4), %%eax\n" /* eax = dcode[val+(hold&mask[op])]*/
-" jmp .L_dodist\n"
-
-".align 32,0x90\n"
-".L_clip_window:\n"
-" movl %%eax, %%ecx\n"
-" movl 48(%%esp), %%eax\n" /* eax = wsize */
-" negl %%ecx\n" /* nbytes = -nbytes */
-" movl 28(%%esp), %%esi\n" /* from = window */
-
-" cmpl %%ebp, %%eax\n"
-" jb .L_invalid_distance_too_far\n" /* if (dist > wsize) */
-
-" addl %%ebp, %%ecx\n" /* nbytes = dist - nbytes */
-" cmpl $0, 52(%%esp)\n"
-" jne .L_wrap_around_window\n" /* if (write != 0) */
-
-" subl %%ecx, %%eax\n"
-" addl %%eax, %%esi\n" /* from += wsize - nbytes */
-
-" movl 64(%%esp), %%eax\n" /* eax = len */
-" cmpl %%ecx, %%eax\n"
-" jbe .L_do_copy\n" /* if (nbytes >= len) */
-
-" subl %%ecx, %%eax\n" /* len -= nbytes */
-" rep movsb\n"
-" movl %%edi, %%esi\n"
-" subl %%ebp, %%esi\n" /* from = out - dist */
-" jmp .L_do_copy\n"
-
-".align 32,0x90\n"
-".L_wrap_around_window:\n"
-" movl 52(%%esp), %%eax\n" /* eax = write */
-" cmpl %%eax, %%ecx\n"
-" jbe .L_contiguous_in_window\n" /* if (write >= nbytes) */
-
-" addl 48(%%esp), %%esi\n" /* from += wsize */
-" addl %%eax, %%esi\n" /* from += write */
-" subl %%ecx, %%esi\n" /* from -= nbytes */
-" subl %%eax, %%ecx\n" /* nbytes -= write */
-
-" movl 64(%%esp), %%eax\n" /* eax = len */
-" cmpl %%ecx, %%eax\n"
-" jbe .L_do_copy\n" /* if (nbytes >= len) */
-
-" subl %%ecx, %%eax\n" /* len -= nbytes */
-" rep movsb\n"
-" movl 28(%%esp), %%esi\n" /* from = window */
-" movl 52(%%esp), %%ecx\n" /* nbytes = write */
-" cmpl %%ecx, %%eax\n"
-" jbe .L_do_copy\n" /* if (nbytes >= len) */
-
-" subl %%ecx, %%eax\n" /* len -= nbytes */
-" rep movsb\n"
-" movl %%edi, %%esi\n"
-" subl %%ebp, %%esi\n" /* from = out - dist */
-" jmp .L_do_copy\n"
-
-".align 32,0x90\n"
-".L_contiguous_in_window:\n"
-" addl %%eax, %%esi\n"
-" subl %%ecx, %%esi\n" /* from += write - nbytes */
-
-" movl 64(%%esp), %%eax\n" /* eax = len */
-" cmpl %%ecx, %%eax\n"
-" jbe .L_do_copy\n" /* if (nbytes >= len) */
-
-" subl %%ecx, %%eax\n" /* len -= nbytes */
-" rep movsb\n"
-" movl %%edi, %%esi\n"
-" subl %%ebp, %%esi\n" /* from = out - dist */
-" jmp .L_do_copy\n" /* if (nbytes >= len) */
-
-".align 32,0x90\n"
-".L_do_copy:\n"
-" movl %%eax, %%ecx\n"
-" rep movsb\n"
-
-" movl 8(%%esp), %%esi\n" /* move in back to %esi, toss from */
-" movl 32(%%esp), %%ebp\n" /* ebp = lcode */
-" jmp .L_while_test\n"
-
-".L_test_for_end_of_block:\n"
-" testb $32, %%al\n"
-" jz .L_invalid_literal_length_code\n"
-" movl $1, 72(%%esp)\n"
-" jmp .L_break_loop_with_status\n"
-
-".L_invalid_literal_length_code:\n"
-" movl $2, 72(%%esp)\n"
-" jmp .L_break_loop_with_status\n"
-
-".L_invalid_distance_code:\n"
-" movl $3, 72(%%esp)\n"
-" jmp .L_break_loop_with_status\n"
-
-".L_invalid_distance_too_far:\n"
-" movl 8(%%esp), %%esi\n"
-" movl $4, 72(%%esp)\n"
-" jmp .L_break_loop_with_status\n"
-
-".L_break_loop:\n"
-" movl $0, 72(%%esp)\n"
-
-".L_break_loop_with_status:\n"
-/* put in, out, bits, and hold back into ar and pop esp */
-" movl %%esi, 8(%%esp)\n" /* save in */
-" movl %%edi, 16(%%esp)\n" /* save out */
-" movl %%ebx, 44(%%esp)\n" /* save bits */
-" movl %%edx, 40(%%esp)\n" /* save hold */
-" movl 4(%%esp), %%ebp\n" /* restore esp, ebp */
-" movl (%%esp), %%esp\n"
- :
- : "m" (ar)
- : "memory", "%eax", "%ebx", "%ecx", "%edx", "%esi", "%edi"
- );
-#elif defined( _MSC_VER ) && ! defined( _M_AMD64 )
- __asm {
- lea eax, ar
- mov [eax], esp /* save esp, ebp */
- mov [eax+4], ebp
- mov esp, eax
- mov esi, [esp+8] /* esi = in */
- mov edi, [esp+16] /* edi = out */
- mov edx, [esp+40] /* edx = hold */
- mov ebx, [esp+44] /* ebx = bits */
- mov ebp, [esp+32] /* ebp = lcode */
-
- cld
- jmp L_do_loop
-
-ALIGN 4
-L_while_test:
- cmp [esp+24], edi
- jbe L_break_loop
- cmp [esp+12], esi
- jbe L_break_loop
-
-L_do_loop:
- cmp bl, 15
- ja L_get_length_code /* if (15 < bits) */
-
- xor eax, eax
- lodsw /* al = *(ushort *)in++ */
- mov cl, bl /* cl = bits, needs it for shifting */
- add bl, 16 /* bits += 16 */
- shl eax, cl
- or edx, eax /* hold |= *((ushort *)in)++ << bits */
-
-L_get_length_code:
- mov eax, [esp+56] /* eax = lmask */
- and eax, edx /* eax &= hold */
- mov eax, [ebp+eax*4] /* eax = lcode[hold & lmask] */
-
-L_dolen:
- mov cl, ah /* cl = this.bits */
- sub bl, ah /* bits -= this.bits */
- shr edx, cl /* hold >>= this.bits */
-
- test al, al
- jnz L_test_for_length_base /* if (op != 0) 45.7% */
-
- shr eax, 16 /* output this.val char */
- stosb
- jmp L_while_test
-
-ALIGN 4
-L_test_for_length_base:
- mov ecx, eax /* len = this */
- shr ecx, 16 /* len = this.val */
- mov [esp+64], ecx /* save len */
- mov cl, al
-
- test al, 16
- jz L_test_for_second_level_length /* if ((op & 16) == 0) 8% */
- and cl, 15 /* op &= 15 */
- jz L_decode_distance /* if (!op) */
- cmp bl, cl
- jae L_add_bits_to_len /* if (op <= bits) */
-
- mov ch, cl /* stash op in ch, freeing cl */
- xor eax, eax
- lodsw /* al = *(ushort *)in++ */
- mov cl, bl /* cl = bits, needs it for shifting */
- add bl, 16 /* bits += 16 */
- shl eax, cl
- or edx, eax /* hold |= *((ushort *)in)++ << bits */
- mov cl, ch /* move op back to ecx */
-
-L_add_bits_to_len:
- sub bl, cl
- xor eax, eax
- inc eax
- shl eax, cl
- dec eax
- and eax, edx /* eax &= hold */
- shr edx, cl
- add [esp+64], eax /* len += hold & mask[op] */
-
-L_decode_distance:
- cmp bl, 15
- ja L_get_distance_code /* if (15 < bits) */
-
- xor eax, eax
- lodsw /* al = *(ushort *)in++ */
- mov cl, bl /* cl = bits, needs it for shifting */
- add bl, 16 /* bits += 16 */
- shl eax, cl
- or edx, eax /* hold |= *((ushort *)in)++ << bits */
-
-L_get_distance_code:
- mov eax, [esp+60] /* eax = dmask */
- mov ecx, [esp+36] /* ecx = dcode */
- and eax, edx /* eax &= hold */
- mov eax, [ecx+eax*4]/* eax = dcode[hold & dmask] */
-
-L_dodist:
- mov ebp, eax /* dist = this */
- shr ebp, 16 /* dist = this.val */
- mov cl, ah
- sub bl, ah /* bits -= this.bits */
- shr edx, cl /* hold >>= this.bits */
- mov cl, al /* cl = this.op */
-
- test al, 16 /* if ((op & 16) == 0) */
- jz L_test_for_second_level_dist
- and cl, 15 /* op &= 15 */
- jz L_check_dist_one
- cmp bl, cl
- jae L_add_bits_to_dist /* if (op <= bits) 97.6% */
-
- mov ch, cl /* stash op in ch, freeing cl */
- xor eax, eax
- lodsw /* al = *(ushort *)in++ */
- mov cl, bl /* cl = bits, needs it for shifting */
- add bl, 16 /* bits += 16 */
- shl eax, cl
- or edx, eax /* hold |= *((ushort *)in)++ << bits */
- mov cl, ch /* move op back to ecx */
-
-L_add_bits_to_dist:
- sub bl, cl
- xor eax, eax
- inc eax
- shl eax, cl
- dec eax /* (1 << op) - 1 */
- and eax, edx /* eax &= hold */
- shr edx, cl
- add ebp, eax /* dist += hold & ((1 << op) - 1) */
-
-L_check_window:
- mov [esp+8], esi /* save in so from can use it's reg */
- mov eax, edi
- sub eax, [esp+20] /* nbytes = out - beg */
-
- cmp eax, ebp
- jb L_clip_window /* if (dist > nbytes) 4.2% */
-
- mov ecx, [esp+64] /* ecx = len */
- mov esi, edi
- sub esi, ebp /* from = out - dist */
-
- sar ecx, 1
- jnc L_copy_two
-
- rep movsw
- mov al, [esi]
- mov [edi], al
- inc edi
-
- mov esi, [esp+8] /* move in back to %esi, toss from */
- mov ebp, [esp+32] /* ebp = lcode */
- jmp L_while_test
-
-L_copy_two:
- rep movsw
- mov esi, [esp+8] /* move in back to %esi, toss from */
- mov ebp, [esp+32] /* ebp = lcode */
- jmp L_while_test
-
-ALIGN 4
-L_check_dist_one:
- cmp ebp, 1 /* if dist 1, is a memset */
- jne L_check_window
- cmp [esp+20], edi
- je L_check_window /* out == beg, if outside window */
-
- mov ecx, [esp+64] /* ecx = len */
- mov al, [edi-1]
- mov ah, al
-
- sar ecx, 1
- jnc L_set_two
- mov [edi], al /* memset out with from[-1] */
- inc edi
-
-L_set_two:
- rep stosw
- mov ebp, [esp+32] /* ebp = lcode */
- jmp L_while_test
-
-ALIGN 4
-L_test_for_second_level_length:
- test al, 64
- jnz L_test_for_end_of_block /* if ((op & 64) != 0) */
-
- xor eax, eax
- inc eax
- shl eax, cl
- dec eax
- and eax, edx /* eax &= hold */
- add eax, [esp+64] /* eax += len */
- mov eax, [ebp+eax*4] /* eax = lcode[val+(hold&mask[op])]*/
- jmp L_dolen
-
-ALIGN 4
-L_test_for_second_level_dist:
- test al, 64
- jnz L_invalid_distance_code /* if ((op & 64) != 0) */
-
- xor eax, eax
- inc eax
- shl eax, cl
- dec eax
- and eax, edx /* eax &= hold */
- add eax, ebp /* eax += dist */
- mov ecx, [esp+36] /* ecx = dcode */
- mov eax, [ecx+eax*4] /* eax = dcode[val+(hold&mask[op])]*/
- jmp L_dodist
-
-ALIGN 4
-L_clip_window:
- mov ecx, eax
- mov eax, [esp+48] /* eax = wsize */
- neg ecx /* nbytes = -nbytes */
- mov esi, [esp+28] /* from = window */
-
- cmp eax, ebp
- jb L_invalid_distance_too_far /* if (dist > wsize) */
-
- add ecx, ebp /* nbytes = dist - nbytes */
- cmp dword ptr [esp+52], 0
- jne L_wrap_around_window /* if (write != 0) */
-
- sub eax, ecx
- add esi, eax /* from += wsize - nbytes */
-
- mov eax, [esp+64] /* eax = len */
- cmp eax, ecx
- jbe L_do_copy /* if (nbytes >= len) */
-
- sub eax, ecx /* len -= nbytes */
- rep movsb
- mov esi, edi
- sub esi, ebp /* from = out - dist */
- jmp L_do_copy
-
-ALIGN 4
-L_wrap_around_window:
- mov eax, [esp+52] /* eax = write */
- cmp ecx, eax
- jbe L_contiguous_in_window /* if (write >= nbytes) */
-
- add esi, [esp+48] /* from += wsize */
- add esi, eax /* from += write */
- sub esi, ecx /* from -= nbytes */
- sub ecx, eax /* nbytes -= write */
-
- mov eax, [esp+64] /* eax = len */
- cmp eax, ecx
- jbe L_do_copy /* if (nbytes >= len) */
-
- sub eax, ecx /* len -= nbytes */
- rep movsb
- mov esi, [esp+28] /* from = window */
- mov ecx, [esp+52] /* nbytes = write */
- cmp eax, ecx
- jbe L_do_copy /* if (nbytes >= len) */
-
- sub eax, ecx /* len -= nbytes */
- rep movsb
- mov esi, edi
- sub esi, ebp /* from = out - dist */
- jmp L_do_copy
-
-ALIGN 4
-L_contiguous_in_window:
- add esi, eax
- sub esi, ecx /* from += write - nbytes */
-
- mov eax, [esp+64] /* eax = len */
- cmp eax, ecx
- jbe L_do_copy /* if (nbytes >= len) */
-
- sub eax, ecx /* len -= nbytes */
- rep movsb
- mov esi, edi
- sub esi, ebp /* from = out - dist */
- jmp L_do_copy
-
-ALIGN 4
-L_do_copy:
- mov ecx, eax
- rep movsb
-
- mov esi, [esp+8] /* move in back to %esi, toss from */
- mov ebp, [esp+32] /* ebp = lcode */
- jmp L_while_test
-
-L_test_for_end_of_block:
- test al, 32
- jz L_invalid_literal_length_code
- mov dword ptr [esp+72], 1
- jmp L_break_loop_with_status
-
-L_invalid_literal_length_code:
- mov dword ptr [esp+72], 2
- jmp L_break_loop_with_status
-
-L_invalid_distance_code:
- mov dword ptr [esp+72], 3
- jmp L_break_loop_with_status
-
-L_invalid_distance_too_far:
- mov esi, [esp+4]
- mov dword ptr [esp+72], 4
- jmp L_break_loop_with_status
-
-L_break_loop:
- mov dword ptr [esp+72], 0
-
-L_break_loop_with_status:
-/* put in, out, bits, and hold back into ar and pop esp */
- mov [esp+8], esi /* save in */
- mov [esp+16], edi /* save out */
- mov [esp+44], ebx /* save bits */
- mov [esp+40], edx /* save hold */
- mov ebp, [esp+4] /* restore esp, ebp */
- mov esp, [esp]
- }
-#else
-#error "x86 architecture not defined"
-#endif
-
- if (ar.status > 1) {
- if (ar.status == 2)
- strm->msg = "invalid literal/length code";
- else if (ar.status == 3)
- strm->msg = "invalid distance code";
- else
- strm->msg = "invalid distance too far back";
- state->mode = BAD;
- }
- else if ( ar.status == 1 ) {
- state->mode = TYPE;
- }
-
- /* return unused bytes (on entry, bits < 8, so in won't go too far back) */
- ar.len = ar.bits >> 3;
- ar.in -= ar.len;
- ar.bits -= ar.len << 3;
- ar.hold &= (1U << ar.bits) - 1;
-
- /* update state and return */
- strm->next_in = ar.in;
- strm->next_out = ar.out;
- strm->avail_in = (unsigned)(ar.in < ar.last ?
- PAD_AVAIL_IN + (ar.last - ar.in) :
- PAD_AVAIL_IN - (ar.in - ar.last));
- strm->avail_out = (unsigned)(ar.out < ar.end ?
- PAD_AVAIL_OUT + (ar.end - ar.out) :
- PAD_AVAIL_OUT - (ar.out - ar.end));
- state->hold = ar.hold;
- state->bits = ar.bits;
- return;
-}
-
diff --git a/third-party/zlib/contrib/inflate86/inffast.S b/third-party/zlib/contrib/inflate86/inffast.S
deleted file mode 100644
index 2245a29..0000000
--- a/third-party/zlib/contrib/inflate86/inffast.S
+++ /dev/null
@@ -1,1368 +0,0 @@
-/*
- * inffast.S is a hand tuned assembler version of:
- *
- * inffast.c -- fast decoding
- * Copyright (C) 1995-2003 Mark Adler
- * For conditions of distribution and use, see copyright notice in zlib.h
- *
- * Copyright (C) 2003 Chris Anderson <christop at charm.net>
- * Please use the copyright conditions above.
- *
- * This version (Jan-23-2003) of inflate_fast was coded and tested under
- * GNU/Linux on a pentium 3, using the gcc-3.2 compiler distribution. On that
- * machine, I found that gzip style archives decompressed about 20% faster than
- * the gcc-3.2 -O3 -fomit-frame-pointer compiled version. Your results will
- * depend on how large of a buffer is used for z_stream.next_in & next_out
- * (8K-32K worked best for my 256K cpu cache) and how much overhead there is in
- * stream processing I/O and crc32/addler32. In my case, this routine used
- * 70% of the cpu time and crc32 used 20%.
- *
- * I am confident that this version will work in the general case, but I have
- * not tested a wide variety of datasets or a wide variety of platforms.
- *
- * Jan-24-2003 -- Added -DUSE_MMX define for slightly faster inflating.
- * It should be a runtime flag instead of compile time flag...
- *
- * Jan-26-2003 -- Added runtime check for MMX support with cpuid instruction.
- * With -DUSE_MMX, only MMX code is compiled. With -DNO_MMX, only non-MMX code
- * is compiled. Without either option, runtime detection is enabled. Runtime
- * detection should work on all modern cpus and the recomended algorithm (flip
- * ID bit on eflags and then use the cpuid instruction) is used in many
- * multimedia applications. Tested under win2k with gcc-2.95 and gas-2.12
- * distributed with cygwin3. Compiling with gcc-2.95 -c inffast.S -o
- * inffast.obj generates a COFF object which can then be linked with MSVC++
- * compiled code. Tested under FreeBSD 4.7 with gcc-2.95.
- *
- * Jan-28-2003 -- Tested Athlon XP... MMX mode is slower than no MMX (and
- * slower than compiler generated code). Adjusted cpuid check to use the MMX
- * code only for Pentiums < P4 until I have more data on the P4. Speed
- * improvment is only about 15% on the Athlon when compared with code generated
- * with MSVC++. Not sure yet, but I think the P4 will also be slower using the
- * MMX mode because many of it's x86 ALU instructions execute in .5 cycles and
- * have less latency than MMX ops. Added code to buffer the last 11 bytes of
- * the input stream since the MMX code grabs bits in chunks of 32, which
- * differs from the inffast.c algorithm. I don't think there would have been
- * read overruns where a page boundary was crossed (a segfault), but there
- * could have been overruns when next_in ends on unaligned memory (unintialized
- * memory read).
- *
- * Mar-13-2003 -- P4 MMX is slightly slower than P4 NO_MMX. I created a C
- * version of the non-MMX code so that it doesn't depend on zstrm and zstate
- * structure offsets which are hard coded in this file. This was last tested
- * with zlib-1.2.0 which is currently in beta testing, newer versions of this
- * and inffas86.c can be found at http://www.eetbeetee.com/zlib/ and
- * http://www.charm.net/~christop/zlib/
- */
-
-
-/*
- * if you have underscore linking problems (_inflate_fast undefined), try
- * using -DGAS_COFF
- */
-#if ! defined( GAS_COFF ) && ! defined( GAS_ELF )
-
-#if defined( WIN32 ) || defined( __CYGWIN__ )
-#define GAS_COFF /* windows object format */
-#else
-#define GAS_ELF
-#endif
-
-#endif /* ! GAS_COFF && ! GAS_ELF */
-
-
-#if defined( GAS_COFF )
-
-/* coff externals have underscores */
-#define inflate_fast _inflate_fast
-#define inflate_fast_use_mmx _inflate_fast_use_mmx
-
-#endif /* GAS_COFF */
-
-
-.file "inffast.S"
-
-.globl inflate_fast
-
-.text
-.align 4,0
-.L_invalid_literal_length_code_msg:
-.string "invalid literal/length code"
-
-.align 4,0
-.L_invalid_distance_code_msg:
-.string "invalid distance code"
-
-.align 4,0
-.L_invalid_distance_too_far_msg:
-.string "invalid distance too far back"
-
-#if ! defined( NO_MMX )
-.align 4,0
-.L_mask: /* mask[N] = ( 1 << N ) - 1 */
-.long 0
-.long 1
-.long 3
-.long 7
-.long 15
-.long 31
-.long 63
-.long 127
-.long 255
-.long 511
-.long 1023
-.long 2047
-.long 4095
-.long 8191
-.long 16383
-.long 32767
-.long 65535
-.long 131071
-.long 262143
-.long 524287
-.long 1048575
-.long 2097151
-.long 4194303
-.long 8388607
-.long 16777215
-.long 33554431
-.long 67108863
-.long 134217727
-.long 268435455
-.long 536870911
-.long 1073741823
-.long 2147483647
-.long 4294967295
-#endif /* NO_MMX */
-
-.text
-
-/*
- * struct z_stream offsets, in zlib.h
- */
-#define next_in_strm 0 /* strm->next_in */
-#define avail_in_strm 4 /* strm->avail_in */
-#define next_out_strm 12 /* strm->next_out */
-#define avail_out_strm 16 /* strm->avail_out */
-#define msg_strm 24 /* strm->msg */
-#define state_strm 28 /* strm->state */
-
-/*
- * struct inflate_state offsets, in inflate.h
- */
-#define mode_state 0 /* state->mode */
-#define wsize_state 32 /* state->wsize */
-#define write_state 40 /* state->write */
-#define window_state 44 /* state->window */
-#define hold_state 48 /* state->hold */
-#define bits_state 52 /* state->bits */
-#define lencode_state 68 /* state->lencode */
-#define distcode_state 72 /* state->distcode */
-#define lenbits_state 76 /* state->lenbits */
-#define distbits_state 80 /* state->distbits */
-
-/*
- * inflate_fast's activation record
- */
-#define local_var_size 64 /* how much local space for vars */
-#define strm_sp 88 /* first arg: z_stream * (local_var_size + 24) */
-#define start_sp 92 /* second arg: unsigned int (local_var_size + 28) */
-
-/*
- * offsets for local vars on stack
- */
-#define out 60 /* unsigned char* */
-#define window 56 /* unsigned char* */
-#define wsize 52 /* unsigned int */
-#define write 48 /* unsigned int */
-#define in 44 /* unsigned char* */
-#define beg 40 /* unsigned char* */
-#define buf 28 /* char[ 12 ] */
-#define len 24 /* unsigned int */
-#define last 20 /* unsigned char* */
-#define end 16 /* unsigned char* */
-#define dcode 12 /* code* */
-#define lcode 8 /* code* */
-#define dmask 4 /* unsigned int */
-#define lmask 0 /* unsigned int */
-
-/*
- * typedef enum inflate_mode consts, in inflate.h
- */
-#define INFLATE_MODE_TYPE 11 /* state->mode flags enum-ed in inflate.h */
-#define INFLATE_MODE_BAD 26
-
-
-#if ! defined( USE_MMX ) && ! defined( NO_MMX )
-
-#define RUN_TIME_MMX
-
-#define CHECK_MMX 1
-#define DO_USE_MMX 2
-#define DONT_USE_MMX 3
-
-.globl inflate_fast_use_mmx
-
-.data
-
-.align 4,0
-inflate_fast_use_mmx: /* integer flag for run time control 1=check,2=mmx,3=no */
-.long CHECK_MMX
-
-#if defined( GAS_ELF )
-/* elf info */
-.type inflate_fast_use_mmx, at object
-.size inflate_fast_use_mmx,4
-#endif
-
-#endif /* RUN_TIME_MMX */
-
-#if defined( GAS_COFF )
-/* coff info: scl 2 = extern, type 32 = function */
-.def inflate_fast; .scl 2; .type 32; .endef
-#endif
-
-.text
-
-.align 32,0x90
-inflate_fast:
- pushl %edi
- pushl %esi
- pushl %ebp
- pushl %ebx
- pushf /* save eflags (strm_sp, state_sp assumes this is 32 bits) */
- subl $local_var_size, %esp
- cld
-
-#define strm_r %esi
-#define state_r %edi
-
- movl strm_sp(%esp), strm_r
- movl state_strm(strm_r), state_r
-
- /* in = strm->next_in;
- * out = strm->next_out;
- * last = in + strm->avail_in - 11;
- * beg = out - (start - strm->avail_out);
- * end = out + (strm->avail_out - 257);
- */
- movl avail_in_strm(strm_r), %edx
- movl next_in_strm(strm_r), %eax
-
- addl %eax, %edx /* avail_in += next_in */
- subl $11, %edx /* avail_in -= 11 */
-
- movl %eax, in(%esp)
- movl %edx, last(%esp)
-
- movl start_sp(%esp), %ebp
- movl avail_out_strm(strm_r), %ecx
- movl next_out_strm(strm_r), %ebx
-
- subl %ecx, %ebp /* start -= avail_out */
- negl %ebp /* start = -start */
- addl %ebx, %ebp /* start += next_out */
-
- subl $257, %ecx /* avail_out -= 257 */
- addl %ebx, %ecx /* avail_out += out */
-
- movl %ebx, out(%esp)
- movl %ebp, beg(%esp)
- movl %ecx, end(%esp)
-
- /* wsize = state->wsize;
- * write = state->write;
- * window = state->window;
- * hold = state->hold;
- * bits = state->bits;
- * lcode = state->lencode;
- * dcode = state->distcode;
- * lmask = ( 1 << state->lenbits ) - 1;
- * dmask = ( 1 << state->distbits ) - 1;
- */
-
- movl lencode_state(state_r), %eax
- movl distcode_state(state_r), %ecx
-
- movl %eax, lcode(%esp)
- movl %ecx, dcode(%esp)
-
- movl $1, %eax
- movl lenbits_state(state_r), %ecx
- shll %cl, %eax
- decl %eax
- movl %eax, lmask(%esp)
-
- movl $1, %eax
- movl distbits_state(state_r), %ecx
- shll %cl, %eax
- decl %eax
- movl %eax, dmask(%esp)
-
- movl wsize_state(state_r), %eax
- movl write_state(state_r), %ecx
- movl window_state(state_r), %edx
-
- movl %eax, wsize(%esp)
- movl %ecx, write(%esp)
- movl %edx, window(%esp)
-
- movl hold_state(state_r), %ebp
- movl bits_state(state_r), %ebx
-
-#undef strm_r
-#undef state_r
-
-#define in_r %esi
-#define from_r %esi
-#define out_r %edi
-
- movl in(%esp), in_r
- movl last(%esp), %ecx
- cmpl in_r, %ecx
- ja .L_align_long /* if in < last */
-
- addl $11, %ecx /* ecx = &in[ avail_in ] */
- subl in_r, %ecx /* ecx = avail_in */
- movl $12, %eax
- subl %ecx, %eax /* eax = 12 - avail_in */
- leal buf(%esp), %edi
- rep movsb /* memcpy( buf, in, avail_in ) */
- movl %eax, %ecx
- xorl %eax, %eax
- rep stosb /* memset( &buf[ avail_in ], 0, 12 - avail_in ) */
- leal buf(%esp), in_r /* in = buf */
- movl in_r, last(%esp) /* last = in, do just one iteration */
- jmp .L_is_aligned
-
- /* align in_r on long boundary */
-.L_align_long:
- testl $3, in_r
- jz .L_is_aligned
- xorl %eax, %eax
- movb (in_r), %al
- incl in_r
- movl %ebx, %ecx
- addl $8, %ebx
- shll %cl, %eax
- orl %eax, %ebp
- jmp .L_align_long
-
-.L_is_aligned:
- movl out(%esp), out_r
-
-#if defined( NO_MMX )
- jmp .L_do_loop
-#endif
-
-#if defined( USE_MMX )
- jmp .L_init_mmx
-#endif
-
-/*** Runtime MMX check ***/
-
-#if defined( RUN_TIME_MMX )
-.L_check_mmx:
- cmpl $DO_USE_MMX, inflate_fast_use_mmx
- je .L_init_mmx
- ja .L_do_loop /* > 2 */
-
- pushl %eax
- pushl %ebx
- pushl %ecx
- pushl %edx
- pushf
- movl (%esp), %eax /* copy eflags to eax */
- xorl $0x200000, (%esp) /* try toggling ID bit of eflags (bit 21)
- * to see if cpu supports cpuid...
- * ID bit method not supported by NexGen but
- * bios may load a cpuid instruction and
- * cpuid may be disabled on Cyrix 5-6x86 */
- popf
- pushf
- popl %edx /* copy new eflags to edx */
- xorl %eax, %edx /* test if ID bit is flipped */
- jz .L_dont_use_mmx /* not flipped if zero */
- xorl %eax, %eax
- cpuid
- cmpl $0x756e6547, %ebx /* check for GenuineIntel in ebx,ecx,edx */
- jne .L_dont_use_mmx
- cmpl $0x6c65746e, %ecx
- jne .L_dont_use_mmx
- cmpl $0x49656e69, %edx
- jne .L_dont_use_mmx
- movl $1, %eax
- cpuid /* get cpu features */
- shrl $8, %eax
- andl $15, %eax
- cmpl $6, %eax /* check for Pentium family, is 0xf for P4 */
- jne .L_dont_use_mmx
- testl $0x800000, %edx /* test if MMX feature is set (bit 23) */
- jnz .L_use_mmx
- jmp .L_dont_use_mmx
-.L_use_mmx:
- movl $DO_USE_MMX, inflate_fast_use_mmx
- jmp .L_check_mmx_pop
-.L_dont_use_mmx:
- movl $DONT_USE_MMX, inflate_fast_use_mmx
-.L_check_mmx_pop:
- popl %edx
- popl %ecx
- popl %ebx
- popl %eax
- jmp .L_check_mmx
-#endif
-
-
-/*** Non-MMX code ***/
-
-#if defined ( NO_MMX ) || defined( RUN_TIME_MMX )
-
-#define hold_r %ebp
-#define bits_r %bl
-#define bitslong_r %ebx
-
-.align 32,0x90
-.L_while_test:
- /* while (in < last && out < end)
- */
- cmpl out_r, end(%esp)
- jbe .L_break_loop /* if (out >= end) */
-
- cmpl in_r, last(%esp)
- jbe .L_break_loop
-
-.L_do_loop:
- /* regs: %esi = in, %ebp = hold, %bl = bits, %edi = out
- *
- * do {
- * if (bits < 15) {
- * hold |= *((unsigned short *)in)++ << bits;
- * bits += 16
- * }
- * this = lcode[hold & lmask]
- */
- cmpb $15, bits_r
- ja .L_get_length_code /* if (15 < bits) */
-
- xorl %eax, %eax
- lodsw /* al = *(ushort *)in++ */
- movb bits_r, %cl /* cl = bits, needs it for shifting */
- addb $16, bits_r /* bits += 16 */
- shll %cl, %eax
- orl %eax, hold_r /* hold |= *((ushort *)in)++ << bits */
-
-.L_get_length_code:
- movl lmask(%esp), %edx /* edx = lmask */
- movl lcode(%esp), %ecx /* ecx = lcode */
- andl hold_r, %edx /* edx &= hold */
- movl (%ecx,%edx,4), %eax /* eax = lcode[hold & lmask] */
-
-.L_dolen:
- /* regs: %esi = in, %ebp = hold, %bl = bits, %edi = out
- *
- * dolen:
- * bits -= this.bits;
- * hold >>= this.bits
- */
- movb %ah, %cl /* cl = this.bits */
- subb %ah, bits_r /* bits -= this.bits */
- shrl %cl, hold_r /* hold >>= this.bits */
-
- /* check if op is a literal
- * if (op == 0) {
- * PUP(out) = this.val;
- * }
- */
- testb %al, %al
- jnz .L_test_for_length_base /* if (op != 0) 45.7% */
-
- shrl $16, %eax /* output this.val char */
- stosb
- jmp .L_while_test
-
-.L_test_for_length_base:
- /* regs: %esi = in, %ebp = hold, %bl = bits, %edi = out, %edx = len
- *
- * else if (op & 16) {
- * len = this.val
- * op &= 15
- * if (op) {
- * if (op > bits) {
- * hold |= *((unsigned short *)in)++ << bits;
- * bits += 16
- * }
- * len += hold & mask[op];
- * bits -= op;
- * hold >>= op;
- * }
- */
-#define len_r %edx
- movl %eax, len_r /* len = this */
- shrl $16, len_r /* len = this.val */
- movb %al, %cl
-
- testb $16, %al
- jz .L_test_for_second_level_length /* if ((op & 16) == 0) 8% */
- andb $15, %cl /* op &= 15 */
- jz .L_save_len /* if (!op) */
- cmpb %cl, bits_r
- jae .L_add_bits_to_len /* if (op <= bits) */
-
- movb %cl, %ch /* stash op in ch, freeing cl */
- xorl %eax, %eax
- lodsw /* al = *(ushort *)in++ */
- movb bits_r, %cl /* cl = bits, needs it for shifting */
- addb $16, bits_r /* bits += 16 */
- shll %cl, %eax
- orl %eax, hold_r /* hold |= *((ushort *)in)++ << bits */
- movb %ch, %cl /* move op back to ecx */
-
-.L_add_bits_to_len:
- movl $1, %eax
- shll %cl, %eax
- decl %eax
- subb %cl, bits_r
- andl hold_r, %eax /* eax &= hold */
- shrl %cl, hold_r
- addl %eax, len_r /* len += hold & mask[op] */
-
-.L_save_len:
- movl len_r, len(%esp) /* save len */
-#undef len_r
-
-.L_decode_distance:
- /* regs: %esi = in, %ebp = hold, %bl = bits, %edi = out, %edx = dist
- *
- * if (bits < 15) {
- * hold |= *((unsigned short *)in)++ << bits;
- * bits += 16
- * }
- * this = dcode[hold & dmask];
- * dodist:
- * bits -= this.bits;
- * hold >>= this.bits;
- * op = this.op;
- */
-
- cmpb $15, bits_r
- ja .L_get_distance_code /* if (15 < bits) */
-
- xorl %eax, %eax
- lodsw /* al = *(ushort *)in++ */
- movb bits_r, %cl /* cl = bits, needs it for shifting */
- addb $16, bits_r /* bits += 16 */
- shll %cl, %eax
- orl %eax, hold_r /* hold |= *((ushort *)in)++ << bits */
-
-.L_get_distance_code:
- movl dmask(%esp), %edx /* edx = dmask */
- movl dcode(%esp), %ecx /* ecx = dcode */
- andl hold_r, %edx /* edx &= hold */
- movl (%ecx,%edx,4), %eax /* eax = dcode[hold & dmask] */
-
-#define dist_r %edx
-.L_dodist:
- movl %eax, dist_r /* dist = this */
- shrl $16, dist_r /* dist = this.val */
- movb %ah, %cl
- subb %ah, bits_r /* bits -= this.bits */
- shrl %cl, hold_r /* hold >>= this.bits */
-
- /* if (op & 16) {
- * dist = this.val
- * op &= 15
- * if (op > bits) {
- * hold |= *((unsigned short *)in)++ << bits;
- * bits += 16
- * }
- * dist += hold & mask[op];
- * bits -= op;
- * hold >>= op;
- */
- movb %al, %cl /* cl = this.op */
-
- testb $16, %al /* if ((op & 16) == 0) */
- jz .L_test_for_second_level_dist
- andb $15, %cl /* op &= 15 */
- jz .L_check_dist_one
- cmpb %cl, bits_r
- jae .L_add_bits_to_dist /* if (op <= bits) 97.6% */
-
- movb %cl, %ch /* stash op in ch, freeing cl */
- xorl %eax, %eax
- lodsw /* al = *(ushort *)in++ */
- movb bits_r, %cl /* cl = bits, needs it for shifting */
- addb $16, bits_r /* bits += 16 */
- shll %cl, %eax
- orl %eax, hold_r /* hold |= *((ushort *)in)++ << bits */
- movb %ch, %cl /* move op back to ecx */
-
-.L_add_bits_to_dist:
- movl $1, %eax
- shll %cl, %eax
- decl %eax /* (1 << op) - 1 */
- subb %cl, bits_r
- andl hold_r, %eax /* eax &= hold */
- shrl %cl, hold_r
- addl %eax, dist_r /* dist += hold & ((1 << op) - 1) */
- jmp .L_check_window
-
-.L_check_window:
- /* regs: %esi = from, %ebp = hold, %bl = bits, %edi = out, %edx = dist
- * %ecx = nbytes
- *
- * nbytes = out - beg;
- * if (dist <= nbytes) {
- * from = out - dist;
- * do {
- * PUP(out) = PUP(from);
- * } while (--len > 0) {
- * }
- */
-
- movl in_r, in(%esp) /* save in so from can use it's reg */
- movl out_r, %eax
- subl beg(%esp), %eax /* nbytes = out - beg */
-
- cmpl dist_r, %eax
- jb .L_clip_window /* if (dist > nbytes) 4.2% */
-
- movl len(%esp), %ecx
- movl out_r, from_r
- subl dist_r, from_r /* from = out - dist */
-
- subl $3, %ecx
- movb (from_r), %al
- movb %al, (out_r)
- movb 1(from_r), %al
- movb 2(from_r), %dl
- addl $3, from_r
- movb %al, 1(out_r)
- movb %dl, 2(out_r)
- addl $3, out_r
- rep movsb
-
- movl in(%esp), in_r /* move in back to %esi, toss from */
- jmp .L_while_test
-
-.align 16,0x90
-.L_check_dist_one:
- cmpl $1, dist_r
- jne .L_check_window
- cmpl out_r, beg(%esp)
- je .L_check_window
-
- decl out_r
- movl len(%esp), %ecx
- movb (out_r), %al
- subl $3, %ecx
-
- movb %al, 1(out_r)
- movb %al, 2(out_r)
- movb %al, 3(out_r)
- addl $4, out_r
- rep stosb
-
- jmp .L_while_test
-
-.align 16,0x90
-.L_test_for_second_level_length:
- /* else if ((op & 64) == 0) {
- * this = lcode[this.val + (hold & mask[op])];
- * }
- */
- testb $64, %al
- jnz .L_test_for_end_of_block /* if ((op & 64) != 0) */
-
- movl $1, %eax
- shll %cl, %eax
- decl %eax
- andl hold_r, %eax /* eax &= hold */
- addl %edx, %eax /* eax += this.val */
- movl lcode(%esp), %edx /* edx = lcode */
- movl (%edx,%eax,4), %eax /* eax = lcode[val + (hold&mask[op])] */
- jmp .L_dolen
-
-.align 16,0x90
-.L_test_for_second_level_dist:
- /* else if ((op & 64) == 0) {
- * this = dcode[this.val + (hold & mask[op])];
- * }
- */
- testb $64, %al
- jnz .L_invalid_distance_code /* if ((op & 64) != 0) */
-
- movl $1, %eax
- shll %cl, %eax
- decl %eax
- andl hold_r, %eax /* eax &= hold */
- addl %edx, %eax /* eax += this.val */
- movl dcode(%esp), %edx /* edx = dcode */
- movl (%edx,%eax,4), %eax /* eax = dcode[val + (hold&mask[op])] */
- jmp .L_dodist
-
-.align 16,0x90
-.L_clip_window:
- /* regs: %esi = from, %ebp = hold, %bl = bits, %edi = out, %edx = dist
- * %ecx = nbytes
- *
- * else {
- * if (dist > wsize) {
- * invalid distance
- * }
- * from = window;
- * nbytes = dist - nbytes;
- * if (write == 0) {
- * from += wsize - nbytes;
- */
-#define nbytes_r %ecx
- movl %eax, nbytes_r
- movl wsize(%esp), %eax /* prepare for dist compare */
- negl nbytes_r /* nbytes = -nbytes */
- movl window(%esp), from_r /* from = window */
-
- cmpl dist_r, %eax
- jb .L_invalid_distance_too_far /* if (dist > wsize) */
-
- addl dist_r, nbytes_r /* nbytes = dist - nbytes */
- cmpl $0, write(%esp)
- jne .L_wrap_around_window /* if (write != 0) */
-
- subl nbytes_r, %eax
- addl %eax, from_r /* from += wsize - nbytes */
-
- /* regs: %esi = from, %ebp = hold, %bl = bits, %edi = out, %edx = dist
- * %ecx = nbytes, %eax = len
- *
- * if (nbytes < len) {
- * len -= nbytes;
- * do {
- * PUP(out) = PUP(from);
- * } while (--nbytes);
- * from = out - dist;
- * }
- * }
- */
-#define len_r %eax
- movl len(%esp), len_r
- cmpl nbytes_r, len_r
- jbe .L_do_copy1 /* if (nbytes >= len) */
-
- subl nbytes_r, len_r /* len -= nbytes */
- rep movsb
- movl out_r, from_r
- subl dist_r, from_r /* from = out - dist */
- jmp .L_do_copy1
-
- cmpl nbytes_r, len_r
- jbe .L_do_copy1 /* if (nbytes >= len) */
-
- subl nbytes_r, len_r /* len -= nbytes */
- rep movsb
- movl out_r, from_r
- subl dist_r, from_r /* from = out - dist */
- jmp .L_do_copy1
-
-.L_wrap_around_window:
- /* regs: %esi = from, %ebp = hold, %bl = bits, %edi = out, %edx = dist
- * %ecx = nbytes, %eax = write, %eax = len
- *
- * else if (write < nbytes) {
- * from += wsize + write - nbytes;
- * nbytes -= write;
- * if (nbytes < len) {
- * len -= nbytes;
- * do {
- * PUP(out) = PUP(from);
- * } while (--nbytes);
- * from = window;
- * nbytes = write;
- * if (nbytes < len) {
- * len -= nbytes;
- * do {
- * PUP(out) = PUP(from);
- * } while(--nbytes);
- * from = out - dist;
- * }
- * }
- * }
- */
-#define write_r %eax
- movl write(%esp), write_r
- cmpl write_r, nbytes_r
- jbe .L_contiguous_in_window /* if (write >= nbytes) */
-
- addl wsize(%esp), from_r
- addl write_r, from_r
- subl nbytes_r, from_r /* from += wsize + write - nbytes */
- subl write_r, nbytes_r /* nbytes -= write */
-#undef write_r
-
- movl len(%esp), len_r
- cmpl nbytes_r, len_r
- jbe .L_do_copy1 /* if (nbytes >= len) */
-
- subl nbytes_r, len_r /* len -= nbytes */
- rep movsb
- movl window(%esp), from_r /* from = window */
- movl write(%esp), nbytes_r /* nbytes = write */
- cmpl nbytes_r, len_r
- jbe .L_do_copy1 /* if (nbytes >= len) */
-
- subl nbytes_r, len_r /* len -= nbytes */
- rep movsb
- movl out_r, from_r
- subl dist_r, from_r /* from = out - dist */
- jmp .L_do_copy1
-
-.L_contiguous_in_window:
- /* regs: %esi = from, %ebp = hold, %bl = bits, %edi = out, %edx = dist
- * %ecx = nbytes, %eax = write, %eax = len
- *
- * else {
- * from += write - nbytes;
- * if (nbytes < len) {
- * len -= nbytes;
- * do {
- * PUP(out) = PUP(from);
- * } while (--nbytes);
- * from = out - dist;
- * }
- * }
- */
-#define write_r %eax
- addl write_r, from_r
- subl nbytes_r, from_r /* from += write - nbytes */
-#undef write_r
-
- movl len(%esp), len_r
- cmpl nbytes_r, len_r
- jbe .L_do_copy1 /* if (nbytes >= len) */
-
- subl nbytes_r, len_r /* len -= nbytes */
- rep movsb
- movl out_r, from_r
- subl dist_r, from_r /* from = out - dist */
-
-.L_do_copy1:
- /* regs: %esi = from, %esi = in, %ebp = hold, %bl = bits, %edi = out
- * %eax = len
- *
- * while (len > 0) {
- * PUP(out) = PUP(from);
- * len--;
- * }
- * }
- * } while (in < last && out < end);
- */
-#undef nbytes_r
-#define in_r %esi
- movl len_r, %ecx
- rep movsb
-
- movl in(%esp), in_r /* move in back to %esi, toss from */
- jmp .L_while_test
-
-#undef len_r
-#undef dist_r
-
-#endif /* NO_MMX || RUN_TIME_MMX */
-
-
-/*** MMX code ***/
-
-#if defined( USE_MMX ) || defined( RUN_TIME_MMX )
-
-.align 32,0x90
-.L_init_mmx:
- emms
-
-#undef bits_r
-#undef bitslong_r
-#define bitslong_r %ebp
-#define hold_mm %mm0
- movd %ebp, hold_mm
- movl %ebx, bitslong_r
-
-#define used_mm %mm1
-#define dmask2_mm %mm2
-#define lmask2_mm %mm3
-#define lmask_mm %mm4
-#define dmask_mm %mm5
-#define tmp_mm %mm6
-
- movd lmask(%esp), lmask_mm
- movq lmask_mm, lmask2_mm
- movd dmask(%esp), dmask_mm
- movq dmask_mm, dmask2_mm
- pxor used_mm, used_mm
- movl lcode(%esp), %ebx /* ebx = lcode */
- jmp .L_do_loop_mmx
-
-.align 32,0x90
-.L_while_test_mmx:
- /* while (in < last && out < end)
- */
- cmpl out_r, end(%esp)
- jbe .L_break_loop /* if (out >= end) */
-
- cmpl in_r, last(%esp)
- jbe .L_break_loop
-
-.L_do_loop_mmx:
- psrlq used_mm, hold_mm /* hold_mm >>= last bit length */
-
- cmpl $32, bitslong_r
- ja .L_get_length_code_mmx /* if (32 < bits) */
-
- movd bitslong_r, tmp_mm
- movd (in_r), %mm7
- addl $4, in_r
- psllq tmp_mm, %mm7
- addl $32, bitslong_r
- por %mm7, hold_mm /* hold_mm |= *((uint *)in)++ << bits */
-
-.L_get_length_code_mmx:
- pand hold_mm, lmask_mm
- movd lmask_mm, %eax
- movq lmask2_mm, lmask_mm
- movl (%ebx,%eax,4), %eax /* eax = lcode[hold & lmask] */
-
-.L_dolen_mmx:
- movzbl %ah, %ecx /* ecx = this.bits */
- movd %ecx, used_mm
- subl %ecx, bitslong_r /* bits -= this.bits */
-
- testb %al, %al
- jnz .L_test_for_length_base_mmx /* if (op != 0) 45.7% */
-
- shrl $16, %eax /* output this.val char */
- stosb
- jmp .L_while_test_mmx
-
-.L_test_for_length_base_mmx:
-#define len_r %edx
- movl %eax, len_r /* len = this */
- shrl $16, len_r /* len = this.val */
-
- testb $16, %al
- jz .L_test_for_second_level_length_mmx /* if ((op & 16) == 0) 8% */
- andl $15, %eax /* op &= 15 */
- jz .L_decode_distance_mmx /* if (!op) */
-
- psrlq used_mm, hold_mm /* hold_mm >>= last bit length */
- movd %eax, used_mm
- movd hold_mm, %ecx
- subl %eax, bitslong_r
- andl .L_mask(,%eax,4), %ecx
- addl %ecx, len_r /* len += hold & mask[op] */
-
-.L_decode_distance_mmx:
- psrlq used_mm, hold_mm /* hold_mm >>= last bit length */
-
- cmpl $32, bitslong_r
- ja .L_get_dist_code_mmx /* if (32 < bits) */
-
- movd bitslong_r, tmp_mm
- movd (in_r), %mm7
- addl $4, in_r
- psllq tmp_mm, %mm7
- addl $32, bitslong_r
- por %mm7, hold_mm /* hold_mm |= *((uint *)in)++ << bits */
-
-.L_get_dist_code_mmx:
- movl dcode(%esp), %ebx /* ebx = dcode */
- pand hold_mm, dmask_mm
- movd dmask_mm, %eax
- movq dmask2_mm, dmask_mm
- movl (%ebx,%eax,4), %eax /* eax = dcode[hold & lmask] */
-
-.L_dodist_mmx:
-#define dist_r %ebx
- movzbl %ah, %ecx /* ecx = this.bits */
- movl %eax, dist_r
- shrl $16, dist_r /* dist = this.val */
- subl %ecx, bitslong_r /* bits -= this.bits */
- movd %ecx, used_mm
-
- testb $16, %al /* if ((op & 16) == 0) */
- jz .L_test_for_second_level_dist_mmx
- andl $15, %eax /* op &= 15 */
- jz .L_check_dist_one_mmx
-
-.L_add_bits_to_dist_mmx:
- psrlq used_mm, hold_mm /* hold_mm >>= last bit length */
- movd %eax, used_mm /* save bit length of current op */
- movd hold_mm, %ecx /* get the next bits on input stream */
- subl %eax, bitslong_r /* bits -= op bits */
- andl .L_mask(,%eax,4), %ecx /* ecx = hold & mask[op] */
- addl %ecx, dist_r /* dist += hold & mask[op] */
-
-.L_check_window_mmx:
- movl in_r, in(%esp) /* save in so from can use it's reg */
- movl out_r, %eax
- subl beg(%esp), %eax /* nbytes = out - beg */
-
- cmpl dist_r, %eax
- jb .L_clip_window_mmx /* if (dist > nbytes) 4.2% */
-
- movl len_r, %ecx
- movl out_r, from_r
- subl dist_r, from_r /* from = out - dist */
-
- subl $3, %ecx
- movb (from_r), %al
- movb %al, (out_r)
- movb 1(from_r), %al
- movb 2(from_r), %dl
- addl $3, from_r
- movb %al, 1(out_r)
- movb %dl, 2(out_r)
- addl $3, out_r
- rep movsb
-
- movl in(%esp), in_r /* move in back to %esi, toss from */
- movl lcode(%esp), %ebx /* move lcode back to %ebx, toss dist */
- jmp .L_while_test_mmx
-
-.align 16,0x90
-.L_check_dist_one_mmx:
- cmpl $1, dist_r
- jne .L_check_window_mmx
- cmpl out_r, beg(%esp)
- je .L_check_window_mmx
-
- decl out_r
- movl len_r, %ecx
- movb (out_r), %al
- subl $3, %ecx
-
- movb %al, 1(out_r)
- movb %al, 2(out_r)
- movb %al, 3(out_r)
- addl $4, out_r
- rep stosb
-
- movl lcode(%esp), %ebx /* move lcode back to %ebx, toss dist */
- jmp .L_while_test_mmx
-
-.align 16,0x90
-.L_test_for_second_level_length_mmx:
- testb $64, %al
- jnz .L_test_for_end_of_block /* if ((op & 64) != 0) */
-
- andl $15, %eax
- psrlq used_mm, hold_mm /* hold_mm >>= last bit length */
- movd hold_mm, %ecx
- andl .L_mask(,%eax,4), %ecx
- addl len_r, %ecx
- movl (%ebx,%ecx,4), %eax /* eax = lcode[hold & lmask] */
- jmp .L_dolen_mmx
-
-.align 16,0x90
-.L_test_for_second_level_dist_mmx:
- testb $64, %al
- jnz .L_invalid_distance_code /* if ((op & 64) != 0) */
-
- andl $15, %eax
- psrlq used_mm, hold_mm /* hold_mm >>= last bit length */
- movd hold_mm, %ecx
- andl .L_mask(,%eax,4), %ecx
- movl dcode(%esp), %eax /* ecx = dcode */
- addl dist_r, %ecx
- movl (%eax,%ecx,4), %eax /* eax = lcode[hold & lmask] */
- jmp .L_dodist_mmx
-
-.align 16,0x90
-.L_clip_window_mmx:
-#define nbytes_r %ecx
- movl %eax, nbytes_r
- movl wsize(%esp), %eax /* prepare for dist compare */
- negl nbytes_r /* nbytes = -nbytes */
- movl window(%esp), from_r /* from = window */
-
- cmpl dist_r, %eax
- jb .L_invalid_distance_too_far /* if (dist > wsize) */
-
- addl dist_r, nbytes_r /* nbytes = dist - nbytes */
- cmpl $0, write(%esp)
- jne .L_wrap_around_window_mmx /* if (write != 0) */
-
- subl nbytes_r, %eax
- addl %eax, from_r /* from += wsize - nbytes */
-
- cmpl nbytes_r, len_r
- jbe .L_do_copy1_mmx /* if (nbytes >= len) */
-
- subl nbytes_r, len_r /* len -= nbytes */
- rep movsb
- movl out_r, from_r
- subl dist_r, from_r /* from = out - dist */
- jmp .L_do_copy1_mmx
-
- cmpl nbytes_r, len_r
- jbe .L_do_copy1_mmx /* if (nbytes >= len) */
-
- subl nbytes_r, len_r /* len -= nbytes */
- rep movsb
- movl out_r, from_r
- subl dist_r, from_r /* from = out - dist */
- jmp .L_do_copy1_mmx
-
-.L_wrap_around_window_mmx:
-#define write_r %eax
- movl write(%esp), write_r
- cmpl write_r, nbytes_r
- jbe .L_contiguous_in_window_mmx /* if (write >= nbytes) */
-
- addl wsize(%esp), from_r
- addl write_r, from_r
- subl nbytes_r, from_r /* from += wsize + write - nbytes */
- subl write_r, nbytes_r /* nbytes -= write */
-#undef write_r
-
- cmpl nbytes_r, len_r
- jbe .L_do_copy1_mmx /* if (nbytes >= len) */
-
- subl nbytes_r, len_r /* len -= nbytes */
- rep movsb
- movl window(%esp), from_r /* from = window */
- movl write(%esp), nbytes_r /* nbytes = write */
- cmpl nbytes_r, len_r
- jbe .L_do_copy1_mmx /* if (nbytes >= len) */
-
- subl nbytes_r, len_r /* len -= nbytes */
- rep movsb
- movl out_r, from_r
- subl dist_r, from_r /* from = out - dist */
- jmp .L_do_copy1_mmx
-
-.L_contiguous_in_window_mmx:
-#define write_r %eax
- addl write_r, from_r
- subl nbytes_r, from_r /* from += write - nbytes */
-#undef write_r
-
- cmpl nbytes_r, len_r
- jbe .L_do_copy1_mmx /* if (nbytes >= len) */
-
- subl nbytes_r, len_r /* len -= nbytes */
- rep movsb
- movl out_r, from_r
- subl dist_r, from_r /* from = out - dist */
-
-.L_do_copy1_mmx:
-#undef nbytes_r
-#define in_r %esi
- movl len_r, %ecx
- rep movsb
-
- movl in(%esp), in_r /* move in back to %esi, toss from */
- movl lcode(%esp), %ebx /* move lcode back to %ebx, toss dist */
- jmp .L_while_test_mmx
-
-#undef hold_r
-#undef bitslong_r
-
-#endif /* USE_MMX || RUN_TIME_MMX */
-
-
-/*** USE_MMX, NO_MMX, and RUNTIME_MMX from here on ***/
-
-.L_invalid_distance_code:
- /* else {
- * strm->msg = "invalid distance code";
- * state->mode = BAD;
- * }
- */
- movl $.L_invalid_distance_code_msg, %ecx
- movl $INFLATE_MODE_BAD, %edx
- jmp .L_update_stream_state
-
-.L_test_for_end_of_block:
- /* else if (op & 32) {
- * state->mode = TYPE;
- * break;
- * }
- */
- testb $32, %al
- jz .L_invalid_literal_length_code /* if ((op & 32) == 0) */
-
- movl $0, %ecx
- movl $INFLATE_MODE_TYPE, %edx
- jmp .L_update_stream_state
-
-.L_invalid_literal_length_code:
- /* else {
- * strm->msg = "invalid literal/length code";
- * state->mode = BAD;
- * }
- */
- movl $.L_invalid_literal_length_code_msg, %ecx
- movl $INFLATE_MODE_BAD, %edx
- jmp .L_update_stream_state
-
-.L_invalid_distance_too_far:
- /* strm->msg = "invalid distance too far back";
- * state->mode = BAD;
- */
- movl in(%esp), in_r /* from_r has in's reg, put in back */
- movl $.L_invalid_distance_too_far_msg, %ecx
- movl $INFLATE_MODE_BAD, %edx
- jmp .L_update_stream_state
-
-.L_update_stream_state:
- /* set strm->msg = %ecx, strm->state->mode = %edx */
- movl strm_sp(%esp), %eax
- testl %ecx, %ecx /* if (msg != NULL) */
- jz .L_skip_msg
- movl %ecx, msg_strm(%eax) /* strm->msg = msg */
-.L_skip_msg:
- movl state_strm(%eax), %eax /* state = strm->state */
- movl %edx, mode_state(%eax) /* state->mode = edx (BAD | TYPE) */
- jmp .L_break_loop
-
-.align 32,0x90
-.L_break_loop:
-
-/*
- * Regs:
- *
- * bits = %ebp when mmx, and in %ebx when non-mmx
- * hold = %hold_mm when mmx, and in %ebp when non-mmx
- * in = %esi
- * out = %edi
- */
-
-#if defined( USE_MMX ) || defined( RUN_TIME_MMX )
-
-#if defined( RUN_TIME_MMX )
-
- cmpl $DO_USE_MMX, inflate_fast_use_mmx
- jne .L_update_next_in
-
-#endif /* RUN_TIME_MMX */
-
- movl %ebp, %ebx
-
-.L_update_next_in:
-
-#endif
-
-#define strm_r %eax
-#define state_r %edx
-
- /* len = bits >> 3;
- * in -= len;
- * bits -= len << 3;
- * hold &= (1U << bits) - 1;
- * state->hold = hold;
- * state->bits = bits;
- * strm->next_in = in;
- * strm->next_out = out;
- */
- movl strm_sp(%esp), strm_r
- movl %ebx, %ecx
- movl state_strm(strm_r), state_r
- shrl $3, %ecx
- subl %ecx, in_r
- shll $3, %ecx
- subl %ecx, %ebx
- movl out_r, next_out_strm(strm_r)
- movl %ebx, bits_state(state_r)
- movl %ebx, %ecx
-
- leal buf(%esp), %ebx
- cmpl %ebx, last(%esp)
- jne .L_buf_not_used /* if buf != last */
-
- subl %ebx, in_r /* in -= buf */
- movl next_in_strm(strm_r), %ebx
- movl %ebx, last(%esp) /* last = strm->next_in */
- addl %ebx, in_r /* in += strm->next_in */
- movl avail_in_strm(strm_r), %ebx
- subl $11, %ebx
- addl %ebx, last(%esp) /* last = &strm->next_in[ avail_in - 11 ] */
-
-.L_buf_not_used:
- movl in_r, next_in_strm(strm_r)
-
- movl $1, %ebx
- shll %cl, %ebx
- decl %ebx
-
-#if defined( USE_MMX ) || defined( RUN_TIME_MMX )
-
-#if defined( RUN_TIME_MMX )
-
- cmpl $DO_USE_MMX, inflate_fast_use_mmx
- jne .L_update_hold
-
-#endif /* RUN_TIME_MMX */
-
- psrlq used_mm, hold_mm /* hold_mm >>= last bit length */
- movd hold_mm, %ebp
-
- emms
-
-.L_update_hold:
-
-#endif /* USE_MMX || RUN_TIME_MMX */
-
- andl %ebx, %ebp
- movl %ebp, hold_state(state_r)
-
-#define last_r %ebx
-
- /* strm->avail_in = in < last ? 11 + (last - in) : 11 - (in - last) */
- movl last(%esp), last_r
- cmpl in_r, last_r
- jbe .L_last_is_smaller /* if (in >= last) */
-
- subl in_r, last_r /* last -= in */
- addl $11, last_r /* last += 11 */
- movl last_r, avail_in_strm(strm_r)
- jmp .L_fixup_out
-.L_last_is_smaller:
- subl last_r, in_r /* in -= last */
- negl in_r /* in = -in */
- addl $11, in_r /* in += 11 */
- movl in_r, avail_in_strm(strm_r)
-
-#undef last_r
-#define end_r %ebx
-
-.L_fixup_out:
- /* strm->avail_out = out < end ? 257 + (end - out) : 257 - (out - end)*/
- movl end(%esp), end_r
- cmpl out_r, end_r
- jbe .L_end_is_smaller /* if (out >= end) */
-
- subl out_r, end_r /* end -= out */
- addl $257, end_r /* end += 257 */
- movl end_r, avail_out_strm(strm_r)
- jmp .L_done
-.L_end_is_smaller:
- subl end_r, out_r /* out -= end */
- negl out_r /* out = -out */
- addl $257, out_r /* out += 257 */
- movl out_r, avail_out_strm(strm_r)
-
-#undef end_r
-#undef strm_r
-#undef state_r
-
-.L_done:
- addl $local_var_size, %esp
- popf
- popl %ebx
- popl %ebp
- popl %esi
- popl %edi
- ret
-
-#if defined( GAS_ELF )
-/* elf info */
-.type inflate_fast, at function
-.size inflate_fast,.-inflate_fast
-#endif
diff --git a/third-party/zlib/contrib/iostream/test.cpp b/third-party/zlib/contrib/iostream/test.cpp
deleted file mode 100644
index 7d265b3..0000000
--- a/third-party/zlib/contrib/iostream/test.cpp
+++ /dev/null
@@ -1,24 +0,0 @@
-
-#include "zfstream.h"
-
-int main() {
-
- // Construct a stream object with this filebuffer. Anything sent
- // to this stream will go to standard out.
- gzofstream os( 1, ios::out );
-
- // This text is getting compressed and sent to stdout.
- // To prove this, run 'test | zcat'.
- os << "Hello, Mommy" << endl;
-
- os << setcompressionlevel( Z_NO_COMPRESSION );
- os << "hello, hello, hi, ho!" << endl;
-
- setcompressionlevel( os, Z_DEFAULT_COMPRESSION )
- << "I'm compressing again" << endl;
-
- os.close();
-
- return 0;
-
-}
diff --git a/third-party/zlib/contrib/iostream/zfstream.cpp b/third-party/zlib/contrib/iostream/zfstream.cpp
deleted file mode 100644
index d0cd85f..0000000
--- a/third-party/zlib/contrib/iostream/zfstream.cpp
+++ /dev/null
@@ -1,329 +0,0 @@
-
-#include "zfstream.h"
-
-gzfilebuf::gzfilebuf() :
- file(NULL),
- mode(0),
- own_file_descriptor(0)
-{ }
-
-gzfilebuf::~gzfilebuf() {
-
- sync();
- if ( own_file_descriptor )
- close();
-
-}
-
-gzfilebuf *gzfilebuf::open( const char *name,
- int io_mode ) {
-
- if ( is_open() )
- return NULL;
-
- char char_mode[10];
- char *p = char_mode;
-
- if ( io_mode & ios::in ) {
- mode = ios::in;
- *p++ = 'r';
- } else if ( io_mode & ios::app ) {
- mode = ios::app;
- *p++ = 'a';
- } else {
- mode = ios::out;
- *p++ = 'w';
- }
-
- if ( io_mode & ios::binary ) {
- mode |= ios::binary;
- *p++ = 'b';
- }
-
- // Hard code the compression level
- if ( io_mode & (ios::out|ios::app )) {
- *p++ = '9';
- }
-
- // Put the end-of-string indicator
- *p = '\0';
-
- if ( (file = gzopen(name, char_mode)) == NULL )
- return NULL;
-
- own_file_descriptor = 1;
-
- return this;
-
-}
-
-gzfilebuf *gzfilebuf::attach( int file_descriptor,
- int io_mode ) {
-
- if ( is_open() )
- return NULL;
-
- char char_mode[10];
- char *p = char_mode;
-
- if ( io_mode & ios::in ) {
- mode = ios::in;
- *p++ = 'r';
- } else if ( io_mode & ios::app ) {
- mode = ios::app;
- *p++ = 'a';
- } else {
- mode = ios::out;
- *p++ = 'w';
- }
-
- if ( io_mode & ios::binary ) {
- mode |= ios::binary;
- *p++ = 'b';
- }
-
- // Hard code the compression level
- if ( io_mode & (ios::out|ios::app )) {
- *p++ = '9';
- }
-
- // Put the end-of-string indicator
- *p = '\0';
-
- if ( (file = gzdopen(file_descriptor, char_mode)) == NULL )
- return NULL;
-
- own_file_descriptor = 0;
-
- return this;
-
-}
-
-gzfilebuf *gzfilebuf::close() {
-
- if ( is_open() ) {
-
- sync();
- gzclose( file );
- file = NULL;
-
- }
-
- return this;
-
-}
-
-int gzfilebuf::setcompressionlevel( int comp_level ) {
-
- return gzsetparams(file, comp_level, -2);
-
-}
-
-int gzfilebuf::setcompressionstrategy( int comp_strategy ) {
-
- return gzsetparams(file, -2, comp_strategy);
-
-}
-
-
-streampos gzfilebuf::seekoff( streamoff off, ios::seek_dir dir, int which ) {
-
- return streampos(EOF);
-
-}
-
-int gzfilebuf::underflow() {
-
- // If the file hasn't been opened for reading, error.
- if ( !is_open() || !(mode & ios::in) )
- return EOF;
-
- // if a buffer doesn't exists, allocate one.
- if ( !base() ) {
-
- if ( (allocate()) == EOF )
- return EOF;
- setp(0,0);
-
- } else {
-
- if ( in_avail() )
- return (unsigned char) *gptr();
-
- if ( out_waiting() ) {
- if ( flushbuf() == EOF )
- return EOF;
- }
-
- }
-
- // Attempt to fill the buffer.
-
- int result = fillbuf();
- if ( result == EOF ) {
- // disable get area
- setg(0,0,0);
- return EOF;
- }
-
- return (unsigned char) *gptr();
-
-}
-
-int gzfilebuf::overflow( int c ) {
-
- if ( !is_open() || !(mode & ios::out) )
- return EOF;
-
- if ( !base() ) {
- if ( allocate() == EOF )
- return EOF;
- setg(0,0,0);
- } else {
- if (in_avail()) {
- return EOF;
- }
- if (out_waiting()) {
- if (flushbuf() == EOF)
- return EOF;
- }
- }
-
- int bl = blen();
- setp( base(), base() + bl);
-
- if ( c != EOF ) {
-
- *pptr() = c;
- pbump(1);
-
- }
-
- return 0;
-
-}
-
-int gzfilebuf::sync() {
-
- if ( !is_open() )
- return EOF;
-
- if ( out_waiting() )
- return flushbuf();
-
- return 0;
-
-}
-
-int gzfilebuf::flushbuf() {
-
- int n;
- char *q;
-
- q = pbase();
- n = pptr() - q;
-
- if ( gzwrite( file, q, n) < n )
- return EOF;
-
- setp(0,0);
-
- return 0;
-
-}
-
-int gzfilebuf::fillbuf() {
-
- int required;
- char *p;
-
- p = base();
-
- required = blen();
-
- int t = gzread( file, p, required );
-
- if ( t <= 0) return EOF;
-
- setg( base(), base(), base()+t);
-
- return t;
-
-}
-
-gzfilestream_common::gzfilestream_common() :
- ios( gzfilestream_common::rdbuf() )
-{ }
-
-gzfilestream_common::~gzfilestream_common()
-{ }
-
-void gzfilestream_common::attach( int fd, int io_mode ) {
-
- if ( !buffer.attach( fd, io_mode) )
- clear( ios::failbit | ios::badbit );
- else
- clear();
-
-}
-
-void gzfilestream_common::open( const char *name, int io_mode ) {
-
- if ( !buffer.open( name, io_mode ) )
- clear( ios::failbit | ios::badbit );
- else
- clear();
-
-}
-
-void gzfilestream_common::close() {
-
- if ( !buffer.close() )
- clear( ios::failbit | ios::badbit );
-
-}
-
-gzfilebuf *gzfilestream_common::rdbuf()
-{
- return &buffer;
-}
-
-gzifstream::gzifstream() :
- ios( gzfilestream_common::rdbuf() )
-{
- clear( ios::badbit );
-}
-
-gzifstream::gzifstream( const char *name, int io_mode ) :
- ios( gzfilestream_common::rdbuf() )
-{
- gzfilestream_common::open( name, io_mode );
-}
-
-gzifstream::gzifstream( int fd, int io_mode ) :
- ios( gzfilestream_common::rdbuf() )
-{
- gzfilestream_common::attach( fd, io_mode );
-}
-
-gzifstream::~gzifstream() { }
-
-gzofstream::gzofstream() :
- ios( gzfilestream_common::rdbuf() )
-{
- clear( ios::badbit );
-}
-
-gzofstream::gzofstream( const char *name, int io_mode ) :
- ios( gzfilestream_common::rdbuf() )
-{
- gzfilestream_common::open( name, io_mode );
-}
-
-gzofstream::gzofstream( int fd, int io_mode ) :
- ios( gzfilestream_common::rdbuf() )
-{
- gzfilestream_common::attach( fd, io_mode );
-}
-
-gzofstream::~gzofstream() { }
diff --git a/third-party/zlib/contrib/iostream/zfstream.h b/third-party/zlib/contrib/iostream/zfstream.h
deleted file mode 100644
index ed79098..0000000
--- a/third-party/zlib/contrib/iostream/zfstream.h
+++ /dev/null
@@ -1,128 +0,0 @@
-
-#ifndef zfstream_h
-#define zfstream_h
-
-#include <fstream.h>
-#include "zlib.h"
-
-class gzfilebuf : public streambuf {
-
-public:
-
- gzfilebuf( );
- virtual ~gzfilebuf();
-
- gzfilebuf *open( const char *name, int io_mode );
- gzfilebuf *attach( int file_descriptor, int io_mode );
- gzfilebuf *close();
-
- int setcompressionlevel( int comp_level );
- int setcompressionstrategy( int comp_strategy );
-
- inline int is_open() const { return (file !=NULL); }
-
- virtual streampos seekoff( streamoff, ios::seek_dir, int );
-
- virtual int sync();
-
-protected:
-
- virtual int underflow();
- virtual int overflow( int = EOF );
-
-private:
-
- gzFile file;
- short mode;
- short own_file_descriptor;
-
- int flushbuf();
- int fillbuf();
-
-};
-
-class gzfilestream_common : virtual public ios {
-
- friend class gzifstream;
- friend class gzofstream;
- friend gzofstream &setcompressionlevel( gzofstream &, int );
- friend gzofstream &setcompressionstrategy( gzofstream &, int );
-
-public:
- virtual ~gzfilestream_common();
-
- void attach( int fd, int io_mode );
- void open( const char *name, int io_mode );
- void close();
-
-protected:
- gzfilestream_common();
-
-private:
- gzfilebuf *rdbuf();
-
- gzfilebuf buffer;
-
-};
-
-class gzifstream : public gzfilestream_common, public istream {
-
-public:
-
- gzifstream();
- gzifstream( const char *name, int io_mode = ios::in );
- gzifstream( int fd, int io_mode = ios::in );
-
- virtual ~gzifstream();
-
-};
-
-class gzofstream : public gzfilestream_common, public ostream {
-
-public:
-
- gzofstream();
- gzofstream( const char *name, int io_mode = ios::out );
- gzofstream( int fd, int io_mode = ios::out );
-
- virtual ~gzofstream();
-
-};
-
-template<class T> class gzomanip {
- friend gzofstream &operator<<(gzofstream &, const gzomanip<T> &);
-public:
- gzomanip(gzofstream &(*f)(gzofstream &, T), T v) : func(f), val(v) { }
-private:
- gzofstream &(*func)(gzofstream &, T);
- T val;
-};
-
-template<class T> gzofstream &operator<<(gzofstream &s, const gzomanip<T> &m)
-{
- return (*m.func)(s, m.val);
-}
-
-inline gzofstream &setcompressionlevel( gzofstream &s, int l )
-{
- (s.rdbuf())->setcompressionlevel(l);
- return s;
-}
-
-inline gzofstream &setcompressionstrategy( gzofstream &s, int l )
-{
- (s.rdbuf())->setcompressionstrategy(l);
- return s;
-}
-
-inline gzomanip<int> setcompressionlevel(int l)
-{
- return gzomanip<int>(&setcompressionlevel,l);
-}
-
-inline gzomanip<int> setcompressionstrategy(int l)
-{
- return gzomanip<int>(&setcompressionstrategy,l);
-}
-
-#endif
diff --git a/third-party/zlib/contrib/iostream2/zstream.h b/third-party/zlib/contrib/iostream2/zstream.h
deleted file mode 100644
index 43d2332..0000000
--- a/third-party/zlib/contrib/iostream2/zstream.h
+++ /dev/null
@@ -1,307 +0,0 @@
-/*
- *
- * Copyright (c) 1997
- * Christian Michelsen Research AS
- * Advanced Computing
- * Fantoftvegen 38, 5036 BERGEN, Norway
- * http://www.cmr.no
- *
- * Permission to use, copy, modify, distribute and sell this software
- * and its documentation for any purpose is hereby granted without fee,
- * provided that the above copyright notice appear in all copies and
- * that both that copyright notice and this permission notice appear
- * in supporting documentation. Christian Michelsen Research AS makes no
- * representations about the suitability of this software for any
- * purpose. It is provided "as is" without express or implied warranty.
- *
- */
-
-#ifndef ZSTREAM__H
-#define ZSTREAM__H
-
-/*
- * zstream.h - C++ interface to the 'zlib' general purpose compression library
- * $Id: zstream.h 1.1 1997-06-25 12:00:56+02 tyge Exp tyge $
- */
-
-#include <strstream.h>
-#include <string.h>
-#include <stdio.h>
-#include "zlib.h"
-
-#if defined(_WIN32)
-# include <fcntl.h>
-# include <io.h>
-# define SET_BINARY_MODE(file) setmode(fileno(file), O_BINARY)
-#else
-# define SET_BINARY_MODE(file)
-#endif
-
-class zstringlen {
-public:
- zstringlen(class izstream&);
- zstringlen(class ozstream&, const char*);
- size_t value() const { return val.word; }
-private:
- struct Val { unsigned char byte; size_t word; } val;
-};
-
-// ----------------------------- izstream -----------------------------
-
-class izstream
-{
- public:
- izstream() : m_fp(0) {}
- izstream(FILE* fp) : m_fp(0) { open(fp); }
- izstream(const char* name) : m_fp(0) { open(name); }
- ~izstream() { close(); }
-
- /* Opens a gzip (.gz) file for reading.
- * open() can be used to read a file which is not in gzip format;
- * in this case read() will directly read from the file without
- * decompression. errno can be checked to distinguish two error
- * cases (if errno is zero, the zlib error is Z_MEM_ERROR).
- */
- void open(const char* name) {
- if (m_fp) close();
- m_fp = ::gzopen(name, "rb");
- }
-
- void open(FILE* fp) {
- SET_BINARY_MODE(fp);
- if (m_fp) close();
- m_fp = ::gzdopen(fileno(fp), "rb");
- }
-
- /* Flushes all pending input if necessary, closes the compressed file
- * and deallocates all the (de)compression state. The return value is
- * the zlib error number (see function error() below).
- */
- int close() {
- int r = ::gzclose(m_fp);
- m_fp = 0; return r;
- }
-
- /* Binary read the given number of bytes from the compressed file.
- */
- int read(void* buf, size_t len) {
- return ::gzread(m_fp, buf, len);
- }
-
- /* Returns the error message for the last error which occurred on the
- * given compressed file. errnum is set to zlib error number. If an
- * error occurred in the file system and not in the compression library,
- * errnum is set to Z_ERRNO and the application may consult errno
- * to get the exact error code.
- */
- const char* error(int* errnum) {
- return ::gzerror(m_fp, errnum);
- }
-
- gzFile fp() { return m_fp; }
-
- private:
- gzFile m_fp;
-};
-
-/*
- * Binary read the given (array of) object(s) from the compressed file.
- * If the input file was not in gzip format, read() copies the objects number
- * of bytes into the buffer.
- * returns the number of uncompressed bytes actually read
- * (0 for end of file, -1 for error).
- */
-template <class T, class Items>
-inline int read(izstream& zs, T* x, Items items) {
- return ::gzread(zs.fp(), x, items*sizeof(T));
-}
-
-/*
- * Binary input with the '>' operator.
- */
-template <class T>
-inline izstream& operator>(izstream& zs, T& x) {
- ::gzread(zs.fp(), &x, sizeof(T));
- return zs;
-}
-
-
-inline zstringlen::zstringlen(izstream& zs) {
- zs > val.byte;
- if (val.byte == 255) zs > val.word;
- else val.word = val.byte;
-}
-
-/*
- * Read length of string + the string with the '>' operator.
- */
-inline izstream& operator>(izstream& zs, char* x) {
- zstringlen len(zs);
- ::gzread(zs.fp(), x, len.value());
- x[len.value()] = '\0';
- return zs;
-}
-
-inline char* read_string(izstream& zs) {
- zstringlen len(zs);
- char* x = new char[len.value()+1];
- ::gzread(zs.fp(), x, len.value());
- x[len.value()] = '\0';
- return x;
-}
-
-// ----------------------------- ozstream -----------------------------
-
-class ozstream
-{
- public:
- ozstream() : m_fp(0), m_os(0) {
- }
- ozstream(FILE* fp, int level = Z_DEFAULT_COMPRESSION)
- : m_fp(0), m_os(0) {
- open(fp, level);
- }
- ozstream(const char* name, int level = Z_DEFAULT_COMPRESSION)
- : m_fp(0), m_os(0) {
- open(name, level);
- }
- ~ozstream() {
- close();
- }
-
- /* Opens a gzip (.gz) file for writing.
- * The compression level parameter should be in 0..9
- * errno can be checked to distinguish two error cases
- * (if errno is zero, the zlib error is Z_MEM_ERROR).
- */
- void open(const char* name, int level = Z_DEFAULT_COMPRESSION) {
- char mode[4] = "wb\0";
- if (level != Z_DEFAULT_COMPRESSION) mode[2] = '0'+level;
- if (m_fp) close();
- m_fp = ::gzopen(name, mode);
- }
-
- /* open from a FILE pointer.
- */
- void open(FILE* fp, int level = Z_DEFAULT_COMPRESSION) {
- SET_BINARY_MODE(fp);
- char mode[4] = "wb\0";
- if (level != Z_DEFAULT_COMPRESSION) mode[2] = '0'+level;
- if (m_fp) close();
- m_fp = ::gzdopen(fileno(fp), mode);
- }
-
- /* Flushes all pending output if necessary, closes the compressed file
- * and deallocates all the (de)compression state. The return value is
- * the zlib error number (see function error() below).
- */
- int close() {
- if (m_os) {
- ::gzwrite(m_fp, m_os->str(), m_os->pcount());
- delete[] m_os->str(); delete m_os; m_os = 0;
- }
- int r = ::gzclose(m_fp); m_fp = 0; return r;
- }
-
- /* Binary write the given number of bytes into the compressed file.
- */
- int write(const void* buf, size_t len) {
- return ::gzwrite(m_fp, (voidp) buf, len);
- }
-
- /* Flushes all pending output into the compressed file. The parameter
- * _flush is as in the deflate() function. The return value is the zlib
- * error number (see function gzerror below). flush() returns Z_OK if
- * the flush_ parameter is Z_FINISH and all output could be flushed.
- * flush() should be called only when strictly necessary because it can
- * degrade compression.
- */
- int flush(int _flush) {
- os_flush();
- return ::gzflush(m_fp, _flush);
- }
-
- /* Returns the error message for the last error which occurred on the
- * given compressed file. errnum is set to zlib error number. If an
- * error occurred in the file system and not in the compression library,
- * errnum is set to Z_ERRNO and the application may consult errno
- * to get the exact error code.
- */
- const char* error(int* errnum) {
- return ::gzerror(m_fp, errnum);
- }
-
- gzFile fp() { return m_fp; }
-
- ostream& os() {
- if (m_os == 0) m_os = new ostrstream;
- return *m_os;
- }
-
- void os_flush() {
- if (m_os && m_os->pcount()>0) {
- ostrstream* oss = new ostrstream;
- oss->fill(m_os->fill());
- oss->flags(m_os->flags());
- oss->precision(m_os->precision());
- oss->width(m_os->width());
- ::gzwrite(m_fp, m_os->str(), m_os->pcount());
- delete[] m_os->str(); delete m_os; m_os = oss;
- }
- }
-
- private:
- gzFile m_fp;
- ostrstream* m_os;
-};
-
-/*
- * Binary write the given (array of) object(s) into the compressed file.
- * returns the number of uncompressed bytes actually written
- * (0 in case of error).
- */
-template <class T, class Items>
-inline int write(ozstream& zs, const T* x, Items items) {
- return ::gzwrite(zs.fp(), (voidp) x, items*sizeof(T));
-}
-
-/*
- * Binary output with the '<' operator.
- */
-template <class T>
-inline ozstream& operator<(ozstream& zs, const T& x) {
- ::gzwrite(zs.fp(), (voidp) &x, sizeof(T));
- return zs;
-}
-
-inline zstringlen::zstringlen(ozstream& zs, const char* x) {
- val.byte = 255; val.word = ::strlen(x);
- if (val.word < 255) zs < (val.byte = val.word);
- else zs < val;
-}
-
-/*
- * Write length of string + the string with the '<' operator.
- */
-inline ozstream& operator<(ozstream& zs, const char* x) {
- zstringlen len(zs, x);
- ::gzwrite(zs.fp(), (voidp) x, len.value());
- return zs;
-}
-
-#ifdef _MSC_VER
-inline ozstream& operator<(ozstream& zs, char* const& x) {
- return zs < (const char*) x;
-}
-#endif
-
-/*
- * Ascii write with the << operator;
- */
-template <class T>
-inline ostream& operator<<(ozstream& zs, const T& x) {
- zs.os_flush();
- return zs.os() << x;
-}
-
-#endif
diff --git a/third-party/zlib/contrib/iostream2/zstream_test.cpp b/third-party/zlib/contrib/iostream2/zstream_test.cpp
deleted file mode 100644
index 6273f62..0000000
--- a/third-party/zlib/contrib/iostream2/zstream_test.cpp
+++ /dev/null
@@ -1,25 +0,0 @@
-#include "zstream.h"
-#include <math.h>
-#include <stdlib.h>
-#include <iomanip.h>
-
-void main() {
- char h[256] = "Hello";
- char* g = "Goodbye";
- ozstream out("temp.gz");
- out < "This works well" < h < g;
- out.close();
-
- izstream in("temp.gz"); // read it back
- char *x = read_string(in), *y = new char[256], z[256];
- in > y > z;
- in.close();
- cout << x << endl << y << endl << z << endl;
-
- out.open("temp.gz"); // try ascii output; zcat temp.gz to see the results
- out << setw(50) << setfill('#') << setprecision(20) << x << endl << y << endl << z << endl;
- out << z << endl << y << endl << x << endl;
- out << 1.1234567890123456789 << endl;
-
- delete[] x; delete[] y;
-}
diff --git a/third-party/zlib/contrib/iostream3/README b/third-party/zlib/contrib/iostream3/README
deleted file mode 100644
index f7b319a..0000000
--- a/third-party/zlib/contrib/iostream3/README
+++ /dev/null
@@ -1,35 +0,0 @@
-These classes provide a C++ stream interface to the zlib library. It allows you
-to do things like:
-
- gzofstream outf("blah.gz");
- outf << "These go into the gzip file " << 123 << endl;
-
-It does this by deriving a specialized stream buffer for gzipped files, which is
-the way Stroustrup would have done it. :->
-
-The gzifstream and gzofstream classes were originally written by Kevin Ruland
-and made available in the zlib contrib/iostream directory. The older version still
-compiles under gcc 2.xx, but not under gcc 3.xx, which sparked the development of
-this version.
-
-The new classes are as standard-compliant as possible, closely following the
-approach of the standard library's fstream classes. It compiles under gcc versions
-3.2 and 3.3, but not under gcc 2.xx. This is mainly due to changes in the standard
-library naming scheme. The new version of gzifstream/gzofstream/gzfilebuf differs
-from the previous one in the following respects:
-- added showmanyc
-- added setbuf, with support for unbuffered output via setbuf(0,0)
-- a few bug fixes of stream behavior
-- gzipped output file opened with default compression level instead of maximum level
-- setcompressionlevel()/strategy() members replaced by single setcompression()
-
-The code is provided "as is", with the permission to use, copy, modify, distribute
-and sell it for any purpose without fee.
-
-Ludwig Schwardt
-<schwardt at sun.ac.za>
-
-DSP Lab
-Electrical & Electronic Engineering Department
-University of Stellenbosch
-South Africa
diff --git a/third-party/zlib/contrib/iostream3/TODO b/third-party/zlib/contrib/iostream3/TODO
deleted file mode 100644
index 7032f97..0000000
--- a/third-party/zlib/contrib/iostream3/TODO
+++ /dev/null
@@ -1,17 +0,0 @@
-Possible upgrades to gzfilebuf:
-
-- The ability to do putback (e.g. putbackfail)
-
-- The ability to seek (zlib supports this, but could be slow/tricky)
-
-- Simultaneous read/write access (does it make sense?)
-
-- Support for ios_base::ate open mode
-
-- Locale support?
-
-- Check public interface to see which calls give problems
- (due to dependence on library internals)
-
-- Override operator<<(ostream&, gzfilebuf*) to allow direct copying
- of stream buffer to stream ( i.e. os << is.rdbuf(); )
diff --git a/third-party/zlib/contrib/iostream3/test.cc b/third-party/zlib/contrib/iostream3/test.cc
deleted file mode 100644
index 9423533..0000000
--- a/third-party/zlib/contrib/iostream3/test.cc
+++ /dev/null
@@ -1,50 +0,0 @@
-/*
- * Test program for gzifstream and gzofstream
- *
- * by Ludwig Schwardt <schwardt at sun.ac.za>
- * original version by Kevin Ruland <kevin at rodin.wustl.edu>
- */
-
-#include "zfstream.h"
-#include <iostream> // for cout
-
-int main() {
-
- gzofstream outf;
- gzifstream inf;
- char buf[80];
-
- outf.open("test1.txt.gz");
- outf << "The quick brown fox sidestepped the lazy canine\n"
- << 1.3 << "\nPlan " << 9 << std::endl;
- outf.close();
- std::cout << "Wrote the following message to 'test1.txt.gz' (check with zcat or zless):\n"
- << "The quick brown fox sidestepped the lazy canine\n"
- << 1.3 << "\nPlan " << 9 << std::endl;
-
- std::cout << "\nReading 'test1.txt.gz' (buffered) produces:\n";
- inf.open("test1.txt.gz");
- while (inf.getline(buf,80,'\n')) {
- std::cout << buf << "\t(" << inf.rdbuf()->in_avail() << " chars left in buffer)\n";
- }
- inf.close();
-
- outf.rdbuf()->pubsetbuf(0,0);
- outf.open("test2.txt.gz");
- outf << setcompression(Z_NO_COMPRESSION)
- << "The quick brown fox sidestepped the lazy canine\n"
- << 1.3 << "\nPlan " << 9 << std::endl;
- outf.close();
- std::cout << "\nWrote the same message to 'test2.txt.gz' in uncompressed form";
-
- std::cout << "\nReading 'test2.txt.gz' (unbuffered) produces:\n";
- inf.rdbuf()->pubsetbuf(0,0);
- inf.open("test2.txt.gz");
- while (inf.getline(buf,80,'\n')) {
- std::cout << buf << "\t(" << inf.rdbuf()->in_avail() << " chars left in buffer)\n";
- }
- inf.close();
-
- return 0;
-
-}
diff --git a/third-party/zlib/contrib/iostream3/zfstream.cc b/third-party/zlib/contrib/iostream3/zfstream.cc
deleted file mode 100644
index 94eb933..0000000
--- a/third-party/zlib/contrib/iostream3/zfstream.cc
+++ /dev/null
@@ -1,479 +0,0 @@
-/*
- * A C++ I/O streams interface to the zlib gz* functions
- *
- * by Ludwig Schwardt <schwardt at sun.ac.za>
- * original version by Kevin Ruland <kevin at rodin.wustl.edu>
- *
- * This version is standard-compliant and compatible with gcc 3.x.
- */
-
-#include "zfstream.h"
-#include <cstring> // for strcpy, strcat, strlen (mode strings)
-#include <cstdio> // for BUFSIZ
-
-// Internal buffer sizes (default and "unbuffered" versions)
-#define BIGBUFSIZE BUFSIZ
-#define SMALLBUFSIZE 1
-
-/*****************************************************************************/
-
-// Default constructor
-gzfilebuf::gzfilebuf()
-: file(NULL), io_mode(std::ios_base::openmode(0)), own_fd(false),
- buffer(NULL), buffer_size(BIGBUFSIZE), own_buffer(true)
-{
- // No buffers to start with
- this->disable_buffer();
-}
-
-// Destructor
-gzfilebuf::~gzfilebuf()
-{
- // Sync output buffer and close only if responsible for file
- // (i.e. attached streams should be left open at this stage)
- this->sync();
- if (own_fd)
- this->close();
- // Make sure internal buffer is deallocated
- this->disable_buffer();
-}
-
-// Set compression level and strategy
-int
-gzfilebuf::setcompression(int comp_level,
- int comp_strategy)
-{
- return gzsetparams(file, comp_level, comp_strategy);
-}
-
-// Open gzipped file
-gzfilebuf*
-gzfilebuf::open(const char *name,
- std::ios_base::openmode mode)
-{
- // Fail if file already open
- if (this->is_open())
- return NULL;
- // Don't support simultaneous read/write access (yet)
- if ((mode & std::ios_base::in) && (mode & std::ios_base::out))
- return NULL;
-
- // Build mode string for gzopen and check it [27.8.1.3.2]
- char char_mode[6] = "\0\0\0\0\0";
- if (!this->open_mode(mode, char_mode))
- return NULL;
-
- // Attempt to open file
- if ((file = gzopen(name, char_mode)) == NULL)
- return NULL;
-
- // On success, allocate internal buffer and set flags
- this->enable_buffer();
- io_mode = mode;
- own_fd = true;
- return this;
-}
-
-// Attach to gzipped file
-gzfilebuf*
-gzfilebuf::attach(int fd,
- std::ios_base::openmode mode)
-{
- // Fail if file already open
- if (this->is_open())
- return NULL;
- // Don't support simultaneous read/write access (yet)
- if ((mode & std::ios_base::in) && (mode & std::ios_base::out))
- return NULL;
-
- // Build mode string for gzdopen and check it [27.8.1.3.2]
- char char_mode[6] = "\0\0\0\0\0";
- if (!this->open_mode(mode, char_mode))
- return NULL;
-
- // Attempt to attach to file
- if ((file = gzdopen(fd, char_mode)) == NULL)
- return NULL;
-
- // On success, allocate internal buffer and set flags
- this->enable_buffer();
- io_mode = mode;
- own_fd = false;
- return this;
-}
-
-// Close gzipped file
-gzfilebuf*
-gzfilebuf::close()
-{
- // Fail immediately if no file is open
- if (!this->is_open())
- return NULL;
- // Assume success
- gzfilebuf* retval = this;
- // Attempt to sync and close gzipped file
- if (this->sync() == -1)
- retval = NULL;
- if (gzclose(file) < 0)
- retval = NULL;
- // File is now gone anyway (postcondition [27.8.1.3.8])
- file = NULL;
- own_fd = false;
- // Destroy internal buffer if it exists
- this->disable_buffer();
- return retval;
-}
-
-/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
-
-// Convert int open mode to mode string
-bool
-gzfilebuf::open_mode(std::ios_base::openmode mode,
- char* c_mode) const
-{
- bool testb = mode & std::ios_base::binary;
- bool testi = mode & std::ios_base::in;
- bool testo = mode & std::ios_base::out;
- bool testt = mode & std::ios_base::trunc;
- bool testa = mode & std::ios_base::app;
-
- // Check for valid flag combinations - see [27.8.1.3.2] (Table 92)
- // Original zfstream hardcoded the compression level to maximum here...
- // Double the time for less than 1% size improvement seems
- // excessive though - keeping it at the default level
- // To change back, just append "9" to the next three mode strings
- if (!testi && testo && !testt && !testa)
- strcpy(c_mode, "w");
- if (!testi && testo && !testt && testa)
- strcpy(c_mode, "a");
- if (!testi && testo && testt && !testa)
- strcpy(c_mode, "w");
- if (testi && !testo && !testt && !testa)
- strcpy(c_mode, "r");
- // No read/write mode yet
-// if (testi && testo && !testt && !testa)
-// strcpy(c_mode, "r+");
-// if (testi && testo && testt && !testa)
-// strcpy(c_mode, "w+");
-
- // Mode string should be empty for invalid combination of flags
- if (strlen(c_mode) == 0)
- return false;
- if (testb)
- strcat(c_mode, "b");
- return true;
-}
-
-// Determine number of characters in internal get buffer
-std::streamsize
-gzfilebuf::showmanyc()
-{
- // Calls to underflow will fail if file not opened for reading
- if (!this->is_open() || !(io_mode & std::ios_base::in))
- return -1;
- // Make sure get area is in use
- if (this->gptr() && (this->gptr() < this->egptr()))
- return std::streamsize(this->egptr() - this->gptr());
- else
- return 0;
-}
-
-// Fill get area from gzipped file
-gzfilebuf::int_type
-gzfilebuf::underflow()
-{
- // If something is left in the get area by chance, return it
- // (this shouldn't normally happen, as underflow is only supposed
- // to be called when gptr >= egptr, but it serves as error check)
- if (this->gptr() && (this->gptr() < this->egptr()))
- return traits_type::to_int_type(*(this->gptr()));
-
- // If the file hasn't been opened for reading, produce error
- if (!this->is_open() || !(io_mode & std::ios_base::in))
- return traits_type::eof();
-
- // Attempt to fill internal buffer from gzipped file
- // (buffer must be guaranteed to exist...)
- int bytes_read = gzread(file, buffer, buffer_size);
- // Indicates error or EOF
- if (bytes_read <= 0)
- {
- // Reset get area
- this->setg(buffer, buffer, buffer);
- return traits_type::eof();
- }
- // Make all bytes read from file available as get area
- this->setg(buffer, buffer, buffer + bytes_read);
-
- // Return next character in get area
- return traits_type::to_int_type(*(this->gptr()));
-}
-
-// Write put area to gzipped file
-gzfilebuf::int_type
-gzfilebuf::overflow(int_type c)
-{
- // Determine whether put area is in use
- if (this->pbase())
- {
- // Double-check pointer range
- if (this->pptr() > this->epptr() || this->pptr() < this->pbase())
- return traits_type::eof();
- // Add extra character to buffer if not EOF
- if (!traits_type::eq_int_type(c, traits_type::eof()))
- {
- *(this->pptr()) = traits_type::to_char_type(c);
- this->pbump(1);
- }
- // Number of characters to write to file
- int bytes_to_write = this->pptr() - this->pbase();
- // Overflow doesn't fail if nothing is to be written
- if (bytes_to_write > 0)
- {
- // If the file hasn't been opened for writing, produce error
- if (!this->is_open() || !(io_mode & std::ios_base::out))
- return traits_type::eof();
- // If gzipped file won't accept all bytes written to it, fail
- if (gzwrite(file, this->pbase(), bytes_to_write) != bytes_to_write)
- return traits_type::eof();
- // Reset next pointer to point to pbase on success
- this->pbump(-bytes_to_write);
- }
- }
- // Write extra character to file if not EOF
- else if (!traits_type::eq_int_type(c, traits_type::eof()))
- {
- // If the file hasn't been opened for writing, produce error
- if (!this->is_open() || !(io_mode & std::ios_base::out))
- return traits_type::eof();
- // Impromptu char buffer (allows "unbuffered" output)
- char_type last_char = traits_type::to_char_type(c);
- // If gzipped file won't accept this character, fail
- if (gzwrite(file, &last_char, 1) != 1)
- return traits_type::eof();
- }
-
- // If you got here, you have succeeded (even if c was EOF)
- // The return value should therefore be non-EOF
- if (traits_type::eq_int_type(c, traits_type::eof()))
- return traits_type::not_eof(c);
- else
- return c;
-}
-
-// Assign new buffer
-std::streambuf*
-gzfilebuf::setbuf(char_type* p,
- std::streamsize n)
-{
- // First make sure stuff is sync'ed, for safety
- if (this->sync() == -1)
- return NULL;
- // If buffering is turned off on purpose via setbuf(0,0), still allocate one...
- // "Unbuffered" only really refers to put [27.8.1.4.10], while get needs at
- // least a buffer of size 1 (very inefficient though, therefore make it bigger?)
- // This follows from [27.5.2.4.3]/12 (gptr needs to point at something, it seems)
- if (!p || !n)
- {
- // Replace existing buffer (if any) with small internal buffer
- this->disable_buffer();
- buffer = NULL;
- buffer_size = 0;
- own_buffer = true;
- this->enable_buffer();
- }
- else
- {
- // Replace existing buffer (if any) with external buffer
- this->disable_buffer();
- buffer = p;
- buffer_size = n;
- own_buffer = false;
- this->enable_buffer();
- }
- return this;
-}
-
-// Write put area to gzipped file (i.e. ensures that put area is empty)
-int
-gzfilebuf::sync()
-{
- return traits_type::eq_int_type(this->overflow(), traits_type::eof()) ? -1 : 0;
-}
-
-/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
-
-// Allocate internal buffer
-void
-gzfilebuf::enable_buffer()
-{
- // If internal buffer required, allocate one
- if (own_buffer && !buffer)
- {
- // Check for buffered vs. "unbuffered"
- if (buffer_size > 0)
- {
- // Allocate internal buffer
- buffer = new char_type[buffer_size];
- // Get area starts empty and will be expanded by underflow as need arises
- this->setg(buffer, buffer, buffer);
- // Setup entire internal buffer as put area.
- // The one-past-end pointer actually points to the last element of the buffer,
- // so that overflow(c) can safely add the extra character c to the sequence.
- // These pointers remain in place for the duration of the buffer
- this->setp(buffer, buffer + buffer_size - 1);
- }
- else
- {
- // Even in "unbuffered" case, (small?) get buffer is still required
- buffer_size = SMALLBUFSIZE;
- buffer = new char_type[buffer_size];
- this->setg(buffer, buffer, buffer);
- // "Unbuffered" means no put buffer
- this->setp(0, 0);
- }
- }
- else
- {
- // If buffer already allocated, reset buffer pointers just to make sure no
- // stale chars are lying around
- this->setg(buffer, buffer, buffer);
- this->setp(buffer, buffer + buffer_size - 1);
- }
-}
-
-// Destroy internal buffer
-void
-gzfilebuf::disable_buffer()
-{
- // If internal buffer exists, deallocate it
- if (own_buffer && buffer)
- {
- // Preserve unbuffered status by zeroing size
- if (!this->pbase())
- buffer_size = 0;
- delete[] buffer;
- buffer = NULL;
- this->setg(0, 0, 0);
- this->setp(0, 0);
- }
- else
- {
- // Reset buffer pointers to initial state if external buffer exists
- this->setg(buffer, buffer, buffer);
- if (buffer)
- this->setp(buffer, buffer + buffer_size - 1);
- else
- this->setp(0, 0);
- }
-}
-
-/*****************************************************************************/
-
-// Default constructor initializes stream buffer
-gzifstream::gzifstream()
-: std::istream(NULL), sb()
-{ this->init(&sb); }
-
-// Initialize stream buffer and open file
-gzifstream::gzifstream(const char* name,
- std::ios_base::openmode mode)
-: std::istream(NULL), sb()
-{
- this->init(&sb);
- this->open(name, mode);
-}
-
-// Initialize stream buffer and attach to file
-gzifstream::gzifstream(int fd,
- std::ios_base::openmode mode)
-: std::istream(NULL), sb()
-{
- this->init(&sb);
- this->attach(fd, mode);
-}
-
-// Open file and go into fail() state if unsuccessful
-void
-gzifstream::open(const char* name,
- std::ios_base::openmode mode)
-{
- if (!sb.open(name, mode | std::ios_base::in))
- this->setstate(std::ios_base::failbit);
- else
- this->clear();
-}
-
-// Attach to file and go into fail() state if unsuccessful
-void
-gzifstream::attach(int fd,
- std::ios_base::openmode mode)
-{
- if (!sb.attach(fd, mode | std::ios_base::in))
- this->setstate(std::ios_base::failbit);
- else
- this->clear();
-}
-
-// Close file
-void
-gzifstream::close()
-{
- if (!sb.close())
- this->setstate(std::ios_base::failbit);
-}
-
-/*****************************************************************************/
-
-// Default constructor initializes stream buffer
-gzofstream::gzofstream()
-: std::ostream(NULL), sb()
-{ this->init(&sb); }
-
-// Initialize stream buffer and open file
-gzofstream::gzofstream(const char* name,
- std::ios_base::openmode mode)
-: std::ostream(NULL), sb()
-{
- this->init(&sb);
- this->open(name, mode);
-}
-
-// Initialize stream buffer and attach to file
-gzofstream::gzofstream(int fd,
- std::ios_base::openmode mode)
-: std::ostream(NULL), sb()
-{
- this->init(&sb);
- this->attach(fd, mode);
-}
-
-// Open file and go into fail() state if unsuccessful
-void
-gzofstream::open(const char* name,
- std::ios_base::openmode mode)
-{
- if (!sb.open(name, mode | std::ios_base::out))
- this->setstate(std::ios_base::failbit);
- else
- this->clear();
-}
-
-// Attach to file and go into fail() state if unsuccessful
-void
-gzofstream::attach(int fd,
- std::ios_base::openmode mode)
-{
- if (!sb.attach(fd, mode | std::ios_base::out))
- this->setstate(std::ios_base::failbit);
- else
- this->clear();
-}
-
-// Close file
-void
-gzofstream::close()
-{
- if (!sb.close())
- this->setstate(std::ios_base::failbit);
-}
diff --git a/third-party/zlib/contrib/iostream3/zfstream.h b/third-party/zlib/contrib/iostream3/zfstream.h
deleted file mode 100644
index 8574479..0000000
--- a/third-party/zlib/contrib/iostream3/zfstream.h
+++ /dev/null
@@ -1,466 +0,0 @@
-/*
- * A C++ I/O streams interface to the zlib gz* functions
- *
- * by Ludwig Schwardt <schwardt at sun.ac.za>
- * original version by Kevin Ruland <kevin at rodin.wustl.edu>
- *
- * This version is standard-compliant and compatible with gcc 3.x.
- */
-
-#ifndef ZFSTREAM_H
-#define ZFSTREAM_H
-
-#include <istream> // not iostream, since we don't need cin/cout
-#include <ostream>
-#include "zlib.h"
-
-/*****************************************************************************/
-
-/**
- * @brief Gzipped file stream buffer class.
- *
- * This class implements basic_filebuf for gzipped files. It doesn't yet support
- * seeking (allowed by zlib but slow/limited), putback and read/write access
- * (tricky). Otherwise, it attempts to be a drop-in replacement for the standard
- * file streambuf.
-*/
-class gzfilebuf : public std::streambuf
-{
-public:
- // Default constructor.
- gzfilebuf();
-
- // Destructor.
- virtual
- ~gzfilebuf();
-
- /**
- * @brief Set compression level and strategy on the fly.
- * @param comp_level Compression level (see zlib.h for allowed values)
- * @param comp_strategy Compression strategy (see zlib.h for allowed values)
- * @return Z_OK on success, Z_STREAM_ERROR otherwise.
- *
- * Unfortunately, these parameters cannot be modified separately, as the
- * previous zfstream version assumed. Since the strategy is seldom changed,
- * it can default and setcompression(level) then becomes like the old
- * setcompressionlevel(level).
- */
- int
- setcompression(int comp_level,
- int comp_strategy = Z_DEFAULT_STRATEGY);
-
- /**
- * @brief Check if file is open.
- * @return True if file is open.
- */
- bool
- is_open() const { return (file != NULL); }
-
- /**
- * @brief Open gzipped file.
- * @param name File name.
- * @param mode Open mode flags.
- * @return @c this on success, NULL on failure.
- */
- gzfilebuf*
- open(const char* name,
- std::ios_base::openmode mode);
-
- /**
- * @brief Attach to already open gzipped file.
- * @param fd File descriptor.
- * @param mode Open mode flags.
- * @return @c this on success, NULL on failure.
- */
- gzfilebuf*
- attach(int fd,
- std::ios_base::openmode mode);
-
- /**
- * @brief Close gzipped file.
- * @return @c this on success, NULL on failure.
- */
- gzfilebuf*
- close();
-
-protected:
- /**
- * @brief Convert ios open mode int to mode string used by zlib.
- * @return True if valid mode flag combination.
- */
- bool
- open_mode(std::ios_base::openmode mode,
- char* c_mode) const;
-
- /**
- * @brief Number of characters available in stream buffer.
- * @return Number of characters.
- *
- * This indicates number of characters in get area of stream buffer.
- * These characters can be read without accessing the gzipped file.
- */
- virtual std::streamsize
- showmanyc();
-
- /**
- * @brief Fill get area from gzipped file.
- * @return First character in get area on success, EOF on error.
- *
- * This actually reads characters from gzipped file to stream
- * buffer. Always buffered.
- */
- virtual int_type
- underflow();
-
- /**
- * @brief Write put area to gzipped file.
- * @param c Extra character to add to buffer contents.
- * @return Non-EOF on success, EOF on error.
- *
- * This actually writes characters in stream buffer to
- * gzipped file. With unbuffered output this is done one
- * character at a time.
- */
- virtual int_type
- overflow(int_type c = traits_type::eof());
-
- /**
- * @brief Installs external stream buffer.
- * @param p Pointer to char buffer.
- * @param n Size of external buffer.
- * @return @c this on success, NULL on failure.
- *
- * Call setbuf(0,0) to enable unbuffered output.
- */
- virtual std::streambuf*
- setbuf(char_type* p,
- std::streamsize n);
-
- /**
- * @brief Flush stream buffer to file.
- * @return 0 on success, -1 on error.
- *
- * This calls underflow(EOF) to do the job.
- */
- virtual int
- sync();
-
-//
-// Some future enhancements
-//
-// virtual int_type uflow();
-// virtual int_type pbackfail(int_type c = traits_type::eof());
-// virtual pos_type
-// seekoff(off_type off,
-// std::ios_base::seekdir way,
-// std::ios_base::openmode mode = std::ios_base::in|std::ios_base::out);
-// virtual pos_type
-// seekpos(pos_type sp,
-// std::ios_base::openmode mode = std::ios_base::in|std::ios_base::out);
-
-private:
- /**
- * @brief Allocate internal buffer.
- *
- * This function is safe to call multiple times. It will ensure
- * that a proper internal buffer exists if it is required. If the
- * buffer already exists or is external, the buffer pointers will be
- * reset to their original state.
- */
- void
- enable_buffer();
-
- /**
- * @brief Destroy internal buffer.
- *
- * This function is safe to call multiple times. It will ensure
- * that the internal buffer is deallocated if it exists. In any
- * case, it will also reset the buffer pointers.
- */
- void
- disable_buffer();
-
- /**
- * Underlying file pointer.
- */
- gzFile file;
-
- /**
- * Mode in which file was opened.
- */
- std::ios_base::openmode io_mode;
-
- /**
- * @brief True if this object owns file descriptor.
- *
- * This makes the class responsible for closing the file
- * upon destruction.
- */
- bool own_fd;
-
- /**
- * @brief Stream buffer.
- *
- * For simplicity this remains allocated on the free store for the
- * entire life span of the gzfilebuf object, unless replaced by setbuf.
- */
- char_type* buffer;
-
- /**
- * @brief Stream buffer size.
- *
- * Defaults to system default buffer size (typically 8192 bytes).
- * Modified by setbuf.
- */
- std::streamsize buffer_size;
-
- /**
- * @brief True if this object owns stream buffer.
- *
- * This makes the class responsible for deleting the buffer
- * upon destruction.
- */
- bool own_buffer;
-};
-
-/*****************************************************************************/
-
-/**
- * @brief Gzipped file input stream class.
- *
- * This class implements ifstream for gzipped files. Seeking and putback
- * is not supported yet.
-*/
-class gzifstream : public std::istream
-{
-public:
- // Default constructor
- gzifstream();
-
- /**
- * @brief Construct stream on gzipped file to be opened.
- * @param name File name.
- * @param mode Open mode flags (forced to contain ios::in).
- */
- explicit
- gzifstream(const char* name,
- std::ios_base::openmode mode = std::ios_base::in);
-
- /**
- * @brief Construct stream on already open gzipped file.
- * @param fd File descriptor.
- * @param mode Open mode flags (forced to contain ios::in).
- */
- explicit
- gzifstream(int fd,
- std::ios_base::openmode mode = std::ios_base::in);
-
- /**
- * Obtain underlying stream buffer.
- */
- gzfilebuf*
- rdbuf() const
- { return const_cast<gzfilebuf*>(&sb); }
-
- /**
- * @brief Check if file is open.
- * @return True if file is open.
- */
- bool
- is_open() { return sb.is_open(); }
-
- /**
- * @brief Open gzipped file.
- * @param name File name.
- * @param mode Open mode flags (forced to contain ios::in).
- *
- * Stream will be in state good() if file opens successfully;
- * otherwise in state fail(). This differs from the behavior of
- * ifstream, which never sets the state to good() and therefore
- * won't allow you to reuse the stream for a second file unless
- * you manually clear() the state. The choice is a matter of
- * convenience.
- */
- void
- open(const char* name,
- std::ios_base::openmode mode = std::ios_base::in);
-
- /**
- * @brief Attach to already open gzipped file.
- * @param fd File descriptor.
- * @param mode Open mode flags (forced to contain ios::in).
- *
- * Stream will be in state good() if attach succeeded; otherwise
- * in state fail().
- */
- void
- attach(int fd,
- std::ios_base::openmode mode = std::ios_base::in);
-
- /**
- * @brief Close gzipped file.
- *
- * Stream will be in state fail() if close failed.
- */
- void
- close();
-
-private:
- /**
- * Underlying stream buffer.
- */
- gzfilebuf sb;
-};
-
-/*****************************************************************************/
-
-/**
- * @brief Gzipped file output stream class.
- *
- * This class implements ofstream for gzipped files. Seeking and putback
- * is not supported yet.
-*/
-class gzofstream : public std::ostream
-{
-public:
- // Default constructor
- gzofstream();
-
- /**
- * @brief Construct stream on gzipped file to be opened.
- * @param name File name.
- * @param mode Open mode flags (forced to contain ios::out).
- */
- explicit
- gzofstream(const char* name,
- std::ios_base::openmode mode = std::ios_base::out);
-
- /**
- * @brief Construct stream on already open gzipped file.
- * @param fd File descriptor.
- * @param mode Open mode flags (forced to contain ios::out).
- */
- explicit
- gzofstream(int fd,
- std::ios_base::openmode mode = std::ios_base::out);
-
- /**
- * Obtain underlying stream buffer.
- */
- gzfilebuf*
- rdbuf() const
- { return const_cast<gzfilebuf*>(&sb); }
-
- /**
- * @brief Check if file is open.
- * @return True if file is open.
- */
- bool
- is_open() { return sb.is_open(); }
-
- /**
- * @brief Open gzipped file.
- * @param name File name.
- * @param mode Open mode flags (forced to contain ios::out).
- *
- * Stream will be in state good() if file opens successfully;
- * otherwise in state fail(). This differs from the behavior of
- * ofstream, which never sets the state to good() and therefore
- * won't allow you to reuse the stream for a second file unless
- * you manually clear() the state. The choice is a matter of
- * convenience.
- */
- void
- open(const char* name,
- std::ios_base::openmode mode = std::ios_base::out);
-
- /**
- * @brief Attach to already open gzipped file.
- * @param fd File descriptor.
- * @param mode Open mode flags (forced to contain ios::out).
- *
- * Stream will be in state good() if attach succeeded; otherwise
- * in state fail().
- */
- void
- attach(int fd,
- std::ios_base::openmode mode = std::ios_base::out);
-
- /**
- * @brief Close gzipped file.
- *
- * Stream will be in state fail() if close failed.
- */
- void
- close();
-
-private:
- /**
- * Underlying stream buffer.
- */
- gzfilebuf sb;
-};
-
-/*****************************************************************************/
-
-/**
- * @brief Gzipped file output stream manipulator class.
- *
- * This class defines a two-argument manipulator for gzofstream. It is used
- * as base for the setcompression(int,int) manipulator.
-*/
-template<typename T1, typename T2>
- class gzomanip2
- {
- public:
- // Allows insertor to peek at internals
- template <typename Ta, typename Tb>
- friend gzofstream&
- operator<<(gzofstream&,
- const gzomanip2<Ta,Tb>&);
-
- // Constructor
- gzomanip2(gzofstream& (*f)(gzofstream&, T1, T2),
- T1 v1,
- T2 v2);
- private:
- // Underlying manipulator function
- gzofstream&
- (*func)(gzofstream&, T1, T2);
-
- // Arguments for manipulator function
- T1 val1;
- T2 val2;
- };
-
-/*****************************************************************************/
-
-// Manipulator function thunks through to stream buffer
-inline gzofstream&
-setcompression(gzofstream &gzs, int l, int s = Z_DEFAULT_STRATEGY)
-{
- (gzs.rdbuf())->setcompression(l, s);
- return gzs;
-}
-
-// Manipulator constructor stores arguments
-template<typename T1, typename T2>
- inline
- gzomanip2<T1,T2>::gzomanip2(gzofstream &(*f)(gzofstream &, T1, T2),
- T1 v1,
- T2 v2)
- : func(f), val1(v1), val2(v2)
- { }
-
-// Insertor applies underlying manipulator function to stream
-template<typename T1, typename T2>
- inline gzofstream&
- operator<<(gzofstream& s, const gzomanip2<T1,T2>& m)
- { return (*m.func)(s, m.val1, m.val2); }
-
-// Insert this onto stream to simplify setting of compression level
-inline gzomanip2<int,int>
-setcompression(int l, int s = Z_DEFAULT_STRATEGY)
-{ return gzomanip2<int,int>(&setcompression, l, s); }
-
-#endif // ZFSTREAM_H
diff --git a/third-party/zlib/contrib/masmx64/bld_ml64.bat b/third-party/zlib/contrib/masmx64/bld_ml64.bat
deleted file mode 100644
index 8f9343d..0000000
--- a/third-party/zlib/contrib/masmx64/bld_ml64.bat
+++ /dev/null
@@ -1,2 +0,0 @@
-ml64.exe /Flinffasx64 /c /Zi inffasx64.asm
-ml64.exe /Flgvmat64 /c /Zi gvmat64.asm
diff --git a/third-party/zlib/contrib/masmx64/gvmat64.asm b/third-party/zlib/contrib/masmx64/gvmat64.asm
deleted file mode 100644
index 9879c28..0000000
--- a/third-party/zlib/contrib/masmx64/gvmat64.asm
+++ /dev/null
@@ -1,553 +0,0 @@
-;uInt longest_match_x64(
-; deflate_state *s,
-; IPos cur_match); /* current match */
-
-; gvmat64.asm -- Asm portion of the optimized longest_match for 32 bits x86_64
-; (AMD64 on Athlon 64, Opteron, Phenom
-; and Intel EM64T on Pentium 4 with EM64T, Pentium D, Core 2 Duo, Core I5/I7)
-; Copyright (C) 1995-2010 Jean-loup Gailly, Brian Raiter and Gilles Vollant.
-;
-; File written by Gilles Vollant, by converting to assembly the longest_match
-; from Jean-loup Gailly in deflate.c of zLib and infoZip zip.
-;
-; and by taking inspiration on asm686 with masm, optimised assembly code
-; from Brian Raiter, written 1998
-;
-; This software is provided 'as-is', without any express or implied
-; warranty. In no event will the authors be held liable for any damages
-; arising from the use of this software.
-;
-; Permission is granted to anyone to use this software for any purpose,
-; including commercial applications, and to alter it and redistribute it
-; freely, subject to the following restrictions:
-;
-; 1. The origin of this software must not be misrepresented; you must not
-; claim that you wrote the original software. If you use this software
-; in a product, an acknowledgment in the product documentation would be
-; appreciated but is not required.
-; 2. Altered source versions must be plainly marked as such, and must not be
-; misrepresented as being the original software
-; 3. This notice may not be removed or altered from any source distribution.
-;
-;
-;
-; http://www.zlib.net
-; http://www.winimage.com/zLibDll
-; http://www.muppetlabs.com/~breadbox/software/assembly.html
-;
-; to compile this file for infozip Zip, I use option:
-; ml64.exe /Flgvmat64 /c /Zi /DINFOZIP gvmat64.asm
-;
-; to compile this file for zLib, I use option:
-; ml64.exe /Flgvmat64 /c /Zi gvmat64.asm
-; Be carrefull to adapt zlib1222add below to your version of zLib
-; (if you use a version of zLib before 1.0.4 or after 1.2.2.2, change
-; value of zlib1222add later)
-;
-; This file compile with Microsoft Macro Assembler (x64) for AMD64
-;
-; ml64.exe is given with Visual Studio 2005/2008/2010 and Windows WDK
-;
-; (you can get Windows WDK with ml64 for AMD64 from
-; http://www.microsoft.com/whdc/Devtools/wdk/default.mspx for low price)
-;
-
-
-;uInt longest_match(s, cur_match)
-; deflate_state *s;
-; IPos cur_match; /* current match */
-.code
-longest_match PROC
-
-
-;LocalVarsSize equ 88
- LocalVarsSize equ 72
-
-; register used : rax,rbx,rcx,rdx,rsi,rdi,r8,r9,r10,r11,r12
-; free register : r14,r15
-; register can be saved : rsp
-
- chainlenwmask equ rsp + 8 - LocalVarsSize ; high word: current chain len
- ; low word: s->wmask
-;window equ rsp + xx - LocalVarsSize ; local copy of s->window ; stored in r10
-;windowbestlen equ rsp + xx - LocalVarsSize ; s->window + bestlen , use r10+r11
-;scanstart equ rsp + xx - LocalVarsSize ; first two bytes of string ; stored in r12w
-;scanend equ rsp + xx - LocalVarsSize ; last two bytes of string use ebx
-;scanalign equ rsp + xx - LocalVarsSize ; dword-misalignment of string r13
-;bestlen equ rsp + xx - LocalVarsSize ; size of best match so far -> r11d
-;scan equ rsp + xx - LocalVarsSize ; ptr to string wanting match -> r9
-IFDEF INFOZIP
-ELSE
- nicematch equ (rsp + 16 - LocalVarsSize) ; a good enough match size
-ENDIF
-
-save_rdi equ rsp + 24 - LocalVarsSize
-save_rsi equ rsp + 32 - LocalVarsSize
-save_rbx equ rsp + 40 - LocalVarsSize
-save_rbp equ rsp + 48 - LocalVarsSize
-save_r12 equ rsp + 56 - LocalVarsSize
-save_r13 equ rsp + 64 - LocalVarsSize
-;save_r14 equ rsp + 72 - LocalVarsSize
-;save_r15 equ rsp + 80 - LocalVarsSize
-
-
-; summary of register usage
-; scanend ebx
-; scanendw bx
-; chainlenwmask edx
-; curmatch rsi
-; curmatchd esi
-; windowbestlen r8
-; scanalign r9
-; scanalignd r9d
-; window r10
-; bestlen r11
-; bestlend r11d
-; scanstart r12d
-; scanstartw r12w
-; scan r13
-; nicematch r14d
-; limit r15
-; limitd r15d
-; prev rcx
-
-; all the +4 offsets are due to the addition of pending_buf_size (in zlib
-; in the deflate_state structure since the asm code was first written
-; (if you compile with zlib 1.0.4 or older, remove the +4).
-; Note : these value are good with a 8 bytes boundary pack structure
-
-
- MAX_MATCH equ 258
- MIN_MATCH equ 3
- MIN_LOOKAHEAD equ (MAX_MATCH+MIN_MATCH+1)
-
-
-;;; Offsets for fields in the deflate_state structure. These numbers
-;;; are calculated from the definition of deflate_state, with the
-;;; assumption that the compiler will dword-align the fields. (Thus,
-;;; changing the definition of deflate_state could easily cause this
-;;; program to crash horribly, without so much as a warning at
-;;; compile time. Sigh.)
-
-; all the +zlib1222add offsets are due to the addition of fields
-; in zlib in the deflate_state structure since the asm code was first written
-; (if you compile with zlib 1.0.4 or older, use "zlib1222add equ (-4)").
-; (if you compile with zlib between 1.0.5 and 1.2.2.1, use "zlib1222add equ 0").
-; if you compile with zlib 1.2.2.2 or later , use "zlib1222add equ 8").
-
-
-IFDEF INFOZIP
-
-_DATA SEGMENT
-COMM window_size:DWORD
-; WMask ; 7fff
-COMM window:BYTE:010040H
-COMM prev:WORD:08000H
-; MatchLen : unused
-; PrevMatch : unused
-COMM strstart:DWORD
-COMM match_start:DWORD
-; Lookahead : ignore
-COMM prev_length:DWORD ; PrevLen
-COMM max_chain_length:DWORD
-COMM good_match:DWORD
-COMM nice_match:DWORD
-prev_ad equ OFFSET prev
-window_ad equ OFFSET window
-nicematch equ nice_match
-_DATA ENDS
-WMask equ 07fffh
-
-ELSE
-
- IFNDEF zlib1222add
- zlib1222add equ 8
- ENDIF
-dsWSize equ 56+zlib1222add+(zlib1222add/2)
-dsWMask equ 64+zlib1222add+(zlib1222add/2)
-dsWindow equ 72+zlib1222add
-dsPrev equ 88+zlib1222add
-dsMatchLen equ 128+zlib1222add
-dsPrevMatch equ 132+zlib1222add
-dsStrStart equ 140+zlib1222add
-dsMatchStart equ 144+zlib1222add
-dsLookahead equ 148+zlib1222add
-dsPrevLen equ 152+zlib1222add
-dsMaxChainLen equ 156+zlib1222add
-dsGoodMatch equ 172+zlib1222add
-dsNiceMatch equ 176+zlib1222add
-
-window_size equ [ rcx + dsWSize]
-WMask equ [ rcx + dsWMask]
-window_ad equ [ rcx + dsWindow]
-prev_ad equ [ rcx + dsPrev]
-strstart equ [ rcx + dsStrStart]
-match_start equ [ rcx + dsMatchStart]
-Lookahead equ [ rcx + dsLookahead] ; 0ffffffffh on infozip
-prev_length equ [ rcx + dsPrevLen]
-max_chain_length equ [ rcx + dsMaxChainLen]
-good_match equ [ rcx + dsGoodMatch]
-nice_match equ [ rcx + dsNiceMatch]
-ENDIF
-
-; parameter 1 in r8(deflate state s), param 2 in rdx (cur match)
-
-; see http://weblogs.asp.net/oldnewthing/archive/2004/01/14/58579.aspx and
-; http://msdn.microsoft.com/library/en-us/kmarch/hh/kmarch/64bitAMD_8e951dd2-ee77-4728-8702-55ce4b5dd24a.xml.asp
-;
-; All registers must be preserved across the call, except for
-; rax, rcx, rdx, r8, r9, r10, and r11, which are scratch.
-
-
-
-;;; Save registers that the compiler may be using, and adjust esp to
-;;; make room for our stack frame.
-
-
-;;; Retrieve the function arguments. r8d will hold cur_match
-;;; throughout the entire function. edx will hold the pointer to the
-;;; deflate_state structure during the function's setup (before
-;;; entering the main loop.
-
-; parameter 1 in rcx (deflate_state* s), param 2 in edx -> r8 (cur match)
-
-; this clear high 32 bits of r8, which can be garbage in both r8 and rdx
-
- mov [save_rdi],rdi
- mov [save_rsi],rsi
- mov [save_rbx],rbx
- mov [save_rbp],rbp
-IFDEF INFOZIP
- mov r8d,ecx
-ELSE
- mov r8d,edx
-ENDIF
- mov [save_r12],r12
- mov [save_r13],r13
-; mov [save_r14],r14
-; mov [save_r15],r15
-
-
-;;; uInt wmask = s->w_mask;
-;;; unsigned chain_length = s->max_chain_length;
-;;; if (s->prev_length >= s->good_match) {
-;;; chain_length >>= 2;
-;;; }
-
- mov edi, prev_length
- mov esi, good_match
- mov eax, WMask
- mov ebx, max_chain_length
- cmp edi, esi
- jl LastMatchGood
- shr ebx, 2
-LastMatchGood:
-
-;;; chainlen is decremented once beforehand so that the function can
-;;; use the sign flag instead of the zero flag for the exit test.
-;;; It is then shifted into the high word, to make room for the wmask
-;;; value, which it will always accompany.
-
- dec ebx
- shl ebx, 16
- or ebx, eax
-
-;;; on zlib only
-;;; if ((uInt)nice_match > s->lookahead) nice_match = s->lookahead;
-
-IFDEF INFOZIP
- mov [chainlenwmask], ebx
-; on infozip nice_match = [nice_match]
-ELSE
- mov eax, nice_match
- mov [chainlenwmask], ebx
- mov r10d, Lookahead
- cmp r10d, eax
- cmovnl r10d, eax
- mov [nicematch],r10d
-ENDIF
-
-;;; register Bytef *scan = s->window + s->strstart;
- mov r10, window_ad
- mov ebp, strstart
- lea r13, [r10 + rbp]
-
-;;; Determine how many bytes the scan ptr is off from being
-;;; dword-aligned.
-
- mov r9,r13
- neg r13
- and r13,3
-
-;;; IPos limit = s->strstart > (IPos)MAX_DIST(s) ?
-;;; s->strstart - (IPos)MAX_DIST(s) : NIL;
-IFDEF INFOZIP
- mov eax,07efah ; MAX_DIST = (WSIZE-MIN_LOOKAHEAD) (0x8000-(3+8+1))
-ELSE
- mov eax, window_size
- sub eax, MIN_LOOKAHEAD
-ENDIF
- xor edi,edi
- sub ebp, eax
-
- mov r11d, prev_length
-
- cmovng ebp,edi
-
-;;; int best_len = s->prev_length;
-
-
-;;; Store the sum of s->window + best_len in esi locally, and in esi.
-
- lea rsi,[r10+r11]
-
-;;; register ush scan_start = *(ushf*)scan;
-;;; register ush scan_end = *(ushf*)(scan+best_len-1);
-;;; Posf *prev = s->prev;
-
- movzx r12d,word ptr [r9]
- movzx ebx, word ptr [r9 + r11 - 1]
-
- mov rdi, prev_ad
-
-;;; Jump into the main loop.
-
- mov edx, [chainlenwmask]
-
- cmp bx,word ptr [rsi + r8 - 1]
- jz LookupLoopIsZero
-
-LookupLoop1:
- and r8d, edx
-
- movzx r8d, word ptr [rdi + r8*2]
- cmp r8d, ebp
- jbe LeaveNow
- sub edx, 00010000h
- js LeaveNow
-
-LoopEntry1:
- cmp bx,word ptr [rsi + r8 - 1]
- jz LookupLoopIsZero
-
-LookupLoop2:
- and r8d, edx
-
- movzx r8d, word ptr [rdi + r8*2]
- cmp r8d, ebp
- jbe LeaveNow
- sub edx, 00010000h
- js LeaveNow
-
-LoopEntry2:
- cmp bx,word ptr [rsi + r8 - 1]
- jz LookupLoopIsZero
-
-LookupLoop4:
- and r8d, edx
-
- movzx r8d, word ptr [rdi + r8*2]
- cmp r8d, ebp
- jbe LeaveNow
- sub edx, 00010000h
- js LeaveNow
-
-LoopEntry4:
-
- cmp bx,word ptr [rsi + r8 - 1]
- jnz LookupLoop1
- jmp LookupLoopIsZero
-
-
-;;; do {
-;;; match = s->window + cur_match;
-;;; if (*(ushf*)(match+best_len-1) != scan_end ||
-;;; *(ushf*)match != scan_start) continue;
-;;; [...]
-;;; } while ((cur_match = prev[cur_match & wmask]) > limit
-;;; && --chain_length != 0);
-;;;
-;;; Here is the inner loop of the function. The function will spend the
-;;; majority of its time in this loop, and majority of that time will
-;;; be spent in the first ten instructions.
-;;;
-;;; Within this loop:
-;;; ebx = scanend
-;;; r8d = curmatch
-;;; edx = chainlenwmask - i.e., ((chainlen << 16) | wmask)
-;;; esi = windowbestlen - i.e., (window + bestlen)
-;;; edi = prev
-;;; ebp = limit
-
-LookupLoop:
- and r8d, edx
-
- movzx r8d, word ptr [rdi + r8*2]
- cmp r8d, ebp
- jbe LeaveNow
- sub edx, 00010000h
- js LeaveNow
-
-LoopEntry:
-
- cmp bx,word ptr [rsi + r8 - 1]
- jnz LookupLoop1
-LookupLoopIsZero:
- cmp r12w, word ptr [r10 + r8]
- jnz LookupLoop1
-
-
-;;; Store the current value of chainlen.
- mov [chainlenwmask], edx
-
-;;; Point edi to the string under scrutiny, and esi to the string we
-;;; are hoping to match it up with. In actuality, esi and edi are
-;;; both pointed (MAX_MATCH_8 - scanalign) bytes ahead, and edx is
-;;; initialized to -(MAX_MATCH_8 - scanalign).
-
- lea rsi,[r8+r10]
- mov rdx, 0fffffffffffffef8h; -(MAX_MATCH_8)
- lea rsi, [rsi + r13 + 0108h] ;MAX_MATCH_8]
- lea rdi, [r9 + r13 + 0108h] ;MAX_MATCH_8]
-
- prefetcht1 [rsi+rdx]
- prefetcht1 [rdi+rdx]
-
-
-;;; Test the strings for equality, 8 bytes at a time. At the end,
-;;; adjust rdx so that it is offset to the exact byte that mismatched.
-;;;
-;;; We already know at this point that the first three bytes of the
-;;; strings match each other, and they can be safely passed over before
-;;; starting the compare loop. So what this code does is skip over 0-3
-;;; bytes, as much as necessary in order to dword-align the edi
-;;; pointer. (rsi will still be misaligned three times out of four.)
-;;;
-;;; It should be confessed that this loop usually does not represent
-;;; much of the total running time. Replacing it with a more
-;;; straightforward "rep cmpsb" would not drastically degrade
-;;; performance.
-
-
-LoopCmps:
- mov rax, [rsi + rdx]
- xor rax, [rdi + rdx]
- jnz LeaveLoopCmps
-
- mov rax, [rsi + rdx + 8]
- xor rax, [rdi + rdx + 8]
- jnz LeaveLoopCmps8
-
-
- mov rax, [rsi + rdx + 8+8]
- xor rax, [rdi + rdx + 8+8]
- jnz LeaveLoopCmps16
-
- add rdx,8+8+8
-
- jnz short LoopCmps
- jmp short LenMaximum
-LeaveLoopCmps16: add rdx,8
-LeaveLoopCmps8: add rdx,8
-LeaveLoopCmps:
-
- test eax, 0000FFFFh
- jnz LenLower
-
- test eax,0ffffffffh
-
- jnz LenLower32
-
- add rdx,4
- shr rax,32
- or ax,ax
- jnz LenLower
-
-LenLower32:
- shr eax,16
- add rdx,2
-LenLower: sub al, 1
- adc rdx, 0
-;;; Calculate the length of the match. If it is longer than MAX_MATCH,
-;;; then automatically accept it as the best possible match and leave.
-
- lea rax, [rdi + rdx]
- sub rax, r9
- cmp eax, MAX_MATCH
- jge LenMaximum
-
-;;; If the length of the match is not longer than the best match we
-;;; have so far, then forget it and return to the lookup loop.
-;///////////////////////////////////
-
- cmp eax, r11d
- jg LongerMatch
-
- lea rsi,[r10+r11]
-
- mov rdi, prev_ad
- mov edx, [chainlenwmask]
- jmp LookupLoop
-
-;;; s->match_start = cur_match;
-;;; best_len = len;
-;;; if (len >= nice_match) break;
-;;; scan_end = *(ushf*)(scan+best_len-1);
-
-LongerMatch:
- mov r11d, eax
- mov match_start, r8d
- cmp eax, [nicematch]
- jge LeaveNow
-
- lea rsi,[r10+rax]
-
- movzx ebx, word ptr [r9 + rax - 1]
- mov rdi, prev_ad
- mov edx, [chainlenwmask]
- jmp LookupLoop
-
-;;; Accept the current string, with the maximum possible length.
-
-LenMaximum:
- mov r11d,MAX_MATCH
- mov match_start, r8d
-
-;;; if ((uInt)best_len <= s->lookahead) return (uInt)best_len;
-;;; return s->lookahead;
-
-LeaveNow:
-IFDEF INFOZIP
- mov eax,r11d
-ELSE
- mov eax, Lookahead
- cmp r11d, eax
- cmovng eax, r11d
-ENDIF
-
-;;; Restore the stack and return from whence we came.
-
-
- mov rsi,[save_rsi]
- mov rdi,[save_rdi]
- mov rbx,[save_rbx]
- mov rbp,[save_rbp]
- mov r12,[save_r12]
- mov r13,[save_r13]
-; mov r14,[save_r14]
-; mov r15,[save_r15]
-
-
- ret 0
-; please don't remove this string !
-; Your can freely use gvmat64 in any free or commercial app
-; but it is far better don't remove the string in the binary!
- db 0dh,0ah,"asm686 with masm, optimised assembly code from Brian Raiter, written 1998, converted to amd 64 by Gilles Vollant 2005",0dh,0ah,0
-longest_match ENDP
-
-match_init PROC
- ret 0
-match_init ENDP
-
-
-END
diff --git a/third-party/zlib/contrib/masmx64/inffas8664.c b/third-party/zlib/contrib/masmx64/inffas8664.c
deleted file mode 100644
index e8af06f..0000000
--- a/third-party/zlib/contrib/masmx64/inffas8664.c
+++ /dev/null
@@ -1,186 +0,0 @@
-/* inffas8664.c is a hand tuned assembler version of inffast.c - fast decoding
- * version for AMD64 on Windows using Microsoft C compiler
- *
- * Copyright (C) 1995-2003 Mark Adler
- * For conditions of distribution and use, see copyright notice in zlib.h
- *
- * Copyright (C) 2003 Chris Anderson <christop at charm.net>
- * Please use the copyright conditions above.
- *
- * 2005 - Adaptation to Microsoft C Compiler for AMD64 by Gilles Vollant
- *
- * inffas8664.c call function inffas8664fnc in inffasx64.asm
- * inffasx64.asm is automatically convert from AMD64 portion of inffas86.c
- *
- * Dec-29-2003 -- I added AMD64 inflate asm support. This version is also
- * slightly quicker on x86 systems because, instead of using rep movsb to copy
- * data, it uses rep movsw, which moves data in 2-byte chunks instead of single
- * bytes. I've tested the AMD64 code on a Fedora Core 1 + the x86_64 updates
- * from http://fedora.linux.duke.edu/fc1_x86_64
- * which is running on an Athlon 64 3000+ / Gigabyte GA-K8VT800M system with
- * 1GB ram. The 64-bit version is about 4% faster than the 32-bit version,
- * when decompressing mozilla-source-1.3.tar.gz.
- *
- * Mar-13-2003 -- Most of this is derived from inffast.S which is derived from
- * the gcc -S output of zlib-1.2.0/inffast.c. Zlib-1.2.0 is in beta release at
- * the moment. I have successfully compiled and tested this code with gcc2.96,
- * gcc3.2, icc5.0, msvc6.0. It is very close to the speed of inffast.S
- * compiled with gcc -DNO_MMX, but inffast.S is still faster on the P3 with MMX
- * enabled. I will attempt to merge the MMX code into this version. Newer
- * versions of this and inffast.S can be found at
- * http://www.eetbeetee.com/zlib/ and http://www.charm.net/~christop/zlib/
- *
- */
-
-#include <stdio.h>
-#include "zutil.h"
-#include "inftrees.h"
-#include "inflate.h"
-#include "inffast.h"
-
-/* Mark Adler's comments from inffast.c: */
-
-/*
- Decode literal, length, and distance codes and write out the resulting
- literal and match bytes until either not enough input or output is
- available, an end-of-block is encountered, or a data error is encountered.
- When large enough input and output buffers are supplied to inflate(), for
- example, a 16K input buffer and a 64K output buffer, more than 95% of the
- inflate execution time is spent in this routine.
-
- Entry assumptions:
-
- state->mode == LEN
- strm->avail_in >= 6
- strm->avail_out >= 258
- start >= strm->avail_out
- state->bits < 8
-
- On return, state->mode is one of:
-
- LEN -- ran out of enough output space or enough available input
- TYPE -- reached end of block code, inflate() to interpret next block
- BAD -- error in block data
-
- Notes:
-
- - The maximum input bits used by a length/distance pair is 15 bits for the
- length code, 5 bits for the length extra, 15 bits for the distance code,
- and 13 bits for the distance extra. This totals 48 bits, or six bytes.
- Therefore if strm->avail_in >= 6, then there is enough input to avoid
- checking for available input while decoding.
-
- - The maximum bytes that a single length/distance pair can output is 258
- bytes, which is the maximum length that can be coded. inflate_fast()
- requires strm->avail_out >= 258 for each loop to avoid checking for
- output space.
- */
-
-
-
- typedef struct inffast_ar {
-/* 64 32 x86 x86_64 */
-/* ar offset register */
-/* 0 0 */ void *esp; /* esp save */
-/* 8 4 */ void *ebp; /* ebp save */
-/* 16 8 */ unsigned char FAR *in; /* esi rsi local strm->next_in */
-/* 24 12 */ unsigned char FAR *last; /* r9 while in < last */
-/* 32 16 */ unsigned char FAR *out; /* edi rdi local strm->next_out */
-/* 40 20 */ unsigned char FAR *beg; /* inflate()'s init next_out */
-/* 48 24 */ unsigned char FAR *end; /* r10 while out < end */
-/* 56 28 */ unsigned char FAR *window;/* size of window, wsize!=0 */
-/* 64 32 */ code const FAR *lcode; /* ebp rbp local strm->lencode */
-/* 72 36 */ code const FAR *dcode; /* r11 local strm->distcode */
-/* 80 40 */ size_t /*unsigned long */hold; /* edx rdx local strm->hold */
-/* 88 44 */ unsigned bits; /* ebx rbx local strm->bits */
-/* 92 48 */ unsigned wsize; /* window size */
-/* 96 52 */ unsigned write; /* window write index */
-/*100 56 */ unsigned lmask; /* r12 mask for lcode */
-/*104 60 */ unsigned dmask; /* r13 mask for dcode */
-/*108 64 */ unsigned len; /* r14 match length */
-/*112 68 */ unsigned dist; /* r15 match distance */
-/*116 72 */ unsigned status; /* set when state chng*/
- } type_ar;
-#ifdef ASMINF
-
-void inflate_fast(strm, start)
-z_streamp strm;
-unsigned start; /* inflate()'s starting value for strm->avail_out */
-{
- struct inflate_state FAR *state;
- type_ar ar;
- void inffas8664fnc(struct inffast_ar * par);
-
-
-
-#if (defined( __GNUC__ ) && defined( __amd64__ ) && ! defined( __i386 )) || (defined(_MSC_VER) && defined(_M_AMD64))
-#define PAD_AVAIL_IN 6
-#define PAD_AVAIL_OUT 258
-#else
-#define PAD_AVAIL_IN 5
-#define PAD_AVAIL_OUT 257
-#endif
-
- /* copy state to local variables */
- state = (struct inflate_state FAR *)strm->state;
-
- ar.in = strm->next_in;
- ar.last = ar.in + (strm->avail_in - PAD_AVAIL_IN);
- ar.out = strm->next_out;
- ar.beg = ar.out - (start - strm->avail_out);
- ar.end = ar.out + (strm->avail_out - PAD_AVAIL_OUT);
- ar.wsize = state->wsize;
- ar.write = state->wnext;
- ar.window = state->window;
- ar.hold = state->hold;
- ar.bits = state->bits;
- ar.lcode = state->lencode;
- ar.dcode = state->distcode;
- ar.lmask = (1U << state->lenbits) - 1;
- ar.dmask = (1U << state->distbits) - 1;
-
- /* decode literals and length/distances until end-of-block or not enough
- input data or output space */
-
- /* align in on 1/2 hold size boundary */
- while (((size_t)(void *)ar.in & (sizeof(ar.hold) / 2 - 1)) != 0) {
- ar.hold += (unsigned long)*ar.in++ << ar.bits;
- ar.bits += 8;
- }
-
- inffas8664fnc(&ar);
-
- if (ar.status > 1) {
- if (ar.status == 2)
- strm->msg = "invalid literal/length code";
- else if (ar.status == 3)
- strm->msg = "invalid distance code";
- else
- strm->msg = "invalid distance too far back";
- state->mode = BAD;
- }
- else if ( ar.status == 1 ) {
- state->mode = TYPE;
- }
-
- /* return unused bytes (on entry, bits < 8, so in won't go too far back) */
- ar.len = ar.bits >> 3;
- ar.in -= ar.len;
- ar.bits -= ar.len << 3;
- ar.hold &= (1U << ar.bits) - 1;
-
- /* update state and return */
- strm->next_in = ar.in;
- strm->next_out = ar.out;
- strm->avail_in = (unsigned)(ar.in < ar.last ?
- PAD_AVAIL_IN + (ar.last - ar.in) :
- PAD_AVAIL_IN - (ar.in - ar.last));
- strm->avail_out = (unsigned)(ar.out < ar.end ?
- PAD_AVAIL_OUT + (ar.end - ar.out) :
- PAD_AVAIL_OUT - (ar.out - ar.end));
- state->hold = (unsigned long)ar.hold;
- state->bits = ar.bits;
- return;
-}
-
-#endif
diff --git a/third-party/zlib/contrib/masmx64/inffasx64.asm b/third-party/zlib/contrib/masmx64/inffasx64.asm
deleted file mode 100644
index 60a8d89..0000000
--- a/third-party/zlib/contrib/masmx64/inffasx64.asm
+++ /dev/null
@@ -1,396 +0,0 @@
-; inffasx64.asm is a hand tuned assembler version of inffast.c - fast decoding
-; version for AMD64 on Windows using Microsoft C compiler
-;
-; inffasx64.asm is automatically convert from AMD64 portion of inffas86.c
-; inffasx64.asm is called by inffas8664.c, which contain more info.
-
-
-; to compile this file, I use option
-; ml64.exe /Flinffasx64 /c /Zi inffasx64.asm
-; with Microsoft Macro Assembler (x64) for AMD64
-;
-
-; This file compile with Microsoft Macro Assembler (x64) for AMD64
-;
-; ml64.exe is given with Visual Studio 2005/2008/2010 and Windows WDK
-;
-; (you can get Windows WDK with ml64 for AMD64 from
-; http://www.microsoft.com/whdc/Devtools/wdk/default.mspx for low price)
-;
-
-
-.code
-inffas8664fnc PROC
-
-; see http://weblogs.asp.net/oldnewthing/archive/2004/01/14/58579.aspx and
-; http://msdn.microsoft.com/library/en-us/kmarch/hh/kmarch/64bitAMD_8e951dd2-ee77-4728-8702-55ce4b5dd24a.xml.asp
-;
-; All registers must be preserved across the call, except for
-; rax, rcx, rdx, r8, r-9, r10, and r11, which are scratch.
-
-
- mov [rsp-8],rsi
- mov [rsp-16],rdi
- mov [rsp-24],r12
- mov [rsp-32],r13
- mov [rsp-40],r14
- mov [rsp-48],r15
- mov [rsp-56],rbx
-
- mov rax,rcx
-
- mov [rax+8], rbp ; /* save regs rbp and rsp */
- mov [rax], rsp
-
- mov rsp, rax ; /* make rsp point to &ar */
-
- mov rsi, [rsp+16] ; /* rsi = in */
- mov rdi, [rsp+32] ; /* rdi = out */
- mov r9, [rsp+24] ; /* r9 = last */
- mov r10, [rsp+48] ; /* r10 = end */
- mov rbp, [rsp+64] ; /* rbp = lcode */
- mov r11, [rsp+72] ; /* r11 = dcode */
- mov rdx, [rsp+80] ; /* rdx = hold */
- mov ebx, [rsp+88] ; /* ebx = bits */
- mov r12d, [rsp+100] ; /* r12d = lmask */
- mov r13d, [rsp+104] ; /* r13d = dmask */
- ; /* r14d = len */
- ; /* r15d = dist */
-
-
- cld
- cmp r10, rdi
- je L_one_time ; /* if only one decode left */
- cmp r9, rsi
-
- jne L_do_loop
-
-
-L_one_time:
- mov r8, r12 ; /* r8 = lmask */
- cmp bl, 32
- ja L_get_length_code_one_time
-
- lodsd ; /* eax = *(uint *)in++ */
- mov cl, bl ; /* cl = bits, needs it for shifting */
- add bl, 32 ; /* bits += 32 */
- shl rax, cl
- or rdx, rax ; /* hold |= *((uint *)in)++ << bits */
- jmp L_get_length_code_one_time
-
-ALIGN 4
-L_while_test:
- cmp r10, rdi
- jbe L_break_loop
- cmp r9, rsi
- jbe L_break_loop
-
-L_do_loop:
- mov r8, r12 ; /* r8 = lmask */
- cmp bl, 32
- ja L_get_length_code ; /* if (32 < bits) */
-
- lodsd ; /* eax = *(uint *)in++ */
- mov cl, bl ; /* cl = bits, needs it for shifting */
- add bl, 32 ; /* bits += 32 */
- shl rax, cl
- or rdx, rax ; /* hold |= *((uint *)in)++ << bits */
-
-L_get_length_code:
- and r8, rdx ; /* r8 &= hold */
- mov eax, [rbp+r8*4] ; /* eax = lcode[hold & lmask] */
-
- mov cl, ah ; /* cl = this.bits */
- sub bl, ah ; /* bits -= this.bits */
- shr rdx, cl ; /* hold >>= this.bits */
-
- test al, al
- jnz L_test_for_length_base ; /* if (op != 0) 45.7% */
-
- mov r8, r12 ; /* r8 = lmask */
- shr eax, 16 ; /* output this.val char */
- stosb
-
-L_get_length_code_one_time:
- and r8, rdx ; /* r8 &= hold */
- mov eax, [rbp+r8*4] ; /* eax = lcode[hold & lmask] */
-
-L_dolen:
- mov cl, ah ; /* cl = this.bits */
- sub bl, ah ; /* bits -= this.bits */
- shr rdx, cl ; /* hold >>= this.bits */
-
- test al, al
- jnz L_test_for_length_base ; /* if (op != 0) 45.7% */
-
- shr eax, 16 ; /* output this.val char */
- stosb
- jmp L_while_test
-
-ALIGN 4
-L_test_for_length_base:
- mov r14d, eax ; /* len = this */
- shr r14d, 16 ; /* len = this.val */
- mov cl, al
-
- test al, 16
- jz L_test_for_second_level_length ; /* if ((op & 16) == 0) 8% */
- and cl, 15 ; /* op &= 15 */
- jz L_decode_distance ; /* if (!op) */
-
-L_add_bits_to_len:
- sub bl, cl
- xor eax, eax
- inc eax
- shl eax, cl
- dec eax
- and eax, edx ; /* eax &= hold */
- shr rdx, cl
- add r14d, eax ; /* len += hold & mask[op] */
-
-L_decode_distance:
- mov r8, r13 ; /* r8 = dmask */
- cmp bl, 32
- ja L_get_distance_code ; /* if (32 < bits) */
-
- lodsd ; /* eax = *(uint *)in++ */
- mov cl, bl ; /* cl = bits, needs it for shifting */
- add bl, 32 ; /* bits += 32 */
- shl rax, cl
- or rdx, rax ; /* hold |= *((uint *)in)++ << bits */
-
-L_get_distance_code:
- and r8, rdx ; /* r8 &= hold */
- mov eax, [r11+r8*4] ; /* eax = dcode[hold & dmask] */
-
-L_dodist:
- mov r15d, eax ; /* dist = this */
- shr r15d, 16 ; /* dist = this.val */
- mov cl, ah
- sub bl, ah ; /* bits -= this.bits */
- shr rdx, cl ; /* hold >>= this.bits */
- mov cl, al ; /* cl = this.op */
-
- test al, 16 ; /* if ((op & 16) == 0) */
- jz L_test_for_second_level_dist
- and cl, 15 ; /* op &= 15 */
- jz L_check_dist_one
-
-L_add_bits_to_dist:
- sub bl, cl
- xor eax, eax
- inc eax
- shl eax, cl
- dec eax ; /* (1 << op) - 1 */
- and eax, edx ; /* eax &= hold */
- shr rdx, cl
- add r15d, eax ; /* dist += hold & ((1 << op) - 1) */
-
-L_check_window:
- mov r8, rsi ; /* save in so from can use it's reg */
- mov rax, rdi
- sub rax, [rsp+40] ; /* nbytes = out - beg */
-
- cmp eax, r15d
- jb L_clip_window ; /* if (dist > nbytes) 4.2% */
-
- mov ecx, r14d ; /* ecx = len */
- mov rsi, rdi
- sub rsi, r15 ; /* from = out - dist */
-
- sar ecx, 1
- jnc L_copy_two ; /* if len % 2 == 0 */
-
- rep movsw
- mov al, [rsi]
- mov [rdi], al
- inc rdi
-
- mov rsi, r8 ; /* move in back to %rsi, toss from */
- jmp L_while_test
-
-L_copy_two:
- rep movsw
- mov rsi, r8 ; /* move in back to %rsi, toss from */
- jmp L_while_test
-
-ALIGN 4
-L_check_dist_one:
- cmp r15d, 1 ; /* if dist 1, is a memset */
- jne L_check_window
- cmp [rsp+40], rdi ; /* if out == beg, outside window */
- je L_check_window
-
- mov ecx, r14d ; /* ecx = len */
- mov al, [rdi-1]
- mov ah, al
-
- sar ecx, 1
- jnc L_set_two
- mov [rdi], al
- inc rdi
-
-L_set_two:
- rep stosw
- jmp L_while_test
-
-ALIGN 4
-L_test_for_second_level_length:
- test al, 64
- jnz L_test_for_end_of_block ; /* if ((op & 64) != 0) */
-
- xor eax, eax
- inc eax
- shl eax, cl
- dec eax
- and eax, edx ; /* eax &= hold */
- add eax, r14d ; /* eax += len */
- mov eax, [rbp+rax*4] ; /* eax = lcode[val+(hold&mask[op])]*/
- jmp L_dolen
-
-ALIGN 4
-L_test_for_second_level_dist:
- test al, 64
- jnz L_invalid_distance_code ; /* if ((op & 64) != 0) */
-
- xor eax, eax
- inc eax
- shl eax, cl
- dec eax
- and eax, edx ; /* eax &= hold */
- add eax, r15d ; /* eax += dist */
- mov eax, [r11+rax*4] ; /* eax = dcode[val+(hold&mask[op])]*/
- jmp L_dodist
-
-ALIGN 4
-L_clip_window:
- mov ecx, eax ; /* ecx = nbytes */
- mov eax, [rsp+92] ; /* eax = wsize, prepare for dist cmp */
- neg ecx ; /* nbytes = -nbytes */
-
- cmp eax, r15d
- jb L_invalid_distance_too_far ; /* if (dist > wsize) */
-
- add ecx, r15d ; /* nbytes = dist - nbytes */
- cmp dword ptr [rsp+96], 0
- jne L_wrap_around_window ; /* if (write != 0) */
-
- mov rsi, [rsp+56] ; /* from = window */
- sub eax, ecx ; /* eax -= nbytes */
- add rsi, rax ; /* from += wsize - nbytes */
-
- mov eax, r14d ; /* eax = len */
- cmp r14d, ecx
- jbe L_do_copy ; /* if (nbytes >= len) */
-
- sub eax, ecx ; /* eax -= nbytes */
- rep movsb
- mov rsi, rdi
- sub rsi, r15 ; /* from = &out[ -dist ] */
- jmp L_do_copy
-
-ALIGN 4
-L_wrap_around_window:
- mov eax, [rsp+96] ; /* eax = write */
- cmp ecx, eax
- jbe L_contiguous_in_window ; /* if (write >= nbytes) */
-
- mov esi, [rsp+92] ; /* from = wsize */
- add rsi, [rsp+56] ; /* from += window */
- add rsi, rax ; /* from += write */
- sub rsi, rcx ; /* from -= nbytes */
- sub ecx, eax ; /* nbytes -= write */
-
- mov eax, r14d ; /* eax = len */
- cmp eax, ecx
- jbe L_do_copy ; /* if (nbytes >= len) */
-
- sub eax, ecx ; /* len -= nbytes */
- rep movsb
- mov rsi, [rsp+56] ; /* from = window */
- mov ecx, [rsp+96] ; /* nbytes = write */
- cmp eax, ecx
- jbe L_do_copy ; /* if (nbytes >= len) */
-
- sub eax, ecx ; /* len -= nbytes */
- rep movsb
- mov rsi, rdi
- sub rsi, r15 ; /* from = out - dist */
- jmp L_do_copy
-
-ALIGN 4
-L_contiguous_in_window:
- mov rsi, [rsp+56] ; /* rsi = window */
- add rsi, rax
- sub rsi, rcx ; /* from += write - nbytes */
-
- mov eax, r14d ; /* eax = len */
- cmp eax, ecx
- jbe L_do_copy ; /* if (nbytes >= len) */
-
- sub eax, ecx ; /* len -= nbytes */
- rep movsb
- mov rsi, rdi
- sub rsi, r15 ; /* from = out - dist */
- jmp L_do_copy ; /* if (nbytes >= len) */
-
-ALIGN 4
-L_do_copy:
- mov ecx, eax ; /* ecx = len */
- rep movsb
-
- mov rsi, r8 ; /* move in back to %esi, toss from */
- jmp L_while_test
-
-L_test_for_end_of_block:
- test al, 32
- jz L_invalid_literal_length_code
- mov dword ptr [rsp+116], 1
- jmp L_break_loop_with_status
-
-L_invalid_literal_length_code:
- mov dword ptr [rsp+116], 2
- jmp L_break_loop_with_status
-
-L_invalid_distance_code:
- mov dword ptr [rsp+116], 3
- jmp L_break_loop_with_status
-
-L_invalid_distance_too_far:
- mov dword ptr [rsp+116], 4
- jmp L_break_loop_with_status
-
-L_break_loop:
- mov dword ptr [rsp+116], 0
-
-L_break_loop_with_status:
-; /* put in, out, bits, and hold back into ar and pop esp */
- mov [rsp+16], rsi ; /* in */
- mov [rsp+32], rdi ; /* out */
- mov [rsp+88], ebx ; /* bits */
- mov [rsp+80], rdx ; /* hold */
-
- mov rax, [rsp] ; /* restore rbp and rsp */
- mov rbp, [rsp+8]
- mov rsp, rax
-
-
-
- mov rsi,[rsp-8]
- mov rdi,[rsp-16]
- mov r12,[rsp-24]
- mov r13,[rsp-32]
- mov r14,[rsp-40]
- mov r15,[rsp-48]
- mov rbx,[rsp-56]
-
- ret 0
-; :
-; : "m" (ar)
-; : "memory", "%rax", "%rbx", "%rcx", "%rdx", "%rsi", "%rdi",
-; "%r8", "%r9", "%r10", "%r11", "%r12", "%r13", "%r14", "%r15"
-; );
-
-inffas8664fnc ENDP
-;_TEXT ENDS
-END
diff --git a/third-party/zlib/contrib/masmx64/readme.txt b/third-party/zlib/contrib/masmx64/readme.txt
deleted file mode 100644
index 2da6733..0000000
--- a/third-party/zlib/contrib/masmx64/readme.txt
+++ /dev/null
@@ -1,31 +0,0 @@
-Summary
--------
-This directory contains ASM implementations of the functions
-longest_match() and inflate_fast(), for 64 bits x86 (both AMD64 and Intel EM64t),
-for use with Microsoft Macro Assembler (x64) for AMD64 and Microsoft C++ 64 bits.
-
-gvmat64.asm is written by Gilles Vollant (2005), by using Brian Raiter 686/32 bits
- assembly optimized version from Jean-loup Gailly original longest_match function
-
-inffasx64.asm and inffas8664.c were written by Chris Anderson, by optimizing
- original function from Mark Adler
-
-Use instructions
-----------------
-Assemble the .asm files using MASM and put the object files into the zlib source
-directory. You can also get object files here:
-
- http://www.winimage.com/zLibDll/zlib124_masm_obj.zip
-
-define ASMV and ASMINF in your project. Include inffas8664.c in your source tree,
-and inffasx64.obj and gvmat64.obj as object to link.
-
-
-Build instructions
-------------------
-run bld_64.bat with Microsoft Macro Assembler (x64) for AMD64 (ml64.exe)
-
-ml64.exe is given with Visual Studio 2005, Windows 2003 server DDK
-
-You can get Windows 2003 server DDK with ml64 and cl for AMD64 from
- http://www.microsoft.com/whdc/devtools/ddk/default.mspx for low price)
diff --git a/third-party/zlib/contrib/masmx86/bld_ml32.bat b/third-party/zlib/contrib/masmx86/bld_ml32.bat
deleted file mode 100644
index e1b86bf..0000000
--- a/third-party/zlib/contrib/masmx86/bld_ml32.bat
+++ /dev/null
@@ -1,2 +0,0 @@
-ml /coff /Zi /c /Flmatch686.lst match686.asm
-ml /coff /Zi /c /Flinffas32.lst inffas32.asm
diff --git a/third-party/zlib/contrib/masmx86/inffas32.asm b/third-party/zlib/contrib/masmx86/inffas32.asm
deleted file mode 100644
index 03d20f8..0000000
--- a/third-party/zlib/contrib/masmx86/inffas32.asm
+++ /dev/null
@@ -1,1080 +0,0 @@
-;/* inffas32.asm is a hand tuned assembler version of inffast.c -- fast decoding
-; *
-; * inffas32.asm is derivated from inffas86.c, with translation of assembly code
-; *
-; * Copyright (C) 1995-2003 Mark Adler
-; * For conditions of distribution and use, see copyright notice in zlib.h
-; *
-; * Copyright (C) 2003 Chris Anderson <christop at charm.net>
-; * Please use the copyright conditions above.
-; *
-; * Mar-13-2003 -- Most of this is derived from inffast.S which is derived from
-; * the gcc -S output of zlib-1.2.0/inffast.c. Zlib-1.2.0 is in beta release at
-; * the moment. I have successfully compiled and tested this code with gcc2.96,
-; * gcc3.2, icc5.0, msvc6.0. It is very close to the speed of inffast.S
-; * compiled with gcc -DNO_MMX, but inffast.S is still faster on the P3 with MMX
-; * enabled. I will attempt to merge the MMX code into this version. Newer
-; * versions of this and inffast.S can be found at
-; * http://www.eetbeetee.com/zlib/ and http://www.charm.net/~christop/zlib/
-; *
-; * 2005 : modification by Gilles Vollant
-; */
-; For Visual C++ 4.x and higher and ML 6.x and higher
-; ml.exe is in directory \MASM611C of Win95 DDK
-; ml.exe is also distributed in http://www.masm32.com/masmdl.htm
-; and in VC++2003 toolkit at http://msdn.microsoft.com/visualc/vctoolkit2003/
-;
-;
-; compile with command line option
-; ml /coff /Zi /c /Flinffas32.lst inffas32.asm
-
-; if you define NO_GZIP (see inflate.h), compile with
-; ml /coff /Zi /c /Flinffas32.lst /DNO_GUNZIP inffas32.asm
-
-
-; zlib122sup is 0 fort zlib 1.2.2.1 and lower
-; zlib122sup is 8 fort zlib 1.2.2.2 and more (with addition of dmax and head
-; in inflate_state in inflate.h)
-zlib1222sup equ 8
-
-
-IFDEF GUNZIP
- INFLATE_MODE_TYPE equ 11
- INFLATE_MODE_BAD equ 26
-ELSE
- IFNDEF NO_GUNZIP
- INFLATE_MODE_TYPE equ 11
- INFLATE_MODE_BAD equ 26
- ELSE
- INFLATE_MODE_TYPE equ 3
- INFLATE_MODE_BAD equ 17
- ENDIF
-ENDIF
-
-
-; 75 "inffast.S"
-;FILE "inffast.S"
-
-;;;GLOBAL _inflate_fast
-
-;;;SECTION .text
-
-
-
- .586p
- .mmx
-
- name inflate_fast_x86
- .MODEL FLAT
-
-_DATA segment
-inflate_fast_use_mmx:
- dd 1
-
-
-_TEXT segment
-
-
-
-ALIGN 4
- db 'Fast decoding Code from Chris Anderson'
- db 0
-
-ALIGN 4
-invalid_literal_length_code_msg:
- db 'invalid literal/length code'
- db 0
-
-ALIGN 4
-invalid_distance_code_msg:
- db 'invalid distance code'
- db 0
-
-ALIGN 4
-invalid_distance_too_far_msg:
- db 'invalid distance too far back'
- db 0
-
-
-ALIGN 4
-inflate_fast_mask:
-dd 0
-dd 1
-dd 3
-dd 7
-dd 15
-dd 31
-dd 63
-dd 127
-dd 255
-dd 511
-dd 1023
-dd 2047
-dd 4095
-dd 8191
-dd 16383
-dd 32767
-dd 65535
-dd 131071
-dd 262143
-dd 524287
-dd 1048575
-dd 2097151
-dd 4194303
-dd 8388607
-dd 16777215
-dd 33554431
-dd 67108863
-dd 134217727
-dd 268435455
-dd 536870911
-dd 1073741823
-dd 2147483647
-dd 4294967295
-
-
-mode_state equ 0 ;/* state->mode */
-wsize_state equ (32+zlib1222sup) ;/* state->wsize */
-write_state equ (36+4+zlib1222sup) ;/* state->write */
-window_state equ (40+4+zlib1222sup) ;/* state->window */
-hold_state equ (44+4+zlib1222sup) ;/* state->hold */
-bits_state equ (48+4+zlib1222sup) ;/* state->bits */
-lencode_state equ (64+4+zlib1222sup) ;/* state->lencode */
-distcode_state equ (68+4+zlib1222sup) ;/* state->distcode */
-lenbits_state equ (72+4+zlib1222sup) ;/* state->lenbits */
-distbits_state equ (76+4+zlib1222sup) ;/* state->distbits */
-
-
-;;SECTION .text
-; 205 "inffast.S"
-;GLOBAL inflate_fast_use_mmx
-
-;SECTION .data
-
-
-; GLOBAL inflate_fast_use_mmx:object
-;.size inflate_fast_use_mmx, 4
-; 226 "inffast.S"
-;SECTION .text
-
-ALIGN 4
-_inflate_fast proc near
-.FPO (16, 4, 0, 0, 1, 0)
- push edi
- push esi
- push ebp
- push ebx
- pushfd
- sub esp,64
- cld
-
-
-
-
- mov esi, [esp+88]
- mov edi, [esi+28]
-
-
-
-
-
-
-
- mov edx, [esi+4]
- mov eax, [esi+0]
-
- add edx,eax
- sub edx,11
-
- mov [esp+44],eax
- mov [esp+20],edx
-
- mov ebp, [esp+92]
- mov ecx, [esi+16]
- mov ebx, [esi+12]
-
- sub ebp,ecx
- neg ebp
- add ebp,ebx
-
- sub ecx,257
- add ecx,ebx
-
- mov [esp+60],ebx
- mov [esp+40],ebp
- mov [esp+16],ecx
-; 285 "inffast.S"
- mov eax, [edi+lencode_state]
- mov ecx, [edi+distcode_state]
-
- mov [esp+8],eax
- mov [esp+12],ecx
-
- mov eax,1
- mov ecx, [edi+lenbits_state]
- shl eax,cl
- dec eax
- mov [esp+0],eax
-
- mov eax,1
- mov ecx, [edi+distbits_state]
- shl eax,cl
- dec eax
- mov [esp+4],eax
-
- mov eax, [edi+wsize_state]
- mov ecx, [edi+write_state]
- mov edx, [edi+window_state]
-
- mov [esp+52],eax
- mov [esp+48],ecx
- mov [esp+56],edx
-
- mov ebp, [edi+hold_state]
- mov ebx, [edi+bits_state]
-; 321 "inffast.S"
- mov esi, [esp+44]
- mov ecx, [esp+20]
- cmp ecx,esi
- ja L_align_long
-
- add ecx,11
- sub ecx,esi
- mov eax,12
- sub eax,ecx
- lea edi, [esp+28]
- rep movsb
- mov ecx,eax
- xor eax,eax
- rep stosb
- lea esi, [esp+28]
- mov [esp+20],esi
- jmp L_is_aligned
-
-
-L_align_long:
- test esi,3
- jz L_is_aligned
- xor eax,eax
- mov al, [esi]
- inc esi
- mov ecx,ebx
- add ebx,8
- shl eax,cl
- or ebp,eax
- jmp L_align_long
-
-L_is_aligned:
- mov edi, [esp+60]
-; 366 "inffast.S"
-L_check_mmx:
- cmp dword ptr [inflate_fast_use_mmx],2
- je L_init_mmx
- ja L_do_loop
-
- push eax
- push ebx
- push ecx
- push edx
- pushfd
- mov eax, [esp]
- xor dword ptr [esp],0200000h
-
-
-
-
- popfd
- pushfd
- pop edx
- xor edx,eax
- jz L_dont_use_mmx
- xor eax,eax
- cpuid
- cmp ebx,0756e6547h
- jne L_dont_use_mmx
- cmp ecx,06c65746eh
- jne L_dont_use_mmx
- cmp edx,049656e69h
- jne L_dont_use_mmx
- mov eax,1
- cpuid
- shr eax,8
- and eax,15
- cmp eax,6
- jne L_dont_use_mmx
- test edx,0800000h
- jnz L_use_mmx
- jmp L_dont_use_mmx
-L_use_mmx:
- mov dword ptr [inflate_fast_use_mmx],2
- jmp L_check_mmx_pop
-L_dont_use_mmx:
- mov dword ptr [inflate_fast_use_mmx],3
-L_check_mmx_pop:
- pop edx
- pop ecx
- pop ebx
- pop eax
- jmp L_check_mmx
-; 426 "inffast.S"
-ALIGN 4
-L_do_loop:
-; 437 "inffast.S"
- cmp bl,15
- ja L_get_length_code
-
- xor eax,eax
- lodsw
- mov cl,bl
- add bl,16
- shl eax,cl
- or ebp,eax
-
-L_get_length_code:
- mov edx, [esp+0]
- mov ecx, [esp+8]
- and edx,ebp
- mov eax, [ecx+edx*4]
-
-L_dolen:
-
-
-
-
-
-
- mov cl,ah
- sub bl,ah
- shr ebp,cl
-
-
-
-
-
-
- test al,al
- jnz L_test_for_length_base
-
- shr eax,16
- stosb
-
-L_while_test:
-
-
- cmp [esp+16],edi
- jbe L_break_loop
-
- cmp [esp+20],esi
- ja L_do_loop
- jmp L_break_loop
-
-L_test_for_length_base:
-; 502 "inffast.S"
- mov edx,eax
- shr edx,16
- mov cl,al
-
- test al,16
- jz L_test_for_second_level_length
- and cl,15
- jz L_save_len
- cmp bl,cl
- jae L_add_bits_to_len
-
- mov ch,cl
- xor eax,eax
- lodsw
- mov cl,bl
- add bl,16
- shl eax,cl
- or ebp,eax
- mov cl,ch
-
-L_add_bits_to_len:
- mov eax,1
- shl eax,cl
- dec eax
- sub bl,cl
- and eax,ebp
- shr ebp,cl
- add edx,eax
-
-L_save_len:
- mov [esp+24],edx
-
-
-L_decode_distance:
-; 549 "inffast.S"
- cmp bl,15
- ja L_get_distance_code
-
- xor eax,eax
- lodsw
- mov cl,bl
- add bl,16
- shl eax,cl
- or ebp,eax
-
-L_get_distance_code:
- mov edx, [esp+4]
- mov ecx, [esp+12]
- and edx,ebp
- mov eax, [ecx+edx*4]
-
-
-L_dodist:
- mov edx,eax
- shr edx,16
- mov cl,ah
- sub bl,ah
- shr ebp,cl
-; 584 "inffast.S"
- mov cl,al
-
- test al,16
- jz L_test_for_second_level_dist
- and cl,15
- jz L_check_dist_one
- cmp bl,cl
- jae L_add_bits_to_dist
-
- mov ch,cl
- xor eax,eax
- lodsw
- mov cl,bl
- add bl,16
- shl eax,cl
- or ebp,eax
- mov cl,ch
-
-L_add_bits_to_dist:
- mov eax,1
- shl eax,cl
- dec eax
- sub bl,cl
- and eax,ebp
- shr ebp,cl
- add edx,eax
- jmp L_check_window
-
-L_check_window:
-; 625 "inffast.S"
- mov [esp+44],esi
- mov eax,edi
- sub eax, [esp+40]
-
- cmp eax,edx
- jb L_clip_window
-
- mov ecx, [esp+24]
- mov esi,edi
- sub esi,edx
-
- sub ecx,3
- mov al, [esi]
- mov [edi],al
- mov al, [esi+1]
- mov dl, [esi+2]
- add esi,3
- mov [edi+1],al
- mov [edi+2],dl
- add edi,3
- rep movsb
-
- mov esi, [esp+44]
- jmp L_while_test
-
-ALIGN 4
-L_check_dist_one:
- cmp edx,1
- jne L_check_window
- cmp [esp+40],edi
- je L_check_window
-
- dec edi
- mov ecx, [esp+24]
- mov al, [edi]
- sub ecx,3
-
- mov [edi+1],al
- mov [edi+2],al
- mov [edi+3],al
- add edi,4
- rep stosb
-
- jmp L_while_test
-
-ALIGN 4
-L_test_for_second_level_length:
-
-
-
-
- test al,64
- jnz L_test_for_end_of_block
-
- mov eax,1
- shl eax,cl
- dec eax
- and eax,ebp
- add eax,edx
- mov edx, [esp+8]
- mov eax, [edx+eax*4]
- jmp L_dolen
-
-ALIGN 4
-L_test_for_second_level_dist:
-
-
-
-
- test al,64
- jnz L_invalid_distance_code
-
- mov eax,1
- shl eax,cl
- dec eax
- and eax,ebp
- add eax,edx
- mov edx, [esp+12]
- mov eax, [edx+eax*4]
- jmp L_dodist
-
-ALIGN 4
-L_clip_window:
-; 721 "inffast.S"
- mov ecx,eax
- mov eax, [esp+52]
- neg ecx
- mov esi, [esp+56]
-
- cmp eax,edx
- jb L_invalid_distance_too_far
-
- add ecx,edx
- cmp dword ptr [esp+48],0
- jne L_wrap_around_window
-
- sub eax,ecx
- add esi,eax
-; 749 "inffast.S"
- mov eax, [esp+24]
- cmp eax,ecx
- jbe L_do_copy1
-
- sub eax,ecx
- rep movsb
- mov esi,edi
- sub esi,edx
- jmp L_do_copy1
-
- cmp eax,ecx
- jbe L_do_copy1
-
- sub eax,ecx
- rep movsb
- mov esi,edi
- sub esi,edx
- jmp L_do_copy1
-
-L_wrap_around_window:
-; 793 "inffast.S"
- mov eax, [esp+48]
- cmp ecx,eax
- jbe L_contiguous_in_window
-
- add esi, [esp+52]
- add esi,eax
- sub esi,ecx
- sub ecx,eax
-
-
- mov eax, [esp+24]
- cmp eax,ecx
- jbe L_do_copy1
-
- sub eax,ecx
- rep movsb
- mov esi, [esp+56]
- mov ecx, [esp+48]
- cmp eax,ecx
- jbe L_do_copy1
-
- sub eax,ecx
- rep movsb
- mov esi,edi
- sub esi,edx
- jmp L_do_copy1
-
-L_contiguous_in_window:
-; 836 "inffast.S"
- add esi,eax
- sub esi,ecx
-
-
- mov eax, [esp+24]
- cmp eax,ecx
- jbe L_do_copy1
-
- sub eax,ecx
- rep movsb
- mov esi,edi
- sub esi,edx
-
-L_do_copy1:
-; 862 "inffast.S"
- mov ecx,eax
- rep movsb
-
- mov esi, [esp+44]
- jmp L_while_test
-; 878 "inffast.S"
-ALIGN 4
-L_init_mmx:
- emms
-
-
-
-
-
- movd mm0,ebp
- mov ebp,ebx
-; 896 "inffast.S"
- movd mm4,dword ptr [esp+0]
- movq mm3,mm4
- movd mm5,dword ptr [esp+4]
- movq mm2,mm5
- pxor mm1,mm1
- mov ebx, [esp+8]
- jmp L_do_loop_mmx
-
-ALIGN 4
-L_do_loop_mmx:
- psrlq mm0,mm1
-
- cmp ebp,32
- ja L_get_length_code_mmx
-
- movd mm6,ebp
- movd mm7,dword ptr [esi]
- add esi,4
- psllq mm7,mm6
- add ebp,32
- por mm0,mm7
-
-L_get_length_code_mmx:
- pand mm4,mm0
- movd eax,mm4
- movq mm4,mm3
- mov eax, [ebx+eax*4]
-
-L_dolen_mmx:
- movzx ecx,ah
- movd mm1,ecx
- sub ebp,ecx
-
- test al,al
- jnz L_test_for_length_base_mmx
-
- shr eax,16
- stosb
-
-L_while_test_mmx:
-
-
- cmp [esp+16],edi
- jbe L_break_loop
-
- cmp [esp+20],esi
- ja L_do_loop_mmx
- jmp L_break_loop
-
-L_test_for_length_base_mmx:
-
- mov edx,eax
- shr edx,16
-
- test al,16
- jz L_test_for_second_level_length_mmx
- and eax,15
- jz L_decode_distance_mmx
-
- psrlq mm0,mm1
- movd mm1,eax
- movd ecx,mm0
- sub ebp,eax
- and ecx, [inflate_fast_mask+eax*4]
- add edx,ecx
-
-L_decode_distance_mmx:
- psrlq mm0,mm1
-
- cmp ebp,32
- ja L_get_dist_code_mmx
-
- movd mm6,ebp
- movd mm7,dword ptr [esi]
- add esi,4
- psllq mm7,mm6
- add ebp,32
- por mm0,mm7
-
-L_get_dist_code_mmx:
- mov ebx, [esp+12]
- pand mm5,mm0
- movd eax,mm5
- movq mm5,mm2
- mov eax, [ebx+eax*4]
-
-L_dodist_mmx:
-
- movzx ecx,ah
- mov ebx,eax
- shr ebx,16
- sub ebp,ecx
- movd mm1,ecx
-
- test al,16
- jz L_test_for_second_level_dist_mmx
- and eax,15
- jz L_check_dist_one_mmx
-
-L_add_bits_to_dist_mmx:
- psrlq mm0,mm1
- movd mm1,eax
- movd ecx,mm0
- sub ebp,eax
- and ecx, [inflate_fast_mask+eax*4]
- add ebx,ecx
-
-L_check_window_mmx:
- mov [esp+44],esi
- mov eax,edi
- sub eax, [esp+40]
-
- cmp eax,ebx
- jb L_clip_window_mmx
-
- mov ecx,edx
- mov esi,edi
- sub esi,ebx
-
- sub ecx,3
- mov al, [esi]
- mov [edi],al
- mov al, [esi+1]
- mov dl, [esi+2]
- add esi,3
- mov [edi+1],al
- mov [edi+2],dl
- add edi,3
- rep movsb
-
- mov esi, [esp+44]
- mov ebx, [esp+8]
- jmp L_while_test_mmx
-
-ALIGN 4
-L_check_dist_one_mmx:
- cmp ebx,1
- jne L_check_window_mmx
- cmp [esp+40],edi
- je L_check_window_mmx
-
- dec edi
- mov ecx,edx
- mov al, [edi]
- sub ecx,3
-
- mov [edi+1],al
- mov [edi+2],al
- mov [edi+3],al
- add edi,4
- rep stosb
-
- mov ebx, [esp+8]
- jmp L_while_test_mmx
-
-ALIGN 4
-L_test_for_second_level_length_mmx:
- test al,64
- jnz L_test_for_end_of_block
-
- and eax,15
- psrlq mm0,mm1
- movd ecx,mm0
- and ecx, [inflate_fast_mask+eax*4]
- add ecx,edx
- mov eax, [ebx+ecx*4]
- jmp L_dolen_mmx
-
-ALIGN 4
-L_test_for_second_level_dist_mmx:
- test al,64
- jnz L_invalid_distance_code
-
- and eax,15
- psrlq mm0,mm1
- movd ecx,mm0
- and ecx, [inflate_fast_mask+eax*4]
- mov eax, [esp+12]
- add ecx,ebx
- mov eax, [eax+ecx*4]
- jmp L_dodist_mmx
-
-ALIGN 4
-L_clip_window_mmx:
-
- mov ecx,eax
- mov eax, [esp+52]
- neg ecx
- mov esi, [esp+56]
-
- cmp eax,ebx
- jb L_invalid_distance_too_far
-
- add ecx,ebx
- cmp dword ptr [esp+48],0
- jne L_wrap_around_window_mmx
-
- sub eax,ecx
- add esi,eax
-
- cmp edx,ecx
- jbe L_do_copy1_mmx
-
- sub edx,ecx
- rep movsb
- mov esi,edi
- sub esi,ebx
- jmp L_do_copy1_mmx
-
- cmp edx,ecx
- jbe L_do_copy1_mmx
-
- sub edx,ecx
- rep movsb
- mov esi,edi
- sub esi,ebx
- jmp L_do_copy1_mmx
-
-L_wrap_around_window_mmx:
-
- mov eax, [esp+48]
- cmp ecx,eax
- jbe L_contiguous_in_window_mmx
-
- add esi, [esp+52]
- add esi,eax
- sub esi,ecx
- sub ecx,eax
-
-
- cmp edx,ecx
- jbe L_do_copy1_mmx
-
- sub edx,ecx
- rep movsb
- mov esi, [esp+56]
- mov ecx, [esp+48]
- cmp edx,ecx
- jbe L_do_copy1_mmx
-
- sub edx,ecx
- rep movsb
- mov esi,edi
- sub esi,ebx
- jmp L_do_copy1_mmx
-
-L_contiguous_in_window_mmx:
-
- add esi,eax
- sub esi,ecx
-
-
- cmp edx,ecx
- jbe L_do_copy1_mmx
-
- sub edx,ecx
- rep movsb
- mov esi,edi
- sub esi,ebx
-
-L_do_copy1_mmx:
-
-
- mov ecx,edx
- rep movsb
-
- mov esi, [esp+44]
- mov ebx, [esp+8]
- jmp L_while_test_mmx
-; 1174 "inffast.S"
-L_invalid_distance_code:
-
-
-
-
-
- mov ecx, invalid_distance_code_msg
- mov edx,INFLATE_MODE_BAD
- jmp L_update_stream_state
-
-L_test_for_end_of_block:
-
-
-
-
-
- test al,32
- jz L_invalid_literal_length_code
-
- mov ecx,0
- mov edx,INFLATE_MODE_TYPE
- jmp L_update_stream_state
-
-L_invalid_literal_length_code:
-
-
-
-
-
- mov ecx, invalid_literal_length_code_msg
- mov edx,INFLATE_MODE_BAD
- jmp L_update_stream_state
-
-L_invalid_distance_too_far:
-
-
-
- mov esi, [esp+44]
- mov ecx, invalid_distance_too_far_msg
- mov edx,INFLATE_MODE_BAD
- jmp L_update_stream_state
-
-L_update_stream_state:
-
- mov eax, [esp+88]
- test ecx,ecx
- jz L_skip_msg
- mov [eax+24],ecx
-L_skip_msg:
- mov eax, [eax+28]
- mov [eax+mode_state],edx
- jmp L_break_loop
-
-ALIGN 4
-L_break_loop:
-; 1243 "inffast.S"
- cmp dword ptr [inflate_fast_use_mmx],2
- jne L_update_next_in
-
-
-
- mov ebx,ebp
-
-L_update_next_in:
-; 1266 "inffast.S"
- mov eax, [esp+88]
- mov ecx,ebx
- mov edx, [eax+28]
- shr ecx,3
- sub esi,ecx
- shl ecx,3
- sub ebx,ecx
- mov [eax+12],edi
- mov [edx+bits_state],ebx
- mov ecx,ebx
-
- lea ebx, [esp+28]
- cmp [esp+20],ebx
- jne L_buf_not_used
-
- sub esi,ebx
- mov ebx, [eax+0]
- mov [esp+20],ebx
- add esi,ebx
- mov ebx, [eax+4]
- sub ebx,11
- add [esp+20],ebx
-
-L_buf_not_used:
- mov [eax+0],esi
-
- mov ebx,1
- shl ebx,cl
- dec ebx
-
-
-
-
-
- cmp dword ptr [inflate_fast_use_mmx],2
- jne L_update_hold
-
-
-
- psrlq mm0,mm1
- movd ebp,mm0
-
- emms
-
-L_update_hold:
-
-
-
- and ebp,ebx
- mov [edx+hold_state],ebp
-
-
-
-
- mov ebx, [esp+20]
- cmp ebx,esi
- jbe L_last_is_smaller
-
- sub ebx,esi
- add ebx,11
- mov [eax+4],ebx
- jmp L_fixup_out
-L_last_is_smaller:
- sub esi,ebx
- neg esi
- add esi,11
- mov [eax+4],esi
-
-
-
-
-L_fixup_out:
-
- mov ebx, [esp+16]
- cmp ebx,edi
- jbe L_end_is_smaller
-
- sub ebx,edi
- add ebx,257
- mov [eax+16],ebx
- jmp L_done
-L_end_is_smaller:
- sub edi,ebx
- neg edi
- add edi,257
- mov [eax+16],edi
-
-
-
-
-
-L_done:
- add esp,64
- popfd
- pop ebx
- pop ebp
- pop esi
- pop edi
- ret
-_inflate_fast endp
-
-_TEXT ends
-end
diff --git a/third-party/zlib/contrib/masmx86/match686.asm b/third-party/zlib/contrib/masmx86/match686.asm
deleted file mode 100644
index 3b09212..0000000
--- a/third-party/zlib/contrib/masmx86/match686.asm
+++ /dev/null
@@ -1,479 +0,0 @@
-; match686.asm -- Asm portion of the optimized longest_match for 32 bits x86
-; Copyright (C) 1995-1996 Jean-loup Gailly, Brian Raiter and Gilles Vollant.
-; File written by Gilles Vollant, by converting match686.S from Brian Raiter
-; for MASM. This is as assembly version of longest_match
-; from Jean-loup Gailly in deflate.c
-;
-; http://www.zlib.net
-; http://www.winimage.com/zLibDll
-; http://www.muppetlabs.com/~breadbox/software/assembly.html
-;
-; For Visual C++ 4.x and higher and ML 6.x and higher
-; ml.exe is distributed in
-; http://www.microsoft.com/downloads/details.aspx?FamilyID=7a1c9da0-0510-44a2-b042-7ef370530c64
-;
-; this file contain two implementation of longest_match
-;
-; this longest_match was written by Brian raiter (1998), optimized for Pentium Pro
-; (and the faster known version of match_init on modern Core 2 Duo and AMD Phenom)
-;
-; for using an assembly version of longest_match, you need define ASMV in project
-;
-; compile the asm file running
-; ml /coff /Zi /c /Flmatch686.lst match686.asm
-; and do not include match686.obj in your project
-;
-; note: contrib of zLib 1.2.3 and earlier contained both a deprecated version for
-; Pentium (prior Pentium Pro) and this version for Pentium Pro and modern processor
-; with autoselect (with cpu detection code)
-; if you want support the old pentium optimization, you can still use these version
-;
-; this file is not optimized for old pentium, but it compatible with all x86 32 bits
-; processor (starting 80386)
-;
-;
-; see below : zlib1222add must be adjuster if you use a zlib version < 1.2.2.2
-
-;uInt longest_match(s, cur_match)
-; deflate_state *s;
-; IPos cur_match; /* current match */
-
- NbStack equ 76
- cur_match equ dword ptr[esp+NbStack-0]
- str_s equ dword ptr[esp+NbStack-4]
-; 5 dword on top (ret,ebp,esi,edi,ebx)
- adrret equ dword ptr[esp+NbStack-8]
- pushebp equ dword ptr[esp+NbStack-12]
- pushedi equ dword ptr[esp+NbStack-16]
- pushesi equ dword ptr[esp+NbStack-20]
- pushebx equ dword ptr[esp+NbStack-24]
-
- chain_length equ dword ptr [esp+NbStack-28]
- limit equ dword ptr [esp+NbStack-32]
- best_len equ dword ptr [esp+NbStack-36]
- window equ dword ptr [esp+NbStack-40]
- prev equ dword ptr [esp+NbStack-44]
- scan_start equ word ptr [esp+NbStack-48]
- wmask equ dword ptr [esp+NbStack-52]
- match_start_ptr equ dword ptr [esp+NbStack-56]
- nice_match equ dword ptr [esp+NbStack-60]
- scan equ dword ptr [esp+NbStack-64]
-
- windowlen equ dword ptr [esp+NbStack-68]
- match_start equ dword ptr [esp+NbStack-72]
- strend equ dword ptr [esp+NbStack-76]
- NbStackAdd equ (NbStack-24)
-
- .386p
-
- name gvmatch
- .MODEL FLAT
-
-
-
-; all the +zlib1222add offsets are due to the addition of fields
-; in zlib in the deflate_state structure since the asm code was first written
-; (if you compile with zlib 1.0.4 or older, use "zlib1222add equ (-4)").
-; (if you compile with zlib between 1.0.5 and 1.2.2.1, use "zlib1222add equ 0").
-; if you compile with zlib 1.2.2.2 or later , use "zlib1222add equ 8").
-
- zlib1222add equ 8
-
-; Note : these value are good with a 8 bytes boundary pack structure
- dep_chain_length equ 74h+zlib1222add
- dep_window equ 30h+zlib1222add
- dep_strstart equ 64h+zlib1222add
- dep_prev_length equ 70h+zlib1222add
- dep_nice_match equ 88h+zlib1222add
- dep_w_size equ 24h+zlib1222add
- dep_prev equ 38h+zlib1222add
- dep_w_mask equ 2ch+zlib1222add
- dep_good_match equ 84h+zlib1222add
- dep_match_start equ 68h+zlib1222add
- dep_lookahead equ 6ch+zlib1222add
-
-
-_TEXT segment
-
-IFDEF NOUNDERLINE
- public longest_match
- public match_init
-ELSE
- public _longest_match
- public _match_init
-ENDIF
-
- MAX_MATCH equ 258
- MIN_MATCH equ 3
- MIN_LOOKAHEAD equ (MAX_MATCH+MIN_MATCH+1)
-
-
-
-MAX_MATCH equ 258
-MIN_MATCH equ 3
-MIN_LOOKAHEAD equ (MAX_MATCH + MIN_MATCH + 1)
-MAX_MATCH_8_ equ ((MAX_MATCH + 7) AND 0FFF0h)
-
-
-;;; stack frame offsets
-
-chainlenwmask equ esp + 0 ; high word: current chain len
- ; low word: s->wmask
-window equ esp + 4 ; local copy of s->window
-windowbestlen equ esp + 8 ; s->window + bestlen
-scanstart equ esp + 16 ; first two bytes of string
-scanend equ esp + 12 ; last two bytes of string
-scanalign equ esp + 20 ; dword-misalignment of string
-nicematch equ esp + 24 ; a good enough match size
-bestlen equ esp + 28 ; size of best match so far
-scan equ esp + 32 ; ptr to string wanting match
-
-LocalVarsSize equ 36
-; saved ebx byte esp + 36
-; saved edi byte esp + 40
-; saved esi byte esp + 44
-; saved ebp byte esp + 48
-; return address byte esp + 52
-deflatestate equ esp + 56 ; the function arguments
-curmatch equ esp + 60
-
-;;; Offsets for fields in the deflate_state structure. These numbers
-;;; are calculated from the definition of deflate_state, with the
-;;; assumption that the compiler will dword-align the fields. (Thus,
-;;; changing the definition of deflate_state could easily cause this
-;;; program to crash horribly, without so much as a warning at
-;;; compile time. Sigh.)
-
-dsWSize equ 36+zlib1222add
-dsWMask equ 44+zlib1222add
-dsWindow equ 48+zlib1222add
-dsPrev equ 56+zlib1222add
-dsMatchLen equ 88+zlib1222add
-dsPrevMatch equ 92+zlib1222add
-dsStrStart equ 100+zlib1222add
-dsMatchStart equ 104+zlib1222add
-dsLookahead equ 108+zlib1222add
-dsPrevLen equ 112+zlib1222add
-dsMaxChainLen equ 116+zlib1222add
-dsGoodMatch equ 132+zlib1222add
-dsNiceMatch equ 136+zlib1222add
-
-
-;;; match686.asm -- Pentium-Pro-optimized version of longest_match()
-;;; Written for zlib 1.1.2
-;;; Copyright (C) 1998 Brian Raiter <breadbox at muppetlabs.com>
-;;; You can look at http://www.muppetlabs.com/~breadbox/software/assembly.html
-;;;
-;;
-;; This software is provided 'as-is', without any express or implied
-;; warranty. In no event will the authors be held liable for any damages
-;; arising from the use of this software.
-;;
-;; Permission is granted to anyone to use this software for any purpose,
-;; including commercial applications, and to alter it and redistribute it
-;; freely, subject to the following restrictions:
-;;
-;; 1. The origin of this software must not be misrepresented; you must not
-;; claim that you wrote the original software. If you use this software
-;; in a product, an acknowledgment in the product documentation would be
-;; appreciated but is not required.
-;; 2. Altered source versions must be plainly marked as such, and must not be
-;; misrepresented as being the original software
-;; 3. This notice may not be removed or altered from any source distribution.
-;;
-
-;GLOBAL _longest_match, _match_init
-
-
-;SECTION .text
-
-;;; uInt longest_match(deflate_state *deflatestate, IPos curmatch)
-
-;_longest_match:
- IFDEF NOUNDERLINE
- longest_match proc near
- ELSE
- _longest_match proc near
- ENDIF
-.FPO (9, 4, 0, 0, 1, 0)
-
-;;; Save registers that the compiler may be using, and adjust esp to
-;;; make room for our stack frame.
-
- push ebp
- push edi
- push esi
- push ebx
- sub esp, LocalVarsSize
-
-;;; Retrieve the function arguments. ecx will hold cur_match
-;;; throughout the entire function. edx will hold the pointer to the
-;;; deflate_state structure during the function's setup (before
-;;; entering the main loop.
-
- mov edx, [deflatestate]
- mov ecx, [curmatch]
-
-;;; uInt wmask = s->w_mask;
-;;; unsigned chain_length = s->max_chain_length;
-;;; if (s->prev_length >= s->good_match) {
-;;; chain_length >>= 2;
-;;; }
-
- mov eax, [edx + dsPrevLen]
- mov ebx, [edx + dsGoodMatch]
- cmp eax, ebx
- mov eax, [edx + dsWMask]
- mov ebx, [edx + dsMaxChainLen]
- jl LastMatchGood
- shr ebx, 2
-LastMatchGood:
-
-;;; chainlen is decremented once beforehand so that the function can
-;;; use the sign flag instead of the zero flag for the exit test.
-;;; It is then shifted into the high word, to make room for the wmask
-;;; value, which it will always accompany.
-
- dec ebx
- shl ebx, 16
- or ebx, eax
- mov [chainlenwmask], ebx
-
-;;; if ((uInt)nice_match > s->lookahead) nice_match = s->lookahead;
-
- mov eax, [edx + dsNiceMatch]
- mov ebx, [edx + dsLookahead]
- cmp ebx, eax
- jl LookaheadLess
- mov ebx, eax
-LookaheadLess: mov [nicematch], ebx
-
-;;; register Bytef *scan = s->window + s->strstart;
-
- mov esi, [edx + dsWindow]
- mov [window], esi
- mov ebp, [edx + dsStrStart]
- lea edi, [esi + ebp]
- mov [scan], edi
-
-;;; Determine how many bytes the scan ptr is off from being
-;;; dword-aligned.
-
- mov eax, edi
- neg eax
- and eax, 3
- mov [scanalign], eax
-
-;;; IPos limit = s->strstart > (IPos)MAX_DIST(s) ?
-;;; s->strstart - (IPos)MAX_DIST(s) : NIL;
-
- mov eax, [edx + dsWSize]
- sub eax, MIN_LOOKAHEAD
- sub ebp, eax
- jg LimitPositive
- xor ebp, ebp
-LimitPositive:
-
-;;; int best_len = s->prev_length;
-
- mov eax, [edx + dsPrevLen]
- mov [bestlen], eax
-
-;;; Store the sum of s->window + best_len in esi locally, and in esi.
-
- add esi, eax
- mov [windowbestlen], esi
-
-;;; register ush scan_start = *(ushf*)scan;
-;;; register ush scan_end = *(ushf*)(scan+best_len-1);
-;;; Posf *prev = s->prev;
-
- movzx ebx, word ptr [edi]
- mov [scanstart], ebx
- movzx ebx, word ptr [edi + eax - 1]
- mov [scanend], ebx
- mov edi, [edx + dsPrev]
-
-;;; Jump into the main loop.
-
- mov edx, [chainlenwmask]
- jmp short LoopEntry
-
-align 4
-
-;;; do {
-;;; match = s->window + cur_match;
-;;; if (*(ushf*)(match+best_len-1) != scan_end ||
-;;; *(ushf*)match != scan_start) continue;
-;;; [...]
-;;; } while ((cur_match = prev[cur_match & wmask]) > limit
-;;; && --chain_length != 0);
-;;;
-;;; Here is the inner loop of the function. The function will spend the
-;;; majority of its time in this loop, and majority of that time will
-;;; be spent in the first ten instructions.
-;;;
-;;; Within this loop:
-;;; ebx = scanend
-;;; ecx = curmatch
-;;; edx = chainlenwmask - i.e., ((chainlen << 16) | wmask)
-;;; esi = windowbestlen - i.e., (window + bestlen)
-;;; edi = prev
-;;; ebp = limit
-
-LookupLoop:
- and ecx, edx
- movzx ecx, word ptr [edi + ecx*2]
- cmp ecx, ebp
- jbe LeaveNow
- sub edx, 00010000h
- js LeaveNow
-LoopEntry: movzx eax, word ptr [esi + ecx - 1]
- cmp eax, ebx
- jnz LookupLoop
- mov eax, [window]
- movzx eax, word ptr [eax + ecx]
- cmp eax, [scanstart]
- jnz LookupLoop
-
-;;; Store the current value of chainlen.
-
- mov [chainlenwmask], edx
-
-;;; Point edi to the string under scrutiny, and esi to the string we
-;;; are hoping to match it up with. In actuality, esi and edi are
-;;; both pointed (MAX_MATCH_8 - scanalign) bytes ahead, and edx is
-;;; initialized to -(MAX_MATCH_8 - scanalign).
-
- mov esi, [window]
- mov edi, [scan]
- add esi, ecx
- mov eax, [scanalign]
- mov edx, 0fffffef8h; -(MAX_MATCH_8)
- lea edi, [edi + eax + 0108h] ;MAX_MATCH_8]
- lea esi, [esi + eax + 0108h] ;MAX_MATCH_8]
-
-;;; Test the strings for equality, 8 bytes at a time. At the end,
-;;; adjust edx so that it is offset to the exact byte that mismatched.
-;;;
-;;; We already know at this point that the first three bytes of the
-;;; strings match each other, and they can be safely passed over before
-;;; starting the compare loop. So what this code does is skip over 0-3
-;;; bytes, as much as necessary in order to dword-align the edi
-;;; pointer. (esi will still be misaligned three times out of four.)
-;;;
-;;; It should be confessed that this loop usually does not represent
-;;; much of the total running time. Replacing it with a more
-;;; straightforward "rep cmpsb" would not drastically degrade
-;;; performance.
-
-LoopCmps:
- mov eax, [esi + edx]
- xor eax, [edi + edx]
- jnz LeaveLoopCmps
- mov eax, [esi + edx + 4]
- xor eax, [edi + edx + 4]
- jnz LeaveLoopCmps4
- add edx, 8
- jnz LoopCmps
- jmp short LenMaximum
-LeaveLoopCmps4: add edx, 4
-LeaveLoopCmps: test eax, 0000FFFFh
- jnz LenLower
- add edx, 2
- shr eax, 16
-LenLower: sub al, 1
- adc edx, 0
-
-;;; Calculate the length of the match. If it is longer than MAX_MATCH,
-;;; then automatically accept it as the best possible match and leave.
-
- lea eax, [edi + edx]
- mov edi, [scan]
- sub eax, edi
- cmp eax, MAX_MATCH
- jge LenMaximum
-
-;;; If the length of the match is not longer than the best match we
-;;; have so far, then forget it and return to the lookup loop.
-
- mov edx, [deflatestate]
- mov ebx, [bestlen]
- cmp eax, ebx
- jg LongerMatch
- mov esi, [windowbestlen]
- mov edi, [edx + dsPrev]
- mov ebx, [scanend]
- mov edx, [chainlenwmask]
- jmp LookupLoop
-
-;;; s->match_start = cur_match;
-;;; best_len = len;
-;;; if (len >= nice_match) break;
-;;; scan_end = *(ushf*)(scan+best_len-1);
-
-LongerMatch: mov ebx, [nicematch]
- mov [bestlen], eax
- mov [edx + dsMatchStart], ecx
- cmp eax, ebx
- jge LeaveNow
- mov esi, [window]
- add esi, eax
- mov [windowbestlen], esi
- movzx ebx, word ptr [edi + eax - 1]
- mov edi, [edx + dsPrev]
- mov [scanend], ebx
- mov edx, [chainlenwmask]
- jmp LookupLoop
-
-;;; Accept the current string, with the maximum possible length.
-
-LenMaximum: mov edx, [deflatestate]
- mov dword ptr [bestlen], MAX_MATCH
- mov [edx + dsMatchStart], ecx
-
-;;; if ((uInt)best_len <= s->lookahead) return (uInt)best_len;
-;;; return s->lookahead;
-
-LeaveNow:
- mov edx, [deflatestate]
- mov ebx, [bestlen]
- mov eax, [edx + dsLookahead]
- cmp ebx, eax
- jg LookaheadRet
- mov eax, ebx
-LookaheadRet:
-
-;;; Restore the stack and return from whence we came.
-
- add esp, LocalVarsSize
- pop ebx
- pop esi
- pop edi
- pop ebp
-
- ret
-; please don't remove this string !
-; Your can freely use match686 in any free or commercial app if you don't remove the string in the binary!
- db 0dh,0ah,"asm686 with masm, optimised assembly code from Brian Raiter, written 1998",0dh,0ah
-
-
- IFDEF NOUNDERLINE
- longest_match endp
- ELSE
- _longest_match endp
- ENDIF
-
- IFDEF NOUNDERLINE
- match_init proc near
- ret
- match_init endp
- ELSE
- _match_init proc near
- ret
- _match_init endp
- ENDIF
-
-
-_TEXT ends
-end
diff --git a/third-party/zlib/contrib/masmx86/readme.txt b/third-party/zlib/contrib/masmx86/readme.txt
deleted file mode 100644
index 3271f72..0000000
--- a/third-party/zlib/contrib/masmx86/readme.txt
+++ /dev/null
@@ -1,27 +0,0 @@
-
-Summary
--------
-This directory contains ASM implementations of the functions
-longest_match() and inflate_fast().
-
-
-Use instructions
-----------------
-Assemble using MASM, and copy the object files into the zlib source
-directory, then run the appropriate makefile, as suggested below. You can
-donwload MASM from here:
-
- http://www.microsoft.com/downloads/details.aspx?displaylang=en&FamilyID=7a1c9da0-0510-44a2-b042-7ef370530c64
-
-You can also get objects files here:
-
- http://www.winimage.com/zLibDll/zlib124_masm_obj.zip
-
-Build instructions
-------------------
-* With Microsoft C and MASM:
-nmake -f win32/Makefile.msc LOC="-DASMV -DASMINF" OBJA="match686.obj inffas32.obj"
-
-* With Borland C and TASM:
-make -f win32/Makefile.bor LOCAL_ZLIB="-DASMV -DASMINF" OBJA="match686.obj inffas32.obj" OBJPA="+match686c.obj+match686.obj+inffas32.obj"
-
diff --git a/third-party/zlib/contrib/minizip/Makefile b/third-party/zlib/contrib/minizip/Makefile
deleted file mode 100644
index 84eaad2..0000000
--- a/third-party/zlib/contrib/minizip/Makefile
+++ /dev/null
@@ -1,25 +0,0 @@
-CC=cc
-CFLAGS=-O -I../..
-
-UNZ_OBJS = miniunz.o unzip.o ioapi.o ../../libz.a
-ZIP_OBJS = minizip.o zip.o ioapi.o ../../libz.a
-
-.c.o:
- $(CC) -c $(CFLAGS) $*.c
-
-all: miniunz minizip
-
-miniunz: $(UNZ_OBJS)
- $(CC) $(CFLAGS) -o $@ $(UNZ_OBJS)
-
-minizip: $(ZIP_OBJS)
- $(CC) $(CFLAGS) -o $@ $(ZIP_OBJS)
-
-test: miniunz minizip
- ./minizip test readme.txt
- ./miniunz -l test.zip
- mv readme.txt readme.old
- ./miniunz test.zip
-
-clean:
- /bin/rm -f *.o *~ minizip miniunz
diff --git a/third-party/zlib/contrib/minizip/Makefile.am b/third-party/zlib/contrib/minizip/Makefile.am
deleted file mode 100644
index d343011..0000000
--- a/third-party/zlib/contrib/minizip/Makefile.am
+++ /dev/null
@@ -1,45 +0,0 @@
-lib_LTLIBRARIES = libminizip.la
-
-if COND_DEMOS
-bin_PROGRAMS = miniunzip minizip
-endif
-
-zlib_top_srcdir = $(top_srcdir)/../..
-zlib_top_builddir = $(top_builddir)/../..
-
-AM_CPPFLAGS = -I$(zlib_top_srcdir)
-AM_LDFLAGS = -L$(zlib_top_builddir)
-
-if WIN32
-iowin32_src = iowin32.c
-iowin32_h = iowin32.h
-endif
-
-libminizip_la_SOURCES = \
- ioapi.c \
- mztools.c \
- unzip.c \
- zip.c \
- ${iowin32_src}
-
-libminizip_la_LDFLAGS = $(AM_LDFLAGS) -version-info 1:0:0 -lz
-
-minizip_includedir = $(includedir)/minizip
-minizip_include_HEADERS = \
- crypt.h \
- ioapi.h \
- mztools.h \
- unzip.h \
- zip.h \
- ${iowin32_h}
-
-pkgconfigdir = $(libdir)/pkgconfig
-pkgconfig_DATA = minizip.pc
-
-EXTRA_PROGRAMS = miniunzip minizip
-
-miniunzip_SOURCES = miniunz.c
-miniunzip_LDADD = libminizip.la
-
-minizip_SOURCES = minizip.c
-minizip_LDADD = libminizip.la -lz
diff --git a/third-party/zlib/contrib/minizip/MiniZip64_Changes.txt b/third-party/zlib/contrib/minizip/MiniZip64_Changes.txt
deleted file mode 100644
index 13a1bd9..0000000
--- a/third-party/zlib/contrib/minizip/MiniZip64_Changes.txt
+++ /dev/null
@@ -1,6 +0,0 @@
-
-MiniZip 1.1 was derrived from MiniZip at version 1.01f
-
-Change in 1.0 (Okt 2009)
- - **TODO - Add history**
-
diff --git a/third-party/zlib/contrib/minizip/MiniZip64_info.txt b/third-party/zlib/contrib/minizip/MiniZip64_info.txt
deleted file mode 100644
index 57d7152..0000000
--- a/third-party/zlib/contrib/minizip/MiniZip64_info.txt
+++ /dev/null
@@ -1,74 +0,0 @@
-MiniZip - Copyright (c) 1998-2010 - by Gilles Vollant - version 1.1 64 bits from Mathias Svensson
-
-Introduction
----------------------
-MiniZip 1.1 is built from MiniZip 1.0 by Gilles Vollant ( http://www.winimage.com/zLibDll/minizip.html )
-
-When adding ZIP64 support into minizip it would result into risk of breaking compatibility with minizip 1.0.
-All possible work was done for compatibility.
-
-
-Background
----------------------
-When adding ZIP64 support Mathias Svensson found that Even Rouault have added ZIP64
-support for unzip.c into minizip for a open source project called gdal ( http://www.gdal.org/ )
-
-That was used as a starting point. And after that ZIP64 support was added to zip.c
-some refactoring and code cleanup was also done.
-
-
-Changed from MiniZip 1.0 to MiniZip 1.1
----------------------------------------
-* Added ZIP64 support for unzip ( by Even Rouault )
-* Added ZIP64 support for zip ( by Mathias Svensson )
-* Reverted some changed that Even Rouault did.
-* Bunch of patches received from Gulles Vollant that he received for MiniZip from various users.
-* Added unzip patch for BZIP Compression method (patch create by Daniel Borca)
-* Added BZIP Compress method for zip
-* Did some refactoring and code cleanup
-
-
-Credits
-
- Gilles Vollant - Original MiniZip author
- Even Rouault - ZIP64 unzip Support
- Daniel Borca - BZip Compression method support in unzip
- Mathias Svensson - ZIP64 zip support
- Mathias Svensson - BZip Compression method support in zip
-
- Resources
-
- ZipLayout http://result42.com/projects/ZipFileLayout
- Command line tool for Windows that shows the layout and information of the headers in a zip archive.
- Used when debugging and validating the creation of zip files using MiniZip64
-
-
- ZIP App Note http://www.pkware.com/documents/casestudies/APPNOTE.TXT
- Zip File specification
-
-
-Notes.
- * To be able to use BZip compression method in zip64.c or unzip64.c the BZIP2 lib is needed and HAVE_BZIP2 need to be defined.
-
-License
-----------------------------------------------------------
- Condition of use and distribution are the same than zlib :
-
- This software is provided 'as-is', without any express or implied
- warranty. In no event will the authors be held liable for any damages
- arising from the use of this software.
-
- Permission is granted to anyone to use this software for any purpose,
- including commercial applications, and to alter it and redistribute it
- freely, subject to the following restrictions:
-
- 1. The origin of this software must not be misrepresented; you must not
- claim that you wrote the original software. If you use this software
- in a product, an acknowledgment in the product documentation would be
- appreciated but is not required.
- 2. Altered source versions must be plainly marked as such, and must not be
- misrepresented as being the original software.
- 3. This notice may not be removed or altered from any source distribution.
-
-----------------------------------------------------------
-
diff --git a/third-party/zlib/contrib/minizip/configure.ac b/third-party/zlib/contrib/minizip/configure.ac
deleted file mode 100644
index 827a4e0..0000000
--- a/third-party/zlib/contrib/minizip/configure.ac
+++ /dev/null
@@ -1,32 +0,0 @@
-# -*- Autoconf -*-
-# Process this file with autoconf to produce a configure script.
-
-AC_INIT([minizip], [1.2.8], [bugzilla.redhat.com])
-AC_CONFIG_SRCDIR([minizip.c])
-AM_INIT_AUTOMAKE([foreign])
-LT_INIT
-
-AC_MSG_CHECKING([whether to build example programs])
-AC_ARG_ENABLE([demos], AC_HELP_STRING([--enable-demos], [build example programs]))
-AM_CONDITIONAL([COND_DEMOS], [test "$enable_demos" = yes])
-if test "$enable_demos" = yes
-then
- AC_MSG_RESULT([yes])
-else
- AC_MSG_RESULT([no])
-fi
-
-case "${host}" in
- *-mingw* | mingw*)
- WIN32="yes"
- ;;
- *)
- ;;
-esac
-AM_CONDITIONAL([WIN32], [test "${WIN32}" = "yes"])
-
-
-AC_SUBST([HAVE_UNISTD_H], [0])
-AC_CHECK_HEADER([unistd.h], [HAVE_UNISTD_H=1], [])
-AC_CONFIG_FILES([Makefile minizip.pc])
-AC_OUTPUT
diff --git a/third-party/zlib/contrib/minizip/crypt.h b/third-party/zlib/contrib/minizip/crypt.h
deleted file mode 100644
index 1e9e820..0000000
--- a/third-party/zlib/contrib/minizip/crypt.h
+++ /dev/null
@@ -1,131 +0,0 @@
-/* crypt.h -- base code for crypt/uncrypt ZIPfile
-
-
- Version 1.01e, February 12th, 2005
-
- Copyright (C) 1998-2005 Gilles Vollant
-
- This code is a modified version of crypting code in Infozip distribution
-
- The encryption/decryption parts of this source code (as opposed to the
- non-echoing password parts) were originally written in Europe. The
- whole source package can be freely distributed, including from the USA.
- (Prior to January 2000, re-export from the US was a violation of US law.)
-
- This encryption code is a direct transcription of the algorithm from
- Roger Schlafly, described by Phil Katz in the file appnote.txt. This
- file (appnote.txt) is distributed with the PKZIP program (even in the
- version without encryption capabilities).
-
- If you don't need crypting in your application, just define symbols
- NOCRYPT and NOUNCRYPT.
-
- This code support the "Traditional PKWARE Encryption".
-
- The new AES encryption added on Zip format by Winzip (see the page
- http://www.winzip.com/aes_info.htm ) and PKWare PKZip 5.x Strong
- Encryption is not supported.
-*/
-
-#define CRC32(c, b) ((*(pcrc_32_tab+(((int)(c) ^ (b)) & 0xff))) ^ ((c) >> 8))
-
-/***********************************************************************
- * Return the next byte in the pseudo-random sequence
- */
-static int decrypt_byte(unsigned long* pkeys, const z_crc_t* pcrc_32_tab)
-{
- unsigned temp; /* POTENTIAL BUG: temp*(temp^1) may overflow in an
- * unpredictable manner on 16-bit systems; not a problem
- * with any known compiler so far, though */
-
- temp = ((unsigned)(*(pkeys+2)) & 0xffff) | 2;
- return (int)(((temp * (temp ^ 1)) >> 8) & 0xff);
-}
-
-/***********************************************************************
- * Update the encryption keys with the next byte of plain text
- */
-static int update_keys(unsigned long* pkeys,const z_crc_t* pcrc_32_tab,int c)
-{
- (*(pkeys+0)) = CRC32((*(pkeys+0)), c);
- (*(pkeys+1)) += (*(pkeys+0)) & 0xff;
- (*(pkeys+1)) = (*(pkeys+1)) * 134775813L + 1;
- {
- register int keyshift = (int)((*(pkeys+1)) >> 24);
- (*(pkeys+2)) = CRC32((*(pkeys+2)), keyshift);
- }
- return c;
-}
-
-
-/***********************************************************************
- * Initialize the encryption keys and the random header according to
- * the given password.
- */
-static void init_keys(const char* passwd,unsigned long* pkeys,const z_crc_t* pcrc_32_tab)
-{
- *(pkeys+0) = 305419896L;
- *(pkeys+1) = 591751049L;
- *(pkeys+2) = 878082192L;
- while (*passwd != '\0') {
- update_keys(pkeys,pcrc_32_tab,(int)*passwd);
- passwd++;
- }
-}
-
-#define zdecode(pkeys,pcrc_32_tab,c) \
- (update_keys(pkeys,pcrc_32_tab,c ^= decrypt_byte(pkeys,pcrc_32_tab)))
-
-#define zencode(pkeys,pcrc_32_tab,c,t) \
- (t=decrypt_byte(pkeys,pcrc_32_tab), update_keys(pkeys,pcrc_32_tab,c), t^(c))
-
-#ifdef INCLUDECRYPTINGCODE_IFCRYPTALLOWED
-
-#define RAND_HEAD_LEN 12
- /* "last resort" source for second part of crypt seed pattern */
-# ifndef ZCR_SEED2
-# define ZCR_SEED2 3141592654UL /* use PI as default pattern */
-# endif
-
-static int crypthead(const char* passwd, /* password string */
- unsigned char* buf, /* where to write header */
- int bufSize,
- unsigned long* pkeys,
- const z_crc_t* pcrc_32_tab,
- unsigned long crcForCrypting)
-{
- int n; /* index in random header */
- int t; /* temporary */
- int c; /* random byte */
- unsigned char header[RAND_HEAD_LEN-2]; /* random header */
- static unsigned calls = 0; /* ensure different random header each time */
-
- if (bufSize<RAND_HEAD_LEN)
- return 0;
-
- /* First generate RAND_HEAD_LEN-2 random bytes. We encrypt the
- * output of rand() to get less predictability, since rand() is
- * often poorly implemented.
- */
- if (++calls == 1)
- {
- srand((unsigned)(time(NULL) ^ ZCR_SEED2));
- }
- init_keys(passwd, pkeys, pcrc_32_tab);
- for (n = 0; n < RAND_HEAD_LEN-2; n++)
- {
- c = (rand() >> 7) & 0xff;
- header[n] = (unsigned char)zencode(pkeys, pcrc_32_tab, c, t);
- }
- /* Encrypt random header (last two bytes is high word of crc) */
- init_keys(passwd, pkeys, pcrc_32_tab);
- for (n = 0; n < RAND_HEAD_LEN-2; n++)
- {
- buf[n] = (unsigned char)zencode(pkeys, pcrc_32_tab, header[n], t);
- }
- buf[n++] = (unsigned char)zencode(pkeys, pcrc_32_tab, (int)(crcForCrypting >> 16) & 0xff, t);
- buf[n++] = (unsigned char)zencode(pkeys, pcrc_32_tab, (int)(crcForCrypting >> 24) & 0xff, t);
- return n;
-}
-
-#endif
diff --git a/third-party/zlib/contrib/minizip/ioapi.c b/third-party/zlib/contrib/minizip/ioapi.c
deleted file mode 100644
index 7f5c191..0000000
--- a/third-party/zlib/contrib/minizip/ioapi.c
+++ /dev/null
@@ -1,247 +0,0 @@
-/* ioapi.h -- IO base function header for compress/uncompress .zip
- part of the MiniZip project - ( http://www.winimage.com/zLibDll/minizip.html )
-
- Copyright (C) 1998-2010 Gilles Vollant (minizip) ( http://www.winimage.com/zLibDll/minizip.html )
-
- Modifications for Zip64 support
- Copyright (C) 2009-2010 Mathias Svensson ( http://result42.com )
-
- For more info read MiniZip_info.txt
-
-*/
-
-#if defined(_WIN32) && (!(defined(_CRT_SECURE_NO_WARNINGS)))
- #define _CRT_SECURE_NO_WARNINGS
-#endif
-
-#if defined(__APPLE__) || defined(IOAPI_NO_64)
-// In darwin and perhaps other BSD variants off_t is a 64 bit value, hence no need for specific 64 bit functions
-#define FOPEN_FUNC(filename, mode) fopen(filename, mode)
-#define FTELLO_FUNC(stream) ftello(stream)
-#define FSEEKO_FUNC(stream, offset, origin) fseeko(stream, offset, origin)
-#else
-#define FOPEN_FUNC(filename, mode) fopen64(filename, mode)
-#define FTELLO_FUNC(stream) ftello64(stream)
-#define FSEEKO_FUNC(stream, offset, origin) fseeko64(stream, offset, origin)
-#endif
-
-
-#include "ioapi.h"
-
-voidpf call_zopen64 (const zlib_filefunc64_32_def* pfilefunc,const void*filename,int mode)
-{
- if (pfilefunc->zfile_func64.zopen64_file != NULL)
- return (*(pfilefunc->zfile_func64.zopen64_file)) (pfilefunc->zfile_func64.opaque,filename,mode);
- else
- {
- return (*(pfilefunc->zopen32_file))(pfilefunc->zfile_func64.opaque,(const char*)filename,mode);
- }
-}
-
-long call_zseek64 (const zlib_filefunc64_32_def* pfilefunc,voidpf filestream, ZPOS64_T offset, int origin)
-{
- if (pfilefunc->zfile_func64.zseek64_file != NULL)
- return (*(pfilefunc->zfile_func64.zseek64_file)) (pfilefunc->zfile_func64.opaque,filestream,offset,origin);
- else
- {
- uLong offsetTruncated = (uLong)offset;
- if (offsetTruncated != offset)
- return -1;
- else
- return (*(pfilefunc->zseek32_file))(pfilefunc->zfile_func64.opaque,filestream,offsetTruncated,origin);
- }
-}
-
-ZPOS64_T call_ztell64 (const zlib_filefunc64_32_def* pfilefunc,voidpf filestream)
-{
- if (pfilefunc->zfile_func64.zseek64_file != NULL)
- return (*(pfilefunc->zfile_func64.ztell64_file)) (pfilefunc->zfile_func64.opaque,filestream);
- else
- {
- uLong tell_uLong = (*(pfilefunc->ztell32_file))(pfilefunc->zfile_func64.opaque,filestream);
- if ((tell_uLong) == MAXU32)
- return (ZPOS64_T)-1;
- else
- return tell_uLong;
- }
-}
-
-void fill_zlib_filefunc64_32_def_from_filefunc32(zlib_filefunc64_32_def* p_filefunc64_32,const zlib_filefunc_def* p_filefunc32)
-{
- p_filefunc64_32->zfile_func64.zopen64_file = NULL;
- p_filefunc64_32->zopen32_file = p_filefunc32->zopen_file;
- p_filefunc64_32->zfile_func64.zerror_file = p_filefunc32->zerror_file;
- p_filefunc64_32->zfile_func64.zread_file = p_filefunc32->zread_file;
- p_filefunc64_32->zfile_func64.zwrite_file = p_filefunc32->zwrite_file;
- p_filefunc64_32->zfile_func64.ztell64_file = NULL;
- p_filefunc64_32->zfile_func64.zseek64_file = NULL;
- p_filefunc64_32->zfile_func64.zclose_file = p_filefunc32->zclose_file;
- p_filefunc64_32->zfile_func64.zerror_file = p_filefunc32->zerror_file;
- p_filefunc64_32->zfile_func64.opaque = p_filefunc32->opaque;
- p_filefunc64_32->zseek32_file = p_filefunc32->zseek_file;
- p_filefunc64_32->ztell32_file = p_filefunc32->ztell_file;
-}
-
-
-
-static voidpf ZCALLBACK fopen_file_func OF((voidpf opaque, const char* filename, int mode));
-static uLong ZCALLBACK fread_file_func OF((voidpf opaque, voidpf stream, void* buf, uLong size));
-static uLong ZCALLBACK fwrite_file_func OF((voidpf opaque, voidpf stream, const void* buf,uLong size));
-static ZPOS64_T ZCALLBACK ftell64_file_func OF((voidpf opaque, voidpf stream));
-static long ZCALLBACK fseek64_file_func OF((voidpf opaque, voidpf stream, ZPOS64_T offset, int origin));
-static int ZCALLBACK fclose_file_func OF((voidpf opaque, voidpf stream));
-static int ZCALLBACK ferror_file_func OF((voidpf opaque, voidpf stream));
-
-static voidpf ZCALLBACK fopen_file_func (voidpf opaque, const char* filename, int mode)
-{
- FILE* file = NULL;
- const char* mode_fopen = NULL;
- if ((mode & ZLIB_FILEFUNC_MODE_READWRITEFILTER)==ZLIB_FILEFUNC_MODE_READ)
- mode_fopen = "rb";
- else
- if (mode & ZLIB_FILEFUNC_MODE_EXISTING)
- mode_fopen = "r+b";
- else
- if (mode & ZLIB_FILEFUNC_MODE_CREATE)
- mode_fopen = "wb";
-
- if ((filename!=NULL) && (mode_fopen != NULL))
- file = fopen(filename, mode_fopen);
- return file;
-}
-
-static voidpf ZCALLBACK fopen64_file_func (voidpf opaque, const void* filename, int mode)
-{
- FILE* file = NULL;
- const char* mode_fopen = NULL;
- if ((mode & ZLIB_FILEFUNC_MODE_READWRITEFILTER)==ZLIB_FILEFUNC_MODE_READ)
- mode_fopen = "rb";
- else
- if (mode & ZLIB_FILEFUNC_MODE_EXISTING)
- mode_fopen = "r+b";
- else
- if (mode & ZLIB_FILEFUNC_MODE_CREATE)
- mode_fopen = "wb";
-
- if ((filename!=NULL) && (mode_fopen != NULL))
- file = FOPEN_FUNC((const char*)filename, mode_fopen);
- return file;
-}
-
-
-static uLong ZCALLBACK fread_file_func (voidpf opaque, voidpf stream, void* buf, uLong size)
-{
- uLong ret;
- ret = (uLong)fread(buf, 1, (size_t)size, (FILE *)stream);
- return ret;
-}
-
-static uLong ZCALLBACK fwrite_file_func (voidpf opaque, voidpf stream, const void* buf, uLong size)
-{
- uLong ret;
- ret = (uLong)fwrite(buf, 1, (size_t)size, (FILE *)stream);
- return ret;
-}
-
-static long ZCALLBACK ftell_file_func (voidpf opaque, voidpf stream)
-{
- long ret;
- ret = ftell((FILE *)stream);
- return ret;
-}
-
-
-static ZPOS64_T ZCALLBACK ftell64_file_func (voidpf opaque, voidpf stream)
-{
- ZPOS64_T ret;
- ret = FTELLO_FUNC((FILE *)stream);
- return ret;
-}
-
-static long ZCALLBACK fseek_file_func (voidpf opaque, voidpf stream, uLong offset, int origin)
-{
- int fseek_origin=0;
- long ret;
- switch (origin)
- {
- case ZLIB_FILEFUNC_SEEK_CUR :
- fseek_origin = SEEK_CUR;
- break;
- case ZLIB_FILEFUNC_SEEK_END :
- fseek_origin = SEEK_END;
- break;
- case ZLIB_FILEFUNC_SEEK_SET :
- fseek_origin = SEEK_SET;
- break;
- default: return -1;
- }
- ret = 0;
- if (fseek((FILE *)stream, offset, fseek_origin) != 0)
- ret = -1;
- return ret;
-}
-
-static long ZCALLBACK fseek64_file_func (voidpf opaque, voidpf stream, ZPOS64_T offset, int origin)
-{
- int fseek_origin=0;
- long ret;
- switch (origin)
- {
- case ZLIB_FILEFUNC_SEEK_CUR :
- fseek_origin = SEEK_CUR;
- break;
- case ZLIB_FILEFUNC_SEEK_END :
- fseek_origin = SEEK_END;
- break;
- case ZLIB_FILEFUNC_SEEK_SET :
- fseek_origin = SEEK_SET;
- break;
- default: return -1;
- }
- ret = 0;
-
- if(FSEEKO_FUNC((FILE *)stream, offset, fseek_origin) != 0)
- ret = -1;
-
- return ret;
-}
-
-
-static int ZCALLBACK fclose_file_func (voidpf opaque, voidpf stream)
-{
- int ret;
- ret = fclose((FILE *)stream);
- return ret;
-}
-
-static int ZCALLBACK ferror_file_func (voidpf opaque, voidpf stream)
-{
- int ret;
- ret = ferror((FILE *)stream);
- return ret;
-}
-
-void fill_fopen_filefunc (pzlib_filefunc_def)
- zlib_filefunc_def* pzlib_filefunc_def;
-{
- pzlib_filefunc_def->zopen_file = fopen_file_func;
- pzlib_filefunc_def->zread_file = fread_file_func;
- pzlib_filefunc_def->zwrite_file = fwrite_file_func;
- pzlib_filefunc_def->ztell_file = ftell_file_func;
- pzlib_filefunc_def->zseek_file = fseek_file_func;
- pzlib_filefunc_def->zclose_file = fclose_file_func;
- pzlib_filefunc_def->zerror_file = ferror_file_func;
- pzlib_filefunc_def->opaque = NULL;
-}
-
-void fill_fopen64_filefunc (zlib_filefunc64_def* pzlib_filefunc_def)
-{
- pzlib_filefunc_def->zopen64_file = fopen64_file_func;
- pzlib_filefunc_def->zread_file = fread_file_func;
- pzlib_filefunc_def->zwrite_file = fwrite_file_func;
- pzlib_filefunc_def->ztell64_file = ftell64_file_func;
- pzlib_filefunc_def->zseek64_file = fseek64_file_func;
- pzlib_filefunc_def->zclose_file = fclose_file_func;
- pzlib_filefunc_def->zerror_file = ferror_file_func;
- pzlib_filefunc_def->opaque = NULL;
-}
diff --git a/third-party/zlib/contrib/minizip/ioapi.h b/third-party/zlib/contrib/minizip/ioapi.h
deleted file mode 100644
index 8dcbdb0..0000000
--- a/third-party/zlib/contrib/minizip/ioapi.h
+++ /dev/null
@@ -1,208 +0,0 @@
-/* ioapi.h -- IO base function header for compress/uncompress .zip
- part of the MiniZip project - ( http://www.winimage.com/zLibDll/minizip.html )
-
- Copyright (C) 1998-2010 Gilles Vollant (minizip) ( http://www.winimage.com/zLibDll/minizip.html )
-
- Modifications for Zip64 support
- Copyright (C) 2009-2010 Mathias Svensson ( http://result42.com )
-
- For more info read MiniZip_info.txt
-
- Changes
-
- Oct-2009 - Defined ZPOS64_T to fpos_t on windows and u_int64_t on linux. (might need to find a better why for this)
- Oct-2009 - Change to fseeko64, ftello64 and fopen64 so large files would work on linux.
- More if/def section may be needed to support other platforms
- Oct-2009 - Defined fxxxx64 calls to normal fopen/ftell/fseek so they would compile on windows.
- (but you should use iowin32.c for windows instead)
-
-*/
-
-#ifndef _ZLIBIOAPI64_H
-#define _ZLIBIOAPI64_H
-
-#if (!defined(_WIN32)) && (!defined(WIN32)) && (!defined(__APPLE__))
-
- // Linux needs this to support file operation on files larger then 4+GB
- // But might need better if/def to select just the platforms that needs them.
-
- #ifndef __USE_FILE_OFFSET64
- #define __USE_FILE_OFFSET64
- #endif
- #ifndef __USE_LARGEFILE64
- #define __USE_LARGEFILE64
- #endif
- #ifndef _LARGEFILE64_SOURCE
- #define _LARGEFILE64_SOURCE
- #endif
- #ifndef _FILE_OFFSET_BIT
- #define _FILE_OFFSET_BIT 64
- #endif
-
-#endif
-
-#include <stdio.h>
-#include <stdlib.h>
-#include "zlib.h"
-
-#if defined(USE_FILE32API)
-#define fopen64 fopen
-#define ftello64 ftell
-#define fseeko64 fseek
-#else
-#ifdef __FreeBSD__
-#define fopen64 fopen
-#define ftello64 ftello
-#define fseeko64 fseeko
-#endif
-#ifdef _MSC_VER
- #define fopen64 fopen
- #if (_MSC_VER >= 1400) && (!(defined(NO_MSCVER_FILE64_FUNC)))
- #define ftello64 _ftelli64
- #define fseeko64 _fseeki64
- #else // old MSC
- #define ftello64 ftell
- #define fseeko64 fseek
- #endif
-#endif
-#endif
-
-/*
-#ifndef ZPOS64_T
- #ifdef _WIN32
- #define ZPOS64_T fpos_t
- #else
- #include <stdint.h>
- #define ZPOS64_T uint64_t
- #endif
-#endif
-*/
-
-#ifdef HAVE_MINIZIP64_CONF_H
-#include "mz64conf.h"
-#endif
-
-/* a type choosen by DEFINE */
-#ifdef HAVE_64BIT_INT_CUSTOM
-typedef 64BIT_INT_CUSTOM_TYPE ZPOS64_T;
-#else
-#ifdef HAS_STDINT_H
-#include "stdint.h"
-typedef uint64_t ZPOS64_T;
-#else
-
-/* Maximum unsigned 32-bit value used as placeholder for zip64 */
-#define MAXU32 0xffffffff
-
-#if defined(_MSC_VER) || defined(__BORLANDC__)
-typedef unsigned __int64 ZPOS64_T;
-#else
-typedef unsigned long long int ZPOS64_T;
-#endif
-#endif
-#endif
-
-
-
-#ifdef __cplusplus
-extern "C" {
-#endif
-
-
-#define ZLIB_FILEFUNC_SEEK_CUR (1)
-#define ZLIB_FILEFUNC_SEEK_END (2)
-#define ZLIB_FILEFUNC_SEEK_SET (0)
-
-#define ZLIB_FILEFUNC_MODE_READ (1)
-#define ZLIB_FILEFUNC_MODE_WRITE (2)
-#define ZLIB_FILEFUNC_MODE_READWRITEFILTER (3)
-
-#define ZLIB_FILEFUNC_MODE_EXISTING (4)
-#define ZLIB_FILEFUNC_MODE_CREATE (8)
-
-
-#ifndef ZCALLBACK
- #if (defined(WIN32) || defined(_WIN32) || defined (WINDOWS) || defined (_WINDOWS)) && defined(CALLBACK) && defined (USEWINDOWS_CALLBACK)
- #define ZCALLBACK CALLBACK
- #else
- #define ZCALLBACK
- #endif
-#endif
-
-
-
-
-typedef voidpf (ZCALLBACK *open_file_func) OF((voidpf opaque, const char* filename, int mode));
-typedef uLong (ZCALLBACK *read_file_func) OF((voidpf opaque, voidpf stream, void* buf, uLong size));
-typedef uLong (ZCALLBACK *write_file_func) OF((voidpf opaque, voidpf stream, const void* buf, uLong size));
-typedef int (ZCALLBACK *close_file_func) OF((voidpf opaque, voidpf stream));
-typedef int (ZCALLBACK *testerror_file_func) OF((voidpf opaque, voidpf stream));
-
-typedef long (ZCALLBACK *tell_file_func) OF((voidpf opaque, voidpf stream));
-typedef long (ZCALLBACK *seek_file_func) OF((voidpf opaque, voidpf stream, uLong offset, int origin));
-
-
-/* here is the "old" 32 bits structure structure */
-typedef struct zlib_filefunc_def_s
-{
- open_file_func zopen_file;
- read_file_func zread_file;
- write_file_func zwrite_file;
- tell_file_func ztell_file;
- seek_file_func zseek_file;
- close_file_func zclose_file;
- testerror_file_func zerror_file;
- voidpf opaque;
-} zlib_filefunc_def;
-
-typedef ZPOS64_T (ZCALLBACK *tell64_file_func) OF((voidpf opaque, voidpf stream));
-typedef long (ZCALLBACK *seek64_file_func) OF((voidpf opaque, voidpf stream, ZPOS64_T offset, int origin));
-typedef voidpf (ZCALLBACK *open64_file_func) OF((voidpf opaque, const void* filename, int mode));
-
-typedef struct zlib_filefunc64_def_s
-{
- open64_file_func zopen64_file;
- read_file_func zread_file;
- write_file_func zwrite_file;
- tell64_file_func ztell64_file;
- seek64_file_func zseek64_file;
- close_file_func zclose_file;
- testerror_file_func zerror_file;
- voidpf opaque;
-} zlib_filefunc64_def;
-
-void fill_fopen64_filefunc OF((zlib_filefunc64_def* pzlib_filefunc_def));
-void fill_fopen_filefunc OF((zlib_filefunc_def* pzlib_filefunc_def));
-
-/* now internal definition, only for zip.c and unzip.h */
-typedef struct zlib_filefunc64_32_def_s
-{
- zlib_filefunc64_def zfile_func64;
- open_file_func zopen32_file;
- tell_file_func ztell32_file;
- seek_file_func zseek32_file;
-} zlib_filefunc64_32_def;
-
-
-#define ZREAD64(filefunc,filestream,buf,size) ((*((filefunc).zfile_func64.zread_file)) ((filefunc).zfile_func64.opaque,filestream,buf,size))
-#define ZWRITE64(filefunc,filestream,buf,size) ((*((filefunc).zfile_func64.zwrite_file)) ((filefunc).zfile_func64.opaque,filestream,buf,size))
-//#define ZTELL64(filefunc,filestream) ((*((filefunc).ztell64_file)) ((filefunc).opaque,filestream))
-//#define ZSEEK64(filefunc,filestream,pos,mode) ((*((filefunc).zseek64_file)) ((filefunc).opaque,filestream,pos,mode))
-#define ZCLOSE64(filefunc,filestream) ((*((filefunc).zfile_func64.zclose_file)) ((filefunc).zfile_func64.opaque,filestream))
-#define ZERROR64(filefunc,filestream) ((*((filefunc).zfile_func64.zerror_file)) ((filefunc).zfile_func64.opaque,filestream))
-
-voidpf call_zopen64 OF((const zlib_filefunc64_32_def* pfilefunc,const void*filename,int mode));
-long call_zseek64 OF((const zlib_filefunc64_32_def* pfilefunc,voidpf filestream, ZPOS64_T offset, int origin));
-ZPOS64_T call_ztell64 OF((const zlib_filefunc64_32_def* pfilefunc,voidpf filestream));
-
-void fill_zlib_filefunc64_32_def_from_filefunc32(zlib_filefunc64_32_def* p_filefunc64_32,const zlib_filefunc_def* p_filefunc32);
-
-#define ZOPEN64(filefunc,filename,mode) (call_zopen64((&(filefunc)),(filename),(mode)))
-#define ZTELL64(filefunc,filestream) (call_ztell64((&(filefunc)),(filestream)))
-#define ZSEEK64(filefunc,filestream,pos,mode) (call_zseek64((&(filefunc)),(filestream),(pos),(mode)))
-
-#ifdef __cplusplus
-}
-#endif
-
-#endif
diff --git a/third-party/zlib/contrib/minizip/iowin32.c b/third-party/zlib/contrib/minizip/iowin32.c
deleted file mode 100644
index a46d96c..0000000
--- a/third-party/zlib/contrib/minizip/iowin32.c
+++ /dev/null
@@ -1,461 +0,0 @@
-/* iowin32.c -- IO base function header for compress/uncompress .zip
- Version 1.1, February 14h, 2010
- part of the MiniZip project - ( http://www.winimage.com/zLibDll/minizip.html )
-
- Copyright (C) 1998-2010 Gilles Vollant (minizip) ( http://www.winimage.com/zLibDll/minizip.html )
-
- Modifications for Zip64 support
- Copyright (C) 2009-2010 Mathias Svensson ( http://result42.com )
-
- For more info read MiniZip_info.txt
-
-*/
-
-#include <stdlib.h>
-
-#include "zlib.h"
-#include "ioapi.h"
-#include "iowin32.h"
-
-#ifndef INVALID_HANDLE_VALUE
-#define INVALID_HANDLE_VALUE (0xFFFFFFFF)
-#endif
-
-#ifndef INVALID_SET_FILE_POINTER
-#define INVALID_SET_FILE_POINTER ((DWORD)-1)
-#endif
-
-
-#if defined(WINAPI_FAMILY_PARTITION) && (!(defined(IOWIN32_USING_WINRT_API)))
-#if WINAPI_FAMILY_PARTITION(WINAPI_PARTITION_APP)
-#define IOWIN32_USING_WINRT_API 1
-#endif
-#endif
-
-voidpf ZCALLBACK win32_open_file_func OF((voidpf opaque, const char* filename, int mode));
-uLong ZCALLBACK win32_read_file_func OF((voidpf opaque, voidpf stream, void* buf, uLong size));
-uLong ZCALLBACK win32_write_file_func OF((voidpf opaque, voidpf stream, const void* buf, uLong size));
-ZPOS64_T ZCALLBACK win32_tell64_file_func OF((voidpf opaque, voidpf stream));
-long ZCALLBACK win32_seek64_file_func OF((voidpf opaque, voidpf stream, ZPOS64_T offset, int origin));
-int ZCALLBACK win32_close_file_func OF((voidpf opaque, voidpf stream));
-int ZCALLBACK win32_error_file_func OF((voidpf opaque, voidpf stream));
-
-typedef struct
-{
- HANDLE hf;
- int error;
-} WIN32FILE_IOWIN;
-
-
-static void win32_translate_open_mode(int mode,
- DWORD* lpdwDesiredAccess,
- DWORD* lpdwCreationDisposition,
- DWORD* lpdwShareMode,
- DWORD* lpdwFlagsAndAttributes)
-{
- *lpdwDesiredAccess = *lpdwShareMode = *lpdwFlagsAndAttributes = *lpdwCreationDisposition = 0;
-
- if ((mode & ZLIB_FILEFUNC_MODE_READWRITEFILTER)==ZLIB_FILEFUNC_MODE_READ)
- {
- *lpdwDesiredAccess = GENERIC_READ;
- *lpdwCreationDisposition = OPEN_EXISTING;
- *lpdwShareMode = FILE_SHARE_READ;
- }
- else if (mode & ZLIB_FILEFUNC_MODE_EXISTING)
- {
- *lpdwDesiredAccess = GENERIC_WRITE | GENERIC_READ;
- *lpdwCreationDisposition = OPEN_EXISTING;
- }
- else if (mode & ZLIB_FILEFUNC_MODE_CREATE)
- {
- *lpdwDesiredAccess = GENERIC_WRITE | GENERIC_READ;
- *lpdwCreationDisposition = CREATE_ALWAYS;
- }
-}
-
-static voidpf win32_build_iowin(HANDLE hFile)
-{
- voidpf ret=NULL;
-
- if ((hFile != NULL) && (hFile != INVALID_HANDLE_VALUE))
- {
- WIN32FILE_IOWIN w32fiow;
- w32fiow.hf = hFile;
- w32fiow.error = 0;
- ret = malloc(sizeof(WIN32FILE_IOWIN));
-
- if (ret==NULL)
- CloseHandle(hFile);
- else
- *((WIN32FILE_IOWIN*)ret) = w32fiow;
- }
- return ret;
-}
-
-voidpf ZCALLBACK win32_open64_file_func (voidpf opaque,const void* filename,int mode)
-{
- const char* mode_fopen = NULL;
- DWORD dwDesiredAccess,dwCreationDisposition,dwShareMode,dwFlagsAndAttributes ;
- HANDLE hFile = NULL;
-
- win32_translate_open_mode(mode,&dwDesiredAccess,&dwCreationDisposition,&dwShareMode,&dwFlagsAndAttributes);
-
-#ifdef IOWIN32_USING_WINRT_API
-#ifdef UNICODE
- if ((filename!=NULL) && (dwDesiredAccess != 0))
- hFile = CreateFile2((LPCTSTR)filename, dwDesiredAccess, dwShareMode, dwCreationDisposition, NULL);
-#else
- if ((filename!=NULL) && (dwDesiredAccess != 0))
- {
- WCHAR filenameW[FILENAME_MAX + 0x200 + 1];
- MultiByteToWideChar(CP_ACP,0,(const char*)filename,-1,filenameW,FILENAME_MAX + 0x200);
- hFile = CreateFile2(filenameW, dwDesiredAccess, dwShareMode, dwCreationDisposition, NULL);
- }
-#endif
-#else
- if ((filename!=NULL) && (dwDesiredAccess != 0))
- hFile = CreateFile((LPCTSTR)filename, dwDesiredAccess, dwShareMode, NULL, dwCreationDisposition, dwFlagsAndAttributes, NULL);
-#endif
-
- return win32_build_iowin(hFile);
-}
-
-
-voidpf ZCALLBACK win32_open64_file_funcA (voidpf opaque,const void* filename,int mode)
-{
- const char* mode_fopen = NULL;
- DWORD dwDesiredAccess,dwCreationDisposition,dwShareMode,dwFlagsAndAttributes ;
- HANDLE hFile = NULL;
-
- win32_translate_open_mode(mode,&dwDesiredAccess,&dwCreationDisposition,&dwShareMode,&dwFlagsAndAttributes);
-
-#ifdef IOWIN32_USING_WINRT_API
- if ((filename!=NULL) && (dwDesiredAccess != 0))
- {
- WCHAR filenameW[FILENAME_MAX + 0x200 + 1];
- MultiByteToWideChar(CP_ACP,0,(const char*)filename,-1,filenameW,FILENAME_MAX + 0x200);
- hFile = CreateFile2(filenameW, dwDesiredAccess, dwShareMode, dwCreationDisposition, NULL);
- }
-#else
- if ((filename!=NULL) && (dwDesiredAccess != 0))
- hFile = CreateFileA((LPCSTR)filename, dwDesiredAccess, dwShareMode, NULL, dwCreationDisposition, dwFlagsAndAttributes, NULL);
-#endif
-
- return win32_build_iowin(hFile);
-}
-
-
-voidpf ZCALLBACK win32_open64_file_funcW (voidpf opaque,const void* filename,int mode)
-{
- const char* mode_fopen = NULL;
- DWORD dwDesiredAccess,dwCreationDisposition,dwShareMode,dwFlagsAndAttributes ;
- HANDLE hFile = NULL;
-
- win32_translate_open_mode(mode,&dwDesiredAccess,&dwCreationDisposition,&dwShareMode,&dwFlagsAndAttributes);
-
-#ifdef IOWIN32_USING_WINRT_API
- if ((filename!=NULL) && (dwDesiredAccess != 0))
- hFile = CreateFile2((LPCWSTR)filename, dwDesiredAccess, dwShareMode, dwCreationDisposition,NULL);
-#else
- if ((filename!=NULL) && (dwDesiredAccess != 0))
- hFile = CreateFileW((LPCWSTR)filename, dwDesiredAccess, dwShareMode, NULL, dwCreationDisposition, dwFlagsAndAttributes, NULL);
-#endif
-
- return win32_build_iowin(hFile);
-}
-
-
-voidpf ZCALLBACK win32_open_file_func (voidpf opaque,const char* filename,int mode)
-{
- const char* mode_fopen = NULL;
- DWORD dwDesiredAccess,dwCreationDisposition,dwShareMode,dwFlagsAndAttributes ;
- HANDLE hFile = NULL;
-
- win32_translate_open_mode(mode,&dwDesiredAccess,&dwCreationDisposition,&dwShareMode,&dwFlagsAndAttributes);
-
-#ifdef IOWIN32_USING_WINRT_API
-#ifdef UNICODE
- if ((filename!=NULL) && (dwDesiredAccess != 0))
- hFile = CreateFile2((LPCTSTR)filename, dwDesiredAccess, dwShareMode, dwCreationDisposition, NULL);
-#else
- if ((filename!=NULL) && (dwDesiredAccess != 0))
- {
- WCHAR filenameW[FILENAME_MAX + 0x200 + 1];
- MultiByteToWideChar(CP_ACP,0,(const char*)filename,-1,filenameW,FILENAME_MAX + 0x200);
- hFile = CreateFile2(filenameW, dwDesiredAccess, dwShareMode, dwCreationDisposition, NULL);
- }
-#endif
-#else
- if ((filename!=NULL) && (dwDesiredAccess != 0))
- hFile = CreateFile((LPCTSTR)filename, dwDesiredAccess, dwShareMode, NULL, dwCreationDisposition, dwFlagsAndAttributes, NULL);
-#endif
-
- return win32_build_iowin(hFile);
-}
-
-
-uLong ZCALLBACK win32_read_file_func (voidpf opaque, voidpf stream, void* buf,uLong size)
-{
- uLong ret=0;
- HANDLE hFile = NULL;
- if (stream!=NULL)
- hFile = ((WIN32FILE_IOWIN*)stream) -> hf;
-
- if (hFile != NULL)
- {
- if (!ReadFile(hFile, buf, size, &ret, NULL))
- {
- DWORD dwErr = GetLastError();
- if (dwErr == ERROR_HANDLE_EOF)
- dwErr = 0;
- ((WIN32FILE_IOWIN*)stream) -> error=(int)dwErr;
- }
- }
-
- return ret;
-}
-
-
-uLong ZCALLBACK win32_write_file_func (voidpf opaque,voidpf stream,const void* buf,uLong size)
-{
- uLong ret=0;
- HANDLE hFile = NULL;
- if (stream!=NULL)
- hFile = ((WIN32FILE_IOWIN*)stream) -> hf;
-
- if (hFile != NULL)
- {
- if (!WriteFile(hFile, buf, size, &ret, NULL))
- {
- DWORD dwErr = GetLastError();
- if (dwErr == ERROR_HANDLE_EOF)
- dwErr = 0;
- ((WIN32FILE_IOWIN*)stream) -> error=(int)dwErr;
- }
- }
-
- return ret;
-}
-
-static BOOL MySetFilePointerEx(HANDLE hFile, LARGE_INTEGER pos, LARGE_INTEGER *newPos, DWORD dwMoveMethod)
-{
-#ifdef IOWIN32_USING_WINRT_API
- return SetFilePointerEx(hFile, pos, newPos, dwMoveMethod);
-#else
- LONG lHigh = pos.HighPart;
- DWORD dwNewPos = SetFilePointer(hFile, pos.LowPart, &lHigh, FILE_CURRENT);
- BOOL fOk = TRUE;
- if (dwNewPos == 0xFFFFFFFF)
- if (GetLastError() != NO_ERROR)
- fOk = FALSE;
- if ((newPos != NULL) && (fOk))
- {
- newPos->LowPart = dwNewPos;
- newPos->HighPart = lHigh;
- }
- return fOk;
-#endif
-}
-
-long ZCALLBACK win32_tell_file_func (voidpf opaque,voidpf stream)
-{
- long ret=-1;
- HANDLE hFile = NULL;
- if (stream!=NULL)
- hFile = ((WIN32FILE_IOWIN*)stream) -> hf;
- if (hFile != NULL)
- {
- LARGE_INTEGER pos;
- pos.QuadPart = 0;
-
- if (!MySetFilePointerEx(hFile, pos, &pos, FILE_CURRENT))
- {
- DWORD dwErr = GetLastError();
- ((WIN32FILE_IOWIN*)stream) -> error=(int)dwErr;
- ret = -1;
- }
- else
- ret=(long)pos.LowPart;
- }
- return ret;
-}
-
-ZPOS64_T ZCALLBACK win32_tell64_file_func (voidpf opaque, voidpf stream)
-{
- ZPOS64_T ret= (ZPOS64_T)-1;
- HANDLE hFile = NULL;
- if (stream!=NULL)
- hFile = ((WIN32FILE_IOWIN*)stream)->hf;
-
- if (hFile)
- {
- LARGE_INTEGER pos;
- pos.QuadPart = 0;
-
- if (!MySetFilePointerEx(hFile, pos, &pos, FILE_CURRENT))
- {
- DWORD dwErr = GetLastError();
- ((WIN32FILE_IOWIN*)stream) -> error=(int)dwErr;
- ret = (ZPOS64_T)-1;
- }
- else
- ret=pos.QuadPart;
- }
- return ret;
-}
-
-
-long ZCALLBACK win32_seek_file_func (voidpf opaque,voidpf stream,uLong offset,int origin)
-{
- DWORD dwMoveMethod=0xFFFFFFFF;
- HANDLE hFile = NULL;
-
- long ret=-1;
- if (stream!=NULL)
- hFile = ((WIN32FILE_IOWIN*)stream) -> hf;
- switch (origin)
- {
- case ZLIB_FILEFUNC_SEEK_CUR :
- dwMoveMethod = FILE_CURRENT;
- break;
- case ZLIB_FILEFUNC_SEEK_END :
- dwMoveMethod = FILE_END;
- break;
- case ZLIB_FILEFUNC_SEEK_SET :
- dwMoveMethod = FILE_BEGIN;
- break;
- default: return -1;
- }
-
- if (hFile != NULL)
- {
- LARGE_INTEGER pos;
- pos.QuadPart = offset;
- if (!MySetFilePointerEx(hFile, pos, NULL, dwMoveMethod))
- {
- DWORD dwErr = GetLastError();
- ((WIN32FILE_IOWIN*)stream) -> error=(int)dwErr;
- ret = -1;
- }
- else
- ret=0;
- }
- return ret;
-}
-
-long ZCALLBACK win32_seek64_file_func (voidpf opaque, voidpf stream,ZPOS64_T offset,int origin)
-{
- DWORD dwMoveMethod=0xFFFFFFFF;
- HANDLE hFile = NULL;
- long ret=-1;
-
- if (stream!=NULL)
- hFile = ((WIN32FILE_IOWIN*)stream)->hf;
-
- switch (origin)
- {
- case ZLIB_FILEFUNC_SEEK_CUR :
- dwMoveMethod = FILE_CURRENT;
- break;
- case ZLIB_FILEFUNC_SEEK_END :
- dwMoveMethod = FILE_END;
- break;
- case ZLIB_FILEFUNC_SEEK_SET :
- dwMoveMethod = FILE_BEGIN;
- break;
- default: return -1;
- }
-
- if (hFile)
- {
- LARGE_INTEGER pos;
- pos.QuadPart = offset;
- if (!MySetFilePointerEx(hFile, pos, NULL, FILE_CURRENT))
- {
- DWORD dwErr = GetLastError();
- ((WIN32FILE_IOWIN*)stream) -> error=(int)dwErr;
- ret = -1;
- }
- else
- ret=0;
- }
- return ret;
-}
-
-int ZCALLBACK win32_close_file_func (voidpf opaque, voidpf stream)
-{
- int ret=-1;
-
- if (stream!=NULL)
- {
- HANDLE hFile;
- hFile = ((WIN32FILE_IOWIN*)stream) -> hf;
- if (hFile != NULL)
- {
- CloseHandle(hFile);
- ret=0;
- }
- free(stream);
- }
- return ret;
-}
-
-int ZCALLBACK win32_error_file_func (voidpf opaque,voidpf stream)
-{
- int ret=-1;
- if (stream!=NULL)
- {
- ret = ((WIN32FILE_IOWIN*)stream) -> error;
- }
- return ret;
-}
-
-void fill_win32_filefunc (zlib_filefunc_def* pzlib_filefunc_def)
-{
- pzlib_filefunc_def->zopen_file = win32_open_file_func;
- pzlib_filefunc_def->zread_file = win32_read_file_func;
- pzlib_filefunc_def->zwrite_file = win32_write_file_func;
- pzlib_filefunc_def->ztell_file = win32_tell_file_func;
- pzlib_filefunc_def->zseek_file = win32_seek_file_func;
- pzlib_filefunc_def->zclose_file = win32_close_file_func;
- pzlib_filefunc_def->zerror_file = win32_error_file_func;
- pzlib_filefunc_def->opaque = NULL;
-}
-
-void fill_win32_filefunc64(zlib_filefunc64_def* pzlib_filefunc_def)
-{
- pzlib_filefunc_def->zopen64_file = win32_open64_file_func;
- pzlib_filefunc_def->zread_file = win32_read_file_func;
- pzlib_filefunc_def->zwrite_file = win32_write_file_func;
- pzlib_filefunc_def->ztell64_file = win32_tell64_file_func;
- pzlib_filefunc_def->zseek64_file = win32_seek64_file_func;
- pzlib_filefunc_def->zclose_file = win32_close_file_func;
- pzlib_filefunc_def->zerror_file = win32_error_file_func;
- pzlib_filefunc_def->opaque = NULL;
-}
-
-
-void fill_win32_filefunc64A(zlib_filefunc64_def* pzlib_filefunc_def)
-{
- pzlib_filefunc_def->zopen64_file = win32_open64_file_funcA;
- pzlib_filefunc_def->zread_file = win32_read_file_func;
- pzlib_filefunc_def->zwrite_file = win32_write_file_func;
- pzlib_filefunc_def->ztell64_file = win32_tell64_file_func;
- pzlib_filefunc_def->zseek64_file = win32_seek64_file_func;
- pzlib_filefunc_def->zclose_file = win32_close_file_func;
- pzlib_filefunc_def->zerror_file = win32_error_file_func;
- pzlib_filefunc_def->opaque = NULL;
-}
-
-
-void fill_win32_filefunc64W(zlib_filefunc64_def* pzlib_filefunc_def)
-{
- pzlib_filefunc_def->zopen64_file = win32_open64_file_funcW;
- pzlib_filefunc_def->zread_file = win32_read_file_func;
- pzlib_filefunc_def->zwrite_file = win32_write_file_func;
- pzlib_filefunc_def->ztell64_file = win32_tell64_file_func;
- pzlib_filefunc_def->zseek64_file = win32_seek64_file_func;
- pzlib_filefunc_def->zclose_file = win32_close_file_func;
- pzlib_filefunc_def->zerror_file = win32_error_file_func;
- pzlib_filefunc_def->opaque = NULL;
-}
diff --git a/third-party/zlib/contrib/minizip/iowin32.h b/third-party/zlib/contrib/minizip/iowin32.h
deleted file mode 100644
index 0ca0969..0000000
--- a/third-party/zlib/contrib/minizip/iowin32.h
+++ /dev/null
@@ -1,28 +0,0 @@
-/* iowin32.h -- IO base function header for compress/uncompress .zip
- Version 1.1, February 14h, 2010
- part of the MiniZip project - ( http://www.winimage.com/zLibDll/minizip.html )
-
- Copyright (C) 1998-2010 Gilles Vollant (minizip) ( http://www.winimage.com/zLibDll/minizip.html )
-
- Modifications for Zip64 support
- Copyright (C) 2009-2010 Mathias Svensson ( http://result42.com )
-
- For more info read MiniZip_info.txt
-
-*/
-
-#include <windows.h>
-
-
-#ifdef __cplusplus
-extern "C" {
-#endif
-
-void fill_win32_filefunc OF((zlib_filefunc_def* pzlib_filefunc_def));
-void fill_win32_filefunc64 OF((zlib_filefunc64_def* pzlib_filefunc_def));
-void fill_win32_filefunc64A OF((zlib_filefunc64_def* pzlib_filefunc_def));
-void fill_win32_filefunc64W OF((zlib_filefunc64_def* pzlib_filefunc_def));
-
-#ifdef __cplusplus
-}
-#endif
diff --git a/third-party/zlib/contrib/minizip/make_vms.com b/third-party/zlib/contrib/minizip/make_vms.com
deleted file mode 100644
index 9ac13a9..0000000
--- a/third-party/zlib/contrib/minizip/make_vms.com
+++ /dev/null
@@ -1,25 +0,0 @@
-$ if f$search("ioapi.h_orig") .eqs. "" then copy ioapi.h ioapi.h_orig
-$ open/write zdef vmsdefs.h
-$ copy sys$input: zdef
-$ deck
-#define unix
-#define fill_zlib_filefunc64_32_def_from_filefunc32 fillzffunc64from
-#define Write_Zip64EndOfCentralDirectoryLocator Write_Zip64EoDLocator
-#define Write_Zip64EndOfCentralDirectoryRecord Write_Zip64EoDRecord
-#define Write_EndOfCentralDirectoryRecord Write_EoDRecord
-$ eod
-$ close zdef
-$ copy vmsdefs.h,ioapi.h_orig ioapi.h
-$ cc/include=[--]/prefix=all ioapi.c
-$ cc/include=[--]/prefix=all miniunz.c
-$ cc/include=[--]/prefix=all unzip.c
-$ cc/include=[--]/prefix=all minizip.c
-$ cc/include=[--]/prefix=all zip.c
-$ link miniunz,unzip,ioapi,[--]libz.olb/lib
-$ link minizip,zip,ioapi,[--]libz.olb/lib
-$ mcr []minizip test minizip_info.txt
-$ mcr []miniunz -l test.zip
-$ rename minizip_info.txt; minizip_info.txt_old
-$ mcr []miniunz test.zip
-$ delete test.zip;*
-$exit
diff --git a/third-party/zlib/contrib/minizip/miniunz.c b/third-party/zlib/contrib/minizip/miniunz.c
deleted file mode 100644
index 3d65401..0000000
--- a/third-party/zlib/contrib/minizip/miniunz.c
+++ /dev/null
@@ -1,660 +0,0 @@
-/*
- miniunz.c
- Version 1.1, February 14h, 2010
- sample part of the MiniZip project - ( http://www.winimage.com/zLibDll/minizip.html )
-
- Copyright (C) 1998-2010 Gilles Vollant (minizip) ( http://www.winimage.com/zLibDll/minizip.html )
-
- Modifications of Unzip for Zip64
- Copyright (C) 2007-2008 Even Rouault
-
- Modifications for Zip64 support on both zip and unzip
- Copyright (C) 2009-2010 Mathias Svensson ( http://result42.com )
-*/
-
-#if (!defined(_WIN32)) && (!defined(WIN32)) && (!defined(__APPLE__))
- #ifndef __USE_FILE_OFFSET64
- #define __USE_FILE_OFFSET64
- #endif
- #ifndef __USE_LARGEFILE64
- #define __USE_LARGEFILE64
- #endif
- #ifndef _LARGEFILE64_SOURCE
- #define _LARGEFILE64_SOURCE
- #endif
- #ifndef _FILE_OFFSET_BIT
- #define _FILE_OFFSET_BIT 64
- #endif
-#endif
-
-#ifdef __APPLE__
-// In darwin and perhaps other BSD variants off_t is a 64 bit value, hence no need for specific 64 bit functions
-#define FOPEN_FUNC(filename, mode) fopen(filename, mode)
-#define FTELLO_FUNC(stream) ftello(stream)
-#define FSEEKO_FUNC(stream, offset, origin) fseeko(stream, offset, origin)
-#else
-#define FOPEN_FUNC(filename, mode) fopen64(filename, mode)
-#define FTELLO_FUNC(stream) ftello64(stream)
-#define FSEEKO_FUNC(stream, offset, origin) fseeko64(stream, offset, origin)
-#endif
-
-
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
-#include <time.h>
-#include <errno.h>
-#include <fcntl.h>
-
-#ifdef _WIN32
-# include <direct.h>
-# include <io.h>
-#else
-# include <unistd.h>
-# include <utime.h>
-#endif
-
-
-#include "unzip.h"
-
-#define CASESENSITIVITY (0)
-#define WRITEBUFFERSIZE (8192)
-#define MAXFILENAME (256)
-
-#ifdef _WIN32
-#define USEWIN32IOAPI
-#include "iowin32.h"
-#endif
-/*
- mini unzip, demo of unzip package
-
- usage :
- Usage : miniunz [-exvlo] file.zip [file_to_extract] [-d extractdir]
-
- list the file in the zipfile, and print the content of FILE_ID.ZIP or README.TXT
- if it exists
-*/
-
-
-/* change_file_date : change the date/time of a file
- filename : the filename of the file where date/time must be modified
- dosdate : the new date at the MSDos format (4 bytes)
- tmu_date : the SAME new date at the tm_unz format */
-void change_file_date(filename,dosdate,tmu_date)
- const char *filename;
- uLong dosdate;
- tm_unz tmu_date;
-{
-#ifdef _WIN32
- HANDLE hFile;
- FILETIME ftm,ftLocal,ftCreate,ftLastAcc,ftLastWrite;
-
- hFile = CreateFileA(filename,GENERIC_READ | GENERIC_WRITE,
- 0,NULL,OPEN_EXISTING,0,NULL);
- GetFileTime(hFile,&ftCreate,&ftLastAcc,&ftLastWrite);
- DosDateTimeToFileTime((WORD)(dosdate>>16),(WORD)dosdate,&ftLocal);
- LocalFileTimeToFileTime(&ftLocal,&ftm);
- SetFileTime(hFile,&ftm,&ftLastAcc,&ftm);
- CloseHandle(hFile);
-#else
-#ifdef unix || __APPLE__
- struct utimbuf ut;
- struct tm newdate;
- newdate.tm_sec = tmu_date.tm_sec;
- newdate.tm_min=tmu_date.tm_min;
- newdate.tm_hour=tmu_date.tm_hour;
- newdate.tm_mday=tmu_date.tm_mday;
- newdate.tm_mon=tmu_date.tm_mon;
- if (tmu_date.tm_year > 1900)
- newdate.tm_year=tmu_date.tm_year - 1900;
- else
- newdate.tm_year=tmu_date.tm_year ;
- newdate.tm_isdst=-1;
-
- ut.actime=ut.modtime=mktime(&newdate);
- utime(filename,&ut);
-#endif
-#endif
-}
-
-
-/* mymkdir and change_file_date are not 100 % portable
- As I don't know well Unix, I wait feedback for the unix portion */
-
-int mymkdir(dirname)
- const char* dirname;
-{
- int ret=0;
-#ifdef _WIN32
- ret = _mkdir(dirname);
-#elif unix
- ret = mkdir (dirname,0775);
-#elif __APPLE__
- ret = mkdir (dirname,0775);
-#endif
- return ret;
-}
-
-int makedir (newdir)
- char *newdir;
-{
- char *buffer ;
- char *p;
- int len = (int)strlen(newdir);
-
- if (len <= 0)
- return 0;
-
- buffer = (char*)malloc(len+1);
- if (buffer==NULL)
- {
- printf("Error allocating memory\n");
- return UNZ_INTERNALERROR;
- }
- strcpy(buffer,newdir);
-
- if (buffer[len-1] == '/') {
- buffer[len-1] = '\0';
- }
- if (mymkdir(buffer) == 0)
- {
- free(buffer);
- return 1;
- }
-
- p = buffer+1;
- while (1)
- {
- char hold;
-
- while(*p && *p != '\\' && *p != '/')
- p++;
- hold = *p;
- *p = 0;
- if ((mymkdir(buffer) == -1) && (errno == ENOENT))
- {
- printf("couldn't create directory %s\n",buffer);
- free(buffer);
- return 0;
- }
- if (hold == 0)
- break;
- *p++ = hold;
- }
- free(buffer);
- return 1;
-}
-
-void do_banner()
-{
- printf("MiniUnz 1.01b, demo of zLib + Unz package written by Gilles Vollant\n");
- printf("more info at http://www.winimage.com/zLibDll/unzip.html\n\n");
-}
-
-void do_help()
-{
- printf("Usage : miniunz [-e] [-x] [-v] [-l] [-o] [-p password] file.zip [file_to_extr.] [-d extractdir]\n\n" \
- " -e Extract without pathname (junk paths)\n" \
- " -x Extract with pathname\n" \
- " -v list files\n" \
- " -l list files\n" \
- " -d directory to extract into\n" \
- " -o overwrite files without prompting\n" \
- " -p extract crypted file using password\n\n");
-}
-
-void Display64BitsSize(ZPOS64_T n, int size_char)
-{
- /* to avoid compatibility problem , we do here the conversion */
- char number[21];
- int offset=19;
- int pos_string = 19;
- number[20]=0;
- for (;;) {
- number[offset]=(char)((n%10)+'0');
- if (number[offset] != '0')
- pos_string=offset;
- n/=10;
- if (offset==0)
- break;
- offset--;
- }
- {
- int size_display_string = 19-pos_string;
- while (size_char > size_display_string)
- {
- size_char--;
- printf(" ");
- }
- }
-
- printf("%s",&number[pos_string]);
-}
-
-int do_list(uf)
- unzFile uf;
-{
- uLong i;
- unz_global_info64 gi;
- int err;
-
- err = unzGetGlobalInfo64(uf,&gi);
- if (err!=UNZ_OK)
- printf("error %d with zipfile in unzGetGlobalInfo \n",err);
- printf(" Length Method Size Ratio Date Time CRC-32 Name\n");
- printf(" ------ ------ ---- ----- ---- ---- ------ ----\n");
- for (i=0;i<gi.number_entry;i++)
- {
- char filename_inzip[256];
- unz_file_info64 file_info;
- uLong ratio=0;
- const char *string_method;
- char charCrypt=' ';
- err = unzGetCurrentFileInfo64(uf,&file_info,filename_inzip,sizeof(filename_inzip),NULL,0,NULL,0);
- if (err!=UNZ_OK)
- {
- printf("error %d with zipfile in unzGetCurrentFileInfo\n",err);
- break;
- }
- if (file_info.uncompressed_size>0)
- ratio = (uLong)((file_info.compressed_size*100)/file_info.uncompressed_size);
-
- /* display a '*' if the file is crypted */
- if ((file_info.flag & 1) != 0)
- charCrypt='*';
-
- if (file_info.compression_method==0)
- string_method="Stored";
- else
- if (file_info.compression_method==Z_DEFLATED)
- {
- uInt iLevel=(uInt)((file_info.flag & 0x6)/2);
- if (iLevel==0)
- string_method="Defl:N";
- else if (iLevel==1)
- string_method="Defl:X";
- else if ((iLevel==2) || (iLevel==3))
- string_method="Defl:F"; /* 2:fast , 3 : extra fast*/
- }
- else
- if (file_info.compression_method==Z_BZIP2ED)
- {
- string_method="BZip2 ";
- }
- else
- string_method="Unkn. ";
-
- Display64BitsSize(file_info.uncompressed_size,7);
- printf(" %6s%c",string_method,charCrypt);
- Display64BitsSize(file_info.compressed_size,7);
- printf(" %3lu%% %2.2lu-%2.2lu-%2.2lu %2.2lu:%2.2lu %8.8lx %s\n",
- ratio,
- (uLong)file_info.tmu_date.tm_mon + 1,
- (uLong)file_info.tmu_date.tm_mday,
- (uLong)file_info.tmu_date.tm_year % 100,
- (uLong)file_info.tmu_date.tm_hour,(uLong)file_info.tmu_date.tm_min,
- (uLong)file_info.crc,filename_inzip);
- if ((i+1)<gi.number_entry)
- {
- err = unzGoToNextFile(uf);
- if (err!=UNZ_OK)
- {
- printf("error %d with zipfile in unzGoToNextFile\n",err);
- break;
- }
- }
- }
-
- return 0;
-}
-
-
-int do_extract_currentfile(uf,popt_extract_without_path,popt_overwrite,password)
- unzFile uf;
- const int* popt_extract_without_path;
- int* popt_overwrite;
- const char* password;
-{
- char filename_inzip[256];
- char* filename_withoutpath;
- char* p;
- int err=UNZ_OK;
- FILE *fout=NULL;
- void* buf;
- uInt size_buf;
-
- unz_file_info64 file_info;
- uLong ratio=0;
- err = unzGetCurrentFileInfo64(uf,&file_info,filename_inzip,sizeof(filename_inzip),NULL,0,NULL,0);
-
- if (err!=UNZ_OK)
- {
- printf("error %d with zipfile in unzGetCurrentFileInfo\n",err);
- return err;
- }
-
- size_buf = WRITEBUFFERSIZE;
- buf = (void*)malloc(size_buf);
- if (buf==NULL)
- {
- printf("Error allocating memory\n");
- return UNZ_INTERNALERROR;
- }
-
- p = filename_withoutpath = filename_inzip;
- while ((*p) != '\0')
- {
- if (((*p)=='/') || ((*p)=='\\'))
- filename_withoutpath = p+1;
- p++;
- }
-
- if ((*filename_withoutpath)=='\0')
- {
- if ((*popt_extract_without_path)==0)
- {
- printf("creating directory: %s\n",filename_inzip);
- mymkdir(filename_inzip);
- }
- }
- else
- {
- const char* write_filename;
- int skip=0;
-
- if ((*popt_extract_without_path)==0)
- write_filename = filename_inzip;
- else
- write_filename = filename_withoutpath;
-
- err = unzOpenCurrentFilePassword(uf,password);
- if (err!=UNZ_OK)
- {
- printf("error %d with zipfile in unzOpenCurrentFilePassword\n",err);
- }
-
- if (((*popt_overwrite)==0) && (err==UNZ_OK))
- {
- char rep=0;
- FILE* ftestexist;
- ftestexist = FOPEN_FUNC(write_filename,"rb");
- if (ftestexist!=NULL)
- {
- fclose(ftestexist);
- do
- {
- char answer[128];
- int ret;
-
- printf("The file %s exists. Overwrite ? [y]es, [n]o, [A]ll: ",write_filename);
- ret = scanf("%1s",answer);
- if (ret != 1)
- {
- exit(EXIT_FAILURE);
- }
- rep = answer[0] ;
- if ((rep>='a') && (rep<='z'))
- rep -= 0x20;
- }
- while ((rep!='Y') && (rep!='N') && (rep!='A'));
- }
-
- if (rep == 'N')
- skip = 1;
-
- if (rep == 'A')
- *popt_overwrite=1;
- }
-
- if ((skip==0) && (err==UNZ_OK))
- {
- fout=FOPEN_FUNC(write_filename,"wb");
- /* some zipfile don't contain directory alone before file */
- if ((fout==NULL) && ((*popt_extract_without_path)==0) &&
- (filename_withoutpath!=(char*)filename_inzip))
- {
- char c=*(filename_withoutpath-1);
- *(filename_withoutpath-1)='\0';
- makedir(write_filename);
- *(filename_withoutpath-1)=c;
- fout=FOPEN_FUNC(write_filename,"wb");
- }
-
- if (fout==NULL)
- {
- printf("error opening %s\n",write_filename);
- }
- }
-
- if (fout!=NULL)
- {
- printf(" extracting: %s\n",write_filename);
-
- do
- {
- err = unzReadCurrentFile(uf,buf,size_buf);
- if (err<0)
- {
- printf("error %d with zipfile in unzReadCurrentFile\n",err);
- break;
- }
- if (err>0)
- if (fwrite(buf,err,1,fout)!=1)
- {
- printf("error in writing extracted file\n");
- err=UNZ_ERRNO;
- break;
- }
- }
- while (err>0);
- if (fout)
- fclose(fout);
-
- if (err==0)
- change_file_date(write_filename,file_info.dosDate,
- file_info.tmu_date);
- }
-
- if (err==UNZ_OK)
- {
- err = unzCloseCurrentFile (uf);
- if (err!=UNZ_OK)
- {
- printf("error %d with zipfile in unzCloseCurrentFile\n",err);
- }
- }
- else
- unzCloseCurrentFile(uf); /* don't lose the error */
- }
-
- free(buf);
- return err;
-}
-
-
-int do_extract(uf,opt_extract_without_path,opt_overwrite,password)
- unzFile uf;
- int opt_extract_without_path;
- int opt_overwrite;
- const char* password;
-{
- uLong i;
- unz_global_info64 gi;
- int err;
- FILE* fout=NULL;
-
- err = unzGetGlobalInfo64(uf,&gi);
- if (err!=UNZ_OK)
- printf("error %d with zipfile in unzGetGlobalInfo \n",err);
-
- for (i=0;i<gi.number_entry;i++)
- {
- if (do_extract_currentfile(uf,&opt_extract_without_path,
- &opt_overwrite,
- password) != UNZ_OK)
- break;
-
- if ((i+1)<gi.number_entry)
- {
- err = unzGoToNextFile(uf);
- if (err!=UNZ_OK)
- {
- printf("error %d with zipfile in unzGoToNextFile\n",err);
- break;
- }
- }
- }
-
- return 0;
-}
-
-int do_extract_onefile(uf,filename,opt_extract_without_path,opt_overwrite,password)
- unzFile uf;
- const char* filename;
- int opt_extract_without_path;
- int opt_overwrite;
- const char* password;
-{
- int err = UNZ_OK;
- if (unzLocateFile(uf,filename,CASESENSITIVITY)!=UNZ_OK)
- {
- printf("file %s not found in the zipfile\n",filename);
- return 2;
- }
-
- if (do_extract_currentfile(uf,&opt_extract_without_path,
- &opt_overwrite,
- password) == UNZ_OK)
- return 0;
- else
- return 1;
-}
-
-
-int main(argc,argv)
- int argc;
- char *argv[];
-{
- const char *zipfilename=NULL;
- const char *filename_to_extract=NULL;
- const char *password=NULL;
- char filename_try[MAXFILENAME+16] = "";
- int i;
- int ret_value=0;
- int opt_do_list=0;
- int opt_do_extract=1;
- int opt_do_extract_withoutpath=0;
- int opt_overwrite=0;
- int opt_extractdir=0;
- const char *dirname=NULL;
- unzFile uf=NULL;
-
- do_banner();
- if (argc==1)
- {
- do_help();
- return 0;
- }
- else
- {
- for (i=1;i<argc;i++)
- {
- if ((*argv[i])=='-')
- {
- const char *p=argv[i]+1;
-
- while ((*p)!='\0')
- {
- char c=*(p++);;
- if ((c=='l') || (c=='L'))
- opt_do_list = 1;
- if ((c=='v') || (c=='V'))
- opt_do_list = 1;
- if ((c=='x') || (c=='X'))
- opt_do_extract = 1;
- if ((c=='e') || (c=='E'))
- opt_do_extract = opt_do_extract_withoutpath = 1;
- if ((c=='o') || (c=='O'))
- opt_overwrite=1;
- if ((c=='d') || (c=='D'))
- {
- opt_extractdir=1;
- dirname=argv[i+1];
- }
-
- if (((c=='p') || (c=='P')) && (i+1<argc))
- {
- password=argv[i+1];
- i++;
- }
- }
- }
- else
- {
- if (zipfilename == NULL)
- zipfilename = argv[i];
- else if ((filename_to_extract==NULL) && (!opt_extractdir))
- filename_to_extract = argv[i] ;
- }
- }
- }
-
- if (zipfilename!=NULL)
- {
-
-# ifdef USEWIN32IOAPI
- zlib_filefunc64_def ffunc;
-# endif
-
- strncpy(filename_try, zipfilename,MAXFILENAME-1);
- /* strncpy doesnt append the trailing NULL, of the string is too long. */
- filename_try[ MAXFILENAME ] = '\0';
-
-# ifdef USEWIN32IOAPI
- fill_win32_filefunc64A(&ffunc);
- uf = unzOpen2_64(zipfilename,&ffunc);
-# else
- uf = unzOpen64(zipfilename);
-# endif
- if (uf==NULL)
- {
- strcat(filename_try,".zip");
-# ifdef USEWIN32IOAPI
- uf = unzOpen2_64(filename_try,&ffunc);
-# else
- uf = unzOpen64(filename_try);
-# endif
- }
- }
-
- if (uf==NULL)
- {
- printf("Cannot open %s or %s.zip\n",zipfilename,zipfilename);
- return 1;
- }
- printf("%s opened\n",filename_try);
-
- if (opt_do_list==1)
- ret_value = do_list(uf);
- else if (opt_do_extract==1)
- {
-#ifdef _WIN32
- if (opt_extractdir && _chdir(dirname))
-#else
- if (opt_extractdir && chdir(dirname))
-#endif
- {
- printf("Error changing into %s, aborting\n", dirname);
- exit(-1);
- }
-
- if (filename_to_extract == NULL)
- ret_value = do_extract(uf, opt_do_extract_withoutpath, opt_overwrite, password);
- else
- ret_value = do_extract_onefile(uf, filename_to_extract, opt_do_extract_withoutpath, opt_overwrite, password);
- }
-
- unzClose(uf);
-
- return ret_value;
-}
diff --git a/third-party/zlib/contrib/minizip/miniunzip.1 b/third-party/zlib/contrib/minizip/miniunzip.1
deleted file mode 100644
index 111ac69..0000000
--- a/third-party/zlib/contrib/minizip/miniunzip.1
+++ /dev/null
@@ -1,63 +0,0 @@
-.\" Hey, EMACS: -*- nroff -*-
-.TH miniunzip 1 "Nov 7, 2001"
-.\" Please adjust this date whenever revising the manpage.
-.\"
-.\" Some roff macros, for reference:
-.\" .nh disable hyphenation
-.\" .hy enable hyphenation
-.\" .ad l left justify
-.\" .ad b justify to both left and right margins
-.\" .nf disable filling
-.\" .fi enable filling
-.\" .br insert line break
-.\" .sp <n> insert n+1 empty lines
-.\" for manpage-specific macros, see man(7)
-.SH NAME
-miniunzip - uncompress and examine ZIP archives
-.SH SYNOPSIS
-.B miniunzip
-.RI [ -exvlo ]
-zipfile [ files_to_extract ] [-d tempdir]
-.SH DESCRIPTION
-.B minizip
-is a simple tool which allows the extraction of compressed file
-archives in the ZIP format used by the MS-DOS utility PKZIP. It was
-written as a demonstration of the
-.IR zlib (3)
-library and therefore lack many of the features of the
-.IR unzip (1)
-program.
-.SH OPTIONS
-A number of options are supported. With the exception of
-.BI \-d\ tempdir
-these must be supplied before any
-other arguments and are:
-.TP
-.BI \-l\ ,\ \-\-v
-List the files in the archive without extracting them.
-.TP
-.B \-o
-Overwrite files without prompting for confirmation.
-.TP
-.B \-x
-Extract files (default).
-.PP
-The
-.I zipfile
-argument is the name of the archive to process. The next argument can be used
-to specify a single file to extract from the archive.
-
-Lastly, the following option can be specified at the end of the command-line:
-.TP
-.BI \-d\ tempdir
-Extract the archive in the directory
-.I tempdir
-rather than the current directory.
-.SH SEE ALSO
-.BR minizip (1),
-.BR zlib (3),
-.BR unzip (1).
-.SH AUTHOR
-This program was written by Gilles Vollant. This manual page was
-written by Mark Brown <broonie at sirena.org.uk>. The -d tempdir option
-was added by Dirk Eddelbuettel <edd at debian.org>.
diff --git a/third-party/zlib/contrib/minizip/minizip.1 b/third-party/zlib/contrib/minizip/minizip.1
deleted file mode 100644
index 1154484..0000000
--- a/third-party/zlib/contrib/minizip/minizip.1
+++ /dev/null
@@ -1,46 +0,0 @@
-.\" Hey, EMACS: -*- nroff -*-
-.TH minizip 1 "May 2, 2001"
-.\" Please adjust this date whenever revising the manpage.
-.\"
-.\" Some roff macros, for reference:
-.\" .nh disable hyphenation
-.\" .hy enable hyphenation
-.\" .ad l left justify
-.\" .ad b justify to both left and right margins
-.\" .nf disable filling
-.\" .fi enable filling
-.\" .br insert line break
-.\" .sp <n> insert n+1 empty lines
-.\" for manpage-specific macros, see man(7)
-.SH NAME
-minizip - create ZIP archives
-.SH SYNOPSIS
-.B minizip
-.RI [ -o ]
-zipfile [ " files" ... ]
-.SH DESCRIPTION
-.B minizip
-is a simple tool which allows the creation of compressed file archives
-in the ZIP format used by the MS-DOS utility PKZIP. It was written as
-a demonstration of the
-.IR zlib (3)
-library and therefore lack many of the features of the
-.IR zip (1)
-program.
-.SH OPTIONS
-The first argument supplied is the name of the ZIP archive to create or
-.RI -o
-in which case it is ignored and the second argument treated as the
-name of the ZIP file. If the ZIP file already exists it will be
-overwritten.
-.PP
-Subsequent arguments specify a list of files to place in the ZIP
-archive. If none are specified then an empty archive will be created.
-.SH SEE ALSO
-.BR miniunzip (1),
-.BR zlib (3),
-.BR zip (1).
-.SH AUTHOR
-This program was written by Gilles Vollant. This manual page was
-written by Mark Brown <broonie at sirena.org.uk>.
-
diff --git a/third-party/zlib/contrib/minizip/minizip.c b/third-party/zlib/contrib/minizip/minizip.c
deleted file mode 100644
index 4288962..0000000
--- a/third-party/zlib/contrib/minizip/minizip.c
+++ /dev/null
@@ -1,520 +0,0 @@
-/*
- minizip.c
- Version 1.1, February 14h, 2010
- sample part of the MiniZip project - ( http://www.winimage.com/zLibDll/minizip.html )
-
- Copyright (C) 1998-2010 Gilles Vollant (minizip) ( http://www.winimage.com/zLibDll/minizip.html )
-
- Modifications of Unzip for Zip64
- Copyright (C) 2007-2008 Even Rouault
-
- Modifications for Zip64 support on both zip and unzip
- Copyright (C) 2009-2010 Mathias Svensson ( http://result42.com )
-*/
-
-
-#if (!defined(_WIN32)) && (!defined(WIN32)) && (!defined(__APPLE__))
- #ifndef __USE_FILE_OFFSET64
- #define __USE_FILE_OFFSET64
- #endif
- #ifndef __USE_LARGEFILE64
- #define __USE_LARGEFILE64
- #endif
- #ifndef _LARGEFILE64_SOURCE
- #define _LARGEFILE64_SOURCE
- #endif
- #ifndef _FILE_OFFSET_BIT
- #define _FILE_OFFSET_BIT 64
- #endif
-#endif
-
-#ifdef __APPLE__
-// In darwin and perhaps other BSD variants off_t is a 64 bit value, hence no need for specific 64 bit functions
-#define FOPEN_FUNC(filename, mode) fopen(filename, mode)
-#define FTELLO_FUNC(stream) ftello(stream)
-#define FSEEKO_FUNC(stream, offset, origin) fseeko(stream, offset, origin)
-#else
-#define FOPEN_FUNC(filename, mode) fopen64(filename, mode)
-#define FTELLO_FUNC(stream) ftello64(stream)
-#define FSEEKO_FUNC(stream, offset, origin) fseeko64(stream, offset, origin)
-#endif
-
-
-
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
-#include <time.h>
-#include <errno.h>
-#include <fcntl.h>
-
-#ifdef _WIN32
-# include <direct.h>
-# include <io.h>
-#else
-# include <unistd.h>
-# include <utime.h>
-# include <sys/types.h>
-# include <sys/stat.h>
-#endif
-
-#include "zip.h"
-
-#ifdef _WIN32
- #define USEWIN32IOAPI
- #include "iowin32.h"
-#endif
-
-
-
-#define WRITEBUFFERSIZE (16384)
-#define MAXFILENAME (256)
-
-#ifdef _WIN32
-uLong filetime(f, tmzip, dt)
- char *f; /* name of file to get info on */
- tm_zip *tmzip; /* return value: access, modific. and creation times */
- uLong *dt; /* dostime */
-{
- int ret = 0;
- {
- FILETIME ftLocal;
- HANDLE hFind;
- WIN32_FIND_DATAA ff32;
-
- hFind = FindFirstFileA(f,&ff32);
- if (hFind != INVALID_HANDLE_VALUE)
- {
- FileTimeToLocalFileTime(&(ff32.ftLastWriteTime),&ftLocal);
- FileTimeToDosDateTime(&ftLocal,((LPWORD)dt)+1,((LPWORD)dt)+0);
- FindClose(hFind);
- ret = 1;
- }
- }
- return ret;
-}
-#else
-#ifdef unix || __APPLE__
-uLong filetime(f, tmzip, dt)
- char *f; /* name of file to get info on */
- tm_zip *tmzip; /* return value: access, modific. and creation times */
- uLong *dt; /* dostime */
-{
- int ret=0;
- struct stat s; /* results of stat() */
- struct tm* filedate;
- time_t tm_t=0;
-
- if (strcmp(f,"-")!=0)
- {
- char name[MAXFILENAME+1];
- int len = strlen(f);
- if (len > MAXFILENAME)
- len = MAXFILENAME;
-
- strncpy(name, f,MAXFILENAME-1);
- /* strncpy doesnt append the trailing NULL, of the string is too long. */
- name[ MAXFILENAME ] = '\0';
-
- if (name[len - 1] == '/')
- name[len - 1] = '\0';
- /* not all systems allow stat'ing a file with / appended */
- if (stat(name,&s)==0)
- {
- tm_t = s.st_mtime;
- ret = 1;
- }
- }
- filedate = localtime(&tm_t);
-
- tmzip->tm_sec = filedate->tm_sec;
- tmzip->tm_min = filedate->tm_min;
- tmzip->tm_hour = filedate->tm_hour;
- tmzip->tm_mday = filedate->tm_mday;
- tmzip->tm_mon = filedate->tm_mon ;
- tmzip->tm_year = filedate->tm_year;
-
- return ret;
-}
-#else
-uLong filetime(f, tmzip, dt)
- char *f; /* name of file to get info on */
- tm_zip *tmzip; /* return value: access, modific. and creation times */
- uLong *dt; /* dostime */
-{
- return 0;
-}
-#endif
-#endif
-
-
-
-
-int check_exist_file(filename)
- const char* filename;
-{
- FILE* ftestexist;
- int ret = 1;
- ftestexist = FOPEN_FUNC(filename,"rb");
- if (ftestexist==NULL)
- ret = 0;
- else
- fclose(ftestexist);
- return ret;
-}
-
-void do_banner()
-{
- printf("MiniZip 1.1, demo of zLib + MiniZip64 package, written by Gilles Vollant\n");
- printf("more info on MiniZip at http://www.winimage.com/zLibDll/minizip.html\n\n");
-}
-
-void do_help()
-{
- printf("Usage : minizip [-o] [-a] [-0 to -9] [-p password] [-j] file.zip [files_to_add]\n\n" \
- " -o Overwrite existing file.zip\n" \
- " -a Append to existing file.zip\n" \
- " -0 Store only\n" \
- " -1 Compress faster\n" \
- " -9 Compress better\n\n" \
- " -j exclude path. store only the file name.\n\n");
-}
-
-/* calculate the CRC32 of a file,
- because to encrypt a file, we need known the CRC32 of the file before */
-int getFileCrc(const char* filenameinzip,void*buf,unsigned long size_buf,unsigned long* result_crc)
-{
- unsigned long calculate_crc=0;
- int err=ZIP_OK;
- FILE * fin = FOPEN_FUNC(filenameinzip,"rb");
-
- unsigned long size_read = 0;
- unsigned long total_read = 0;
- if (fin==NULL)
- {
- err = ZIP_ERRNO;
- }
-
- if (err == ZIP_OK)
- do
- {
- err = ZIP_OK;
- size_read = (int)fread(buf,1,size_buf,fin);
- if (size_read < size_buf)
- if (feof(fin)==0)
- {
- printf("error in reading %s\n",filenameinzip);
- err = ZIP_ERRNO;
- }
-
- if (size_read>0)
- calculate_crc = crc32(calculate_crc,buf,size_read);
- total_read += size_read;
-
- } while ((err == ZIP_OK) && (size_read>0));
-
- if (fin)
- fclose(fin);
-
- *result_crc=calculate_crc;
- printf("file %s crc %lx\n", filenameinzip, calculate_crc);
- return err;
-}
-
-int isLargeFile(const char* filename)
-{
- int largeFile = 0;
- ZPOS64_T pos = 0;
- FILE* pFile = FOPEN_FUNC(filename, "rb");
-
- if(pFile != NULL)
- {
- int n = FSEEKO_FUNC(pFile, 0, SEEK_END);
- pos = FTELLO_FUNC(pFile);
-
- printf("File : %s is %lld bytes\n", filename, pos);
-
- if(pos >= 0xffffffff)
- largeFile = 1;
-
- fclose(pFile);
- }
-
- return largeFile;
-}
-
-int main(argc,argv)
- int argc;
- char *argv[];
-{
- int i;
- int opt_overwrite=0;
- int opt_compress_level=Z_DEFAULT_COMPRESSION;
- int opt_exclude_path=0;
- int zipfilenamearg = 0;
- char filename_try[MAXFILENAME+16];
- int zipok;
- int err=0;
- int size_buf=0;
- void* buf=NULL;
- const char* password=NULL;
-
-
- do_banner();
- if (argc==1)
- {
- do_help();
- return 0;
- }
- else
- {
- for (i=1;i<argc;i++)
- {
- if ((*argv[i])=='-')
- {
- const char *p=argv[i]+1;
-
- while ((*p)!='\0')
- {
- char c=*(p++);;
- if ((c=='o') || (c=='O'))
- opt_overwrite = 1;
- if ((c=='a') || (c=='A'))
- opt_overwrite = 2;
- if ((c>='0') && (c<='9'))
- opt_compress_level = c-'0';
- if ((c=='j') || (c=='J'))
- opt_exclude_path = 1;
-
- if (((c=='p') || (c=='P')) && (i+1<argc))
- {
- password=argv[i+1];
- i++;
- }
- }
- }
- else
- {
- if (zipfilenamearg == 0)
- {
- zipfilenamearg = i ;
- }
- }
- }
- }
-
- size_buf = WRITEBUFFERSIZE;
- buf = (void*)malloc(size_buf);
- if (buf==NULL)
- {
- printf("Error allocating memory\n");
- return ZIP_INTERNALERROR;
- }
-
- if (zipfilenamearg==0)
- {
- zipok=0;
- }
- else
- {
- int i,len;
- int dot_found=0;
-
- zipok = 1 ;
- strncpy(filename_try, argv[zipfilenamearg],MAXFILENAME-1);
- /* strncpy doesnt append the trailing NULL, of the string is too long. */
- filename_try[ MAXFILENAME ] = '\0';
-
- len=(int)strlen(filename_try);
- for (i=0;i<len;i++)
- if (filename_try[i]=='.')
- dot_found=1;
-
- if (dot_found==0)
- strcat(filename_try,".zip");
-
- if (opt_overwrite==2)
- {
- /* if the file don't exist, we not append file */
- if (check_exist_file(filename_try)==0)
- opt_overwrite=1;
- }
- else
- if (opt_overwrite==0)
- if (check_exist_file(filename_try)!=0)
- {
- char rep=0;
- do
- {
- char answer[128];
- int ret;
- printf("The file %s exists. Overwrite ? [y]es, [n]o, [a]ppend : ",filename_try);
- ret = scanf("%1s",answer);
- if (ret != 1)
- {
- exit(EXIT_FAILURE);
- }
- rep = answer[0] ;
- if ((rep>='a') && (rep<='z'))
- rep -= 0x20;
- }
- while ((rep!='Y') && (rep!='N') && (rep!='A'));
- if (rep=='N')
- zipok = 0;
- if (rep=='A')
- opt_overwrite = 2;
- }
- }
-
- if (zipok==1)
- {
- zipFile zf;
- int errclose;
-# ifdef USEWIN32IOAPI
- zlib_filefunc64_def ffunc;
- fill_win32_filefunc64A(&ffunc);
- zf = zipOpen2_64(filename_try,(opt_overwrite==2) ? 2 : 0,NULL,&ffunc);
-# else
- zf = zipOpen64(filename_try,(opt_overwrite==2) ? 2 : 0);
-# endif
-
- if (zf == NULL)
- {
- printf("error opening %s\n",filename_try);
- err= ZIP_ERRNO;
- }
- else
- printf("creating %s\n",filename_try);
-
- for (i=zipfilenamearg+1;(i<argc) && (err==ZIP_OK);i++)
- {
- if (!((((*(argv[i]))=='-') || ((*(argv[i]))=='/')) &&
- ((argv[i][1]=='o') || (argv[i][1]=='O') ||
- (argv[i][1]=='a') || (argv[i][1]=='A') ||
- (argv[i][1]=='p') || (argv[i][1]=='P') ||
- ((argv[i][1]>='0') || (argv[i][1]<='9'))) &&
- (strlen(argv[i]) == 2)))
- {
- FILE * fin;
- int size_read;
- const char* filenameinzip = argv[i];
- const char *savefilenameinzip;
- zip_fileinfo zi;
- unsigned long crcFile=0;
- int zip64 = 0;
-
- zi.tmz_date.tm_sec = zi.tmz_date.tm_min = zi.tmz_date.tm_hour =
- zi.tmz_date.tm_mday = zi.tmz_date.tm_mon = zi.tmz_date.tm_year = 0;
- zi.dosDate = 0;
- zi.internal_fa = 0;
- zi.external_fa = 0;
- filetime(filenameinzip,&zi.tmz_date,&zi.dosDate);
-
-/*
- err = zipOpenNewFileInZip(zf,filenameinzip,&zi,
- NULL,0,NULL,0,NULL / * comment * /,
- (opt_compress_level != 0) ? Z_DEFLATED : 0,
- opt_compress_level);
-*/
- if ((password != NULL) && (err==ZIP_OK))
- err = getFileCrc(filenameinzip,buf,size_buf,&crcFile);
-
- zip64 = isLargeFile(filenameinzip);
-
- /* The path name saved, should not include a leading slash. */
- /*if it did, windows/xp and dynazip couldn't read the zip file. */
- savefilenameinzip = filenameinzip;
- while( savefilenameinzip[0] == '\\' || savefilenameinzip[0] == '/' )
- {
- savefilenameinzip++;
- }
-
- /*should the zip file contain any path at all?*/
- if( opt_exclude_path )
- {
- const char *tmpptr;
- const char *lastslash = 0;
- for( tmpptr = savefilenameinzip; *tmpptr; tmpptr++)
- {
- if( *tmpptr == '\\' || *tmpptr == '/')
- {
- lastslash = tmpptr;
- }
- }
- if( lastslash != NULL )
- {
- savefilenameinzip = lastslash+1; // base filename follows last slash.
- }
- }
-
- /**/
- err = zipOpenNewFileInZip3_64(zf,savefilenameinzip,&zi,
- NULL,0,NULL,0,NULL /* comment*/,
- (opt_compress_level != 0) ? Z_DEFLATED : 0,
- opt_compress_level,0,
- /* -MAX_WBITS, DEF_MEM_LEVEL, Z_DEFAULT_STRATEGY, */
- -MAX_WBITS, DEF_MEM_LEVEL, Z_DEFAULT_STRATEGY,
- password,crcFile, zip64);
-
- if (err != ZIP_OK)
- printf("error in opening %s in zipfile\n",filenameinzip);
- else
- {
- fin = FOPEN_FUNC(filenameinzip,"rb");
- if (fin==NULL)
- {
- err=ZIP_ERRNO;
- printf("error in opening %s for reading\n",filenameinzip);
- }
- }
-
- if (err == ZIP_OK)
- do
- {
- err = ZIP_OK;
- size_read = (int)fread(buf,1,size_buf,fin);
- if (size_read < size_buf)
- if (feof(fin)==0)
- {
- printf("error in reading %s\n",filenameinzip);
- err = ZIP_ERRNO;
- }
-
- if (size_read>0)
- {
- err = zipWriteInFileInZip (zf,buf,size_read);
- if (err<0)
- {
- printf("error in writing %s in the zipfile\n",
- filenameinzip);
- }
-
- }
- } while ((err == ZIP_OK) && (size_read>0));
-
- if (fin)
- fclose(fin);
-
- if (err<0)
- err=ZIP_ERRNO;
- else
- {
- err = zipCloseFileInZip(zf);
- if (err!=ZIP_OK)
- printf("error in closing %s in the zipfile\n",
- filenameinzip);
- }
- }
- }
- errclose = zipClose(zf,NULL);
- if (errclose != ZIP_OK)
- printf("error in closing %s\n",filename_try);
- }
- else
- {
- do_help();
- }
-
- free(buf);
- return 0;
-}
diff --git a/third-party/zlib/contrib/minizip/minizip.pc.in b/third-party/zlib/contrib/minizip/minizip.pc.in
deleted file mode 100644
index 69b5b7f..0000000
--- a/third-party/zlib/contrib/minizip/minizip.pc.in
+++ /dev/null
@@ -1,12 +0,0 @@
-prefix=@prefix@
-exec_prefix=@exec_prefix@
-libdir=@libdir@
-includedir=@includedir@/minizip
-
-Name: minizip
-Description: Minizip zip file manipulation library
-Requires:
-Version: @PACKAGE_VERSION@
-Libs: -L${libdir} -lminizip
-Libs.private: -lz
-Cflags: -I${includedir}
diff --git a/third-party/zlib/contrib/minizip/mztools.c b/third-party/zlib/contrib/minizip/mztools.c
deleted file mode 100644
index 96891c2..0000000
--- a/third-party/zlib/contrib/minizip/mztools.c
+++ /dev/null
@@ -1,291 +0,0 @@
-/*
- Additional tools for Minizip
- Code: Xavier Roche '2004
- License: Same as ZLIB (www.gzip.org)
-*/
-
-/* Code */
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
-#include "zlib.h"
-#include "unzip.h"
-
-#define READ_8(adr) ((unsigned char)*(adr))
-#define READ_16(adr) ( READ_8(adr) | (READ_8(adr+1) << 8) )
-#define READ_32(adr) ( READ_16(adr) | (READ_16((adr)+2) << 16) )
-
-#define WRITE_8(buff, n) do { \
- *((unsigned char*)(buff)) = (unsigned char) ((n) & 0xff); \
-} while(0)
-#define WRITE_16(buff, n) do { \
- WRITE_8((unsigned char*)(buff), n); \
- WRITE_8(((unsigned char*)(buff)) + 1, (n) >> 8); \
-} while(0)
-#define WRITE_32(buff, n) do { \
- WRITE_16((unsigned char*)(buff), (n) & 0xffff); \
- WRITE_16((unsigned char*)(buff) + 2, (n) >> 16); \
-} while(0)
-
-extern int ZEXPORT unzRepair(file, fileOut, fileOutTmp, nRecovered, bytesRecovered)
-const char* file;
-const char* fileOut;
-const char* fileOutTmp;
-uLong* nRecovered;
-uLong* bytesRecovered;
-{
- int err = Z_OK;
- FILE* fpZip = fopen(file, "rb");
- FILE* fpOut = fopen(fileOut, "wb");
- FILE* fpOutCD = fopen(fileOutTmp, "wb");
- if (fpZip != NULL && fpOut != NULL) {
- int entries = 0;
- uLong totalBytes = 0;
- char header[30];
- char filename[1024];
- char extra[1024];
- int offset = 0;
- int offsetCD = 0;
- while ( fread(header, 1, 30, fpZip) == 30 ) {
- int currentOffset = offset;
-
- /* File entry */
- if (READ_32(header) == 0x04034b50) {
- unsigned int version = READ_16(header + 4);
- unsigned int gpflag = READ_16(header + 6);
- unsigned int method = READ_16(header + 8);
- unsigned int filetime = READ_16(header + 10);
- unsigned int filedate = READ_16(header + 12);
- unsigned int crc = READ_32(header + 14); /* crc */
- unsigned int cpsize = READ_32(header + 18); /* compressed size */
- unsigned int uncpsize = READ_32(header + 22); /* uncompressed sz */
- unsigned int fnsize = READ_16(header + 26); /* file name length */
- unsigned int extsize = READ_16(header + 28); /* extra field length */
- filename[0] = extra[0] = '\0';
-
- /* Header */
- if (fwrite(header, 1, 30, fpOut) == 30) {
- offset += 30;
- } else {
- err = Z_ERRNO;
- break;
- }
-
- /* Filename */
- if (fnsize > 0) {
- if (fnsize < sizeof(filename)) {
- if (fread(filename, 1, fnsize, fpZip) == fnsize) {
- if (fwrite(filename, 1, fnsize, fpOut) == fnsize) {
- offset += fnsize;
- } else {
- err = Z_ERRNO;
- break;
- }
- } else {
- err = Z_ERRNO;
- break;
- }
- } else {
- err = Z_ERRNO;
- break;
- }
- } else {
- err = Z_STREAM_ERROR;
- break;
- }
-
- /* Extra field */
- if (extsize > 0) {
- if (extsize < sizeof(extra)) {
- if (fread(extra, 1, extsize, fpZip) == extsize) {
- if (fwrite(extra, 1, extsize, fpOut) == extsize) {
- offset += extsize;
- } else {
- err = Z_ERRNO;
- break;
- }
- } else {
- err = Z_ERRNO;
- break;
- }
- } else {
- err = Z_ERRNO;
- break;
- }
- }
-
- /* Data */
- {
- int dataSize = cpsize;
- if (dataSize == 0) {
- dataSize = uncpsize;
- }
- if (dataSize > 0) {
- char* data = malloc(dataSize);
- if (data != NULL) {
- if ((int)fread(data, 1, dataSize, fpZip) == dataSize) {
- if ((int)fwrite(data, 1, dataSize, fpOut) == dataSize) {
- offset += dataSize;
- totalBytes += dataSize;
- } else {
- err = Z_ERRNO;
- }
- } else {
- err = Z_ERRNO;
- }
- free(data);
- if (err != Z_OK) {
- break;
- }
- } else {
- err = Z_MEM_ERROR;
- break;
- }
- }
- }
-
- /* Central directory entry */
- {
- char header[46];
- char* comment = "";
- int comsize = (int) strlen(comment);
- WRITE_32(header, 0x02014b50);
- WRITE_16(header + 4, version);
- WRITE_16(header + 6, version);
- WRITE_16(header + 8, gpflag);
- WRITE_16(header + 10, method);
- WRITE_16(header + 12, filetime);
- WRITE_16(header + 14, filedate);
- WRITE_32(header + 16, crc);
- WRITE_32(header + 20, cpsize);
- WRITE_32(header + 24, uncpsize);
- WRITE_16(header + 28, fnsize);
- WRITE_16(header + 30, extsize);
- WRITE_16(header + 32, comsize);
- WRITE_16(header + 34, 0); /* disk # */
- WRITE_16(header + 36, 0); /* int attrb */
- WRITE_32(header + 38, 0); /* ext attrb */
- WRITE_32(header + 42, currentOffset);
- /* Header */
- if (fwrite(header, 1, 46, fpOutCD) == 46) {
- offsetCD += 46;
-
- /* Filename */
- if (fnsize > 0) {
- if (fwrite(filename, 1, fnsize, fpOutCD) == fnsize) {
- offsetCD += fnsize;
- } else {
- err = Z_ERRNO;
- break;
- }
- } else {
- err = Z_STREAM_ERROR;
- break;
- }
-
- /* Extra field */
- if (extsize > 0) {
- if (fwrite(extra, 1, extsize, fpOutCD) == extsize) {
- offsetCD += extsize;
- } else {
- err = Z_ERRNO;
- break;
- }
- }
-
- /* Comment field */
- if (comsize > 0) {
- if ((int)fwrite(comment, 1, comsize, fpOutCD) == comsize) {
- offsetCD += comsize;
- } else {
- err = Z_ERRNO;
- break;
- }
- }
-
-
- } else {
- err = Z_ERRNO;
- break;
- }
- }
-
- /* Success */
- entries++;
-
- } else {
- break;
- }
- }
-
- /* Final central directory */
- {
- int entriesZip = entries;
- char header[22];
- char* comment = ""; // "ZIP File recovered by zlib/minizip/mztools";
- int comsize = (int) strlen(comment);
- if (entriesZip > 0xffff) {
- entriesZip = 0xffff;
- }
- WRITE_32(header, 0x06054b50);
- WRITE_16(header + 4, 0); /* disk # */
- WRITE_16(header + 6, 0); /* disk # */
- WRITE_16(header + 8, entriesZip); /* hack */
- WRITE_16(header + 10, entriesZip); /* hack */
- WRITE_32(header + 12, offsetCD); /* size of CD */
- WRITE_32(header + 16, offset); /* offset to CD */
- WRITE_16(header + 20, comsize); /* comment */
-
- /* Header */
- if (fwrite(header, 1, 22, fpOutCD) == 22) {
-
- /* Comment field */
- if (comsize > 0) {
- if ((int)fwrite(comment, 1, comsize, fpOutCD) != comsize) {
- err = Z_ERRNO;
- }
- }
-
- } else {
- err = Z_ERRNO;
- }
- }
-
- /* Final merge (file + central directory) */
- fclose(fpOutCD);
- if (err == Z_OK) {
- fpOutCD = fopen(fileOutTmp, "rb");
- if (fpOutCD != NULL) {
- int nRead;
- char buffer[8192];
- while ( (nRead = (int)fread(buffer, 1, sizeof(buffer), fpOutCD)) > 0) {
- if ((int)fwrite(buffer, 1, nRead, fpOut) != nRead) {
- err = Z_ERRNO;
- break;
- }
- }
- fclose(fpOutCD);
- }
- }
-
- /* Close */
- fclose(fpZip);
- fclose(fpOut);
-
- /* Wipe temporary file */
- (void)remove(fileOutTmp);
-
- /* Number of recovered entries */
- if (err == Z_OK) {
- if (nRecovered != NULL) {
- *nRecovered = entries;
- }
- if (bytesRecovered != NULL) {
- *bytesRecovered = totalBytes;
- }
- }
- } else {
- err = Z_STREAM_ERROR;
- }
- return err;
-}
diff --git a/third-party/zlib/contrib/minizip/mztools.h b/third-party/zlib/contrib/minizip/mztools.h
deleted file mode 100644
index a49a426..0000000
--- a/third-party/zlib/contrib/minizip/mztools.h
+++ /dev/null
@@ -1,37 +0,0 @@
-/*
- Additional tools for Minizip
- Code: Xavier Roche '2004
- License: Same as ZLIB (www.gzip.org)
-*/
-
-#ifndef _zip_tools_H
-#define _zip_tools_H
-
-#ifdef __cplusplus
-extern "C" {
-#endif
-
-#ifndef _ZLIB_H
-#include "zlib.h"
-#endif
-
-#include "unzip.h"
-
-/* Repair a ZIP file (missing central directory)
- file: file to recover
- fileOut: output file after recovery
- fileOutTmp: temporary file name used for recovery
-*/
-extern int ZEXPORT unzRepair(const char* file,
- const char* fileOut,
- const char* fileOutTmp,
- uLong* nRecovered,
- uLong* bytesRecovered);
-
-
-#ifdef __cplusplus
-}
-#endif
-
-
-#endif
diff --git a/third-party/zlib/contrib/minizip/unzip.c b/third-party/zlib/contrib/minizip/unzip.c
deleted file mode 100644
index 9093504..0000000
--- a/third-party/zlib/contrib/minizip/unzip.c
+++ /dev/null
@@ -1,2125 +0,0 @@
-/* unzip.c -- IO for uncompress .zip files using zlib
- Version 1.1, February 14h, 2010
- part of the MiniZip project - ( http://www.winimage.com/zLibDll/minizip.html )
-
- Copyright (C) 1998-2010 Gilles Vollant (minizip) ( http://www.winimage.com/zLibDll/minizip.html )
-
- Modifications of Unzip for Zip64
- Copyright (C) 2007-2008 Even Rouault
-
- Modifications for Zip64 support on both zip and unzip
- Copyright (C) 2009-2010 Mathias Svensson ( http://result42.com )
-
- For more info read MiniZip_info.txt
-
-
- ------------------------------------------------------------------------------------
- Decryption code comes from crypt.c by Info-ZIP but has been greatly reduced in terms of
- compatibility with older software. The following is from the original crypt.c.
- Code woven in by Terry Thorsen 1/2003.
-
- Copyright (c) 1990-2000 Info-ZIP. All rights reserved.
-
- See the accompanying file LICENSE, version 2000-Apr-09 or later
- (the contents of which are also included in zip.h) for terms of use.
- If, for some reason, all these files are missing, the Info-ZIP license
- also may be found at: ftp://ftp.info-zip.org/pub/infozip/license.html
-
- crypt.c (full version) by Info-ZIP. Last revised: [see crypt.h]
-
- The encryption/decryption parts of this source code (as opposed to the
- non-echoing password parts) were originally written in Europe. The
- whole source package can be freely distributed, including from the USA.
- (Prior to January 2000, re-export from the US was a violation of US law.)
-
- This encryption code is a direct transcription of the algorithm from
- Roger Schlafly, described by Phil Katz in the file appnote.txt. This
- file (appnote.txt) is distributed with the PKZIP program (even in the
- version without encryption capabilities).
-
- ------------------------------------------------------------------------------------
-
- Changes in unzip.c
-
- 2007-2008 - Even Rouault - Addition of cpl_unzGetCurrentFileZStreamPos
- 2007-2008 - Even Rouault - Decoration of symbol names unz* -> cpl_unz*
- 2007-2008 - Even Rouault - Remove old C style function prototypes
- 2007-2008 - Even Rouault - Add unzip support for ZIP64
-
- Copyright (C) 2007-2008 Even Rouault
-
-
- Oct-2009 - Mathias Svensson - Removed cpl_* from symbol names (Even Rouault added them but since this is now moved to a new project (minizip64) I renamed them again).
- Oct-2009 - Mathias Svensson - Fixed problem if uncompressed size was > 4G and compressed size was <4G
- should only read the compressed/uncompressed size from the Zip64 format if
- the size from normal header was 0xFFFFFFFF
- Oct-2009 - Mathias Svensson - Applied some bug fixes from paches recived from Gilles Vollant
- Oct-2009 - Mathias Svensson - Applied support to unzip files with compression mathod BZIP2 (bzip2 lib is required)
- Patch created by Daniel Borca
-
- Jan-2010 - back to unzip and minizip 1.0 name scheme, with compatibility layer
-
- Copyright (C) 1998 - 2010 Gilles Vollant, Even Rouault, Mathias Svensson
-
-*/
-
-
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
-
-#ifndef NOUNCRYPT
- #define NOUNCRYPT
-#endif
-
-#include "zlib.h"
-#include "unzip.h"
-
-#ifdef STDC
-# include <stddef.h>
-# include <string.h>
-# include <stdlib.h>
-#endif
-#ifdef NO_ERRNO_H
- extern int errno;
-#else
-# include <errno.h>
-#endif
-
-
-#ifndef local
-# define local static
-#endif
-/* compile with -Dlocal if your debugger can't find static symbols */
-
-
-#ifndef CASESENSITIVITYDEFAULT_NO
-# if !defined(unix) && !defined(CASESENSITIVITYDEFAULT_YES)
-# define CASESENSITIVITYDEFAULT_NO
-# endif
-#endif
-
-
-#ifndef UNZ_BUFSIZE
-#define UNZ_BUFSIZE (16384)
-#endif
-
-#ifndef UNZ_MAXFILENAMEINZIP
-#define UNZ_MAXFILENAMEINZIP (256)
-#endif
-
-#ifndef ALLOC
-# define ALLOC(size) (malloc(size))
-#endif
-#ifndef TRYFREE
-# define TRYFREE(p) {if (p) free(p);}
-#endif
-
-#define SIZECENTRALDIRITEM (0x2e)
-#define SIZEZIPLOCALHEADER (0x1e)
-
-
-const char unz_copyright[] =
- " unzip 1.01 Copyright 1998-2004 Gilles Vollant - http://www.winimage.com/zLibDll";
-
-/* unz_file_info_interntal contain internal info about a file in zipfile*/
-typedef struct unz_file_info64_internal_s
-{
- ZPOS64_T offset_curfile;/* relative offset of local header 8 bytes */
-} unz_file_info64_internal;
-
-
-/* file_in_zip_read_info_s contain internal information about a file in zipfile,
- when reading and decompress it */
-typedef struct
-{
- char *read_buffer; /* internal buffer for compressed data */
- z_stream stream; /* zLib stream structure for inflate */
-
-#ifdef HAVE_BZIP2
- bz_stream bstream; /* bzLib stream structure for bziped */
-#endif
-
- ZPOS64_T pos_in_zipfile; /* position in byte on the zipfile, for fseek*/
- uLong stream_initialised; /* flag set if stream structure is initialised*/
-
- ZPOS64_T offset_local_extrafield;/* offset of the local extra field */
- uInt size_local_extrafield;/* size of the local extra field */
- ZPOS64_T pos_local_extrafield; /* position in the local extra field in read*/
- ZPOS64_T total_out_64;
-
- uLong crc32; /* crc32 of all data uncompressed */
- uLong crc32_wait; /* crc32 we must obtain after decompress all */
- ZPOS64_T rest_read_compressed; /* number of byte to be decompressed */
- ZPOS64_T rest_read_uncompressed;/*number of byte to be obtained after decomp*/
- zlib_filefunc64_32_def z_filefunc;
- voidpf filestream; /* io structore of the zipfile */
- uLong compression_method; /* compression method (0==store) */
- ZPOS64_T byte_before_the_zipfile;/* byte before the zipfile, (>0 for sfx)*/
- int raw;
-} file_in_zip64_read_info_s;
-
-
-/* unz64_s contain internal information about the zipfile
-*/
-typedef struct
-{
- zlib_filefunc64_32_def z_filefunc;
- int is64bitOpenFunction;
- voidpf filestream; /* io structore of the zipfile */
- unz_global_info64 gi; /* public global information */
- ZPOS64_T byte_before_the_zipfile;/* byte before the zipfile, (>0 for sfx)*/
- ZPOS64_T num_file; /* number of the current file in the zipfile*/
- ZPOS64_T pos_in_central_dir; /* pos of the current file in the central dir*/
- ZPOS64_T current_file_ok; /* flag about the usability of the current file*/
- ZPOS64_T central_pos; /* position of the beginning of the central dir*/
-
- ZPOS64_T size_central_dir; /* size of the central directory */
- ZPOS64_T offset_central_dir; /* offset of start of central directory with
- respect to the starting disk number */
-
- unz_file_info64 cur_file_info; /* public info about the current file in zip*/
- unz_file_info64_internal cur_file_info_internal; /* private info about it*/
- file_in_zip64_read_info_s* pfile_in_zip_read; /* structure about the current
- file if we are decompressing it */
- int encrypted;
-
- int isZip64;
-
-# ifndef NOUNCRYPT
- unsigned long keys[3]; /* keys defining the pseudo-random sequence */
- const z_crc_t* pcrc_32_tab;
-# endif
-} unz64_s;
-
-
-#ifndef NOUNCRYPT
-#include "crypt.h"
-#endif
-
-/* ===========================================================================
- Read a byte from a gz_stream; update next_in and avail_in. Return EOF
- for end of file.
- IN assertion: the stream s has been sucessfully opened for reading.
-*/
-
-
-local int unz64local_getByte OF((
- const zlib_filefunc64_32_def* pzlib_filefunc_def,
- voidpf filestream,
- int *pi));
-
-local int unz64local_getByte(const zlib_filefunc64_32_def* pzlib_filefunc_def, voidpf filestream, int *pi)
-{
- unsigned char c;
- int err = (int)ZREAD64(*pzlib_filefunc_def,filestream,&c,1);
- if (err==1)
- {
- *pi = (int)c;
- return UNZ_OK;
- }
- else
- {
- if (ZERROR64(*pzlib_filefunc_def,filestream))
- return UNZ_ERRNO;
- else
- return UNZ_EOF;
- }
-}
-
-
-/* ===========================================================================
- Reads a long in LSB order from the given gz_stream. Sets
-*/
-local int unz64local_getShort OF((
- const zlib_filefunc64_32_def* pzlib_filefunc_def,
- voidpf filestream,
- uLong *pX));
-
-local int unz64local_getShort (const zlib_filefunc64_32_def* pzlib_filefunc_def,
- voidpf filestream,
- uLong *pX)
-{
- uLong x ;
- int i = 0;
- int err;
-
- err = unz64local_getByte(pzlib_filefunc_def,filestream,&i);
- x = (uLong)i;
-
- if (err==UNZ_OK)
- err = unz64local_getByte(pzlib_filefunc_def,filestream,&i);
- x |= ((uLong)i)<<8;
-
- if (err==UNZ_OK)
- *pX = x;
- else
- *pX = 0;
- return err;
-}
-
-local int unz64local_getLong OF((
- const zlib_filefunc64_32_def* pzlib_filefunc_def,
- voidpf filestream,
- uLong *pX));
-
-local int unz64local_getLong (const zlib_filefunc64_32_def* pzlib_filefunc_def,
- voidpf filestream,
- uLong *pX)
-{
- uLong x ;
- int i = 0;
- int err;
-
- err = unz64local_getByte(pzlib_filefunc_def,filestream,&i);
- x = (uLong)i;
-
- if (err==UNZ_OK)
- err = unz64local_getByte(pzlib_filefunc_def,filestream,&i);
- x |= ((uLong)i)<<8;
-
- if (err==UNZ_OK)
- err = unz64local_getByte(pzlib_filefunc_def,filestream,&i);
- x |= ((uLong)i)<<16;
-
- if (err==UNZ_OK)
- err = unz64local_getByte(pzlib_filefunc_def,filestream,&i);
- x += ((uLong)i)<<24;
-
- if (err==UNZ_OK)
- *pX = x;
- else
- *pX = 0;
- return err;
-}
-
-local int unz64local_getLong64 OF((
- const zlib_filefunc64_32_def* pzlib_filefunc_def,
- voidpf filestream,
- ZPOS64_T *pX));
-
-
-local int unz64local_getLong64 (const zlib_filefunc64_32_def* pzlib_filefunc_def,
- voidpf filestream,
- ZPOS64_T *pX)
-{
- ZPOS64_T x ;
- int i = 0;
- int err;
-
- err = unz64local_getByte(pzlib_filefunc_def,filestream,&i);
- x = (ZPOS64_T)i;
-
- if (err==UNZ_OK)
- err = unz64local_getByte(pzlib_filefunc_def,filestream,&i);
- x |= ((ZPOS64_T)i)<<8;
-
- if (err==UNZ_OK)
- err = unz64local_getByte(pzlib_filefunc_def,filestream,&i);
- x |= ((ZPOS64_T)i)<<16;
-
- if (err==UNZ_OK)
- err = unz64local_getByte(pzlib_filefunc_def,filestream,&i);
- x |= ((ZPOS64_T)i)<<24;
-
- if (err==UNZ_OK)
- err = unz64local_getByte(pzlib_filefunc_def,filestream,&i);
- x |= ((ZPOS64_T)i)<<32;
-
- if (err==UNZ_OK)
- err = unz64local_getByte(pzlib_filefunc_def,filestream,&i);
- x |= ((ZPOS64_T)i)<<40;
-
- if (err==UNZ_OK)
- err = unz64local_getByte(pzlib_filefunc_def,filestream,&i);
- x |= ((ZPOS64_T)i)<<48;
-
- if (err==UNZ_OK)
- err = unz64local_getByte(pzlib_filefunc_def,filestream,&i);
- x |= ((ZPOS64_T)i)<<56;
-
- if (err==UNZ_OK)
- *pX = x;
- else
- *pX = 0;
- return err;
-}
-
-/* My own strcmpi / strcasecmp */
-local int strcmpcasenosensitive_internal (const char* fileName1, const char* fileName2)
-{
- for (;;)
- {
- char c1=*(fileName1++);
- char c2=*(fileName2++);
- if ((c1>='a') && (c1<='z'))
- c1 -= 0x20;
- if ((c2>='a') && (c2<='z'))
- c2 -= 0x20;
- if (c1=='\0')
- return ((c2=='\0') ? 0 : -1);
- if (c2=='\0')
- return 1;
- if (c1<c2)
- return -1;
- if (c1>c2)
- return 1;
- }
-}
-
-
-#ifdef CASESENSITIVITYDEFAULT_NO
-#define CASESENSITIVITYDEFAULTVALUE 2
-#else
-#define CASESENSITIVITYDEFAULTVALUE 1
-#endif
-
-#ifndef STRCMPCASENOSENTIVEFUNCTION
-#define STRCMPCASENOSENTIVEFUNCTION strcmpcasenosensitive_internal
-#endif
-
-/*
- Compare two filename (fileName1,fileName2).
- If iCaseSenisivity = 1, comparision is case sensitivity (like strcmp)
- If iCaseSenisivity = 2, comparision is not case sensitivity (like strcmpi
- or strcasecmp)
- If iCaseSenisivity = 0, case sensitivity is defaut of your operating system
- (like 1 on Unix, 2 on Windows)
-
-*/
-extern int ZEXPORT unzStringFileNameCompare (const char* fileName1,
- const char* fileName2,
- int iCaseSensitivity)
-
-{
- if (iCaseSensitivity==0)
- iCaseSensitivity=CASESENSITIVITYDEFAULTVALUE;
-
- if (iCaseSensitivity==1)
- return strcmp(fileName1,fileName2);
-
- return STRCMPCASENOSENTIVEFUNCTION(fileName1,fileName2);
-}
-
-#ifndef BUFREADCOMMENT
-#define BUFREADCOMMENT (0x400)
-#endif
-
-/*
- Locate the Central directory of a zipfile (at the end, just before
- the global comment)
-*/
-local ZPOS64_T unz64local_SearchCentralDir OF((const zlib_filefunc64_32_def* pzlib_filefunc_def, voidpf filestream));
-local ZPOS64_T unz64local_SearchCentralDir(const zlib_filefunc64_32_def* pzlib_filefunc_def, voidpf filestream)
-{
- unsigned char* buf;
- ZPOS64_T uSizeFile;
- ZPOS64_T uBackRead;
- ZPOS64_T uMaxBack=0xffff; /* maximum size of global comment */
- ZPOS64_T uPosFound=0;
-
- if (ZSEEK64(*pzlib_filefunc_def,filestream,0,ZLIB_FILEFUNC_SEEK_END) != 0)
- return 0;
-
-
- uSizeFile = ZTELL64(*pzlib_filefunc_def,filestream);
-
- if (uMaxBack>uSizeFile)
- uMaxBack = uSizeFile;
-
- buf = (unsigned char*)ALLOC(BUFREADCOMMENT+4);
- if (buf==NULL)
- return 0;
-
- uBackRead = 4;
- while (uBackRead<uMaxBack)
- {
- uLong uReadSize;
- ZPOS64_T uReadPos ;
- int i;
- if (uBackRead+BUFREADCOMMENT>uMaxBack)
- uBackRead = uMaxBack;
- else
- uBackRead+=BUFREADCOMMENT;
- uReadPos = uSizeFile-uBackRead ;
-
- uReadSize = ((BUFREADCOMMENT+4) < (uSizeFile-uReadPos)) ?
- (BUFREADCOMMENT+4) : (uLong)(uSizeFile-uReadPos);
- if (ZSEEK64(*pzlib_filefunc_def,filestream,uReadPos,ZLIB_FILEFUNC_SEEK_SET)!=0)
- break;
-
- if (ZREAD64(*pzlib_filefunc_def,filestream,buf,uReadSize)!=uReadSize)
- break;
-
- for (i=(int)uReadSize-3; (i--)>0;)
- if (((*(buf+i))==0x50) && ((*(buf+i+1))==0x4b) &&
- ((*(buf+i+2))==0x05) && ((*(buf+i+3))==0x06))
- {
- uPosFound = uReadPos+i;
- break;
- }
-
- if (uPosFound!=0)
- break;
- }
- TRYFREE(buf);
- return uPosFound;
-}
-
-
-/*
- Locate the Central directory 64 of a zipfile (at the end, just before
- the global comment)
-*/
-local ZPOS64_T unz64local_SearchCentralDir64 OF((
- const zlib_filefunc64_32_def* pzlib_filefunc_def,
- voidpf filestream));
-
-local ZPOS64_T unz64local_SearchCentralDir64(const zlib_filefunc64_32_def* pzlib_filefunc_def,
- voidpf filestream)
-{
- unsigned char* buf;
- ZPOS64_T uSizeFile;
- ZPOS64_T uBackRead;
- ZPOS64_T uMaxBack=0xffff; /* maximum size of global comment */
- ZPOS64_T uPosFound=0;
- uLong uL;
- ZPOS64_T relativeOffset;
-
- if (ZSEEK64(*pzlib_filefunc_def,filestream,0,ZLIB_FILEFUNC_SEEK_END) != 0)
- return 0;
-
-
- uSizeFile = ZTELL64(*pzlib_filefunc_def,filestream);
-
- if (uMaxBack>uSizeFile)
- uMaxBack = uSizeFile;
-
- buf = (unsigned char*)ALLOC(BUFREADCOMMENT+4);
- if (buf==NULL)
- return 0;
-
- uBackRead = 4;
- while (uBackRead<uMaxBack)
- {
- uLong uReadSize;
- ZPOS64_T uReadPos;
- int i;
- if (uBackRead+BUFREADCOMMENT>uMaxBack)
- uBackRead = uMaxBack;
- else
- uBackRead+=BUFREADCOMMENT;
- uReadPos = uSizeFile-uBackRead ;
-
- uReadSize = ((BUFREADCOMMENT+4) < (uSizeFile-uReadPos)) ?
- (BUFREADCOMMENT+4) : (uLong)(uSizeFile-uReadPos);
- if (ZSEEK64(*pzlib_filefunc_def,filestream,uReadPos,ZLIB_FILEFUNC_SEEK_SET)!=0)
- break;
-
- if (ZREAD64(*pzlib_filefunc_def,filestream,buf,uReadSize)!=uReadSize)
- break;
-
- for (i=(int)uReadSize-3; (i--)>0;)
- if (((*(buf+i))==0x50) && ((*(buf+i+1))==0x4b) &&
- ((*(buf+i+2))==0x06) && ((*(buf+i+3))==0x07))
- {
- uPosFound = uReadPos+i;
- break;
- }
-
- if (uPosFound!=0)
- break;
- }
- TRYFREE(buf);
- if (uPosFound == 0)
- return 0;
-
- /* Zip64 end of central directory locator */
- if (ZSEEK64(*pzlib_filefunc_def,filestream, uPosFound,ZLIB_FILEFUNC_SEEK_SET)!=0)
- return 0;
-
- /* the signature, already checked */
- if (unz64local_getLong(pzlib_filefunc_def,filestream,&uL)!=UNZ_OK)
- return 0;
-
- /* number of the disk with the start of the zip64 end of central directory */
- if (unz64local_getLong(pzlib_filefunc_def,filestream,&uL)!=UNZ_OK)
- return 0;
- if (uL != 0)
- return 0;
-
- /* relative offset of the zip64 end of central directory record */
- if (unz64local_getLong64(pzlib_filefunc_def,filestream,&relativeOffset)!=UNZ_OK)
- return 0;
-
- /* total number of disks */
- if (unz64local_getLong(pzlib_filefunc_def,filestream,&uL)!=UNZ_OK)
- return 0;
- if (uL != 1)
- return 0;
-
- /* Goto end of central directory record */
- if (ZSEEK64(*pzlib_filefunc_def,filestream, relativeOffset,ZLIB_FILEFUNC_SEEK_SET)!=0)
- return 0;
-
- /* the signature */
- if (unz64local_getLong(pzlib_filefunc_def,filestream,&uL)!=UNZ_OK)
- return 0;
-
- if (uL != 0x06064b50)
- return 0;
-
- return relativeOffset;
-}
-
-/*
- Open a Zip file. path contain the full pathname (by example,
- on a Windows NT computer "c:\\test\\zlib114.zip" or on an Unix computer
- "zlib/zlib114.zip".
- If the zipfile cannot be opened (file doesn't exist or in not valid), the
- return value is NULL.
- Else, the return value is a unzFile Handle, usable with other function
- of this unzip package.
-*/
-local unzFile unzOpenInternal (const void *path,
- zlib_filefunc64_32_def* pzlib_filefunc64_32_def,
- int is64bitOpenFunction)
-{
- unz64_s us;
- unz64_s *s;
- ZPOS64_T central_pos;
- uLong uL;
-
- uLong number_disk; /* number of the current dist, used for
- spaning ZIP, unsupported, always 0*/
- uLong number_disk_with_CD; /* number the the disk with central dir, used
- for spaning ZIP, unsupported, always 0*/
- ZPOS64_T number_entry_CD; /* total number of entries in
- the central dir
- (same than number_entry on nospan) */
-
- int err=UNZ_OK;
-
- if (unz_copyright[0]!=' ')
- return NULL;
-
- us.z_filefunc.zseek32_file = NULL;
- us.z_filefunc.ztell32_file = NULL;
- if (pzlib_filefunc64_32_def==NULL)
- fill_fopen64_filefunc(&us.z_filefunc.zfile_func64);
- else
- us.z_filefunc = *pzlib_filefunc64_32_def;
- us.is64bitOpenFunction = is64bitOpenFunction;
-
-
-
- us.filestream = ZOPEN64(us.z_filefunc,
- path,
- ZLIB_FILEFUNC_MODE_READ |
- ZLIB_FILEFUNC_MODE_EXISTING);
- if (us.filestream==NULL)
- return NULL;
-
- central_pos = unz64local_SearchCentralDir64(&us.z_filefunc,us.filestream);
- if (central_pos)
- {
- uLong uS;
- ZPOS64_T uL64;
-
- us.isZip64 = 1;
-
- if (ZSEEK64(us.z_filefunc, us.filestream,
- central_pos,ZLIB_FILEFUNC_SEEK_SET)!=0)
- err=UNZ_ERRNO;
-
- /* the signature, already checked */
- if (unz64local_getLong(&us.z_filefunc, us.filestream,&uL)!=UNZ_OK)
- err=UNZ_ERRNO;
-
- /* size of zip64 end of central directory record */
- if (unz64local_getLong64(&us.z_filefunc, us.filestream,&uL64)!=UNZ_OK)
- err=UNZ_ERRNO;
-
- /* version made by */
- if (unz64local_getShort(&us.z_filefunc, us.filestream,&uS)!=UNZ_OK)
- err=UNZ_ERRNO;
-
- /* version needed to extract */
- if (unz64local_getShort(&us.z_filefunc, us.filestream,&uS)!=UNZ_OK)
- err=UNZ_ERRNO;
-
- /* number of this disk */
- if (unz64local_getLong(&us.z_filefunc, us.filestream,&number_disk)!=UNZ_OK)
- err=UNZ_ERRNO;
-
- /* number of the disk with the start of the central directory */
- if (unz64local_getLong(&us.z_filefunc, us.filestream,&number_disk_with_CD)!=UNZ_OK)
- err=UNZ_ERRNO;
-
- /* total number of entries in the central directory on this disk */
- if (unz64local_getLong64(&us.z_filefunc, us.filestream,&us.gi.number_entry)!=UNZ_OK)
- err=UNZ_ERRNO;
-
- /* total number of entries in the central directory */
- if (unz64local_getLong64(&us.z_filefunc, us.filestream,&number_entry_CD)!=UNZ_OK)
- err=UNZ_ERRNO;
-
- if ((number_entry_CD!=us.gi.number_entry) ||
- (number_disk_with_CD!=0) ||
- (number_disk!=0))
- err=UNZ_BADZIPFILE;
-
- /* size of the central directory */
- if (unz64local_getLong64(&us.z_filefunc, us.filestream,&us.size_central_dir)!=UNZ_OK)
- err=UNZ_ERRNO;
-
- /* offset of start of central directory with respect to the
- starting disk number */
- if (unz64local_getLong64(&us.z_filefunc, us.filestream,&us.offset_central_dir)!=UNZ_OK)
- err=UNZ_ERRNO;
-
- us.gi.size_comment = 0;
- }
- else
- {
- central_pos = unz64local_SearchCentralDir(&us.z_filefunc,us.filestream);
- if (central_pos==0)
- err=UNZ_ERRNO;
-
- us.isZip64 = 0;
-
- if (ZSEEK64(us.z_filefunc, us.filestream,
- central_pos,ZLIB_FILEFUNC_SEEK_SET)!=0)
- err=UNZ_ERRNO;
-
- /* the signature, already checked */
- if (unz64local_getLong(&us.z_filefunc, us.filestream,&uL)!=UNZ_OK)
- err=UNZ_ERRNO;
-
- /* number of this disk */
- if (unz64local_getShort(&us.z_filefunc, us.filestream,&number_disk)!=UNZ_OK)
- err=UNZ_ERRNO;
-
- /* number of the disk with the start of the central directory */
- if (unz64local_getShort(&us.z_filefunc, us.filestream,&number_disk_with_CD)!=UNZ_OK)
- err=UNZ_ERRNO;
-
- /* total number of entries in the central dir on this disk */
- if (unz64local_getShort(&us.z_filefunc, us.filestream,&uL)!=UNZ_OK)
- err=UNZ_ERRNO;
- us.gi.number_entry = uL;
-
- /* total number of entries in the central dir */
- if (unz64local_getShort(&us.z_filefunc, us.filestream,&uL)!=UNZ_OK)
- err=UNZ_ERRNO;
- number_entry_CD = uL;
-
- if ((number_entry_CD!=us.gi.number_entry) ||
- (number_disk_with_CD!=0) ||
- (number_disk!=0))
- err=UNZ_BADZIPFILE;
-
- /* size of the central directory */
- if (unz64local_getLong(&us.z_filefunc, us.filestream,&uL)!=UNZ_OK)
- err=UNZ_ERRNO;
- us.size_central_dir = uL;
-
- /* offset of start of central directory with respect to the
- starting disk number */
- if (unz64local_getLong(&us.z_filefunc, us.filestream,&uL)!=UNZ_OK)
- err=UNZ_ERRNO;
- us.offset_central_dir = uL;
-
- /* zipfile comment length */
- if (unz64local_getShort(&us.z_filefunc, us.filestream,&us.gi.size_comment)!=UNZ_OK)
- err=UNZ_ERRNO;
- }
-
- if ((central_pos<us.offset_central_dir+us.size_central_dir) &&
- (err==UNZ_OK))
- err=UNZ_BADZIPFILE;
-
- if (err!=UNZ_OK)
- {
- ZCLOSE64(us.z_filefunc, us.filestream);
- return NULL;
- }
-
- us.byte_before_the_zipfile = central_pos -
- (us.offset_central_dir+us.size_central_dir);
- us.central_pos = central_pos;
- us.pfile_in_zip_read = NULL;
- us.encrypted = 0;
-
-
- s=(unz64_s*)ALLOC(sizeof(unz64_s));
- if( s != NULL)
- {
- *s=us;
- unzGoToFirstFile((unzFile)s);
- }
- return (unzFile)s;
-}
-
-
-extern unzFile ZEXPORT unzOpen2 (const char *path,
- zlib_filefunc_def* pzlib_filefunc32_def)
-{
- if (pzlib_filefunc32_def != NULL)
- {
- zlib_filefunc64_32_def zlib_filefunc64_32_def_fill;
- fill_zlib_filefunc64_32_def_from_filefunc32(&zlib_filefunc64_32_def_fill,pzlib_filefunc32_def);
- return unzOpenInternal(path, &zlib_filefunc64_32_def_fill, 0);
- }
- else
- return unzOpenInternal(path, NULL, 0);
-}
-
-extern unzFile ZEXPORT unzOpen2_64 (const void *path,
- zlib_filefunc64_def* pzlib_filefunc_def)
-{
- if (pzlib_filefunc_def != NULL)
- {
- zlib_filefunc64_32_def zlib_filefunc64_32_def_fill;
- zlib_filefunc64_32_def_fill.zfile_func64 = *pzlib_filefunc_def;
- zlib_filefunc64_32_def_fill.ztell32_file = NULL;
- zlib_filefunc64_32_def_fill.zseek32_file = NULL;
- return unzOpenInternal(path, &zlib_filefunc64_32_def_fill, 1);
- }
- else
- return unzOpenInternal(path, NULL, 1);
-}
-
-extern unzFile ZEXPORT unzOpen (const char *path)
-{
- return unzOpenInternal(path, NULL, 0);
-}
-
-extern unzFile ZEXPORT unzOpen64 (const void *path)
-{
- return unzOpenInternal(path, NULL, 1);
-}
-
-/*
- Close a ZipFile opened with unzOpen.
- If there is files inside the .Zip opened with unzOpenCurrentFile (see later),
- these files MUST be closed with unzCloseCurrentFile before call unzClose.
- return UNZ_OK if there is no problem. */
-extern int ZEXPORT unzClose (unzFile file)
-{
- unz64_s* s;
- if (file==NULL)
- return UNZ_PARAMERROR;
- s=(unz64_s*)file;
-
- if (s->pfile_in_zip_read!=NULL)
- unzCloseCurrentFile(file);
-
- ZCLOSE64(s->z_filefunc, s->filestream);
- TRYFREE(s);
- return UNZ_OK;
-}
-
-
-/*
- Write info about the ZipFile in the *pglobal_info structure.
- No preparation of the structure is needed
- return UNZ_OK if there is no problem. */
-extern int ZEXPORT unzGetGlobalInfo64 (unzFile file, unz_global_info64* pglobal_info)
-{
- unz64_s* s;
- if (file==NULL)
- return UNZ_PARAMERROR;
- s=(unz64_s*)file;
- *pglobal_info=s->gi;
- return UNZ_OK;
-}
-
-extern int ZEXPORT unzGetGlobalInfo (unzFile file, unz_global_info* pglobal_info32)
-{
- unz64_s* s;
- if (file==NULL)
- return UNZ_PARAMERROR;
- s=(unz64_s*)file;
- /* to do : check if number_entry is not truncated */
- pglobal_info32->number_entry = (uLong)s->gi.number_entry;
- pglobal_info32->size_comment = s->gi.size_comment;
- return UNZ_OK;
-}
-/*
- Translate date/time from Dos format to tm_unz (readable more easilty)
-*/
-local void unz64local_DosDateToTmuDate (ZPOS64_T ulDosDate, tm_unz* ptm)
-{
- ZPOS64_T uDate;
- uDate = (ZPOS64_T)(ulDosDate>>16);
- ptm->tm_mday = (uInt)(uDate&0x1f) ;
- ptm->tm_mon = (uInt)((((uDate)&0x1E0)/0x20)-1) ;
- ptm->tm_year = (uInt)(((uDate&0x0FE00)/0x0200)+1980) ;
-
- ptm->tm_hour = (uInt) ((ulDosDate &0xF800)/0x800);
- ptm->tm_min = (uInt) ((ulDosDate&0x7E0)/0x20) ;
- ptm->tm_sec = (uInt) (2*(ulDosDate&0x1f)) ;
-}
-
-/*
- Get Info about the current file in the zipfile, with internal only info
-*/
-local int unz64local_GetCurrentFileInfoInternal OF((unzFile file,
- unz_file_info64 *pfile_info,
- unz_file_info64_internal
- *pfile_info_internal,
- char *szFileName,
- uLong fileNameBufferSize,
- void *extraField,
- uLong extraFieldBufferSize,
- char *szComment,
- uLong commentBufferSize));
-
-local int unz64local_GetCurrentFileInfoInternal (unzFile file,
- unz_file_info64 *pfile_info,
- unz_file_info64_internal
- *pfile_info_internal,
- char *szFileName,
- uLong fileNameBufferSize,
- void *extraField,
- uLong extraFieldBufferSize,
- char *szComment,
- uLong commentBufferSize)
-{
- unz64_s* s;
- unz_file_info64 file_info;
- unz_file_info64_internal file_info_internal;
- int err=UNZ_OK;
- uLong uMagic;
- long lSeek=0;
- uLong uL;
-
- if (file==NULL)
- return UNZ_PARAMERROR;
- s=(unz64_s*)file;
- if (ZSEEK64(s->z_filefunc, s->filestream,
- s->pos_in_central_dir+s->byte_before_the_zipfile,
- ZLIB_FILEFUNC_SEEK_SET)!=0)
- err=UNZ_ERRNO;
-
-
- /* we check the magic */
- if (err==UNZ_OK)
- {
- if (unz64local_getLong(&s->z_filefunc, s->filestream,&uMagic) != UNZ_OK)
- err=UNZ_ERRNO;
- else if (uMagic!=0x02014b50)
- err=UNZ_BADZIPFILE;
- }
-
- if (unz64local_getShort(&s->z_filefunc, s->filestream,&file_info.version) != UNZ_OK)
- err=UNZ_ERRNO;
-
- if (unz64local_getShort(&s->z_filefunc, s->filestream,&file_info.version_needed) != UNZ_OK)
- err=UNZ_ERRNO;
-
- if (unz64local_getShort(&s->z_filefunc, s->filestream,&file_info.flag) != UNZ_OK)
- err=UNZ_ERRNO;
-
- if (unz64local_getShort(&s->z_filefunc, s->filestream,&file_info.compression_method) != UNZ_OK)
- err=UNZ_ERRNO;
-
- if (unz64local_getLong(&s->z_filefunc, s->filestream,&file_info.dosDate) != UNZ_OK)
- err=UNZ_ERRNO;
-
- unz64local_DosDateToTmuDate(file_info.dosDate,&file_info.tmu_date);
-
- if (unz64local_getLong(&s->z_filefunc, s->filestream,&file_info.crc) != UNZ_OK)
- err=UNZ_ERRNO;
-
- if (unz64local_getLong(&s->z_filefunc, s->filestream,&uL) != UNZ_OK)
- err=UNZ_ERRNO;
- file_info.compressed_size = uL;
-
- if (unz64local_getLong(&s->z_filefunc, s->filestream,&uL) != UNZ_OK)
- err=UNZ_ERRNO;
- file_info.uncompressed_size = uL;
-
- if (unz64local_getShort(&s->z_filefunc, s->filestream,&file_info.size_filename) != UNZ_OK)
- err=UNZ_ERRNO;
-
- if (unz64local_getShort(&s->z_filefunc, s->filestream,&file_info.size_file_extra) != UNZ_OK)
- err=UNZ_ERRNO;
-
- if (unz64local_getShort(&s->z_filefunc, s->filestream,&file_info.size_file_comment) != UNZ_OK)
- err=UNZ_ERRNO;
-
- if (unz64local_getShort(&s->z_filefunc, s->filestream,&file_info.disk_num_start) != UNZ_OK)
- err=UNZ_ERRNO;
-
- if (unz64local_getShort(&s->z_filefunc, s->filestream,&file_info.internal_fa) != UNZ_OK)
- err=UNZ_ERRNO;
-
- if (unz64local_getLong(&s->z_filefunc, s->filestream,&file_info.external_fa) != UNZ_OK)
- err=UNZ_ERRNO;
-
- // relative offset of local header
- if (unz64local_getLong(&s->z_filefunc, s->filestream,&uL) != UNZ_OK)
- err=UNZ_ERRNO;
- file_info_internal.offset_curfile = uL;
-
- lSeek+=file_info.size_filename;
- if ((err==UNZ_OK) && (szFileName!=NULL))
- {
- uLong uSizeRead ;
- if (file_info.size_filename<fileNameBufferSize)
- {
- *(szFileName+file_info.size_filename)='\0';
- uSizeRead = file_info.size_filename;
- }
- else
- uSizeRead = fileNameBufferSize;
-
- if ((file_info.size_filename>0) && (fileNameBufferSize>0))
- if (ZREAD64(s->z_filefunc, s->filestream,szFileName,uSizeRead)!=uSizeRead)
- err=UNZ_ERRNO;
- lSeek -= uSizeRead;
- }
-
- // Read extrafield
- if ((err==UNZ_OK) && (extraField!=NULL))
- {
- ZPOS64_T uSizeRead ;
- if (file_info.size_file_extra<extraFieldBufferSize)
- uSizeRead = file_info.size_file_extra;
- else
- uSizeRead = extraFieldBufferSize;
-
- if (lSeek!=0)
- {
- if (ZSEEK64(s->z_filefunc, s->filestream,lSeek,ZLIB_FILEFUNC_SEEK_CUR)==0)
- lSeek=0;
- else
- err=UNZ_ERRNO;
- }
-
- if ((file_info.size_file_extra>0) && (extraFieldBufferSize>0))
- if (ZREAD64(s->z_filefunc, s->filestream,extraField,(uLong)uSizeRead)!=uSizeRead)
- err=UNZ_ERRNO;
-
- lSeek += file_info.size_file_extra - (uLong)uSizeRead;
- }
- else
- lSeek += file_info.size_file_extra;
-
-
- if ((err==UNZ_OK) && (file_info.size_file_extra != 0))
- {
- uLong acc = 0;
-
- // since lSeek now points to after the extra field we need to move back
- lSeek -= file_info.size_file_extra;
-
- if (lSeek!=0)
- {
- if (ZSEEK64(s->z_filefunc, s->filestream,lSeek,ZLIB_FILEFUNC_SEEK_CUR)==0)
- lSeek=0;
- else
- err=UNZ_ERRNO;
- }
-
- while(acc < file_info.size_file_extra)
- {
- uLong headerId;
- uLong dataSize;
-
- if (unz64local_getShort(&s->z_filefunc, s->filestream,&headerId) != UNZ_OK)
- err=UNZ_ERRNO;
-
- if (unz64local_getShort(&s->z_filefunc, s->filestream,&dataSize) != UNZ_OK)
- err=UNZ_ERRNO;
-
- /* ZIP64 extra fields */
- if (headerId == 0x0001)
- {
- uLong uL;
-
- if(file_info.uncompressed_size == MAXU32)
- {
- if (unz64local_getLong64(&s->z_filefunc, s->filestream,&file_info.uncompressed_size) != UNZ_OK)
- err=UNZ_ERRNO;
- }
-
- if(file_info.compressed_size == MAXU32)
- {
- if (unz64local_getLong64(&s->z_filefunc, s->filestream,&file_info.compressed_size) != UNZ_OK)
- err=UNZ_ERRNO;
- }
-
- if(file_info_internal.offset_curfile == MAXU32)
- {
- /* Relative Header offset */
- if (unz64local_getLong64(&s->z_filefunc, s->filestream,&file_info_internal.offset_curfile) != UNZ_OK)
- err=UNZ_ERRNO;
- }
-
- if(file_info.disk_num_start == MAXU32)
- {
- /* Disk Start Number */
- if (unz64local_getLong(&s->z_filefunc, s->filestream,&uL) != UNZ_OK)
- err=UNZ_ERRNO;
- }
-
- }
- else
- {
- if (ZSEEK64(s->z_filefunc, s->filestream,dataSize,ZLIB_FILEFUNC_SEEK_CUR)!=0)
- err=UNZ_ERRNO;
- }
-
- acc += 2 + 2 + dataSize;
- }
- }
-
- if ((err==UNZ_OK) && (szComment!=NULL))
- {
- uLong uSizeRead ;
- if (file_info.size_file_comment<commentBufferSize)
- {
- *(szComment+file_info.size_file_comment)='\0';
- uSizeRead = file_info.size_file_comment;
- }
- else
- uSizeRead = commentBufferSize;
-
- if (lSeek!=0)
- {
- if (ZSEEK64(s->z_filefunc, s->filestream,lSeek,ZLIB_FILEFUNC_SEEK_CUR)==0)
- lSeek=0;
- else
- err=UNZ_ERRNO;
- }
-
- if ((file_info.size_file_comment>0) && (commentBufferSize>0))
- if (ZREAD64(s->z_filefunc, s->filestream,szComment,uSizeRead)!=uSizeRead)
- err=UNZ_ERRNO;
- lSeek+=file_info.size_file_comment - uSizeRead;
- }
- else
- lSeek+=file_info.size_file_comment;
-
-
- if ((err==UNZ_OK) && (pfile_info!=NULL))
- *pfile_info=file_info;
-
- if ((err==UNZ_OK) && (pfile_info_internal!=NULL))
- *pfile_info_internal=file_info_internal;
-
- return err;
-}
-
-
-
-/*
- Write info about the ZipFile in the *pglobal_info structure.
- No preparation of the structure is needed
- return UNZ_OK if there is no problem.
-*/
-extern int ZEXPORT unzGetCurrentFileInfo64 (unzFile file,
- unz_file_info64 * pfile_info,
- char * szFileName, uLong fileNameBufferSize,
- void *extraField, uLong extraFieldBufferSize,
- char* szComment, uLong commentBufferSize)
-{
- return unz64local_GetCurrentFileInfoInternal(file,pfile_info,NULL,
- szFileName,fileNameBufferSize,
- extraField,extraFieldBufferSize,
- szComment,commentBufferSize);
-}
-
-extern int ZEXPORT unzGetCurrentFileInfo (unzFile file,
- unz_file_info * pfile_info,
- char * szFileName, uLong fileNameBufferSize,
- void *extraField, uLong extraFieldBufferSize,
- char* szComment, uLong commentBufferSize)
-{
- int err;
- unz_file_info64 file_info64;
- err = unz64local_GetCurrentFileInfoInternal(file,&file_info64,NULL,
- szFileName,fileNameBufferSize,
- extraField,extraFieldBufferSize,
- szComment,commentBufferSize);
- if ((err==UNZ_OK) && (pfile_info != NULL))
- {
- pfile_info->version = file_info64.version;
- pfile_info->version_needed = file_info64.version_needed;
- pfile_info->flag = file_info64.flag;
- pfile_info->compression_method = file_info64.compression_method;
- pfile_info->dosDate = file_info64.dosDate;
- pfile_info->crc = file_info64.crc;
-
- pfile_info->size_filename = file_info64.size_filename;
- pfile_info->size_file_extra = file_info64.size_file_extra;
- pfile_info->size_file_comment = file_info64.size_file_comment;
-
- pfile_info->disk_num_start = file_info64.disk_num_start;
- pfile_info->internal_fa = file_info64.internal_fa;
- pfile_info->external_fa = file_info64.external_fa;
-
- pfile_info->tmu_date = file_info64.tmu_date,
-
-
- pfile_info->compressed_size = (uLong)file_info64.compressed_size;
- pfile_info->uncompressed_size = (uLong)file_info64.uncompressed_size;
-
- }
- return err;
-}
-/*
- Set the current file of the zipfile to the first file.
- return UNZ_OK if there is no problem
-*/
-extern int ZEXPORT unzGoToFirstFile (unzFile file)
-{
- int err=UNZ_OK;
- unz64_s* s;
- if (file==NULL)
- return UNZ_PARAMERROR;
- s=(unz64_s*)file;
- s->pos_in_central_dir=s->offset_central_dir;
- s->num_file=0;
- err=unz64local_GetCurrentFileInfoInternal(file,&s->cur_file_info,
- &s->cur_file_info_internal,
- NULL,0,NULL,0,NULL,0);
- s->current_file_ok = (err == UNZ_OK);
- return err;
-}
-
-/*
- Set the current file of the zipfile to the next file.
- return UNZ_OK if there is no problem
- return UNZ_END_OF_LIST_OF_FILE if the actual file was the latest.
-*/
-extern int ZEXPORT unzGoToNextFile (unzFile file)
-{
- unz64_s* s;
- int err;
-
- if (file==NULL)
- return UNZ_PARAMERROR;
- s=(unz64_s*)file;
- if (!s->current_file_ok)
- return UNZ_END_OF_LIST_OF_FILE;
- if (s->gi.number_entry != 0xffff) /* 2^16 files overflow hack */
- if (s->num_file+1==s->gi.number_entry)
- return UNZ_END_OF_LIST_OF_FILE;
-
- s->pos_in_central_dir += SIZECENTRALDIRITEM + s->cur_file_info.size_filename +
- s->cur_file_info.size_file_extra + s->cur_file_info.size_file_comment ;
- s->num_file++;
- err = unz64local_GetCurrentFileInfoInternal(file,&s->cur_file_info,
- &s->cur_file_info_internal,
- NULL,0,NULL,0,NULL,0);
- s->current_file_ok = (err == UNZ_OK);
- return err;
-}
-
-
-/*
- Try locate the file szFileName in the zipfile.
- For the iCaseSensitivity signification, see unzStringFileNameCompare
-
- return value :
- UNZ_OK if the file is found. It becomes the current file.
- UNZ_END_OF_LIST_OF_FILE if the file is not found
-*/
-extern int ZEXPORT unzLocateFile (unzFile file, const char *szFileName, int iCaseSensitivity)
-{
- unz64_s* s;
- int err;
-
- /* We remember the 'current' position in the file so that we can jump
- * back there if we fail.
- */
- unz_file_info64 cur_file_infoSaved;
- unz_file_info64_internal cur_file_info_internalSaved;
- ZPOS64_T num_fileSaved;
- ZPOS64_T pos_in_central_dirSaved;
-
-
- if (file==NULL)
- return UNZ_PARAMERROR;
-
- if (strlen(szFileName)>=UNZ_MAXFILENAMEINZIP)
- return UNZ_PARAMERROR;
-
- s=(unz64_s*)file;
- if (!s->current_file_ok)
- return UNZ_END_OF_LIST_OF_FILE;
-
- /* Save the current state */
- num_fileSaved = s->num_file;
- pos_in_central_dirSaved = s->pos_in_central_dir;
- cur_file_infoSaved = s->cur_file_info;
- cur_file_info_internalSaved = s->cur_file_info_internal;
-
- err = unzGoToFirstFile(file);
-
- while (err == UNZ_OK)
- {
- char szCurrentFileName[UNZ_MAXFILENAMEINZIP+1];
- err = unzGetCurrentFileInfo64(file,NULL,
- szCurrentFileName,sizeof(szCurrentFileName)-1,
- NULL,0,NULL,0);
- if (err == UNZ_OK)
- {
- if (unzStringFileNameCompare(szCurrentFileName,
- szFileName,iCaseSensitivity)==0)
- return UNZ_OK;
- err = unzGoToNextFile(file);
- }
- }
-
- /* We failed, so restore the state of the 'current file' to where we
- * were.
- */
- s->num_file = num_fileSaved ;
- s->pos_in_central_dir = pos_in_central_dirSaved ;
- s->cur_file_info = cur_file_infoSaved;
- s->cur_file_info_internal = cur_file_info_internalSaved;
- return err;
-}
-
-
-/*
-///////////////////////////////////////////
-// Contributed by Ryan Haksi (mailto://cryogen@infoserve.net)
-// I need random access
-//
-// Further optimization could be realized by adding an ability
-// to cache the directory in memory. The goal being a single
-// comprehensive file read to put the file I need in a memory.
-*/
-
-/*
-typedef struct unz_file_pos_s
-{
- ZPOS64_T pos_in_zip_directory; // offset in file
- ZPOS64_T num_of_file; // # of file
-} unz_file_pos;
-*/
-
-extern int ZEXPORT unzGetFilePos64(unzFile file, unz64_file_pos* file_pos)
-{
- unz64_s* s;
-
- if (file==NULL || file_pos==NULL)
- return UNZ_PARAMERROR;
- s=(unz64_s*)file;
- if (!s->current_file_ok)
- return UNZ_END_OF_LIST_OF_FILE;
-
- file_pos->pos_in_zip_directory = s->pos_in_central_dir;
- file_pos->num_of_file = s->num_file;
-
- return UNZ_OK;
-}
-
-extern int ZEXPORT unzGetFilePos(
- unzFile file,
- unz_file_pos* file_pos)
-{
- unz64_file_pos file_pos64;
- int err = unzGetFilePos64(file,&file_pos64);
- if (err==UNZ_OK)
- {
- file_pos->pos_in_zip_directory = (uLong)file_pos64.pos_in_zip_directory;
- file_pos->num_of_file = (uLong)file_pos64.num_of_file;
- }
- return err;
-}
-
-extern int ZEXPORT unzGoToFilePos64(unzFile file, const unz64_file_pos* file_pos)
-{
- unz64_s* s;
- int err;
-
- if (file==NULL || file_pos==NULL)
- return UNZ_PARAMERROR;
- s=(unz64_s*)file;
-
- /* jump to the right spot */
- s->pos_in_central_dir = file_pos->pos_in_zip_directory;
- s->num_file = file_pos->num_of_file;
-
- /* set the current file */
- err = unz64local_GetCurrentFileInfoInternal(file,&s->cur_file_info,
- &s->cur_file_info_internal,
- NULL,0,NULL,0,NULL,0);
- /* return results */
- s->current_file_ok = (err == UNZ_OK);
- return err;
-}
-
-extern int ZEXPORT unzGoToFilePos(
- unzFile file,
- unz_file_pos* file_pos)
-{
- unz64_file_pos file_pos64;
- if (file_pos == NULL)
- return UNZ_PARAMERROR;
-
- file_pos64.pos_in_zip_directory = file_pos->pos_in_zip_directory;
- file_pos64.num_of_file = file_pos->num_of_file;
- return unzGoToFilePos64(file,&file_pos64);
-}
-
-/*
-// Unzip Helper Functions - should be here?
-///////////////////////////////////////////
-*/
-
-/*
- Read the local header of the current zipfile
- Check the coherency of the local header and info in the end of central
- directory about this file
- store in *piSizeVar the size of extra info in local header
- (filename and size of extra field data)
-*/
-local int unz64local_CheckCurrentFileCoherencyHeader (unz64_s* s, uInt* piSizeVar,
- ZPOS64_T * poffset_local_extrafield,
- uInt * psize_local_extrafield)
-{
- uLong uMagic,uData,uFlags;
- uLong size_filename;
- uLong size_extra_field;
- int err=UNZ_OK;
-
- *piSizeVar = 0;
- *poffset_local_extrafield = 0;
- *psize_local_extrafield = 0;
-
- if (ZSEEK64(s->z_filefunc, s->filestream,s->cur_file_info_internal.offset_curfile +
- s->byte_before_the_zipfile,ZLIB_FILEFUNC_SEEK_SET)!=0)
- return UNZ_ERRNO;
-
-
- if (err==UNZ_OK)
- {
- if (unz64local_getLong(&s->z_filefunc, s->filestream,&uMagic) != UNZ_OK)
- err=UNZ_ERRNO;
- else if (uMagic!=0x04034b50)
- err=UNZ_BADZIPFILE;
- }
-
- if (unz64local_getShort(&s->z_filefunc, s->filestream,&uData) != UNZ_OK)
- err=UNZ_ERRNO;
-/*
- else if ((err==UNZ_OK) && (uData!=s->cur_file_info.wVersion))
- err=UNZ_BADZIPFILE;
-*/
- if (unz64local_getShort(&s->z_filefunc, s->filestream,&uFlags) != UNZ_OK)
- err=UNZ_ERRNO;
-
- if (unz64local_getShort(&s->z_filefunc, s->filestream,&uData) != UNZ_OK)
- err=UNZ_ERRNO;
- else if ((err==UNZ_OK) && (uData!=s->cur_file_info.compression_method))
- err=UNZ_BADZIPFILE;
-
- if ((err==UNZ_OK) && (s->cur_file_info.compression_method!=0) &&
-/* #ifdef HAVE_BZIP2 */
- (s->cur_file_info.compression_method!=Z_BZIP2ED) &&
-/* #endif */
- (s->cur_file_info.compression_method!=Z_DEFLATED))
- err=UNZ_BADZIPFILE;
-
- if (unz64local_getLong(&s->z_filefunc, s->filestream,&uData) != UNZ_OK) /* date/time */
- err=UNZ_ERRNO;
-
- if (unz64local_getLong(&s->z_filefunc, s->filestream,&uData) != UNZ_OK) /* crc */
- err=UNZ_ERRNO;
- else if ((err==UNZ_OK) && (uData!=s->cur_file_info.crc) && ((uFlags & 8)==0))
- err=UNZ_BADZIPFILE;
-
- if (unz64local_getLong(&s->z_filefunc, s->filestream,&uData) != UNZ_OK) /* size compr */
- err=UNZ_ERRNO;
- else if (uData != 0xFFFFFFFF && (err==UNZ_OK) && (uData!=s->cur_file_info.compressed_size) && ((uFlags & 8)==0))
- err=UNZ_BADZIPFILE;
-
- if (unz64local_getLong(&s->z_filefunc, s->filestream,&uData) != UNZ_OK) /* size uncompr */
- err=UNZ_ERRNO;
- else if (uData != 0xFFFFFFFF && (err==UNZ_OK) && (uData!=s->cur_file_info.uncompressed_size) && ((uFlags & 8)==0))
- err=UNZ_BADZIPFILE;
-
- if (unz64local_getShort(&s->z_filefunc, s->filestream,&size_filename) != UNZ_OK)
- err=UNZ_ERRNO;
- else if ((err==UNZ_OK) && (size_filename!=s->cur_file_info.size_filename))
- err=UNZ_BADZIPFILE;
-
- *piSizeVar += (uInt)size_filename;
-
- if (unz64local_getShort(&s->z_filefunc, s->filestream,&size_extra_field) != UNZ_OK)
- err=UNZ_ERRNO;
- *poffset_local_extrafield= s->cur_file_info_internal.offset_curfile +
- SIZEZIPLOCALHEADER + size_filename;
- *psize_local_extrafield = (uInt)size_extra_field;
-
- *piSizeVar += (uInt)size_extra_field;
-
- return err;
-}
-
-/*
- Open for reading data the current file in the zipfile.
- If there is no error and the file is opened, the return value is UNZ_OK.
-*/
-extern int ZEXPORT unzOpenCurrentFile3 (unzFile file, int* method,
- int* level, int raw, const char* password)
-{
- int err=UNZ_OK;
- uInt iSizeVar;
- unz64_s* s;
- file_in_zip64_read_info_s* pfile_in_zip_read_info;
- ZPOS64_T offset_local_extrafield; /* offset of the local extra field */
- uInt size_local_extrafield; /* size of the local extra field */
-# ifndef NOUNCRYPT
- char source[12];
-# else
- if (password != NULL)
- return UNZ_PARAMERROR;
-# endif
-
- if (file==NULL)
- return UNZ_PARAMERROR;
- s=(unz64_s*)file;
- if (!s->current_file_ok)
- return UNZ_PARAMERROR;
-
- if (s->pfile_in_zip_read != NULL)
- unzCloseCurrentFile(file);
-
- if (unz64local_CheckCurrentFileCoherencyHeader(s,&iSizeVar, &offset_local_extrafield,&size_local_extrafield)!=UNZ_OK)
- return UNZ_BADZIPFILE;
-
- pfile_in_zip_read_info = (file_in_zip64_read_info_s*)ALLOC(sizeof(file_in_zip64_read_info_s));
- if (pfile_in_zip_read_info==NULL)
- return UNZ_INTERNALERROR;
-
- pfile_in_zip_read_info->read_buffer=(char*)ALLOC(UNZ_BUFSIZE);
- pfile_in_zip_read_info->offset_local_extrafield = offset_local_extrafield;
- pfile_in_zip_read_info->size_local_extrafield = size_local_extrafield;
- pfile_in_zip_read_info->pos_local_extrafield=0;
- pfile_in_zip_read_info->raw=raw;
-
- if (pfile_in_zip_read_info->read_buffer==NULL)
- {
- TRYFREE(pfile_in_zip_read_info);
- return UNZ_INTERNALERROR;
- }
-
- pfile_in_zip_read_info->stream_initialised=0;
-
- if (method!=NULL)
- *method = (int)s->cur_file_info.compression_method;
-
- if (level!=NULL)
- {
- *level = 6;
- switch (s->cur_file_info.flag & 0x06)
- {
- case 6 : *level = 1; break;
- case 4 : *level = 2; break;
- case 2 : *level = 9; break;
- }
- }
-
- if ((s->cur_file_info.compression_method!=0) &&
-/* #ifdef HAVE_BZIP2 */
- (s->cur_file_info.compression_method!=Z_BZIP2ED) &&
-/* #endif */
- (s->cur_file_info.compression_method!=Z_DEFLATED))
-
- err=UNZ_BADZIPFILE;
-
- pfile_in_zip_read_info->crc32_wait=s->cur_file_info.crc;
- pfile_in_zip_read_info->crc32=0;
- pfile_in_zip_read_info->total_out_64=0;
- pfile_in_zip_read_info->compression_method = s->cur_file_info.compression_method;
- pfile_in_zip_read_info->filestream=s->filestream;
- pfile_in_zip_read_info->z_filefunc=s->z_filefunc;
- pfile_in_zip_read_info->byte_before_the_zipfile=s->byte_before_the_zipfile;
-
- pfile_in_zip_read_info->stream.total_out = 0;
-
- if ((s->cur_file_info.compression_method==Z_BZIP2ED) && (!raw))
- {
-#ifdef HAVE_BZIP2
- pfile_in_zip_read_info->bstream.bzalloc = (void *(*) (void *, int, int))0;
- pfile_in_zip_read_info->bstream.bzfree = (free_func)0;
- pfile_in_zip_read_info->bstream.opaque = (voidpf)0;
- pfile_in_zip_read_info->bstream.state = (voidpf)0;
-
- pfile_in_zip_read_info->stream.zalloc = (alloc_func)0;
- pfile_in_zip_read_info->stream.zfree = (free_func)0;
- pfile_in_zip_read_info->stream.opaque = (voidpf)0;
- pfile_in_zip_read_info->stream.next_in = (voidpf)0;
- pfile_in_zip_read_info->stream.avail_in = 0;
-
- err=BZ2_bzDecompressInit(&pfile_in_zip_read_info->bstream, 0, 0);
- if (err == Z_OK)
- pfile_in_zip_read_info->stream_initialised=Z_BZIP2ED;
- else
- {
- TRYFREE(pfile_in_zip_read_info);
- return err;
- }
-#else
- pfile_in_zip_read_info->raw=1;
-#endif
- }
- else if ((s->cur_file_info.compression_method==Z_DEFLATED) && (!raw))
- {
- pfile_in_zip_read_info->stream.zalloc = (alloc_func)0;
- pfile_in_zip_read_info->stream.zfree = (free_func)0;
- pfile_in_zip_read_info->stream.opaque = (voidpf)0;
- pfile_in_zip_read_info->stream.next_in = 0;
- pfile_in_zip_read_info->stream.avail_in = 0;
-
- err=inflateInit2(&pfile_in_zip_read_info->stream, -MAX_WBITS);
- if (err == Z_OK)
- pfile_in_zip_read_info->stream_initialised=Z_DEFLATED;
- else
- {
- TRYFREE(pfile_in_zip_read_info);
- return err;
- }
- /* windowBits is passed < 0 to tell that there is no zlib header.
- * Note that in this case inflate *requires* an extra "dummy" byte
- * after the compressed stream in order to complete decompression and
- * return Z_STREAM_END.
- * In unzip, i don't wait absolutely Z_STREAM_END because I known the
- * size of both compressed and uncompressed data
- */
- }
- pfile_in_zip_read_info->rest_read_compressed =
- s->cur_file_info.compressed_size ;
- pfile_in_zip_read_info->rest_read_uncompressed =
- s->cur_file_info.uncompressed_size ;
-
-
- pfile_in_zip_read_info->pos_in_zipfile =
- s->cur_file_info_internal.offset_curfile + SIZEZIPLOCALHEADER +
- iSizeVar;
-
- pfile_in_zip_read_info->stream.avail_in = (uInt)0;
-
- s->pfile_in_zip_read = pfile_in_zip_read_info;
- s->encrypted = 0;
-
-# ifndef NOUNCRYPT
- if (password != NULL)
- {
- int i;
- s->pcrc_32_tab = get_crc_table();
- init_keys(password,s->keys,s->pcrc_32_tab);
- if (ZSEEK64(s->z_filefunc, s->filestream,
- s->pfile_in_zip_read->pos_in_zipfile +
- s->pfile_in_zip_read->byte_before_the_zipfile,
- SEEK_SET)!=0)
- return UNZ_INTERNALERROR;
- if(ZREAD64(s->z_filefunc, s->filestream,source, 12)<12)
- return UNZ_INTERNALERROR;
-
- for (i = 0; i<12; i++)
- zdecode(s->keys,s->pcrc_32_tab,source[i]);
-
- s->pfile_in_zip_read->pos_in_zipfile+=12;
- s->encrypted=1;
- }
-# endif
-
-
- return UNZ_OK;
-}
-
-extern int ZEXPORT unzOpenCurrentFile (unzFile file)
-{
- return unzOpenCurrentFile3(file, NULL, NULL, 0, NULL);
-}
-
-extern int ZEXPORT unzOpenCurrentFilePassword (unzFile file, const char* password)
-{
- return unzOpenCurrentFile3(file, NULL, NULL, 0, password);
-}
-
-extern int ZEXPORT unzOpenCurrentFile2 (unzFile file, int* method, int* level, int raw)
-{
- return unzOpenCurrentFile3(file, method, level, raw, NULL);
-}
-
-/** Addition for GDAL : START */
-
-extern ZPOS64_T ZEXPORT unzGetCurrentFileZStreamPos64( unzFile file)
-{
- unz64_s* s;
- file_in_zip64_read_info_s* pfile_in_zip_read_info;
- s=(unz64_s*)file;
- if (file==NULL)
- return 0; //UNZ_PARAMERROR;
- pfile_in_zip_read_info=s->pfile_in_zip_read;
- if (pfile_in_zip_read_info==NULL)
- return 0; //UNZ_PARAMERROR;
- return pfile_in_zip_read_info->pos_in_zipfile +
- pfile_in_zip_read_info->byte_before_the_zipfile;
-}
-
-/** Addition for GDAL : END */
-
-/*
- Read bytes from the current file.
- buf contain buffer where data must be copied
- len the size of buf.
-
- return the number of byte copied if somes bytes are copied
- return 0 if the end of file was reached
- return <0 with error code if there is an error
- (UNZ_ERRNO for IO error, or zLib error for uncompress error)
-*/
-extern int ZEXPORT unzReadCurrentFile (unzFile file, voidp buf, unsigned len)
-{
- int err=UNZ_OK;
- uInt iRead = 0;
- unz64_s* s;
- file_in_zip64_read_info_s* pfile_in_zip_read_info;
- if (file==NULL)
- return UNZ_PARAMERROR;
- s=(unz64_s*)file;
- pfile_in_zip_read_info=s->pfile_in_zip_read;
-
- if (pfile_in_zip_read_info==NULL)
- return UNZ_PARAMERROR;
-
-
- if (pfile_in_zip_read_info->read_buffer == NULL)
- return UNZ_END_OF_LIST_OF_FILE;
- if (len==0)
- return 0;
-
- pfile_in_zip_read_info->stream.next_out = (Bytef*)buf;
-
- pfile_in_zip_read_info->stream.avail_out = (uInt)len;
-
- if ((len>pfile_in_zip_read_info->rest_read_uncompressed) &&
- (!(pfile_in_zip_read_info->raw)))
- pfile_in_zip_read_info->stream.avail_out =
- (uInt)pfile_in_zip_read_info->rest_read_uncompressed;
-
- if ((len>pfile_in_zip_read_info->rest_read_compressed+
- pfile_in_zip_read_info->stream.avail_in) &&
- (pfile_in_zip_read_info->raw))
- pfile_in_zip_read_info->stream.avail_out =
- (uInt)pfile_in_zip_read_info->rest_read_compressed+
- pfile_in_zip_read_info->stream.avail_in;
-
- while (pfile_in_zip_read_info->stream.avail_out>0)
- {
- if ((pfile_in_zip_read_info->stream.avail_in==0) &&
- (pfile_in_zip_read_info->rest_read_compressed>0))
- {
- uInt uReadThis = UNZ_BUFSIZE;
- if (pfile_in_zip_read_info->rest_read_compressed<uReadThis)
- uReadThis = (uInt)pfile_in_zip_read_info->rest_read_compressed;
- if (uReadThis == 0)
- return UNZ_EOF;
- if (ZSEEK64(pfile_in_zip_read_info->z_filefunc,
- pfile_in_zip_read_info->filestream,
- pfile_in_zip_read_info->pos_in_zipfile +
- pfile_in_zip_read_info->byte_before_the_zipfile,
- ZLIB_FILEFUNC_SEEK_SET)!=0)
- return UNZ_ERRNO;
- if (ZREAD64(pfile_in_zip_read_info->z_filefunc,
- pfile_in_zip_read_info->filestream,
- pfile_in_zip_read_info->read_buffer,
- uReadThis)!=uReadThis)
- return UNZ_ERRNO;
-
-
-# ifndef NOUNCRYPT
- if(s->encrypted)
- {
- uInt i;
- for(i=0;i<uReadThis;i++)
- pfile_in_zip_read_info->read_buffer[i] =
- zdecode(s->keys,s->pcrc_32_tab,
- pfile_in_zip_read_info->read_buffer[i]);
- }
-# endif
-
-
- pfile_in_zip_read_info->pos_in_zipfile += uReadThis;
-
- pfile_in_zip_read_info->rest_read_compressed-=uReadThis;
-
- pfile_in_zip_read_info->stream.next_in =
- (Bytef*)pfile_in_zip_read_info->read_buffer;
- pfile_in_zip_read_info->stream.avail_in = (uInt)uReadThis;
- }
-
- if ((pfile_in_zip_read_info->compression_method==0) || (pfile_in_zip_read_info->raw))
- {
- uInt uDoCopy,i ;
-
- if ((pfile_in_zip_read_info->stream.avail_in == 0) &&
- (pfile_in_zip_read_info->rest_read_compressed == 0))
- return (iRead==0) ? UNZ_EOF : iRead;
-
- if (pfile_in_zip_read_info->stream.avail_out <
- pfile_in_zip_read_info->stream.avail_in)
- uDoCopy = pfile_in_zip_read_info->stream.avail_out ;
- else
- uDoCopy = pfile_in_zip_read_info->stream.avail_in ;
-
- for (i=0;i<uDoCopy;i++)
- *(pfile_in_zip_read_info->stream.next_out+i) =
- *(pfile_in_zip_read_info->stream.next_in+i);
-
- pfile_in_zip_read_info->total_out_64 = pfile_in_zip_read_info->total_out_64 + uDoCopy;
-
- pfile_in_zip_read_info->crc32 = crc32(pfile_in_zip_read_info->crc32,
- pfile_in_zip_read_info->stream.next_out,
- uDoCopy);
- pfile_in_zip_read_info->rest_read_uncompressed-=uDoCopy;
- pfile_in_zip_read_info->stream.avail_in -= uDoCopy;
- pfile_in_zip_read_info->stream.avail_out -= uDoCopy;
- pfile_in_zip_read_info->stream.next_out += uDoCopy;
- pfile_in_zip_read_info->stream.next_in += uDoCopy;
- pfile_in_zip_read_info->stream.total_out += uDoCopy;
- iRead += uDoCopy;
- }
- else if (pfile_in_zip_read_info->compression_method==Z_BZIP2ED)
- {
-#ifdef HAVE_BZIP2
- uLong uTotalOutBefore,uTotalOutAfter;
- const Bytef *bufBefore;
- uLong uOutThis;
-
- pfile_in_zip_read_info->bstream.next_in = (char*)pfile_in_zip_read_info->stream.next_in;
- pfile_in_zip_read_info->bstream.avail_in = pfile_in_zip_read_info->stream.avail_in;
- pfile_in_zip_read_info->bstream.total_in_lo32 = pfile_in_zip_read_info->stream.total_in;
- pfile_in_zip_read_info->bstream.total_in_hi32 = 0;
- pfile_in_zip_read_info->bstream.next_out = (char*)pfile_in_zip_read_info->stream.next_out;
- pfile_in_zip_read_info->bstream.avail_out = pfile_in_zip_read_info->stream.avail_out;
- pfile_in_zip_read_info->bstream.total_out_lo32 = pfile_in_zip_read_info->stream.total_out;
- pfile_in_zip_read_info->bstream.total_out_hi32 = 0;
-
- uTotalOutBefore = pfile_in_zip_read_info->bstream.total_out_lo32;
- bufBefore = (const Bytef *)pfile_in_zip_read_info->bstream.next_out;
-
- err=BZ2_bzDecompress(&pfile_in_zip_read_info->bstream);
-
- uTotalOutAfter = pfile_in_zip_read_info->bstream.total_out_lo32;
- uOutThis = uTotalOutAfter-uTotalOutBefore;
-
- pfile_in_zip_read_info->total_out_64 = pfile_in_zip_read_info->total_out_64 + uOutThis;
-
- pfile_in_zip_read_info->crc32 = crc32(pfile_in_zip_read_info->crc32,bufBefore, (uInt)(uOutThis));
- pfile_in_zip_read_info->rest_read_uncompressed -= uOutThis;
- iRead += (uInt)(uTotalOutAfter - uTotalOutBefore);
-
- pfile_in_zip_read_info->stream.next_in = (Bytef*)pfile_in_zip_read_info->bstream.next_in;
- pfile_in_zip_read_info->stream.avail_in = pfile_in_zip_read_info->bstream.avail_in;
- pfile_in_zip_read_info->stream.total_in = pfile_in_zip_read_info->bstream.total_in_lo32;
- pfile_in_zip_read_info->stream.next_out = (Bytef*)pfile_in_zip_read_info->bstream.next_out;
- pfile_in_zip_read_info->stream.avail_out = pfile_in_zip_read_info->bstream.avail_out;
- pfile_in_zip_read_info->stream.total_out = pfile_in_zip_read_info->bstream.total_out_lo32;
-
- if (err==BZ_STREAM_END)
- return (iRead==0) ? UNZ_EOF : iRead;
- if (err!=BZ_OK)
- break;
-#endif
- } // end Z_BZIP2ED
- else
- {
- ZPOS64_T uTotalOutBefore,uTotalOutAfter;
- const Bytef *bufBefore;
- ZPOS64_T uOutThis;
- int flush=Z_SYNC_FLUSH;
-
- uTotalOutBefore = pfile_in_zip_read_info->stream.total_out;
- bufBefore = pfile_in_zip_read_info->stream.next_out;
-
- /*
- if ((pfile_in_zip_read_info->rest_read_uncompressed ==
- pfile_in_zip_read_info->stream.avail_out) &&
- (pfile_in_zip_read_info->rest_read_compressed == 0))
- flush = Z_FINISH;
- */
- err=inflate(&pfile_in_zip_read_info->stream,flush);
-
- if ((err>=0) && (pfile_in_zip_read_info->stream.msg!=NULL))
- err = Z_DATA_ERROR;
-
- uTotalOutAfter = pfile_in_zip_read_info->stream.total_out;
- uOutThis = uTotalOutAfter-uTotalOutBefore;
-
- pfile_in_zip_read_info->total_out_64 = pfile_in_zip_read_info->total_out_64 + uOutThis;
-
- pfile_in_zip_read_info->crc32 =
- crc32(pfile_in_zip_read_info->crc32,bufBefore,
- (uInt)(uOutThis));
-
- pfile_in_zip_read_info->rest_read_uncompressed -=
- uOutThis;
-
- iRead += (uInt)(uTotalOutAfter - uTotalOutBefore);
-
- if (err==Z_STREAM_END)
- return (iRead==0) ? UNZ_EOF : iRead;
- if (err!=Z_OK)
- break;
- }
- }
-
- if (err==Z_OK)
- return iRead;
- return err;
-}
-
-
-/*
- Give the current position in uncompressed data
-*/
-extern z_off_t ZEXPORT unztell (unzFile file)
-{
- unz64_s* s;
- file_in_zip64_read_info_s* pfile_in_zip_read_info;
- if (file==NULL)
- return UNZ_PARAMERROR;
- s=(unz64_s*)file;
- pfile_in_zip_read_info=s->pfile_in_zip_read;
-
- if (pfile_in_zip_read_info==NULL)
- return UNZ_PARAMERROR;
-
- return (z_off_t)pfile_in_zip_read_info->stream.total_out;
-}
-
-extern ZPOS64_T ZEXPORT unztell64 (unzFile file)
-{
-
- unz64_s* s;
- file_in_zip64_read_info_s* pfile_in_zip_read_info;
- if (file==NULL)
- return (ZPOS64_T)-1;
- s=(unz64_s*)file;
- pfile_in_zip_read_info=s->pfile_in_zip_read;
-
- if (pfile_in_zip_read_info==NULL)
- return (ZPOS64_T)-1;
-
- return pfile_in_zip_read_info->total_out_64;
-}
-
-
-/*
- return 1 if the end of file was reached, 0 elsewhere
-*/
-extern int ZEXPORT unzeof (unzFile file)
-{
- unz64_s* s;
- file_in_zip64_read_info_s* pfile_in_zip_read_info;
- if (file==NULL)
- return UNZ_PARAMERROR;
- s=(unz64_s*)file;
- pfile_in_zip_read_info=s->pfile_in_zip_read;
-
- if (pfile_in_zip_read_info==NULL)
- return UNZ_PARAMERROR;
-
- if (pfile_in_zip_read_info->rest_read_uncompressed == 0)
- return 1;
- else
- return 0;
-}
-
-
-
-/*
-Read extra field from the current file (opened by unzOpenCurrentFile)
-This is the local-header version of the extra field (sometimes, there is
-more info in the local-header version than in the central-header)
-
- if buf==NULL, it return the size of the local extra field that can be read
-
- if buf!=NULL, len is the size of the buffer, the extra header is copied in
- buf.
- the return value is the number of bytes copied in buf, or (if <0)
- the error code
-*/
-extern int ZEXPORT unzGetLocalExtrafield (unzFile file, voidp buf, unsigned len)
-{
- unz64_s* s;
- file_in_zip64_read_info_s* pfile_in_zip_read_info;
- uInt read_now;
- ZPOS64_T size_to_read;
-
- if (file==NULL)
- return UNZ_PARAMERROR;
- s=(unz64_s*)file;
- pfile_in_zip_read_info=s->pfile_in_zip_read;
-
- if (pfile_in_zip_read_info==NULL)
- return UNZ_PARAMERROR;
-
- size_to_read = (pfile_in_zip_read_info->size_local_extrafield -
- pfile_in_zip_read_info->pos_local_extrafield);
-
- if (buf==NULL)
- return (int)size_to_read;
-
- if (len>size_to_read)
- read_now = (uInt)size_to_read;
- else
- read_now = (uInt)len ;
-
- if (read_now==0)
- return 0;
-
- if (ZSEEK64(pfile_in_zip_read_info->z_filefunc,
- pfile_in_zip_read_info->filestream,
- pfile_in_zip_read_info->offset_local_extrafield +
- pfile_in_zip_read_info->pos_local_extrafield,
- ZLIB_FILEFUNC_SEEK_SET)!=0)
- return UNZ_ERRNO;
-
- if (ZREAD64(pfile_in_zip_read_info->z_filefunc,
- pfile_in_zip_read_info->filestream,
- buf,read_now)!=read_now)
- return UNZ_ERRNO;
-
- return (int)read_now;
-}
-
-/*
- Close the file in zip opened with unzOpenCurrentFile
- Return UNZ_CRCERROR if all the file was read but the CRC is not good
-*/
-extern int ZEXPORT unzCloseCurrentFile (unzFile file)
-{
- int err=UNZ_OK;
-
- unz64_s* s;
- file_in_zip64_read_info_s* pfile_in_zip_read_info;
- if (file==NULL)
- return UNZ_PARAMERROR;
- s=(unz64_s*)file;
- pfile_in_zip_read_info=s->pfile_in_zip_read;
-
- if (pfile_in_zip_read_info==NULL)
- return UNZ_PARAMERROR;
-
-
- if ((pfile_in_zip_read_info->rest_read_uncompressed == 0) &&
- (!pfile_in_zip_read_info->raw))
- {
- if (pfile_in_zip_read_info->crc32 != pfile_in_zip_read_info->crc32_wait)
- err=UNZ_CRCERROR;
- }
-
-
- TRYFREE(pfile_in_zip_read_info->read_buffer);
- pfile_in_zip_read_info->read_buffer = NULL;
- if (pfile_in_zip_read_info->stream_initialised == Z_DEFLATED)
- inflateEnd(&pfile_in_zip_read_info->stream);
-#ifdef HAVE_BZIP2
- else if (pfile_in_zip_read_info->stream_initialised == Z_BZIP2ED)
- BZ2_bzDecompressEnd(&pfile_in_zip_read_info->bstream);
-#endif
-
-
- pfile_in_zip_read_info->stream_initialised = 0;
- TRYFREE(pfile_in_zip_read_info);
-
- s->pfile_in_zip_read=NULL;
-
- return err;
-}
-
-
-/*
- Get the global comment string of the ZipFile, in the szComment buffer.
- uSizeBuf is the size of the szComment buffer.
- return the number of byte copied or an error code <0
-*/
-extern int ZEXPORT unzGetGlobalComment (unzFile file, char * szComment, uLong uSizeBuf)
-{
- unz64_s* s;
- uLong uReadThis ;
- if (file==NULL)
- return (int)UNZ_PARAMERROR;
- s=(unz64_s*)file;
-
- uReadThis = uSizeBuf;
- if (uReadThis>s->gi.size_comment)
- uReadThis = s->gi.size_comment;
-
- if (ZSEEK64(s->z_filefunc,s->filestream,s->central_pos+22,ZLIB_FILEFUNC_SEEK_SET)!=0)
- return UNZ_ERRNO;
-
- if (uReadThis>0)
- {
- *szComment='\0';
- if (ZREAD64(s->z_filefunc,s->filestream,szComment,uReadThis)!=uReadThis)
- return UNZ_ERRNO;
- }
-
- if ((szComment != NULL) && (uSizeBuf > s->gi.size_comment))
- *(szComment+s->gi.size_comment)='\0';
- return (int)uReadThis;
-}
-
-/* Additions by RX '2004 */
-extern ZPOS64_T ZEXPORT unzGetOffset64(unzFile file)
-{
- unz64_s* s;
-
- if (file==NULL)
- return 0; //UNZ_PARAMERROR;
- s=(unz64_s*)file;
- if (!s->current_file_ok)
- return 0;
- if (s->gi.number_entry != 0 && s->gi.number_entry != 0xffff)
- if (s->num_file==s->gi.number_entry)
- return 0;
- return s->pos_in_central_dir;
-}
-
-extern uLong ZEXPORT unzGetOffset (unzFile file)
-{
- ZPOS64_T offset64;
-
- if (file==NULL)
- return 0; //UNZ_PARAMERROR;
- offset64 = unzGetOffset64(file);
- return (uLong)offset64;
-}
-
-extern int ZEXPORT unzSetOffset64(unzFile file, ZPOS64_T pos)
-{
- unz64_s* s;
- int err;
-
- if (file==NULL)
- return UNZ_PARAMERROR;
- s=(unz64_s*)file;
-
- s->pos_in_central_dir = pos;
- s->num_file = s->gi.number_entry; /* hack */
- err = unz64local_GetCurrentFileInfoInternal(file,&s->cur_file_info,
- &s->cur_file_info_internal,
- NULL,0,NULL,0,NULL,0);
- s->current_file_ok = (err == UNZ_OK);
- return err;
-}
-
-extern int ZEXPORT unzSetOffset (unzFile file, uLong pos)
-{
- return unzSetOffset64(file,pos);
-}
diff --git a/third-party/zlib/contrib/minizip/unzip.h b/third-party/zlib/contrib/minizip/unzip.h
deleted file mode 100644
index 2104e39..0000000
--- a/third-party/zlib/contrib/minizip/unzip.h
+++ /dev/null
@@ -1,437 +0,0 @@
-/* unzip.h -- IO for uncompress .zip files using zlib
- Version 1.1, February 14h, 2010
- part of the MiniZip project - ( http://www.winimage.com/zLibDll/minizip.html )
-
- Copyright (C) 1998-2010 Gilles Vollant (minizip) ( http://www.winimage.com/zLibDll/minizip.html )
-
- Modifications of Unzip for Zip64
- Copyright (C) 2007-2008 Even Rouault
-
- Modifications for Zip64 support on both zip and unzip
- Copyright (C) 2009-2010 Mathias Svensson ( http://result42.com )
-
- For more info read MiniZip_info.txt
-
- ---------------------------------------------------------------------------------
-
- Condition of use and distribution are the same than zlib :
-
- This software is provided 'as-is', without any express or implied
- warranty. In no event will the authors be held liable for any damages
- arising from the use of this software.
-
- Permission is granted to anyone to use this software for any purpose,
- including commercial applications, and to alter it and redistribute it
- freely, subject to the following restrictions:
-
- 1. The origin of this software must not be misrepresented; you must not
- claim that you wrote the original software. If you use this software
- in a product, an acknowledgment in the product documentation would be
- appreciated but is not required.
- 2. Altered source versions must be plainly marked as such, and must not be
- misrepresented as being the original software.
- 3. This notice may not be removed or altered from any source distribution.
-
- ---------------------------------------------------------------------------------
-
- Changes
-
- See header of unzip64.c
-
-*/
-
-#ifndef _unz64_H
-#define _unz64_H
-
-#ifdef __cplusplus
-extern "C" {
-#endif
-
-#ifndef _ZLIB_H
-#include "zlib.h"
-#endif
-
-#ifndef _ZLIBIOAPI_H
-#include "ioapi.h"
-#endif
-
-#ifdef HAVE_BZIP2
-#include "bzlib.h"
-#endif
-
-#define Z_BZIP2ED 12
-
-#if defined(STRICTUNZIP) || defined(STRICTZIPUNZIP)
-/* like the STRICT of WIN32, we define a pointer that cannot be converted
- from (void*) without cast */
-typedef struct TagunzFile__ { int unused; } unzFile__;
-typedef unzFile__ *unzFile;
-#else
-typedef voidp unzFile;
-#endif
-
-
-#define UNZ_OK (0)
-#define UNZ_END_OF_LIST_OF_FILE (-100)
-#define UNZ_ERRNO (Z_ERRNO)
-#define UNZ_EOF (0)
-#define UNZ_PARAMERROR (-102)
-#define UNZ_BADZIPFILE (-103)
-#define UNZ_INTERNALERROR (-104)
-#define UNZ_CRCERROR (-105)
-
-/* tm_unz contain date/time info */
-typedef struct tm_unz_s
-{
- uInt tm_sec; /* seconds after the minute - [0,59] */
- uInt tm_min; /* minutes after the hour - [0,59] */
- uInt tm_hour; /* hours since midnight - [0,23] */
- uInt tm_mday; /* day of the month - [1,31] */
- uInt tm_mon; /* months since January - [0,11] */
- uInt tm_year; /* years - [1980..2044] */
-} tm_unz;
-
-/* unz_global_info structure contain global data about the ZIPfile
- These data comes from the end of central dir */
-typedef struct unz_global_info64_s
-{
- ZPOS64_T number_entry; /* total number of entries in
- the central dir on this disk */
- uLong size_comment; /* size of the global comment of the zipfile */
-} unz_global_info64;
-
-typedef struct unz_global_info_s
-{
- uLong number_entry; /* total number of entries in
- the central dir on this disk */
- uLong size_comment; /* size of the global comment of the zipfile */
-} unz_global_info;
-
-/* unz_file_info contain information about a file in the zipfile */
-typedef struct unz_file_info64_s
-{
- uLong version; /* version made by 2 bytes */
- uLong version_needed; /* version needed to extract 2 bytes */
- uLong flag; /* general purpose bit flag 2 bytes */
- uLong compression_method; /* compression method 2 bytes */
- uLong dosDate; /* last mod file date in Dos fmt 4 bytes */
- uLong crc; /* crc-32 4 bytes */
- ZPOS64_T compressed_size; /* compressed size 8 bytes */
- ZPOS64_T uncompressed_size; /* uncompressed size 8 bytes */
- uLong size_filename; /* filename length 2 bytes */
- uLong size_file_extra; /* extra field length 2 bytes */
- uLong size_file_comment; /* file comment length 2 bytes */
-
- uLong disk_num_start; /* disk number start 2 bytes */
- uLong internal_fa; /* internal file attributes 2 bytes */
- uLong external_fa; /* external file attributes 4 bytes */
-
- tm_unz tmu_date;
-} unz_file_info64;
-
-typedef struct unz_file_info_s
-{
- uLong version; /* version made by 2 bytes */
- uLong version_needed; /* version needed to extract 2 bytes */
- uLong flag; /* general purpose bit flag 2 bytes */
- uLong compression_method; /* compression method 2 bytes */
- uLong dosDate; /* last mod file date in Dos fmt 4 bytes */
- uLong crc; /* crc-32 4 bytes */
- uLong compressed_size; /* compressed size 4 bytes */
- uLong uncompressed_size; /* uncompressed size 4 bytes */
- uLong size_filename; /* filename length 2 bytes */
- uLong size_file_extra; /* extra field length 2 bytes */
- uLong size_file_comment; /* file comment length 2 bytes */
-
- uLong disk_num_start; /* disk number start 2 bytes */
- uLong internal_fa; /* internal file attributes 2 bytes */
- uLong external_fa; /* external file attributes 4 bytes */
-
- tm_unz tmu_date;
-} unz_file_info;
-
-extern int ZEXPORT unzStringFileNameCompare OF ((const char* fileName1,
- const char* fileName2,
- int iCaseSensitivity));
-/*
- Compare two filename (fileName1,fileName2).
- If iCaseSenisivity = 1, comparision is case sensitivity (like strcmp)
- If iCaseSenisivity = 2, comparision is not case sensitivity (like strcmpi
- or strcasecmp)
- If iCaseSenisivity = 0, case sensitivity is defaut of your operating system
- (like 1 on Unix, 2 on Windows)
-*/
-
-
-extern unzFile ZEXPORT unzOpen OF((const char *path));
-extern unzFile ZEXPORT unzOpen64 OF((const void *path));
-/*
- Open a Zip file. path contain the full pathname (by example,
- on a Windows XP computer "c:\\zlib\\zlib113.zip" or on an Unix computer
- "zlib/zlib113.zip".
- If the zipfile cannot be opened (file don't exist or in not valid), the
- return value is NULL.
- Else, the return value is a unzFile Handle, usable with other function
- of this unzip package.
- the "64" function take a const void* pointer, because the path is just the
- value passed to the open64_file_func callback.
- Under Windows, if UNICODE is defined, using fill_fopen64_filefunc, the path
- is a pointer to a wide unicode string (LPCTSTR is LPCWSTR), so const char*
- does not describe the reality
-*/
-
-
-extern unzFile ZEXPORT unzOpen2 OF((const char *path,
- zlib_filefunc_def* pzlib_filefunc_def));
-/*
- Open a Zip file, like unzOpen, but provide a set of file low level API
- for read/write the zip file (see ioapi.h)
-*/
-
-extern unzFile ZEXPORT unzOpen2_64 OF((const void *path,
- zlib_filefunc64_def* pzlib_filefunc_def));
-/*
- Open a Zip file, like unz64Open, but provide a set of file low level API
- for read/write the zip file (see ioapi.h)
-*/
-
-extern int ZEXPORT unzClose OF((unzFile file));
-/*
- Close a ZipFile opened with unzOpen.
- If there is files inside the .Zip opened with unzOpenCurrentFile (see later),
- these files MUST be closed with unzCloseCurrentFile before call unzClose.
- return UNZ_OK if there is no problem. */
-
-extern int ZEXPORT unzGetGlobalInfo OF((unzFile file,
- unz_global_info *pglobal_info));
-
-extern int ZEXPORT unzGetGlobalInfo64 OF((unzFile file,
- unz_global_info64 *pglobal_info));
-/*
- Write info about the ZipFile in the *pglobal_info structure.
- No preparation of the structure is needed
- return UNZ_OK if there is no problem. */
-
-
-extern int ZEXPORT unzGetGlobalComment OF((unzFile file,
- char *szComment,
- uLong uSizeBuf));
-/*
- Get the global comment string of the ZipFile, in the szComment buffer.
- uSizeBuf is the size of the szComment buffer.
- return the number of byte copied or an error code <0
-*/
-
-
-/***************************************************************************/
-/* Unzip package allow you browse the directory of the zipfile */
-
-extern int ZEXPORT unzGoToFirstFile OF((unzFile file));
-/*
- Set the current file of the zipfile to the first file.
- return UNZ_OK if there is no problem
-*/
-
-extern int ZEXPORT unzGoToNextFile OF((unzFile file));
-/*
- Set the current file of the zipfile to the next file.
- return UNZ_OK if there is no problem
- return UNZ_END_OF_LIST_OF_FILE if the actual file was the latest.
-*/
-
-extern int ZEXPORT unzLocateFile OF((unzFile file,
- const char *szFileName,
- int iCaseSensitivity));
-/*
- Try locate the file szFileName in the zipfile.
- For the iCaseSensitivity signification, see unzStringFileNameCompare
-
- return value :
- UNZ_OK if the file is found. It becomes the current file.
- UNZ_END_OF_LIST_OF_FILE if the file is not found
-*/
-
-
-/* ****************************************** */
-/* Ryan supplied functions */
-/* unz_file_info contain information about a file in the zipfile */
-typedef struct unz_file_pos_s
-{
- uLong pos_in_zip_directory; /* offset in zip file directory */
- uLong num_of_file; /* # of file */
-} unz_file_pos;
-
-extern int ZEXPORT unzGetFilePos(
- unzFile file,
- unz_file_pos* file_pos);
-
-extern int ZEXPORT unzGoToFilePos(
- unzFile file,
- unz_file_pos* file_pos);
-
-typedef struct unz64_file_pos_s
-{
- ZPOS64_T pos_in_zip_directory; /* offset in zip file directory */
- ZPOS64_T num_of_file; /* # of file */
-} unz64_file_pos;
-
-extern int ZEXPORT unzGetFilePos64(
- unzFile file,
- unz64_file_pos* file_pos);
-
-extern int ZEXPORT unzGoToFilePos64(
- unzFile file,
- const unz64_file_pos* file_pos);
-
-/* ****************************************** */
-
-extern int ZEXPORT unzGetCurrentFileInfo64 OF((unzFile file,
- unz_file_info64 *pfile_info,
- char *szFileName,
- uLong fileNameBufferSize,
- void *extraField,
- uLong extraFieldBufferSize,
- char *szComment,
- uLong commentBufferSize));
-
-extern int ZEXPORT unzGetCurrentFileInfo OF((unzFile file,
- unz_file_info *pfile_info,
- char *szFileName,
- uLong fileNameBufferSize,
- void *extraField,
- uLong extraFieldBufferSize,
- char *szComment,
- uLong commentBufferSize));
-/*
- Get Info about the current file
- if pfile_info!=NULL, the *pfile_info structure will contain somes info about
- the current file
- if szFileName!=NULL, the filemane string will be copied in szFileName
- (fileNameBufferSize is the size of the buffer)
- if extraField!=NULL, the extra field information will be copied in extraField
- (extraFieldBufferSize is the size of the buffer).
- This is the Central-header version of the extra field
- if szComment!=NULL, the comment string of the file will be copied in szComment
- (commentBufferSize is the size of the buffer)
-*/
-
-
-/** Addition for GDAL : START */
-
-extern ZPOS64_T ZEXPORT unzGetCurrentFileZStreamPos64 OF((unzFile file));
-
-/** Addition for GDAL : END */
-
-
-/***************************************************************************/
-/* for reading the content of the current zipfile, you can open it, read data
- from it, and close it (you can close it before reading all the file)
- */
-
-extern int ZEXPORT unzOpenCurrentFile OF((unzFile file));
-/*
- Open for reading data the current file in the zipfile.
- If there is no error, the return value is UNZ_OK.
-*/
-
-extern int ZEXPORT unzOpenCurrentFilePassword OF((unzFile file,
- const char* password));
-/*
- Open for reading data the current file in the zipfile.
- password is a crypting password
- If there is no error, the return value is UNZ_OK.
-*/
-
-extern int ZEXPORT unzOpenCurrentFile2 OF((unzFile file,
- int* method,
- int* level,
- int raw));
-/*
- Same than unzOpenCurrentFile, but open for read raw the file (not uncompress)
- if raw==1
- *method will receive method of compression, *level will receive level of
- compression
- note : you can set level parameter as NULL (if you did not want known level,
- but you CANNOT set method parameter as NULL
-*/
-
-extern int ZEXPORT unzOpenCurrentFile3 OF((unzFile file,
- int* method,
- int* level,
- int raw,
- const char* password));
-/*
- Same than unzOpenCurrentFile, but open for read raw the file (not uncompress)
- if raw==1
- *method will receive method of compression, *level will receive level of
- compression
- note : you can set level parameter as NULL (if you did not want known level,
- but you CANNOT set method parameter as NULL
-*/
-
-
-extern int ZEXPORT unzCloseCurrentFile OF((unzFile file));
-/*
- Close the file in zip opened with unzOpenCurrentFile
- Return UNZ_CRCERROR if all the file was read but the CRC is not good
-*/
-
-extern int ZEXPORT unzReadCurrentFile OF((unzFile file,
- voidp buf,
- unsigned len));
-/*
- Read bytes from the current file (opened by unzOpenCurrentFile)
- buf contain buffer where data must be copied
- len the size of buf.
-
- return the number of byte copied if somes bytes are copied
- return 0 if the end of file was reached
- return <0 with error code if there is an error
- (UNZ_ERRNO for IO error, or zLib error for uncompress error)
-*/
-
-extern z_off_t ZEXPORT unztell OF((unzFile file));
-
-extern ZPOS64_T ZEXPORT unztell64 OF((unzFile file));
-/*
- Give the current position in uncompressed data
-*/
-
-extern int ZEXPORT unzeof OF((unzFile file));
-/*
- return 1 if the end of file was reached, 0 elsewhere
-*/
-
-extern int ZEXPORT unzGetLocalExtrafield OF((unzFile file,
- voidp buf,
- unsigned len));
-/*
- Read extra field from the current file (opened by unzOpenCurrentFile)
- This is the local-header version of the extra field (sometimes, there is
- more info in the local-header version than in the central-header)
-
- if buf==NULL, it return the size of the local extra field
-
- if buf!=NULL, len is the size of the buffer, the extra header is copied in
- buf.
- the return value is the number of bytes copied in buf, or (if <0)
- the error code
-*/
-
-/***************************************************************************/
-
-/* Get the current file offset */
-extern ZPOS64_T ZEXPORT unzGetOffset64 (unzFile file);
-extern uLong ZEXPORT unzGetOffset (unzFile file);
-
-/* Set the current file offset */
-extern int ZEXPORT unzSetOffset64 (unzFile file, ZPOS64_T pos);
-extern int ZEXPORT unzSetOffset (unzFile file, uLong pos);
-
-
-
-#ifdef __cplusplus
-}
-#endif
-
-#endif /* _unz64_H */
diff --git a/third-party/zlib/contrib/minizip/zip.c b/third-party/zlib/contrib/minizip/zip.c
deleted file mode 100644
index ea54853..0000000
--- a/third-party/zlib/contrib/minizip/zip.c
+++ /dev/null
@@ -1,2007 +0,0 @@
-/* zip.c -- IO on .zip files using zlib
- Version 1.1, February 14h, 2010
- part of the MiniZip project - ( http://www.winimage.com/zLibDll/minizip.html )
-
- Copyright (C) 1998-2010 Gilles Vollant (minizip) ( http://www.winimage.com/zLibDll/minizip.html )
-
- Modifications for Zip64 support
- Copyright (C) 2009-2010 Mathias Svensson ( http://result42.com )
-
- For more info read MiniZip_info.txt
-
- Changes
- Oct-2009 - Mathias Svensson - Remove old C style function prototypes
- Oct-2009 - Mathias Svensson - Added Zip64 Support when creating new file archives
- Oct-2009 - Mathias Svensson - Did some code cleanup and refactoring to get better overview of some functions.
- Oct-2009 - Mathias Svensson - Added zipRemoveExtraInfoBlock to strip extra field data from its ZIP64 data
- It is used when recreting zip archive with RAW when deleting items from a zip.
- ZIP64 data is automaticly added to items that needs it, and existing ZIP64 data need to be removed.
- Oct-2009 - Mathias Svensson - Added support for BZIP2 as compression mode (bzip2 lib is required)
- Jan-2010 - back to unzip and minizip 1.0 name scheme, with compatibility layer
-
-*/
-
-
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
-#include <time.h>
-#include "zlib.h"
-#include "zip.h"
-
-#ifdef STDC
-# include <stddef.h>
-# include <string.h>
-# include <stdlib.h>
-#endif
-#ifdef NO_ERRNO_H
- extern int errno;
-#else
-# include <errno.h>
-#endif
-
-
-#ifndef local
-# define local static
-#endif
-/* compile with -Dlocal if your debugger can't find static symbols */
-
-#ifndef VERSIONMADEBY
-# define VERSIONMADEBY (0x0) /* platform depedent */
-#endif
-
-#ifndef Z_BUFSIZE
-#define Z_BUFSIZE (64*1024) //(16384)
-#endif
-
-#ifndef Z_MAXFILENAMEINZIP
-#define Z_MAXFILENAMEINZIP (256)
-#endif
-
-#ifndef ALLOC
-# define ALLOC(size) (malloc(size))
-#endif
-#ifndef TRYFREE
-# define TRYFREE(p) {if (p) free(p);}
-#endif
-
-/*
-#define SIZECENTRALDIRITEM (0x2e)
-#define SIZEZIPLOCALHEADER (0x1e)
-*/
-
-/* I've found an old Unix (a SunOS 4.1.3_U1) without all SEEK_* defined.... */
-
-
-// NOT sure that this work on ALL platform
-#define MAKEULONG64(a, b) ((ZPOS64_T)(((unsigned long)(a)) | ((ZPOS64_T)((unsigned long)(b))) << 32))
-
-#ifndef SEEK_CUR
-#define SEEK_CUR 1
-#endif
-
-#ifndef SEEK_END
-#define SEEK_END 2
-#endif
-
-#ifndef SEEK_SET
-#define SEEK_SET 0
-#endif
-
-#ifndef DEF_MEM_LEVEL
-#if MAX_MEM_LEVEL >= 8
-# define DEF_MEM_LEVEL 8
-#else
-# define DEF_MEM_LEVEL MAX_MEM_LEVEL
-#endif
-#endif
-const char zip_copyright[] =" zip 1.01 Copyright 1998-2004 Gilles Vollant - http://www.winimage.com/zLibDll";
-
-
-#define SIZEDATA_INDATABLOCK (4096-(4*4))
-
-#define LOCALHEADERMAGIC (0x04034b50)
-#define CENTRALHEADERMAGIC (0x02014b50)
-#define ENDHEADERMAGIC (0x06054b50)
-#define ZIP64ENDHEADERMAGIC (0x6064b50)
-#define ZIP64ENDLOCHEADERMAGIC (0x7064b50)
-
-#define FLAG_LOCALHEADER_OFFSET (0x06)
-#define CRC_LOCALHEADER_OFFSET (0x0e)
-
-#define SIZECENTRALHEADER (0x2e) /* 46 */
-
-typedef struct linkedlist_datablock_internal_s
-{
- struct linkedlist_datablock_internal_s* next_datablock;
- uLong avail_in_this_block;
- uLong filled_in_this_block;
- uLong unused; /* for future use and alignement */
- unsigned char data[SIZEDATA_INDATABLOCK];
-} linkedlist_datablock_internal;
-
-typedef struct linkedlist_data_s
-{
- linkedlist_datablock_internal* first_block;
- linkedlist_datablock_internal* last_block;
-} linkedlist_data;
-
-
-typedef struct
-{
- z_stream stream; /* zLib stream structure for inflate */
-#ifdef HAVE_BZIP2
- bz_stream bstream; /* bzLib stream structure for bziped */
-#endif
-
- int stream_initialised; /* 1 is stream is initialised */
- uInt pos_in_buffered_data; /* last written byte in buffered_data */
-
- ZPOS64_T pos_local_header; /* offset of the local header of the file
- currenty writing */
- char* central_header; /* central header data for the current file */
- uLong size_centralExtra;
- uLong size_centralheader; /* size of the central header for cur file */
- uLong size_centralExtraFree; /* Extra bytes allocated to the centralheader but that are not used */
- uLong flag; /* flag of the file currently writing */
-
- int method; /* compression method of file currenty wr.*/
- int raw; /* 1 for directly writing raw data */
- Byte buffered_data[Z_BUFSIZE];/* buffer contain compressed data to be writ*/
- uLong dosDate;
- uLong crc32;
- int encrypt;
- int zip64; /* Add ZIP64 extened information in the extra field */
- ZPOS64_T pos_zip64extrainfo;
- ZPOS64_T totalCompressedData;
- ZPOS64_T totalUncompressedData;
-#ifndef NOCRYPT
- unsigned long keys[3]; /* keys defining the pseudo-random sequence */
- const z_crc_t* pcrc_32_tab;
- int crypt_header_size;
-#endif
-} curfile64_info;
-
-typedef struct
-{
- zlib_filefunc64_32_def z_filefunc;
- voidpf filestream; /* io structore of the zipfile */
- linkedlist_data central_dir;/* datablock with central dir in construction*/
- int in_opened_file_inzip; /* 1 if a file in the zip is currently writ.*/
- curfile64_info ci; /* info on the file curretly writing */
-
- ZPOS64_T begin_pos; /* position of the beginning of the zipfile */
- ZPOS64_T add_position_when_writting_offset;
- ZPOS64_T number_entry;
-
-#ifndef NO_ADDFILEINEXISTINGZIP
- char *globalcomment;
-#endif
-
-} zip64_internal;
-
-
-#ifndef NOCRYPT
-#define INCLUDECRYPTINGCODE_IFCRYPTALLOWED
-#include "crypt.h"
-#endif
-
-local linkedlist_datablock_internal* allocate_new_datablock()
-{
- linkedlist_datablock_internal* ldi;
- ldi = (linkedlist_datablock_internal*)
- ALLOC(sizeof(linkedlist_datablock_internal));
- if (ldi!=NULL)
- {
- ldi->next_datablock = NULL ;
- ldi->filled_in_this_block = 0 ;
- ldi->avail_in_this_block = SIZEDATA_INDATABLOCK ;
- }
- return ldi;
-}
-
-local void free_datablock(linkedlist_datablock_internal* ldi)
-{
- while (ldi!=NULL)
- {
- linkedlist_datablock_internal* ldinext = ldi->next_datablock;
- TRYFREE(ldi);
- ldi = ldinext;
- }
-}
-
-local void init_linkedlist(linkedlist_data* ll)
-{
- ll->first_block = ll->last_block = NULL;
-}
-
-local void free_linkedlist(linkedlist_data* ll)
-{
- free_datablock(ll->first_block);
- ll->first_block = ll->last_block = NULL;
-}
-
-
-local int add_data_in_datablock(linkedlist_data* ll, const void* buf, uLong len)
-{
- linkedlist_datablock_internal* ldi;
- const unsigned char* from_copy;
-
- if (ll==NULL)
- return ZIP_INTERNALERROR;
-
- if (ll->last_block == NULL)
- {
- ll->first_block = ll->last_block = allocate_new_datablock();
- if (ll->first_block == NULL)
- return ZIP_INTERNALERROR;
- }
-
- ldi = ll->last_block;
- from_copy = (unsigned char*)buf;
-
- while (len>0)
- {
- uInt copy_this;
- uInt i;
- unsigned char* to_copy;
-
- if (ldi->avail_in_this_block==0)
- {
- ldi->next_datablock = allocate_new_datablock();
- if (ldi->next_datablock == NULL)
- return ZIP_INTERNALERROR;
- ldi = ldi->next_datablock ;
- ll->last_block = ldi;
- }
-
- if (ldi->avail_in_this_block < len)
- copy_this = (uInt)ldi->avail_in_this_block;
- else
- copy_this = (uInt)len;
-
- to_copy = &(ldi->data[ldi->filled_in_this_block]);
-
- for (i=0;i<copy_this;i++)
- *(to_copy+i)=*(from_copy+i);
-
- ldi->filled_in_this_block += copy_this;
- ldi->avail_in_this_block -= copy_this;
- from_copy += copy_this ;
- len -= copy_this;
- }
- return ZIP_OK;
-}
-
-
-
-/****************************************************************************/
-
-#ifndef NO_ADDFILEINEXISTINGZIP
-/* ===========================================================================
- Inputs a long in LSB order to the given file
- nbByte == 1, 2 ,4 or 8 (byte, short or long, ZPOS64_T)
-*/
-
-local int zip64local_putValue OF((const zlib_filefunc64_32_def* pzlib_filefunc_def, voidpf filestream, ZPOS64_T x, int nbByte));
-local int zip64local_putValue (const zlib_filefunc64_32_def* pzlib_filefunc_def, voidpf filestream, ZPOS64_T x, int nbByte)
-{
- unsigned char buf[8];
- int n;
- for (n = 0; n < nbByte; n++)
- {
- buf[n] = (unsigned char)(x & 0xff);
- x >>= 8;
- }
- if (x != 0)
- { /* data overflow - hack for ZIP64 (X Roche) */
- for (n = 0; n < nbByte; n++)
- {
- buf[n] = 0xff;
- }
- }
-
- if (ZWRITE64(*pzlib_filefunc_def,filestream,buf,nbByte)!=(uLong)nbByte)
- return ZIP_ERRNO;
- else
- return ZIP_OK;
-}
-
-local void zip64local_putValue_inmemory OF((void* dest, ZPOS64_T x, int nbByte));
-local void zip64local_putValue_inmemory (void* dest, ZPOS64_T x, int nbByte)
-{
- unsigned char* buf=(unsigned char*)dest;
- int n;
- for (n = 0; n < nbByte; n++) {
- buf[n] = (unsigned char)(x & 0xff);
- x >>= 8;
- }
-
- if (x != 0)
- { /* data overflow - hack for ZIP64 */
- for (n = 0; n < nbByte; n++)
- {
- buf[n] = 0xff;
- }
- }
-}
-
-/****************************************************************************/
-
-
-local uLong zip64local_TmzDateToDosDate(const tm_zip* ptm)
-{
- uLong year = (uLong)ptm->tm_year;
- if (year>=1980)
- year-=1980;
- else if (year>=80)
- year-=80;
- return
- (uLong) (((ptm->tm_mday) + (32 * (ptm->tm_mon+1)) + (512 * year)) << 16) |
- ((ptm->tm_sec/2) + (32* ptm->tm_min) + (2048 * (uLong)ptm->tm_hour));
-}
-
-
-/****************************************************************************/
-
-local int zip64local_getByte OF((const zlib_filefunc64_32_def* pzlib_filefunc_def, voidpf filestream, int *pi));
-
-local int zip64local_getByte(const zlib_filefunc64_32_def* pzlib_filefunc_def,voidpf filestream,int* pi)
-{
- unsigned char c;
- int err = (int)ZREAD64(*pzlib_filefunc_def,filestream,&c,1);
- if (err==1)
- {
- *pi = (int)c;
- return ZIP_OK;
- }
- else
- {
- if (ZERROR64(*pzlib_filefunc_def,filestream))
- return ZIP_ERRNO;
- else
- return ZIP_EOF;
- }
-}
-
-
-/* ===========================================================================
- Reads a long in LSB order from the given gz_stream. Sets
-*/
-local int zip64local_getShort OF((const zlib_filefunc64_32_def* pzlib_filefunc_def, voidpf filestream, uLong *pX));
-
-local int zip64local_getShort (const zlib_filefunc64_32_def* pzlib_filefunc_def, voidpf filestream, uLong* pX)
-{
- uLong x ;
- int i = 0;
- int err;
-
- err = zip64local_getByte(pzlib_filefunc_def,filestream,&i);
- x = (uLong)i;
-
- if (err==ZIP_OK)
- err = zip64local_getByte(pzlib_filefunc_def,filestream,&i);
- x += ((uLong)i)<<8;
-
- if (err==ZIP_OK)
- *pX = x;
- else
- *pX = 0;
- return err;
-}
-
-local int zip64local_getLong OF((const zlib_filefunc64_32_def* pzlib_filefunc_def, voidpf filestream, uLong *pX));
-
-local int zip64local_getLong (const zlib_filefunc64_32_def* pzlib_filefunc_def, voidpf filestream, uLong* pX)
-{
- uLong x ;
- int i = 0;
- int err;
-
- err = zip64local_getByte(pzlib_filefunc_def,filestream,&i);
- x = (uLong)i;
-
- if (err==ZIP_OK)
- err = zip64local_getByte(pzlib_filefunc_def,filestream,&i);
- x += ((uLong)i)<<8;
-
- if (err==ZIP_OK)
- err = zip64local_getByte(pzlib_filefunc_def,filestream,&i);
- x += ((uLong)i)<<16;
-
- if (err==ZIP_OK)
- err = zip64local_getByte(pzlib_filefunc_def,filestream,&i);
- x += ((uLong)i)<<24;
-
- if (err==ZIP_OK)
- *pX = x;
- else
- *pX = 0;
- return err;
-}
-
-local int zip64local_getLong64 OF((const zlib_filefunc64_32_def* pzlib_filefunc_def, voidpf filestream, ZPOS64_T *pX));
-
-
-local int zip64local_getLong64 (const zlib_filefunc64_32_def* pzlib_filefunc_def, voidpf filestream, ZPOS64_T *pX)
-{
- ZPOS64_T x;
- int i = 0;
- int err;
-
- err = zip64local_getByte(pzlib_filefunc_def,filestream,&i);
- x = (ZPOS64_T)i;
-
- if (err==ZIP_OK)
- err = zip64local_getByte(pzlib_filefunc_def,filestream,&i);
- x += ((ZPOS64_T)i)<<8;
-
- if (err==ZIP_OK)
- err = zip64local_getByte(pzlib_filefunc_def,filestream,&i);
- x += ((ZPOS64_T)i)<<16;
-
- if (err==ZIP_OK)
- err = zip64local_getByte(pzlib_filefunc_def,filestream,&i);
- x += ((ZPOS64_T)i)<<24;
-
- if (err==ZIP_OK)
- err = zip64local_getByte(pzlib_filefunc_def,filestream,&i);
- x += ((ZPOS64_T)i)<<32;
-
- if (err==ZIP_OK)
- err = zip64local_getByte(pzlib_filefunc_def,filestream,&i);
- x += ((ZPOS64_T)i)<<40;
-
- if (err==ZIP_OK)
- err = zip64local_getByte(pzlib_filefunc_def,filestream,&i);
- x += ((ZPOS64_T)i)<<48;
-
- if (err==ZIP_OK)
- err = zip64local_getByte(pzlib_filefunc_def,filestream,&i);
- x += ((ZPOS64_T)i)<<56;
-
- if (err==ZIP_OK)
- *pX = x;
- else
- *pX = 0;
-
- return err;
-}
-
-#ifndef BUFREADCOMMENT
-#define BUFREADCOMMENT (0x400)
-#endif
-/*
- Locate the Central directory of a zipfile (at the end, just before
- the global comment)
-*/
-local ZPOS64_T zip64local_SearchCentralDir OF((const zlib_filefunc64_32_def* pzlib_filefunc_def, voidpf filestream));
-
-local ZPOS64_T zip64local_SearchCentralDir(const zlib_filefunc64_32_def* pzlib_filefunc_def, voidpf filestream)
-{
- unsigned char* buf;
- ZPOS64_T uSizeFile;
- ZPOS64_T uBackRead;
- ZPOS64_T uMaxBack=0xffff; /* maximum size of global comment */
- ZPOS64_T uPosFound=0;
-
- if (ZSEEK64(*pzlib_filefunc_def,filestream,0,ZLIB_FILEFUNC_SEEK_END) != 0)
- return 0;
-
-
- uSizeFile = ZTELL64(*pzlib_filefunc_def,filestream);
-
- if (uMaxBack>uSizeFile)
- uMaxBack = uSizeFile;
-
- buf = (unsigned char*)ALLOC(BUFREADCOMMENT+4);
- if (buf==NULL)
- return 0;
-
- uBackRead = 4;
- while (uBackRead<uMaxBack)
- {
- uLong uReadSize;
- ZPOS64_T uReadPos ;
- int i;
- if (uBackRead+BUFREADCOMMENT>uMaxBack)
- uBackRead = uMaxBack;
- else
- uBackRead+=BUFREADCOMMENT;
- uReadPos = uSizeFile-uBackRead ;
-
- uReadSize = ((BUFREADCOMMENT+4) < (uSizeFile-uReadPos)) ?
- (BUFREADCOMMENT+4) : (uLong)(uSizeFile-uReadPos);
- if (ZSEEK64(*pzlib_filefunc_def,filestream,uReadPos,ZLIB_FILEFUNC_SEEK_SET)!=0)
- break;
-
- if (ZREAD64(*pzlib_filefunc_def,filestream,buf,uReadSize)!=uReadSize)
- break;
-
- for (i=(int)uReadSize-3; (i--)>0;)
- if (((*(buf+i))==0x50) && ((*(buf+i+1))==0x4b) &&
- ((*(buf+i+2))==0x05) && ((*(buf+i+3))==0x06))
- {
- uPosFound = uReadPos+i;
- break;
- }
-
- if (uPosFound!=0)
- break;
- }
- TRYFREE(buf);
- return uPosFound;
-}
-
-/*
-Locate the End of Zip64 Central directory locator and from there find the CD of a zipfile (at the end, just before
-the global comment)
-*/
-local ZPOS64_T zip64local_SearchCentralDir64 OF((const zlib_filefunc64_32_def* pzlib_filefunc_def, voidpf filestream));
-
-local ZPOS64_T zip64local_SearchCentralDir64(const zlib_filefunc64_32_def* pzlib_filefunc_def, voidpf filestream)
-{
- unsigned char* buf;
- ZPOS64_T uSizeFile;
- ZPOS64_T uBackRead;
- ZPOS64_T uMaxBack=0xffff; /* maximum size of global comment */
- ZPOS64_T uPosFound=0;
- uLong uL;
- ZPOS64_T relativeOffset;
-
- if (ZSEEK64(*pzlib_filefunc_def,filestream,0,ZLIB_FILEFUNC_SEEK_END) != 0)
- return 0;
-
- uSizeFile = ZTELL64(*pzlib_filefunc_def,filestream);
-
- if (uMaxBack>uSizeFile)
- uMaxBack = uSizeFile;
-
- buf = (unsigned char*)ALLOC(BUFREADCOMMENT+4);
- if (buf==NULL)
- return 0;
-
- uBackRead = 4;
- while (uBackRead<uMaxBack)
- {
- uLong uReadSize;
- ZPOS64_T uReadPos;
- int i;
- if (uBackRead+BUFREADCOMMENT>uMaxBack)
- uBackRead = uMaxBack;
- else
- uBackRead+=BUFREADCOMMENT;
- uReadPos = uSizeFile-uBackRead ;
-
- uReadSize = ((BUFREADCOMMENT+4) < (uSizeFile-uReadPos)) ?
- (BUFREADCOMMENT+4) : (uLong)(uSizeFile-uReadPos);
- if (ZSEEK64(*pzlib_filefunc_def,filestream,uReadPos,ZLIB_FILEFUNC_SEEK_SET)!=0)
- break;
-
- if (ZREAD64(*pzlib_filefunc_def,filestream,buf,uReadSize)!=uReadSize)
- break;
-
- for (i=(int)uReadSize-3; (i--)>0;)
- {
- // Signature "0x07064b50" Zip64 end of central directory locater
- if (((*(buf+i))==0x50) && ((*(buf+i+1))==0x4b) && ((*(buf+i+2))==0x06) && ((*(buf+i+3))==0x07))
- {
- uPosFound = uReadPos+i;
- break;
- }
- }
-
- if (uPosFound!=0)
- break;
- }
-
- TRYFREE(buf);
- if (uPosFound == 0)
- return 0;
-
- /* Zip64 end of central directory locator */
- if (ZSEEK64(*pzlib_filefunc_def,filestream, uPosFound,ZLIB_FILEFUNC_SEEK_SET)!=0)
- return 0;
-
- /* the signature, already checked */
- if (zip64local_getLong(pzlib_filefunc_def,filestream,&uL)!=ZIP_OK)
- return 0;
-
- /* number of the disk with the start of the zip64 end of central directory */
- if (zip64local_getLong(pzlib_filefunc_def,filestream,&uL)!=ZIP_OK)
- return 0;
- if (uL != 0)
- return 0;
-
- /* relative offset of the zip64 end of central directory record */
- if (zip64local_getLong64(pzlib_filefunc_def,filestream,&relativeOffset)!=ZIP_OK)
- return 0;
-
- /* total number of disks */
- if (zip64local_getLong(pzlib_filefunc_def,filestream,&uL)!=ZIP_OK)
- return 0;
- if (uL != 1)
- return 0;
-
- /* Goto Zip64 end of central directory record */
- if (ZSEEK64(*pzlib_filefunc_def,filestream, relativeOffset,ZLIB_FILEFUNC_SEEK_SET)!=0)
- return 0;
-
- /* the signature */
- if (zip64local_getLong(pzlib_filefunc_def,filestream,&uL)!=ZIP_OK)
- return 0;
-
- if (uL != 0x06064b50) // signature of 'Zip64 end of central directory'
- return 0;
-
- return relativeOffset;
-}
-
-int LoadCentralDirectoryRecord(zip64_internal* pziinit)
-{
- int err=ZIP_OK;
- ZPOS64_T byte_before_the_zipfile;/* byte before the zipfile, (>0 for sfx)*/
-
- ZPOS64_T size_central_dir; /* size of the central directory */
- ZPOS64_T offset_central_dir; /* offset of start of central directory */
- ZPOS64_T central_pos;
- uLong uL;
-
- uLong number_disk; /* number of the current dist, used for
- spaning ZIP, unsupported, always 0*/
- uLong number_disk_with_CD; /* number the the disk with central dir, used
- for spaning ZIP, unsupported, always 0*/
- ZPOS64_T number_entry;
- ZPOS64_T number_entry_CD; /* total number of entries in
- the central dir
- (same than number_entry on nospan) */
- uLong VersionMadeBy;
- uLong VersionNeeded;
- uLong size_comment;
-
- int hasZIP64Record = 0;
-
- // check first if we find a ZIP64 record
- central_pos = zip64local_SearchCentralDir64(&pziinit->z_filefunc,pziinit->filestream);
- if(central_pos > 0)
- {
- hasZIP64Record = 1;
- }
- else if(central_pos == 0)
- {
- central_pos = zip64local_SearchCentralDir(&pziinit->z_filefunc,pziinit->filestream);
- }
-
-/* disable to allow appending to empty ZIP archive
- if (central_pos==0)
- err=ZIP_ERRNO;
-*/
-
- if(hasZIP64Record)
- {
- ZPOS64_T sizeEndOfCentralDirectory;
- if (ZSEEK64(pziinit->z_filefunc, pziinit->filestream, central_pos, ZLIB_FILEFUNC_SEEK_SET) != 0)
- err=ZIP_ERRNO;
-
- /* the signature, already checked */
- if (zip64local_getLong(&pziinit->z_filefunc, pziinit->filestream,&uL)!=ZIP_OK)
- err=ZIP_ERRNO;
-
- /* size of zip64 end of central directory record */
- if (zip64local_getLong64(&pziinit->z_filefunc, pziinit->filestream, &sizeEndOfCentralDirectory)!=ZIP_OK)
- err=ZIP_ERRNO;
-
- /* version made by */
- if (zip64local_getShort(&pziinit->z_filefunc, pziinit->filestream, &VersionMadeBy)!=ZIP_OK)
- err=ZIP_ERRNO;
-
- /* version needed to extract */
- if (zip64local_getShort(&pziinit->z_filefunc, pziinit->filestream, &VersionNeeded)!=ZIP_OK)
- err=ZIP_ERRNO;
-
- /* number of this disk */
- if (zip64local_getLong(&pziinit->z_filefunc, pziinit->filestream,&number_disk)!=ZIP_OK)
- err=ZIP_ERRNO;
-
- /* number of the disk with the start of the central directory */
- if (zip64local_getLong(&pziinit->z_filefunc, pziinit->filestream,&number_disk_with_CD)!=ZIP_OK)
- err=ZIP_ERRNO;
-
- /* total number of entries in the central directory on this disk */
- if (zip64local_getLong64(&pziinit->z_filefunc, pziinit->filestream, &number_entry)!=ZIP_OK)
- err=ZIP_ERRNO;
-
- /* total number of entries in the central directory */
- if (zip64local_getLong64(&pziinit->z_filefunc, pziinit->filestream,&number_entry_CD)!=ZIP_OK)
- err=ZIP_ERRNO;
-
- if ((number_entry_CD!=number_entry) || (number_disk_with_CD!=0) || (number_disk!=0))
- err=ZIP_BADZIPFILE;
-
- /* size of the central directory */
- if (zip64local_getLong64(&pziinit->z_filefunc, pziinit->filestream,&size_central_dir)!=ZIP_OK)
- err=ZIP_ERRNO;
-
- /* offset of start of central directory with respect to the
- starting disk number */
- if (zip64local_getLong64(&pziinit->z_filefunc, pziinit->filestream,&offset_central_dir)!=ZIP_OK)
- err=ZIP_ERRNO;
-
- // TODO..
- // read the comment from the standard central header.
- size_comment = 0;
- }
- else
- {
- // Read End of central Directory info
- if (ZSEEK64(pziinit->z_filefunc, pziinit->filestream, central_pos,ZLIB_FILEFUNC_SEEK_SET)!=0)
- err=ZIP_ERRNO;
-
- /* the signature, already checked */
- if (zip64local_getLong(&pziinit->z_filefunc, pziinit->filestream,&uL)!=ZIP_OK)
- err=ZIP_ERRNO;
-
- /* number of this disk */
- if (zip64local_getShort(&pziinit->z_filefunc, pziinit->filestream,&number_disk)!=ZIP_OK)
- err=ZIP_ERRNO;
-
- /* number of the disk with the start of the central directory */
- if (zip64local_getShort(&pziinit->z_filefunc, pziinit->filestream,&number_disk_with_CD)!=ZIP_OK)
- err=ZIP_ERRNO;
-
- /* total number of entries in the central dir on this disk */
- number_entry = 0;
- if (zip64local_getShort(&pziinit->z_filefunc, pziinit->filestream, &uL)!=ZIP_OK)
- err=ZIP_ERRNO;
- else
- number_entry = uL;
-
- /* total number of entries in the central dir */
- number_entry_CD = 0;
- if (zip64local_getShort(&pziinit->z_filefunc, pziinit->filestream, &uL)!=ZIP_OK)
- err=ZIP_ERRNO;
- else
- number_entry_CD = uL;
-
- if ((number_entry_CD!=number_entry) || (number_disk_with_CD!=0) || (number_disk!=0))
- err=ZIP_BADZIPFILE;
-
- /* size of the central directory */
- size_central_dir = 0;
- if (zip64local_getLong(&pziinit->z_filefunc, pziinit->filestream, &uL)!=ZIP_OK)
- err=ZIP_ERRNO;
- else
- size_central_dir = uL;
-
- /* offset of start of central directory with respect to the starting disk number */
- offset_central_dir = 0;
- if (zip64local_getLong(&pziinit->z_filefunc, pziinit->filestream, &uL)!=ZIP_OK)
- err=ZIP_ERRNO;
- else
- offset_central_dir = uL;
-
-
- /* zipfile global comment length */
- if (zip64local_getShort(&pziinit->z_filefunc, pziinit->filestream, &size_comment)!=ZIP_OK)
- err=ZIP_ERRNO;
- }
-
- if ((central_pos<offset_central_dir+size_central_dir) &&
- (err==ZIP_OK))
- err=ZIP_BADZIPFILE;
-
- if (err!=ZIP_OK)
- {
- ZCLOSE64(pziinit->z_filefunc, pziinit->filestream);
- return ZIP_ERRNO;
- }
-
- if (size_comment>0)
- {
- pziinit->globalcomment = (char*)ALLOC(size_comment+1);
- if (pziinit->globalcomment)
- {
- size_comment = ZREAD64(pziinit->z_filefunc, pziinit->filestream, pziinit->globalcomment,size_comment);
- pziinit->globalcomment[size_comment]=0;
- }
- }
-
- byte_before_the_zipfile = central_pos - (offset_central_dir+size_central_dir);
- pziinit->add_position_when_writting_offset = byte_before_the_zipfile;
-
- {
- ZPOS64_T size_central_dir_to_read = size_central_dir;
- size_t buf_size = SIZEDATA_INDATABLOCK;
- void* buf_read = (void*)ALLOC(buf_size);
- if (ZSEEK64(pziinit->z_filefunc, pziinit->filestream, offset_central_dir + byte_before_the_zipfile, ZLIB_FILEFUNC_SEEK_SET) != 0)
- err=ZIP_ERRNO;
-
- while ((size_central_dir_to_read>0) && (err==ZIP_OK))
- {
- ZPOS64_T read_this = SIZEDATA_INDATABLOCK;
- if (read_this > size_central_dir_to_read)
- read_this = size_central_dir_to_read;
-
- if (ZREAD64(pziinit->z_filefunc, pziinit->filestream,buf_read,(uLong)read_this) != read_this)
- err=ZIP_ERRNO;
-
- if (err==ZIP_OK)
- err = add_data_in_datablock(&pziinit->central_dir,buf_read, (uLong)read_this);
-
- size_central_dir_to_read-=read_this;
- }
- TRYFREE(buf_read);
- }
- pziinit->begin_pos = byte_before_the_zipfile;
- pziinit->number_entry = number_entry_CD;
-
- if (ZSEEK64(pziinit->z_filefunc, pziinit->filestream, offset_central_dir+byte_before_the_zipfile,ZLIB_FILEFUNC_SEEK_SET) != 0)
- err=ZIP_ERRNO;
-
- return err;
-}
-
-
-#endif /* !NO_ADDFILEINEXISTINGZIP*/
-
-
-/************************************************************/
-extern zipFile ZEXPORT zipOpen3 (const void *pathname, int append, zipcharpc* globalcomment, zlib_filefunc64_32_def* pzlib_filefunc64_32_def)
-{
- zip64_internal ziinit;
- zip64_internal* zi;
- int err=ZIP_OK;
-
- ziinit.z_filefunc.zseek32_file = NULL;
- ziinit.z_filefunc.ztell32_file = NULL;
- if (pzlib_filefunc64_32_def==NULL)
- fill_fopen64_filefunc(&ziinit.z_filefunc.zfile_func64);
- else
- ziinit.z_filefunc = *pzlib_filefunc64_32_def;
-
- ziinit.filestream = ZOPEN64(ziinit.z_filefunc,
- pathname,
- (append == APPEND_STATUS_CREATE) ?
- (ZLIB_FILEFUNC_MODE_READ | ZLIB_FILEFUNC_MODE_WRITE | ZLIB_FILEFUNC_MODE_CREATE) :
- (ZLIB_FILEFUNC_MODE_READ | ZLIB_FILEFUNC_MODE_WRITE | ZLIB_FILEFUNC_MODE_EXISTING));
-
- if (ziinit.filestream == NULL)
- return NULL;
-
- if (append == APPEND_STATUS_CREATEAFTER)
- ZSEEK64(ziinit.z_filefunc,ziinit.filestream,0,SEEK_END);
-
- ziinit.begin_pos = ZTELL64(ziinit.z_filefunc,ziinit.filestream);
- ziinit.in_opened_file_inzip = 0;
- ziinit.ci.stream_initialised = 0;
- ziinit.number_entry = 0;
- ziinit.add_position_when_writting_offset = 0;
- init_linkedlist(&(ziinit.central_dir));
-
-
-
- zi = (zip64_internal*)ALLOC(sizeof(zip64_internal));
- if (zi==NULL)
- {
- ZCLOSE64(ziinit.z_filefunc,ziinit.filestream);
- return NULL;
- }
-
- /* now we add file in a zipfile */
-# ifndef NO_ADDFILEINEXISTINGZIP
- ziinit.globalcomment = NULL;
- if (append == APPEND_STATUS_ADDINZIP)
- {
- // Read and Cache Central Directory Records
- err = LoadCentralDirectoryRecord(&ziinit);
- }
-
- if (globalcomment)
- {
- *globalcomment = ziinit.globalcomment;
- }
-# endif /* !NO_ADDFILEINEXISTINGZIP*/
-
- if (err != ZIP_OK)
- {
-# ifndef NO_ADDFILEINEXISTINGZIP
- TRYFREE(ziinit.globalcomment);
-# endif /* !NO_ADDFILEINEXISTINGZIP*/
- TRYFREE(zi);
- return NULL;
- }
- else
- {
- *zi = ziinit;
- return (zipFile)zi;
- }
-}
-
-extern zipFile ZEXPORT zipOpen2 (const char *pathname, int append, zipcharpc* globalcomment, zlib_filefunc_def* pzlib_filefunc32_def)
-{
- if (pzlib_filefunc32_def != NULL)
- {
- zlib_filefunc64_32_def zlib_filefunc64_32_def_fill;
- fill_zlib_filefunc64_32_def_from_filefunc32(&zlib_filefunc64_32_def_fill,pzlib_filefunc32_def);
- return zipOpen3(pathname, append, globalcomment, &zlib_filefunc64_32_def_fill);
- }
- else
- return zipOpen3(pathname, append, globalcomment, NULL);
-}
-
-extern zipFile ZEXPORT zipOpen2_64 (const void *pathname, int append, zipcharpc* globalcomment, zlib_filefunc64_def* pzlib_filefunc_def)
-{
- if (pzlib_filefunc_def != NULL)
- {
- zlib_filefunc64_32_def zlib_filefunc64_32_def_fill;
- zlib_filefunc64_32_def_fill.zfile_func64 = *pzlib_filefunc_def;
- zlib_filefunc64_32_def_fill.ztell32_file = NULL;
- zlib_filefunc64_32_def_fill.zseek32_file = NULL;
- return zipOpen3(pathname, append, globalcomment, &zlib_filefunc64_32_def_fill);
- }
- else
- return zipOpen3(pathname, append, globalcomment, NULL);
-}
-
-
-
-extern zipFile ZEXPORT zipOpen (const char* pathname, int append)
-{
- return zipOpen3((const void*)pathname,append,NULL,NULL);
-}
-
-extern zipFile ZEXPORT zipOpen64 (const void* pathname, int append)
-{
- return zipOpen3(pathname,append,NULL,NULL);
-}
-
-int Write_LocalFileHeader(zip64_internal* zi, const char* filename, uInt size_extrafield_local, const void* extrafield_local)
-{
- /* write the local header */
- int err;
- uInt size_filename = (uInt)strlen(filename);
- uInt size_extrafield = size_extrafield_local;
-
- err = zip64local_putValue(&zi->z_filefunc,zi->filestream,(uLong)LOCALHEADERMAGIC, 4);
-
- if (err==ZIP_OK)
- {
- if(zi->ci.zip64)
- err = zip64local_putValue(&zi->z_filefunc,zi->filestream,(uLong)45,2);/* version needed to extract */
- else
- err = zip64local_putValue(&zi->z_filefunc,zi->filestream,(uLong)20,2);/* version needed to extract */
- }
-
- if (err==ZIP_OK)
- err = zip64local_putValue(&zi->z_filefunc,zi->filestream,(uLong)zi->ci.flag,2);
-
- if (err==ZIP_OK)
- err = zip64local_putValue(&zi->z_filefunc,zi->filestream,(uLong)zi->ci.method,2);
-
- if (err==ZIP_OK)
- err = zip64local_putValue(&zi->z_filefunc,zi->filestream,(uLong)zi->ci.dosDate,4);
-
- // CRC / Compressed size / Uncompressed size will be filled in later and rewritten later
- if (err==ZIP_OK)
- err = zip64local_putValue(&zi->z_filefunc,zi->filestream,(uLong)0,4); /* crc 32, unknown */
- if (err==ZIP_OK)
- {
- if(zi->ci.zip64)
- err = zip64local_putValue(&zi->z_filefunc,zi->filestream,(uLong)0xFFFFFFFF,4); /* compressed size, unknown */
- else
- err = zip64local_putValue(&zi->z_filefunc,zi->filestream,(uLong)0,4); /* compressed size, unknown */
- }
- if (err==ZIP_OK)
- {
- if(zi->ci.zip64)
- err = zip64local_putValue(&zi->z_filefunc,zi->filestream,(uLong)0xFFFFFFFF,4); /* uncompressed size, unknown */
- else
- err = zip64local_putValue(&zi->z_filefunc,zi->filestream,(uLong)0,4); /* uncompressed size, unknown */
- }
-
- if (err==ZIP_OK)
- err = zip64local_putValue(&zi->z_filefunc,zi->filestream,(uLong)size_filename,2);
-
- if(zi->ci.zip64)
- {
- size_extrafield += 20;
- }
-
- if (err==ZIP_OK)
- err = zip64local_putValue(&zi->z_filefunc,zi->filestream,(uLong)size_extrafield,2);
-
- if ((err==ZIP_OK) && (size_filename > 0))
- {
- if (ZWRITE64(zi->z_filefunc,zi->filestream,filename,size_filename)!=size_filename)
- err = ZIP_ERRNO;
- }
-
- if ((err==ZIP_OK) && (size_extrafield_local > 0))
- {
- if (ZWRITE64(zi->z_filefunc, zi->filestream, extrafield_local, size_extrafield_local) != size_extrafield_local)
- err = ZIP_ERRNO;
- }
-
-
- if ((err==ZIP_OK) && (zi->ci.zip64))
- {
- // write the Zip64 extended info
- short HeaderID = 1;
- short DataSize = 16;
- ZPOS64_T CompressedSize = 0;
- ZPOS64_T UncompressedSize = 0;
-
- // Remember position of Zip64 extended info for the local file header. (needed when we update size after done with file)
- zi->ci.pos_zip64extrainfo = ZTELL64(zi->z_filefunc,zi->filestream);
-
- err = zip64local_putValue(&zi->z_filefunc, zi->filestream, (short)HeaderID,2);
- err = zip64local_putValue(&zi->z_filefunc, zi->filestream, (short)DataSize,2);
-
- err = zip64local_putValue(&zi->z_filefunc, zi->filestream, (ZPOS64_T)UncompressedSize,8);
- err = zip64local_putValue(&zi->z_filefunc, zi->filestream, (ZPOS64_T)CompressedSize,8);
- }
-
- return err;
-}
-
-/*
- NOTE.
- When writing RAW the ZIP64 extended information in extrafield_local and extrafield_global needs to be stripped
- before calling this function it can be done with zipRemoveExtraInfoBlock
-
- It is not done here because then we need to realloc a new buffer since parameters are 'const' and I want to minimize
- unnecessary allocations.
- */
-extern int ZEXPORT zipOpenNewFileInZip4_64 (zipFile file, const char* filename, const zip_fileinfo* zipfi,
- const void* extrafield_local, uInt size_extrafield_local,
- const void* extrafield_global, uInt size_extrafield_global,
- const char* comment, int method, int level, int raw,
- int windowBits,int memLevel, int strategy,
- const char* password, uLong crcForCrypting,
- uLong versionMadeBy, uLong flagBase, int zip64)
-{
- zip64_internal* zi;
- uInt size_filename;
- uInt size_comment;
- uInt i;
- int err = ZIP_OK;
-
-# ifdef NOCRYPT
- (crcForCrypting);
- if (password != NULL)
- return ZIP_PARAMERROR;
-# endif
-
- if (file == NULL)
- return ZIP_PARAMERROR;
-
-#ifdef HAVE_BZIP2
- if ((method!=0) && (method!=Z_DEFLATED) && (method!=Z_BZIP2ED))
- return ZIP_PARAMERROR;
-#else
- if ((method!=0) && (method!=Z_DEFLATED))
- return ZIP_PARAMERROR;
-#endif
-
- zi = (zip64_internal*)file;
-
- if (zi->in_opened_file_inzip == 1)
- {
- err = zipCloseFileInZip (file);
- if (err != ZIP_OK)
- return err;
- }
-
- if (filename==NULL)
- filename="-";
-
- if (comment==NULL)
- size_comment = 0;
- else
- size_comment = (uInt)strlen(comment);
-
- size_filename = (uInt)strlen(filename);
-
- if (zipfi == NULL)
- zi->ci.dosDate = 0;
- else
- {
- if (zipfi->dosDate != 0)
- zi->ci.dosDate = zipfi->dosDate;
- else
- zi->ci.dosDate = zip64local_TmzDateToDosDate(&zipfi->tmz_date);
- }
-
- zi->ci.flag = flagBase;
- if ((level==8) || (level==9))
- zi->ci.flag |= 2;
- if (level==2)
- zi->ci.flag |= 4;
- if (level==1)
- zi->ci.flag |= 6;
- if (password != NULL)
- zi->ci.flag |= 1;
-
- zi->ci.crc32 = 0;
- zi->ci.method = method;
- zi->ci.encrypt = 0;
- zi->ci.stream_initialised = 0;
- zi->ci.pos_in_buffered_data = 0;
- zi->ci.raw = raw;
- zi->ci.pos_local_header = ZTELL64(zi->z_filefunc,zi->filestream);
-
- zi->ci.size_centralheader = SIZECENTRALHEADER + size_filename + size_extrafield_global + size_comment;
- zi->ci.size_centralExtraFree = 32; // Extra space we have reserved in case we need to add ZIP64 extra info data
-
- zi->ci.central_header = (char*)ALLOC((uInt)zi->ci.size_centralheader + zi->ci.size_centralExtraFree);
-
- zi->ci.size_centralExtra = size_extrafield_global;
- zip64local_putValue_inmemory(zi->ci.central_header,(uLong)CENTRALHEADERMAGIC,4);
- /* version info */
- zip64local_putValue_inmemory(zi->ci.central_header+4,(uLong)versionMadeBy,2);
- zip64local_putValue_inmemory(zi->ci.central_header+6,(uLong)20,2);
- zip64local_putValue_inmemory(zi->ci.central_header+8,(uLong)zi->ci.flag,2);
- zip64local_putValue_inmemory(zi->ci.central_header+10,(uLong)zi->ci.method,2);
- zip64local_putValue_inmemory(zi->ci.central_header+12,(uLong)zi->ci.dosDate,4);
- zip64local_putValue_inmemory(zi->ci.central_header+16,(uLong)0,4); /*crc*/
- zip64local_putValue_inmemory(zi->ci.central_header+20,(uLong)0,4); /*compr size*/
- zip64local_putValue_inmemory(zi->ci.central_header+24,(uLong)0,4); /*uncompr size*/
- zip64local_putValue_inmemory(zi->ci.central_header+28,(uLong)size_filename,2);
- zip64local_putValue_inmemory(zi->ci.central_header+30,(uLong)size_extrafield_global,2);
- zip64local_putValue_inmemory(zi->ci.central_header+32,(uLong)size_comment,2);
- zip64local_putValue_inmemory(zi->ci.central_header+34,(uLong)0,2); /*disk nm start*/
-
- if (zipfi==NULL)
- zip64local_putValue_inmemory(zi->ci.central_header+36,(uLong)0,2);
- else
- zip64local_putValue_inmemory(zi->ci.central_header+36,(uLong)zipfi->internal_fa,2);
-
- if (zipfi==NULL)
- zip64local_putValue_inmemory(zi->ci.central_header+38,(uLong)0,4);
- else
- zip64local_putValue_inmemory(zi->ci.central_header+38,(uLong)zipfi->external_fa,4);
-
- if(zi->ci.pos_local_header >= 0xffffffff)
- zip64local_putValue_inmemory(zi->ci.central_header+42,(uLong)0xffffffff,4);
- else
- zip64local_putValue_inmemory(zi->ci.central_header+42,(uLong)zi->ci.pos_local_header - zi->add_position_when_writting_offset,4);
-
- for (i=0;i<size_filename;i++)
- *(zi->ci.central_header+SIZECENTRALHEADER+i) = *(filename+i);
-
- for (i=0;i<size_extrafield_global;i++)
- *(zi->ci.central_header+SIZECENTRALHEADER+size_filename+i) =
- *(((const char*)extrafield_global)+i);
-
- for (i=0;i<size_comment;i++)
- *(zi->ci.central_header+SIZECENTRALHEADER+size_filename+
- size_extrafield_global+i) = *(comment+i);
- if (zi->ci.central_header == NULL)
- return ZIP_INTERNALERROR;
-
- zi->ci.zip64 = zip64;
- zi->ci.totalCompressedData = 0;
- zi->ci.totalUncompressedData = 0;
- zi->ci.pos_zip64extrainfo = 0;
-
- err = Write_LocalFileHeader(zi, filename, size_extrafield_local, extrafield_local);
-
-#ifdef HAVE_BZIP2
- zi->ci.bstream.avail_in = (uInt)0;
- zi->ci.bstream.avail_out = (uInt)Z_BUFSIZE;
- zi->ci.bstream.next_out = (char*)zi->ci.buffered_data;
- zi->ci.bstream.total_in_hi32 = 0;
- zi->ci.bstream.total_in_lo32 = 0;
- zi->ci.bstream.total_out_hi32 = 0;
- zi->ci.bstream.total_out_lo32 = 0;
-#endif
-
- zi->ci.stream.avail_in = (uInt)0;
- zi->ci.stream.avail_out = (uInt)Z_BUFSIZE;
- zi->ci.stream.next_out = zi->ci.buffered_data;
- zi->ci.stream.total_in = 0;
- zi->ci.stream.total_out = 0;
- zi->ci.stream.data_type = Z_BINARY;
-
-#ifdef HAVE_BZIP2
- if ((err==ZIP_OK) && (zi->ci.method == Z_DEFLATED || zi->ci.method == Z_BZIP2ED) && (!zi->ci.raw))
-#else
- if ((err==ZIP_OK) && (zi->ci.method == Z_DEFLATED) && (!zi->ci.raw))
-#endif
- {
- if(zi->ci.method == Z_DEFLATED)
- {
- zi->ci.stream.zalloc = (alloc_func)0;
- zi->ci.stream.zfree = (free_func)0;
- zi->ci.stream.opaque = (voidpf)0;
-
- if (windowBits>0)
- windowBits = -windowBits;
-
- err = deflateInit2(&zi->ci.stream, level, Z_DEFLATED, windowBits, memLevel, strategy);
-
- if (err==Z_OK)
- zi->ci.stream_initialised = Z_DEFLATED;
- }
- else if(zi->ci.method == Z_BZIP2ED)
- {
-#ifdef HAVE_BZIP2
- // Init BZip stuff here
- zi->ci.bstream.bzalloc = 0;
- zi->ci.bstream.bzfree = 0;
- zi->ci.bstream.opaque = (voidpf)0;
-
- err = BZ2_bzCompressInit(&zi->ci.bstream, level, 0,35);
- if(err == BZ_OK)
- zi->ci.stream_initialised = Z_BZIP2ED;
-#endif
- }
-
- }
-
-# ifndef NOCRYPT
- zi->ci.crypt_header_size = 0;
- if ((err==Z_OK) && (password != NULL))
- {
- unsigned char bufHead[RAND_HEAD_LEN];
- unsigned int sizeHead;
- zi->ci.encrypt = 1;
- zi->ci.pcrc_32_tab = get_crc_table();
- /*init_keys(password,zi->ci.keys,zi->ci.pcrc_32_tab);*/
-
- sizeHead=crypthead(password,bufHead,RAND_HEAD_LEN,zi->ci.keys,zi->ci.pcrc_32_tab,crcForCrypting);
- zi->ci.crypt_header_size = sizeHead;
-
- if (ZWRITE64(zi->z_filefunc,zi->filestream,bufHead,sizeHead) != sizeHead)
- err = ZIP_ERRNO;
- }
-# endif
-
- if (err==Z_OK)
- zi->in_opened_file_inzip = 1;
- return err;
-}
-
-extern int ZEXPORT zipOpenNewFileInZip4 (zipFile file, const char* filename, const zip_fileinfo* zipfi,
- const void* extrafield_local, uInt size_extrafield_local,
- const void* extrafield_global, uInt size_extrafield_global,
- const char* comment, int method, int level, int raw,
- int windowBits,int memLevel, int strategy,
- const char* password, uLong crcForCrypting,
- uLong versionMadeBy, uLong flagBase)
-{
- return zipOpenNewFileInZip4_64 (file, filename, zipfi,
- extrafield_local, size_extrafield_local,
- extrafield_global, size_extrafield_global,
- comment, method, level, raw,
- windowBits, memLevel, strategy,
- password, crcForCrypting, versionMadeBy, flagBase, 0);
-}
-
-extern int ZEXPORT zipOpenNewFileInZip3 (zipFile file, const char* filename, const zip_fileinfo* zipfi,
- const void* extrafield_local, uInt size_extrafield_local,
- const void* extrafield_global, uInt size_extrafield_global,
- const char* comment, int method, int level, int raw,
- int windowBits,int memLevel, int strategy,
- const char* password, uLong crcForCrypting)
-{
- return zipOpenNewFileInZip4_64 (file, filename, zipfi,
- extrafield_local, size_extrafield_local,
- extrafield_global, size_extrafield_global,
- comment, method, level, raw,
- windowBits, memLevel, strategy,
- password, crcForCrypting, VERSIONMADEBY, 0, 0);
-}
-
-extern int ZEXPORT zipOpenNewFileInZip3_64(zipFile file, const char* filename, const zip_fileinfo* zipfi,
- const void* extrafield_local, uInt size_extrafield_local,
- const void* extrafield_global, uInt size_extrafield_global,
- const char* comment, int method, int level, int raw,
- int windowBits,int memLevel, int strategy,
- const char* password, uLong crcForCrypting, int zip64)
-{
- return zipOpenNewFileInZip4_64 (file, filename, zipfi,
- extrafield_local, size_extrafield_local,
- extrafield_global, size_extrafield_global,
- comment, method, level, raw,
- windowBits, memLevel, strategy,
- password, crcForCrypting, VERSIONMADEBY, 0, zip64);
-}
-
-extern int ZEXPORT zipOpenNewFileInZip2(zipFile file, const char* filename, const zip_fileinfo* zipfi,
- const void* extrafield_local, uInt size_extrafield_local,
- const void* extrafield_global, uInt size_extrafield_global,
- const char* comment, int method, int level, int raw)
-{
- return zipOpenNewFileInZip4_64 (file, filename, zipfi,
- extrafield_local, size_extrafield_local,
- extrafield_global, size_extrafield_global,
- comment, method, level, raw,
- -MAX_WBITS, DEF_MEM_LEVEL, Z_DEFAULT_STRATEGY,
- NULL, 0, VERSIONMADEBY, 0, 0);
-}
-
-extern int ZEXPORT zipOpenNewFileInZip2_64(zipFile file, const char* filename, const zip_fileinfo* zipfi,
- const void* extrafield_local, uInt size_extrafield_local,
- const void* extrafield_global, uInt size_extrafield_global,
- const char* comment, int method, int level, int raw, int zip64)
-{
- return zipOpenNewFileInZip4_64 (file, filename, zipfi,
- extrafield_local, size_extrafield_local,
- extrafield_global, size_extrafield_global,
- comment, method, level, raw,
- -MAX_WBITS, DEF_MEM_LEVEL, Z_DEFAULT_STRATEGY,
- NULL, 0, VERSIONMADEBY, 0, zip64);
-}
-
-extern int ZEXPORT zipOpenNewFileInZip64 (zipFile file, const char* filename, const zip_fileinfo* zipfi,
- const void* extrafield_local, uInt size_extrafield_local,
- const void*extrafield_global, uInt size_extrafield_global,
- const char* comment, int method, int level, int zip64)
-{
- return zipOpenNewFileInZip4_64 (file, filename, zipfi,
- extrafield_local, size_extrafield_local,
- extrafield_global, size_extrafield_global,
- comment, method, level, 0,
- -MAX_WBITS, DEF_MEM_LEVEL, Z_DEFAULT_STRATEGY,
- NULL, 0, VERSIONMADEBY, 0, zip64);
-}
-
-extern int ZEXPORT zipOpenNewFileInZip (zipFile file, const char* filename, const zip_fileinfo* zipfi,
- const void* extrafield_local, uInt size_extrafield_local,
- const void*extrafield_global, uInt size_extrafield_global,
- const char* comment, int method, int level)
-{
- return zipOpenNewFileInZip4_64 (file, filename, zipfi,
- extrafield_local, size_extrafield_local,
- extrafield_global, size_extrafield_global,
- comment, method, level, 0,
- -MAX_WBITS, DEF_MEM_LEVEL, Z_DEFAULT_STRATEGY,
- NULL, 0, VERSIONMADEBY, 0, 0);
-}
-
-local int zip64FlushWriteBuffer(zip64_internal* zi)
-{
- int err=ZIP_OK;
-
- if (zi->ci.encrypt != 0)
- {
-#ifndef NOCRYPT
- uInt i;
- int t;
- for (i=0;i<zi->ci.pos_in_buffered_data;i++)
- zi->ci.buffered_data[i] = zencode(zi->ci.keys, zi->ci.pcrc_32_tab, zi->ci.buffered_data[i],t);
-#endif
- }
-
- if (ZWRITE64(zi->z_filefunc,zi->filestream,zi->ci.buffered_data,zi->ci.pos_in_buffered_data) != zi->ci.pos_in_buffered_data)
- err = ZIP_ERRNO;
-
- zi->ci.totalCompressedData += zi->ci.pos_in_buffered_data;
-
-#ifdef HAVE_BZIP2
- if(zi->ci.method == Z_BZIP2ED)
- {
- zi->ci.totalUncompressedData += zi->ci.bstream.total_in_lo32;
- zi->ci.bstream.total_in_lo32 = 0;
- zi->ci.bstream.total_in_hi32 = 0;
- }
- else
-#endif
- {
- zi->ci.totalUncompressedData += zi->ci.stream.total_in;
- zi->ci.stream.total_in = 0;
- }
-
-
- zi->ci.pos_in_buffered_data = 0;
-
- return err;
-}
-
-extern int ZEXPORT zipWriteInFileInZip (zipFile file,const void* buf,unsigned int len)
-{
- zip64_internal* zi;
- int err=ZIP_OK;
-
- if (file == NULL)
- return ZIP_PARAMERROR;
- zi = (zip64_internal*)file;
-
- if (zi->in_opened_file_inzip == 0)
- return ZIP_PARAMERROR;
-
- zi->ci.crc32 = crc32(zi->ci.crc32,buf,(uInt)len);
-
-#ifdef HAVE_BZIP2
- if(zi->ci.method == Z_BZIP2ED && (!zi->ci.raw))
- {
- zi->ci.bstream.next_in = (void*)buf;
- zi->ci.bstream.avail_in = len;
- err = BZ_RUN_OK;
-
- while ((err==BZ_RUN_OK) && (zi->ci.bstream.avail_in>0))
- {
- if (zi->ci.bstream.avail_out == 0)
- {
- if (zip64FlushWriteBuffer(zi) == ZIP_ERRNO)
- err = ZIP_ERRNO;
- zi->ci.bstream.avail_out = (uInt)Z_BUFSIZE;
- zi->ci.bstream.next_out = (char*)zi->ci.buffered_data;
- }
-
-
- if(err != BZ_RUN_OK)
- break;
-
- if ((zi->ci.method == Z_BZIP2ED) && (!zi->ci.raw))
- {
- uLong uTotalOutBefore_lo = zi->ci.bstream.total_out_lo32;
-// uLong uTotalOutBefore_hi = zi->ci.bstream.total_out_hi32;
- err=BZ2_bzCompress(&zi->ci.bstream, BZ_RUN);
-
- zi->ci.pos_in_buffered_data += (uInt)(zi->ci.bstream.total_out_lo32 - uTotalOutBefore_lo) ;
- }
- }
-
- if(err == BZ_RUN_OK)
- err = ZIP_OK;
- }
- else
-#endif
- {
- zi->ci.stream.next_in = (Bytef*)buf;
- zi->ci.stream.avail_in = len;
-
- while ((err==ZIP_OK) && (zi->ci.stream.avail_in>0))
- {
- if (zi->ci.stream.avail_out == 0)
- {
- if (zip64FlushWriteBuffer(zi) == ZIP_ERRNO)
- err = ZIP_ERRNO;
- zi->ci.stream.avail_out = (uInt)Z_BUFSIZE;
- zi->ci.stream.next_out = zi->ci.buffered_data;
- }
-
-
- if(err != ZIP_OK)
- break;
-
- if ((zi->ci.method == Z_DEFLATED) && (!zi->ci.raw))
- {
- uLong uTotalOutBefore = zi->ci.stream.total_out;
- err=deflate(&zi->ci.stream, Z_NO_FLUSH);
- if(uTotalOutBefore > zi->ci.stream.total_out)
- {
- int bBreak = 0;
- bBreak++;
- }
-
- zi->ci.pos_in_buffered_data += (uInt)(zi->ci.stream.total_out - uTotalOutBefore) ;
- }
- else
- {
- uInt copy_this,i;
- if (zi->ci.stream.avail_in < zi->ci.stream.avail_out)
- copy_this = zi->ci.stream.avail_in;
- else
- copy_this = zi->ci.stream.avail_out;
-
- for (i = 0; i < copy_this; i++)
- *(((char*)zi->ci.stream.next_out)+i) =
- *(((const char*)zi->ci.stream.next_in)+i);
- {
- zi->ci.stream.avail_in -= copy_this;
- zi->ci.stream.avail_out-= copy_this;
- zi->ci.stream.next_in+= copy_this;
- zi->ci.stream.next_out+= copy_this;
- zi->ci.stream.total_in+= copy_this;
- zi->ci.stream.total_out+= copy_this;
- zi->ci.pos_in_buffered_data += copy_this;
- }
- }
- }// while(...)
- }
-
- return err;
-}
-
-extern int ZEXPORT zipCloseFileInZipRaw (zipFile file, uLong uncompressed_size, uLong crc32)
-{
- return zipCloseFileInZipRaw64 (file, uncompressed_size, crc32);
-}
-
-extern int ZEXPORT zipCloseFileInZipRaw64 (zipFile file, ZPOS64_T uncompressed_size, uLong crc32)
-{
- zip64_internal* zi;
- ZPOS64_T compressed_size;
- uLong invalidValue = 0xffffffff;
- short datasize = 0;
- int err=ZIP_OK;
-
- if (file == NULL)
- return ZIP_PARAMERROR;
- zi = (zip64_internal*)file;
-
- if (zi->in_opened_file_inzip == 0)
- return ZIP_PARAMERROR;
- zi->ci.stream.avail_in = 0;
-
- if ((zi->ci.method == Z_DEFLATED) && (!zi->ci.raw))
- {
- while (err==ZIP_OK)
- {
- uLong uTotalOutBefore;
- if (zi->ci.stream.avail_out == 0)
- {
- if (zip64FlushWriteBuffer(zi) == ZIP_ERRNO)
- err = ZIP_ERRNO;
- zi->ci.stream.avail_out = (uInt)Z_BUFSIZE;
- zi->ci.stream.next_out = zi->ci.buffered_data;
- }
- uTotalOutBefore = zi->ci.stream.total_out;
- err=deflate(&zi->ci.stream, Z_FINISH);
- zi->ci.pos_in_buffered_data += (uInt)(zi->ci.stream.total_out - uTotalOutBefore) ;
- }
- }
- else if ((zi->ci.method == Z_BZIP2ED) && (!zi->ci.raw))
- {
-#ifdef HAVE_BZIP2
- err = BZ_FINISH_OK;
- while (err==BZ_FINISH_OK)
- {
- uLong uTotalOutBefore;
- if (zi->ci.bstream.avail_out == 0)
- {
- if (zip64FlushWriteBuffer(zi) == ZIP_ERRNO)
- err = ZIP_ERRNO;
- zi->ci.bstream.avail_out = (uInt)Z_BUFSIZE;
- zi->ci.bstream.next_out = (char*)zi->ci.buffered_data;
- }
- uTotalOutBefore = zi->ci.bstream.total_out_lo32;
- err=BZ2_bzCompress(&zi->ci.bstream, BZ_FINISH);
- if(err == BZ_STREAM_END)
- err = Z_STREAM_END;
-
- zi->ci.pos_in_buffered_data += (uInt)(zi->ci.bstream.total_out_lo32 - uTotalOutBefore);
- }
-
- if(err == BZ_FINISH_OK)
- err = ZIP_OK;
-#endif
- }
-
- if (err==Z_STREAM_END)
- err=ZIP_OK; /* this is normal */
-
- if ((zi->ci.pos_in_buffered_data>0) && (err==ZIP_OK))
- {
- if (zip64FlushWriteBuffer(zi)==ZIP_ERRNO)
- err = ZIP_ERRNO;
- }
-
- if ((zi->ci.method == Z_DEFLATED) && (!zi->ci.raw))
- {
- int tmp_err = deflateEnd(&zi->ci.stream);
- if (err == ZIP_OK)
- err = tmp_err;
- zi->ci.stream_initialised = 0;
- }
-#ifdef HAVE_BZIP2
- else if((zi->ci.method == Z_BZIP2ED) && (!zi->ci.raw))
- {
- int tmperr = BZ2_bzCompressEnd(&zi->ci.bstream);
- if (err==ZIP_OK)
- err = tmperr;
- zi->ci.stream_initialised = 0;
- }
-#endif
-
- if (!zi->ci.raw)
- {
- crc32 = (uLong)zi->ci.crc32;
- uncompressed_size = zi->ci.totalUncompressedData;
- }
- compressed_size = zi->ci.totalCompressedData;
-
-# ifndef NOCRYPT
- compressed_size += zi->ci.crypt_header_size;
-# endif
-
- // update Current Item crc and sizes,
- if(compressed_size >= 0xffffffff || uncompressed_size >= 0xffffffff || zi->ci.pos_local_header >= 0xffffffff)
- {
- /*version Made by*/
- zip64local_putValue_inmemory(zi->ci.central_header+4,(uLong)45,2);
- /*version needed*/
- zip64local_putValue_inmemory(zi->ci.central_header+6,(uLong)45,2);
-
- }
-
- zip64local_putValue_inmemory(zi->ci.central_header+16,crc32,4); /*crc*/
-
-
- if(compressed_size >= 0xffffffff)
- zip64local_putValue_inmemory(zi->ci.central_header+20, invalidValue,4); /*compr size*/
- else
- zip64local_putValue_inmemory(zi->ci.central_header+20, compressed_size,4); /*compr size*/
-
- /// set internal file attributes field
- if (zi->ci.stream.data_type == Z_ASCII)
- zip64local_putValue_inmemory(zi->ci.central_header+36,(uLong)Z_ASCII,2);
-
- if(uncompressed_size >= 0xffffffff)
- zip64local_putValue_inmemory(zi->ci.central_header+24, invalidValue,4); /*uncompr size*/
- else
- zip64local_putValue_inmemory(zi->ci.central_header+24, uncompressed_size,4); /*uncompr size*/
-
- // Add ZIP64 extra info field for uncompressed size
- if(uncompressed_size >= 0xffffffff)
- datasize += 8;
-
- // Add ZIP64 extra info field for compressed size
- if(compressed_size >= 0xffffffff)
- datasize += 8;
-
- // Add ZIP64 extra info field for relative offset to local file header of current file
- if(zi->ci.pos_local_header >= 0xffffffff)
- datasize += 8;
-
- if(datasize > 0)
- {
- char* p = NULL;
-
- if((uLong)(datasize + 4) > zi->ci.size_centralExtraFree)
- {
- // we can not write more data to the buffer that we have room for.
- return ZIP_BADZIPFILE;
- }
-
- p = zi->ci.central_header + zi->ci.size_centralheader;
-
- // Add Extra Information Header for 'ZIP64 information'
- zip64local_putValue_inmemory(p, 0x0001, 2); // HeaderID
- p += 2;
- zip64local_putValue_inmemory(p, datasize, 2); // DataSize
- p += 2;
-
- if(uncompressed_size >= 0xffffffff)
- {
- zip64local_putValue_inmemory(p, uncompressed_size, 8);
- p += 8;
- }
-
- if(compressed_size >= 0xffffffff)
- {
- zip64local_putValue_inmemory(p, compressed_size, 8);
- p += 8;
- }
-
- if(zi->ci.pos_local_header >= 0xffffffff)
- {
- zip64local_putValue_inmemory(p, zi->ci.pos_local_header, 8);
- p += 8;
- }
-
- // Update how much extra free space we got in the memory buffer
- // and increase the centralheader size so the new ZIP64 fields are included
- // ( 4 below is the size of HeaderID and DataSize field )
- zi->ci.size_centralExtraFree -= datasize + 4;
- zi->ci.size_centralheader += datasize + 4;
-
- // Update the extra info size field
- zi->ci.size_centralExtra += datasize + 4;
- zip64local_putValue_inmemory(zi->ci.central_header+30,(uLong)zi->ci.size_centralExtra,2);
- }
-
- if (err==ZIP_OK)
- err = add_data_in_datablock(&zi->central_dir, zi->ci.central_header, (uLong)zi->ci.size_centralheader);
-
- free(zi->ci.central_header);
-
- if (err==ZIP_OK)
- {
- // Update the LocalFileHeader with the new values.
-
- ZPOS64_T cur_pos_inzip = ZTELL64(zi->z_filefunc,zi->filestream);
-
- if (ZSEEK64(zi->z_filefunc,zi->filestream, zi->ci.pos_local_header + 14,ZLIB_FILEFUNC_SEEK_SET)!=0)
- err = ZIP_ERRNO;
-
- if (err==ZIP_OK)
- err = zip64local_putValue(&zi->z_filefunc,zi->filestream,crc32,4); /* crc 32, unknown */
-
- if(uncompressed_size >= 0xffffffff || compressed_size >= 0xffffffff )
- {
- if(zi->ci.pos_zip64extrainfo > 0)
- {
- // Update the size in the ZIP64 extended field.
- if (ZSEEK64(zi->z_filefunc,zi->filestream, zi->ci.pos_zip64extrainfo + 4,ZLIB_FILEFUNC_SEEK_SET)!=0)
- err = ZIP_ERRNO;
-
- if (err==ZIP_OK) /* compressed size, unknown */
- err = zip64local_putValue(&zi->z_filefunc, zi->filestream, uncompressed_size, 8);
-
- if (err==ZIP_OK) /* uncompressed size, unknown */
- err = zip64local_putValue(&zi->z_filefunc, zi->filestream, compressed_size, 8);
- }
- else
- err = ZIP_BADZIPFILE; // Caller passed zip64 = 0, so no room for zip64 info -> fatal
- }
- else
- {
- if (err==ZIP_OK) /* compressed size, unknown */
- err = zip64local_putValue(&zi->z_filefunc,zi->filestream,compressed_size,4);
-
- if (err==ZIP_OK) /* uncompressed size, unknown */
- err = zip64local_putValue(&zi->z_filefunc,zi->filestream,uncompressed_size,4);
- }
-
- if (ZSEEK64(zi->z_filefunc,zi->filestream, cur_pos_inzip,ZLIB_FILEFUNC_SEEK_SET)!=0)
- err = ZIP_ERRNO;
- }
-
- zi->number_entry ++;
- zi->in_opened_file_inzip = 0;
-
- return err;
-}
-
-extern int ZEXPORT zipCloseFileInZip (zipFile file)
-{
- return zipCloseFileInZipRaw (file,0,0);
-}
-
-int Write_Zip64EndOfCentralDirectoryLocator(zip64_internal* zi, ZPOS64_T zip64eocd_pos_inzip)
-{
- int err = ZIP_OK;
- ZPOS64_T pos = zip64eocd_pos_inzip - zi->add_position_when_writting_offset;
-
- err = zip64local_putValue(&zi->z_filefunc,zi->filestream,(uLong)ZIP64ENDLOCHEADERMAGIC,4);
-
- /*num disks*/
- if (err==ZIP_OK) /* number of the disk with the start of the central directory */
- err = zip64local_putValue(&zi->z_filefunc,zi->filestream,(uLong)0,4);
-
- /*relative offset*/
- if (err==ZIP_OK) /* Relative offset to the Zip64EndOfCentralDirectory */
- err = zip64local_putValue(&zi->z_filefunc,zi->filestream, pos,8);
-
- /*total disks*/ /* Do not support spawning of disk so always say 1 here*/
- if (err==ZIP_OK) /* number of the disk with the start of the central directory */
- err = zip64local_putValue(&zi->z_filefunc,zi->filestream,(uLong)1,4);
-
- return err;
-}
-
-int Write_Zip64EndOfCentralDirectoryRecord(zip64_internal* zi, uLong size_centraldir, ZPOS64_T centraldir_pos_inzip)
-{
- int err = ZIP_OK;
-
- uLong Zip64DataSize = 44;
-
- err = zip64local_putValue(&zi->z_filefunc,zi->filestream,(uLong)ZIP64ENDHEADERMAGIC,4);
-
- if (err==ZIP_OK) /* size of this 'zip64 end of central directory' */
- err = zip64local_putValue(&zi->z_filefunc,zi->filestream,(ZPOS64_T)Zip64DataSize,8); // why ZPOS64_T of this ?
-
- if (err==ZIP_OK) /* version made by */
- err = zip64local_putValue(&zi->z_filefunc,zi->filestream,(uLong)45,2);
-
- if (err==ZIP_OK) /* version needed */
- err = zip64local_putValue(&zi->z_filefunc,zi->filestream,(uLong)45,2);
-
- if (err==ZIP_OK) /* number of this disk */
- err = zip64local_putValue(&zi->z_filefunc,zi->filestream,(uLong)0,4);
-
- if (err==ZIP_OK) /* number of the disk with the start of the central directory */
- err = zip64local_putValue(&zi->z_filefunc,zi->filestream,(uLong)0,4);
-
- if (err==ZIP_OK) /* total number of entries in the central dir on this disk */
- err = zip64local_putValue(&zi->z_filefunc, zi->filestream, zi->number_entry, 8);
-
- if (err==ZIP_OK) /* total number of entries in the central dir */
- err = zip64local_putValue(&zi->z_filefunc, zi->filestream, zi->number_entry, 8);
-
- if (err==ZIP_OK) /* size of the central directory */
- err = zip64local_putValue(&zi->z_filefunc,zi->filestream,(ZPOS64_T)size_centraldir,8);
-
- if (err==ZIP_OK) /* offset of start of central directory with respect to the starting disk number */
- {
- ZPOS64_T pos = centraldir_pos_inzip - zi->add_position_when_writting_offset;
- err = zip64local_putValue(&zi->z_filefunc,zi->filestream, (ZPOS64_T)pos,8);
- }
- return err;
-}
-int Write_EndOfCentralDirectoryRecord(zip64_internal* zi, uLong size_centraldir, ZPOS64_T centraldir_pos_inzip)
-{
- int err = ZIP_OK;
-
- /*signature*/
- err = zip64local_putValue(&zi->z_filefunc,zi->filestream,(uLong)ENDHEADERMAGIC,4);
-
- if (err==ZIP_OK) /* number of this disk */
- err = zip64local_putValue(&zi->z_filefunc,zi->filestream,(uLong)0,2);
-
- if (err==ZIP_OK) /* number of the disk with the start of the central directory */
- err = zip64local_putValue(&zi->z_filefunc,zi->filestream,(uLong)0,2);
-
- if (err==ZIP_OK) /* total number of entries in the central dir on this disk */
- {
- {
- if(zi->number_entry >= 0xFFFF)
- err = zip64local_putValue(&zi->z_filefunc,zi->filestream,(uLong)0xffff,2); // use value in ZIP64 record
- else
- err = zip64local_putValue(&zi->z_filefunc,zi->filestream,(uLong)zi->number_entry,2);
- }
- }
-
- if (err==ZIP_OK) /* total number of entries in the central dir */
- {
- if(zi->number_entry >= 0xFFFF)
- err = zip64local_putValue(&zi->z_filefunc,zi->filestream,(uLong)0xffff,2); // use value in ZIP64 record
- else
- err = zip64local_putValue(&zi->z_filefunc,zi->filestream,(uLong)zi->number_entry,2);
- }
-
- if (err==ZIP_OK) /* size of the central directory */
- err = zip64local_putValue(&zi->z_filefunc,zi->filestream,(uLong)size_centraldir,4);
-
- if (err==ZIP_OK) /* offset of start of central directory with respect to the starting disk number */
- {
- ZPOS64_T pos = centraldir_pos_inzip - zi->add_position_when_writting_offset;
- if(pos >= 0xffffffff)
- {
- err = zip64local_putValue(&zi->z_filefunc,zi->filestream, (uLong)0xffffffff,4);
- }
- else
- err = zip64local_putValue(&zi->z_filefunc,zi->filestream, (uLong)(centraldir_pos_inzip - zi->add_position_when_writting_offset),4);
- }
-
- return err;
-}
-
-int Write_GlobalComment(zip64_internal* zi, const char* global_comment)
-{
- int err = ZIP_OK;
- uInt size_global_comment = 0;
-
- if(global_comment != NULL)
- size_global_comment = (uInt)strlen(global_comment);
-
- err = zip64local_putValue(&zi->z_filefunc,zi->filestream,(uLong)size_global_comment,2);
-
- if (err == ZIP_OK && size_global_comment > 0)
- {
- if (ZWRITE64(zi->z_filefunc,zi->filestream, global_comment, size_global_comment) != size_global_comment)
- err = ZIP_ERRNO;
- }
- return err;
-}
-
-extern int ZEXPORT zipClose (zipFile file, const char* global_comment)
-{
- zip64_internal* zi;
- int err = 0;
- uLong size_centraldir = 0;
- ZPOS64_T centraldir_pos_inzip;
- ZPOS64_T pos;
-
- if (file == NULL)
- return ZIP_PARAMERROR;
-
- zi = (zip64_internal*)file;
-
- if (zi->in_opened_file_inzip == 1)
- {
- err = zipCloseFileInZip (file);
- }
-
-#ifndef NO_ADDFILEINEXISTINGZIP
- if (global_comment==NULL)
- global_comment = zi->globalcomment;
-#endif
-
- centraldir_pos_inzip = ZTELL64(zi->z_filefunc,zi->filestream);
-
- if (err==ZIP_OK)
- {
- linkedlist_datablock_internal* ldi = zi->central_dir.first_block;
- while (ldi!=NULL)
- {
- if ((err==ZIP_OK) && (ldi->filled_in_this_block>0))
- {
- if (ZWRITE64(zi->z_filefunc,zi->filestream, ldi->data, ldi->filled_in_this_block) != ldi->filled_in_this_block)
- err = ZIP_ERRNO;
- }
-
- size_centraldir += ldi->filled_in_this_block;
- ldi = ldi->next_datablock;
- }
- }
- free_linkedlist(&(zi->central_dir));
-
- pos = centraldir_pos_inzip - zi->add_position_when_writting_offset;
- if(pos >= 0xffffffff || zi->number_entry > 0xFFFF)
- {
- ZPOS64_T Zip64EOCDpos = ZTELL64(zi->z_filefunc,zi->filestream);
- Write_Zip64EndOfCentralDirectoryRecord(zi, size_centraldir, centraldir_pos_inzip);
-
- Write_Zip64EndOfCentralDirectoryLocator(zi, Zip64EOCDpos);
- }
-
- if (err==ZIP_OK)
- err = Write_EndOfCentralDirectoryRecord(zi, size_centraldir, centraldir_pos_inzip);
-
- if(err == ZIP_OK)
- err = Write_GlobalComment(zi, global_comment);
-
- if (ZCLOSE64(zi->z_filefunc,zi->filestream) != 0)
- if (err == ZIP_OK)
- err = ZIP_ERRNO;
-
-#ifndef NO_ADDFILEINEXISTINGZIP
- TRYFREE(zi->globalcomment);
-#endif
- TRYFREE(zi);
-
- return err;
-}
-
-extern int ZEXPORT zipRemoveExtraInfoBlock (char* pData, int* dataLen, short sHeader)
-{
- char* p = pData;
- int size = 0;
- char* pNewHeader;
- char* pTmp;
- short header;
- short dataSize;
-
- int retVal = ZIP_OK;
-
- if(pData == NULL || *dataLen < 4)
- return ZIP_PARAMERROR;
-
- pNewHeader = (char*)ALLOC(*dataLen);
- pTmp = pNewHeader;
-
- while(p < (pData + *dataLen))
- {
- header = *(short*)p;
- dataSize = *(((short*)p)+1);
-
- if( header == sHeader ) // Header found.
- {
- p += dataSize + 4; // skip it. do not copy to temp buffer
- }
- else
- {
- // Extra Info block should not be removed, So copy it to the temp buffer.
- memcpy(pTmp, p, dataSize + 4);
- p += dataSize + 4;
- size += dataSize + 4;
- }
-
- }
-
- if(size < *dataLen)
- {
- // clean old extra info block.
- memset(pData,0, *dataLen);
-
- // copy the new extra info block over the old
- if(size > 0)
- memcpy(pData, pNewHeader, size);
-
- // set the new extra info size
- *dataLen = size;
-
- retVal = ZIP_OK;
- }
- else
- retVal = ZIP_ERRNO;
-
- TRYFREE(pNewHeader);
-
- return retVal;
-}
diff --git a/third-party/zlib/contrib/minizip/zip.h b/third-party/zlib/contrib/minizip/zip.h
deleted file mode 100644
index 8aaebb6..0000000
--- a/third-party/zlib/contrib/minizip/zip.h
+++ /dev/null
@@ -1,362 +0,0 @@
-/* zip.h -- IO on .zip files using zlib
- Version 1.1, February 14h, 2010
- part of the MiniZip project - ( http://www.winimage.com/zLibDll/minizip.html )
-
- Copyright (C) 1998-2010 Gilles Vollant (minizip) ( http://www.winimage.com/zLibDll/minizip.html )
-
- Modifications for Zip64 support
- Copyright (C) 2009-2010 Mathias Svensson ( http://result42.com )
-
- For more info read MiniZip_info.txt
-
- ---------------------------------------------------------------------------
-
- Condition of use and distribution are the same than zlib :
-
- This software is provided 'as-is', without any express or implied
- warranty. In no event will the authors be held liable for any damages
- arising from the use of this software.
-
- Permission is granted to anyone to use this software for any purpose,
- including commercial applications, and to alter it and redistribute it
- freely, subject to the following restrictions:
-
- 1. The origin of this software must not be misrepresented; you must not
- claim that you wrote the original software. If you use this software
- in a product, an acknowledgment in the product documentation would be
- appreciated but is not required.
- 2. Altered source versions must be plainly marked as such, and must not be
- misrepresented as being the original software.
- 3. This notice may not be removed or altered from any source distribution.
-
- ---------------------------------------------------------------------------
-
- Changes
-
- See header of zip.h
-
-*/
-
-#ifndef _zip12_H
-#define _zip12_H
-
-#ifdef __cplusplus
-extern "C" {
-#endif
-
-//#define HAVE_BZIP2
-
-#ifndef _ZLIB_H
-#include "zlib.h"
-#endif
-
-#ifndef _ZLIBIOAPI_H
-#include "ioapi.h"
-#endif
-
-#ifdef HAVE_BZIP2
-#include "bzlib.h"
-#endif
-
-#define Z_BZIP2ED 12
-
-#if defined(STRICTZIP) || defined(STRICTZIPUNZIP)
-/* like the STRICT of WIN32, we define a pointer that cannot be converted
- from (void*) without cast */
-typedef struct TagzipFile__ { int unused; } zipFile__;
-typedef zipFile__ *zipFile;
-#else
-typedef voidp zipFile;
-#endif
-
-#define ZIP_OK (0)
-#define ZIP_EOF (0)
-#define ZIP_ERRNO (Z_ERRNO)
-#define ZIP_PARAMERROR (-102)
-#define ZIP_BADZIPFILE (-103)
-#define ZIP_INTERNALERROR (-104)
-
-#ifndef DEF_MEM_LEVEL
-# if MAX_MEM_LEVEL >= 8
-# define DEF_MEM_LEVEL 8
-# else
-# define DEF_MEM_LEVEL MAX_MEM_LEVEL
-# endif
-#endif
-/* default memLevel */
-
-/* tm_zip contain date/time info */
-typedef struct tm_zip_s
-{
- uInt tm_sec; /* seconds after the minute - [0,59] */
- uInt tm_min; /* minutes after the hour - [0,59] */
- uInt tm_hour; /* hours since midnight - [0,23] */
- uInt tm_mday; /* day of the month - [1,31] */
- uInt tm_mon; /* months since January - [0,11] */
- uInt tm_year; /* years - [1980..2044] */
-} tm_zip;
-
-typedef struct
-{
- tm_zip tmz_date; /* date in understandable format */
- uLong dosDate; /* if dos_date == 0, tmu_date is used */
-/* uLong flag; */ /* general purpose bit flag 2 bytes */
-
- uLong internal_fa; /* internal file attributes 2 bytes */
- uLong external_fa; /* external file attributes 4 bytes */
-} zip_fileinfo;
-
-typedef const char* zipcharpc;
-
-
-#define APPEND_STATUS_CREATE (0)
-#define APPEND_STATUS_CREATEAFTER (1)
-#define APPEND_STATUS_ADDINZIP (2)
-
-extern zipFile ZEXPORT zipOpen OF((const char *pathname, int append));
-extern zipFile ZEXPORT zipOpen64 OF((const void *pathname, int append));
-/*
- Create a zipfile.
- pathname contain on Windows XP a filename like "c:\\zlib\\zlib113.zip" or on
- an Unix computer "zlib/zlib113.zip".
- if the file pathname exist and append==APPEND_STATUS_CREATEAFTER, the zip
- will be created at the end of the file.
- (useful if the file contain a self extractor code)
- if the file pathname exist and append==APPEND_STATUS_ADDINZIP, we will
- add files in existing zip (be sure you don't add file that doesn't exist)
- If the zipfile cannot be opened, the return value is NULL.
- Else, the return value is a zipFile Handle, usable with other function
- of this zip package.
-*/
-
-/* Note : there is no delete function into a zipfile.
- If you want delete file into a zipfile, you must open a zipfile, and create another
- Of couse, you can use RAW reading and writing to copy the file you did not want delte
-*/
-
-extern zipFile ZEXPORT zipOpen2 OF((const char *pathname,
- int append,
- zipcharpc* globalcomment,
- zlib_filefunc_def* pzlib_filefunc_def));
-
-extern zipFile ZEXPORT zipOpen2_64 OF((const void *pathname,
- int append,
- zipcharpc* globalcomment,
- zlib_filefunc64_def* pzlib_filefunc_def));
-
-extern int ZEXPORT zipOpenNewFileInZip OF((zipFile file,
- const char* filename,
- const zip_fileinfo* zipfi,
- const void* extrafield_local,
- uInt size_extrafield_local,
- const void* extrafield_global,
- uInt size_extrafield_global,
- const char* comment,
- int method,
- int level));
-
-extern int ZEXPORT zipOpenNewFileInZip64 OF((zipFile file,
- const char* filename,
- const zip_fileinfo* zipfi,
- const void* extrafield_local,
- uInt size_extrafield_local,
- const void* extrafield_global,
- uInt size_extrafield_global,
- const char* comment,
- int method,
- int level,
- int zip64));
-
-/*
- Open a file in the ZIP for writing.
- filename : the filename in zip (if NULL, '-' without quote will be used
- *zipfi contain supplemental information
- if extrafield_local!=NULL and size_extrafield_local>0, extrafield_local
- contains the extrafield data the the local header
- if extrafield_global!=NULL and size_extrafield_global>0, extrafield_global
- contains the extrafield data the the local header
- if comment != NULL, comment contain the comment string
- method contain the compression method (0 for store, Z_DEFLATED for deflate)
- level contain the level of compression (can be Z_DEFAULT_COMPRESSION)
- zip64 is set to 1 if a zip64 extended information block should be added to the local file header.
- this MUST be '1' if the uncompressed size is >= 0xffffffff.
-
-*/
-
-
-extern int ZEXPORT zipOpenNewFileInZip2 OF((zipFile file,
- const char* filename,
- const zip_fileinfo* zipfi,
- const void* extrafield_local,
- uInt size_extrafield_local,
- const void* extrafield_global,
- uInt size_extrafield_global,
- const char* comment,
- int method,
- int level,
- int raw));
-
-
-extern int ZEXPORT zipOpenNewFileInZip2_64 OF((zipFile file,
- const char* filename,
- const zip_fileinfo* zipfi,
- const void* extrafield_local,
- uInt size_extrafield_local,
- const void* extrafield_global,
- uInt size_extrafield_global,
- const char* comment,
- int method,
- int level,
- int raw,
- int zip64));
-/*
- Same than zipOpenNewFileInZip, except if raw=1, we write raw file
- */
-
-extern int ZEXPORT zipOpenNewFileInZip3 OF((zipFile file,
- const char* filename,
- const zip_fileinfo* zipfi,
- const void* extrafield_local,
- uInt size_extrafield_local,
- const void* extrafield_global,
- uInt size_extrafield_global,
- const char* comment,
- int method,
- int level,
- int raw,
- int windowBits,
- int memLevel,
- int strategy,
- const char* password,
- uLong crcForCrypting));
-
-extern int ZEXPORT zipOpenNewFileInZip3_64 OF((zipFile file,
- const char* filename,
- const zip_fileinfo* zipfi,
- const void* extrafield_local,
- uInt size_extrafield_local,
- const void* extrafield_global,
- uInt size_extrafield_global,
- const char* comment,
- int method,
- int level,
- int raw,
- int windowBits,
- int memLevel,
- int strategy,
- const char* password,
- uLong crcForCrypting,
- int zip64
- ));
-
-/*
- Same than zipOpenNewFileInZip2, except
- windowBits,memLevel,,strategy : see parameter strategy in deflateInit2
- password : crypting password (NULL for no crypting)
- crcForCrypting : crc of file to compress (needed for crypting)
- */
-
-extern int ZEXPORT zipOpenNewFileInZip4 OF((zipFile file,
- const char* filename,
- const zip_fileinfo* zipfi,
- const void* extrafield_local,
- uInt size_extrafield_local,
- const void* extrafield_global,
- uInt size_extrafield_global,
- const char* comment,
- int method,
- int level,
- int raw,
- int windowBits,
- int memLevel,
- int strategy,
- const char* password,
- uLong crcForCrypting,
- uLong versionMadeBy,
- uLong flagBase
- ));
-
-
-extern int ZEXPORT zipOpenNewFileInZip4_64 OF((zipFile file,
- const char* filename,
- const zip_fileinfo* zipfi,
- const void* extrafield_local,
- uInt size_extrafield_local,
- const void* extrafield_global,
- uInt size_extrafield_global,
- const char* comment,
- int method,
- int level,
- int raw,
- int windowBits,
- int memLevel,
- int strategy,
- const char* password,
- uLong crcForCrypting,
- uLong versionMadeBy,
- uLong flagBase,
- int zip64
- ));
-/*
- Same than zipOpenNewFileInZip4, except
- versionMadeBy : value for Version made by field
- flag : value for flag field (compression level info will be added)
- */
-
-
-extern int ZEXPORT zipWriteInFileInZip OF((zipFile file,
- const void* buf,
- unsigned len));
-/*
- Write data in the zipfile
-*/
-
-extern int ZEXPORT zipCloseFileInZip OF((zipFile file));
-/*
- Close the current file in the zipfile
-*/
-
-extern int ZEXPORT zipCloseFileInZipRaw OF((zipFile file,
- uLong uncompressed_size,
- uLong crc32));
-
-extern int ZEXPORT zipCloseFileInZipRaw64 OF((zipFile file,
- ZPOS64_T uncompressed_size,
- uLong crc32));
-
-/*
- Close the current file in the zipfile, for file opened with
- parameter raw=1 in zipOpenNewFileInZip2
- uncompressed_size and crc32 are value for the uncompressed size
-*/
-
-extern int ZEXPORT zipClose OF((zipFile file,
- const char* global_comment));
-/*
- Close the zipfile
-*/
-
-
-extern int ZEXPORT zipRemoveExtraInfoBlock OF((char* pData, int* dataLen, short sHeader));
-/*
- zipRemoveExtraInfoBlock - Added by Mathias Svensson
-
- Remove extra information block from a extra information data for the local file header or central directory header
-
- It is needed to remove ZIP64 extra information blocks when before data is written if using RAW mode.
-
- 0x0001 is the signature header for the ZIP64 extra information blocks
-
- usage.
- Remove ZIP64 Extra information from a central director extra field data
- zipRemoveExtraInfoBlock(pCenDirExtraFieldData, &nCenDirExtraFieldDataLen, 0x0001);
-
- Remove ZIP64 Extra information from a Local File Header extra field data
- zipRemoveExtraInfoBlock(pLocalHeaderExtraFieldData, &nLocalHeaderExtraFieldDataLen, 0x0001);
-*/
-
-#ifdef __cplusplus
-}
-#endif
-
-#endif /* _zip64_H */
diff --git a/third-party/zlib/contrib/pascal/example.pas b/third-party/zlib/contrib/pascal/example.pas
deleted file mode 100644
index 5518b36..0000000
--- a/third-party/zlib/contrib/pascal/example.pas
+++ /dev/null
@@ -1,599 +0,0 @@
-(* example.c -- usage example of the zlib compression library
- * Copyright (C) 1995-2003 Jean-loup Gailly.
- * For conditions of distribution and use, see copyright notice in zlib.h
- *
- * Pascal translation
- * Copyright (C) 1998 by Jacques Nomssi Nzali.
- * For conditions of distribution and use, see copyright notice in readme.txt
- *
- * Adaptation to the zlibpas interface
- * Copyright (C) 2003 by Cosmin Truta.
- * For conditions of distribution and use, see copyright notice in readme.txt
- *)
-
-program example;
-
-{$DEFINE TEST_COMPRESS}
-{DO NOT $DEFINE TEST_GZIO}
-{$DEFINE TEST_DEFLATE}
-{$DEFINE TEST_INFLATE}
-{$DEFINE TEST_FLUSH}
-{$DEFINE TEST_SYNC}
-{$DEFINE TEST_DICT}
-
-uses SysUtils, zlibpas;
-
-const TESTFILE = 'foo.gz';
-
-(* "hello world" would be more standard, but the repeated "hello"
- * stresses the compression code better, sorry...
- *)
-const hello: PChar = 'hello, hello!';
-
-const dictionary: PChar = 'hello';
-
-var dictId: LongInt; (* Adler32 value of the dictionary *)
-
-procedure CHECK_ERR(err: Integer; msg: String);
-begin
- if err <> Z_OK then
- begin
- WriteLn(msg, ' error: ', err);
- Halt(1);
- end;
-end;
-
-procedure EXIT_ERR(const msg: String);
-begin
- WriteLn('Error: ', msg);
- Halt(1);
-end;
-
-(* ===========================================================================
- * Test compress and uncompress
- *)
-{$IFDEF TEST_COMPRESS}
-procedure test_compress(compr: Pointer; comprLen: LongInt;
- uncompr: Pointer; uncomprLen: LongInt);
-var err: Integer;
- len: LongInt;
-begin
- len := StrLen(hello)+1;
-
- err := compress(compr, comprLen, hello, len);
- CHECK_ERR(err, 'compress');
-
- StrCopy(PChar(uncompr), 'garbage');
-
- err := uncompress(uncompr, uncomprLen, compr, comprLen);
- CHECK_ERR(err, 'uncompress');
-
- if StrComp(PChar(uncompr), hello) <> 0 then
- EXIT_ERR('bad uncompress')
- else
- WriteLn('uncompress(): ', PChar(uncompr));
-end;
-{$ENDIF}
-
-(* ===========================================================================
- * Test read/write of .gz files
- *)
-{$IFDEF TEST_GZIO}
-procedure test_gzio(const fname: PChar; (* compressed file name *)
- uncompr: Pointer;
- uncomprLen: LongInt);
-var err: Integer;
- len: Integer;
- zfile: gzFile;
- pos: LongInt;
-begin
- len := StrLen(hello)+1;
-
- zfile := gzopen(fname, 'wb');
- if zfile = NIL then
- begin
- WriteLn('gzopen error');
- Halt(1);
- end;
- gzputc(zfile, 'h');
- if gzputs(zfile, 'ello') <> 4 then
- begin
- WriteLn('gzputs err: ', gzerror(zfile, err));
- Halt(1);
- end;
- {$IFDEF GZ_FORMAT_STRING}
- if gzprintf(zfile, ', %s!', 'hello') <> 8 then
- begin
- WriteLn('gzprintf err: ', gzerror(zfile, err));
- Halt(1);
- end;
- {$ELSE}
- if gzputs(zfile, ', hello!') <> 8 then
- begin
- WriteLn('gzputs err: ', gzerror(zfile, err));
- Halt(1);
- end;
- {$ENDIF}
- gzseek(zfile, 1, SEEK_CUR); (* add one zero byte *)
- gzclose(zfile);
-
- zfile := gzopen(fname, 'rb');
- if zfile = NIL then
- begin
- WriteLn('gzopen error');
- Halt(1);
- end;
-
- StrCopy(PChar(uncompr), 'garbage');
-
- if gzread(zfile, uncompr, uncomprLen) <> len then
- begin
- WriteLn('gzread err: ', gzerror(zfile, err));
- Halt(1);
- end;
- if StrComp(PChar(uncompr), hello) <> 0 then
- begin
- WriteLn('bad gzread: ', PChar(uncompr));
- Halt(1);
- end
- else
- WriteLn('gzread(): ', PChar(uncompr));
-
- pos := gzseek(zfile, -8, SEEK_CUR);
- if (pos <> 6) or (gztell(zfile) <> pos) then
- begin
- WriteLn('gzseek error, pos=', pos, ', gztell=', gztell(zfile));
- Halt(1);
- end;
-
- if gzgetc(zfile) <> ' ' then
- begin
- WriteLn('gzgetc error');
- Halt(1);
- end;
-
- if gzungetc(' ', zfile) <> ' ' then
- begin
- WriteLn('gzungetc error');
- Halt(1);
- end;
-
- gzgets(zfile, PChar(uncompr), uncomprLen);
- uncomprLen := StrLen(PChar(uncompr));
- if uncomprLen <> 7 then (* " hello!" *)
- begin
- WriteLn('gzgets err after gzseek: ', gzerror(zfile, err));
- Halt(1);
- end;
- if StrComp(PChar(uncompr), hello + 6) <> 0 then
- begin
- WriteLn('bad gzgets after gzseek');
- Halt(1);
- end
- else
- WriteLn('gzgets() after gzseek: ', PChar(uncompr));
-
- gzclose(zfile);
-end;
-{$ENDIF}
-
-(* ===========================================================================
- * Test deflate with small buffers
- *)
-{$IFDEF TEST_DEFLATE}
-procedure test_deflate(compr: Pointer; comprLen: LongInt);
-var c_stream: z_stream; (* compression stream *)
- err: Integer;
- len: LongInt;
-begin
- len := StrLen(hello)+1;
-
- c_stream.zalloc := NIL;
- c_stream.zfree := NIL;
- c_stream.opaque := NIL;
-
- err := deflateInit(c_stream, Z_DEFAULT_COMPRESSION);
- CHECK_ERR(err, 'deflateInit');
-
- c_stream.next_in := hello;
- c_stream.next_out := compr;
-
- while (c_stream.total_in <> len) and
- (c_stream.total_out < comprLen) do
- begin
- c_stream.avail_out := 1; { force small buffers }
- c_stream.avail_in := 1;
- err := deflate(c_stream, Z_NO_FLUSH);
- CHECK_ERR(err, 'deflate');
- end;
-
- (* Finish the stream, still forcing small buffers: *)
- while TRUE do
- begin
- c_stream.avail_out := 1;
- err := deflate(c_stream, Z_FINISH);
- if err = Z_STREAM_END then
- break;
- CHECK_ERR(err, 'deflate');
- end;
-
- err := deflateEnd(c_stream);
- CHECK_ERR(err, 'deflateEnd');
-end;
-{$ENDIF}
-
-(* ===========================================================================
- * Test inflate with small buffers
- *)
-{$IFDEF TEST_INFLATE}
-procedure test_inflate(compr: Pointer; comprLen : LongInt;
- uncompr: Pointer; uncomprLen : LongInt);
-var err: Integer;
- d_stream: z_stream; (* decompression stream *)
-begin
- StrCopy(PChar(uncompr), 'garbage');
-
- d_stream.zalloc := NIL;
- d_stream.zfree := NIL;
- d_stream.opaque := NIL;
-
- d_stream.next_in := compr;
- d_stream.avail_in := 0;
- d_stream.next_out := uncompr;
-
- err := inflateInit(d_stream);
- CHECK_ERR(err, 'inflateInit');
-
- while (d_stream.total_out < uncomprLen) and
- (d_stream.total_in < comprLen) do
- begin
- d_stream.avail_out := 1; (* force small buffers *)
- d_stream.avail_in := 1;
- err := inflate(d_stream, Z_NO_FLUSH);
- if err = Z_STREAM_END then
- break;
- CHECK_ERR(err, 'inflate');
- end;
-
- err := inflateEnd(d_stream);
- CHECK_ERR(err, 'inflateEnd');
-
- if StrComp(PChar(uncompr), hello) <> 0 then
- EXIT_ERR('bad inflate')
- else
- WriteLn('inflate(): ', PChar(uncompr));
-end;
-{$ENDIF}
-
-(* ===========================================================================
- * Test deflate with large buffers and dynamic change of compression level
- *)
-{$IFDEF TEST_DEFLATE}
-procedure test_large_deflate(compr: Pointer; comprLen: LongInt;
- uncompr: Pointer; uncomprLen: LongInt);
-var c_stream: z_stream; (* compression stream *)
- err: Integer;
-begin
- c_stream.zalloc := NIL;
- c_stream.zfree := NIL;
- c_stream.opaque := NIL;
-
- err := deflateInit(c_stream, Z_BEST_SPEED);
- CHECK_ERR(err, 'deflateInit');
-
- c_stream.next_out := compr;
- c_stream.avail_out := Integer(comprLen);
-
- (* At this point, uncompr is still mostly zeroes, so it should compress
- * very well:
- *)
- c_stream.next_in := uncompr;
- c_stream.avail_in := Integer(uncomprLen);
- err := deflate(c_stream, Z_NO_FLUSH);
- CHECK_ERR(err, 'deflate');
- if c_stream.avail_in <> 0 then
- EXIT_ERR('deflate not greedy');
-
- (* Feed in already compressed data and switch to no compression: *)
- deflateParams(c_stream, Z_NO_COMPRESSION, Z_DEFAULT_STRATEGY);
- c_stream.next_in := compr;
- c_stream.avail_in := Integer(comprLen div 2);
- err := deflate(c_stream, Z_NO_FLUSH);
- CHECK_ERR(err, 'deflate');
-
- (* Switch back to compressing mode: *)
- deflateParams(c_stream, Z_BEST_COMPRESSION, Z_FILTERED);
- c_stream.next_in := uncompr;
- c_stream.avail_in := Integer(uncomprLen);
- err := deflate(c_stream, Z_NO_FLUSH);
- CHECK_ERR(err, 'deflate');
-
- err := deflate(c_stream, Z_FINISH);
- if err <> Z_STREAM_END then
- EXIT_ERR('deflate should report Z_STREAM_END');
-
- err := deflateEnd(c_stream);
- CHECK_ERR(err, 'deflateEnd');
-end;
-{$ENDIF}
-
-(* ===========================================================================
- * Test inflate with large buffers
- *)
-{$IFDEF TEST_INFLATE}
-procedure test_large_inflate(compr: Pointer; comprLen: LongInt;
- uncompr: Pointer; uncomprLen: LongInt);
-var err: Integer;
- d_stream: z_stream; (* decompression stream *)
-begin
- StrCopy(PChar(uncompr), 'garbage');
-
- d_stream.zalloc := NIL;
- d_stream.zfree := NIL;
- d_stream.opaque := NIL;
-
- d_stream.next_in := compr;
- d_stream.avail_in := Integer(comprLen);
-
- err := inflateInit(d_stream);
- CHECK_ERR(err, 'inflateInit');
-
- while TRUE do
- begin
- d_stream.next_out := uncompr; (* discard the output *)
- d_stream.avail_out := Integer(uncomprLen);
- err := inflate(d_stream, Z_NO_FLUSH);
- if err = Z_STREAM_END then
- break;
- CHECK_ERR(err, 'large inflate');
- end;
-
- err := inflateEnd(d_stream);
- CHECK_ERR(err, 'inflateEnd');
-
- if d_stream.total_out <> 2 * uncomprLen + comprLen div 2 then
- begin
- WriteLn('bad large inflate: ', d_stream.total_out);
- Halt(1);
- end
- else
- WriteLn('large_inflate(): OK');
-end;
-{$ENDIF}
-
-(* ===========================================================================
- * Test deflate with full flush
- *)
-{$IFDEF TEST_FLUSH}
-procedure test_flush(compr: Pointer; var comprLen : LongInt);
-var c_stream: z_stream; (* compression stream *)
- err: Integer;
- len: Integer;
-begin
- len := StrLen(hello)+1;
-
- c_stream.zalloc := NIL;
- c_stream.zfree := NIL;
- c_stream.opaque := NIL;
-
- err := deflateInit(c_stream, Z_DEFAULT_COMPRESSION);
- CHECK_ERR(err, 'deflateInit');
-
- c_stream.next_in := hello;
- c_stream.next_out := compr;
- c_stream.avail_in := 3;
- c_stream.avail_out := Integer(comprLen);
- err := deflate(c_stream, Z_FULL_FLUSH);
- CHECK_ERR(err, 'deflate');
-
- Inc(PByteArray(compr)^[3]); (* force an error in first compressed block *)
- c_stream.avail_in := len - 3;
-
- err := deflate(c_stream, Z_FINISH);
- if err <> Z_STREAM_END then
- CHECK_ERR(err, 'deflate');
-
- err := deflateEnd(c_stream);
- CHECK_ERR(err, 'deflateEnd');
-
- comprLen := c_stream.total_out;
-end;
-{$ENDIF}
-
-(* ===========================================================================
- * Test inflateSync()
- *)
-{$IFDEF TEST_SYNC}
-procedure test_sync(compr: Pointer; comprLen: LongInt;
- uncompr: Pointer; uncomprLen : LongInt);
-var err: Integer;
- d_stream: z_stream; (* decompression stream *)
-begin
- StrCopy(PChar(uncompr), 'garbage');
-
- d_stream.zalloc := NIL;
- d_stream.zfree := NIL;
- d_stream.opaque := NIL;
-
- d_stream.next_in := compr;
- d_stream.avail_in := 2; (* just read the zlib header *)
-
- err := inflateInit(d_stream);
- CHECK_ERR(err, 'inflateInit');
-
- d_stream.next_out := uncompr;
- d_stream.avail_out := Integer(uncomprLen);
-
- inflate(d_stream, Z_NO_FLUSH);
- CHECK_ERR(err, 'inflate');
-
- d_stream.avail_in := Integer(comprLen-2); (* read all compressed data *)
- err := inflateSync(d_stream); (* but skip the damaged part *)
- CHECK_ERR(err, 'inflateSync');
-
- err := inflate(d_stream, Z_FINISH);
- if err <> Z_DATA_ERROR then
- EXIT_ERR('inflate should report DATA_ERROR');
- (* Because of incorrect adler32 *)
-
- err := inflateEnd(d_stream);
- CHECK_ERR(err, 'inflateEnd');
-
- WriteLn('after inflateSync(): hel', PChar(uncompr));
-end;
-{$ENDIF}
-
-(* ===========================================================================
- * Test deflate with preset dictionary
- *)
-{$IFDEF TEST_DICT}
-procedure test_dict_deflate(compr: Pointer; comprLen: LongInt);
-var c_stream: z_stream; (* compression stream *)
- err: Integer;
-begin
- c_stream.zalloc := NIL;
- c_stream.zfree := NIL;
- c_stream.opaque := NIL;
-
- err := deflateInit(c_stream, Z_BEST_COMPRESSION);
- CHECK_ERR(err, 'deflateInit');
-
- err := deflateSetDictionary(c_stream, dictionary, StrLen(dictionary));
- CHECK_ERR(err, 'deflateSetDictionary');
-
- dictId := c_stream.adler;
- c_stream.next_out := compr;
- c_stream.avail_out := Integer(comprLen);
-
- c_stream.next_in := hello;
- c_stream.avail_in := StrLen(hello)+1;
-
- err := deflate(c_stream, Z_FINISH);
- if err <> Z_STREAM_END then
- EXIT_ERR('deflate should report Z_STREAM_END');
-
- err := deflateEnd(c_stream);
- CHECK_ERR(err, 'deflateEnd');
-end;
-{$ENDIF}
-
-(* ===========================================================================
- * Test inflate with a preset dictionary
- *)
-{$IFDEF TEST_DICT}
-procedure test_dict_inflate(compr: Pointer; comprLen: LongInt;
- uncompr: Pointer; uncomprLen: LongInt);
-var err: Integer;
- d_stream: z_stream; (* decompression stream *)
-begin
- StrCopy(PChar(uncompr), 'garbage');
-
- d_stream.zalloc := NIL;
- d_stream.zfree := NIL;
- d_stream.opaque := NIL;
-
- d_stream.next_in := compr;
- d_stream.avail_in := Integer(comprLen);
-
- err := inflateInit(d_stream);
- CHECK_ERR(err, 'inflateInit');
-
- d_stream.next_out := uncompr;
- d_stream.avail_out := Integer(uncomprLen);
-
- while TRUE do
- begin
- err := inflate(d_stream, Z_NO_FLUSH);
- if err = Z_STREAM_END then
- break;
- if err = Z_NEED_DICT then
- begin
- if d_stream.adler <> dictId then
- EXIT_ERR('unexpected dictionary');
- err := inflateSetDictionary(d_stream, dictionary, StrLen(dictionary));
- end;
- CHECK_ERR(err, 'inflate with dict');
- end;
-
- err := inflateEnd(d_stream);
- CHECK_ERR(err, 'inflateEnd');
-
- if StrComp(PChar(uncompr), hello) <> 0 then
- EXIT_ERR('bad inflate with dict')
- else
- WriteLn('inflate with dictionary: ', PChar(uncompr));
-end;
-{$ENDIF}
-
-var compr, uncompr: Pointer;
- comprLen, uncomprLen: LongInt;
-
-begin
- if zlibVersion^ <> ZLIB_VERSION[1] then
- EXIT_ERR('Incompatible zlib version');
-
- WriteLn('zlib version: ', zlibVersion);
- WriteLn('zlib compile flags: ', Format('0x%x', [zlibCompileFlags]));
-
- comprLen := 10000 * SizeOf(Integer); (* don't overflow on MSDOS *)
- uncomprLen := comprLen;
- GetMem(compr, comprLen);
- GetMem(uncompr, uncomprLen);
- if (compr = NIL) or (uncompr = NIL) then
- EXIT_ERR('Out of memory');
- (* compr and uncompr are cleared to avoid reading uninitialized
- * data and to ensure that uncompr compresses well.
- *)
- FillChar(compr^, comprLen, 0);
- FillChar(uncompr^, uncomprLen, 0);
-
- {$IFDEF TEST_COMPRESS}
- WriteLn('** Testing compress');
- test_compress(compr, comprLen, uncompr, uncomprLen);
- {$ENDIF}
-
- {$IFDEF TEST_GZIO}
- WriteLn('** Testing gzio');
- if ParamCount >= 1 then
- test_gzio(ParamStr(1), uncompr, uncomprLen)
- else
- test_gzio(TESTFILE, uncompr, uncomprLen);
- {$ENDIF}
-
- {$IFDEF TEST_DEFLATE}
- WriteLn('** Testing deflate with small buffers');
- test_deflate(compr, comprLen);
- {$ENDIF}
- {$IFDEF TEST_INFLATE}
- WriteLn('** Testing inflate with small buffers');
- test_inflate(compr, comprLen, uncompr, uncomprLen);
- {$ENDIF}
-
- {$IFDEF TEST_DEFLATE}
- WriteLn('** Testing deflate with large buffers');
- test_large_deflate(compr, comprLen, uncompr, uncomprLen);
- {$ENDIF}
- {$IFDEF TEST_INFLATE}
- WriteLn('** Testing inflate with large buffers');
- test_large_inflate(compr, comprLen, uncompr, uncomprLen);
- {$ENDIF}
-
- {$IFDEF TEST_FLUSH}
- WriteLn('** Testing deflate with full flush');
- test_flush(compr, comprLen);
- {$ENDIF}
- {$IFDEF TEST_SYNC}
- WriteLn('** Testing inflateSync');
- test_sync(compr, comprLen, uncompr, uncomprLen);
- {$ENDIF}
- comprLen := uncomprLen;
-
- {$IFDEF TEST_DICT}
- WriteLn('** Testing deflate and inflate with preset dictionary');
- test_dict_deflate(compr, comprLen);
- test_dict_inflate(compr, comprLen, uncompr, uncomprLen);
- {$ENDIF}
-
- FreeMem(compr, comprLen);
- FreeMem(uncompr, uncomprLen);
-end.
diff --git a/third-party/zlib/contrib/pascal/readme.txt b/third-party/zlib/contrib/pascal/readme.txt
deleted file mode 100644
index 60e87c8..0000000
--- a/third-party/zlib/contrib/pascal/readme.txt
+++ /dev/null
@@ -1,76 +0,0 @@
-
-This directory contains a Pascal (Delphi, Kylix) interface to the
-zlib data compression library.
-
-
-Directory listing
-=================
-
-zlibd32.mak makefile for Borland C++
-example.pas usage example of zlib
-zlibpas.pas the Pascal interface to zlib
-readme.txt this file
-
-
-Compatibility notes
-===================
-
-- Although the name "zlib" would have been more normal for the
- zlibpas unit, this name is already taken by Borland's ZLib unit.
- This is somehow unfortunate, because that unit is not a genuine
- interface to the full-fledged zlib functionality, but a suite of
- class wrappers around zlib streams. Other essential features,
- such as checksums, are missing.
- It would have been more appropriate for that unit to have a name
- like "ZStreams", or something similar.
-
-- The C and zlib-supplied types int, uInt, long, uLong, etc. are
- translated directly into Pascal types of similar sizes (Integer,
- LongInt, etc.), to avoid namespace pollution. In particular,
- there is no conversion of unsigned int into a Pascal unsigned
- integer. The Word type is non-portable and has the same size
- (16 bits) both in a 16-bit and in a 32-bit environment, unlike
- Integer. Even if there is a 32-bit Cardinal type, there is no
- real need for unsigned int in zlib under a 32-bit environment.
-
-- Except for the callbacks, the zlib function interfaces are
- assuming the calling convention normally used in Pascal
- (__pascal for DOS and Windows16, __fastcall for Windows32).
- Since the cdecl keyword is used, the old Turbo Pascal does
- not work with this interface.
-
-- The gz* function interfaces are not translated, to avoid
- interfacing problems with the C runtime library. Besides,
- gzprintf(gzFile file, const char *format, ...)
- cannot be translated into Pascal.
-
-
-Legal issues
-============
-
-The zlibpas interface is:
- Copyright (C) 1995-2003 Jean-loup Gailly and Mark Adler.
- Copyright (C) 1998 by Bob Dellaca.
- Copyright (C) 2003 by Cosmin Truta.
-
-The example program is:
- Copyright (C) 1995-2003 by Jean-loup Gailly.
- Copyright (C) 1998,1999,2000 by Jacques Nomssi Nzali.
- Copyright (C) 2003 by Cosmin Truta.
-
- This software is provided 'as-is', without any express or implied
- warranty. In no event will the author be held liable for any damages
- arising from the use of this software.
-
- Permission is granted to anyone to use this software for any purpose,
- including commercial applications, and to alter it and redistribute it
- freely, subject to the following restrictions:
-
- 1. The origin of this software must not be misrepresented; you must not
- claim that you wrote the original software. If you use this software
- in a product, an acknowledgment in the product documentation would be
- appreciated but is not required.
- 2. Altered source versions must be plainly marked as such, and must not be
- misrepresented as being the original software.
- 3. This notice may not be removed or altered from any source distribution.
-
diff --git a/third-party/zlib/contrib/pascal/zlibd32.mak b/third-party/zlib/contrib/pascal/zlibd32.mak
deleted file mode 100644
index 9bb00b7..0000000
--- a/third-party/zlib/contrib/pascal/zlibd32.mak
+++ /dev/null
@@ -1,99 +0,0 @@
-# Makefile for zlib
-# For use with Delphi and C++ Builder under Win32
-# Updated for zlib 1.2.x by Cosmin Truta
-
-# ------------ Borland C++ ------------
-
-# This project uses the Delphi (fastcall/register) calling convention:
-LOC = -DZEXPORT=__fastcall -DZEXPORTVA=__cdecl
-
-CC = bcc32
-LD = bcc32
-AR = tlib
-# do not use "-pr" in CFLAGS
-CFLAGS = -a -d -k- -O2 $(LOC)
-LDFLAGS =
-
-
-# variables
-ZLIB_LIB = zlib.lib
-
-OBJ1 = adler32.obj compress.obj crc32.obj deflate.obj gzclose.obj gzlib.obj gzread.obj
-OBJ2 = gzwrite.obj infback.obj inffast.obj inflate.obj inftrees.obj trees.obj uncompr.obj zutil.obj
-OBJP1 = +adler32.obj+compress.obj+crc32.obj+deflate.obj+gzclose.obj+gzlib.obj+gzread.obj
-OBJP2 = +gzwrite.obj+infback.obj+inffast.obj+inflate.obj+inftrees.obj+trees.obj+uncompr.obj+zutil.obj
-
-
-# targets
-all: $(ZLIB_LIB) example.exe minigzip.exe
-
-.c.obj:
- $(CC) -c $(CFLAGS) $*.c
-
-adler32.obj: adler32.c zlib.h zconf.h
-
-compress.obj: compress.c zlib.h zconf.h
-
-crc32.obj: crc32.c zlib.h zconf.h crc32.h
-
-deflate.obj: deflate.c deflate.h zutil.h zlib.h zconf.h
-
-gzclose.obj: gzclose.c zlib.h zconf.h gzguts.h
-
-gzlib.obj: gzlib.c zlib.h zconf.h gzguts.h
-
-gzread.obj: gzread.c zlib.h zconf.h gzguts.h
-
-gzwrite.obj: gzwrite.c zlib.h zconf.h gzguts.h
-
-infback.obj: infback.c zutil.h zlib.h zconf.h inftrees.h inflate.h \
- inffast.h inffixed.h
-
-inffast.obj: inffast.c zutil.h zlib.h zconf.h inftrees.h inflate.h \
- inffast.h
-
-inflate.obj: inflate.c zutil.h zlib.h zconf.h inftrees.h inflate.h \
- inffast.h inffixed.h
-
-inftrees.obj: inftrees.c zutil.h zlib.h zconf.h inftrees.h
-
-trees.obj: trees.c zutil.h zlib.h zconf.h deflate.h trees.h
-
-uncompr.obj: uncompr.c zlib.h zconf.h
-
-zutil.obj: zutil.c zutil.h zlib.h zconf.h
-
-example.obj: test/example.c zlib.h zconf.h
-
-minigzip.obj: test/minigzip.c zlib.h zconf.h
-
-
-# For the sake of the old Borland make,
-# the command line is cut to fit in the MS-DOS 128 byte limit:
-$(ZLIB_LIB): $(OBJ1) $(OBJ2)
- -del $(ZLIB_LIB)
- $(AR) $(ZLIB_LIB) $(OBJP1)
- $(AR) $(ZLIB_LIB) $(OBJP2)
-
-
-# testing
-test: example.exe minigzip.exe
- example
- echo hello world | minigzip | minigzip -d
-
-example.exe: example.obj $(ZLIB_LIB)
- $(LD) $(LDFLAGS) example.obj $(ZLIB_LIB)
-
-minigzip.exe: minigzip.obj $(ZLIB_LIB)
- $(LD) $(LDFLAGS) minigzip.obj $(ZLIB_LIB)
-
-
-# cleanup
-clean:
- -del *.obj
- -del *.exe
- -del *.lib
- -del *.tds
- -del zlib.bak
- -del foo.gz
-
diff --git a/third-party/zlib/contrib/pascal/zlibpas.pas b/third-party/zlib/contrib/pascal/zlibpas.pas
deleted file mode 100644
index e6a0782..0000000
--- a/third-party/zlib/contrib/pascal/zlibpas.pas
+++ /dev/null
@@ -1,276 +0,0 @@
-(* zlibpas -- Pascal interface to the zlib data compression library
- *
- * Copyright (C) 2003 Cosmin Truta.
- * Derived from original sources by Bob Dellaca.
- * For conditions of distribution and use, see copyright notice in readme.txt
- *)
-
-unit zlibpas;
-
-interface
-
-const
- ZLIB_VERSION = '1.2.8';
- ZLIB_VERNUM = $1280;
-
-type
- alloc_func = function(opaque: Pointer; items, size: Integer): Pointer;
- cdecl;
- free_func = procedure(opaque, address: Pointer);
- cdecl;
-
- in_func = function(opaque: Pointer; var buf: PByte): Integer;
- cdecl;
- out_func = function(opaque: Pointer; buf: PByte; size: Integer): Integer;
- cdecl;
-
- z_streamp = ^z_stream;
- z_stream = packed record
- next_in: PChar; (* next input byte *)
- avail_in: Integer; (* number of bytes available at next_in *)
- total_in: LongInt; (* total nb of input bytes read so far *)
-
- next_out: PChar; (* next output byte should be put there *)
- avail_out: Integer; (* remaining free space at next_out *)
- total_out: LongInt; (* total nb of bytes output so far *)
-
- msg: PChar; (* last error message, NULL if no error *)
- state: Pointer; (* not visible by applications *)
-
- zalloc: alloc_func; (* used to allocate the internal state *)
- zfree: free_func; (* used to free the internal state *)
- opaque: Pointer; (* private data object passed to zalloc and zfree *)
-
- data_type: Integer; (* best guess about the data type: ascii or binary *)
- adler: LongInt; (* adler32 value of the uncompressed data *)
- reserved: LongInt; (* reserved for future use *)
- end;
-
- gz_headerp = ^gz_header;
- gz_header = packed record
- text: Integer; (* true if compressed data believed to be text *)
- time: LongInt; (* modification time *)
- xflags: Integer; (* extra flags (not used when writing a gzip file) *)
- os: Integer; (* operating system *)
- extra: PChar; (* pointer to extra field or Z_NULL if none *)
- extra_len: Integer; (* extra field length (valid if extra != Z_NULL) *)
- extra_max: Integer; (* space at extra (only when reading header) *)
- name: PChar; (* pointer to zero-terminated file name or Z_NULL *)
- name_max: Integer; (* space at name (only when reading header) *)
- comment: PChar; (* pointer to zero-terminated comment or Z_NULL *)
- comm_max: Integer; (* space at comment (only when reading header) *)
- hcrc: Integer; (* true if there was or will be a header crc *)
- done: Integer; (* true when done reading gzip header *)
- end;
-
-(* constants *)
-const
- Z_NO_FLUSH = 0;
- Z_PARTIAL_FLUSH = 1;
- Z_SYNC_FLUSH = 2;
- Z_FULL_FLUSH = 3;
- Z_FINISH = 4;
- Z_BLOCK = 5;
- Z_TREES = 6;
-
- Z_OK = 0;
- Z_STREAM_END = 1;
- Z_NEED_DICT = 2;
- Z_ERRNO = -1;
- Z_STREAM_ERROR = -2;
- Z_DATA_ERROR = -3;
- Z_MEM_ERROR = -4;
- Z_BUF_ERROR = -5;
- Z_VERSION_ERROR = -6;
-
- Z_NO_COMPRESSION = 0;
- Z_BEST_SPEED = 1;
- Z_BEST_COMPRESSION = 9;
- Z_DEFAULT_COMPRESSION = -1;
-
- Z_FILTERED = 1;
- Z_HUFFMAN_ONLY = 2;
- Z_RLE = 3;
- Z_FIXED = 4;
- Z_DEFAULT_STRATEGY = 0;
-
- Z_BINARY = 0;
- Z_TEXT = 1;
- Z_ASCII = 1;
- Z_UNKNOWN = 2;
-
- Z_DEFLATED = 8;
-
-(* basic functions *)
-function zlibVersion: PChar;
-function deflateInit(var strm: z_stream; level: Integer): Integer;
-function deflate(var strm: z_stream; flush: Integer): Integer;
-function deflateEnd(var strm: z_stream): Integer;
-function inflateInit(var strm: z_stream): Integer;
-function inflate(var strm: z_stream; flush: Integer): Integer;
-function inflateEnd(var strm: z_stream): Integer;
-
-(* advanced functions *)
-function deflateInit2(var strm: z_stream; level, method, windowBits,
- memLevel, strategy: Integer): Integer;
-function deflateSetDictionary(var strm: z_stream; const dictionary: PChar;
- dictLength: Integer): Integer;
-function deflateCopy(var dest, source: z_stream): Integer;
-function deflateReset(var strm: z_stream): Integer;
-function deflateParams(var strm: z_stream; level, strategy: Integer): Integer;
-function deflateTune(var strm: z_stream; good_length, max_lazy, nice_length, max_chain: Integer): Integer;
-function deflateBound(var strm: z_stream; sourceLen: LongInt): LongInt;
-function deflatePending(var strm: z_stream; var pending: Integer; var bits: Integer): Integer;
-function deflatePrime(var strm: z_stream; bits, value: Integer): Integer;
-function deflateSetHeader(var strm: z_stream; head: gz_header): Integer;
-function inflateInit2(var strm: z_stream; windowBits: Integer): Integer;
-function inflateSetDictionary(var strm: z_stream; const dictionary: PChar;
- dictLength: Integer): Integer;
-function inflateSync(var strm: z_stream): Integer;
-function inflateCopy(var dest, source: z_stream): Integer;
-function inflateReset(var strm: z_stream): Integer;
-function inflateReset2(var strm: z_stream; windowBits: Integer): Integer;
-function inflatePrime(var strm: z_stream; bits, value: Integer): Integer;
-function inflateMark(var strm: z_stream): LongInt;
-function inflateGetHeader(var strm: z_stream; var head: gz_header): Integer;
-function inflateBackInit(var strm: z_stream;
- windowBits: Integer; window: PChar): Integer;
-function inflateBack(var strm: z_stream; in_fn: in_func; in_desc: Pointer;
- out_fn: out_func; out_desc: Pointer): Integer;
-function inflateBackEnd(var strm: z_stream): Integer;
-function zlibCompileFlags: LongInt;
-
-(* utility functions *)
-function compress(dest: PChar; var destLen: LongInt;
- const source: PChar; sourceLen: LongInt): Integer;
-function compress2(dest: PChar; var destLen: LongInt;
- const source: PChar; sourceLen: LongInt;
- level: Integer): Integer;
-function compressBound(sourceLen: LongInt): LongInt;
-function uncompress(dest: PChar; var destLen: LongInt;
- const source: PChar; sourceLen: LongInt): Integer;
-
-(* checksum functions *)
-function adler32(adler: LongInt; const buf: PChar; len: Integer): LongInt;
-function adler32_combine(adler1, adler2, len2: LongInt): LongInt;
-function crc32(crc: LongInt; const buf: PChar; len: Integer): LongInt;
-function crc32_combine(crc1, crc2, len2: LongInt): LongInt;
-
-(* various hacks, don't look :) *)
-function deflateInit_(var strm: z_stream; level: Integer;
- const version: PChar; stream_size: Integer): Integer;
-function inflateInit_(var strm: z_stream; const version: PChar;
- stream_size: Integer): Integer;
-function deflateInit2_(var strm: z_stream;
- level, method, windowBits, memLevel, strategy: Integer;
- const version: PChar; stream_size: Integer): Integer;
-function inflateInit2_(var strm: z_stream; windowBits: Integer;
- const version: PChar; stream_size: Integer): Integer;
-function inflateBackInit_(var strm: z_stream;
- windowBits: Integer; window: PChar;
- const version: PChar; stream_size: Integer): Integer;
-
-
-implementation
-
-{$L adler32.obj}
-{$L compress.obj}
-{$L crc32.obj}
-{$L deflate.obj}
-{$L infback.obj}
-{$L inffast.obj}
-{$L inflate.obj}
-{$L inftrees.obj}
-{$L trees.obj}
-{$L uncompr.obj}
-{$L zutil.obj}
-
-function adler32; external;
-function adler32_combine; external;
-function compress; external;
-function compress2; external;
-function compressBound; external;
-function crc32; external;
-function crc32_combine; external;
-function deflate; external;
-function deflateBound; external;
-function deflateCopy; external;
-function deflateEnd; external;
-function deflateInit_; external;
-function deflateInit2_; external;
-function deflateParams; external;
-function deflatePending; external;
-function deflatePrime; external;
-function deflateReset; external;
-function deflateSetDictionary; external;
-function deflateSetHeader; external;
-function deflateTune; external;
-function inflate; external;
-function inflateBack; external;
-function inflateBackEnd; external;
-function inflateBackInit_; external;
-function inflateCopy; external;
-function inflateEnd; external;
-function inflateGetHeader; external;
-function inflateInit_; external;
-function inflateInit2_; external;
-function inflateMark; external;
-function inflatePrime; external;
-function inflateReset; external;
-function inflateReset2; external;
-function inflateSetDictionary; external;
-function inflateSync; external;
-function uncompress; external;
-function zlibCompileFlags; external;
-function zlibVersion; external;
-
-function deflateInit(var strm: z_stream; level: Integer): Integer;
-begin
- Result := deflateInit_(strm, level, ZLIB_VERSION, sizeof(z_stream));
-end;
-
-function deflateInit2(var strm: z_stream; level, method, windowBits, memLevel,
- strategy: Integer): Integer;
-begin
- Result := deflateInit2_(strm, level, method, windowBits, memLevel, strategy,
- ZLIB_VERSION, sizeof(z_stream));
-end;
-
-function inflateInit(var strm: z_stream): Integer;
-begin
- Result := inflateInit_(strm, ZLIB_VERSION, sizeof(z_stream));
-end;
-
-function inflateInit2(var strm: z_stream; windowBits: Integer): Integer;
-begin
- Result := inflateInit2_(strm, windowBits, ZLIB_VERSION, sizeof(z_stream));
-end;
-
-function inflateBackInit(var strm: z_stream;
- windowBits: Integer; window: PChar): Integer;
-begin
- Result := inflateBackInit_(strm, windowBits, window,
- ZLIB_VERSION, sizeof(z_stream));
-end;
-
-function _malloc(Size: Integer): Pointer; cdecl;
-begin
- GetMem(Result, Size);
-end;
-
-procedure _free(Block: Pointer); cdecl;
-begin
- FreeMem(Block);
-end;
-
-procedure _memset(P: Pointer; B: Byte; count: Integer); cdecl;
-begin
- FillChar(P^, count, B);
-end;
-
-procedure _memcpy(dest, source: Pointer; count: Integer); cdecl;
-begin
- Move(source^, dest^, count);
-end;
-
-end.
diff --git a/third-party/zlib/contrib/puff/Makefile b/third-party/zlib/contrib/puff/Makefile
deleted file mode 100644
index 0e2594c..0000000
--- a/third-party/zlib/contrib/puff/Makefile
+++ /dev/null
@@ -1,42 +0,0 @@
-CFLAGS=-O
-
-puff: puff.o pufftest.o
-
-puff.o: puff.h
-
-pufftest.o: puff.h
-
-test: puff
- puff zeros.raw
-
-puft: puff.c puff.h pufftest.o
- cc -fprofile-arcs -ftest-coverage -o puft puff.c pufftest.o
-
-# puff full coverage test (should say 100%)
-cov: puft
- @rm -f *.gcov *.gcda
- @puft -w zeros.raw 2>&1 | cat > /dev/null
- @echo '04' | xxd -r -p | puft 2> /dev/null || test $$? -eq 2
- @echo '00' | xxd -r -p | puft 2> /dev/null || test $$? -eq 2
- @echo '00 00 00 00 00' | xxd -r -p | puft 2> /dev/null || test $$? -eq 254
- @echo '00 01 00 fe ff' | xxd -r -p | puft 2> /dev/null || test $$? -eq 2
- @echo '01 01 00 fe ff 0a' | xxd -r -p | puft -f 2>&1 | cat > /dev/null
- @echo '02 7e ff ff' | xxd -r -p | puft 2> /dev/null || test $$? -eq 246
- @echo '02' | xxd -r -p | puft 2> /dev/null || test $$? -eq 2
- @echo '04 80 49 92 24 49 92 24 0f b4 ff ff c3 04' | xxd -r -p | puft 2> /dev/null || test $$? -eq 2
- @echo '04 80 49 92 24 49 92 24 71 ff ff 93 11 00' | xxd -r -p | puft 2> /dev/null || test $$? -eq 249
- @echo '04 c0 81 08 00 00 00 00 20 7f eb 0b 00 00' | xxd -r -p | puft 2> /dev/null || test $$? -eq 246
- @echo '0b 00 00' | xxd -r -p | puft -f 2>&1 | cat > /dev/null
- @echo '1a 07' | xxd -r -p | puft 2> /dev/null || test $$? -eq 246
- @echo '0c c0 81 00 00 00 00 00 90 ff 6b 04' | xxd -r -p | puft 2> /dev/null || test $$? -eq 245
- @puft -f zeros.raw 2>&1 | cat > /dev/null
- @echo 'fc 00 00' | xxd -r -p | puft 2> /dev/null || test $$? -eq 253
- @echo '04 00 fe ff' | xxd -r -p | puft 2> /dev/null || test $$? -eq 252
- @echo '04 00 24 49' | xxd -r -p | puft 2> /dev/null || test $$? -eq 251
- @echo '04 80 49 92 24 49 92 24 0f b4 ff ff c3 84' | xxd -r -p | puft 2> /dev/null || test $$? -eq 248
- @echo '04 00 24 e9 ff ff' | xxd -r -p | puft 2> /dev/null || test $$? -eq 250
- @echo '04 00 24 e9 ff 6d' | xxd -r -p | puft 2> /dev/null || test $$? -eq 247
- @gcov -n puff.c
-
-clean:
- rm -f puff puft *.o *.gc*
diff --git a/third-party/zlib/contrib/puff/README b/third-party/zlib/contrib/puff/README
deleted file mode 100644
index bbc4cb5..0000000
--- a/third-party/zlib/contrib/puff/README
+++ /dev/null
@@ -1,63 +0,0 @@
-Puff -- A Simple Inflate
-3 Mar 2003
-Mark Adler
-madler at alumni.caltech.edu
-
-What this is --
-
-puff.c provides the routine puff() to decompress the deflate data format. It
-does so more slowly than zlib, but the code is about one-fifth the size of the
-inflate code in zlib, and written to be very easy to read.
-
-Why I wrote this --
-
-puff.c was written to document the deflate format unambiguously, by virtue of
-being working C code. It is meant to supplement RFC 1951, which formally
-describes the deflate format. I have received many questions on details of the
-deflate format, and I hope that reading this code will answer those questions.
-puff.c is heavily commented with details of the deflate format, especially
-those little nooks and cranies of the format that might not be obvious from a
-specification.
-
-puff.c may also be useful in applications where code size or memory usage is a
-very limited resource, and speed is not as important.
-
-How to use it --
-
-Well, most likely you should just be reading puff.c and using zlib for actual
-applications, but if you must ...
-
-Include puff.h in your code, which provides this prototype:
-
-int puff(unsigned char *dest, /* pointer to destination pointer */
- unsigned long *destlen, /* amount of output space */
- unsigned char *source, /* pointer to source data pointer */
- unsigned long *sourcelen); /* amount of input available */
-
-Then you can call puff() to decompress a deflate stream that is in memory in
-its entirety at source, to a sufficiently sized block of memory for the
-decompressed data at dest. puff() is the only external symbol in puff.c The
-only C library functions that puff.c needs are setjmp() and longjmp(), which
-are used to simplify error checking in the code to improve readabilty. puff.c
-does no memory allocation, and uses less than 2K bytes off of the stack.
-
-If destlen is not enough space for the uncompressed data, then inflate will
-return an error without writing more than destlen bytes. Note that this means
-that in order to decompress the deflate data successfully, you need to know
-the size of the uncompressed data ahead of time.
-
-If needed, puff() can determine the size of the uncompressed data with no
-output space. This is done by passing dest equal to (unsigned char *)0. Then
-the initial value of *destlen is ignored and *destlen is set to the length of
-the uncompressed data. So if the size of the uncompressed data is not known,
-then two passes of puff() can be used--first to determine the size, and second
-to do the actual inflation after allocating the appropriate memory. Not
-pretty, but it works. (This is one of the reasons you should be using zlib.)
-
-The deflate format is self-terminating. If the deflate stream does not end
-in *sourcelen bytes, puff() will return an error without reading at or past
-endsource.
-
-On return, *sourcelen is updated to the amount of input data consumed, and
-*destlen is updated to the size of the uncompressed data. See the comments
-in puff.c for the possible return codes for puff().
diff --git a/third-party/zlib/contrib/puff/puff.c b/third-party/zlib/contrib/puff/puff.c
deleted file mode 100644
index ba58483..0000000
--- a/third-party/zlib/contrib/puff/puff.c
+++ /dev/null
@@ -1,840 +0,0 @@
-/*
- * puff.c
- * Copyright (C) 2002-2013 Mark Adler
- * For conditions of distribution and use, see copyright notice in puff.h
- * version 2.3, 21 Jan 2013
- *
- * puff.c is a simple inflate written to be an unambiguous way to specify the
- * deflate format. It is not written for speed but rather simplicity. As a
- * side benefit, this code might actually be useful when small code is more
- * important than speed, such as bootstrap applications. For typical deflate
- * data, zlib's inflate() is about four times as fast as puff(). zlib's
- * inflate compiles to around 20K on my machine, whereas puff.c compiles to
- * around 4K on my machine (a PowerPC using GNU cc). If the faster decode()
- * function here is used, then puff() is only twice as slow as zlib's
- * inflate().
- *
- * All dynamically allocated memory comes from the stack. The stack required
- * is less than 2K bytes. This code is compatible with 16-bit int's and
- * assumes that long's are at least 32 bits. puff.c uses the short data type,
- * assumed to be 16 bits, for arrays in order to to conserve memory. The code
- * works whether integers are stored big endian or little endian.
- *
- * In the comments below are "Format notes" that describe the inflate process
- * and document some of the less obvious aspects of the format. This source
- * code is meant to supplement RFC 1951, which formally describes the deflate
- * format:
- *
- * http://www.zlib.org/rfc-deflate.html
- */
-
-/*
- * Change history:
- *
- * 1.0 10 Feb 2002 - First version
- * 1.1 17 Feb 2002 - Clarifications of some comments and notes
- * - Update puff() dest and source pointers on negative
- * errors to facilitate debugging deflators
- * - Remove longest from struct huffman -- not needed
- * - Simplify offs[] index in construct()
- * - Add input size and checking, using longjmp() to
- * maintain easy readability
- * - Use short data type for large arrays
- * - Use pointers instead of long to specify source and
- * destination sizes to avoid arbitrary 4 GB limits
- * 1.2 17 Mar 2002 - Add faster version of decode(), doubles speed (!),
- * but leave simple version for readabilty
- * - Make sure invalid distances detected if pointers
- * are 16 bits
- * - Fix fixed codes table error
- * - Provide a scanning mode for determining size of
- * uncompressed data
- * 1.3 20 Mar 2002 - Go back to lengths for puff() parameters [Gailly]
- * - Add a puff.h file for the interface
- * - Add braces in puff() for else do [Gailly]
- * - Use indexes instead of pointers for readability
- * 1.4 31 Mar 2002 - Simplify construct() code set check
- * - Fix some comments
- * - Add FIXLCODES #define
- * 1.5 6 Apr 2002 - Minor comment fixes
- * 1.6 7 Aug 2002 - Minor format changes
- * 1.7 3 Mar 2003 - Added test code for distribution
- * - Added zlib-like license
- * 1.8 9 Jan 2004 - Added some comments on no distance codes case
- * 1.9 21 Feb 2008 - Fix bug on 16-bit integer architectures [Pohland]
- * - Catch missing end-of-block symbol error
- * 2.0 25 Jul 2008 - Add #define to permit distance too far back
- * - Add option in TEST code for puff to write the data
- * - Add option in TEST code to skip input bytes
- * - Allow TEST code to read from piped stdin
- * 2.1 4 Apr 2010 - Avoid variable initialization for happier compilers
- * - Avoid unsigned comparisons for even happier compilers
- * 2.2 25 Apr 2010 - Fix bug in variable initializations [Oberhumer]
- * - Add const where appropriate [Oberhumer]
- * - Split if's and ?'s for coverage testing
- * - Break out test code to separate file
- * - Move NIL to puff.h
- * - Allow incomplete code only if single code length is 1
- * - Add full code coverage test to Makefile
- * 2.3 21 Jan 2013 - Check for invalid code length codes in dynamic blocks
- */
-
-#include <setjmp.h> /* for setjmp(), longjmp(), and jmp_buf */
-#include "puff.h" /* prototype for puff() */
-
-#define local static /* for local function definitions */
-
-/*
- * Maximums for allocations and loops. It is not useful to change these --
- * they are fixed by the deflate format.
- */
-#define MAXBITS 15 /* maximum bits in a code */
-#define MAXLCODES 286 /* maximum number of literal/length codes */
-#define MAXDCODES 30 /* maximum number of distance codes */
-#define MAXCODES (MAXLCODES+MAXDCODES) /* maximum codes lengths to read */
-#define FIXLCODES 288 /* number of fixed literal/length codes */
-
-/* input and output state */
-struct state {
- /* output state */
- unsigned char *out; /* output buffer */
- unsigned long outlen; /* available space at out */
- unsigned long outcnt; /* bytes written to out so far */
-
- /* input state */
- const unsigned char *in; /* input buffer */
- unsigned long inlen; /* available input at in */
- unsigned long incnt; /* bytes read so far */
- int bitbuf; /* bit buffer */
- int bitcnt; /* number of bits in bit buffer */
-
- /* input limit error return state for bits() and decode() */
- jmp_buf env;
-};
-
-/*
- * Return need bits from the input stream. This always leaves less than
- * eight bits in the buffer. bits() works properly for need == 0.
- *
- * Format notes:
- *
- * - Bits are stored in bytes from the least significant bit to the most
- * significant bit. Therefore bits are dropped from the bottom of the bit
- * buffer, using shift right, and new bytes are appended to the top of the
- * bit buffer, using shift left.
- */
-local int bits(struct state *s, int need)
-{
- long val; /* bit accumulator (can use up to 20 bits) */
-
- /* load at least need bits into val */
- val = s->bitbuf;
- while (s->bitcnt < need) {
- if (s->incnt == s->inlen)
- longjmp(s->env, 1); /* out of input */
- val |= (long)(s->in[s->incnt++]) << s->bitcnt; /* load eight bits */
- s->bitcnt += 8;
- }
-
- /* drop need bits and update buffer, always zero to seven bits left */
- s->bitbuf = (int)(val >> need);
- s->bitcnt -= need;
-
- /* return need bits, zeroing the bits above that */
- return (int)(val & ((1L << need) - 1));
-}
-
-/*
- * Process a stored block.
- *
- * Format notes:
- *
- * - After the two-bit stored block type (00), the stored block length and
- * stored bytes are byte-aligned for fast copying. Therefore any leftover
- * bits in the byte that has the last bit of the type, as many as seven, are
- * discarded. The value of the discarded bits are not defined and should not
- * be checked against any expectation.
- *
- * - The second inverted copy of the stored block length does not have to be
- * checked, but it's probably a good idea to do so anyway.
- *
- * - A stored block can have zero length. This is sometimes used to byte-align
- * subsets of the compressed data for random access or partial recovery.
- */
-local int stored(struct state *s)
-{
- unsigned len; /* length of stored block */
-
- /* discard leftover bits from current byte (assumes s->bitcnt < 8) */
- s->bitbuf = 0;
- s->bitcnt = 0;
-
- /* get length and check against its one's complement */
- if (s->incnt + 4 > s->inlen)
- return 2; /* not enough input */
- len = s->in[s->incnt++];
- len |= s->in[s->incnt++] << 8;
- if (s->in[s->incnt++] != (~len & 0xff) ||
- s->in[s->incnt++] != ((~len >> 8) & 0xff))
- return -2; /* didn't match complement! */
-
- /* copy len bytes from in to out */
- if (s->incnt + len > s->inlen)
- return 2; /* not enough input */
- if (s->out != NIL) {
- if (s->outcnt + len > s->outlen)
- return 1; /* not enough output space */
- while (len--)
- s->out[s->outcnt++] = s->in[s->incnt++];
- }
- else { /* just scanning */
- s->outcnt += len;
- s->incnt += len;
- }
-
- /* done with a valid stored block */
- return 0;
-}
-
-/*
- * Huffman code decoding tables. count[1..MAXBITS] is the number of symbols of
- * each length, which for a canonical code are stepped through in order.
- * symbol[] are the symbol values in canonical order, where the number of
- * entries is the sum of the counts in count[]. The decoding process can be
- * seen in the function decode() below.
- */
-struct huffman {
- short *count; /* number of symbols of each length */
- short *symbol; /* canonically ordered symbols */
-};
-
-/*
- * Decode a code from the stream s using huffman table h. Return the symbol or
- * a negative value if there is an error. If all of the lengths are zero, i.e.
- * an empty code, or if the code is incomplete and an invalid code is received,
- * then -10 is returned after reading MAXBITS bits.
- *
- * Format notes:
- *
- * - The codes as stored in the compressed data are bit-reversed relative to
- * a simple integer ordering of codes of the same lengths. Hence below the
- * bits are pulled from the compressed data one at a time and used to
- * build the code value reversed from what is in the stream in order to
- * permit simple integer comparisons for decoding. A table-based decoding
- * scheme (as used in zlib) does not need to do this reversal.
- *
- * - The first code for the shortest length is all zeros. Subsequent codes of
- * the same length are simply integer increments of the previous code. When
- * moving up a length, a zero bit is appended to the code. For a complete
- * code, the last code of the longest length will be all ones.
- *
- * - Incomplete codes are handled by this decoder, since they are permitted
- * in the deflate format. See the format notes for fixed() and dynamic().
- */
-#ifdef SLOW
-local int decode(struct state *s, const struct huffman *h)
-{
- int len; /* current number of bits in code */
- int code; /* len bits being decoded */
- int first; /* first code of length len */
- int count; /* number of codes of length len */
- int index; /* index of first code of length len in symbol table */
-
- code = first = index = 0;
- for (len = 1; len <= MAXBITS; len++) {
- code |= bits(s, 1); /* get next bit */
- count = h->count[len];
- if (code - count < first) /* if length len, return symbol */
- return h->symbol[index + (code - first)];
- index += count; /* else update for next length */
- first += count;
- first <<= 1;
- code <<= 1;
- }
- return -10; /* ran out of codes */
-}
-
-/*
- * A faster version of decode() for real applications of this code. It's not
- * as readable, but it makes puff() twice as fast. And it only makes the code
- * a few percent larger.
- */
-#else /* !SLOW */
-local int decode(struct state *s, const struct huffman *h)
-{
- int len; /* current number of bits in code */
- int code; /* len bits being decoded */
- int first; /* first code of length len */
- int count; /* number of codes of length len */
- int index; /* index of first code of length len in symbol table */
- int bitbuf; /* bits from stream */
- int left; /* bits left in next or left to process */
- short *next; /* next number of codes */
-
- bitbuf = s->bitbuf;
- left = s->bitcnt;
- code = first = index = 0;
- len = 1;
- next = h->count + 1;
- while (1) {
- while (left--) {
- code |= bitbuf & 1;
- bitbuf >>= 1;
- count = *next++;
- if (code - count < first) { /* if length len, return symbol */
- s->bitbuf = bitbuf;
- s->bitcnt = (s->bitcnt - len) & 7;
- return h->symbol[index + (code - first)];
- }
- index += count; /* else update for next length */
- first += count;
- first <<= 1;
- code <<= 1;
- len++;
- }
- left = (MAXBITS+1) - len;
- if (left == 0)
- break;
- if (s->incnt == s->inlen)
- longjmp(s->env, 1); /* out of input */
- bitbuf = s->in[s->incnt++];
- if (left > 8)
- left = 8;
- }
- return -10; /* ran out of codes */
-}
-#endif /* SLOW */
-
-/*
- * Given the list of code lengths length[0..n-1] representing a canonical
- * Huffman code for n symbols, construct the tables required to decode those
- * codes. Those tables are the number of codes of each length, and the symbols
- * sorted by length, retaining their original order within each length. The
- * return value is zero for a complete code set, negative for an over-
- * subscribed code set, and positive for an incomplete code set. The tables
- * can be used if the return value is zero or positive, but they cannot be used
- * if the return value is negative. If the return value is zero, it is not
- * possible for decode() using that table to return an error--any stream of
- * enough bits will resolve to a symbol. If the return value is positive, then
- * it is possible for decode() using that table to return an error for received
- * codes past the end of the incomplete lengths.
- *
- * Not used by decode(), but used for error checking, h->count[0] is the number
- * of the n symbols not in the code. So n - h->count[0] is the number of
- * codes. This is useful for checking for incomplete codes that have more than
- * one symbol, which is an error in a dynamic block.
- *
- * Assumption: for all i in 0..n-1, 0 <= length[i] <= MAXBITS
- * This is assured by the construction of the length arrays in dynamic() and
- * fixed() and is not verified by construct().
- *
- * Format notes:
- *
- * - Permitted and expected examples of incomplete codes are one of the fixed
- * codes and any code with a single symbol which in deflate is coded as one
- * bit instead of zero bits. See the format notes for fixed() and dynamic().
- *
- * - Within a given code length, the symbols are kept in ascending order for
- * the code bits definition.
- */
-local int construct(struct huffman *h, const short *length, int n)
-{
- int symbol; /* current symbol when stepping through length[] */
- int len; /* current length when stepping through h->count[] */
- int left; /* number of possible codes left of current length */
- short offs[MAXBITS+1]; /* offsets in symbol table for each length */
-
- /* count number of codes of each length */
- for (len = 0; len <= MAXBITS; len++)
- h->count[len] = 0;
- for (symbol = 0; symbol < n; symbol++)
- (h->count[length[symbol]])++; /* assumes lengths are within bounds */
- if (h->count[0] == n) /* no codes! */
- return 0; /* complete, but decode() will fail */
-
- /* check for an over-subscribed or incomplete set of lengths */
- left = 1; /* one possible code of zero length */
- for (len = 1; len <= MAXBITS; len++) {
- left <<= 1; /* one more bit, double codes left */
- left -= h->count[len]; /* deduct count from possible codes */
- if (left < 0)
- return left; /* over-subscribed--return negative */
- } /* left > 0 means incomplete */
-
- /* generate offsets into symbol table for each length for sorting */
- offs[1] = 0;
- for (len = 1; len < MAXBITS; len++)
- offs[len + 1] = offs[len] + h->count[len];
-
- /*
- * put symbols in table sorted by length, by symbol order within each
- * length
- */
- for (symbol = 0; symbol < n; symbol++)
- if (length[symbol] != 0)
- h->symbol[offs[length[symbol]]++] = symbol;
-
- /* return zero for complete set, positive for incomplete set */
- return left;
-}
-
-/*
- * Decode literal/length and distance codes until an end-of-block code.
- *
- * Format notes:
- *
- * - Compressed data that is after the block type if fixed or after the code
- * description if dynamic is a combination of literals and length/distance
- * pairs terminated by and end-of-block code. Literals are simply Huffman
- * coded bytes. A length/distance pair is a coded length followed by a
- * coded distance to represent a string that occurs earlier in the
- * uncompressed data that occurs again at the current location.
- *
- * - Literals, lengths, and the end-of-block code are combined into a single
- * code of up to 286 symbols. They are 256 literals (0..255), 29 length
- * symbols (257..285), and the end-of-block symbol (256).
- *
- * - There are 256 possible lengths (3..258), and so 29 symbols are not enough
- * to represent all of those. Lengths 3..10 and 258 are in fact represented
- * by just a length symbol. Lengths 11..257 are represented as a symbol and
- * some number of extra bits that are added as an integer to the base length
- * of the length symbol. The number of extra bits is determined by the base
- * length symbol. These are in the static arrays below, lens[] for the base
- * lengths and lext[] for the corresponding number of extra bits.
- *
- * - The reason that 258 gets its own symbol is that the longest length is used
- * often in highly redundant files. Note that 258 can also be coded as the
- * base value 227 plus the maximum extra value of 31. While a good deflate
- * should never do this, it is not an error, and should be decoded properly.
- *
- * - If a length is decoded, including its extra bits if any, then it is
- * followed a distance code. There are up to 30 distance symbols. Again
- * there are many more possible distances (1..32768), so extra bits are added
- * to a base value represented by the symbol. The distances 1..4 get their
- * own symbol, but the rest require extra bits. The base distances and
- * corresponding number of extra bits are below in the static arrays dist[]
- * and dext[].
- *
- * - Literal bytes are simply written to the output. A length/distance pair is
- * an instruction to copy previously uncompressed bytes to the output. The
- * copy is from distance bytes back in the output stream, copying for length
- * bytes.
- *
- * - Distances pointing before the beginning of the output data are not
- * permitted.
- *
- * - Overlapped copies, where the length is greater than the distance, are
- * allowed and common. For example, a distance of one and a length of 258
- * simply copies the last byte 258 times. A distance of four and a length of
- * twelve copies the last four bytes three times. A simple forward copy
- * ignoring whether the length is greater than the distance or not implements
- * this correctly. You should not use memcpy() since its behavior is not
- * defined for overlapped arrays. You should not use memmove() or bcopy()
- * since though their behavior -is- defined for overlapping arrays, it is
- * defined to do the wrong thing in this case.
- */
-local int codes(struct state *s,
- const struct huffman *lencode,
- const struct huffman *distcode)
-{
- int symbol; /* decoded symbol */
- int len; /* length for copy */
- unsigned dist; /* distance for copy */
- static const short lens[29] = { /* Size base for length codes 257..285 */
- 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 15, 17, 19, 23, 27, 31,
- 35, 43, 51, 59, 67, 83, 99, 115, 131, 163, 195, 227, 258};
- static const short lext[29] = { /* Extra bits for length codes 257..285 */
- 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 2, 2, 2, 2,
- 3, 3, 3, 3, 4, 4, 4, 4, 5, 5, 5, 5, 0};
- static const short dists[30] = { /* Offset base for distance codes 0..29 */
- 1, 2, 3, 4, 5, 7, 9, 13, 17, 25, 33, 49, 65, 97, 129, 193,
- 257, 385, 513, 769, 1025, 1537, 2049, 3073, 4097, 6145,
- 8193, 12289, 16385, 24577};
- static const short dext[30] = { /* Extra bits for distance codes 0..29 */
- 0, 0, 0, 0, 1, 1, 2, 2, 3, 3, 4, 4, 5, 5, 6, 6,
- 7, 7, 8, 8, 9, 9, 10, 10, 11, 11,
- 12, 12, 13, 13};
-
- /* decode literals and length/distance pairs */
- do {
- symbol = decode(s, lencode);
- if (symbol < 0)
- return symbol; /* invalid symbol */
- if (symbol < 256) { /* literal: symbol is the byte */
- /* write out the literal */
- if (s->out != NIL) {
- if (s->outcnt == s->outlen)
- return 1;
- s->out[s->outcnt] = symbol;
- }
- s->outcnt++;
- }
- else if (symbol > 256) { /* length */
- /* get and compute length */
- symbol -= 257;
- if (symbol >= 29)
- return -10; /* invalid fixed code */
- len = lens[symbol] + bits(s, lext[symbol]);
-
- /* get and check distance */
- symbol = decode(s, distcode);
- if (symbol < 0)
- return symbol; /* invalid symbol */
- dist = dists[symbol] + bits(s, dext[symbol]);
-#ifndef INFLATE_ALLOW_INVALID_DISTANCE_TOOFAR_ARRR
- if (dist > s->outcnt)
- return -11; /* distance too far back */
-#endif
-
- /* copy length bytes from distance bytes back */
- if (s->out != NIL) {
- if (s->outcnt + len > s->outlen)
- return 1;
- while (len--) {
- s->out[s->outcnt] =
-#ifdef INFLATE_ALLOW_INVALID_DISTANCE_TOOFAR_ARRR
- dist > s->outcnt ?
- 0 :
-#endif
- s->out[s->outcnt - dist];
- s->outcnt++;
- }
- }
- else
- s->outcnt += len;
- }
- } while (symbol != 256); /* end of block symbol */
-
- /* done with a valid fixed or dynamic block */
- return 0;
-}
-
-/*
- * Process a fixed codes block.
- *
- * Format notes:
- *
- * - This block type can be useful for compressing small amounts of data for
- * which the size of the code descriptions in a dynamic block exceeds the
- * benefit of custom codes for that block. For fixed codes, no bits are
- * spent on code descriptions. Instead the code lengths for literal/length
- * codes and distance codes are fixed. The specific lengths for each symbol
- * can be seen in the "for" loops below.
- *
- * - The literal/length code is complete, but has two symbols that are invalid
- * and should result in an error if received. This cannot be implemented
- * simply as an incomplete code since those two symbols are in the "middle"
- * of the code. They are eight bits long and the longest literal/length\
- * code is nine bits. Therefore the code must be constructed with those
- * symbols, and the invalid symbols must be detected after decoding.
- *
- * - The fixed distance codes also have two invalid symbols that should result
- * in an error if received. Since all of the distance codes are the same
- * length, this can be implemented as an incomplete code. Then the invalid
- * codes are detected while decoding.
- */
-local int fixed(struct state *s)
-{
- static int virgin = 1;
- static short lencnt[MAXBITS+1], lensym[FIXLCODES];
- static short distcnt[MAXBITS+1], distsym[MAXDCODES];
- static struct huffman lencode, distcode;
-
- /* build fixed huffman tables if first call (may not be thread safe) */
- if (virgin) {
- int symbol;
- short lengths[FIXLCODES];
-
- /* construct lencode and distcode */
- lencode.count = lencnt;
- lencode.symbol = lensym;
- distcode.count = distcnt;
- distcode.symbol = distsym;
-
- /* literal/length table */
- for (symbol = 0; symbol < 144; symbol++)
- lengths[symbol] = 8;
- for (; symbol < 256; symbol++)
- lengths[symbol] = 9;
- for (; symbol < 280; symbol++)
- lengths[symbol] = 7;
- for (; symbol < FIXLCODES; symbol++)
- lengths[symbol] = 8;
- construct(&lencode, lengths, FIXLCODES);
-
- /* distance table */
- for (symbol = 0; symbol < MAXDCODES; symbol++)
- lengths[symbol] = 5;
- construct(&distcode, lengths, MAXDCODES);
-
- /* do this just once */
- virgin = 0;
- }
-
- /* decode data until end-of-block code */
- return codes(s, &lencode, &distcode);
-}
-
-/*
- * Process a dynamic codes block.
- *
- * Format notes:
- *
- * - A dynamic block starts with a description of the literal/length and
- * distance codes for that block. New dynamic blocks allow the compressor to
- * rapidly adapt to changing data with new codes optimized for that data.
- *
- * - The codes used by the deflate format are "canonical", which means that
- * the actual bits of the codes are generated in an unambiguous way simply
- * from the number of bits in each code. Therefore the code descriptions
- * are simply a list of code lengths for each symbol.
- *
- * - The code lengths are stored in order for the symbols, so lengths are
- * provided for each of the literal/length symbols, and for each of the
- * distance symbols.
- *
- * - If a symbol is not used in the block, this is represented by a zero as
- * as the code length. This does not mean a zero-length code, but rather
- * that no code should be created for this symbol. There is no way in the
- * deflate format to represent a zero-length code.
- *
- * - The maximum number of bits in a code is 15, so the possible lengths for
- * any code are 1..15.
- *
- * - The fact that a length of zero is not permitted for a code has an
- * interesting consequence. Normally if only one symbol is used for a given
- * code, then in fact that code could be represented with zero bits. However
- * in deflate, that code has to be at least one bit. So for example, if
- * only a single distance base symbol appears in a block, then it will be
- * represented by a single code of length one, in particular one 0 bit. This
- * is an incomplete code, since if a 1 bit is received, it has no meaning,
- * and should result in an error. So incomplete distance codes of one symbol
- * should be permitted, and the receipt of invalid codes should be handled.
- *
- * - It is also possible to have a single literal/length code, but that code
- * must be the end-of-block code, since every dynamic block has one. This
- * is not the most efficient way to create an empty block (an empty fixed
- * block is fewer bits), but it is allowed by the format. So incomplete
- * literal/length codes of one symbol should also be permitted.
- *
- * - If there are only literal codes and no lengths, then there are no distance
- * codes. This is represented by one distance code with zero bits.
- *
- * - The list of up to 286 length/literal lengths and up to 30 distance lengths
- * are themselves compressed using Huffman codes and run-length encoding. In
- * the list of code lengths, a 0 symbol means no code, a 1..15 symbol means
- * that length, and the symbols 16, 17, and 18 are run-length instructions.
- * Each of 16, 17, and 18 are follwed by extra bits to define the length of
- * the run. 16 copies the last length 3 to 6 times. 17 represents 3 to 10
- * zero lengths, and 18 represents 11 to 138 zero lengths. Unused symbols
- * are common, hence the special coding for zero lengths.
- *
- * - The symbols for 0..18 are Huffman coded, and so that code must be
- * described first. This is simply a sequence of up to 19 three-bit values
- * representing no code (0) or the code length for that symbol (1..7).
- *
- * - A dynamic block starts with three fixed-size counts from which is computed
- * the number of literal/length code lengths, the number of distance code
- * lengths, and the number of code length code lengths (ok, you come up with
- * a better name!) in the code descriptions. For the literal/length and
- * distance codes, lengths after those provided are considered zero, i.e. no
- * code. The code length code lengths are received in a permuted order (see
- * the order[] array below) to make a short code length code length list more
- * likely. As it turns out, very short and very long codes are less likely
- * to be seen in a dynamic code description, hence what may appear initially
- * to be a peculiar ordering.
- *
- * - Given the number of literal/length code lengths (nlen) and distance code
- * lengths (ndist), then they are treated as one long list of nlen + ndist
- * code lengths. Therefore run-length coding can and often does cross the
- * boundary between the two sets of lengths.
- *
- * - So to summarize, the code description at the start of a dynamic block is
- * three counts for the number of code lengths for the literal/length codes,
- * the distance codes, and the code length codes. This is followed by the
- * code length code lengths, three bits each. This is used to construct the
- * code length code which is used to read the remainder of the lengths. Then
- * the literal/length code lengths and distance lengths are read as a single
- * set of lengths using the code length codes. Codes are constructed from
- * the resulting two sets of lengths, and then finally you can start
- * decoding actual compressed data in the block.
- *
- * - For reference, a "typical" size for the code description in a dynamic
- * block is around 80 bytes.
- */
-local int dynamic(struct state *s)
-{
- int nlen, ndist, ncode; /* number of lengths in descriptor */
- int index; /* index of lengths[] */
- int err; /* construct() return value */
- short lengths[MAXCODES]; /* descriptor code lengths */
- short lencnt[MAXBITS+1], lensym[MAXLCODES]; /* lencode memory */
- short distcnt[MAXBITS+1], distsym[MAXDCODES]; /* distcode memory */
- struct huffman lencode, distcode; /* length and distance codes */
- static const short order[19] = /* permutation of code length codes */
- {16, 17, 18, 0, 8, 7, 9, 6, 10, 5, 11, 4, 12, 3, 13, 2, 14, 1, 15};
-
- /* construct lencode and distcode */
- lencode.count = lencnt;
- lencode.symbol = lensym;
- distcode.count = distcnt;
- distcode.symbol = distsym;
-
- /* get number of lengths in each table, check lengths */
- nlen = bits(s, 5) + 257;
- ndist = bits(s, 5) + 1;
- ncode = bits(s, 4) + 4;
- if (nlen > MAXLCODES || ndist > MAXDCODES)
- return -3; /* bad counts */
-
- /* read code length code lengths (really), missing lengths are zero */
- for (index = 0; index < ncode; index++)
- lengths[order[index]] = bits(s, 3);
- for (; index < 19; index++)
- lengths[order[index]] = 0;
-
- /* build huffman table for code lengths codes (use lencode temporarily) */
- err = construct(&lencode, lengths, 19);
- if (err != 0) /* require complete code set here */
- return -4;
-
- /* read length/literal and distance code length tables */
- index = 0;
- while (index < nlen + ndist) {
- int symbol; /* decoded value */
- int len; /* last length to repeat */
-
- symbol = decode(s, &lencode);
- if (symbol < 0)
- return symbol; /* invalid symbol */
- if (symbol < 16) /* length in 0..15 */
- lengths[index++] = symbol;
- else { /* repeat instruction */
- len = 0; /* assume repeating zeros */
- if (symbol == 16) { /* repeat last length 3..6 times */
- if (index == 0)
- return -5; /* no last length! */
- len = lengths[index - 1]; /* last length */
- symbol = 3 + bits(s, 2);
- }
- else if (symbol == 17) /* repeat zero 3..10 times */
- symbol = 3 + bits(s, 3);
- else /* == 18, repeat zero 11..138 times */
- symbol = 11 + bits(s, 7);
- if (index + symbol > nlen + ndist)
- return -6; /* too many lengths! */
- while (symbol--) /* repeat last or zero symbol times */
- lengths[index++] = len;
- }
- }
-
- /* check for end-of-block code -- there better be one! */
- if (lengths[256] == 0)
- return -9;
-
- /* build huffman table for literal/length codes */
- err = construct(&lencode, lengths, nlen);
- if (err && (err < 0 || nlen != lencode.count[0] + lencode.count[1]))
- return -7; /* incomplete code ok only for single length 1 code */
-
- /* build huffman table for distance codes */
- err = construct(&distcode, lengths + nlen, ndist);
- if (err && (err < 0 || ndist != distcode.count[0] + distcode.count[1]))
- return -8; /* incomplete code ok only for single length 1 code */
-
- /* decode data until end-of-block code */
- return codes(s, &lencode, &distcode);
-}
-
-/*
- * Inflate source to dest. On return, destlen and sourcelen are updated to the
- * size of the uncompressed data and the size of the deflate data respectively.
- * On success, the return value of puff() is zero. If there is an error in the
- * source data, i.e. it is not in the deflate format, then a negative value is
- * returned. If there is not enough input available or there is not enough
- * output space, then a positive error is returned. In that case, destlen and
- * sourcelen are not updated to facilitate retrying from the beginning with the
- * provision of more input data or more output space. In the case of invalid
- * inflate data (a negative error), the dest and source pointers are updated to
- * facilitate the debugging of deflators.
- *
- * puff() also has a mode to determine the size of the uncompressed output with
- * no output written. For this dest must be (unsigned char *)0. In this case,
- * the input value of *destlen is ignored, and on return *destlen is set to the
- * size of the uncompressed output.
- *
- * The return codes are:
- *
- * 2: available inflate data did not terminate
- * 1: output space exhausted before completing inflate
- * 0: successful inflate
- * -1: invalid block type (type == 3)
- * -2: stored block length did not match one's complement
- * -3: dynamic block code description: too many length or distance codes
- * -4: dynamic block code description: code lengths codes incomplete
- * -5: dynamic block code description: repeat lengths with no first length
- * -6: dynamic block code description: repeat more than specified lengths
- * -7: dynamic block code description: invalid literal/length code lengths
- * -8: dynamic block code description: invalid distance code lengths
- * -9: dynamic block code description: missing end-of-block code
- * -10: invalid literal/length or distance code in fixed or dynamic block
- * -11: distance is too far back in fixed or dynamic block
- *
- * Format notes:
- *
- * - Three bits are read for each block to determine the kind of block and
- * whether or not it is the last block. Then the block is decoded and the
- * process repeated if it was not the last block.
- *
- * - The leftover bits in the last byte of the deflate data after the last
- * block (if it was a fixed or dynamic block) are undefined and have no
- * expected values to check.
- */
-int puff(unsigned char *dest, /* pointer to destination pointer */
- unsigned long *destlen, /* amount of output space */
- const unsigned char *source, /* pointer to source data pointer */
- unsigned long *sourcelen) /* amount of input available */
-{
- struct state s; /* input/output state */
- int last, type; /* block information */
- int err; /* return value */
-
- /* initialize output state */
- s.out = dest;
- s.outlen = *destlen; /* ignored if dest is NIL */
- s.outcnt = 0;
-
- /* initialize input state */
- s.in = source;
- s.inlen = *sourcelen;
- s.incnt = 0;
- s.bitbuf = 0;
- s.bitcnt = 0;
-
- /* return if bits() or decode() tries to read past available input */
- if (setjmp(s.env) != 0) /* if came back here via longjmp() */
- err = 2; /* then skip do-loop, return error */
- else {
- /* process blocks until last block or error */
- do {
- last = bits(&s, 1); /* one if last block */
- type = bits(&s, 2); /* block type 0..3 */
- err = type == 0 ?
- stored(&s) :
- (type == 1 ?
- fixed(&s) :
- (type == 2 ?
- dynamic(&s) :
- -1)); /* type == 3, invalid */
- if (err != 0)
- break; /* return with error */
- } while (!last);
- }
-
- /* update the lengths and return */
- if (err <= 0) {
- *destlen = s.outcnt;
- *sourcelen = s.incnt;
- }
- return err;
-}
diff --git a/third-party/zlib/contrib/puff/puff.h b/third-party/zlib/contrib/puff/puff.h
deleted file mode 100644
index e23a245..0000000
--- a/third-party/zlib/contrib/puff/puff.h
+++ /dev/null
@@ -1,35 +0,0 @@
-/* puff.h
- Copyright (C) 2002-2013 Mark Adler, all rights reserved
- version 2.3, 21 Jan 2013
-
- This software is provided 'as-is', without any express or implied
- warranty. In no event will the author be held liable for any damages
- arising from the use of this software.
-
- Permission is granted to anyone to use this software for any purpose,
- including commercial applications, and to alter it and redistribute it
- freely, subject to the following restrictions:
-
- 1. The origin of this software must not be misrepresented; you must not
- claim that you wrote the original software. If you use this software
- in a product, an acknowledgment in the product documentation would be
- appreciated but is not required.
- 2. Altered source versions must be plainly marked as such, and must not be
- misrepresented as being the original software.
- 3. This notice may not be removed or altered from any source distribution.
-
- Mark Adler madler at alumni.caltech.edu
- */
-
-
-/*
- * See puff.c for purpose and usage.
- */
-#ifndef NIL
-# define NIL ((unsigned char *)0) /* for no output option */
-#endif
-
-int puff(unsigned char *dest, /* pointer to destination pointer */
- unsigned long *destlen, /* amount of output space */
- const unsigned char *source, /* pointer to source data pointer */
- unsigned long *sourcelen); /* amount of input available */
diff --git a/third-party/zlib/contrib/puff/pufftest.c b/third-party/zlib/contrib/puff/pufftest.c
deleted file mode 100644
index 7764814..0000000
--- a/third-party/zlib/contrib/puff/pufftest.c
+++ /dev/null
@@ -1,165 +0,0 @@
-/*
- * pufftest.c
- * Copyright (C) 2002-2013 Mark Adler
- * For conditions of distribution and use, see copyright notice in puff.h
- * version 2.3, 21 Jan 2013
- */
-
-/* Example of how to use puff().
-
- Usage: puff [-w] [-f] [-nnn] file
- ... | puff [-w] [-f] [-nnn]
-
- where file is the input file with deflate data, nnn is the number of bytes
- of input to skip before inflating (e.g. to skip a zlib or gzip header), and
- -w is used to write the decompressed data to stdout. -f is for coverage
- testing, and causes pufftest to fail with not enough output space (-f does
- a write like -w, so -w is not required). */
-
-#include <stdio.h>
-#include <stdlib.h>
-#include "puff.h"
-
-#if defined(MSDOS) || defined(OS2) || defined(WIN32) || defined(__CYGWIN__)
-# include <fcntl.h>
-# include <io.h>
-# define SET_BINARY_MODE(file) setmode(fileno(file), O_BINARY)
-#else
-# define SET_BINARY_MODE(file)
-#endif
-
-#define local static
-
-/* Return size times approximately the cube root of 2, keeping the result as 1,
- 3, or 5 times a power of 2 -- the result is always > size, until the result
- is the maximum value of an unsigned long, where it remains. This is useful
- to keep reallocations less than ~33% over the actual data. */
-local size_t bythirds(size_t size)
-{
- int n;
- size_t m;
-
- m = size;
- for (n = 0; m; n++)
- m >>= 1;
- if (n < 3)
- return size + 1;
- n -= 3;
- m = size >> n;
- m += m == 6 ? 2 : 1;
- m <<= n;
- return m > size ? m : (size_t)(-1);
-}
-
-/* Read the input file *name, or stdin if name is NULL, into allocated memory.
- Reallocate to larger buffers until the entire file is read in. Return a
- pointer to the allocated data, or NULL if there was a memory allocation
- failure. *len is the number of bytes of data read from the input file (even
- if load() returns NULL). If the input file was empty or could not be opened
- or read, *len is zero. */
-local void *load(const char *name, size_t *len)
-{
- size_t size;
- void *buf, *swap;
- FILE *in;
-
- *len = 0;
- buf = malloc(size = 4096);
- if (buf == NULL)
- return NULL;
- in = name == NULL ? stdin : fopen(name, "rb");
- if (in != NULL) {
- for (;;) {
- *len += fread((char *)buf + *len, 1, size - *len, in);
- if (*len < size) break;
- size = bythirds(size);
- if (size == *len || (swap = realloc(buf, size)) == NULL) {
- free(buf);
- buf = NULL;
- break;
- }
- buf = swap;
- }
- fclose(in);
- }
- return buf;
-}
-
-int main(int argc, char **argv)
-{
- int ret, put = 0, fail = 0;
- unsigned skip = 0;
- char *arg, *name = NULL;
- unsigned char *source = NULL, *dest;
- size_t len = 0;
- unsigned long sourcelen, destlen;
-
- /* process arguments */
- while (arg = *++argv, --argc)
- if (arg[0] == '-') {
- if (arg[1] == 'w' && arg[2] == 0)
- put = 1;
- else if (arg[1] == 'f' && arg[2] == 0)
- fail = 1, put = 1;
- else if (arg[1] >= '0' && arg[1] <= '9')
- skip = (unsigned)atoi(arg + 1);
- else {
- fprintf(stderr, "invalid option %s\n", arg);
- return 3;
- }
- }
- else if (name != NULL) {
- fprintf(stderr, "only one file name allowed\n");
- return 3;
- }
- else
- name = arg;
- source = load(name, &len);
- if (source == NULL) {
- fprintf(stderr, "memory allocation failure\n");
- return 4;
- }
- if (len == 0) {
- fprintf(stderr, "could not read %s, or it was empty\n",
- name == NULL ? "<stdin>" : name);
- free(source);
- return 3;
- }
- if (skip >= len) {
- fprintf(stderr, "skip request of %d leaves no input\n", skip);
- free(source);
- return 3;
- }
-
- /* test inflate data with offset skip */
- len -= skip;
- sourcelen = (unsigned long)len;
- ret = puff(NIL, &destlen, source + skip, &sourcelen);
- if (ret)
- fprintf(stderr, "puff() failed with return code %d\n", ret);
- else {
- fprintf(stderr, "puff() succeeded uncompressing %lu bytes\n", destlen);
- if (sourcelen < len) fprintf(stderr, "%lu compressed bytes unused\n",
- len - sourcelen);
- }
-
- /* if requested, inflate again and write decompressd data to stdout */
- if (put && ret == 0) {
- if (fail)
- destlen >>= 1;
- dest = malloc(destlen);
- if (dest == NULL) {
- fprintf(stderr, "memory allocation failure\n");
- free(source);
- return 4;
- }
- puff(dest, &destlen, source + skip, &sourcelen);
- SET_BINARY_MODE(stdout);
- fwrite(dest, 1, destlen, stdout);
- free(dest);
- }
-
- /* clean up */
- free(source);
- return ret;
-}
diff --git a/third-party/zlib/contrib/puff/zeros.raw b/third-party/zlib/contrib/puff/zeros.raw
deleted file mode 100644
index 0a90e76..0000000
Binary files a/third-party/zlib/contrib/puff/zeros.raw and /dev/null differ
diff --git a/third-party/zlib/contrib/testzlib/testzlib.c b/third-party/zlib/contrib/testzlib/testzlib.c
deleted file mode 100644
index 5f659de..0000000
--- a/third-party/zlib/contrib/testzlib/testzlib.c
+++ /dev/null
@@ -1,275 +0,0 @@
-#include <stdio.h>
-#include <stdlib.h>
-#include <windows.h>
-
-#include "zlib.h"
-
-
-void MyDoMinus64(LARGE_INTEGER *R,LARGE_INTEGER A,LARGE_INTEGER B)
-{
- R->HighPart = A.HighPart - B.HighPart;
- if (A.LowPart >= B.LowPart)
- R->LowPart = A.LowPart - B.LowPart;
- else
- {
- R->LowPart = A.LowPart - B.LowPart;
- R->HighPart --;
- }
-}
-
-#ifdef _M_X64
-// see http://msdn2.microsoft.com/library/twchhe95(en-us,vs.80).aspx for __rdtsc
-unsigned __int64 __rdtsc(void);
-void BeginCountRdtsc(LARGE_INTEGER * pbeginTime64)
-{
- // printf("rdtsc = %I64x\n",__rdtsc());
- pbeginTime64->QuadPart=__rdtsc();
-}
-
-LARGE_INTEGER GetResRdtsc(LARGE_INTEGER beginTime64,BOOL fComputeTimeQueryPerf)
-{
- LARGE_INTEGER LIres;
- unsigned _int64 res=__rdtsc()-((unsigned _int64)(beginTime64.QuadPart));
- LIres.QuadPart=res;
- // printf("rdtsc = %I64x\n",__rdtsc());
- return LIres;
-}
-#else
-#ifdef _M_IX86
-void myGetRDTSC32(LARGE_INTEGER * pbeginTime64)
-{
- DWORD dwEdx,dwEax;
- _asm
- {
- rdtsc
- mov dwEax,eax
- mov dwEdx,edx
- }
- pbeginTime64->LowPart=dwEax;
- pbeginTime64->HighPart=dwEdx;
-}
-
-void BeginCountRdtsc(LARGE_INTEGER * pbeginTime64)
-{
- myGetRDTSC32(pbeginTime64);
-}
-
-LARGE_INTEGER GetResRdtsc(LARGE_INTEGER beginTime64,BOOL fComputeTimeQueryPerf)
-{
- LARGE_INTEGER LIres,endTime64;
- myGetRDTSC32(&endTime64);
-
- LIres.LowPart=LIres.HighPart=0;
- MyDoMinus64(&LIres,endTime64,beginTime64);
- return LIres;
-}
-#else
-void myGetRDTSC32(LARGE_INTEGER * pbeginTime64)
-{
-}
-
-void BeginCountRdtsc(LARGE_INTEGER * pbeginTime64)
-{
-}
-
-LARGE_INTEGER GetResRdtsc(LARGE_INTEGER beginTime64,BOOL fComputeTimeQueryPerf)
-{
- LARGE_INTEGER lr;
- lr.QuadPart=0;
- return lr;
-}
-#endif
-#endif
-
-void BeginCountPerfCounter(LARGE_INTEGER * pbeginTime64,BOOL fComputeTimeQueryPerf)
-{
- if ((!fComputeTimeQueryPerf) || (!QueryPerformanceCounter(pbeginTime64)))
- {
- pbeginTime64->LowPart = GetTickCount();
- pbeginTime64->HighPart = 0;
- }
-}
-
-DWORD GetMsecSincePerfCounter(LARGE_INTEGER beginTime64,BOOL fComputeTimeQueryPerf)
-{
- LARGE_INTEGER endTime64,ticksPerSecond,ticks;
- DWORDLONG ticksShifted,tickSecShifted;
- DWORD dwLog=16+0;
- DWORD dwRet;
- if ((!fComputeTimeQueryPerf) || (!QueryPerformanceCounter(&endTime64)))
- dwRet = (GetTickCount() - beginTime64.LowPart)*1;
- else
- {
- MyDoMinus64(&ticks,endTime64,beginTime64);
- QueryPerformanceFrequency(&ticksPerSecond);
-
-
- {
- ticksShifted = Int64ShrlMod32(*(DWORDLONG*)&ticks,dwLog);
- tickSecShifted = Int64ShrlMod32(*(DWORDLONG*)&ticksPerSecond,dwLog);
-
- }
-
- dwRet = (DWORD)((((DWORD)ticksShifted)*1000)/(DWORD)(tickSecShifted));
- dwRet *=1;
- }
- return dwRet;
-}
-
-int ReadFileMemory(const char* filename,long* plFileSize,unsigned char** pFilePtr)
-{
- FILE* stream;
- unsigned char* ptr;
- int retVal=1;
- stream=fopen(filename, "rb");
- if (stream==NULL)
- return 0;
-
- fseek(stream,0,SEEK_END);
-
- *plFileSize=ftell(stream);
- fseek(stream,0,SEEK_SET);
- ptr=malloc((*plFileSize)+1);
- if (ptr==NULL)
- retVal=0;
- else
- {
- if (fread(ptr, 1, *plFileSize,stream) != (*plFileSize))
- retVal=0;
- }
- fclose(stream);
- *pFilePtr=ptr;
- return retVal;
-}
-
-int main(int argc, char *argv[])
-{
- int BlockSizeCompress=0x8000;
- int BlockSizeUncompress=0x8000;
- int cprLevel=Z_DEFAULT_COMPRESSION ;
- long lFileSize;
- unsigned char* FilePtr;
- long lBufferSizeCpr;
- long lBufferSizeUncpr;
- long lCompressedSize=0;
- unsigned char* CprPtr;
- unsigned char* UncprPtr;
- long lSizeCpr,lSizeUncpr;
- DWORD dwGetTick,dwMsecQP;
- LARGE_INTEGER li_qp,li_rdtsc,dwResRdtsc;
-
- if (argc<=1)
- {
- printf("run TestZlib <File> [BlockSizeCompress] [BlockSizeUncompress] [compres. level]\n");
- return 0;
- }
-
- if (ReadFileMemory(argv[1],&lFileSize,&FilePtr)==0)
- {
- printf("error reading %s\n",argv[1]);
- return 1;
- }
- else printf("file %s read, %u bytes\n",argv[1],lFileSize);
-
- if (argc>=3)
- BlockSizeCompress=atol(argv[2]);
-
- if (argc>=4)
- BlockSizeUncompress=atol(argv[3]);
-
- if (argc>=5)
- cprLevel=(int)atol(argv[4]);
-
- lBufferSizeCpr = lFileSize + (lFileSize/0x10) + 0x200;
- lBufferSizeUncpr = lBufferSizeCpr;
-
- CprPtr=(unsigned char*)malloc(lBufferSizeCpr + BlockSizeCompress);
-
- BeginCountPerfCounter(&li_qp,TRUE);
- dwGetTick=GetTickCount();
- BeginCountRdtsc(&li_rdtsc);
- {
- z_stream zcpr;
- int ret=Z_OK;
- long lOrigToDo = lFileSize;
- long lOrigDone = 0;
- int step=0;
- memset(&zcpr,0,sizeof(z_stream));
- deflateInit(&zcpr,cprLevel);
-
- zcpr.next_in = FilePtr;
- zcpr.next_out = CprPtr;
-
-
- do
- {
- long all_read_before = zcpr.total_in;
- zcpr.avail_in = min(lOrigToDo,BlockSizeCompress);
- zcpr.avail_out = BlockSizeCompress;
- ret=deflate(&zcpr,(zcpr.avail_in==lOrigToDo) ? Z_FINISH : Z_SYNC_FLUSH);
- lOrigDone += (zcpr.total_in-all_read_before);
- lOrigToDo -= (zcpr.total_in-all_read_before);
- step++;
- } while (ret==Z_OK);
-
- lSizeCpr=zcpr.total_out;
- deflateEnd(&zcpr);
- dwGetTick=GetTickCount()-dwGetTick;
- dwMsecQP=GetMsecSincePerfCounter(li_qp,TRUE);
- dwResRdtsc=GetResRdtsc(li_rdtsc,TRUE);
- printf("total compress size = %u, in %u step\n",lSizeCpr,step);
- printf("time = %u msec = %f sec\n",dwGetTick,dwGetTick/(double)1000.);
- printf("defcpr time QP = %u msec = %f sec\n",dwMsecQP,dwMsecQP/(double)1000.);
- printf("defcpr result rdtsc = %I64x\n\n",dwResRdtsc.QuadPart);
- }
-
- CprPtr=(unsigned char*)realloc(CprPtr,lSizeCpr);
- UncprPtr=(unsigned char*)malloc(lBufferSizeUncpr + BlockSizeUncompress);
-
- BeginCountPerfCounter(&li_qp,TRUE);
- dwGetTick=GetTickCount();
- BeginCountRdtsc(&li_rdtsc);
- {
- z_stream zcpr;
- int ret=Z_OK;
- long lOrigToDo = lSizeCpr;
- long lOrigDone = 0;
- int step=0;
- memset(&zcpr,0,sizeof(z_stream));
- inflateInit(&zcpr);
-
- zcpr.next_in = CprPtr;
- zcpr.next_out = UncprPtr;
-
-
- do
- {
- long all_read_before = zcpr.total_in;
- zcpr.avail_in = min(lOrigToDo,BlockSizeUncompress);
- zcpr.avail_out = BlockSizeUncompress;
- ret=inflate(&zcpr,Z_SYNC_FLUSH);
- lOrigDone += (zcpr.total_in-all_read_before);
- lOrigToDo -= (zcpr.total_in-all_read_before);
- step++;
- } while (ret==Z_OK);
-
- lSizeUncpr=zcpr.total_out;
- inflateEnd(&zcpr);
- dwGetTick=GetTickCount()-dwGetTick;
- dwMsecQP=GetMsecSincePerfCounter(li_qp,TRUE);
- dwResRdtsc=GetResRdtsc(li_rdtsc,TRUE);
- printf("total uncompress size = %u, in %u step\n",lSizeUncpr,step);
- printf("time = %u msec = %f sec\n",dwGetTick,dwGetTick/(double)1000.);
- printf("uncpr time QP = %u msec = %f sec\n",dwMsecQP,dwMsecQP/(double)1000.);
- printf("uncpr result rdtsc = %I64x\n\n",dwResRdtsc.QuadPart);
- }
-
- if (lSizeUncpr==lFileSize)
- {
- if (memcmp(FilePtr,UncprPtr,lFileSize)==0)
- printf("compare ok\n");
-
- }
-
- return 0;
-}
diff --git a/third-party/zlib/contrib/testzlib/testzlib.txt b/third-party/zlib/contrib/testzlib/testzlib.txt
deleted file mode 100644
index 62258f1..0000000
--- a/third-party/zlib/contrib/testzlib/testzlib.txt
+++ /dev/null
@@ -1,10 +0,0 @@
-To build testzLib with Visual Studio 2005:
-
-copy to a directory file from :
-- root of zLib tree
-- contrib/testzlib
-- contrib/masmx86
-- contrib/masmx64
-- contrib/vstudio/vc7
-
-and open testzlib8.sln
\ No newline at end of file
diff --git a/third-party/zlib/contrib/untgz/Makefile b/third-party/zlib/contrib/untgz/Makefile
deleted file mode 100644
index b54266f..0000000
--- a/third-party/zlib/contrib/untgz/Makefile
+++ /dev/null
@@ -1,14 +0,0 @@
-CC=cc
-CFLAGS=-g
-
-untgz: untgz.o ../../libz.a
- $(CC) $(CFLAGS) -o untgz untgz.o -L../.. -lz
-
-untgz.o: untgz.c ../../zlib.h
- $(CC) $(CFLAGS) -c -I../.. untgz.c
-
-../../libz.a:
- cd ../..; ./configure; make
-
-clean:
- rm -f untgz untgz.o *~
diff --git a/third-party/zlib/contrib/untgz/Makefile.msc b/third-party/zlib/contrib/untgz/Makefile.msc
deleted file mode 100644
index 77b8602..0000000
--- a/third-party/zlib/contrib/untgz/Makefile.msc
+++ /dev/null
@@ -1,17 +0,0 @@
-CC=cl
-CFLAGS=-MD
-
-untgz.exe: untgz.obj ..\..\zlib.lib
- $(CC) $(CFLAGS) untgz.obj ..\..\zlib.lib
-
-untgz.obj: untgz.c ..\..\zlib.h
- $(CC) $(CFLAGS) -c -I..\.. untgz.c
-
-..\..\zlib.lib:
- cd ..\..
- $(MAKE) -f win32\makefile.msc
- cd contrib\untgz
-
-clean:
- -del untgz.obj
- -del untgz.exe
diff --git a/third-party/zlib/contrib/untgz/untgz.c b/third-party/zlib/contrib/untgz/untgz.c
deleted file mode 100644
index 2c391e5..0000000
--- a/third-party/zlib/contrib/untgz/untgz.c
+++ /dev/null
@@ -1,674 +0,0 @@
-/*
- * untgz.c -- Display contents and extract files from a gzip'd TAR file
- *
- * written by Pedro A. Aranda Gutierrez <paag at tid.es>
- * adaptation to Unix by Jean-loup Gailly <jloup at gzip.org>
- * various fixes by Cosmin Truta <cosmint at cs.ubbcluj.ro>
- */
-
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
-#include <time.h>
-#include <errno.h>
-
-#include "zlib.h"
-
-#ifdef unix
-# include <unistd.h>
-#else
-# include <direct.h>
-# include <io.h>
-#endif
-
-#ifdef WIN32
-#include <windows.h>
-# ifndef F_OK
-# define F_OK 0
-# endif
-# define mkdir(dirname,mode) _mkdir(dirname)
-# ifdef _MSC_VER
-# define access(path,mode) _access(path,mode)
-# define chmod(path,mode) _chmod(path,mode)
-# define strdup(str) _strdup(str)
-# endif
-#else
-# include <utime.h>
-#endif
-
-
-/* values used in typeflag field */
-
-#define REGTYPE '0' /* regular file */
-#define AREGTYPE '\0' /* regular file */
-#define LNKTYPE '1' /* link */
-#define SYMTYPE '2' /* reserved */
-#define CHRTYPE '3' /* character special */
-#define BLKTYPE '4' /* block special */
-#define DIRTYPE '5' /* directory */
-#define FIFOTYPE '6' /* FIFO special */
-#define CONTTYPE '7' /* reserved */
-
-/* GNU tar extensions */
-
-#define GNUTYPE_DUMPDIR 'D' /* file names from dumped directory */
-#define GNUTYPE_LONGLINK 'K' /* long link name */
-#define GNUTYPE_LONGNAME 'L' /* long file name */
-#define GNUTYPE_MULTIVOL 'M' /* continuation of file from another volume */
-#define GNUTYPE_NAMES 'N' /* file name that does not fit into main hdr */
-#define GNUTYPE_SPARSE 'S' /* sparse file */
-#define GNUTYPE_VOLHDR 'V' /* tape/volume header */
-
-
-/* tar header */
-
-#define BLOCKSIZE 512
-#define SHORTNAMESIZE 100
-
-struct tar_header
-{ /* byte offset */
- char name[100]; /* 0 */
- char mode[8]; /* 100 */
- char uid[8]; /* 108 */
- char gid[8]; /* 116 */
- char size[12]; /* 124 */
- char mtime[12]; /* 136 */
- char chksum[8]; /* 148 */
- char typeflag; /* 156 */
- char linkname[100]; /* 157 */
- char magic[6]; /* 257 */
- char version[2]; /* 263 */
- char uname[32]; /* 265 */
- char gname[32]; /* 297 */
- char devmajor[8]; /* 329 */
- char devminor[8]; /* 337 */
- char prefix[155]; /* 345 */
- /* 500 */
-};
-
-union tar_buffer
-{
- char buffer[BLOCKSIZE];
- struct tar_header header;
-};
-
-struct attr_item
-{
- struct attr_item *next;
- char *fname;
- int mode;
- time_t time;
-};
-
-enum { TGZ_EXTRACT, TGZ_LIST, TGZ_INVALID };
-
-char *TGZfname OF((const char *));
-void TGZnotfound OF((const char *));
-
-int getoct OF((char *, int));
-char *strtime OF((time_t *));
-int setfiletime OF((char *, time_t));
-void push_attr OF((struct attr_item **, char *, int, time_t));
-void restore_attr OF((struct attr_item **));
-
-int ExprMatch OF((char *, char *));
-
-int makedir OF((char *));
-int matchname OF((int, int, char **, char *));
-
-void error OF((const char *));
-int tar OF((gzFile, int, int, int, char **));
-
-void help OF((int));
-int main OF((int, char **));
-
-char *prog;
-
-const char *TGZsuffix[] = { "\0", ".tar", ".tar.gz", ".taz", ".tgz", NULL };
-
-/* return the file name of the TGZ archive */
-/* or NULL if it does not exist */
-
-char *TGZfname (const char *arcname)
-{
- static char buffer[1024];
- int origlen,i;
-
- strcpy(buffer,arcname);
- origlen = strlen(buffer);
-
- for (i=0; TGZsuffix[i]; i++)
- {
- strcpy(buffer+origlen,TGZsuffix[i]);
- if (access(buffer,F_OK) == 0)
- return buffer;
- }
- return NULL;
-}
-
-
-/* error message for the filename */
-
-void TGZnotfound (const char *arcname)
-{
- int i;
-
- fprintf(stderr,"%s: Couldn't find ",prog);
- for (i=0;TGZsuffix[i];i++)
- fprintf(stderr,(TGZsuffix[i+1]) ? "%s%s, " : "or %s%s\n",
- arcname,
- TGZsuffix[i]);
- exit(1);
-}
-
-
-/* convert octal digits to int */
-/* on error return -1 */
-
-int getoct (char *p,int width)
-{
- int result = 0;
- char c;
-
- while (width--)
- {
- c = *p++;
- if (c == 0)
- break;
- if (c == ' ')
- continue;
- if (c < '0' || c > '7')
- return -1;
- result = result * 8 + (c - '0');
- }
- return result;
-}
-
-
-/* convert time_t to string */
-/* use the "YYYY/MM/DD hh:mm:ss" format */
-
-char *strtime (time_t *t)
-{
- struct tm *local;
- static char result[32];
-
- local = localtime(t);
- sprintf(result,"%4d/%02d/%02d %02d:%02d:%02d",
- local->tm_year+1900, local->tm_mon+1, local->tm_mday,
- local->tm_hour, local->tm_min, local->tm_sec);
- return result;
-}
-
-
-/* set file time */
-
-int setfiletime (char *fname,time_t ftime)
-{
-#ifdef WIN32
- static int isWinNT = -1;
- SYSTEMTIME st;
- FILETIME locft, modft;
- struct tm *loctm;
- HANDLE hFile;
- int result;
-
- loctm = localtime(&ftime);
- if (loctm == NULL)
- return -1;
-
- st.wYear = (WORD)loctm->tm_year + 1900;
- st.wMonth = (WORD)loctm->tm_mon + 1;
- st.wDayOfWeek = (WORD)loctm->tm_wday;
- st.wDay = (WORD)loctm->tm_mday;
- st.wHour = (WORD)loctm->tm_hour;
- st.wMinute = (WORD)loctm->tm_min;
- st.wSecond = (WORD)loctm->tm_sec;
- st.wMilliseconds = 0;
- if (!SystemTimeToFileTime(&st, &locft) ||
- !LocalFileTimeToFileTime(&locft, &modft))
- return -1;
-
- if (isWinNT < 0)
- isWinNT = (GetVersion() < 0x80000000) ? 1 : 0;
- hFile = CreateFile(fname, GENERIC_WRITE, 0, NULL, OPEN_EXISTING,
- (isWinNT ? FILE_FLAG_BACKUP_SEMANTICS : 0),
- NULL);
- if (hFile == INVALID_HANDLE_VALUE)
- return -1;
- result = SetFileTime(hFile, NULL, NULL, &modft) ? 0 : -1;
- CloseHandle(hFile);
- return result;
-#else
- struct utimbuf settime;
-
- settime.actime = settime.modtime = ftime;
- return utime(fname,&settime);
-#endif
-}
-
-
-/* push file attributes */
-
-void push_attr(struct attr_item **list,char *fname,int mode,time_t time)
-{
- struct attr_item *item;
-
- item = (struct attr_item *)malloc(sizeof(struct attr_item));
- if (item == NULL)
- error("Out of memory");
- item->fname = strdup(fname);
- item->mode = mode;
- item->time = time;
- item->next = *list;
- *list = item;
-}
-
-
-/* restore file attributes */
-
-void restore_attr(struct attr_item **list)
-{
- struct attr_item *item, *prev;
-
- for (item = *list; item != NULL; )
- {
- setfiletime(item->fname,item->time);
- chmod(item->fname,item->mode);
- prev = item;
- item = item->next;
- free(prev);
- }
- *list = NULL;
-}
-
-
-/* match regular expression */
-
-#define ISSPECIAL(c) (((c) == '*') || ((c) == '/'))
-
-int ExprMatch (char *string,char *expr)
-{
- while (1)
- {
- if (ISSPECIAL(*expr))
- {
- if (*expr == '/')
- {
- if (*string != '\\' && *string != '/')
- return 0;
- string ++; expr++;
- }
- else if (*expr == '*')
- {
- if (*expr ++ == 0)
- return 1;
- while (*++string != *expr)
- if (*string == 0)
- return 0;
- }
- }
- else
- {
- if (*string != *expr)
- return 0;
- if (*expr++ == 0)
- return 1;
- string++;
- }
- }
-}
-
-
-/* recursive mkdir */
-/* abort on ENOENT; ignore other errors like "directory already exists" */
-/* return 1 if OK */
-/* 0 on error */
-
-int makedir (char *newdir)
-{
- char *buffer = strdup(newdir);
- char *p;
- int len = strlen(buffer);
-
- if (len <= 0) {
- free(buffer);
- return 0;
- }
- if (buffer[len-1] == '/') {
- buffer[len-1] = '\0';
- }
- if (mkdir(buffer, 0755) == 0)
- {
- free(buffer);
- return 1;
- }
-
- p = buffer+1;
- while (1)
- {
- char hold;
-
- while(*p && *p != '\\' && *p != '/')
- p++;
- hold = *p;
- *p = 0;
- if ((mkdir(buffer, 0755) == -1) && (errno == ENOENT))
- {
- fprintf(stderr,"%s: Couldn't create directory %s\n",prog,buffer);
- free(buffer);
- return 0;
- }
- if (hold == 0)
- break;
- *p++ = hold;
- }
- free(buffer);
- return 1;
-}
-
-
-int matchname (int arg,int argc,char **argv,char *fname)
-{
- if (arg == argc) /* no arguments given (untgz tgzarchive) */
- return 1;
-
- while (arg < argc)
- if (ExprMatch(fname,argv[arg++]))
- return 1;
-
- return 0; /* ignore this for the moment being */
-}
-
-
-/* tar file list or extract */
-
-int tar (gzFile in,int action,int arg,int argc,char **argv)
-{
- union tar_buffer buffer;
- int len;
- int err;
- int getheader = 1;
- int remaining = 0;
- FILE *outfile = NULL;
- char fname[BLOCKSIZE];
- int tarmode;
- time_t tartime;
- struct attr_item *attributes = NULL;
-
- if (action == TGZ_LIST)
- printf(" date time size file\n"
- " ---------- -------- --------- -------------------------------------\n");
- while (1)
- {
- len = gzread(in, &buffer, BLOCKSIZE);
- if (len < 0)
- error(gzerror(in, &err));
- /*
- * Always expect complete blocks to process
- * the tar information.
- */
- if (len != BLOCKSIZE)
- {
- action = TGZ_INVALID; /* force error exit */
- remaining = 0; /* force I/O cleanup */
- }
-
- /*
- * If we have to get a tar header
- */
- if (getheader >= 1)
- {
- /*
- * if we met the end of the tar
- * or the end-of-tar block,
- * we are done
- */
- if (len == 0 || buffer.header.name[0] == 0)
- break;
-
- tarmode = getoct(buffer.header.mode,8);
- tartime = (time_t)getoct(buffer.header.mtime,12);
- if (tarmode == -1 || tartime == (time_t)-1)
- {
- buffer.header.name[0] = 0;
- action = TGZ_INVALID;
- }
-
- if (getheader == 1)
- {
- strncpy(fname,buffer.header.name,SHORTNAMESIZE);
- if (fname[SHORTNAMESIZE-1] != 0)
- fname[SHORTNAMESIZE] = 0;
- }
- else
- {
- /*
- * The file name is longer than SHORTNAMESIZE
- */
- if (strncmp(fname,buffer.header.name,SHORTNAMESIZE-1) != 0)
- error("bad long name");
- getheader = 1;
- }
-
- /*
- * Act according to the type flag
- */
- switch (buffer.header.typeflag)
- {
- case DIRTYPE:
- if (action == TGZ_LIST)
- printf(" %s <dir> %s\n",strtime(&tartime),fname);
- if (action == TGZ_EXTRACT)
- {
- makedir(fname);
- push_attr(&attributes,fname,tarmode,tartime);
- }
- break;
- case REGTYPE:
- case AREGTYPE:
- remaining = getoct(buffer.header.size,12);
- if (remaining == -1)
- {
- action = TGZ_INVALID;
- break;
- }
- if (action == TGZ_LIST)
- printf(" %s %9d %s\n",strtime(&tartime),remaining,fname);
- else if (action == TGZ_EXTRACT)
- {
- if (matchname(arg,argc,argv,fname))
- {
- outfile = fopen(fname,"wb");
- if (outfile == NULL) {
- /* try creating directory */
- char *p = strrchr(fname, '/');
- if (p != NULL) {
- *p = '\0';
- makedir(fname);
- *p = '/';
- outfile = fopen(fname,"wb");
- }
- }
- if (outfile != NULL)
- printf("Extracting %s\n",fname);
- else
- fprintf(stderr, "%s: Couldn't create %s",prog,fname);
- }
- else
- outfile = NULL;
- }
- getheader = 0;
- break;
- case GNUTYPE_LONGLINK:
- case GNUTYPE_LONGNAME:
- remaining = getoct(buffer.header.size,12);
- if (remaining < 0 || remaining >= BLOCKSIZE)
- {
- action = TGZ_INVALID;
- break;
- }
- len = gzread(in, fname, BLOCKSIZE);
- if (len < 0)
- error(gzerror(in, &err));
- if (fname[BLOCKSIZE-1] != 0 || (int)strlen(fname) > remaining)
- {
- action = TGZ_INVALID;
- break;
- }
- getheader = 2;
- break;
- default:
- if (action == TGZ_LIST)
- printf(" %s <---> %s\n",strtime(&tartime),fname);
- break;
- }
- }
- else
- {
- unsigned int bytes = (remaining > BLOCKSIZE) ? BLOCKSIZE : remaining;
-
- if (outfile != NULL)
- {
- if (fwrite(&buffer,sizeof(char),bytes,outfile) != bytes)
- {
- fprintf(stderr,
- "%s: Error writing %s -- skipping\n",prog,fname);
- fclose(outfile);
- outfile = NULL;
- remove(fname);
- }
- }
- remaining -= bytes;
- }
-
- if (remaining == 0)
- {
- getheader = 1;
- if (outfile != NULL)
- {
- fclose(outfile);
- outfile = NULL;
- if (action != TGZ_INVALID)
- push_attr(&attributes,fname,tarmode,tartime);
- }
- }
-
- /*
- * Abandon if errors are found
- */
- if (action == TGZ_INVALID)
- {
- error("broken archive");
- break;
- }
- }
-
- /*
- * Restore file modes and time stamps
- */
- restore_attr(&attributes);
-
- if (gzclose(in) != Z_OK)
- error("failed gzclose");
-
- return 0;
-}
-
-
-/* ============================================================ */
-
-void help(int exitval)
-{
- printf("untgz version 0.2.1\n"
- " using zlib version %s\n\n",
- zlibVersion());
- printf("Usage: untgz file.tgz extract all files\n"
- " untgz file.tgz fname ... extract selected files\n"
- " untgz -l file.tgz list archive contents\n"
- " untgz -h display this help\n");
- exit(exitval);
-}
-
-void error(const char *msg)
-{
- fprintf(stderr, "%s: %s\n", prog, msg);
- exit(1);
-}
-
-
-/* ============================================================ */
-
-#if defined(WIN32) && defined(__GNUC__)
-int _CRT_glob = 0; /* disable argument globbing in MinGW */
-#endif
-
-int main(int argc,char **argv)
-{
- int action = TGZ_EXTRACT;
- int arg = 1;
- char *TGZfile;
- gzFile *f;
-
- prog = strrchr(argv[0],'\\');
- if (prog == NULL)
- {
- prog = strrchr(argv[0],'/');
- if (prog == NULL)
- {
- prog = strrchr(argv[0],':');
- if (prog == NULL)
- prog = argv[0];
- else
- prog++;
- }
- else
- prog++;
- }
- else
- prog++;
-
- if (argc == 1)
- help(0);
-
- if (strcmp(argv[arg],"-l") == 0)
- {
- action = TGZ_LIST;
- if (argc == ++arg)
- help(0);
- }
- else if (strcmp(argv[arg],"-h") == 0)
- {
- help(0);
- }
-
- if ((TGZfile = TGZfname(argv[arg])) == NULL)
- TGZnotfound(argv[arg]);
-
- ++arg;
- if ((action == TGZ_LIST) && (arg != argc))
- help(1);
-
-/*
- * Process the TGZ file
- */
- switch(action)
- {
- case TGZ_LIST:
- case TGZ_EXTRACT:
- f = gzopen(TGZfile,"rb");
- if (f == NULL)
- {
- fprintf(stderr,"%s: Couldn't gzopen %s\n",prog,TGZfile);
- return 1;
- }
- exit(tar(f, action, arg, argc, argv));
- break;
-
- default:
- error("Unknown option");
- exit(1);
- }
-
- return 0;
-}
diff --git a/third-party/zlib/contrib/vstudio/readme.txt b/third-party/zlib/contrib/vstudio/readme.txt
deleted file mode 100644
index bfdcd9d..0000000
--- a/third-party/zlib/contrib/vstudio/readme.txt
+++ /dev/null
@@ -1,65 +0,0 @@
-Building instructions for the DLL versions of Zlib 1.2.8
-========================================================
-
-This directory contains projects that build zlib and minizip using
-Microsoft Visual C++ 9.0/10.0.
-
-You don't need to build these projects yourself. You can download the
-binaries from:
- http://www.winimage.com/zLibDll
-
-More information can be found at this site.
-
-
-
-
-
-Build instructions for Visual Studio 2008 (32 bits or 64 bits)
---------------------------------------------------------------
-- Uncompress current zlib, including all contrib/* files
-- Compile assembly code (with Visual Studio Command Prompt) by running:
- bld_ml64.bat (in contrib\masmx64)
- bld_ml32.bat (in contrib\masmx86)
-- Open contrib\vstudio\vc9\zlibvc.sln with Microsoft Visual C++ 2008
-- Or run: vcbuild /rebuild contrib\vstudio\vc9\zlibvc.sln "Release|Win32"
-
-Build instructions for Visual Studio 2010 (32 bits or 64 bits)
---------------------------------------------------------------
-- Uncompress current zlib, including all contrib/* files
-- Open contrib\vstudio\vc10\zlibvc.sln with Microsoft Visual C++ 2010
-
-Build instructions for Visual Studio 2012 (32 bits or 64 bits)
---------------------------------------------------------------
-- Uncompress current zlib, including all contrib/* files
-- Open contrib\vstudio\vc11\zlibvc.sln with Microsoft Visual C++ 2012
-
-
-Important
----------
-- To use zlibwapi.dll in your application, you must define the
- macro ZLIB_WINAPI when compiling your application's source files.
-
-
-Additional notes
-----------------
-- This DLL, named zlibwapi.dll, is compatible to the old zlib.dll built
- by Gilles Vollant from the zlib 1.1.x sources, and distributed at
- http://www.winimage.com/zLibDll
- It uses the WINAPI calling convention for the exported functions, and
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-
-- The new DLL was renamed because there exist several incompatible
- versions of zlib.dll on the Internet.
-
-- There is also an official DLL build of zlib, named zlib1.dll. This one
- is exporting the functions using the CDECL convention. See the file
- win32\DLL_FAQ.txt found in this zlib distribution.
-
-- There used to be a ZLIB_DLL macro in zlib 1.1.x, but now this symbol
- has a slightly different effect. To avoid compatibility problems, do
- not define it here.
-
-
-Gilles Vollant
-info at winimage.com
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diff --git a/third-party/zlib/contrib/vstudio/vc10/testzlibdll.vcxproj.filters b/third-party/zlib/contrib/vstudio/vc10/testzlibdll.vcxproj.filters
deleted file mode 100644
index 53a8693..0000000
--- a/third-party/zlib/contrib/vstudio/vc10/testzlibdll.vcxproj.filters
+++ /dev/null
@@ -1,22 +0,0 @@
-<?xml version="1.0" encoding="utf-8"?>
-<Project ToolsVersion="4.0" xmlns="http://schemas.microsoft.com/developer/msbuild/2003">
- <ItemGroup>
- <Filter Include="Source Files">
- <UniqueIdentifier>{fa61a89f-93fc-4c89-b29e-36224b7592f4}</UniqueIdentifier>
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- <Extensions>h;hpp;hxx;hm;inl;inc</Extensions>
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diff --git a/third-party/zlib/contrib/vstudio/vc10/zlib.rc b/third-party/zlib/contrib/vstudio/vc10/zlib.rc
deleted file mode 100644
index 73f6476..0000000
--- a/third-party/zlib/contrib/vstudio/vc10/zlib.rc
+++ /dev/null
@@ -1,32 +0,0 @@
-#include <windows.h>
-
-#define IDR_VERSION1 1
-IDR_VERSION1 VERSIONINFO MOVEABLE IMPURE LOADONCALL DISCARDABLE
- FILEVERSION 1,2,8,0
- PRODUCTVERSION 1,2,8,0
- FILEFLAGSMASK VS_FFI_FILEFLAGSMASK
- FILEFLAGS 0
- FILEOS VOS_DOS_WINDOWS32
- FILETYPE VFT_DLL
- FILESUBTYPE 0 // not used
-BEGIN
- BLOCK "StringFileInfo"
- BEGIN
- BLOCK "040904E4"
- //language ID = U.S. English, char set = Windows, Multilingual
-
- BEGIN
- VALUE "FileDescription", "zlib data compression and ZIP file I/O library\0"
- VALUE "FileVersion", "1.2.8\0"
- VALUE "InternalName", "zlib\0"
- VALUE "OriginalFilename", "zlibwapi.dll\0"
- VALUE "ProductName", "ZLib.DLL\0"
- VALUE "Comments","DLL support by Alessandro Iacopetti & Gilles Vollant\0"
- VALUE "LegalCopyright", "(C) 1995-2013 Jean-loup Gailly & Mark Adler\0"
- END
- END
- BLOCK "VarFileInfo"
- BEGIN
- VALUE "Translation", 0x0409, 1252
- END
-END
diff --git a/third-party/zlib/contrib/vstudio/vc10/zlibstat.vcxproj b/third-party/zlib/contrib/vstudio/vc10/zlibstat.vcxproj
deleted file mode 100644
index b9f2bbe..0000000
--- a/third-party/zlib/contrib/vstudio/vc10/zlibstat.vcxproj
+++ /dev/null
@@ -1,473 +0,0 @@
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- <Optimization>Disabled</Optimization>
- <AdditionalIncludeDirectories>..\..\..;..\..\masmx86;%(AdditionalIncludeDirectories)</AdditionalIncludeDirectories>
- <PreprocessorDefinitions>ZLIB_WINAPI;_CRT_NONSTDC_NO_DEPRECATE;_CRT_SECURE_NO_DEPRECATE;_CRT_NONSTDC_NO_WARNINGS;WIN64;%(PreprocessorDefinitions)</PreprocessorDefinitions>
- <ExceptionHandling>
- </ExceptionHandling>
- <RuntimeLibrary>MultiThreadedDebugDLL</RuntimeLibrary>
- <BufferSecurityCheck>false</BufferSecurityCheck>
- <PrecompiledHeaderOutputFile>$(IntDir)zlibstat.pch</PrecompiledHeaderOutputFile>
- <AssemblerListingLocation>$(IntDir)</AssemblerListingLocation>
- <ObjectFileName>$(IntDir)</ObjectFileName>
- <ProgramDataBaseFileName>$(OutDir)</ProgramDataBaseFileName>
- <WarningLevel>Level3</WarningLevel>
- <SuppressStartupBanner>true</SuppressStartupBanner>
- <DebugInformationFormat>OldStyle</DebugInformationFormat>
- </ClCompile>
- <ResourceCompile>
- <Culture>0x040c</Culture>
- </ResourceCompile>
- <Lib>
- <AdditionalOptions>/MACHINE:IA64 /NODEFAULTLIB %(AdditionalOptions)</AdditionalOptions>
- <OutputFile>$(OutDir)zlibstat.lib</OutputFile>
- <SuppressStartupBanner>true</SuppressStartupBanner>
- </Lib>
- </ItemDefinitionGroup>
- <ItemDefinitionGroup Condition="'$(Configuration)|$(Platform)'=='Release|x64'">
- <Midl>
- <TargetEnvironment>X64</TargetEnvironment>
- </Midl>
- <ClCompile>
- <InlineFunctionExpansion>OnlyExplicitInline</InlineFunctionExpansion>
- <AdditionalIncludeDirectories>..\..\..;..\..\masmx86;%(AdditionalIncludeDirectories)</AdditionalIncludeDirectories>
- <PreprocessorDefinitions>ZLIB_WINAPI;_CRT_NONSTDC_NO_DEPRECATE;_CRT_SECURE_NO_DEPRECATE;_CRT_NONSTDC_NO_WARNINGS;ASMV;ASMINF;WIN64;%(PreprocessorDefinitions)</PreprocessorDefinitions>
- <StringPooling>true</StringPooling>
- <ExceptionHandling>
- </ExceptionHandling>
- <RuntimeLibrary>MultiThreadedDLL</RuntimeLibrary>
- <BufferSecurityCheck>false</BufferSecurityCheck>
- <FunctionLevelLinking>true</FunctionLevelLinking>
- <PrecompiledHeaderOutputFile>$(IntDir)zlibstat.pch</PrecompiledHeaderOutputFile>
- <AssemblerListingLocation>$(IntDir)</AssemblerListingLocation>
- <ObjectFileName>$(IntDir)</ObjectFileName>
- <ProgramDataBaseFileName>$(OutDir)</ProgramDataBaseFileName>
- <WarningLevel>Level3</WarningLevel>
- <SuppressStartupBanner>true</SuppressStartupBanner>
- </ClCompile>
- <ResourceCompile>
- <Culture>0x040c</Culture>
- </ResourceCompile>
- <Lib>
- <AdditionalOptions>/MACHINE:AMD64 /NODEFAULTLIB %(AdditionalOptions)</AdditionalOptions>
- <AdditionalDependencies>..\..\masmx64\gvmat64.obj;..\..\masmx64\inffasx64.obj;%(AdditionalDependencies)</AdditionalDependencies>
- <OutputFile>$(OutDir)zlibstat.lib</OutputFile>
- <SuppressStartupBanner>true</SuppressStartupBanner>
- </Lib>
- <PreBuildEvent>
- <Command>cd ..\..\masmx64
-bld_ml64.bat</Command>
- </PreBuildEvent>
- </ItemDefinitionGroup>
- <ItemDefinitionGroup Condition="'$(Configuration)|$(Platform)'=='Release|Itanium'">
- <Midl>
- <TargetEnvironment>Itanium</TargetEnvironment>
- </Midl>
- <ClCompile>
- <InlineFunctionExpansion>OnlyExplicitInline</InlineFunctionExpansion>
- <AdditionalIncludeDirectories>..\..\..;..\..\masmx86;%(AdditionalIncludeDirectories)</AdditionalIncludeDirectories>
- <PreprocessorDefinitions>ZLIB_WINAPI;_CRT_NONSTDC_NO_DEPRECATE;_CRT_SECURE_NO_DEPRECATE;_CRT_NONSTDC_NO_WARNINGS;WIN64;%(PreprocessorDefinitions)</PreprocessorDefinitions>
- <StringPooling>true</StringPooling>
- <ExceptionHandling>
- </ExceptionHandling>
- <RuntimeLibrary>MultiThreadedDLL</RuntimeLibrary>
- <BufferSecurityCheck>false</BufferSecurityCheck>
- <FunctionLevelLinking>true</FunctionLevelLinking>
- <PrecompiledHeaderOutputFile>$(IntDir)zlibstat.pch</PrecompiledHeaderOutputFile>
- <AssemblerListingLocation>$(IntDir)</AssemblerListingLocation>
- <ObjectFileName>$(IntDir)</ObjectFileName>
- <ProgramDataBaseFileName>$(OutDir)</ProgramDataBaseFileName>
- <WarningLevel>Level3</WarningLevel>
- <SuppressStartupBanner>true</SuppressStartupBanner>
- </ClCompile>
- <ResourceCompile>
- <Culture>0x040c</Culture>
- </ResourceCompile>
- <Lib>
- <AdditionalOptions>/MACHINE:IA64 /NODEFAULTLIB %(AdditionalOptions)</AdditionalOptions>
- <OutputFile>$(OutDir)zlibstat.lib</OutputFile>
- <SuppressStartupBanner>true</SuppressStartupBanner>
- </Lib>
- </ItemDefinitionGroup>
- <ItemDefinitionGroup Condition="'$(Configuration)|$(Platform)'=='ReleaseWithoutAsm|x64'">
- <Midl>
- <TargetEnvironment>X64</TargetEnvironment>
- </Midl>
- <ClCompile>
- <InlineFunctionExpansion>OnlyExplicitInline</InlineFunctionExpansion>
- <AdditionalIncludeDirectories>..\..\..;..\..\masmx86;%(AdditionalIncludeDirectories)</AdditionalIncludeDirectories>
- <PreprocessorDefinitions>ZLIB_WINAPI;_CRT_NONSTDC_NO_DEPRECATE;_CRT_SECURE_NO_DEPRECATE;_CRT_NONSTDC_NO_WARNINGS;WIN64;%(PreprocessorDefinitions)</PreprocessorDefinitions>
- <StringPooling>true</StringPooling>
- <ExceptionHandling>
- </ExceptionHandling>
- <RuntimeLibrary>MultiThreadedDLL</RuntimeLibrary>
- <BufferSecurityCheck>false</BufferSecurityCheck>
- <FunctionLevelLinking>true</FunctionLevelLinking>
- <PrecompiledHeaderOutputFile>$(IntDir)zlibstat.pch</PrecompiledHeaderOutputFile>
- <AssemblerListingLocation>$(IntDir)</AssemblerListingLocation>
- <ObjectFileName>$(IntDir)</ObjectFileName>
- <ProgramDataBaseFileName>$(OutDir)</ProgramDataBaseFileName>
- <WarningLevel>Level3</WarningLevel>
- <SuppressStartupBanner>true</SuppressStartupBanner>
- </ClCompile>
- <ResourceCompile>
- <Culture>0x040c</Culture>
- </ResourceCompile>
- <Lib>
- <AdditionalOptions>/MACHINE:AMD64 /NODEFAULTLIB %(AdditionalOptions)</AdditionalOptions>
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- <SuppressStartupBanner>true</SuppressStartupBanner>
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- <Midl>
- <TargetEnvironment>Itanium</TargetEnvironment>
- </Midl>
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- <AdditionalIncludeDirectories>..\..\..;..\..\masmx86;%(AdditionalIncludeDirectories)</AdditionalIncludeDirectories>
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- <StringPooling>true</StringPooling>
- <ExceptionHandling>
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- <SuppressStartupBanner>true</SuppressStartupBanner>
- </ClCompile>
- <ResourceCompile>
- <Culture>0x040c</Culture>
- </ResourceCompile>
- <Lib>
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- <OutputFile>$(OutDir)zlibstat.lib</OutputFile>
- <SuppressStartupBanner>true</SuppressStartupBanner>
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- </ItemDefinitionGroup>
- <ItemGroup>
- <ClCompile Include="..\..\..\adler32.c" />
- <ClCompile Include="..\..\..\compress.c" />
- <ClCompile Include="..\..\..\crc32.c" />
- <ClCompile Include="..\..\..\deflate.c" />
- <ClCompile Include="..\..\..\gzclose.c" />
- <ClCompile Include="..\..\..\gzlib.c" />
- <ClCompile Include="..\..\..\gzread.c" />
- <ClCompile Include="..\..\..\gzwrite.c" />
- <ClCompile Include="..\..\..\infback.c" />
- <ClCompile Include="..\..\masmx64\inffas8664.c">
- <ExcludedFromBuild Condition="'$(Configuration)|$(Platform)'=='Debug|Itanium'">true</ExcludedFromBuild>
- <ExcludedFromBuild Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'">true</ExcludedFromBuild>
- <ExcludedFromBuild Condition="'$(Configuration)|$(Platform)'=='ReleaseWithoutAsm|Itanium'">true</ExcludedFromBuild>
- <ExcludedFromBuild Condition="'$(Configuration)|$(Platform)'=='ReleaseWithoutAsm|Win32'">true</ExcludedFromBuild>
- <ExcludedFromBuild Condition="'$(Configuration)|$(Platform)'=='Release|Itanium'">true</ExcludedFromBuild>
- <ExcludedFromBuild Condition="'$(Configuration)|$(Platform)'=='Release|Win32'">true</ExcludedFromBuild>
- </ClCompile>
- <ClCompile Include="..\..\..\inffast.c" />
- <ClCompile Include="..\..\..\inflate.c" />
- <ClCompile Include="..\..\..\inftrees.c" />
- <ClCompile Include="..\..\minizip\ioapi.c" />
- <ClCompile Include="..\..\..\trees.c" />
- <ClCompile Include="..\..\..\uncompr.c" />
- <ClCompile Include="..\..\minizip\unzip.c" />
- <ClCompile Include="..\..\minizip\zip.c" />
- <ClCompile Include="..\..\..\zutil.c" />
- </ItemGroup>
- <ItemGroup>
- <ResourceCompile Include="zlib.rc" />
- </ItemGroup>
- <ItemGroup>
- <None Include="zlibvc.def" />
- </ItemGroup>
- <Import Project="$(VCTargetsPath)\Microsoft.Cpp.targets" />
- <ImportGroup Label="ExtensionTargets">
- </ImportGroup>
-</Project>
\ No newline at end of file
diff --git a/third-party/zlib/contrib/vstudio/vc10/zlibstat.vcxproj.filters b/third-party/zlib/contrib/vstudio/vc10/zlibstat.vcxproj.filters
deleted file mode 100644
index c8c7f7e..0000000
--- a/third-party/zlib/contrib/vstudio/vc10/zlibstat.vcxproj.filters
+++ /dev/null
@@ -1,77 +0,0 @@
-<?xml version="1.0" encoding="utf-8"?>
-<Project ToolsVersion="4.0" xmlns="http://schemas.microsoft.com/developer/msbuild/2003">
- <ItemGroup>
- <Filter Include="Source Files">
- <UniqueIdentifier>{174213f6-7f66-4ae8-a3a8-a1e0a1e6ffdd}</UniqueIdentifier>
- </Filter>
- </ItemGroup>
- <ItemGroup>
- <ClCompile Include="..\..\..\adler32.c">
- <Filter>Source Files</Filter>
- </ClCompile>
- <ClCompile Include="..\..\..\compress.c">
- <Filter>Source Files</Filter>
- </ClCompile>
- <ClCompile Include="..\..\..\crc32.c">
- <Filter>Source Files</Filter>
- </ClCompile>
- <ClCompile Include="..\..\..\deflate.c">
- <Filter>Source Files</Filter>
- </ClCompile>
- <ClCompile Include="..\..\..\gzclose.c">
- <Filter>Source Files</Filter>
- </ClCompile>
- <ClCompile Include="..\..\..\gzlib.c">
- <Filter>Source Files</Filter>
- </ClCompile>
- <ClCompile Include="..\..\..\gzread.c">
- <Filter>Source Files</Filter>
- </ClCompile>
- <ClCompile Include="..\..\..\gzwrite.c">
- <Filter>Source Files</Filter>
- </ClCompile>
- <ClCompile Include="..\..\..\infback.c">
- <Filter>Source Files</Filter>
- </ClCompile>
- <ClCompile Include="..\..\masmx64\inffas8664.c">
- <Filter>Source Files</Filter>
- </ClCompile>
- <ClCompile Include="..\..\..\inffast.c">
- <Filter>Source Files</Filter>
- </ClCompile>
- <ClCompile Include="..\..\..\inflate.c">
- <Filter>Source Files</Filter>
- </ClCompile>
- <ClCompile Include="..\..\..\inftrees.c">
- <Filter>Source Files</Filter>
- </ClCompile>
- <ClCompile Include="..\..\minizip\ioapi.c">
- <Filter>Source Files</Filter>
- </ClCompile>
- <ClCompile Include="..\..\..\trees.c">
- <Filter>Source Files</Filter>
- </ClCompile>
- <ClCompile Include="..\..\..\uncompr.c">
- <Filter>Source Files</Filter>
- </ClCompile>
- <ClCompile Include="..\..\minizip\unzip.c">
- <Filter>Source Files</Filter>
- </ClCompile>
- <ClCompile Include="..\..\minizip\zip.c">
- <Filter>Source Files</Filter>
- </ClCompile>
- <ClCompile Include="..\..\..\zutil.c">
- <Filter>Source Files</Filter>
- </ClCompile>
- </ItemGroup>
- <ItemGroup>
- <ResourceCompile Include="zlib.rc">
- <Filter>Source Files</Filter>
- </ResourceCompile>
- </ItemGroup>
- <ItemGroup>
- <None Include="zlibvc.def">
- <Filter>Source Files</Filter>
- </None>
- </ItemGroup>
-</Project>
\ No newline at end of file
diff --git a/third-party/zlib/contrib/vstudio/vc10/zlibvc.def b/third-party/zlib/contrib/vstudio/vc10/zlibvc.def
deleted file mode 100644
index 6367046..0000000
--- a/third-party/zlib/contrib/vstudio/vc10/zlibvc.def
+++ /dev/null
@@ -1,143 +0,0 @@
-LIBRARY
-; zlib data compression and ZIP file I/O library
-
-VERSION 1.2.8
-
-EXPORTS
- adler32 @1
- compress @2
- crc32 @3
- deflate @4
- deflateCopy @5
- deflateEnd @6
- deflateInit2_ @7
- deflateInit_ @8
- deflateParams @9
- deflateReset @10
- deflateSetDictionary @11
- gzclose @12
- gzdopen @13
- gzerror @14
- gzflush @15
- gzopen @16
- gzread @17
- gzwrite @18
- inflate @19
- inflateEnd @20
- inflateInit2_ @21
- inflateInit_ @22
- inflateReset @23
- inflateSetDictionary @24
- inflateSync @25
- uncompress @26
- zlibVersion @27
- gzprintf @28
- gzputc @29
- gzgetc @30
- gzseek @31
- gzrewind @32
- gztell @33
- gzeof @34
- gzsetparams @35
- zError @36
- inflateSyncPoint @37
- get_crc_table @38
- compress2 @39
- gzputs @40
- gzgets @41
- inflateCopy @42
- inflateBackInit_ @43
- inflateBack @44
- inflateBackEnd @45
- compressBound @46
- deflateBound @47
- gzclearerr @48
- gzungetc @49
- zlibCompileFlags @50
- deflatePrime @51
- deflatePending @52
-
- unzOpen @61
- unzClose @62
- unzGetGlobalInfo @63
- unzGetCurrentFileInfo @64
- unzGoToFirstFile @65
- unzGoToNextFile @66
- unzOpenCurrentFile @67
- unzReadCurrentFile @68
- unzOpenCurrentFile3 @69
- unztell @70
- unzeof @71
- unzCloseCurrentFile @72
- unzGetGlobalComment @73
- unzStringFileNameCompare @74
- unzLocateFile @75
- unzGetLocalExtrafield @76
- unzOpen2 @77
- unzOpenCurrentFile2 @78
- unzOpenCurrentFilePassword @79
-
- zipOpen @80
- zipOpenNewFileInZip @81
- zipWriteInFileInZip @82
- zipCloseFileInZip @83
- zipClose @84
- zipOpenNewFileInZip2 @86
- zipCloseFileInZipRaw @87
- zipOpen2 @88
- zipOpenNewFileInZip3 @89
-
- unzGetFilePos @100
- unzGoToFilePos @101
-
- fill_win32_filefunc @110
-
-; zlibwapi v1.2.4 added:
- fill_win32_filefunc64 @111
- fill_win32_filefunc64A @112
- fill_win32_filefunc64W @113
-
- unzOpen64 @120
- unzOpen2_64 @121
- unzGetGlobalInfo64 @122
- unzGetCurrentFileInfo64 @124
- unzGetCurrentFileZStreamPos64 @125
- unztell64 @126
- unzGetFilePos64 @127
- unzGoToFilePos64 @128
-
- zipOpen64 @130
- zipOpen2_64 @131
- zipOpenNewFileInZip64 @132
- zipOpenNewFileInZip2_64 @133
- zipOpenNewFileInZip3_64 @134
- zipOpenNewFileInZip4_64 @135
- zipCloseFileInZipRaw64 @136
-
-; zlib1 v1.2.4 added:
- adler32_combine @140
- crc32_combine @142
- deflateSetHeader @144
- deflateTune @145
- gzbuffer @146
- gzclose_r @147
- gzclose_w @148
- gzdirect @149
- gzoffset @150
- inflateGetHeader @156
- inflateMark @157
- inflatePrime @158
- inflateReset2 @159
- inflateUndermine @160
-
-; zlib1 v1.2.6 added:
- gzgetc_ @161
- inflateResetKeep @163
- deflateResetKeep @164
-
-; zlib1 v1.2.7 added:
- gzopen_w @165
-
-; zlib1 v1.2.8 added:
- inflateGetDictionary @166
- gzvprintf @167
diff --git a/third-party/zlib/contrib/vstudio/vc10/zlibvc.sln b/third-party/zlib/contrib/vstudio/vc10/zlibvc.sln
deleted file mode 100644
index 6f6ffd5..0000000
--- a/third-party/zlib/contrib/vstudio/vc10/zlibvc.sln
+++ /dev/null
@@ -1,135 +0,0 @@
-
-Microsoft Visual Studio Solution File, Format Version 11.00
-# Visual Studio 2010
-Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "zlibvc", "zlibvc.vcxproj", "{8FD826F8-3739-44E6-8CC8-997122E53B8D}"
-EndProject
-Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "zlibstat", "zlibstat.vcxproj", "{745DEC58-EBB3-47A9-A9B8-4C6627C01BF8}"
-EndProject
-Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "testzlib", "testzlib.vcxproj", "{AA6666AA-E09F-4135-9C0C-4FE50C3C654B}"
-EndProject
-Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "testzlibdll", "testzlibdll.vcxproj", "{C52F9E7B-498A-42BE-8DB4-85A15694366A}"
-EndProject
-Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "minizip", "minizip.vcxproj", "{48CDD9DC-E09F-4135-9C0C-4FE50C3C654B}"
-EndProject
-Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "miniunz", "miniunz.vcxproj", "{C52F9E7B-498A-42BE-8DB4-85A15694382A}"
-EndProject
-Global
- GlobalSection(SolutionConfigurationPlatforms) = preSolution
- Debug|Itanium = Debug|Itanium
- Debug|Win32 = Debug|Win32
- Debug|x64 = Debug|x64
- Release|Itanium = Release|Itanium
- Release|Win32 = Release|Win32
- Release|x64 = Release|x64
- ReleaseWithoutAsm|Itanium = ReleaseWithoutAsm|Itanium
- ReleaseWithoutAsm|Win32 = ReleaseWithoutAsm|Win32
- ReleaseWithoutAsm|x64 = ReleaseWithoutAsm|x64
- EndGlobalSection
- GlobalSection(ProjectConfigurationPlatforms) = postSolution
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- {8FD826F8-3739-44E6-8CC8-997122E53B8D}.Debug|Itanium.Build.0 = Debug|Itanium
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- {8FD826F8-3739-44E6-8CC8-997122E53B8D}.Debug|x64.ActiveCfg = Debug|x64
- {8FD826F8-3739-44E6-8CC8-997122E53B8D}.Debug|x64.Build.0 = Debug|x64
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- {8FD826F8-3739-44E6-8CC8-997122E53B8D}.Release|Win32.Build.0 = Release|Win32
- {8FD826F8-3739-44E6-8CC8-997122E53B8D}.Release|x64.ActiveCfg = Release|x64
- {8FD826F8-3739-44E6-8CC8-997122E53B8D}.Release|x64.Build.0 = Release|x64
- {8FD826F8-3739-44E6-8CC8-997122E53B8D}.ReleaseWithoutAsm|Itanium.ActiveCfg = ReleaseWithoutAsm|Itanium
- {8FD826F8-3739-44E6-8CC8-997122E53B8D}.ReleaseWithoutAsm|Itanium.Build.0 = ReleaseWithoutAsm|Itanium
- {8FD826F8-3739-44E6-8CC8-997122E53B8D}.ReleaseWithoutAsm|Win32.ActiveCfg = ReleaseWithoutAsm|Win32
- {8FD826F8-3739-44E6-8CC8-997122E53B8D}.ReleaseWithoutAsm|Win32.Build.0 = ReleaseWithoutAsm|Win32
- {8FD826F8-3739-44E6-8CC8-997122E53B8D}.ReleaseWithoutAsm|x64.ActiveCfg = ReleaseWithoutAsm|x64
- {8FD826F8-3739-44E6-8CC8-997122E53B8D}.ReleaseWithoutAsm|x64.Build.0 = ReleaseWithoutAsm|x64
- {745DEC58-EBB3-47A9-A9B8-4C6627C01BF8}.Debug|Itanium.ActiveCfg = Debug|Itanium
- {745DEC58-EBB3-47A9-A9B8-4C6627C01BF8}.Debug|Itanium.Build.0 = Debug|Itanium
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- {745DEC58-EBB3-47A9-A9B8-4C6627C01BF8}.Debug|Win32.Build.0 = Debug|Win32
- {745DEC58-EBB3-47A9-A9B8-4C6627C01BF8}.Debug|x64.ActiveCfg = Debug|x64
- {745DEC58-EBB3-47A9-A9B8-4C6627C01BF8}.Debug|x64.Build.0 = Debug|x64
- {745DEC58-EBB3-47A9-A9B8-4C6627C01BF8}.Release|Itanium.ActiveCfg = Release|Itanium
- {745DEC58-EBB3-47A9-A9B8-4C6627C01BF8}.Release|Itanium.Build.0 = Release|Itanium
- {745DEC58-EBB3-47A9-A9B8-4C6627C01BF8}.Release|Win32.ActiveCfg = Release|Win32
- {745DEC58-EBB3-47A9-A9B8-4C6627C01BF8}.Release|Win32.Build.0 = Release|Win32
- {745DEC58-EBB3-47A9-A9B8-4C6627C01BF8}.Release|x64.ActiveCfg = Release|x64
- {745DEC58-EBB3-47A9-A9B8-4C6627C01BF8}.Release|x64.Build.0 = Release|x64
- {745DEC58-EBB3-47A9-A9B8-4C6627C01BF8}.ReleaseWithoutAsm|Itanium.ActiveCfg = ReleaseWithoutAsm|Itanium
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- {745DEC58-EBB3-47A9-A9B8-4C6627C01BF8}.ReleaseWithoutAsm|Win32.ActiveCfg = ReleaseWithoutAsm|Win32
- {745DEC58-EBB3-47A9-A9B8-4C6627C01BF8}.ReleaseWithoutAsm|Win32.Build.0 = ReleaseWithoutAsm|Win32
- {745DEC58-EBB3-47A9-A9B8-4C6627C01BF8}.ReleaseWithoutAsm|x64.ActiveCfg = ReleaseWithoutAsm|x64
- {745DEC58-EBB3-47A9-A9B8-4C6627C01BF8}.ReleaseWithoutAsm|x64.Build.0 = ReleaseWithoutAsm|x64
- {AA6666AA-E09F-4135-9C0C-4FE50C3C654B}.Debug|Itanium.ActiveCfg = Debug|Itanium
- {AA6666AA-E09F-4135-9C0C-4FE50C3C654B}.Debug|Itanium.Build.0 = Debug|Itanium
- {AA6666AA-E09F-4135-9C0C-4FE50C3C654B}.Debug|Win32.ActiveCfg = Debug|Win32
- {AA6666AA-E09F-4135-9C0C-4FE50C3C654B}.Debug|Win32.Build.0 = Debug|Win32
- {AA6666AA-E09F-4135-9C0C-4FE50C3C654B}.Debug|x64.ActiveCfg = Debug|x64
- {AA6666AA-E09F-4135-9C0C-4FE50C3C654B}.Debug|x64.Build.0 = Debug|x64
- {AA6666AA-E09F-4135-9C0C-4FE50C3C654B}.Release|Itanium.ActiveCfg = Release|Itanium
- {AA6666AA-E09F-4135-9C0C-4FE50C3C654B}.Release|Itanium.Build.0 = Release|Itanium
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deleted file mode 100644
index 9f20c78..0000000
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\ No newline at end of file
diff --git a/third-party/zlib/contrib/vstudio/vc11/zlib.rc b/third-party/zlib/contrib/vstudio/vc11/zlib.rc
deleted file mode 100644
index 73f6476..0000000
--- a/third-party/zlib/contrib/vstudio/vc11/zlib.rc
+++ /dev/null
@@ -1,32 +0,0 @@
-#include <windows.h>
-
-#define IDR_VERSION1 1
-IDR_VERSION1 VERSIONINFO MOVEABLE IMPURE LOADONCALL DISCARDABLE
- FILEVERSION 1,2,8,0
- PRODUCTVERSION 1,2,8,0
- FILEFLAGSMASK VS_FFI_FILEFLAGSMASK
- FILEFLAGS 0
- FILEOS VOS_DOS_WINDOWS32
- FILETYPE VFT_DLL
- FILESUBTYPE 0 // not used
-BEGIN
- BLOCK "StringFileInfo"
- BEGIN
- BLOCK "040904E4"
- //language ID = U.S. English, char set = Windows, Multilingual
-
- BEGIN
- VALUE "FileDescription", "zlib data compression and ZIP file I/O library\0"
- VALUE "FileVersion", "1.2.8\0"
- VALUE "InternalName", "zlib\0"
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- VALUE "ProductName", "ZLib.DLL\0"
- VALUE "Comments","DLL support by Alessandro Iacopetti & Gilles Vollant\0"
- VALUE "LegalCopyright", "(C) 1995-2013 Jean-loup Gailly & Mark Adler\0"
- END
- END
- BLOCK "VarFileInfo"
- BEGIN
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- END
-END
diff --git a/third-party/zlib/contrib/vstudio/vc11/zlibstat.vcxproj b/third-party/zlib/contrib/vstudio/vc11/zlibstat.vcxproj
deleted file mode 100644
index 806b76a..0000000
--- a/third-party/zlib/contrib/vstudio/vc11/zlibstat.vcxproj
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diff --git a/third-party/zlib/contrib/vstudio/vc11/zlibvc.def b/third-party/zlib/contrib/vstudio/vc11/zlibvc.def
deleted file mode 100644
index 6367046..0000000
--- a/third-party/zlib/contrib/vstudio/vc11/zlibvc.def
+++ /dev/null
@@ -1,143 +0,0 @@
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- gzeof @34
- gzsetparams @35
- zError @36
- inflateSyncPoint @37
- get_crc_table @38
- compress2 @39
- gzputs @40
- gzgets @41
- inflateCopy @42
- inflateBackInit_ @43
- inflateBack @44
- inflateBackEnd @45
- compressBound @46
- deflateBound @47
- gzclearerr @48
- gzungetc @49
- zlibCompileFlags @50
- deflatePrime @51
- deflatePending @52
-
- unzOpen @61
- unzClose @62
- unzGetGlobalInfo @63
- unzGetCurrentFileInfo @64
- unzGoToFirstFile @65
- unzGoToNextFile @66
- unzOpenCurrentFile @67
- unzReadCurrentFile @68
- unzOpenCurrentFile3 @69
- unztell @70
- unzeof @71
- unzCloseCurrentFile @72
- unzGetGlobalComment @73
- unzStringFileNameCompare @74
- unzLocateFile @75
- unzGetLocalExtrafield @76
- unzOpen2 @77
- unzOpenCurrentFile2 @78
- unzOpenCurrentFilePassword @79
-
- zipOpen @80
- zipOpenNewFileInZip @81
- zipWriteInFileInZip @82
- zipCloseFileInZip @83
- zipClose @84
- zipOpenNewFileInZip2 @86
- zipCloseFileInZipRaw @87
- zipOpen2 @88
- zipOpenNewFileInZip3 @89
-
- unzGetFilePos @100
- unzGoToFilePos @101
-
- fill_win32_filefunc @110
-
-; zlibwapi v1.2.4 added:
- fill_win32_filefunc64 @111
- fill_win32_filefunc64A @112
- fill_win32_filefunc64W @113
-
- unzOpen64 @120
- unzOpen2_64 @121
- unzGetGlobalInfo64 @122
- unzGetCurrentFileInfo64 @124
- unzGetCurrentFileZStreamPos64 @125
- unztell64 @126
- unzGetFilePos64 @127
- unzGoToFilePos64 @128
-
- zipOpen64 @130
- zipOpen2_64 @131
- zipOpenNewFileInZip64 @132
- zipOpenNewFileInZip2_64 @133
- zipOpenNewFileInZip3_64 @134
- zipOpenNewFileInZip4_64 @135
- zipCloseFileInZipRaw64 @136
-
-; zlib1 v1.2.4 added:
- adler32_combine @140
- crc32_combine @142
- deflateSetHeader @144
- deflateTune @145
- gzbuffer @146
- gzclose_r @147
- gzclose_w @148
- gzdirect @149
- gzoffset @150
- inflateGetHeader @156
- inflateMark @157
- inflatePrime @158
- inflateReset2 @159
- inflateUndermine @160
-
-; zlib1 v1.2.6 added:
- gzgetc_ @161
- inflateResetKeep @163
- deflateResetKeep @164
-
-; zlib1 v1.2.7 added:
- gzopen_w @165
-
-; zlib1 v1.2.8 added:
- inflateGetDictionary @166
- gzvprintf @167
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index 9fcbafd..0000000
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deleted file mode 100644
index c65b95f..0000000
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- <GenerateMapFile>true</GenerateMapFile>
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- <TargetMachine>MachineIA64</TargetMachine>
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- </ItemDefinitionGroup>
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- <ClCompile Include="..\..\..\adler32.c" />
- <ClCompile Include="..\..\..\compress.c" />
- <ClCompile Include="..\..\..\crc32.c" />
- <ClCompile Include="..\..\..\deflate.c" />
- <ClCompile Include="..\..\..\gzclose.c" />
- <ClCompile Include="..\..\..\gzlib.c" />
- <ClCompile Include="..\..\..\gzread.c" />
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- <ExcludedFromBuild Condition="'$(Configuration)|$(Platform)'=='ReleaseWithoutAsm|Itanium'">true</ExcludedFromBuild>
- <ExcludedFromBuild Condition="'$(Configuration)|$(Platform)'=='ReleaseWithoutAsm|Win32'">true</ExcludedFromBuild>
- <ExcludedFromBuild Condition="'$(Configuration)|$(Platform)'=='Release|Itanium'">true</ExcludedFromBuild>
- <ExcludedFromBuild Condition="'$(Configuration)|$(Platform)'=='Release|Win32'">true</ExcludedFromBuild>
- </ClCompile>
- <ClCompile Include="..\..\..\inffast.c" />
- <ClCompile Include="..\..\..\inflate.c" />
- <ClCompile Include="..\..\..\inftrees.c" />
- <ClCompile Include="..\..\minizip\ioapi.c" />
- <ClCompile Include="..\..\minizip\iowin32.c" />
- <ClCompile Include="..\..\..\trees.c" />
- <ClCompile Include="..\..\..\uncompr.c" />
- <ClCompile Include="..\..\minizip\unzip.c">
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- <ResourceCompile Include="zlib.rc" />
- </ItemGroup>
- <ItemGroup>
- <None Include="zlibvc.def" />
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- <ItemGroup>
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- <ClInclude Include="..\..\..\infblock.h" />
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-</Project>
\ No newline at end of file
diff --git a/third-party/zlib/contrib/vstudio/vc9/miniunz.vcproj b/third-party/zlib/contrib/vstudio/vc9/miniunz.vcproj
deleted file mode 100644
index 7da32b9..0000000
--- a/third-party/zlib/contrib/vstudio/vc9/miniunz.vcproj
+++ /dev/null
@@ -1,565 +0,0 @@
-<?xml version="1.0" encoding="Windows-1252"?>
-<VisualStudioProject
- ProjectType="Visual C++"
- Version="9.00"
- Name="miniunz"
- ProjectGUID="{C52F9E7B-498A-42BE-8DB4-85A15694382A}"
- Keyword="Win32Proj"
- TargetFrameworkVersion="131072"
- >
- <Platforms>
- <Platform
- Name="Win32"
- />
- <Platform
- Name="x64"
- />
- <Platform
- Name="Itanium"
- />
- </Platforms>
- <ToolFiles>
- </ToolFiles>
- <Configurations>
- <Configuration
- Name="Debug|Win32"
- OutputDirectory="x86\MiniUnzip$(ConfigurationName)"
- IntermediateDirectory="x86\MiniUnzip$(ConfigurationName)\Tmp"
- ConfigurationType="1"
- InheritedPropertySheets="UpgradeFromVC70.vsprops"
- CharacterSet="2"
- >
- <Tool
- Name="VCPreBuildEventTool"
- />
- <Tool
- Name="VCCustomBuildTool"
- />
- <Tool
- Name="VCXMLDataGeneratorTool"
- />
- <Tool
- Name="VCWebServiceProxyGeneratorTool"
- />
- <Tool
- Name="VCMIDLTool"
- />
- <Tool
- Name="VCCLCompilerTool"
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- AdditionalIncludeDirectories="..\..\..;..\..\minizip"
- PreprocessorDefinitions="WIN32;_CRT_NONSTDC_NO_DEPRECATE;_CRT_SECURE_NO_DEPRECATE;ZLIB_WINAPI;_DEBUG;_CONSOLE"
- MinimalRebuild="true"
- BasicRuntimeChecks="0"
- RuntimeLibrary="1"
- BufferSecurityCheck="false"
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- AssemblerListingLocation="$(IntDir)\"
- WarningLevel="3"
- Detect64BitPortabilityProblems="true"
- DebugInformationFormat="4"
- />
- <Tool
- Name="VCManagedResourceCompilerTool"
- />
- <Tool
- Name="VCResourceCompilerTool"
- />
- <Tool
- Name="VCPreLinkEventTool"
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- <Tool
- Name="VCLinkerTool"
- AdditionalDependencies="x86\ZlibDllDebug\zlibwapi.lib"
- OutputFile="$(OutDir)/miniunz.exe"
- LinkIncremental="2"
- GenerateManifest="false"
- GenerateDebugInformation="true"
- ProgramDatabaseFile="$(OutDir)/miniunz.pdb"
- SubSystem="1"
- RandomizedBaseAddress="1"
- DataExecutionPrevention="0"
- TargetMachine="1"
- />
- <Tool
- Name="VCALinkTool"
- />
- <Tool
- Name="VCManifestTool"
- />
- <Tool
- Name="VCXDCMakeTool"
- />
- <Tool
- Name="VCBscMakeTool"
- />
- <Tool
- Name="VCFxCopTool"
- />
- <Tool
- Name="VCAppVerifierTool"
- />
- <Tool
- Name="VCPostBuildEventTool"
- />
- </Configuration>
- <Configuration
- Name="Release|Win32"
- OutputDirectory="x86\MiniUnzip$(ConfigurationName)"
- IntermediateDirectory="x86\MiniUnzip$(ConfigurationName)\Tmp"
- ConfigurationType="1"
- InheritedPropertySheets="UpgradeFromVC70.vsprops"
- CharacterSet="2"
- >
- <Tool
- Name="VCPreBuildEventTool"
- />
- <Tool
- Name="VCCustomBuildTool"
- />
- <Tool
- Name="VCXMLDataGeneratorTool"
- />
- <Tool
- Name="VCWebServiceProxyGeneratorTool"
- />
- <Tool
- Name="VCMIDLTool"
- />
- <Tool
- Name="VCCLCompilerTool"
- Optimization="2"
- InlineFunctionExpansion="1"
- OmitFramePointers="true"
- AdditionalIncludeDirectories="..\..\..;..\..\minizip"
- PreprocessorDefinitions="WIN32;_CRT_NONSTDC_NO_DEPRECATE;_CRT_SECURE_NO_DEPRECATE;ZLIB_WINAPI;NDEBUG;_CONSOLE"
- StringPooling="true"
- BasicRuntimeChecks="0"
- RuntimeLibrary="0"
- BufferSecurityCheck="false"
- EnableFunctionLevelLinking="true"
- UsePrecompiledHeader="0"
- AssemblerListingLocation="$(IntDir)\"
- WarningLevel="3"
- Detect64BitPortabilityProblems="true"
- DebugInformationFormat="3"
- />
- <Tool
- Name="VCManagedResourceCompilerTool"
- />
- <Tool
- Name="VCResourceCompilerTool"
- />
- <Tool
- Name="VCPreLinkEventTool"
- />
- <Tool
- Name="VCLinkerTool"
- AdditionalDependencies="x86\ZlibDllRelease\zlibwapi.lib"
- OutputFile="$(OutDir)/miniunz.exe"
- LinkIncremental="1"
- GenerateManifest="false"
- GenerateDebugInformation="true"
- SubSystem="1"
- OptimizeReferences="2"
- EnableCOMDATFolding="2"
- OptimizeForWindows98="1"
- RandomizedBaseAddress="1"
- DataExecutionPrevention="0"
- TargetMachine="1"
- />
- <Tool
- Name="VCALinkTool"
- />
- <Tool
- Name="VCManifestTool"
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- InheritedPropertySheets="UpgradeFromVC70.vsprops"
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- PreprocessorDefinitions="_CRT_NONSTDC_NO_DEPRECATE;_CRT_SECURE_NO_DEPRECATE;ZLIB_WINAPI;_DEBUG;_CONSOLE;WIN64"
- MinimalRebuild="true"
- BasicRuntimeChecks="0"
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- AssemblerListingLocation="$(IntDir)\"
- WarningLevel="3"
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- DebugInformationFormat="3"
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diff --git a/third-party/zlib/contrib/vstudio/vc9/minizip.vcproj b/third-party/zlib/contrib/vstudio/vc9/minizip.vcproj
deleted file mode 100644
index e57e07d..0000000
--- a/third-party/zlib/contrib/vstudio/vc9/minizip.vcproj
+++ /dev/null
@@ -1,562 +0,0 @@
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-<VisualStudioProject
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- Version="9.00"
- Name="minizip"
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- Name="VCCustomBuildTool"
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- Name="VCFxCopTool"
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- <Tool
- Name="VCBscMakeTool"
- />
- <Tool
- Name="VCFxCopTool"
- />
- <Tool
- Name="VCAppVerifierTool"
- />
- <Tool
- Name="VCPostBuildEventTool"
- />
- </Configuration>
- <Configuration
- Name="Debug|x64"
- OutputDirectory="x64\$(ConfigurationName)"
- IntermediateDirectory="x64\$(ConfigurationName)"
- ConfigurationType="1"
- InheritedPropertySheets="UpgradeFromVC70.vsprops"
- CharacterSet="2"
- >
- <Tool
- Name="VCPreBuildEventTool"
- />
- <Tool
- Name="VCCustomBuildTool"
- />
- <Tool
- Name="VCXMLDataGeneratorTool"
- />
- <Tool
- Name="VCWebServiceProxyGeneratorTool"
- />
- <Tool
- Name="VCMIDLTool"
- TargetEnvironment="3"
- />
- <Tool
- Name="VCCLCompilerTool"
- Optimization="0"
- AdditionalIncludeDirectories="..\..\..;..\..\minizip"
- PreprocessorDefinitions="_CRT_NONSTDC_NO_DEPRECATE;_CRT_SECURE_NO_DEPRECATE;ZLIB_WINAPI;_DEBUG;_CONSOLE;WIN64"
- MinimalRebuild="true"
- BasicRuntimeChecks="0"
- RuntimeLibrary="3"
- BufferSecurityCheck="false"
- UsePrecompiledHeader="0"
- AssemblerListingLocation="$(IntDir)\"
- WarningLevel="3"
- Detect64BitPortabilityProblems="true"
- DebugInformationFormat="3"
- />
- <Tool
- Name="VCManagedResourceCompilerTool"
- />
- <Tool
- Name="VCResourceCompilerTool"
- />
- <Tool
- Name="VCPreLinkEventTool"
- />
- <Tool
- Name="VCLinkerTool"
- AdditionalDependencies="x64\ZlibDllDebug\zlibwapi.lib"
- OutputFile="$(OutDir)/minizip.exe"
- LinkIncremental="2"
- GenerateManifest="false"
- GenerateDebugInformation="true"
- ProgramDatabaseFile="$(OutDir)/minizip.pdb"
- SubSystem="1"
- TargetMachine="17"
- />
- <Tool
- Name="VCALinkTool"
- />
- <Tool
- Name="VCManifestTool"
- />
- <Tool
- Name="VCXDCMakeTool"
- />
- <Tool
- Name="VCBscMakeTool"
- />
- <Tool
- Name="VCFxCopTool"
- />
- <Tool
- Name="VCAppVerifierTool"
- />
- <Tool
- Name="VCWebDeploymentTool"
- />
- <Tool
- Name="VCPostBuildEventTool"
- />
- </Configuration>
- <Configuration
- Name="Debug|Itanium"
- OutputDirectory="ia64\$(ConfigurationName)"
- IntermediateDirectory="ia64\$(ConfigurationName)"
- ConfigurationType="1"
- InheritedPropertySheets="UpgradeFromVC70.vsprops"
- CharacterSet="2"
- >
- <Tool
- Name="VCPreBuildEventTool"
- />
- <Tool
- Name="VCCustomBuildTool"
- />
- <Tool
- Name="VCXMLDataGeneratorTool"
- />
- <Tool
- Name="VCWebServiceProxyGeneratorTool"
- />
- <Tool
- Name="VCMIDLTool"
- TargetEnvironment="2"
- />
- <Tool
- Name="VCCLCompilerTool"
- Optimization="0"
- AdditionalIncludeDirectories="..\..\..;..\..\minizip"
- PreprocessorDefinitions="_CRT_NONSTDC_NO_DEPRECATE;_CRT_SECURE_NO_DEPRECATE;ZLIB_WINAPI;_DEBUG;_CONSOLE;WIN64"
- MinimalRebuild="true"
- BasicRuntimeChecks="0"
- RuntimeLibrary="3"
- BufferSecurityCheck="false"
- UsePrecompiledHeader="0"
- AssemblerListingLocation="$(IntDir)\"
- WarningLevel="3"
- Detect64BitPortabilityProblems="true"
- DebugInformationFormat="3"
- />
- <Tool
- Name="VCManagedResourceCompilerTool"
- />
- <Tool
- Name="VCResourceCompilerTool"
- />
- <Tool
- Name="VCPreLinkEventTool"
- />
- <Tool
- Name="VCLinkerTool"
- AdditionalDependencies="ia64\ZlibDllDebug\zlibwapi.lib"
- OutputFile="$(OutDir)/minizip.exe"
- LinkIncremental="2"
- GenerateManifest="false"
- GenerateDebugInformation="true"
- ProgramDatabaseFile="$(OutDir)/minizip.pdb"
- SubSystem="1"
- TargetMachine="5"
- />
- <Tool
- Name="VCALinkTool"
- />
- <Tool
- Name="VCManifestTool"
- />
- <Tool
- Name="VCXDCMakeTool"
- />
- <Tool
- Name="VCBscMakeTool"
- />
- <Tool
- Name="VCFxCopTool"
- />
- <Tool
- Name="VCAppVerifierTool"
- />
- <Tool
- Name="VCWebDeploymentTool"
- />
- <Tool
- Name="VCPostBuildEventTool"
- />
- </Configuration>
- <Configuration
- Name="Release|x64"
- OutputDirectory="x64\$(ConfigurationName)"
- IntermediateDirectory="x64\$(ConfigurationName)"
- ConfigurationType="1"
- InheritedPropertySheets="UpgradeFromVC70.vsprops"
- CharacterSet="2"
- >
- <Tool
- Name="VCPreBuildEventTool"
- />
- <Tool
- Name="VCCustomBuildTool"
- />
- <Tool
- Name="VCXMLDataGeneratorTool"
- />
- <Tool
- Name="VCWebServiceProxyGeneratorTool"
- />
- <Tool
- Name="VCMIDLTool"
- TargetEnvironment="3"
- />
- <Tool
- Name="VCCLCompilerTool"
- Optimization="2"
- InlineFunctionExpansion="1"
- OmitFramePointers="true"
- AdditionalIncludeDirectories="..\..\..;..\..\minizip"
- PreprocessorDefinitions="_CRT_NONSTDC_NO_DEPRECATE;_CRT_SECURE_NO_DEPRECATE;ZLIB_WINAPI;NDEBUG;_CONSOLE;WIN64"
- StringPooling="true"
- BasicRuntimeChecks="0"
- RuntimeLibrary="2"
- BufferSecurityCheck="false"
- EnableFunctionLevelLinking="true"
- UsePrecompiledHeader="0"
- AssemblerListingLocation="$(IntDir)\"
- WarningLevel="3"
- Detect64BitPortabilityProblems="true"
- DebugInformationFormat="3"
- />
- <Tool
- Name="VCManagedResourceCompilerTool"
- />
- <Tool
- Name="VCResourceCompilerTool"
- />
- <Tool
- Name="VCPreLinkEventTool"
- />
- <Tool
- Name="VCLinkerTool"
- AdditionalDependencies="x64\ZlibDllRelease\zlibwapi.lib"
- OutputFile="$(OutDir)/minizip.exe"
- LinkIncremental="1"
- GenerateDebugInformation="true"
- SubSystem="1"
- OptimizeReferences="2"
- EnableCOMDATFolding="2"
- OptimizeForWindows98="1"
- TargetMachine="17"
- />
- <Tool
- Name="VCALinkTool"
- />
- <Tool
- Name="VCManifestTool"
- />
- <Tool
- Name="VCXDCMakeTool"
- />
- <Tool
- Name="VCBscMakeTool"
- />
- <Tool
- Name="VCFxCopTool"
- />
- <Tool
- Name="VCAppVerifierTool"
- />
- <Tool
- Name="VCWebDeploymentTool"
- />
- <Tool
- Name="VCPostBuildEventTool"
- />
- </Configuration>
- <Configuration
- Name="Release|Itanium"
- OutputDirectory="ia64\$(ConfigurationName)"
- IntermediateDirectory="ia64\$(ConfigurationName)"
- ConfigurationType="1"
- InheritedPropertySheets="UpgradeFromVC70.vsprops"
- CharacterSet="2"
- >
- <Tool
- Name="VCPreBuildEventTool"
- />
- <Tool
- Name="VCCustomBuildTool"
- />
- <Tool
- Name="VCXMLDataGeneratorTool"
- />
- <Tool
- Name="VCWebServiceProxyGeneratorTool"
- />
- <Tool
- Name="VCMIDLTool"
- TargetEnvironment="2"
- />
- <Tool
- Name="VCCLCompilerTool"
- Optimization="2"
- InlineFunctionExpansion="1"
- OmitFramePointers="true"
- AdditionalIncludeDirectories="..\..\..;..\..\minizip"
- PreprocessorDefinitions="_CRT_NONSTDC_NO_DEPRECATE;_CRT_SECURE_NO_DEPRECATE;ZLIB_WINAPI;NDEBUG;_CONSOLE;WIN64"
- StringPooling="true"
- BasicRuntimeChecks="0"
- RuntimeLibrary="2"
- BufferSecurityCheck="false"
- EnableFunctionLevelLinking="true"
- UsePrecompiledHeader="0"
- AssemblerListingLocation="$(IntDir)\"
- WarningLevel="3"
- Detect64BitPortabilityProblems="true"
- DebugInformationFormat="3"
- />
- <Tool
- Name="VCManagedResourceCompilerTool"
- />
- <Tool
- Name="VCResourceCompilerTool"
- />
- <Tool
- Name="VCPreLinkEventTool"
- />
- <Tool
- Name="VCLinkerTool"
- AdditionalDependencies="ia64\ZlibDllRelease\zlibwapi.lib"
- OutputFile="$(OutDir)/minizip.exe"
- LinkIncremental="1"
- GenerateDebugInformation="true"
- SubSystem="1"
- OptimizeReferences="2"
- EnableCOMDATFolding="2"
- OptimizeForWindows98="1"
- TargetMachine="5"
- />
- <Tool
- Name="VCALinkTool"
- />
- <Tool
- Name="VCManifestTool"
- />
- <Tool
- Name="VCXDCMakeTool"
- />
- <Tool
- Name="VCBscMakeTool"
- />
- <Tool
- Name="VCFxCopTool"
- />
- <Tool
- Name="VCAppVerifierTool"
- />
- <Tool
- Name="VCWebDeploymentTool"
- />
- <Tool
- Name="VCPostBuildEventTool"
- />
- </Configuration>
- </Configurations>
- <References>
- </References>
- <Files>
- <Filter
- Name="Source Files"
- Filter="cpp;c;cxx;def;odl;idl;hpj;bat;asm"
- >
- <File
- RelativePath="..\..\minizip\minizip.c"
- >
- </File>
- </Filter>
- <Filter
- Name="Header Files"
- Filter="h;hpp;hxx;hm;inl;inc"
- >
- </Filter>
- <Filter
- Name="Resource Files"
- Filter="rc;ico;cur;bmp;dlg;rc2;rct;bin;rgs;gif;jpg;jpeg;jpe"
- >
- </Filter>
- </Files>
- <Globals>
- </Globals>
-</VisualStudioProject>
diff --git a/third-party/zlib/contrib/vstudio/vc9/testzlib.vcproj b/third-party/zlib/contrib/vstudio/vc9/testzlib.vcproj
deleted file mode 100644
index 9cb0bf8..0000000
--- a/third-party/zlib/contrib/vstudio/vc9/testzlib.vcproj
+++ /dev/null
@@ -1,852 +0,0 @@
-<?xml version="1.0" encoding="Windows-1252"?>
-<VisualStudioProject
- ProjectType="Visual C++"
- Version="9,00"
- Name="testzlib"
- ProjectGUID="{AA6666AA-E09F-4135-9C0C-4FE50C3C654B}"
- RootNamespace="testzlib"
- Keyword="Win32Proj"
- TargetFrameworkVersion="131072"
- >
- <Platforms>
- <Platform
- Name="Win32"
- />
- <Platform
- Name="x64"
- />
- <Platform
- Name="Itanium"
- />
- </Platforms>
- <ToolFiles>
- </ToolFiles>
- <Configurations>
- <Configuration
- Name="Debug|Win32"
- OutputDirectory="x86\TestZlib$(ConfigurationName)"
- IntermediateDirectory="x86\TestZlib$(ConfigurationName)\Tmp"
- ConfigurationType="1"
- CharacterSet="2"
- >
- <Tool
- Name="VCPreBuildEventTool"
- />
- <Tool
- Name="VCCustomBuildTool"
- />
- <Tool
- Name="VCXMLDataGeneratorTool"
- />
- <Tool
- Name="VCWebServiceProxyGeneratorTool"
- />
- <Tool
- Name="VCMIDLTool"
- />
- <Tool
- Name="VCCLCompilerTool"
- Optimization="0"
- AdditionalIncludeDirectories="..\..\.."
- PreprocessorDefinitions="ASMV;ASMINF;WIN32;ZLIB_WINAPI;_DEBUG;_CONSOLE;_CRT_NONSTDC_NO_DEPRECATE;_CRT_SECURE_NO_DEPRECATE;_CRT_NONSTDC_NO_WARNINGS"
- MinimalRebuild="true"
- BasicRuntimeChecks="0"
- RuntimeLibrary="1"
- BufferSecurityCheck="false"
- UsePrecompiledHeader="0"
- AssemblerOutput="4"
- AssemblerListingLocation="$(IntDir)\"
- WarningLevel="3"
- Detect64BitPortabilityProblems="true"
- DebugInformationFormat="4"
- />
- <Tool
- Name="VCManagedResourceCompilerTool"
- />
- <Tool
- Name="VCResourceCompilerTool"
- />
- <Tool
- Name="VCPreLinkEventTool"
- />
- <Tool
- Name="VCLinkerTool"
- AdditionalDependencies="..\..\masmx86\match686.obj ..\..\masmx86\inffas32.obj"
- OutputFile="$(OutDir)/testzlib.exe"
- LinkIncremental="2"
- GenerateManifest="false"
- GenerateDebugInformation="true"
- ProgramDatabaseFile="$(OutDir)/testzlib.pdb"
- SubSystem="1"
- RandomizedBaseAddress="1"
- DataExecutionPrevention="0"
- TargetMachine="1"
- />
- <Tool
- Name="VCALinkTool"
- />
- <Tool
- Name="VCManifestTool"
- />
- <Tool
- Name="VCXDCMakeTool"
- />
- <Tool
- Name="VCBscMakeTool"
- />
- <Tool
- Name="VCFxCopTool"
- />
- <Tool
- Name="VCAppVerifierTool"
- />
- <Tool
- Name="VCPostBuildEventTool"
- />
- </Configuration>
- <Configuration
- Name="Debug|x64"
- OutputDirectory="x64\TestZlib$(ConfigurationName)"
- IntermediateDirectory="x64\TestZlib$(ConfigurationName)\Tmp"
- ConfigurationType="1"
- >
- <Tool
- Name="VCPreBuildEventTool"
- />
- <Tool
- Name="VCCustomBuildTool"
- />
- <Tool
- Name="VCXMLDataGeneratorTool"
- />
- <Tool
- Name="VCWebServiceProxyGeneratorTool"
- />
- <Tool
- Name="VCMIDLTool"
- />
- <Tool
- Name="VCCLCompilerTool"
- AdditionalIncludeDirectories="..\..\.."
- PreprocessorDefinitions="ASMV;ASMINF;WIN32;ZLIB_WINAPI;_DEBUG;_CONSOLE;_CRT_NONSTDC_NO_DEPRECATE;_CRT_SECURE_NO_DEPRECATE;_CRT_NONSTDC_NO_WARNINGS"
- BasicRuntimeChecks="0"
- RuntimeLibrary="3"
- BufferSecurityCheck="false"
- AssemblerListingLocation="$(IntDir)\"
- />
- <Tool
- Name="VCManagedResourceCompilerTool"
- />
- <Tool
- Name="VCResourceCompilerTool"
- />
- <Tool
- Name="VCPreLinkEventTool"
- />
- <Tool
- Name="VCLinkerTool"
- AdditionalDependencies="..\..\masmx64\gvmat64.obj ..\..\masmx64\inffasx64.obj"
- GenerateManifest="false"
- />
- <Tool
- Name="VCALinkTool"
- />
- <Tool
- Name="VCManifestTool"
- />
- <Tool
- Name="VCXDCMakeTool"
- />
- <Tool
- Name="VCBscMakeTool"
- />
- <Tool
- Name="VCFxCopTool"
- />
- <Tool
- Name="VCAppVerifierTool"
- />
- <Tool
- Name="VCPostBuildEventTool"
- />
- </Configuration>
- <Configuration
- Name="Debug|Itanium"
- OutputDirectory="ia64\TestZlib$(ConfigurationName)"
- IntermediateDirectory="ia64\TestZlib$(ConfigurationName)\Tmp"
- ConfigurationType="1"
- CharacterSet="2"
- >
- <Tool
- Name="VCPreBuildEventTool"
- />
- <Tool
- Name="VCCustomBuildTool"
- />
- <Tool
- Name="VCXMLDataGeneratorTool"
- />
- <Tool
- Name="VCWebServiceProxyGeneratorTool"
- />
- <Tool
- Name="VCMIDLTool"
- TargetEnvironment="2"
- />
- <Tool
- Name="VCCLCompilerTool"
- Optimization="0"
- AdditionalIncludeDirectories="..\..\.."
- PreprocessorDefinitions="ZLIB_WINAPI;_DEBUG;_CONSOLE;_CRT_NONSTDC_NO_DEPRECATE;_CRT_SECURE_NO_DEPRECATE;_CRT_NONSTDC_NO_WARNINGS;WIN64"
- MinimalRebuild="true"
- BasicRuntimeChecks="0"
- RuntimeLibrary="3"
- BufferSecurityCheck="false"
- UsePrecompiledHeader="0"
- AssemblerOutput="4"
- AssemblerListingLocation="$(IntDir)\"
- WarningLevel="3"
- Detect64BitPortabilityProblems="true"
- DebugInformationFormat="3"
- />
- <Tool
- Name="VCManagedResourceCompilerTool"
- />
- <Tool
- Name="VCResourceCompilerTool"
- />
- <Tool
- Name="VCPreLinkEventTool"
- />
- <Tool
- Name="VCLinkerTool"
- OutputFile="$(OutDir)/testzlib.exe"
- LinkIncremental="2"
- GenerateManifest="false"
- GenerateDebugInformation="true"
- ProgramDatabaseFile="$(OutDir)/testzlib.pdb"
- SubSystem="1"
- TargetMachine="5"
- />
- <Tool
- Name="VCALinkTool"
- />
- <Tool
- Name="VCManifestTool"
- />
- <Tool
- Name="VCXDCMakeTool"
- />
- <Tool
- Name="VCBscMakeTool"
- />
- <Tool
- Name="VCFxCopTool"
- />
- <Tool
- Name="VCAppVerifierTool"
- />
- <Tool
- Name="VCPostBuildEventTool"
- />
- </Configuration>
- <Configuration
- Name="ReleaseWithoutAsm|Win32"
- OutputDirectory="x86\TestZlib$(ConfigurationName)"
- IntermediateDirectory="x86\TestZlib$(ConfigurationName)\Tmp"
- ConfigurationType="1"
- CharacterSet="2"
- WholeProgramOptimization="1"
- >
- <Tool
- Name="VCPreBuildEventTool"
- />
- <Tool
- Name="VCCustomBuildTool"
- />
- <Tool
- Name="VCXMLDataGeneratorTool"
- />
- <Tool
- Name="VCWebServiceProxyGeneratorTool"
- />
- <Tool
- Name="VCMIDLTool"
- />
- <Tool
- Name="VCCLCompilerTool"
- Optimization="2"
- InlineFunctionExpansion="1"
- OmitFramePointers="true"
- AdditionalIncludeDirectories="..\..\.."
- PreprocessorDefinitions="WIN32;ZLIB_WINAPI;NDEBUG;_CONSOLE;_CRT_NONSTDC_NO_DEPRECATE;_CRT_SECURE_NO_DEPRECATE;_CRT_NONSTDC_NO_WARNINGS"
- StringPooling="true"
- BasicRuntimeChecks="0"
- RuntimeLibrary="0"
- BufferSecurityCheck="false"
- EnableFunctionLevelLinking="true"
- UsePrecompiledHeader="0"
- AssemblerListingLocation="$(IntDir)\"
- WarningLevel="3"
- Detect64BitPortabilityProblems="true"
- DebugInformationFormat="3"
- />
- <Tool
- Name="VCManagedResourceCompilerTool"
- />
- <Tool
- Name="VCResourceCompilerTool"
- />
- <Tool
- Name="VCPreLinkEventTool"
- />
- <Tool
- Name="VCLinkerTool"
- OutputFile="$(OutDir)/testzlib.exe"
- LinkIncremental="1"
- GenerateManifest="false"
- GenerateDebugInformation="true"
- SubSystem="1"
- OptimizeReferences="2"
- EnableCOMDATFolding="2"
- OptimizeForWindows98="1"
- RandomizedBaseAddress="1"
- DataExecutionPrevention="0"
- TargetMachine="1"
- />
- <Tool
- Name="VCALinkTool"
- />
- <Tool
- Name="VCManifestTool"
- />
- <Tool
- Name="VCXDCMakeTool"
- />
- <Tool
- Name="VCBscMakeTool"
- />
- <Tool
- Name="VCFxCopTool"
- />
- <Tool
- Name="VCAppVerifierTool"
- />
- <Tool
- Name="VCPostBuildEventTool"
- />
- </Configuration>
- <Configuration
- Name="ReleaseWithoutAsm|x64"
- OutputDirectory="x64\TestZlib$(ConfigurationName)"
- IntermediateDirectory="x64\TestZlib$(ConfigurationName)\Tmp"
- ConfigurationType="1"
- WholeProgramOptimization="1"
- >
- <Tool
- Name="VCPreBuildEventTool"
- />
- <Tool
- Name="VCCustomBuildTool"
- />
- <Tool
- Name="VCXMLDataGeneratorTool"
- />
- <Tool
- Name="VCWebServiceProxyGeneratorTool"
- />
- <Tool
- Name="VCMIDLTool"
- />
- <Tool
- Name="VCCLCompilerTool"
- AdditionalIncludeDirectories="..\..\.."
- PreprocessorDefinitions="WIN32;ZLIB_WINAPI;NDEBUG;_CONSOLE;_CRT_NONSTDC_NO_DEPRECATE;_CRT_SECURE_NO_DEPRECATE;_CRT_NONSTDC_NO_WARNINGS"
- BasicRuntimeChecks="0"
- RuntimeLibrary="2"
- BufferSecurityCheck="false"
- AssemblerListingLocation="$(IntDir)\"
- />
- <Tool
- Name="VCManagedResourceCompilerTool"
- />
- <Tool
- Name="VCResourceCompilerTool"
- />
- <Tool
- Name="VCPreLinkEventTool"
- />
- <Tool
- Name="VCLinkerTool"
- AdditionalDependencies=""
- GenerateManifest="false"
- />
- <Tool
- Name="VCALinkTool"
- />
- <Tool
- Name="VCManifestTool"
- />
- <Tool
- Name="VCXDCMakeTool"
- />
- <Tool
- Name="VCBscMakeTool"
- />
- <Tool
- Name="VCFxCopTool"
- />
- <Tool
- Name="VCAppVerifierTool"
- />
- <Tool
- Name="VCPostBuildEventTool"
- />
- </Configuration>
- <Configuration
- Name="ReleaseWithoutAsm|Itanium"
- OutputDirectory="ia64\TestZlib$(ConfigurationName)"
- IntermediateDirectory="ia64\TestZlib$(ConfigurationName)\Tmp"
- ConfigurationType="1"
- CharacterSet="2"
- WholeProgramOptimization="1"
- >
- <Tool
- Name="VCPreBuildEventTool"
- />
- <Tool
- Name="VCCustomBuildTool"
- />
- <Tool
- Name="VCXMLDataGeneratorTool"
- />
- <Tool
- Name="VCWebServiceProxyGeneratorTool"
- />
- <Tool
- Name="VCMIDLTool"
- TargetEnvironment="2"
- />
- <Tool
- Name="VCCLCompilerTool"
- Optimization="2"
- InlineFunctionExpansion="1"
- OmitFramePointers="true"
- AdditionalIncludeDirectories="..\..\.."
- PreprocessorDefinitions="ZLIB_WINAPI;NDEBUG;_CONSOLE;_CRT_NONSTDC_NO_DEPRECATE;_CRT_SECURE_NO_DEPRECATE;_CRT_NONSTDC_NO_WARNINGS;WIN64"
- StringPooling="true"
- BasicRuntimeChecks="0"
- RuntimeLibrary="2"
- BufferSecurityCheck="false"
- EnableFunctionLevelLinking="true"
- UsePrecompiledHeader="0"
- AssemblerListingLocation="$(IntDir)\"
- WarningLevel="3"
- Detect64BitPortabilityProblems="true"
- DebugInformationFormat="3"
- />
- <Tool
- Name="VCManagedResourceCompilerTool"
- />
- <Tool
- Name="VCResourceCompilerTool"
- />
- <Tool
- Name="VCPreLinkEventTool"
- />
- <Tool
- Name="VCLinkerTool"
- OutputFile="$(OutDir)/testzlib.exe"
- LinkIncremental="1"
- GenerateManifest="false"
- GenerateDebugInformation="true"
- SubSystem="1"
- OptimizeReferences="2"
- EnableCOMDATFolding="2"
- OptimizeForWindows98="1"
- TargetMachine="5"
- />
- <Tool
- Name="VCALinkTool"
- />
- <Tool
- Name="VCManifestTool"
- />
- <Tool
- Name="VCXDCMakeTool"
- />
- <Tool
- Name="VCBscMakeTool"
- />
- <Tool
- Name="VCFxCopTool"
- />
- <Tool
- Name="VCAppVerifierTool"
- />
- <Tool
- Name="VCPostBuildEventTool"
- />
- </Configuration>
- <Configuration
- Name="Release|Win32"
- OutputDirectory="x86\TestZlib$(ConfigurationName)"
- IntermediateDirectory="x86\TestZlib$(ConfigurationName)\Tmp"
- ConfigurationType="1"
- CharacterSet="2"
- WholeProgramOptimization="1"
- >
- <Tool
- Name="VCPreBuildEventTool"
- />
- <Tool
- Name="VCCustomBuildTool"
- />
- <Tool
- Name="VCXMLDataGeneratorTool"
- />
- <Tool
- Name="VCWebServiceProxyGeneratorTool"
- />
- <Tool
- Name="VCMIDLTool"
- />
- <Tool
- Name="VCCLCompilerTool"
- Optimization="2"
- InlineFunctionExpansion="1"
- OmitFramePointers="true"
- AdditionalIncludeDirectories="..\..\.."
- PreprocessorDefinitions="ASMV;ASMINF;WIN32;ZLIB_WINAPI;NDEBUG;_CONSOLE;_CRT_NONSTDC_NO_DEPRECATE;_CRT_SECURE_NO_DEPRECATE;_CRT_NONSTDC_NO_WARNINGS"
- StringPooling="true"
- BasicRuntimeChecks="0"
- RuntimeLibrary="0"
- BufferSecurityCheck="false"
- EnableFunctionLevelLinking="true"
- UsePrecompiledHeader="0"
- AssemblerListingLocation="$(IntDir)\"
- WarningLevel="3"
- Detect64BitPortabilityProblems="true"
- DebugInformationFormat="3"
- />
- <Tool
- Name="VCManagedResourceCompilerTool"
- />
- <Tool
- Name="VCResourceCompilerTool"
- />
- <Tool
- Name="VCPreLinkEventTool"
- />
- <Tool
- Name="VCLinkerTool"
- AdditionalDependencies="..\..\masmx86\match686.obj ..\..\masmx86\inffas32.obj"
- OutputFile="$(OutDir)/testzlib.exe"
- LinkIncremental="1"
- GenerateManifest="false"
- GenerateDebugInformation="true"
- SubSystem="1"
- OptimizeReferences="2"
- EnableCOMDATFolding="2"
- OptimizeForWindows98="1"
- RandomizedBaseAddress="1"
- DataExecutionPrevention="0"
- TargetMachine="1"
- />
- <Tool
- Name="VCALinkTool"
- />
- <Tool
- Name="VCManifestTool"
- />
- <Tool
- Name="VCXDCMakeTool"
- />
- <Tool
- Name="VCBscMakeTool"
- />
- <Tool
- Name="VCFxCopTool"
- />
- <Tool
- Name="VCAppVerifierTool"
- />
- <Tool
- Name="VCPostBuildEventTool"
- />
- </Configuration>
- <Configuration
- Name="Release|x64"
- OutputDirectory="x64\TestZlib$(ConfigurationName)"
- IntermediateDirectory="x64\TestZlib$(ConfigurationName)\Tmp"
- ConfigurationType="1"
- WholeProgramOptimization="1"
- >
- <Tool
- Name="VCPreBuildEventTool"
- />
- <Tool
- Name="VCCustomBuildTool"
- />
- <Tool
- Name="VCXMLDataGeneratorTool"
- />
- <Tool
- Name="VCWebServiceProxyGeneratorTool"
- />
- <Tool
- Name="VCMIDLTool"
- />
- <Tool
- Name="VCCLCompilerTool"
- AdditionalIncludeDirectories="..\..\.."
- PreprocessorDefinitions="ASMV;ASMINF;WIN32;ZLIB_WINAPI;NDEBUG;_CONSOLE;_CRT_NONSTDC_NO_DEPRECATE;_CRT_SECURE_NO_DEPRECATE;_CRT_NONSTDC_NO_WARNINGS"
- BasicRuntimeChecks="0"
- RuntimeLibrary="0"
- BufferSecurityCheck="false"
- AssemblerListingLocation="$(IntDir)\"
- />
- <Tool
- Name="VCManagedResourceCompilerTool"
- />
- <Tool
- Name="VCResourceCompilerTool"
- />
- <Tool
- Name="VCPreLinkEventTool"
- />
- <Tool
- Name="VCLinkerTool"
- AdditionalDependencies="..\..\masmx64\gvmat64.obj ..\..\masmx64\inffasx64.obj"
- GenerateManifest="false"
- />
- <Tool
- Name="VCALinkTool"
- />
- <Tool
- Name="VCManifestTool"
- />
- <Tool
- Name="VCXDCMakeTool"
- />
- <Tool
- Name="VCBscMakeTool"
- />
- <Tool
- Name="VCFxCopTool"
- />
- <Tool
- Name="VCAppVerifierTool"
- />
- <Tool
- Name="VCPostBuildEventTool"
- />
- </Configuration>
- <Configuration
- Name="Release|Itanium"
- OutputDirectory="ia64\TestZlib$(ConfigurationName)"
- IntermediateDirectory="ia64\TestZlib$(ConfigurationName)\Tmp"
- ConfigurationType="1"
- CharacterSet="2"
- WholeProgramOptimization="1"
- >
- <Tool
- Name="VCPreBuildEventTool"
- />
- <Tool
- Name="VCCustomBuildTool"
- />
- <Tool
- Name="VCXMLDataGeneratorTool"
- />
- <Tool
- Name="VCWebServiceProxyGeneratorTool"
- />
- <Tool
- Name="VCMIDLTool"
- TargetEnvironment="2"
- />
- <Tool
- Name="VCCLCompilerTool"
- Optimization="2"
- InlineFunctionExpansion="1"
- OmitFramePointers="true"
- AdditionalIncludeDirectories="..\..\.."
- PreprocessorDefinitions="ZLIB_WINAPI;NDEBUG;_CONSOLE;_CRT_NONSTDC_NO_DEPRECATE;_CRT_SECURE_NO_DEPRECATE;_CRT_NONSTDC_NO_WARNINGS;WIN64"
- StringPooling="true"
- BasicRuntimeChecks="0"
- RuntimeLibrary="2"
- BufferSecurityCheck="false"
- EnableFunctionLevelLinking="true"
- UsePrecompiledHeader="0"
- AssemblerListingLocation="$(IntDir)\"
- WarningLevel="3"
- Detect64BitPortabilityProblems="true"
- DebugInformationFormat="3"
- />
- <Tool
- Name="VCManagedResourceCompilerTool"
- />
- <Tool
- Name="VCResourceCompilerTool"
- />
- <Tool
- Name="VCPreLinkEventTool"
- />
- <Tool
- Name="VCLinkerTool"
- OutputFile="$(OutDir)/testzlib.exe"
- LinkIncremental="1"
- GenerateManifest="false"
- GenerateDebugInformation="true"
- SubSystem="1"
- OptimizeReferences="2"
- EnableCOMDATFolding="2"
- OptimizeForWindows98="1"
- TargetMachine="5"
- />
- <Tool
- Name="VCALinkTool"
- />
- <Tool
- Name="VCManifestTool"
- />
- <Tool
- Name="VCXDCMakeTool"
- />
- <Tool
- Name="VCBscMakeTool"
- />
- <Tool
- Name="VCFxCopTool"
- />
- <Tool
- Name="VCAppVerifierTool"
- />
- <Tool
- Name="VCPostBuildEventTool"
- />
- </Configuration>
- </Configurations>
- <References>
- </References>
- <Files>
- <Filter
- Name="Source Files"
- Filter="cpp;c;cxx;def;odl;idl;hpj;bat;asm"
- >
- <File
- RelativePath="..\..\..\adler32.c"
- >
- </File>
- <File
- RelativePath="..\..\..\compress.c"
- >
- </File>
- <File
- RelativePath="..\..\..\crc32.c"
- >
- </File>
- <File
- RelativePath="..\..\..\deflate.c"
- >
- </File>
- <File
- RelativePath="..\..\..\infback.c"
- >
- </File>
- <File
- RelativePath="..\..\masmx64\inffas8664.c"
- >
- <FileConfiguration
- Name="Debug|Win32"
- ExcludedFromBuild="true"
- >
- <Tool
- Name="VCCLCompilerTool"
- />
- </FileConfiguration>
- <FileConfiguration
- Name="Debug|Itanium"
- ExcludedFromBuild="true"
- >
- <Tool
- Name="VCCLCompilerTool"
- />
- </FileConfiguration>
- <FileConfiguration
- Name="ReleaseWithoutAsm|Win32"
- ExcludedFromBuild="true"
- >
- <Tool
- Name="VCCLCompilerTool"
- />
- </FileConfiguration>
- <FileConfiguration
- Name="ReleaseWithoutAsm|Itanium"
- ExcludedFromBuild="true"
- >
- <Tool
- Name="VCCLCompilerTool"
- />
- </FileConfiguration>
- <FileConfiguration
- Name="Release|Win32"
- ExcludedFromBuild="true"
- >
- <Tool
- Name="VCCLCompilerTool"
- />
- </FileConfiguration>
- <FileConfiguration
- Name="Release|Itanium"
- ExcludedFromBuild="true"
- >
- <Tool
- Name="VCCLCompilerTool"
- />
- </FileConfiguration>
- </File>
- <File
- RelativePath="..\..\..\inffast.c"
- >
- </File>
- <File
- RelativePath="..\..\..\inflate.c"
- >
- </File>
- <File
- RelativePath="..\..\..\inftrees.c"
- >
- </File>
- <File
- RelativePath="..\..\testzlib\testzlib.c"
- >
- </File>
- <File
- RelativePath="..\..\..\trees.c"
- >
- </File>
- <File
- RelativePath="..\..\..\uncompr.c"
- >
- </File>
- <File
- RelativePath="..\..\..\zutil.c"
- >
- </File>
- </Filter>
- <Filter
- Name="Header Files"
- Filter="h;hpp;hxx;hm;inl;inc"
- >
- </Filter>
- <Filter
- Name="Resource Files"
- Filter="rc;ico;cur;bmp;dlg;rc2;rct;bin;rgs;gif;jpg;jpeg;jpe"
- >
- </Filter>
- </Files>
- <Globals>
- </Globals>
-</VisualStudioProject>
diff --git a/third-party/zlib/contrib/vstudio/vc9/testzlibdll.vcproj b/third-party/zlib/contrib/vstudio/vc9/testzlibdll.vcproj
deleted file mode 100644
index b1ddde0..0000000
--- a/third-party/zlib/contrib/vstudio/vc9/testzlibdll.vcproj
+++ /dev/null
@@ -1,565 +0,0 @@
-<?xml version="1.0" encoding="Windows-1252"?>
-<VisualStudioProject
- ProjectType="Visual C++"
- Version="9.00"
- Name="TestZlibDll"
- ProjectGUID="{C52F9E7B-498A-42BE-8DB4-85A15694366A}"
- Keyword="Win32Proj"
- TargetFrameworkVersion="131072"
- >
- <Platforms>
- <Platform
- Name="Win32"
- />
- <Platform
- Name="x64"
- />
- <Platform
- Name="Itanium"
- />
- </Platforms>
- <ToolFiles>
- </ToolFiles>
- <Configurations>
- <Configuration
- Name="Debug|Win32"
- OutputDirectory="x86\TestZlibDll$(ConfigurationName)"
- IntermediateDirectory="x86\TestZlibDll$(ConfigurationName)\Tmp"
- ConfigurationType="1"
- InheritedPropertySheets="UpgradeFromVC70.vsprops"
- CharacterSet="2"
- >
- <Tool
- Name="VCPreBuildEventTool"
- />
- <Tool
- Name="VCCustomBuildTool"
- />
- <Tool
- Name="VCXMLDataGeneratorTool"
- />
- <Tool
- Name="VCWebServiceProxyGeneratorTool"
- />
- <Tool
- Name="VCMIDLTool"
- />
- <Tool
- Name="VCCLCompilerTool"
- Optimization="0"
- AdditionalIncludeDirectories="..\..\..;..\..\minizip"
- PreprocessorDefinitions="WIN32;_CRT_NONSTDC_NO_DEPRECATE;_CRT_SECURE_NO_DEPRECATE;ZLIB_WINAPI;_DEBUG;_CONSOLE"
- MinimalRebuild="true"
- BasicRuntimeChecks="0"
- RuntimeLibrary="1"
- BufferSecurityCheck="false"
- UsePrecompiledHeader="0"
- AssemblerListingLocation="$(IntDir)\"
- WarningLevel="3"
- Detect64BitPortabilityProblems="true"
- DebugInformationFormat="4"
- />
- <Tool
- Name="VCManagedResourceCompilerTool"
- />
- <Tool
- Name="VCResourceCompilerTool"
- />
- <Tool
- Name="VCPreLinkEventTool"
- />
- <Tool
- Name="VCLinkerTool"
- AdditionalDependencies="x86\ZlibDllDebug\zlibwapi.lib"
- OutputFile="$(OutDir)/testzlib.exe"
- LinkIncremental="2"
- GenerateManifest="false"
- GenerateDebugInformation="true"
- ProgramDatabaseFile="$(OutDir)/testzlib.pdb"
- SubSystem="1"
- RandomizedBaseAddress="1"
- DataExecutionPrevention="0"
- TargetMachine="1"
- />
- <Tool
- Name="VCALinkTool"
- />
- <Tool
- Name="VCManifestTool"
- />
- <Tool
- Name="VCXDCMakeTool"
- />
- <Tool
- Name="VCBscMakeTool"
- />
- <Tool
- Name="VCFxCopTool"
- />
- <Tool
- Name="VCAppVerifierTool"
- />
- <Tool
- Name="VCPostBuildEventTool"
- />
- </Configuration>
- <Configuration
- Name="Release|Win32"
- OutputDirectory="x86\TestZlibDll$(ConfigurationName)"
- IntermediateDirectory="x86\TestZlibDll$(ConfigurationName)\Tmp"
- ConfigurationType="1"
- InheritedPropertySheets="UpgradeFromVC70.vsprops"
- CharacterSet="2"
- >
- <Tool
- Name="VCPreBuildEventTool"
- />
- <Tool
- Name="VCCustomBuildTool"
- />
- <Tool
- Name="VCXMLDataGeneratorTool"
- />
- <Tool
- Name="VCWebServiceProxyGeneratorTool"
- />
- <Tool
- Name="VCMIDLTool"
- />
- <Tool
- Name="VCCLCompilerTool"
- Optimization="2"
- InlineFunctionExpansion="1"
- OmitFramePointers="true"
- AdditionalIncludeDirectories="..\..\..;..\..\minizip"
- PreprocessorDefinitions="WIN32;_CRT_NONSTDC_NO_DEPRECATE;_CRT_SECURE_NO_DEPRECATE;ZLIB_WINAPI;NDEBUG;_CONSOLE"
- StringPooling="true"
- BasicRuntimeChecks="0"
- RuntimeLibrary="0"
- BufferSecurityCheck="false"
- EnableFunctionLevelLinking="true"
- UsePrecompiledHeader="0"
- AssemblerListingLocation="$(IntDir)\"
- WarningLevel="3"
- Detect64BitPortabilityProblems="true"
- DebugInformationFormat="3"
- />
- <Tool
- Name="VCManagedResourceCompilerTool"
- />
- <Tool
- Name="VCResourceCompilerTool"
- />
- <Tool
- Name="VCPreLinkEventTool"
- />
- <Tool
- Name="VCLinkerTool"
- AdditionalDependencies="x86\ZlibDllRelease\zlibwapi.lib"
- OutputFile="$(OutDir)/testzlib.exe"
- LinkIncremental="1"
- GenerateManifest="false"
- GenerateDebugInformation="true"
- SubSystem="1"
- OptimizeReferences="2"
- EnableCOMDATFolding="2"
- OptimizeForWindows98="1"
- RandomizedBaseAddress="1"
- DataExecutionPrevention="0"
- TargetMachine="1"
- />
- <Tool
- Name="VCALinkTool"
- />
- <Tool
- Name="VCManifestTool"
- />
- <Tool
- Name="VCXDCMakeTool"
- />
- <Tool
- Name="VCBscMakeTool"
- />
- <Tool
- Name="VCFxCopTool"
- />
- <Tool
- Name="VCAppVerifierTool"
- />
- <Tool
- Name="VCPostBuildEventTool"
- />
- </Configuration>
- <Configuration
- Name="Debug|x64"
- OutputDirectory="x64\TestZlibDll$(ConfigurationName)"
- IntermediateDirectory="x64\TestZlibDll$(ConfigurationName)\Tmp"
- ConfigurationType="1"
- InheritedPropertySheets="UpgradeFromVC70.vsprops"
- CharacterSet="2"
- >
- <Tool
- Name="VCPreBuildEventTool"
- />
- <Tool
- Name="VCCustomBuildTool"
- />
- <Tool
- Name="VCXMLDataGeneratorTool"
- />
- <Tool
- Name="VCWebServiceProxyGeneratorTool"
- />
- <Tool
- Name="VCMIDLTool"
- TargetEnvironment="3"
- />
- <Tool
- Name="VCCLCompilerTool"
- Optimization="0"
- AdditionalIncludeDirectories="..\..\..;..\..\minizip"
- PreprocessorDefinitions="_CRT_NONSTDC_NO_DEPRECATE;_CRT_SECURE_NO_DEPRECATE;ZLIB_WINAPI;_DEBUG;_CONSOLE;WIN64"
- MinimalRebuild="true"
- BasicRuntimeChecks="0"
- RuntimeLibrary="3"
- BufferSecurityCheck="false"
- UsePrecompiledHeader="0"
- AssemblerListingLocation="$(IntDir)\"
- WarningLevel="3"
- Detect64BitPortabilityProblems="true"
- DebugInformationFormat="3"
- />
- <Tool
- Name="VCManagedResourceCompilerTool"
- />
- <Tool
- Name="VCResourceCompilerTool"
- />
- <Tool
- Name="VCPreLinkEventTool"
- />
- <Tool
- Name="VCLinkerTool"
- AdditionalDependencies="x64\ZlibDllDebug\zlibwapi.lib"
- OutputFile="$(OutDir)/testzlib.exe"
- LinkIncremental="2"
- GenerateManifest="false"
- GenerateDebugInformation="true"
- ProgramDatabaseFile="$(OutDir)/testzlib.pdb"
- SubSystem="1"
- TargetMachine="17"
- />
- <Tool
- Name="VCALinkTool"
- />
- <Tool
- Name="VCManifestTool"
- />
- <Tool
- Name="VCXDCMakeTool"
- />
- <Tool
- Name="VCBscMakeTool"
- />
- <Tool
- Name="VCFxCopTool"
- />
- <Tool
- Name="VCAppVerifierTool"
- />
- <Tool
- Name="VCWebDeploymentTool"
- />
- <Tool
- Name="VCPostBuildEventTool"
- />
- </Configuration>
- <Configuration
- Name="Debug|Itanium"
- OutputDirectory="ia64\TestZlibDll$(ConfigurationName)"
- IntermediateDirectory="ia64\TestZlibDll$(ConfigurationName)\Tmp"
- ConfigurationType="1"
- InheritedPropertySheets="UpgradeFromVC70.vsprops"
- CharacterSet="2"
- >
- <Tool
- Name="VCPreBuildEventTool"
- />
- <Tool
- Name="VCCustomBuildTool"
- />
- <Tool
- Name="VCXMLDataGeneratorTool"
- />
- <Tool
- Name="VCWebServiceProxyGeneratorTool"
- />
- <Tool
- Name="VCMIDLTool"
- TargetEnvironment="2"
- />
- <Tool
- Name="VCCLCompilerTool"
- Optimization="0"
- AdditionalIncludeDirectories="..\..\..;..\..\minizip"
- PreprocessorDefinitions="_CRT_NONSTDC_NO_DEPRECATE;_CRT_SECURE_NO_DEPRECATE;ZLIB_WINAPI;_DEBUG;_CONSOLE;WIN64"
- MinimalRebuild="true"
- BasicRuntimeChecks="0"
- RuntimeLibrary="3"
- BufferSecurityCheck="false"
- UsePrecompiledHeader="0"
- AssemblerListingLocation="$(IntDir)\"
- WarningLevel="3"
- Detect64BitPortabilityProblems="true"
- DebugInformationFormat="3"
- />
- <Tool
- Name="VCManagedResourceCompilerTool"
- />
- <Tool
- Name="VCResourceCompilerTool"
- />
- <Tool
- Name="VCPreLinkEventTool"
- />
- <Tool
- Name="VCLinkerTool"
- AdditionalDependencies="ia64\ZlibDllDebug\zlibwapi.lib"
- OutputFile="$(OutDir)/testzlib.exe"
- LinkIncremental="2"
- GenerateManifest="false"
- GenerateDebugInformation="true"
- ProgramDatabaseFile="$(OutDir)/testzlib.pdb"
- SubSystem="1"
- TargetMachine="5"
- />
- <Tool
- Name="VCALinkTool"
- />
- <Tool
- Name="VCManifestTool"
- />
- <Tool
- Name="VCXDCMakeTool"
- />
- <Tool
- Name="VCBscMakeTool"
- />
- <Tool
- Name="VCFxCopTool"
- />
- <Tool
- Name="VCAppVerifierTool"
- />
- <Tool
- Name="VCWebDeploymentTool"
- />
- <Tool
- Name="VCPostBuildEventTool"
- />
- </Configuration>
- <Configuration
- Name="Release|x64"
- OutputDirectory="x64\TestZlibDll$(ConfigurationName)"
- IntermediateDirectory="x64\TestZlibDll$(ConfigurationName)\Tmp"
- ConfigurationType="1"
- InheritedPropertySheets="UpgradeFromVC70.vsprops"
- CharacterSet="2"
- >
- <Tool
- Name="VCPreBuildEventTool"
- />
- <Tool
- Name="VCCustomBuildTool"
- />
- <Tool
- Name="VCXMLDataGeneratorTool"
- />
- <Tool
- Name="VCWebServiceProxyGeneratorTool"
- />
- <Tool
- Name="VCMIDLTool"
- TargetEnvironment="3"
- />
- <Tool
- Name="VCCLCompilerTool"
- Optimization="2"
- InlineFunctionExpansion="1"
- OmitFramePointers="true"
- AdditionalIncludeDirectories="..\..\..;..\..\minizip"
- PreprocessorDefinitions="_CRT_NONSTDC_NO_DEPRECATE;_CRT_SECURE_NO_DEPRECATE;ZLIB_WINAPI;NDEBUG;_CONSOLE;WIN64"
- StringPooling="true"
- BasicRuntimeChecks="0"
- RuntimeLibrary="2"
- BufferSecurityCheck="false"
- EnableFunctionLevelLinking="true"
- UsePrecompiledHeader="0"
- AssemblerListingLocation="$(IntDir)\"
- WarningLevel="3"
- Detect64BitPortabilityProblems="true"
- DebugInformationFormat="3"
- />
- <Tool
- Name="VCManagedResourceCompilerTool"
- />
- <Tool
- Name="VCResourceCompilerTool"
- />
- <Tool
- Name="VCPreLinkEventTool"
- />
- <Tool
- Name="VCLinkerTool"
- AdditionalDependencies="x64\ZlibDllRelease\zlibwapi.lib"
- OutputFile="$(OutDir)/testzlib.exe"
- LinkIncremental="1"
- GenerateManifest="false"
- GenerateDebugInformation="true"
- SubSystem="1"
- OptimizeReferences="2"
- EnableCOMDATFolding="2"
- OptimizeForWindows98="1"
- TargetMachine="17"
- />
- <Tool
- Name="VCALinkTool"
- />
- <Tool
- Name="VCManifestTool"
- />
- <Tool
- Name="VCXDCMakeTool"
- />
- <Tool
- Name="VCBscMakeTool"
- />
- <Tool
- Name="VCFxCopTool"
- />
- <Tool
- Name="VCAppVerifierTool"
- />
- <Tool
- Name="VCWebDeploymentTool"
- />
- <Tool
- Name="VCPostBuildEventTool"
- />
- </Configuration>
- <Configuration
- Name="Release|Itanium"
- OutputDirectory="ia64\TestZlibDll$(ConfigurationName)"
- IntermediateDirectory="ia64\TestZlibDll$(ConfigurationName)\Tmp"
- ConfigurationType="1"
- InheritedPropertySheets="UpgradeFromVC70.vsprops"
- CharacterSet="2"
- >
- <Tool
- Name="VCPreBuildEventTool"
- />
- <Tool
- Name="VCCustomBuildTool"
- />
- <Tool
- Name="VCXMLDataGeneratorTool"
- />
- <Tool
- Name="VCWebServiceProxyGeneratorTool"
- />
- <Tool
- Name="VCMIDLTool"
- TargetEnvironment="2"
- />
- <Tool
- Name="VCCLCompilerTool"
- Optimization="2"
- InlineFunctionExpansion="1"
- OmitFramePointers="true"
- AdditionalIncludeDirectories="..\..\..;..\..\minizip"
- PreprocessorDefinitions="_CRT_NONSTDC_NO_DEPRECATE;_CRT_SECURE_NO_DEPRECATE;ZLIB_WINAPI;NDEBUG;_CONSOLE;WIN64"
- StringPooling="true"
- BasicRuntimeChecks="0"
- RuntimeLibrary="2"
- BufferSecurityCheck="false"
- EnableFunctionLevelLinking="true"
- UsePrecompiledHeader="0"
- AssemblerListingLocation="$(IntDir)\"
- WarningLevel="3"
- Detect64BitPortabilityProblems="true"
- DebugInformationFormat="3"
- />
- <Tool
- Name="VCManagedResourceCompilerTool"
- />
- <Tool
- Name="VCResourceCompilerTool"
- />
- <Tool
- Name="VCPreLinkEventTool"
- />
- <Tool
- Name="VCLinkerTool"
- AdditionalDependencies="ia64\ZlibDllRelease\zlibwapi.lib"
- OutputFile="$(OutDir)/testzlib.exe"
- LinkIncremental="1"
- GenerateManifest="false"
- GenerateDebugInformation="true"
- SubSystem="1"
- OptimizeReferences="2"
- EnableCOMDATFolding="2"
- OptimizeForWindows98="1"
- TargetMachine="5"
- />
- <Tool
- Name="VCALinkTool"
- />
- <Tool
- Name="VCManifestTool"
- />
- <Tool
- Name="VCXDCMakeTool"
- />
- <Tool
- Name="VCBscMakeTool"
- />
- <Tool
- Name="VCFxCopTool"
- />
- <Tool
- Name="VCAppVerifierTool"
- />
- <Tool
- Name="VCWebDeploymentTool"
- />
- <Tool
- Name="VCPostBuildEventTool"
- />
- </Configuration>
- </Configurations>
- <References>
- </References>
- <Files>
- <Filter
- Name="Source Files"
- Filter="cpp;c;cxx;def;odl;idl;hpj;bat;asm"
- >
- <File
- RelativePath="..\..\testzlib\testzlib.c"
- >
- </File>
- </Filter>
- <Filter
- Name="Header Files"
- Filter="h;hpp;hxx;hm;inl;inc"
- >
- </Filter>
- <Filter
- Name="Resource Files"
- Filter="rc;ico;cur;bmp;dlg;rc2;rct;bin;rgs;gif;jpg;jpeg;jpe"
- >
- </Filter>
- </Files>
- <Globals>
- </Globals>
-</VisualStudioProject>
diff --git a/third-party/zlib/contrib/vstudio/vc9/zlib.rc b/third-party/zlib/contrib/vstudio/vc9/zlib.rc
deleted file mode 100644
index 73f6476..0000000
--- a/third-party/zlib/contrib/vstudio/vc9/zlib.rc
+++ /dev/null
@@ -1,32 +0,0 @@
-#include <windows.h>
-
-#define IDR_VERSION1 1
-IDR_VERSION1 VERSIONINFO MOVEABLE IMPURE LOADONCALL DISCARDABLE
- FILEVERSION 1,2,8,0
- PRODUCTVERSION 1,2,8,0
- FILEFLAGSMASK VS_FFI_FILEFLAGSMASK
- FILEFLAGS 0
- FILEOS VOS_DOS_WINDOWS32
- FILETYPE VFT_DLL
- FILESUBTYPE 0 // not used
-BEGIN
- BLOCK "StringFileInfo"
- BEGIN
- BLOCK "040904E4"
- //language ID = U.S. English, char set = Windows, Multilingual
-
- BEGIN
- VALUE "FileDescription", "zlib data compression and ZIP file I/O library\0"
- VALUE "FileVersion", "1.2.8\0"
- VALUE "InternalName", "zlib\0"
- VALUE "OriginalFilename", "zlibwapi.dll\0"
- VALUE "ProductName", "ZLib.DLL\0"
- VALUE "Comments","DLL support by Alessandro Iacopetti & Gilles Vollant\0"
- VALUE "LegalCopyright", "(C) 1995-2013 Jean-loup Gailly & Mark Adler\0"
- END
- END
- BLOCK "VarFileInfo"
- BEGIN
- VALUE "Translation", 0x0409, 1252
- END
-END
diff --git a/third-party/zlib/contrib/vstudio/vc9/zlibstat.vcproj b/third-party/zlib/contrib/vstudio/vc9/zlibstat.vcproj
deleted file mode 100644
index 61c76c7..0000000
--- a/third-party/zlib/contrib/vstudio/vc9/zlibstat.vcproj
+++ /dev/null
@@ -1,835 +0,0 @@
-<?xml version="1.0" encoding="Windows-1252"?>
-<VisualStudioProject
- ProjectType="Visual C++"
- Version="9,00"
- Name="zlibstat"
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- </File>
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- <Globals>
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-</VisualStudioProject>
diff --git a/third-party/zlib/contrib/vstudio/vc9/zlibvc.def b/third-party/zlib/contrib/vstudio/vc9/zlibvc.def
deleted file mode 100644
index 6367046..0000000
--- a/third-party/zlib/contrib/vstudio/vc9/zlibvc.def
+++ /dev/null
@@ -1,143 +0,0 @@
-LIBRARY
-; zlib data compression and ZIP file I/O library
-
-VERSION 1.2.8
-
-EXPORTS
- adler32 @1
- compress @2
- crc32 @3
- deflate @4
- deflateCopy @5
- deflateEnd @6
- deflateInit2_ @7
- deflateInit_ @8
- deflateParams @9
- deflateReset @10
- deflateSetDictionary @11
- gzclose @12
- gzdopen @13
- gzerror @14
- gzflush @15
- gzopen @16
- gzread @17
- gzwrite @18
- inflate @19
- inflateEnd @20
- inflateInit2_ @21
- inflateInit_ @22
- inflateReset @23
- inflateSetDictionary @24
- inflateSync @25
- uncompress @26
- zlibVersion @27
- gzprintf @28
- gzputc @29
- gzgetc @30
- gzseek @31
- gzrewind @32
- gztell @33
- gzeof @34
- gzsetparams @35
- zError @36
- inflateSyncPoint @37
- get_crc_table @38
- compress2 @39
- gzputs @40
- gzgets @41
- inflateCopy @42
- inflateBackInit_ @43
- inflateBack @44
- inflateBackEnd @45
- compressBound @46
- deflateBound @47
- gzclearerr @48
- gzungetc @49
- zlibCompileFlags @50
- deflatePrime @51
- deflatePending @52
-
- unzOpen @61
- unzClose @62
- unzGetGlobalInfo @63
- unzGetCurrentFileInfo @64
- unzGoToFirstFile @65
- unzGoToNextFile @66
- unzOpenCurrentFile @67
- unzReadCurrentFile @68
- unzOpenCurrentFile3 @69
- unztell @70
- unzeof @71
- unzCloseCurrentFile @72
- unzGetGlobalComment @73
- unzStringFileNameCompare @74
- unzLocateFile @75
- unzGetLocalExtrafield @76
- unzOpen2 @77
- unzOpenCurrentFile2 @78
- unzOpenCurrentFilePassword @79
-
- zipOpen @80
- zipOpenNewFileInZip @81
- zipWriteInFileInZip @82
- zipCloseFileInZip @83
- zipClose @84
- zipOpenNewFileInZip2 @86
- zipCloseFileInZipRaw @87
- zipOpen2 @88
- zipOpenNewFileInZip3 @89
-
- unzGetFilePos @100
- unzGoToFilePos @101
-
- fill_win32_filefunc @110
-
-; zlibwapi v1.2.4 added:
- fill_win32_filefunc64 @111
- fill_win32_filefunc64A @112
- fill_win32_filefunc64W @113
-
- unzOpen64 @120
- unzOpen2_64 @121
- unzGetGlobalInfo64 @122
- unzGetCurrentFileInfo64 @124
- unzGetCurrentFileZStreamPos64 @125
- unztell64 @126
- unzGetFilePos64 @127
- unzGoToFilePos64 @128
-
- zipOpen64 @130
- zipOpen2_64 @131
- zipOpenNewFileInZip64 @132
- zipOpenNewFileInZip2_64 @133
- zipOpenNewFileInZip3_64 @134
- zipOpenNewFileInZip4_64 @135
- zipCloseFileInZipRaw64 @136
-
-; zlib1 v1.2.4 added:
- adler32_combine @140
- crc32_combine @142
- deflateSetHeader @144
- deflateTune @145
- gzbuffer @146
- gzclose_r @147
- gzclose_w @148
- gzdirect @149
- gzoffset @150
- inflateGetHeader @156
- inflateMark @157
- inflatePrime @158
- inflateReset2 @159
- inflateUndermine @160
-
-; zlib1 v1.2.6 added:
- gzgetc_ @161
- inflateResetKeep @163
- deflateResetKeep @164
-
-; zlib1 v1.2.7 added:
- gzopen_w @165
-
-; zlib1 v1.2.8 added:
- inflateGetDictionary @166
- gzvprintf @167
diff --git a/third-party/zlib/contrib/vstudio/vc9/zlibvc.sln b/third-party/zlib/contrib/vstudio/vc9/zlibvc.sln
deleted file mode 100644
index b482967..0000000
--- a/third-party/zlib/contrib/vstudio/vc9/zlibvc.sln
+++ /dev/null
@@ -1,144 +0,0 @@
-
-Microsoft Visual Studio Solution File, Format Version 10.00
-# Visual Studio 2008
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-EndProject
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-EndProject
-Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "testzlib", "testzlib.vcproj", "{AA6666AA-E09F-4135-9C0C-4FE50C3C654B}"
-EndProject
-Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "TestZlibDll", "testzlibdll.vcproj", "{C52F9E7B-498A-42BE-8DB4-85A15694366A}"
- ProjectSection(ProjectDependencies) = postProject
- {8FD826F8-3739-44E6-8CC8-997122E53B8D} = {8FD826F8-3739-44E6-8CC8-997122E53B8D}
- EndProjectSection
-EndProject
-Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "minizip", "minizip.vcproj", "{48CDD9DC-E09F-4135-9C0C-4FE50C3C654B}"
- ProjectSection(ProjectDependencies) = postProject
- {8FD826F8-3739-44E6-8CC8-997122E53B8D} = {8FD826F8-3739-44E6-8CC8-997122E53B8D}
- EndProjectSection
-EndProject
-Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "miniunz", "miniunz.vcproj", "{C52F9E7B-498A-42BE-8DB4-85A15694382A}"
- ProjectSection(ProjectDependencies) = postProject
- {8FD826F8-3739-44E6-8CC8-997122E53B8D} = {8FD826F8-3739-44E6-8CC8-997122E53B8D}
- EndProjectSection
-EndProject
-Global
- GlobalSection(SolutionConfigurationPlatforms) = preSolution
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- Debug|Win32 = Debug|Win32
- Debug|x64 = Debug|x64
- Release|Itanium = Release|Itanium
- Release|Win32 = Release|Win32
- Release|x64 = Release|x64
- ReleaseWithoutAsm|Itanium = ReleaseWithoutAsm|Itanium
- ReleaseWithoutAsm|Win32 = ReleaseWithoutAsm|Win32
- ReleaseWithoutAsm|x64 = ReleaseWithoutAsm|x64
- EndGlobalSection
- GlobalSection(ProjectConfigurationPlatforms) = postSolution
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- {745DEC58-EBB3-47A9-A9B8-4C6627C01BF8}.ReleaseWithoutAsm|x64.ActiveCfg = ReleaseWithoutAsm|x64
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- {AA6666AA-E09F-4135-9C0C-4FE50C3C654B}.Debug|Itanium.ActiveCfg = Debug|Itanium
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- {AA6666AA-E09F-4135-9C0C-4FE50C3C654B}.Debug|Win32.Build.0 = Debug|Win32
- {AA6666AA-E09F-4135-9C0C-4FE50C3C654B}.Debug|x64.ActiveCfg = Debug|x64
- {AA6666AA-E09F-4135-9C0C-4FE50C3C654B}.Debug|x64.Build.0 = Debug|x64
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- {AA6666AA-E09F-4135-9C0C-4FE50C3C654B}.Release|Win32.Build.0 = Release|Win32
- {AA6666AA-E09F-4135-9C0C-4FE50C3C654B}.Release|x64.ActiveCfg = Release|x64
- {AA6666AA-E09F-4135-9C0C-4FE50C3C654B}.Release|x64.Build.0 = Release|x64
- {AA6666AA-E09F-4135-9C0C-4FE50C3C654B}.ReleaseWithoutAsm|Itanium.ActiveCfg = ReleaseWithoutAsm|Itanium
- {AA6666AA-E09F-4135-9C0C-4FE50C3C654B}.ReleaseWithoutAsm|Itanium.Build.0 = ReleaseWithoutAsm|Itanium
- {AA6666AA-E09F-4135-9C0C-4FE50C3C654B}.ReleaseWithoutAsm|Win32.ActiveCfg = ReleaseWithoutAsm|Win32
- {AA6666AA-E09F-4135-9C0C-4FE50C3C654B}.ReleaseWithoutAsm|Win32.Build.0 = ReleaseWithoutAsm|Win32
- {AA6666AA-E09F-4135-9C0C-4FE50C3C654B}.ReleaseWithoutAsm|x64.ActiveCfg = ReleaseWithoutAsm|x64
- {AA6666AA-E09F-4135-9C0C-4FE50C3C654B}.ReleaseWithoutAsm|x64.Build.0 = ReleaseWithoutAsm|x64
- {C52F9E7B-498A-42BE-8DB4-85A15694366A}.Debug|Itanium.ActiveCfg = Debug|Itanium
- {C52F9E7B-498A-42BE-8DB4-85A15694366A}.Debug|Itanium.Build.0 = Debug|Itanium
- {C52F9E7B-498A-42BE-8DB4-85A15694366A}.Debug|Win32.ActiveCfg = Debug|Win32
- {C52F9E7B-498A-42BE-8DB4-85A15694366A}.Debug|Win32.Build.0 = Debug|Win32
- {C52F9E7B-498A-42BE-8DB4-85A15694366A}.Debug|x64.ActiveCfg = Debug|x64
- {C52F9E7B-498A-42BE-8DB4-85A15694366A}.Debug|x64.Build.0 = Debug|x64
- {C52F9E7B-498A-42BE-8DB4-85A15694366A}.Release|Itanium.ActiveCfg = Release|Itanium
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- EndGlobalSection
- GlobalSection(SolutionProperties) = preSolution
- HideSolutionNode = FALSE
- EndGlobalSection
-EndGlobal
diff --git a/third-party/zlib/contrib/vstudio/vc9/zlibvc.vcproj b/third-party/zlib/contrib/vstudio/vc9/zlibvc.vcproj
deleted file mode 100644
index c9a8947..0000000
--- a/third-party/zlib/contrib/vstudio/vc9/zlibvc.vcproj
+++ /dev/null
@@ -1,1156 +0,0 @@
-<?xml version="1.0" encoding="Windows-1252"?>
-<VisualStudioProject
- ProjectType="Visual C++"
- Version="9,00"
- Name="zlibvc"
- ProjectGUID="{8FD826F8-3739-44E6-8CC8-997122E53B8D}"
- RootNamespace="zlibvc"
- TargetFrameworkVersion="131072"
- >
- <Platforms>
- <Platform
- Name="Win32"
- />
- <Platform
- Name="x64"
- />
- <Platform
- Name="Itanium"
- />
- </Platforms>
- <ToolFiles>
- </ToolFiles>
- <Configurations>
- <Configuration
- Name="Debug|Win32"
- OutputDirectory="x86\ZlibDll$(ConfigurationName)"
- IntermediateDirectory="x86\ZlibDll$(ConfigurationName)\Tmp"
- ConfigurationType="2"
- InheritedPropertySheets="UpgradeFromVC70.vsprops"
- UseOfMFC="0"
- ATLMinimizesCRunTimeLibraryUsage="false"
- >
- <Tool
- Name="VCPreBuildEventTool"
- />
- <Tool
- Name="VCCustomBuildTool"
- />
- <Tool
- Name="VCXMLDataGeneratorTool"
- />
- <Tool
- Name="VCWebServiceProxyGeneratorTool"
- />
- <Tool
- Name="VCMIDLTool"
- PreprocessorDefinitions="_DEBUG"
- MkTypLibCompatible="true"
- SuppressStartupBanner="true"
- TargetEnvironment="1"
- TypeLibraryName="$(OutDir)/zlibvc.tlb"
- />
- <Tool
- Name="VCCLCompilerTool"
- Optimization="0"
- AdditionalIncludeDirectories="..\..\..;..\..\masmx86"
- PreprocessorDefinitions="WIN32;_CRT_NONSTDC_NO_DEPRECATE;_CRT_SECURE_NO_DEPRECATE;_CRT_NONSTDC_NO_WARNINGS;ZLIB_WINAPI;ASMV;ASMINF"
- ExceptionHandling="0"
- RuntimeLibrary="1"
- BufferSecurityCheck="false"
- PrecompiledHeaderFile="$(IntDir)/zlibvc.pch"
- AssemblerListingLocation="$(IntDir)\"
- ObjectFile="$(IntDir)\"
- ProgramDataBaseFileName="$(OutDir)\"
- BrowseInformation="0"
- WarningLevel="3"
- SuppressStartupBanner="true"
- DebugInformationFormat="4"
- />
- <Tool
- Name="VCManagedResourceCompilerTool"
- />
- <Tool
- Name="VCResourceCompilerTool"
- PreprocessorDefinitions="_DEBUG"
- Culture="1036"
- />
- <Tool
- Name="VCPreLinkEventTool"
- />
- <Tool
- Name="VCLinkerTool"
- AdditionalOptions="/MACHINE:I386"
- AdditionalDependencies="..\..\masmx86\match686.obj ..\..\masmx86\inffas32.obj"
- OutputFile="$(OutDir)\zlibwapi.dll"
- LinkIncremental="2"
- SuppressStartupBanner="true"
- GenerateManifest="false"
- ModuleDefinitionFile=".\zlibvc.def"
- GenerateDebugInformation="true"
- ProgramDatabaseFile="$(OutDir)/zlibwapi.pdb"
- GenerateMapFile="true"
- MapFileName="$(OutDir)/zlibwapi.map"
- SubSystem="2"
- RandomizedBaseAddress="1"
- DataExecutionPrevention="0"
- ImportLibrary="$(OutDir)/zlibwapi.lib"
- />
- <Tool
- Name="VCALinkTool"
- />
- <Tool
- Name="VCManifestTool"
- />
- <Tool
- Name="VCXDCMakeTool"
- />
- <Tool
- Name="VCBscMakeTool"
- />
- <Tool
- Name="VCFxCopTool"
- />
- <Tool
- Name="VCAppVerifierTool"
- />
- <Tool
- Name="VCPostBuildEventTool"
- />
- </Configuration>
- <Configuration
- Name="Debug|x64"
- OutputDirectory="x64\ZlibDll$(ConfigurationName)"
- IntermediateDirectory="x64\ZlibDll$(ConfigurationName)\Tmp"
- ConfigurationType="2"
- InheritedPropertySheets="UpgradeFromVC70.vsprops"
- UseOfMFC="0"
- ATLMinimizesCRunTimeLibraryUsage="false"
- >
- <Tool
- Name="VCPreBuildEventTool"
- />
- <Tool
- Name="VCCustomBuildTool"
- />
- <Tool
- Name="VCXMLDataGeneratorTool"
- />
- <Tool
- Name="VCWebServiceProxyGeneratorTool"
- />
- <Tool
- Name="VCMIDLTool"
- PreprocessorDefinitions="_DEBUG"
- MkTypLibCompatible="true"
- SuppressStartupBanner="true"
- TargetEnvironment="3"
- TypeLibraryName="$(OutDir)/zlibvc.tlb"
- />
- <Tool
- Name="VCCLCompilerTool"
- Optimization="0"
- AdditionalIncludeDirectories="..\..\..;..\..\masmx86"
- PreprocessorDefinitions="WIN32;_CRT_NONSTDC_NO_DEPRECATE;_CRT_SECURE_NO_DEPRECATE;_CRT_NONSTDC_NO_WARNINGS;ZLIB_WINAPI;ASMV;ASMINF;WIN64"
- ExceptionHandling="0"
- RuntimeLibrary="3"
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- ProgramDataBaseFileName="$(OutDir)\"
- BrowseInformation="0"
- WarningLevel="3"
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- <Tool
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- <Tool
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- PreprocessorDefinitions="_DEBUG"
- Culture="1036"
- />
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- <Tool
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- AdditionalDependencies="..\..\masmx64\gvmat64.obj ..\..\masmx64\inffasx64.obj "
- OutputFile="$(OutDir)\zlibwapi.dll"
- LinkIncremental="2"
- SuppressStartupBanner="true"
- GenerateManifest="false"
- ModuleDefinitionFile=".\zlibvc.def"
- GenerateDebugInformation="true"
- ProgramDatabaseFile="$(OutDir)/zlibwapi.pdb"
- GenerateMapFile="true"
- MapFileName="$(OutDir)/zlibwapi.map"
- SubSystem="2"
- ImportLibrary="$(OutDir)/zlibwapi.lib"
- TargetMachine="17"
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- <Tool
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- Filter="h;hpp;hxx;hm;inl;fi;fd"
- >
- <File
- RelativePath="..\..\..\deflate.h"
- >
- </File>
- <File
- RelativePath="..\..\..\infblock.h"
- >
- </File>
- <File
- RelativePath="..\..\..\infcodes.h"
- >
- </File>
- <File
- RelativePath="..\..\..\inffast.h"
- >
- </File>
- <File
- RelativePath="..\..\..\inftrees.h"
- >
- </File>
- <File
- RelativePath="..\..\..\infutil.h"
- >
- </File>
- <File
- RelativePath="..\..\..\zconf.h"
- >
- </File>
- <File
- RelativePath="..\..\..\zlib.h"
- >
- </File>
- <File
- RelativePath="..\..\..\zutil.h"
- >
- </File>
- </Filter>
- <Filter
- Name="Resource Files"
- Filter="ico;cur;bmp;dlg;rc2;rct;bin;cnt;rtf;gif;jpg;jpeg;jpe"
- >
- </Filter>
- </Files>
- <Globals>
- </Globals>
-</VisualStudioProject>
diff --git a/third-party/zlib/crc32.c b/third-party/zlib/crc32.c
deleted file mode 100644
index 979a719..0000000
--- a/third-party/zlib/crc32.c
+++ /dev/null
@@ -1,425 +0,0 @@
-/* crc32.c -- compute the CRC-32 of a data stream
- * Copyright (C) 1995-2006, 2010, 2011, 2012 Mark Adler
- * For conditions of distribution and use, see copyright notice in zlib.h
- *
- * Thanks to Rodney Brown <rbrown64 at csc.com.au> for his contribution of faster
- * CRC methods: exclusive-oring 32 bits of data at a time, and pre-computing
- * tables for updating the shift register in one step with three exclusive-ors
- * instead of four steps with four exclusive-ors. This results in about a
- * factor of two increase in speed on a Power PC G4 (PPC7455) using gcc -O3.
- */
-
-/* @(#) $Id$ */
-
-/*
- Note on the use of DYNAMIC_CRC_TABLE: there is no mutex or semaphore
- protection on the static variables used to control the first-use generation
- of the crc tables. Therefore, if you #define DYNAMIC_CRC_TABLE, you should
- first call get_crc_table() to initialize the tables before allowing more than
- one thread to use crc32().
-
- DYNAMIC_CRC_TABLE and MAKECRCH can be #defined to write out crc32.h.
- */
-
-#ifdef MAKECRCH
-# include <stdio.h>
-# ifndef DYNAMIC_CRC_TABLE
-# define DYNAMIC_CRC_TABLE
-# endif /* !DYNAMIC_CRC_TABLE */
-#endif /* MAKECRCH */
-
-#include "zutil.h" /* for STDC and FAR definitions */
-
-#define local static
-
-/* Definitions for doing the crc four data bytes at a time. */
-#if !defined(NOBYFOUR) && defined(Z_U4)
-# define BYFOUR
-#endif
-#ifdef BYFOUR
- local unsigned long crc32_little OF((unsigned long,
- const unsigned char FAR *, unsigned));
- local unsigned long crc32_big OF((unsigned long,
- const unsigned char FAR *, unsigned));
-# define TBLS 8
-#else
-# define TBLS 1
-#endif /* BYFOUR */
-
-/* Local functions for crc concatenation */
-local unsigned long gf2_matrix_times OF((unsigned long *mat,
- unsigned long vec));
-local void gf2_matrix_square OF((unsigned long *square, unsigned long *mat));
-local uLong crc32_combine_ OF((uLong crc1, uLong crc2, z_off64_t len2));
-
-
-#ifdef DYNAMIC_CRC_TABLE
-
-local volatile int crc_table_empty = 1;
-local z_crc_t FAR crc_table[TBLS][256];
-local void make_crc_table OF((void));
-#ifdef MAKECRCH
- local void write_table OF((FILE *, const z_crc_t FAR *));
-#endif /* MAKECRCH */
-/*
- Generate tables for a byte-wise 32-bit CRC calculation on the polynomial:
- x^32+x^26+x^23+x^22+x^16+x^12+x^11+x^10+x^8+x^7+x^5+x^4+x^2+x+1.
-
- Polynomials over GF(2) are represented in binary, one bit per coefficient,
- with the lowest powers in the most significant bit. Then adding polynomials
- is just exclusive-or, and multiplying a polynomial by x is a right shift by
- one. If we call the above polynomial p, and represent a byte as the
- polynomial q, also with the lowest power in the most significant bit (so the
- byte 0xb1 is the polynomial x^7+x^3+x+1), then the CRC is (q*x^32) mod p,
- where a mod b means the remainder after dividing a by b.
-
- This calculation is done using the shift-register method of multiplying and
- taking the remainder. The register is initialized to zero, and for each
- incoming bit, x^32 is added mod p to the register if the bit is a one (where
- x^32 mod p is p+x^32 = x^26+...+1), and the register is multiplied mod p by
- x (which is shifting right by one and adding x^32 mod p if the bit shifted
- out is a one). We start with the highest power (least significant bit) of
- q and repeat for all eight bits of q.
-
- The first table is simply the CRC of all possible eight bit values. This is
- all the information needed to generate CRCs on data a byte at a time for all
- combinations of CRC register values and incoming bytes. The remaining tables
- allow for word-at-a-time CRC calculation for both big-endian and little-
- endian machines, where a word is four bytes.
-*/
-local void make_crc_table()
-{
- z_crc_t c;
- int n, k;
- z_crc_t poly; /* polynomial exclusive-or pattern */
- /* terms of polynomial defining this crc (except x^32): */
- static volatile int first = 1; /* flag to limit concurrent making */
- static const unsigned char p[] = {0,1,2,4,5,7,8,10,11,12,16,22,23,26};
-
- /* See if another task is already doing this (not thread-safe, but better
- than nothing -- significantly reduces duration of vulnerability in
- case the advice about DYNAMIC_CRC_TABLE is ignored) */
- if (first) {
- first = 0;
-
- /* make exclusive-or pattern from polynomial (0xedb88320UL) */
- poly = 0;
- for (n = 0; n < (int)(sizeof(p)/sizeof(unsigned char)); n++)
- poly |= (z_crc_t)1 << (31 - p[n]);
-
- /* generate a crc for every 8-bit value */
- for (n = 0; n < 256; n++) {
- c = (z_crc_t)n;
- for (k = 0; k < 8; k++)
- c = c & 1 ? poly ^ (c >> 1) : c >> 1;
- crc_table[0][n] = c;
- }
-
-#ifdef BYFOUR
- /* generate crc for each value followed by one, two, and three zeros,
- and then the byte reversal of those as well as the first table */
- for (n = 0; n < 256; n++) {
- c = crc_table[0][n];
- crc_table[4][n] = ZSWAP32(c);
- for (k = 1; k < 4; k++) {
- c = crc_table[0][c & 0xff] ^ (c >> 8);
- crc_table[k][n] = c;
- crc_table[k + 4][n] = ZSWAP32(c);
- }
- }
-#endif /* BYFOUR */
-
- crc_table_empty = 0;
- }
- else { /* not first */
- /* wait for the other guy to finish (not efficient, but rare) */
- while (crc_table_empty)
- ;
- }
-
-#ifdef MAKECRCH
- /* write out CRC tables to crc32.h */
- {
- FILE *out;
-
- out = fopen("crc32.h", "w");
- if (out == NULL) return;
- fprintf(out, "/* crc32.h -- tables for rapid CRC calculation\n");
- fprintf(out, " * Generated automatically by crc32.c\n */\n\n");
- fprintf(out, "local const z_crc_t FAR ");
- fprintf(out, "crc_table[TBLS][256] =\n{\n {\n");
- write_table(out, crc_table[0]);
-# ifdef BYFOUR
- fprintf(out, "#ifdef BYFOUR\n");
- for (k = 1; k < 8; k++) {
- fprintf(out, " },\n {\n");
- write_table(out, crc_table[k]);
- }
- fprintf(out, "#endif\n");
-# endif /* BYFOUR */
- fprintf(out, " }\n};\n");
- fclose(out);
- }
-#endif /* MAKECRCH */
-}
-
-#ifdef MAKECRCH
-local void write_table(out, table)
- FILE *out;
- const z_crc_t FAR *table;
-{
- int n;
-
- for (n = 0; n < 256; n++)
- fprintf(out, "%s0x%08lxUL%s", n % 5 ? "" : " ",
- (unsigned long)(table[n]),
- n == 255 ? "\n" : (n % 5 == 4 ? ",\n" : ", "));
-}
-#endif /* MAKECRCH */
-
-#else /* !DYNAMIC_CRC_TABLE */
-/* ========================================================================
- * Tables of CRC-32s of all single-byte values, made by make_crc_table().
- */
-#include "crc32.h"
-#endif /* DYNAMIC_CRC_TABLE */
-
-/* =========================================================================
- * This function can be used by asm versions of crc32()
- */
-const z_crc_t FAR * ZEXPORT get_crc_table()
-{
-#ifdef DYNAMIC_CRC_TABLE
- if (crc_table_empty)
- make_crc_table();
-#endif /* DYNAMIC_CRC_TABLE */
- return (const z_crc_t FAR *)crc_table;
-}
-
-/* ========================================================================= */
-#define DO1 crc = crc_table[0][((int)crc ^ (*buf++)) & 0xff] ^ (crc >> 8)
-#define DO8 DO1; DO1; DO1; DO1; DO1; DO1; DO1; DO1
-
-/* ========================================================================= */
-unsigned long ZEXPORT crc32(crc, buf, len)
- unsigned long crc;
- const unsigned char FAR *buf;
- uInt len;
-{
- if (buf == Z_NULL) return 0UL;
-
-#ifdef DYNAMIC_CRC_TABLE
- if (crc_table_empty)
- make_crc_table();
-#endif /* DYNAMIC_CRC_TABLE */
-
-#ifdef BYFOUR
- if (sizeof(void *) == sizeof(ptrdiff_t)) {
- z_crc_t endian;
-
- endian = 1;
- if (*((unsigned char *)(&endian)))
- return crc32_little(crc, buf, len);
- else
- return crc32_big(crc, buf, len);
- }
-#endif /* BYFOUR */
- crc = crc ^ 0xffffffffUL;
- while (len >= 8) {
- DO8;
- len -= 8;
- }
- if (len) do {
- DO1;
- } while (--len);
- return crc ^ 0xffffffffUL;
-}
-
-#ifdef BYFOUR
-
-/* ========================================================================= */
-#define DOLIT4 c ^= *buf4++; \
- c = crc_table[3][c & 0xff] ^ crc_table[2][(c >> 8) & 0xff] ^ \
- crc_table[1][(c >> 16) & 0xff] ^ crc_table[0][c >> 24]
-#define DOLIT32 DOLIT4; DOLIT4; DOLIT4; DOLIT4; DOLIT4; DOLIT4; DOLIT4; DOLIT4
-
-/* ========================================================================= */
-local unsigned long crc32_little(crc, buf, len)
- unsigned long crc;
- const unsigned char FAR *buf;
- unsigned len;
-{
- register z_crc_t c;
- register const z_crc_t FAR *buf4;
-
- c = (z_crc_t)crc;
- c = ~c;
- while (len && ((ptrdiff_t)buf & 3)) {
- c = crc_table[0][(c ^ *buf++) & 0xff] ^ (c >> 8);
- len--;
- }
-
- buf4 = (const z_crc_t FAR *)(const void FAR *)buf;
- while (len >= 32) {
- DOLIT32;
- len -= 32;
- }
- while (len >= 4) {
- DOLIT4;
- len -= 4;
- }
- buf = (const unsigned char FAR *)buf4;
-
- if (len) do {
- c = crc_table[0][(c ^ *buf++) & 0xff] ^ (c >> 8);
- } while (--len);
- c = ~c;
- return (unsigned long)c;
-}
-
-/* ========================================================================= */
-#define DOBIG4 c ^= *++buf4; \
- c = crc_table[4][c & 0xff] ^ crc_table[5][(c >> 8) & 0xff] ^ \
- crc_table[6][(c >> 16) & 0xff] ^ crc_table[7][c >> 24]
-#define DOBIG32 DOBIG4; DOBIG4; DOBIG4; DOBIG4; DOBIG4; DOBIG4; DOBIG4; DOBIG4
-
-/* ========================================================================= */
-local unsigned long crc32_big(crc, buf, len)
- unsigned long crc;
- const unsigned char FAR *buf;
- unsigned len;
-{
- register z_crc_t c;
- register const z_crc_t FAR *buf4;
-
- c = ZSWAP32((z_crc_t)crc);
- c = ~c;
- while (len && ((ptrdiff_t)buf & 3)) {
- c = crc_table[4][(c >> 24) ^ *buf++] ^ (c << 8);
- len--;
- }
-
- buf4 = (const z_crc_t FAR *)(const void FAR *)buf;
- buf4--;
- while (len >= 32) {
- DOBIG32;
- len -= 32;
- }
- while (len >= 4) {
- DOBIG4;
- len -= 4;
- }
- buf4++;
- buf = (const unsigned char FAR *)buf4;
-
- if (len) do {
- c = crc_table[4][(c >> 24) ^ *buf++] ^ (c << 8);
- } while (--len);
- c = ~c;
- return (unsigned long)(ZSWAP32(c));
-}
-
-#endif /* BYFOUR */
-
-#define GF2_DIM 32 /* dimension of GF(2) vectors (length of CRC) */
-
-/* ========================================================================= */
-local unsigned long gf2_matrix_times(mat, vec)
- unsigned long *mat;
- unsigned long vec;
-{
- unsigned long sum;
-
- sum = 0;
- while (vec) {
- if (vec & 1)
- sum ^= *mat;
- vec >>= 1;
- mat++;
- }
- return sum;
-}
-
-/* ========================================================================= */
-local void gf2_matrix_square(square, mat)
- unsigned long *square;
- unsigned long *mat;
-{
- int n;
-
- for (n = 0; n < GF2_DIM; n++)
- square[n] = gf2_matrix_times(mat, mat[n]);
-}
-
-/* ========================================================================= */
-local uLong crc32_combine_(crc1, crc2, len2)
- uLong crc1;
- uLong crc2;
- z_off64_t len2;
-{
- int n;
- unsigned long row;
- unsigned long even[GF2_DIM]; /* even-power-of-two zeros operator */
- unsigned long odd[GF2_DIM]; /* odd-power-of-two zeros operator */
-
- /* degenerate case (also disallow negative lengths) */
- if (len2 <= 0)
- return crc1;
-
- /* put operator for one zero bit in odd */
- odd[0] = 0xedb88320UL; /* CRC-32 polynomial */
- row = 1;
- for (n = 1; n < GF2_DIM; n++) {
- odd[n] = row;
- row <<= 1;
- }
-
- /* put operator for two zero bits in even */
- gf2_matrix_square(even, odd);
-
- /* put operator for four zero bits in odd */
- gf2_matrix_square(odd, even);
-
- /* apply len2 zeros to crc1 (first square will put the operator for one
- zero byte, eight zero bits, in even) */
- do {
- /* apply zeros operator for this bit of len2 */
- gf2_matrix_square(even, odd);
- if (len2 & 1)
- crc1 = gf2_matrix_times(even, crc1);
- len2 >>= 1;
-
- /* if no more bits set, then done */
- if (len2 == 0)
- break;
-
- /* another iteration of the loop with odd and even swapped */
- gf2_matrix_square(odd, even);
- if (len2 & 1)
- crc1 = gf2_matrix_times(odd, crc1);
- len2 >>= 1;
-
- /* if no more bits set, then done */
- } while (len2 != 0);
-
- /* return combined crc */
- crc1 ^= crc2;
- return crc1;
-}
-
-/* ========================================================================= */
-uLong ZEXPORT crc32_combine(crc1, crc2, len2)
- uLong crc1;
- uLong crc2;
- z_off_t len2;
-{
- return crc32_combine_(crc1, crc2, len2);
-}
-
-uLong ZEXPORT crc32_combine64(crc1, crc2, len2)
- uLong crc1;
- uLong crc2;
- z_off64_t len2;
-{
- return crc32_combine_(crc1, crc2, len2);
-}
diff --git a/third-party/zlib/crc32.h b/third-party/zlib/crc32.h
deleted file mode 100644
index 9e0c778..0000000
--- a/third-party/zlib/crc32.h
+++ /dev/null
@@ -1,441 +0,0 @@
-/* crc32.h -- tables for rapid CRC calculation
- * Generated automatically by crc32.c
- */
-
-local const z_crc_t FAR crc_table[TBLS][256] =
-{
- {
- 0x00000000UL, 0x77073096UL, 0xee0e612cUL, 0x990951baUL, 0x076dc419UL,
- 0x706af48fUL, 0xe963a535UL, 0x9e6495a3UL, 0x0edb8832UL, 0x79dcb8a4UL,
- 0xe0d5e91eUL, 0x97d2d988UL, 0x09b64c2bUL, 0x7eb17cbdUL, 0xe7b82d07UL,
- 0x90bf1d91UL, 0x1db71064UL, 0x6ab020f2UL, 0xf3b97148UL, 0x84be41deUL,
- 0x1adad47dUL, 0x6ddde4ebUL, 0xf4d4b551UL, 0x83d385c7UL, 0x136c9856UL,
- 0x646ba8c0UL, 0xfd62f97aUL, 0x8a65c9ecUL, 0x14015c4fUL, 0x63066cd9UL,
- 0xfa0f3d63UL, 0x8d080df5UL, 0x3b6e20c8UL, 0x4c69105eUL, 0xd56041e4UL,
- 0xa2677172UL, 0x3c03e4d1UL, 0x4b04d447UL, 0xd20d85fdUL, 0xa50ab56bUL,
- 0x35b5a8faUL, 0x42b2986cUL, 0xdbbbc9d6UL, 0xacbcf940UL, 0x32d86ce3UL,
- 0x45df5c75UL, 0xdcd60dcfUL, 0xabd13d59UL, 0x26d930acUL, 0x51de003aUL,
- 0xc8d75180UL, 0xbfd06116UL, 0x21b4f4b5UL, 0x56b3c423UL, 0xcfba9599UL,
- 0xb8bda50fUL, 0x2802b89eUL, 0x5f058808UL, 0xc60cd9b2UL, 0xb10be924UL,
- 0x2f6f7c87UL, 0x58684c11UL, 0xc1611dabUL, 0xb6662d3dUL, 0x76dc4190UL,
- 0x01db7106UL, 0x98d220bcUL, 0xefd5102aUL, 0x71b18589UL, 0x06b6b51fUL,
- 0x9fbfe4a5UL, 0xe8b8d433UL, 0x7807c9a2UL, 0x0f00f934UL, 0x9609a88eUL,
- 0xe10e9818UL, 0x7f6a0dbbUL, 0x086d3d2dUL, 0x91646c97UL, 0xe6635c01UL,
- 0x6b6b51f4UL, 0x1c6c6162UL, 0x856530d8UL, 0xf262004eUL, 0x6c0695edUL,
- 0x1b01a57bUL, 0x8208f4c1UL, 0xf50fc457UL, 0x65b0d9c6UL, 0x12b7e950UL,
- 0x8bbeb8eaUL, 0xfcb9887cUL, 0x62dd1ddfUL, 0x15da2d49UL, 0x8cd37cf3UL,
- 0xfbd44c65UL, 0x4db26158UL, 0x3ab551ceUL, 0xa3bc0074UL, 0xd4bb30e2UL,
- 0x4adfa541UL, 0x3dd895d7UL, 0xa4d1c46dUL, 0xd3d6f4fbUL, 0x4369e96aUL,
- 0x346ed9fcUL, 0xad678846UL, 0xda60b8d0UL, 0x44042d73UL, 0x33031de5UL,
- 0xaa0a4c5fUL, 0xdd0d7cc9UL, 0x5005713cUL, 0x270241aaUL, 0xbe0b1010UL,
- 0xc90c2086UL, 0x5768b525UL, 0x206f85b3UL, 0xb966d409UL, 0xce61e49fUL,
- 0x5edef90eUL, 0x29d9c998UL, 0xb0d09822UL, 0xc7d7a8b4UL, 0x59b33d17UL,
- 0x2eb40d81UL, 0xb7bd5c3bUL, 0xc0ba6cadUL, 0xedb88320UL, 0x9abfb3b6UL,
- 0x03b6e20cUL, 0x74b1d29aUL, 0xead54739UL, 0x9dd277afUL, 0x04db2615UL,
- 0x73dc1683UL, 0xe3630b12UL, 0x94643b84UL, 0x0d6d6a3eUL, 0x7a6a5aa8UL,
- 0xe40ecf0bUL, 0x9309ff9dUL, 0x0a00ae27UL, 0x7d079eb1UL, 0xf00f9344UL,
- 0x8708a3d2UL, 0x1e01f268UL, 0x6906c2feUL, 0xf762575dUL, 0x806567cbUL,
- 0x196c3671UL, 0x6e6b06e7UL, 0xfed41b76UL, 0x89d32be0UL, 0x10da7a5aUL,
- 0x67dd4accUL, 0xf9b9df6fUL, 0x8ebeeff9UL, 0x17b7be43UL, 0x60b08ed5UL,
- 0xd6d6a3e8UL, 0xa1d1937eUL, 0x38d8c2c4UL, 0x4fdff252UL, 0xd1bb67f1UL,
- 0xa6bc5767UL, 0x3fb506ddUL, 0x48b2364bUL, 0xd80d2bdaUL, 0xaf0a1b4cUL,
- 0x36034af6UL, 0x41047a60UL, 0xdf60efc3UL, 0xa867df55UL, 0x316e8eefUL,
- 0x4669be79UL, 0xcb61b38cUL, 0xbc66831aUL, 0x256fd2a0UL, 0x5268e236UL,
- 0xcc0c7795UL, 0xbb0b4703UL, 0x220216b9UL, 0x5505262fUL, 0xc5ba3bbeUL,
- 0xb2bd0b28UL, 0x2bb45a92UL, 0x5cb36a04UL, 0xc2d7ffa7UL, 0xb5d0cf31UL,
- 0x2cd99e8bUL, 0x5bdeae1dUL, 0x9b64c2b0UL, 0xec63f226UL, 0x756aa39cUL,
- 0x026d930aUL, 0x9c0906a9UL, 0xeb0e363fUL, 0x72076785UL, 0x05005713UL,
- 0x95bf4a82UL, 0xe2b87a14UL, 0x7bb12baeUL, 0x0cb61b38UL, 0x92d28e9bUL,
- 0xe5d5be0dUL, 0x7cdcefb7UL, 0x0bdbdf21UL, 0x86d3d2d4UL, 0xf1d4e242UL,
- 0x68ddb3f8UL, 0x1fda836eUL, 0x81be16cdUL, 0xf6b9265bUL, 0x6fb077e1UL,
- 0x18b74777UL, 0x88085ae6UL, 0xff0f6a70UL, 0x66063bcaUL, 0x11010b5cUL,
- 0x8f659effUL, 0xf862ae69UL, 0x616bffd3UL, 0x166ccf45UL, 0xa00ae278UL,
- 0xd70dd2eeUL, 0x4e048354UL, 0x3903b3c2UL, 0xa7672661UL, 0xd06016f7UL,
- 0x4969474dUL, 0x3e6e77dbUL, 0xaed16a4aUL, 0xd9d65adcUL, 0x40df0b66UL,
- 0x37d83bf0UL, 0xa9bcae53UL, 0xdebb9ec5UL, 0x47b2cf7fUL, 0x30b5ffe9UL,
- 0xbdbdf21cUL, 0xcabac28aUL, 0x53b39330UL, 0x24b4a3a6UL, 0xbad03605UL,
- 0xcdd70693UL, 0x54de5729UL, 0x23d967bfUL, 0xb3667a2eUL, 0xc4614ab8UL,
- 0x5d681b02UL, 0x2a6f2b94UL, 0xb40bbe37UL, 0xc30c8ea1UL, 0x5a05df1bUL,
- 0x2d02ef8dUL
-#ifdef BYFOUR
- },
- {
- 0x00000000UL, 0x191b3141UL, 0x32366282UL, 0x2b2d53c3UL, 0x646cc504UL,
- 0x7d77f445UL, 0x565aa786UL, 0x4f4196c7UL, 0xc8d98a08UL, 0xd1c2bb49UL,
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- 0xcdd91092UL, 0xa8beac2aUL, 0x46111938UL, 0x2376a580UL, 0x7566c6d8UL,
- 0x10017a60UL, 0xfeaecf72UL, 0x9bc973caUL, 0x22f1a457UL, 0x479618efUL,
- 0xa939adfdUL, 0xcc5e1145UL, 0x06ee4d76UL, 0x6389f1ceUL, 0x8d2644dcUL,
- 0xe841f864UL, 0x51792ff9UL, 0x341e9341UL, 0xdab12653UL, 0xbfd69aebUL,
- 0xe9c6f9b3UL, 0x8ca1450bUL, 0x620ef019UL, 0x07694ca1UL, 0xbe519b3cUL,
- 0xdb362784UL, 0x35999296UL, 0x50fe2e2eUL, 0x99b95426UL, 0xfcdee89eUL,
- 0x12715d8cUL, 0x7716e134UL, 0xce2e36a9UL, 0xab498a11UL, 0x45e63f03UL,
- 0x208183bbUL, 0x7691e0e3UL, 0x13f65c5bUL, 0xfd59e949UL, 0x983e55f1UL,
- 0x2106826cUL, 0x44613ed4UL, 0xaace8bc6UL, 0xcfa9377eUL, 0x38417fd6UL,
- 0x5d26c36eUL, 0xb389767cUL, 0xd6eecac4UL, 0x6fd61d59UL, 0x0ab1a1e1UL,
- 0xe41e14f3UL, 0x8179a84bUL, 0xd769cb13UL, 0xb20e77abUL, 0x5ca1c2b9UL,
- 0x39c67e01UL, 0x80fea99cUL, 0xe5991524UL, 0x0b36a036UL, 0x6e511c8eUL,
- 0xa7166686UL, 0xc271da3eUL, 0x2cde6f2cUL, 0x49b9d394UL, 0xf0810409UL,
- 0x95e6b8b1UL, 0x7b490da3UL, 0x1e2eb11bUL, 0x483ed243UL, 0x2d596efbUL,
- 0xc3f6dbe9UL, 0xa6916751UL, 0x1fa9b0ccUL, 0x7ace0c74UL, 0x9461b966UL,
- 0xf10605deUL
-#endif
- }
-};
diff --git a/third-party/zlib/deflate.c b/third-party/zlib/deflate.c
deleted file mode 100644
index 6969577..0000000
--- a/third-party/zlib/deflate.c
+++ /dev/null
@@ -1,1967 +0,0 @@
-/* deflate.c -- compress data using the deflation algorithm
- * Copyright (C) 1995-2013 Jean-loup Gailly and Mark Adler
- * For conditions of distribution and use, see copyright notice in zlib.h
- */
-
-/*
- * ALGORITHM
- *
- * The "deflation" process depends on being able to identify portions
- * of the input text which are identical to earlier input (within a
- * sliding window trailing behind the input currently being processed).
- *
- * The most straightforward technique turns out to be the fastest for
- * most input files: try all possible matches and select the longest.
- * The key feature of this algorithm is that insertions into the string
- * dictionary are very simple and thus fast, and deletions are avoided
- * completely. Insertions are performed at each input character, whereas
- * string matches are performed only when the previous match ends. So it
- * is preferable to spend more time in matches to allow very fast string
- * insertions and avoid deletions. The matching algorithm for small
- * strings is inspired from that of Rabin & Karp. A brute force approach
- * is used to find longer strings when a small match has been found.
- * A similar algorithm is used in comic (by Jan-Mark Wams) and freeze
- * (by Leonid Broukhis).
- * A previous version of this file used a more sophisticated algorithm
- * (by Fiala and Greene) which is guaranteed to run in linear amortized
- * time, but has a larger average cost, uses more memory and is patented.
- * However the F&G algorithm may be faster for some highly redundant
- * files if the parameter max_chain_length (described below) is too large.
- *
- * ACKNOWLEDGEMENTS
- *
- * The idea of lazy evaluation of matches is due to Jan-Mark Wams, and
- * I found it in 'freeze' written by Leonid Broukhis.
- * Thanks to many people for bug reports and testing.
- *
- * REFERENCES
- *
- * Deutsch, L.P.,"DEFLATE Compressed Data Format Specification".
- * Available in http://tools.ietf.org/html/rfc1951
- *
- * A description of the Rabin and Karp algorithm is given in the book
- * "Algorithms" by R. Sedgewick, Addison-Wesley, p252.
- *
- * Fiala,E.R., and Greene,D.H.
- * Data Compression with Finite Windows, Comm.ACM, 32,4 (1989) 490-595
- *
- */
-
-/* @(#) $Id$ */
-
-#include "deflate.h"
-
-const char deflate_copyright[] =
- " deflate 1.2.8 Copyright 1995-2013 Jean-loup Gailly and Mark Adler ";
-/*
- If you use the zlib library in a product, an acknowledgment is welcome
- in the documentation of your product. If for some reason you cannot
- include such an acknowledgment, I would appreciate that you keep this
- copyright string in the executable of your product.
- */
-
-/* ===========================================================================
- * Function prototypes.
- */
-typedef enum {
- need_more, /* block not completed, need more input or more output */
- block_done, /* block flush performed */
- finish_started, /* finish started, need only more output at next deflate */
- finish_done /* finish done, accept no more input or output */
-} block_state;
-
-typedef block_state (*compress_func) OF((deflate_state *s, int flush));
-/* Compression function. Returns the block state after the call. */
-
-local void fill_window OF((deflate_state *s));
-local block_state deflate_stored OF((deflate_state *s, int flush));
-local block_state deflate_fast OF((deflate_state *s, int flush));
-#ifndef FASTEST
-local block_state deflate_slow OF((deflate_state *s, int flush));
-#endif
-local block_state deflate_rle OF((deflate_state *s, int flush));
-local block_state deflate_huff OF((deflate_state *s, int flush));
-local void lm_init OF((deflate_state *s));
-local void putShortMSB OF((deflate_state *s, uInt b));
-local void flush_pending OF((z_streamp strm));
-local int read_buf OF((z_streamp strm, Bytef *buf, unsigned size));
-#ifdef ASMV
- void match_init OF((void)); /* asm code initialization */
- uInt longest_match OF((deflate_state *s, IPos cur_match));
-#else
-local uInt longest_match OF((deflate_state *s, IPos cur_match));
-#endif
-
-#ifdef DEBUG
-local void check_match OF((deflate_state *s, IPos start, IPos match,
- int length));
-#endif
-
-/* ===========================================================================
- * Local data
- */
-
-#define NIL 0
-/* Tail of hash chains */
-
-#ifndef TOO_FAR
-# define TOO_FAR 4096
-#endif
-/* Matches of length 3 are discarded if their distance exceeds TOO_FAR */
-
-/* Values for max_lazy_match, good_match and max_chain_length, depending on
- * the desired pack level (0..9). The values given below have been tuned to
- * exclude worst case performance for pathological files. Better values may be
- * found for specific files.
- */
-typedef struct config_s {
- ush good_length; /* reduce lazy search above this match length */
- ush max_lazy; /* do not perform lazy search above this match length */
- ush nice_length; /* quit search above this match length */
- ush max_chain;
- compress_func func;
-} config;
-
-#ifdef FASTEST
-local const config configuration_table[2] = {
-/* good lazy nice chain */
-/* 0 */ {0, 0, 0, 0, deflate_stored}, /* store only */
-/* 1 */ {4, 4, 8, 4, deflate_fast}}; /* max speed, no lazy matches */
-#else
-local const config configuration_table[10] = {
-/* good lazy nice chain */
-/* 0 */ {0, 0, 0, 0, deflate_stored}, /* store only */
-/* 1 */ {4, 4, 8, 4, deflate_fast}, /* max speed, no lazy matches */
-/* 2 */ {4, 5, 16, 8, deflate_fast},
-/* 3 */ {4, 6, 32, 32, deflate_fast},
-
-/* 4 */ {4, 4, 16, 16, deflate_slow}, /* lazy matches */
-/* 5 */ {8, 16, 32, 32, deflate_slow},
-/* 6 */ {8, 16, 128, 128, deflate_slow},
-/* 7 */ {8, 32, 128, 256, deflate_slow},
-/* 8 */ {32, 128, 258, 1024, deflate_slow},
-/* 9 */ {32, 258, 258, 4096, deflate_slow}}; /* max compression */
-#endif
-
-/* Note: the deflate() code requires max_lazy >= MIN_MATCH and max_chain >= 4
- * For deflate_fast() (levels <= 3) good is ignored and lazy has a different
- * meaning.
- */
-
-#define EQUAL 0
-/* result of memcmp for equal strings */
-
-#ifndef NO_DUMMY_DECL
-struct static_tree_desc_s {int dummy;}; /* for buggy compilers */
-#endif
-
-/* rank Z_BLOCK between Z_NO_FLUSH and Z_PARTIAL_FLUSH */
-#define RANK(f) (((f) << 1) - ((f) > 4 ? 9 : 0))
-
-/* ===========================================================================
- * Update a hash value with the given input byte
- * IN assertion: all calls to to UPDATE_HASH are made with consecutive
- * input characters, so that a running hash key can be computed from the
- * previous key instead of complete recalculation each time.
- */
-#define UPDATE_HASH(s,h,c) (h = (((h)<<s->hash_shift) ^ (c)) & s->hash_mask)
-
-
-/* ===========================================================================
- * Insert string str in the dictionary and set match_head to the previous head
- * of the hash chain (the most recent string with same hash key). Return
- * the previous length of the hash chain.
- * If this file is compiled with -DFASTEST, the compression level is forced
- * to 1, and no hash chains are maintained.
- * IN assertion: all calls to to INSERT_STRING are made with consecutive
- * input characters and the first MIN_MATCH bytes of str are valid
- * (except for the last MIN_MATCH-1 bytes of the input file).
- */
-#ifdef FASTEST
-#define INSERT_STRING(s, str, match_head) \
- (UPDATE_HASH(s, s->ins_h, s->window[(str) + (MIN_MATCH-1)]), \
- match_head = s->head[s->ins_h], \
- s->head[s->ins_h] = (Pos)(str))
-#else
-#define INSERT_STRING(s, str, match_head) \
- (UPDATE_HASH(s, s->ins_h, s->window[(str) + (MIN_MATCH-1)]), \
- match_head = s->prev[(str) & s->w_mask] = s->head[s->ins_h], \
- s->head[s->ins_h] = (Pos)(str))
-#endif
-
-/* ===========================================================================
- * Initialize the hash table (avoiding 64K overflow for 16 bit systems).
- * prev[] will be initialized on the fly.
- */
-#define CLEAR_HASH(s) \
- s->head[s->hash_size-1] = NIL; \
- zmemzero((Bytef *)s->head, (unsigned)(s->hash_size-1)*sizeof(*s->head));
-
-/* ========================================================================= */
-int ZEXPORT deflateInit_(strm, level, version, stream_size)
- z_streamp strm;
- int level;
- const char *version;
- int stream_size;
-{
- return deflateInit2_(strm, level, Z_DEFLATED, MAX_WBITS, DEF_MEM_LEVEL,
- Z_DEFAULT_STRATEGY, version, stream_size);
- /* To do: ignore strm->next_in if we use it as window */
-}
-
-/* ========================================================================= */
-int ZEXPORT deflateInit2_(strm, level, method, windowBits, memLevel, strategy,
- version, stream_size)
- z_streamp strm;
- int level;
- int method;
- int windowBits;
- int memLevel;
- int strategy;
- const char *version;
- int stream_size;
-{
- deflate_state *s;
- int wrap = 1;
- static const char my_version[] = ZLIB_VERSION;
-
- ushf *overlay;
- /* We overlay pending_buf and d_buf+l_buf. This works since the average
- * output size for (length,distance) codes is <= 24 bits.
- */
-
- if (version == Z_NULL || version[0] != my_version[0] ||
- stream_size != sizeof(z_stream)) {
- return Z_VERSION_ERROR;
- }
- if (strm == Z_NULL) return Z_STREAM_ERROR;
-
- strm->msg = Z_NULL;
- if (strm->zalloc == (alloc_func)0) {
-#ifdef Z_SOLO
- return Z_STREAM_ERROR;
-#else
- strm->zalloc = zcalloc;
- strm->opaque = (voidpf)0;
-#endif
- }
- if (strm->zfree == (free_func)0)
-#ifdef Z_SOLO
- return Z_STREAM_ERROR;
-#else
- strm->zfree = zcfree;
-#endif
-
-#ifdef FASTEST
- if (level != 0) level = 1;
-#else
- if (level == Z_DEFAULT_COMPRESSION) level = 6;
-#endif
-
- if (windowBits < 0) { /* suppress zlib wrapper */
- wrap = 0;
- windowBits = -windowBits;
- }
-#ifdef GZIP
- else if (windowBits > 15) {
- wrap = 2; /* write gzip wrapper instead */
- windowBits -= 16;
- }
-#endif
- if (memLevel < 1 || memLevel > MAX_MEM_LEVEL || method != Z_DEFLATED ||
- windowBits < 8 || windowBits > 15 || level < 0 || level > 9 ||
- strategy < 0 || strategy > Z_FIXED) {
- return Z_STREAM_ERROR;
- }
- if (windowBits == 8) windowBits = 9; /* until 256-byte window bug fixed */
- s = (deflate_state *) ZALLOC(strm, 1, sizeof(deflate_state));
- if (s == Z_NULL) return Z_MEM_ERROR;
- strm->state = (struct internal_state FAR *)s;
- s->strm = strm;
-
- s->wrap = wrap;
- s->gzhead = Z_NULL;
- s->w_bits = windowBits;
- s->w_size = 1 << s->w_bits;
- s->w_mask = s->w_size - 1;
-
- s->hash_bits = memLevel + 7;
- s->hash_size = 1 << s->hash_bits;
- s->hash_mask = s->hash_size - 1;
- s->hash_shift = ((s->hash_bits+MIN_MATCH-1)/MIN_MATCH);
-
- s->window = (Bytef *) ZALLOC(strm, s->w_size, 2*sizeof(Byte));
- s->prev = (Posf *) ZALLOC(strm, s->w_size, sizeof(Pos));
- s->head = (Posf *) ZALLOC(strm, s->hash_size, sizeof(Pos));
-
- s->high_water = 0; /* nothing written to s->window yet */
-
- s->lit_bufsize = 1 << (memLevel + 6); /* 16K elements by default */
-
- overlay = (ushf *) ZALLOC(strm, s->lit_bufsize, sizeof(ush)+2);
- s->pending_buf = (uchf *) overlay;
- s->pending_buf_size = (ulg)s->lit_bufsize * (sizeof(ush)+2L);
-
- if (s->window == Z_NULL || s->prev == Z_NULL || s->head == Z_NULL ||
- s->pending_buf == Z_NULL) {
- s->status = FINISH_STATE;
- strm->msg = ERR_MSG(Z_MEM_ERROR);
- deflateEnd (strm);
- return Z_MEM_ERROR;
- }
- s->d_buf = overlay + s->lit_bufsize/sizeof(ush);
- s->l_buf = s->pending_buf + (1+sizeof(ush))*s->lit_bufsize;
-
- s->level = level;
- s->strategy = strategy;
- s->method = (Byte)method;
-
- return deflateReset(strm);
-}
-
-/* ========================================================================= */
-int ZEXPORT deflateSetDictionary (strm, dictionary, dictLength)
- z_streamp strm;
- const Bytef *dictionary;
- uInt dictLength;
-{
- deflate_state *s;
- uInt str, n;
- int wrap;
- unsigned avail;
- z_const unsigned char *next;
-
- if (strm == Z_NULL || strm->state == Z_NULL || dictionary == Z_NULL)
- return Z_STREAM_ERROR;
- s = strm->state;
- wrap = s->wrap;
- if (wrap == 2 || (wrap == 1 && s->status != INIT_STATE) || s->lookahead)
- return Z_STREAM_ERROR;
-
- /* when using zlib wrappers, compute Adler-32 for provided dictionary */
- if (wrap == 1)
- strm->adler = adler32(strm->adler, dictionary, dictLength);
- s->wrap = 0; /* avoid computing Adler-32 in read_buf */
-
- /* if dictionary would fill window, just replace the history */
- if (dictLength >= s->w_size) {
- if (wrap == 0) { /* already empty otherwise */
- CLEAR_HASH(s);
- s->strstart = 0;
- s->block_start = 0L;
- s->insert = 0;
- }
- dictionary += dictLength - s->w_size; /* use the tail */
- dictLength = s->w_size;
- }
-
- /* insert dictionary into window and hash */
- avail = strm->avail_in;
- next = strm->next_in;
- strm->avail_in = dictLength;
- strm->next_in = (z_const Bytef *)dictionary;
- fill_window(s);
- while (s->lookahead >= MIN_MATCH) {
- str = s->strstart;
- n = s->lookahead - (MIN_MATCH-1);
- do {
- UPDATE_HASH(s, s->ins_h, s->window[str + MIN_MATCH-1]);
-#ifndef FASTEST
- s->prev[str & s->w_mask] = s->head[s->ins_h];
-#endif
- s->head[s->ins_h] = (Pos)str;
- str++;
- } while (--n);
- s->strstart = str;
- s->lookahead = MIN_MATCH-1;
- fill_window(s);
- }
- s->strstart += s->lookahead;
- s->block_start = (long)s->strstart;
- s->insert = s->lookahead;
- s->lookahead = 0;
- s->match_length = s->prev_length = MIN_MATCH-1;
- s->match_available = 0;
- strm->next_in = next;
- strm->avail_in = avail;
- s->wrap = wrap;
- return Z_OK;
-}
-
-/* ========================================================================= */
-int ZEXPORT deflateResetKeep (strm)
- z_streamp strm;
-{
- deflate_state *s;
-
- if (strm == Z_NULL || strm->state == Z_NULL ||
- strm->zalloc == (alloc_func)0 || strm->zfree == (free_func)0) {
- return Z_STREAM_ERROR;
- }
-
- strm->total_in = strm->total_out = 0;
- strm->msg = Z_NULL; /* use zfree if we ever allocate msg dynamically */
- strm->data_type = Z_UNKNOWN;
-
- s = (deflate_state *)strm->state;
- s->pending = 0;
- s->pending_out = s->pending_buf;
-
- if (s->wrap < 0) {
- s->wrap = -s->wrap; /* was made negative by deflate(..., Z_FINISH); */
- }
- s->status = s->wrap ? INIT_STATE : BUSY_STATE;
- strm->adler =
-#ifdef GZIP
- s->wrap == 2 ? crc32(0L, Z_NULL, 0) :
-#endif
- adler32(0L, Z_NULL, 0);
- s->last_flush = Z_NO_FLUSH;
-
- _tr_init(s);
-
- return Z_OK;
-}
-
-/* ========================================================================= */
-int ZEXPORT deflateReset (strm)
- z_streamp strm;
-{
- int ret;
-
- ret = deflateResetKeep(strm);
- if (ret == Z_OK)
- lm_init(strm->state);
- return ret;
-}
-
-/* ========================================================================= */
-int ZEXPORT deflateSetHeader (strm, head)
- z_streamp strm;
- gz_headerp head;
-{
- if (strm == Z_NULL || strm->state == Z_NULL) return Z_STREAM_ERROR;
- if (strm->state->wrap != 2) return Z_STREAM_ERROR;
- strm->state->gzhead = head;
- return Z_OK;
-}
-
-/* ========================================================================= */
-int ZEXPORT deflatePending (strm, pending, bits)
- unsigned *pending;
- int *bits;
- z_streamp strm;
-{
- if (strm == Z_NULL || strm->state == Z_NULL) return Z_STREAM_ERROR;
- if (pending != Z_NULL)
- *pending = strm->state->pending;
- if (bits != Z_NULL)
- *bits = strm->state->bi_valid;
- return Z_OK;
-}
-
-/* ========================================================================= */
-int ZEXPORT deflatePrime (strm, bits, value)
- z_streamp strm;
- int bits;
- int value;
-{
- deflate_state *s;
- int put;
-
- if (strm == Z_NULL || strm->state == Z_NULL) return Z_STREAM_ERROR;
- s = strm->state;
- if ((Bytef *)(s->d_buf) < s->pending_out + ((Buf_size + 7) >> 3))
- return Z_BUF_ERROR;
- do {
- put = Buf_size - s->bi_valid;
- if (put > bits)
- put = bits;
- s->bi_buf |= (ush)((value & ((1 << put) - 1)) << s->bi_valid);
- s->bi_valid += put;
- _tr_flush_bits(s);
- value >>= put;
- bits -= put;
- } while (bits);
- return Z_OK;
-}
-
-/* ========================================================================= */
-int ZEXPORT deflateParams(strm, level, strategy)
- z_streamp strm;
- int level;
- int strategy;
-{
- deflate_state *s;
- compress_func func;
- int err = Z_OK;
-
- if (strm == Z_NULL || strm->state == Z_NULL) return Z_STREAM_ERROR;
- s = strm->state;
-
-#ifdef FASTEST
- if (level != 0) level = 1;
-#else
- if (level == Z_DEFAULT_COMPRESSION) level = 6;
-#endif
- if (level < 0 || level > 9 || strategy < 0 || strategy > Z_FIXED) {
- return Z_STREAM_ERROR;
- }
- func = configuration_table[s->level].func;
-
- if ((strategy != s->strategy || func != configuration_table[level].func) &&
- strm->total_in != 0) {
- /* Flush the last buffer: */
- err = deflate(strm, Z_BLOCK);
- if (err == Z_BUF_ERROR && s->pending == 0)
- err = Z_OK;
- }
- if (s->level != level) {
- s->level = level;
- s->max_lazy_match = configuration_table[level].max_lazy;
- s->good_match = configuration_table[level].good_length;
- s->nice_match = configuration_table[level].nice_length;
- s->max_chain_length = configuration_table[level].max_chain;
- }
- s->strategy = strategy;
- return err;
-}
-
-/* ========================================================================= */
-int ZEXPORT deflateTune(strm, good_length, max_lazy, nice_length, max_chain)
- z_streamp strm;
- int good_length;
- int max_lazy;
- int nice_length;
- int max_chain;
-{
- deflate_state *s;
-
- if (strm == Z_NULL || strm->state == Z_NULL) return Z_STREAM_ERROR;
- s = strm->state;
- s->good_match = good_length;
- s->max_lazy_match = max_lazy;
- s->nice_match = nice_length;
- s->max_chain_length = max_chain;
- return Z_OK;
-}
-
-/* =========================================================================
- * For the default windowBits of 15 and memLevel of 8, this function returns
- * a close to exact, as well as small, upper bound on the compressed size.
- * They are coded as constants here for a reason--if the #define's are
- * changed, then this function needs to be changed as well. The return
- * value for 15 and 8 only works for those exact settings.
- *
- * For any setting other than those defaults for windowBits and memLevel,
- * the value returned is a conservative worst case for the maximum expansion
- * resulting from using fixed blocks instead of stored blocks, which deflate
- * can emit on compressed data for some combinations of the parameters.
- *
- * This function could be more sophisticated to provide closer upper bounds for
- * every combination of windowBits and memLevel. But even the conservative
- * upper bound of about 14% expansion does not seem onerous for output buffer
- * allocation.
- */
-uLong ZEXPORT deflateBound(strm, sourceLen)
- z_streamp strm;
- uLong sourceLen;
-{
- deflate_state *s;
- uLong complen, wraplen;
- Bytef *str;
-
- /* conservative upper bound for compressed data */
- complen = sourceLen +
- ((sourceLen + 7) >> 3) + ((sourceLen + 63) >> 6) + 5;
-
- /* if can't get parameters, return conservative bound plus zlib wrapper */
- if (strm == Z_NULL || strm->state == Z_NULL)
- return complen + 6;
-
- /* compute wrapper length */
- s = strm->state;
- switch (s->wrap) {
- case 0: /* raw deflate */
- wraplen = 0;
- break;
- case 1: /* zlib wrapper */
- wraplen = 6 + (s->strstart ? 4 : 0);
- break;
- case 2: /* gzip wrapper */
- wraplen = 18;
- if (s->gzhead != Z_NULL) { /* user-supplied gzip header */
- if (s->gzhead->extra != Z_NULL)
- wraplen += 2 + s->gzhead->extra_len;
- str = s->gzhead->name;
- if (str != Z_NULL)
- do {
- wraplen++;
- } while (*str++);
- str = s->gzhead->comment;
- if (str != Z_NULL)
- do {
- wraplen++;
- } while (*str++);
- if (s->gzhead->hcrc)
- wraplen += 2;
- }
- break;
- default: /* for compiler happiness */
- wraplen = 6;
- }
-
- /* if not default parameters, return conservative bound */
- if (s->w_bits != 15 || s->hash_bits != 8 + 7)
- return complen + wraplen;
-
- /* default settings: return tight bound for that case */
- return sourceLen + (sourceLen >> 12) + (sourceLen >> 14) +
- (sourceLen >> 25) + 13 - 6 + wraplen;
-}
-
-/* =========================================================================
- * Put a short in the pending buffer. The 16-bit value is put in MSB order.
- * IN assertion: the stream state is correct and there is enough room in
- * pending_buf.
- */
-local void putShortMSB (s, b)
- deflate_state *s;
- uInt b;
-{
- put_byte(s, (Byte)(b >> 8));
- put_byte(s, (Byte)(b & 0xff));
-}
-
-/* =========================================================================
- * Flush as much pending output as possible. All deflate() output goes
- * through this function so some applications may wish to modify it
- * to avoid allocating a large strm->next_out buffer and copying into it.
- * (See also read_buf()).
- */
-local void flush_pending(strm)
- z_streamp strm;
-{
- unsigned len;
- deflate_state *s = strm->state;
-
- _tr_flush_bits(s);
- len = s->pending;
- if (len > strm->avail_out) len = strm->avail_out;
- if (len == 0) return;
-
- zmemcpy(strm->next_out, s->pending_out, len);
- strm->next_out += len;
- s->pending_out += len;
- strm->total_out += len;
- strm->avail_out -= len;
- s->pending -= len;
- if (s->pending == 0) {
- s->pending_out = s->pending_buf;
- }
-}
-
-/* ========================================================================= */
-int ZEXPORT deflate (strm, flush)
- z_streamp strm;
- int flush;
-{
- int old_flush; /* value of flush param for previous deflate call */
- deflate_state *s;
-
- if (strm == Z_NULL || strm->state == Z_NULL ||
- flush > Z_BLOCK || flush < 0) {
- return Z_STREAM_ERROR;
- }
- s = strm->state;
-
- if (strm->next_out == Z_NULL ||
- (strm->next_in == Z_NULL && strm->avail_in != 0) ||
- (s->status == FINISH_STATE && flush != Z_FINISH)) {
- ERR_RETURN(strm, Z_STREAM_ERROR);
- }
- if (strm->avail_out == 0) ERR_RETURN(strm, Z_BUF_ERROR);
-
- s->strm = strm; /* just in case */
- old_flush = s->last_flush;
- s->last_flush = flush;
-
- /* Write the header */
- if (s->status == INIT_STATE) {
-#ifdef GZIP
- if (s->wrap == 2) {
- strm->adler = crc32(0L, Z_NULL, 0);
- put_byte(s, 31);
- put_byte(s, 139);
- put_byte(s, 8);
- if (s->gzhead == Z_NULL) {
- put_byte(s, 0);
- put_byte(s, 0);
- put_byte(s, 0);
- put_byte(s, 0);
- put_byte(s, 0);
- put_byte(s, s->level == 9 ? 2 :
- (s->strategy >= Z_HUFFMAN_ONLY || s->level < 2 ?
- 4 : 0));
- put_byte(s, OS_CODE);
- s->status = BUSY_STATE;
- }
- else {
- put_byte(s, (s->gzhead->text ? 1 : 0) +
- (s->gzhead->hcrc ? 2 : 0) +
- (s->gzhead->extra == Z_NULL ? 0 : 4) +
- (s->gzhead->name == Z_NULL ? 0 : 8) +
- (s->gzhead->comment == Z_NULL ? 0 : 16)
- );
- put_byte(s, (Byte)(s->gzhead->time & 0xff));
- put_byte(s, (Byte)((s->gzhead->time >> 8) & 0xff));
- put_byte(s, (Byte)((s->gzhead->time >> 16) & 0xff));
- put_byte(s, (Byte)((s->gzhead->time >> 24) & 0xff));
- put_byte(s, s->level == 9 ? 2 :
- (s->strategy >= Z_HUFFMAN_ONLY || s->level < 2 ?
- 4 : 0));
- put_byte(s, s->gzhead->os & 0xff);
- if (s->gzhead->extra != Z_NULL) {
- put_byte(s, s->gzhead->extra_len & 0xff);
- put_byte(s, (s->gzhead->extra_len >> 8) & 0xff);
- }
- if (s->gzhead->hcrc)
- strm->adler = crc32(strm->adler, s->pending_buf,
- s->pending);
- s->gzindex = 0;
- s->status = EXTRA_STATE;
- }
- }
- else
-#endif
- {
- uInt header = (Z_DEFLATED + ((s->w_bits-8)<<4)) << 8;
- uInt level_flags;
-
- if (s->strategy >= Z_HUFFMAN_ONLY || s->level < 2)
- level_flags = 0;
- else if (s->level < 6)
- level_flags = 1;
- else if (s->level == 6)
- level_flags = 2;
- else
- level_flags = 3;
- header |= (level_flags << 6);
- if (s->strstart != 0) header |= PRESET_DICT;
- header += 31 - (header % 31);
-
- s->status = BUSY_STATE;
- putShortMSB(s, header);
-
- /* Save the adler32 of the preset dictionary: */
- if (s->strstart != 0) {
- putShortMSB(s, (uInt)(strm->adler >> 16));
- putShortMSB(s, (uInt)(strm->adler & 0xffff));
- }
- strm->adler = adler32(0L, Z_NULL, 0);
- }
- }
-#ifdef GZIP
- if (s->status == EXTRA_STATE) {
- if (s->gzhead->extra != Z_NULL) {
- uInt beg = s->pending; /* start of bytes to update crc */
-
- while (s->gzindex < (s->gzhead->extra_len & 0xffff)) {
- if (s->pending == s->pending_buf_size) {
- if (s->gzhead->hcrc && s->pending > beg)
- strm->adler = crc32(strm->adler, s->pending_buf + beg,
- s->pending - beg);
- flush_pending(strm);
- beg = s->pending;
- if (s->pending == s->pending_buf_size)
- break;
- }
- put_byte(s, s->gzhead->extra[s->gzindex]);
- s->gzindex++;
- }
- if (s->gzhead->hcrc && s->pending > beg)
- strm->adler = crc32(strm->adler, s->pending_buf + beg,
- s->pending - beg);
- if (s->gzindex == s->gzhead->extra_len) {
- s->gzindex = 0;
- s->status = NAME_STATE;
- }
- }
- else
- s->status = NAME_STATE;
- }
- if (s->status == NAME_STATE) {
- if (s->gzhead->name != Z_NULL) {
- uInt beg = s->pending; /* start of bytes to update crc */
- int val;
-
- do {
- if (s->pending == s->pending_buf_size) {
- if (s->gzhead->hcrc && s->pending > beg)
- strm->adler = crc32(strm->adler, s->pending_buf + beg,
- s->pending - beg);
- flush_pending(strm);
- beg = s->pending;
- if (s->pending == s->pending_buf_size) {
- val = 1;
- break;
- }
- }
- val = s->gzhead->name[s->gzindex++];
- put_byte(s, val);
- } while (val != 0);
- if (s->gzhead->hcrc && s->pending > beg)
- strm->adler = crc32(strm->adler, s->pending_buf + beg,
- s->pending - beg);
- if (val == 0) {
- s->gzindex = 0;
- s->status = COMMENT_STATE;
- }
- }
- else
- s->status = COMMENT_STATE;
- }
- if (s->status == COMMENT_STATE) {
- if (s->gzhead->comment != Z_NULL) {
- uInt beg = s->pending; /* start of bytes to update crc */
- int val;
-
- do {
- if (s->pending == s->pending_buf_size) {
- if (s->gzhead->hcrc && s->pending > beg)
- strm->adler = crc32(strm->adler, s->pending_buf + beg,
- s->pending - beg);
- flush_pending(strm);
- beg = s->pending;
- if (s->pending == s->pending_buf_size) {
- val = 1;
- break;
- }
- }
- val = s->gzhead->comment[s->gzindex++];
- put_byte(s, val);
- } while (val != 0);
- if (s->gzhead->hcrc && s->pending > beg)
- strm->adler = crc32(strm->adler, s->pending_buf + beg,
- s->pending - beg);
- if (val == 0)
- s->status = HCRC_STATE;
- }
- else
- s->status = HCRC_STATE;
- }
- if (s->status == HCRC_STATE) {
- if (s->gzhead->hcrc) {
- if (s->pending + 2 > s->pending_buf_size)
- flush_pending(strm);
- if (s->pending + 2 <= s->pending_buf_size) {
- put_byte(s, (Byte)(strm->adler & 0xff));
- put_byte(s, (Byte)((strm->adler >> 8) & 0xff));
- strm->adler = crc32(0L, Z_NULL, 0);
- s->status = BUSY_STATE;
- }
- }
- else
- s->status = BUSY_STATE;
- }
-#endif
-
- /* Flush as much pending output as possible */
- if (s->pending != 0) {
- flush_pending(strm);
- if (strm->avail_out == 0) {
- /* Since avail_out is 0, deflate will be called again with
- * more output space, but possibly with both pending and
- * avail_in equal to zero. There won't be anything to do,
- * but this is not an error situation so make sure we
- * return OK instead of BUF_ERROR at next call of deflate:
- */
- s->last_flush = -1;
- return Z_OK;
- }
-
- /* Make sure there is something to do and avoid duplicate consecutive
- * flushes. For repeated and useless calls with Z_FINISH, we keep
- * returning Z_STREAM_END instead of Z_BUF_ERROR.
- */
- } else if (strm->avail_in == 0 && RANK(flush) <= RANK(old_flush) &&
- flush != Z_FINISH) {
- ERR_RETURN(strm, Z_BUF_ERROR);
- }
-
- /* User must not provide more input after the first FINISH: */
- if (s->status == FINISH_STATE && strm->avail_in != 0) {
- ERR_RETURN(strm, Z_BUF_ERROR);
- }
-
- /* Start a new block or continue the current one.
- */
- if (strm->avail_in != 0 || s->lookahead != 0 ||
- (flush != Z_NO_FLUSH && s->status != FINISH_STATE)) {
- block_state bstate;
-
- bstate = s->strategy == Z_HUFFMAN_ONLY ? deflate_huff(s, flush) :
- (s->strategy == Z_RLE ? deflate_rle(s, flush) :
- (*(configuration_table[s->level].func))(s, flush));
-
- if (bstate == finish_started || bstate == finish_done) {
- s->status = FINISH_STATE;
- }
- if (bstate == need_more || bstate == finish_started) {
- if (strm->avail_out == 0) {
- s->last_flush = -1; /* avoid BUF_ERROR next call, see above */
- }
- return Z_OK;
- /* If flush != Z_NO_FLUSH && avail_out == 0, the next call
- * of deflate should use the same flush parameter to make sure
- * that the flush is complete. So we don't have to output an
- * empty block here, this will be done at next call. This also
- * ensures that for a very small output buffer, we emit at most
- * one empty block.
- */
- }
- if (bstate == block_done) {
- if (flush == Z_PARTIAL_FLUSH) {
- _tr_align(s);
- } else if (flush != Z_BLOCK) { /* FULL_FLUSH or SYNC_FLUSH */
- _tr_stored_block(s, (char*)0, 0L, 0);
- /* For a full flush, this empty block will be recognized
- * as a special marker by inflate_sync().
- */
- if (flush == Z_FULL_FLUSH) {
- CLEAR_HASH(s); /* forget history */
- if (s->lookahead == 0) {
- s->strstart = 0;
- s->block_start = 0L;
- s->insert = 0;
- }
- }
- }
- flush_pending(strm);
- if (strm->avail_out == 0) {
- s->last_flush = -1; /* avoid BUF_ERROR at next call, see above */
- return Z_OK;
- }
- }
- }
- Assert(strm->avail_out > 0, "bug2");
-
- if (flush != Z_FINISH) return Z_OK;
- if (s->wrap <= 0) return Z_STREAM_END;
-
- /* Write the trailer */
-#ifdef GZIP
- if (s->wrap == 2) {
- put_byte(s, (Byte)(strm->adler & 0xff));
- put_byte(s, (Byte)((strm->adler >> 8) & 0xff));
- put_byte(s, (Byte)((strm->adler >> 16) & 0xff));
- put_byte(s, (Byte)((strm->adler >> 24) & 0xff));
- put_byte(s, (Byte)(strm->total_in & 0xff));
- put_byte(s, (Byte)((strm->total_in >> 8) & 0xff));
- put_byte(s, (Byte)((strm->total_in >> 16) & 0xff));
- put_byte(s, (Byte)((strm->total_in >> 24) & 0xff));
- }
- else
-#endif
- {
- putShortMSB(s, (uInt)(strm->adler >> 16));
- putShortMSB(s, (uInt)(strm->adler & 0xffff));
- }
- flush_pending(strm);
- /* If avail_out is zero, the application will call deflate again
- * to flush the rest.
- */
- if (s->wrap > 0) s->wrap = -s->wrap; /* write the trailer only once! */
- return s->pending != 0 ? Z_OK : Z_STREAM_END;
-}
-
-/* ========================================================================= */
-int ZEXPORT deflateEnd (strm)
- z_streamp strm;
-{
- int status;
-
- if (strm == Z_NULL || strm->state == Z_NULL) return Z_STREAM_ERROR;
-
- status = strm->state->status;
- if (status != INIT_STATE &&
- status != EXTRA_STATE &&
- status != NAME_STATE &&
- status != COMMENT_STATE &&
- status != HCRC_STATE &&
- status != BUSY_STATE &&
- status != FINISH_STATE) {
- return Z_STREAM_ERROR;
- }
-
- /* Deallocate in reverse order of allocations: */
- TRY_FREE(strm, strm->state->pending_buf);
- TRY_FREE(strm, strm->state->head);
- TRY_FREE(strm, strm->state->prev);
- TRY_FREE(strm, strm->state->window);
-
- ZFREE(strm, strm->state);
- strm->state = Z_NULL;
-
- return status == BUSY_STATE ? Z_DATA_ERROR : Z_OK;
-}
-
-/* =========================================================================
- * Copy the source state to the destination state.
- * To simplify the source, this is not supported for 16-bit MSDOS (which
- * doesn't have enough memory anyway to duplicate compression states).
- */
-int ZEXPORT deflateCopy (dest, source)
- z_streamp dest;
- z_streamp source;
-{
-#ifdef MAXSEG_64K
- return Z_STREAM_ERROR;
-#else
- deflate_state *ds;
- deflate_state *ss;
- ushf *overlay;
-
-
- if (source == Z_NULL || dest == Z_NULL || source->state == Z_NULL) {
- return Z_STREAM_ERROR;
- }
-
- ss = source->state;
-
- zmemcpy((voidpf)dest, (voidpf)source, sizeof(z_stream));
-
- ds = (deflate_state *) ZALLOC(dest, 1, sizeof(deflate_state));
- if (ds == Z_NULL) return Z_MEM_ERROR;
- dest->state = (struct internal_state FAR *) ds;
- zmemcpy((voidpf)ds, (voidpf)ss, sizeof(deflate_state));
- ds->strm = dest;
-
- ds->window = (Bytef *) ZALLOC(dest, ds->w_size, 2*sizeof(Byte));
- ds->prev = (Posf *) ZALLOC(dest, ds->w_size, sizeof(Pos));
- ds->head = (Posf *) ZALLOC(dest, ds->hash_size, sizeof(Pos));
- overlay = (ushf *) ZALLOC(dest, ds->lit_bufsize, sizeof(ush)+2);
- ds->pending_buf = (uchf *) overlay;
-
- if (ds->window == Z_NULL || ds->prev == Z_NULL || ds->head == Z_NULL ||
- ds->pending_buf == Z_NULL) {
- deflateEnd (dest);
- return Z_MEM_ERROR;
- }
- /* following zmemcpy do not work for 16-bit MSDOS */
- zmemcpy(ds->window, ss->window, ds->w_size * 2 * sizeof(Byte));
- zmemcpy((voidpf)ds->prev, (voidpf)ss->prev, ds->w_size * sizeof(Pos));
- zmemcpy((voidpf)ds->head, (voidpf)ss->head, ds->hash_size * sizeof(Pos));
- zmemcpy(ds->pending_buf, ss->pending_buf, (uInt)ds->pending_buf_size);
-
- ds->pending_out = ds->pending_buf + (ss->pending_out - ss->pending_buf);
- ds->d_buf = overlay + ds->lit_bufsize/sizeof(ush);
- ds->l_buf = ds->pending_buf + (1+sizeof(ush))*ds->lit_bufsize;
-
- ds->l_desc.dyn_tree = ds->dyn_ltree;
- ds->d_desc.dyn_tree = ds->dyn_dtree;
- ds->bl_desc.dyn_tree = ds->bl_tree;
-
- return Z_OK;
-#endif /* MAXSEG_64K */
-}
-
-/* ===========================================================================
- * Read a new buffer from the current input stream, update the adler32
- * and total number of bytes read. All deflate() input goes through
- * this function so some applications may wish to modify it to avoid
- * allocating a large strm->next_in buffer and copying from it.
- * (See also flush_pending()).
- */
-local int read_buf(strm, buf, size)
- z_streamp strm;
- Bytef *buf;
- unsigned size;
-{
- unsigned len = strm->avail_in;
-
- if (len > size) len = size;
- if (len == 0) return 0;
-
- strm->avail_in -= len;
-
- zmemcpy(buf, strm->next_in, len);
- if (strm->state->wrap == 1) {
- strm->adler = adler32(strm->adler, buf, len);
- }
-#ifdef GZIP
- else if (strm->state->wrap == 2) {
- strm->adler = crc32(strm->adler, buf, len);
- }
-#endif
- strm->next_in += len;
- strm->total_in += len;
-
- return (int)len;
-}
-
-/* ===========================================================================
- * Initialize the "longest match" routines for a new zlib stream
- */
-local void lm_init (s)
- deflate_state *s;
-{
- s->window_size = (ulg)2L*s->w_size;
-
- CLEAR_HASH(s);
-
- /* Set the default configuration parameters:
- */
- s->max_lazy_match = configuration_table[s->level].max_lazy;
- s->good_match = configuration_table[s->level].good_length;
- s->nice_match = configuration_table[s->level].nice_length;
- s->max_chain_length = configuration_table[s->level].max_chain;
-
- s->strstart = 0;
- s->block_start = 0L;
- s->lookahead = 0;
- s->insert = 0;
- s->match_length = s->prev_length = MIN_MATCH-1;
- s->match_available = 0;
- s->ins_h = 0;
-#ifndef FASTEST
-#ifdef ASMV
- match_init(); /* initialize the asm code */
-#endif
-#endif
-}
-
-#ifndef FASTEST
-/* ===========================================================================
- * Set match_start to the longest match starting at the given string and
- * return its length. Matches shorter or equal to prev_length are discarded,
- * in which case the result is equal to prev_length and match_start is
- * garbage.
- * IN assertions: cur_match is the head of the hash chain for the current
- * string (strstart) and its distance is <= MAX_DIST, and prev_length >= 1
- * OUT assertion: the match length is not greater than s->lookahead.
- */
-#ifndef ASMV
-/* For 80x86 and 680x0, an optimized version will be provided in match.asm or
- * match.S. The code will be functionally equivalent.
- */
-local uInt longest_match(s, cur_match)
- deflate_state *s;
- IPos cur_match; /* current match */
-{
- unsigned chain_length = s->max_chain_length;/* max hash chain length */
- register Bytef *scan = s->window + s->strstart; /* current string */
- register Bytef *match; /* matched string */
- register int len; /* length of current match */
- int best_len = s->prev_length; /* best match length so far */
- int nice_match = s->nice_match; /* stop if match long enough */
- IPos limit = s->strstart > (IPos)MAX_DIST(s) ?
- s->strstart - (IPos)MAX_DIST(s) : NIL;
- /* Stop when cur_match becomes <= limit. To simplify the code,
- * we prevent matches with the string of window index 0.
- */
- Posf *prev = s->prev;
- uInt wmask = s->w_mask;
-
-#ifdef UNALIGNED_OK
- /* Compare two bytes at a time. Note: this is not always beneficial.
- * Try with and without -DUNALIGNED_OK to check.
- */
- register Bytef *strend = s->window + s->strstart + MAX_MATCH - 1;
- register ush scan_start = *(ushf*)scan;
- register ush scan_end = *(ushf*)(scan+best_len-1);
-#else
- register Bytef *strend = s->window + s->strstart + MAX_MATCH;
- register Byte scan_end1 = scan[best_len-1];
- register Byte scan_end = scan[best_len];
-#endif
-
- /* The code is optimized for HASH_BITS >= 8 and MAX_MATCH-2 multiple of 16.
- * It is easy to get rid of this optimization if necessary.
- */
- Assert(s->hash_bits >= 8 && MAX_MATCH == 258, "Code too clever");
-
- /* Do not waste too much time if we already have a good match: */
- if (s->prev_length >= s->good_match) {
- chain_length >>= 2;
- }
- /* Do not look for matches beyond the end of the input. This is necessary
- * to make deflate deterministic.
- */
- if ((uInt)nice_match > s->lookahead) nice_match = s->lookahead;
-
- Assert((ulg)s->strstart <= s->window_size-MIN_LOOKAHEAD, "need lookahead");
-
- do {
- Assert(cur_match < s->strstart, "no future");
- match = s->window + cur_match;
-
- /* Skip to next match if the match length cannot increase
- * or if the match length is less than 2. Note that the checks below
- * for insufficient lookahead only occur occasionally for performance
- * reasons. Therefore uninitialized memory will be accessed, and
- * conditional jumps will be made that depend on those values.
- * However the length of the match is limited to the lookahead, so
- * the output of deflate is not affected by the uninitialized values.
- */
-#if (defined(UNALIGNED_OK) && MAX_MATCH == 258)
- /* This code assumes sizeof(unsigned short) == 2. Do not use
- * UNALIGNED_OK if your compiler uses a different size.
- */
- if (*(ushf*)(match+best_len-1) != scan_end ||
- *(ushf*)match != scan_start) continue;
-
- /* It is not necessary to compare scan[2] and match[2] since they are
- * always equal when the other bytes match, given that the hash keys
- * are equal and that HASH_BITS >= 8. Compare 2 bytes at a time at
- * strstart+3, +5, ... up to strstart+257. We check for insufficient
- * lookahead only every 4th comparison; the 128th check will be made
- * at strstart+257. If MAX_MATCH-2 is not a multiple of 8, it is
- * necessary to put more guard bytes at the end of the window, or
- * to check more often for insufficient lookahead.
- */
- Assert(scan[2] == match[2], "scan[2]?");
- scan++, match++;
- do {
- } while (*(ushf*)(scan+=2) == *(ushf*)(match+=2) &&
- *(ushf*)(scan+=2) == *(ushf*)(match+=2) &&
- *(ushf*)(scan+=2) == *(ushf*)(match+=2) &&
- *(ushf*)(scan+=2) == *(ushf*)(match+=2) &&
- scan < strend);
- /* The funny "do {}" generates better code on most compilers */
-
- /* Here, scan <= window+strstart+257 */
- Assert(scan <= s->window+(unsigned)(s->window_size-1), "wild scan");
- if (*scan == *match) scan++;
-
- len = (MAX_MATCH - 1) - (int)(strend-scan);
- scan = strend - (MAX_MATCH-1);
-
-#else /* UNALIGNED_OK */
-
- if (match[best_len] != scan_end ||
- match[best_len-1] != scan_end1 ||
- *match != *scan ||
- *++match != scan[1]) continue;
-
- /* The check at best_len-1 can be removed because it will be made
- * again later. (This heuristic is not always a win.)
- * It is not necessary to compare scan[2] and match[2] since they
- * are always equal when the other bytes match, given that
- * the hash keys are equal and that HASH_BITS >= 8.
- */
- scan += 2, match++;
- Assert(*scan == *match, "match[2]?");
-
- /* We check for insufficient lookahead only every 8th comparison;
- * the 256th check will be made at strstart+258.
- */
- do {
- } while (*++scan == *++match && *++scan == *++match &&
- *++scan == *++match && *++scan == *++match &&
- *++scan == *++match && *++scan == *++match &&
- *++scan == *++match && *++scan == *++match &&
- scan < strend);
-
- Assert(scan <= s->window+(unsigned)(s->window_size-1), "wild scan");
-
- len = MAX_MATCH - (int)(strend - scan);
- scan = strend - MAX_MATCH;
-
-#endif /* UNALIGNED_OK */
-
- if (len > best_len) {
- s->match_start = cur_match;
- best_len = len;
- if (len >= nice_match) break;
-#ifdef UNALIGNED_OK
- scan_end = *(ushf*)(scan+best_len-1);
-#else
- scan_end1 = scan[best_len-1];
- scan_end = scan[best_len];
-#endif
- }
- } while ((cur_match = prev[cur_match & wmask]) > limit
- && --chain_length != 0);
-
- if ((uInt)best_len <= s->lookahead) return (uInt)best_len;
- return s->lookahead;
-}
-#endif /* ASMV */
-
-#else /* FASTEST */
-
-/* ---------------------------------------------------------------------------
- * Optimized version for FASTEST only
- */
-local uInt longest_match(s, cur_match)
- deflate_state *s;
- IPos cur_match; /* current match */
-{
- register Bytef *scan = s->window + s->strstart; /* current string */
- register Bytef *match; /* matched string */
- register int len; /* length of current match */
- register Bytef *strend = s->window + s->strstart + MAX_MATCH;
-
- /* The code is optimized for HASH_BITS >= 8 and MAX_MATCH-2 multiple of 16.
- * It is easy to get rid of this optimization if necessary.
- */
- Assert(s->hash_bits >= 8 && MAX_MATCH == 258, "Code too clever");
-
- Assert((ulg)s->strstart <= s->window_size-MIN_LOOKAHEAD, "need lookahead");
-
- Assert(cur_match < s->strstart, "no future");
-
- match = s->window + cur_match;
-
- /* Return failure if the match length is less than 2:
- */
- if (match[0] != scan[0] || match[1] != scan[1]) return MIN_MATCH-1;
-
- /* The check at best_len-1 can be removed because it will be made
- * again later. (This heuristic is not always a win.)
- * It is not necessary to compare scan[2] and match[2] since they
- * are always equal when the other bytes match, given that
- * the hash keys are equal and that HASH_BITS >= 8.
- */
- scan += 2, match += 2;
- Assert(*scan == *match, "match[2]?");
-
- /* We check for insufficient lookahead only every 8th comparison;
- * the 256th check will be made at strstart+258.
- */
- do {
- } while (*++scan == *++match && *++scan == *++match &&
- *++scan == *++match && *++scan == *++match &&
- *++scan == *++match && *++scan == *++match &&
- *++scan == *++match && *++scan == *++match &&
- scan < strend);
-
- Assert(scan <= s->window+(unsigned)(s->window_size-1), "wild scan");
-
- len = MAX_MATCH - (int)(strend - scan);
-
- if (len < MIN_MATCH) return MIN_MATCH - 1;
-
- s->match_start = cur_match;
- return (uInt)len <= s->lookahead ? (uInt)len : s->lookahead;
-}
-
-#endif /* FASTEST */
-
-#ifdef DEBUG
-/* ===========================================================================
- * Check that the match at match_start is indeed a match.
- */
-local void check_match(s, start, match, length)
- deflate_state *s;
- IPos start, match;
- int length;
-{
- /* check that the match is indeed a match */
- if (zmemcmp(s->window + match,
- s->window + start, length) != EQUAL) {
- fprintf(stderr, " start %u, match %u, length %d\n",
- start, match, length);
- do {
- fprintf(stderr, "%c%c", s->window[match++], s->window[start++]);
- } while (--length != 0);
- z_error("invalid match");
- }
- if (z_verbose > 1) {
- fprintf(stderr,"\\[%d,%d]", start-match, length);
- do { putc(s->window[start++], stderr); } while (--length != 0);
- }
-}
-#else
-# define check_match(s, start, match, length)
-#endif /* DEBUG */
-
-/* ===========================================================================
- * Fill the window when the lookahead becomes insufficient.
- * Updates strstart and lookahead.
- *
- * IN assertion: lookahead < MIN_LOOKAHEAD
- * OUT assertions: strstart <= window_size-MIN_LOOKAHEAD
- * At least one byte has been read, or avail_in == 0; reads are
- * performed for at least two bytes (required for the zip translate_eol
- * option -- not supported here).
- */
-local void fill_window(s)
- deflate_state *s;
-{
- register unsigned n, m;
- register Posf *p;
- unsigned more; /* Amount of free space at the end of the window. */
- uInt wsize = s->w_size;
-
- Assert(s->lookahead < MIN_LOOKAHEAD, "already enough lookahead");
-
- do {
- more = (unsigned)(s->window_size -(ulg)s->lookahead -(ulg)s->strstart);
-
- /* Deal with !@#$% 64K limit: */
- if (sizeof(int) <= 2) {
- if (more == 0 && s->strstart == 0 && s->lookahead == 0) {
- more = wsize;
-
- } else if (more == (unsigned)(-1)) {
- /* Very unlikely, but possible on 16 bit machine if
- * strstart == 0 && lookahead == 1 (input done a byte at time)
- */
- more--;
- }
- }
-
- /* If the window is almost full and there is insufficient lookahead,
- * move the upper half to the lower one to make room in the upper half.
- */
- if (s->strstart >= wsize+MAX_DIST(s)) {
-
- zmemcpy(s->window, s->window+wsize, (unsigned)wsize);
- s->match_start -= wsize;
- s->strstart -= wsize; /* we now have strstart >= MAX_DIST */
- s->block_start -= (long) wsize;
-
- /* Slide the hash table (could be avoided with 32 bit values
- at the expense of memory usage). We slide even when level == 0
- to keep the hash table consistent if we switch back to level > 0
- later. (Using level 0 permanently is not an optimal usage of
- zlib, so we don't care about this pathological case.)
- */
- n = s->hash_size;
- p = &s->head[n];
- do {
- m = *--p;
- *p = (Pos)(m >= wsize ? m-wsize : NIL);
- } while (--n);
-
- n = wsize;
-#ifndef FASTEST
- p = &s->prev[n];
- do {
- m = *--p;
- *p = (Pos)(m >= wsize ? m-wsize : NIL);
- /* If n is not on any hash chain, prev[n] is garbage but
- * its value will never be used.
- */
- } while (--n);
-#endif
- more += wsize;
- }
- if (s->strm->avail_in == 0) break;
-
- /* If there was no sliding:
- * strstart <= WSIZE+MAX_DIST-1 && lookahead <= MIN_LOOKAHEAD - 1 &&
- * more == window_size - lookahead - strstart
- * => more >= window_size - (MIN_LOOKAHEAD-1 + WSIZE + MAX_DIST-1)
- * => more >= window_size - 2*WSIZE + 2
- * In the BIG_MEM or MMAP case (not yet supported),
- * window_size == input_size + MIN_LOOKAHEAD &&
- * strstart + s->lookahead <= input_size => more >= MIN_LOOKAHEAD.
- * Otherwise, window_size == 2*WSIZE so more >= 2.
- * If there was sliding, more >= WSIZE. So in all cases, more >= 2.
- */
- Assert(more >= 2, "more < 2");
-
- n = read_buf(s->strm, s->window + s->strstart + s->lookahead, more);
- s->lookahead += n;
-
- /* Initialize the hash value now that we have some input: */
- if (s->lookahead + s->insert >= MIN_MATCH) {
- uInt str = s->strstart - s->insert;
- s->ins_h = s->window[str];
- UPDATE_HASH(s, s->ins_h, s->window[str + 1]);
-#if MIN_MATCH != 3
- Call UPDATE_HASH() MIN_MATCH-3 more times
-#endif
- while (s->insert) {
- UPDATE_HASH(s, s->ins_h, s->window[str + MIN_MATCH-1]);
-#ifndef FASTEST
- s->prev[str & s->w_mask] = s->head[s->ins_h];
-#endif
- s->head[s->ins_h] = (Pos)str;
- str++;
- s->insert--;
- if (s->lookahead + s->insert < MIN_MATCH)
- break;
- }
- }
- /* If the whole input has less than MIN_MATCH bytes, ins_h is garbage,
- * but this is not important since only literal bytes will be emitted.
- */
-
- } while (s->lookahead < MIN_LOOKAHEAD && s->strm->avail_in != 0);
-
- /* If the WIN_INIT bytes after the end of the current data have never been
- * written, then zero those bytes in order to avoid memory check reports of
- * the use of uninitialized (or uninitialised as Julian writes) bytes by
- * the longest match routines. Update the high water mark for the next
- * time through here. WIN_INIT is set to MAX_MATCH since the longest match
- * routines allow scanning to strstart + MAX_MATCH, ignoring lookahead.
- */
- if (s->high_water < s->window_size) {
- ulg curr = s->strstart + (ulg)(s->lookahead);
- ulg init;
-
- if (s->high_water < curr) {
- /* Previous high water mark below current data -- zero WIN_INIT
- * bytes or up to end of window, whichever is less.
- */
- init = s->window_size - curr;
- if (init > WIN_INIT)
- init = WIN_INIT;
- zmemzero(s->window + curr, (unsigned)init);
- s->high_water = curr + init;
- }
- else if (s->high_water < (ulg)curr + WIN_INIT) {
- /* High water mark at or above current data, but below current data
- * plus WIN_INIT -- zero out to current data plus WIN_INIT, or up
- * to end of window, whichever is less.
- */
- init = (ulg)curr + WIN_INIT - s->high_water;
- if (init > s->window_size - s->high_water)
- init = s->window_size - s->high_water;
- zmemzero(s->window + s->high_water, (unsigned)init);
- s->high_water += init;
- }
- }
-
- Assert((ulg)s->strstart <= s->window_size - MIN_LOOKAHEAD,
- "not enough room for search");
-}
-
-/* ===========================================================================
- * Flush the current block, with given end-of-file flag.
- * IN assertion: strstart is set to the end of the current match.
- */
-#define FLUSH_BLOCK_ONLY(s, last) { \
- _tr_flush_block(s, (s->block_start >= 0L ? \
- (charf *)&s->window[(unsigned)s->block_start] : \
- (charf *)Z_NULL), \
- (ulg)((long)s->strstart - s->block_start), \
- (last)); \
- s->block_start = s->strstart; \
- flush_pending(s->strm); \
- Tracev((stderr,"[FLUSH]")); \
-}
-
-/* Same but force premature exit if necessary. */
-#define FLUSH_BLOCK(s, last) { \
- FLUSH_BLOCK_ONLY(s, last); \
- if (s->strm->avail_out == 0) return (last) ? finish_started : need_more; \
-}
-
-/* ===========================================================================
- * Copy without compression as much as possible from the input stream, return
- * the current block state.
- * This function does not insert new strings in the dictionary since
- * uncompressible data is probably not useful. This function is used
- * only for the level=0 compression option.
- * NOTE: this function should be optimized to avoid extra copying from
- * window to pending_buf.
- */
-local block_state deflate_stored(s, flush)
- deflate_state *s;
- int flush;
-{
- /* Stored blocks are limited to 0xffff bytes, pending_buf is limited
- * to pending_buf_size, and each stored block has a 5 byte header:
- */
- ulg max_block_size = 0xffff;
- ulg max_start;
-
- if (max_block_size > s->pending_buf_size - 5) {
- max_block_size = s->pending_buf_size - 5;
- }
-
- /* Copy as much as possible from input to output: */
- for (;;) {
- /* Fill the window as much as possible: */
- if (s->lookahead <= 1) {
-
- Assert(s->strstart < s->w_size+MAX_DIST(s) ||
- s->block_start >= (long)s->w_size, "slide too late");
-
- fill_window(s);
- if (s->lookahead == 0 && flush == Z_NO_FLUSH) return need_more;
-
- if (s->lookahead == 0) break; /* flush the current block */
- }
- Assert(s->block_start >= 0L, "block gone");
-
- s->strstart += s->lookahead;
- s->lookahead = 0;
-
- /* Emit a stored block if pending_buf will be full: */
- max_start = s->block_start + max_block_size;
- if (s->strstart == 0 || (ulg)s->strstart >= max_start) {
- /* strstart == 0 is possible when wraparound on 16-bit machine */
- s->lookahead = (uInt)(s->strstart - max_start);
- s->strstart = (uInt)max_start;
- FLUSH_BLOCK(s, 0);
- }
- /* Flush if we may have to slide, otherwise block_start may become
- * negative and the data will be gone:
- */
- if (s->strstart - (uInt)s->block_start >= MAX_DIST(s)) {
- FLUSH_BLOCK(s, 0);
- }
- }
- s->insert = 0;
- if (flush == Z_FINISH) {
- FLUSH_BLOCK(s, 1);
- return finish_done;
- }
- if ((long)s->strstart > s->block_start)
- FLUSH_BLOCK(s, 0);
- return block_done;
-}
-
-/* ===========================================================================
- * Compress as much as possible from the input stream, return the current
- * block state.
- * This function does not perform lazy evaluation of matches and inserts
- * new strings in the dictionary only for unmatched strings or for short
- * matches. It is used only for the fast compression options.
- */
-local block_state deflate_fast(s, flush)
- deflate_state *s;
- int flush;
-{
- IPos hash_head; /* head of the hash chain */
- int bflush; /* set if current block must be flushed */
-
- for (;;) {
- /* Make sure that we always have enough lookahead, except
- * at the end of the input file. We need MAX_MATCH bytes
- * for the next match, plus MIN_MATCH bytes to insert the
- * string following the next match.
- */
- if (s->lookahead < MIN_LOOKAHEAD) {
- fill_window(s);
- if (s->lookahead < MIN_LOOKAHEAD && flush == Z_NO_FLUSH) {
- return need_more;
- }
- if (s->lookahead == 0) break; /* flush the current block */
- }
-
- /* Insert the string window[strstart .. strstart+2] in the
- * dictionary, and set hash_head to the head of the hash chain:
- */
- hash_head = NIL;
- if (s->lookahead >= MIN_MATCH) {
- INSERT_STRING(s, s->strstart, hash_head);
- }
-
- /* Find the longest match, discarding those <= prev_length.
- * At this point we have always match_length < MIN_MATCH
- */
- if (hash_head != NIL && s->strstart - hash_head <= MAX_DIST(s)) {
- /* To simplify the code, we prevent matches with the string
- * of window index 0 (in particular we have to avoid a match
- * of the string with itself at the start of the input file).
- */
- s->match_length = longest_match (s, hash_head);
- /* longest_match() sets match_start */
- }
- if (s->match_length >= MIN_MATCH) {
- check_match(s, s->strstart, s->match_start, s->match_length);
-
- _tr_tally_dist(s, s->strstart - s->match_start,
- s->match_length - MIN_MATCH, bflush);
-
- s->lookahead -= s->match_length;
-
- /* Insert new strings in the hash table only if the match length
- * is not too large. This saves time but degrades compression.
- */
-#ifndef FASTEST
- if (s->match_length <= s->max_insert_length &&
- s->lookahead >= MIN_MATCH) {
- s->match_length--; /* string at strstart already in table */
- do {
- s->strstart++;
- INSERT_STRING(s, s->strstart, hash_head);
- /* strstart never exceeds WSIZE-MAX_MATCH, so there are
- * always MIN_MATCH bytes ahead.
- */
- } while (--s->match_length != 0);
- s->strstart++;
- } else
-#endif
- {
- s->strstart += s->match_length;
- s->match_length = 0;
- s->ins_h = s->window[s->strstart];
- UPDATE_HASH(s, s->ins_h, s->window[s->strstart+1]);
-#if MIN_MATCH != 3
- Call UPDATE_HASH() MIN_MATCH-3 more times
-#endif
- /* If lookahead < MIN_MATCH, ins_h is garbage, but it does not
- * matter since it will be recomputed at next deflate call.
- */
- }
- } else {
- /* No match, output a literal byte */
- Tracevv((stderr,"%c", s->window[s->strstart]));
- _tr_tally_lit (s, s->window[s->strstart], bflush);
- s->lookahead--;
- s->strstart++;
- }
- if (bflush) FLUSH_BLOCK(s, 0);
- }
- s->insert = s->strstart < MIN_MATCH-1 ? s->strstart : MIN_MATCH-1;
- if (flush == Z_FINISH) {
- FLUSH_BLOCK(s, 1);
- return finish_done;
- }
- if (s->last_lit)
- FLUSH_BLOCK(s, 0);
- return block_done;
-}
-
-#ifndef FASTEST
-/* ===========================================================================
- * Same as above, but achieves better compression. We use a lazy
- * evaluation for matches: a match is finally adopted only if there is
- * no better match at the next window position.
- */
-local block_state deflate_slow(s, flush)
- deflate_state *s;
- int flush;
-{
- IPos hash_head; /* head of hash chain */
- int bflush; /* set if current block must be flushed */
-
- /* Process the input block. */
- for (;;) {
- /* Make sure that we always have enough lookahead, except
- * at the end of the input file. We need MAX_MATCH bytes
- * for the next match, plus MIN_MATCH bytes to insert the
- * string following the next match.
- */
- if (s->lookahead < MIN_LOOKAHEAD) {
- fill_window(s);
- if (s->lookahead < MIN_LOOKAHEAD && flush == Z_NO_FLUSH) {
- return need_more;
- }
- if (s->lookahead == 0) break; /* flush the current block */
- }
-
- /* Insert the string window[strstart .. strstart+2] in the
- * dictionary, and set hash_head to the head of the hash chain:
- */
- hash_head = NIL;
- if (s->lookahead >= MIN_MATCH) {
- INSERT_STRING(s, s->strstart, hash_head);
- }
-
- /* Find the longest match, discarding those <= prev_length.
- */
- s->prev_length = s->match_length, s->prev_match = s->match_start;
- s->match_length = MIN_MATCH-1;
-
- if (hash_head != NIL && s->prev_length < s->max_lazy_match &&
- s->strstart - hash_head <= MAX_DIST(s)) {
- /* To simplify the code, we prevent matches with the string
- * of window index 0 (in particular we have to avoid a match
- * of the string with itself at the start of the input file).
- */
- s->match_length = longest_match (s, hash_head);
- /* longest_match() sets match_start */
-
- if (s->match_length <= 5 && (s->strategy == Z_FILTERED
-#if TOO_FAR <= 32767
- || (s->match_length == MIN_MATCH &&
- s->strstart - s->match_start > TOO_FAR)
-#endif
- )) {
-
- /* If prev_match is also MIN_MATCH, match_start is garbage
- * but we will ignore the current match anyway.
- */
- s->match_length = MIN_MATCH-1;
- }
- }
- /* If there was a match at the previous step and the current
- * match is not better, output the previous match:
- */
- if (s->prev_length >= MIN_MATCH && s->match_length <= s->prev_length) {
- uInt max_insert = s->strstart + s->lookahead - MIN_MATCH;
- /* Do not insert strings in hash table beyond this. */
-
- check_match(s, s->strstart-1, s->prev_match, s->prev_length);
-
- _tr_tally_dist(s, s->strstart -1 - s->prev_match,
- s->prev_length - MIN_MATCH, bflush);
-
- /* Insert in hash table all strings up to the end of the match.
- * strstart-1 and strstart are already inserted. If there is not
- * enough lookahead, the last two strings are not inserted in
- * the hash table.
- */
- s->lookahead -= s->prev_length-1;
- s->prev_length -= 2;
- do {
- if (++s->strstart <= max_insert) {
- INSERT_STRING(s, s->strstart, hash_head);
- }
- } while (--s->prev_length != 0);
- s->match_available = 0;
- s->match_length = MIN_MATCH-1;
- s->strstart++;
-
- if (bflush) FLUSH_BLOCK(s, 0);
-
- } else if (s->match_available) {
- /* If there was no match at the previous position, output a
- * single literal. If there was a match but the current match
- * is longer, truncate the previous match to a single literal.
- */
- Tracevv((stderr,"%c", s->window[s->strstart-1]));
- _tr_tally_lit(s, s->window[s->strstart-1], bflush);
- if (bflush) {
- FLUSH_BLOCK_ONLY(s, 0);
- }
- s->strstart++;
- s->lookahead--;
- if (s->strm->avail_out == 0) return need_more;
- } else {
- /* There is no previous match to compare with, wait for
- * the next step to decide.
- */
- s->match_available = 1;
- s->strstart++;
- s->lookahead--;
- }
- }
- Assert (flush != Z_NO_FLUSH, "no flush?");
- if (s->match_available) {
- Tracevv((stderr,"%c", s->window[s->strstart-1]));
- _tr_tally_lit(s, s->window[s->strstart-1], bflush);
- s->match_available = 0;
- }
- s->insert = s->strstart < MIN_MATCH-1 ? s->strstart : MIN_MATCH-1;
- if (flush == Z_FINISH) {
- FLUSH_BLOCK(s, 1);
- return finish_done;
- }
- if (s->last_lit)
- FLUSH_BLOCK(s, 0);
- return block_done;
-}
-#endif /* FASTEST */
-
-/* ===========================================================================
- * For Z_RLE, simply look for runs of bytes, generate matches only of distance
- * one. Do not maintain a hash table. (It will be regenerated if this run of
- * deflate switches away from Z_RLE.)
- */
-local block_state deflate_rle(s, flush)
- deflate_state *s;
- int flush;
-{
- int bflush; /* set if current block must be flushed */
- uInt prev; /* byte at distance one to match */
- Bytef *scan, *strend; /* scan goes up to strend for length of run */
-
- for (;;) {
- /* Make sure that we always have enough lookahead, except
- * at the end of the input file. We need MAX_MATCH bytes
- * for the longest run, plus one for the unrolled loop.
- */
- if (s->lookahead <= MAX_MATCH) {
- fill_window(s);
- if (s->lookahead <= MAX_MATCH && flush == Z_NO_FLUSH) {
- return need_more;
- }
- if (s->lookahead == 0) break; /* flush the current block */
- }
-
- /* See how many times the previous byte repeats */
- s->match_length = 0;
- if (s->lookahead >= MIN_MATCH && s->strstart > 0) {
- scan = s->window + s->strstart - 1;
- prev = *scan;
- if (prev == *++scan && prev == *++scan && prev == *++scan) {
- strend = s->window + s->strstart + MAX_MATCH;
- do {
- } while (prev == *++scan && prev == *++scan &&
- prev == *++scan && prev == *++scan &&
- prev == *++scan && prev == *++scan &&
- prev == *++scan && prev == *++scan &&
- scan < strend);
- s->match_length = MAX_MATCH - (int)(strend - scan);
- if (s->match_length > s->lookahead)
- s->match_length = s->lookahead;
- }
- Assert(scan <= s->window+(uInt)(s->window_size-1), "wild scan");
- }
-
- /* Emit match if have run of MIN_MATCH or longer, else emit literal */
- if (s->match_length >= MIN_MATCH) {
- check_match(s, s->strstart, s->strstart - 1, s->match_length);
-
- _tr_tally_dist(s, 1, s->match_length - MIN_MATCH, bflush);
-
- s->lookahead -= s->match_length;
- s->strstart += s->match_length;
- s->match_length = 0;
- } else {
- /* No match, output a literal byte */
- Tracevv((stderr,"%c", s->window[s->strstart]));
- _tr_tally_lit (s, s->window[s->strstart], bflush);
- s->lookahead--;
- s->strstart++;
- }
- if (bflush) FLUSH_BLOCK(s, 0);
- }
- s->insert = 0;
- if (flush == Z_FINISH) {
- FLUSH_BLOCK(s, 1);
- return finish_done;
- }
- if (s->last_lit)
- FLUSH_BLOCK(s, 0);
- return block_done;
-}
-
-/* ===========================================================================
- * For Z_HUFFMAN_ONLY, do not look for matches. Do not maintain a hash table.
- * (It will be regenerated if this run of deflate switches away from Huffman.)
- */
-local block_state deflate_huff(s, flush)
- deflate_state *s;
- int flush;
-{
- int bflush; /* set if current block must be flushed */
-
- for (;;) {
- /* Make sure that we have a literal to write. */
- if (s->lookahead == 0) {
- fill_window(s);
- if (s->lookahead == 0) {
- if (flush == Z_NO_FLUSH)
- return need_more;
- break; /* flush the current block */
- }
- }
-
- /* Output a literal byte */
- s->match_length = 0;
- Tracevv((stderr,"%c", s->window[s->strstart]));
- _tr_tally_lit (s, s->window[s->strstart], bflush);
- s->lookahead--;
- s->strstart++;
- if (bflush) FLUSH_BLOCK(s, 0);
- }
- s->insert = 0;
- if (flush == Z_FINISH) {
- FLUSH_BLOCK(s, 1);
- return finish_done;
- }
- if (s->last_lit)
- FLUSH_BLOCK(s, 0);
- return block_done;
-}
diff --git a/third-party/zlib/deflate.h b/third-party/zlib/deflate.h
deleted file mode 100644
index ce0299e..0000000
--- a/third-party/zlib/deflate.h
+++ /dev/null
@@ -1,346 +0,0 @@
-/* deflate.h -- internal compression state
- * Copyright (C) 1995-2012 Jean-loup Gailly
- * For conditions of distribution and use, see copyright notice in zlib.h
- */
-
-/* WARNING: this file should *not* be used by applications. It is
- part of the implementation of the compression library and is
- subject to change. Applications should only use zlib.h.
- */
-
-/* @(#) $Id$ */
-
-#ifndef DEFLATE_H
-#define DEFLATE_H
-
-#include "zutil.h"
-
-/* define NO_GZIP when compiling if you want to disable gzip header and
- trailer creation by deflate(). NO_GZIP would be used to avoid linking in
- the crc code when it is not needed. For shared libraries, gzip encoding
- should be left enabled. */
-#ifndef NO_GZIP
-# define GZIP
-#endif
-
-/* ===========================================================================
- * Internal compression state.
- */
-
-#define LENGTH_CODES 29
-/* number of length codes, not counting the special END_BLOCK code */
-
-#define LITERALS 256
-/* number of literal bytes 0..255 */
-
-#define L_CODES (LITERALS+1+LENGTH_CODES)
-/* number of Literal or Length codes, including the END_BLOCK code */
-
-#define D_CODES 30
-/* number of distance codes */
-
-#define BL_CODES 19
-/* number of codes used to transfer the bit lengths */
-
-#define HEAP_SIZE (2*L_CODES+1)
-/* maximum heap size */
-
-#define MAX_BITS 15
-/* All codes must not exceed MAX_BITS bits */
-
-#define Buf_size 16
-/* size of bit buffer in bi_buf */
-
-#define INIT_STATE 42
-#define EXTRA_STATE 69
-#define NAME_STATE 73
-#define COMMENT_STATE 91
-#define HCRC_STATE 103
-#define BUSY_STATE 113
-#define FINISH_STATE 666
-/* Stream status */
-
-
-/* Data structure describing a single value and its code string. */
-typedef struct ct_data_s {
- union {
- ush freq; /* frequency count */
- ush code; /* bit string */
- } fc;
- union {
- ush dad; /* father node in Huffman tree */
- ush len; /* length of bit string */
- } dl;
-} FAR ct_data;
-
-#define Freq fc.freq
-#define Code fc.code
-#define Dad dl.dad
-#define Len dl.len
-
-typedef struct static_tree_desc_s static_tree_desc;
-
-typedef struct tree_desc_s {
- ct_data *dyn_tree; /* the dynamic tree */
- int max_code; /* largest code with non zero frequency */
- static_tree_desc *stat_desc; /* the corresponding static tree */
-} FAR tree_desc;
-
-typedef ush Pos;
-typedef Pos FAR Posf;
-typedef unsigned IPos;
-
-/* A Pos is an index in the character window. We use short instead of int to
- * save space in the various tables. IPos is used only for parameter passing.
- */
-
-typedef struct internal_state {
- z_streamp strm; /* pointer back to this zlib stream */
- int status; /* as the name implies */
- Bytef *pending_buf; /* output still pending */
- ulg pending_buf_size; /* size of pending_buf */
- Bytef *pending_out; /* next pending byte to output to the stream */
- uInt pending; /* nb of bytes in the pending buffer */
- int wrap; /* bit 0 true for zlib, bit 1 true for gzip */
- gz_headerp gzhead; /* gzip header information to write */
- uInt gzindex; /* where in extra, name, or comment */
- Byte method; /* can only be DEFLATED */
- int last_flush; /* value of flush param for previous deflate call */
-
- /* used by deflate.c: */
-
- uInt w_size; /* LZ77 window size (32K by default) */
- uInt w_bits; /* log2(w_size) (8..16) */
- uInt w_mask; /* w_size - 1 */
-
- Bytef *window;
- /* Sliding window. Input bytes are read into the second half of the window,
- * and move to the first half later to keep a dictionary of at least wSize
- * bytes. With this organization, matches are limited to a distance of
- * wSize-MAX_MATCH bytes, but this ensures that IO is always
- * performed with a length multiple of the block size. Also, it limits
- * the window size to 64K, which is quite useful on MSDOS.
- * To do: use the user input buffer as sliding window.
- */
-
- ulg window_size;
- /* Actual size of window: 2*wSize, except when the user input buffer
- * is directly used as sliding window.
- */
-
- Posf *prev;
- /* Link to older string with same hash index. To limit the size of this
- * array to 64K, this link is maintained only for the last 32K strings.
- * An index in this array is thus a window index modulo 32K.
- */
-
- Posf *head; /* Heads of the hash chains or NIL. */
-
- uInt ins_h; /* hash index of string to be inserted */
- uInt hash_size; /* number of elements in hash table */
- uInt hash_bits; /* log2(hash_size) */
- uInt hash_mask; /* hash_size-1 */
-
- uInt hash_shift;
- /* Number of bits by which ins_h must be shifted at each input
- * step. It must be such that after MIN_MATCH steps, the oldest
- * byte no longer takes part in the hash key, that is:
- * hash_shift * MIN_MATCH >= hash_bits
- */
-
- long block_start;
- /* Window position at the beginning of the current output block. Gets
- * negative when the window is moved backwards.
- */
-
- uInt match_length; /* length of best match */
- IPos prev_match; /* previous match */
- int match_available; /* set if previous match exists */
- uInt strstart; /* start of string to insert */
- uInt match_start; /* start of matching string */
- uInt lookahead; /* number of valid bytes ahead in window */
-
- uInt prev_length;
- /* Length of the best match at previous step. Matches not greater than this
- * are discarded. This is used in the lazy match evaluation.
- */
-
- uInt max_chain_length;
- /* To speed up deflation, hash chains are never searched beyond this
- * length. A higher limit improves compression ratio but degrades the
- * speed.
- */
-
- uInt max_lazy_match;
- /* Attempt to find a better match only when the current match is strictly
- * smaller than this value. This mechanism is used only for compression
- * levels >= 4.
- */
-# define max_insert_length max_lazy_match
- /* Insert new strings in the hash table only if the match length is not
- * greater than this length. This saves time but degrades compression.
- * max_insert_length is used only for compression levels <= 3.
- */
-
- int level; /* compression level (1..9) */
- int strategy; /* favor or force Huffman coding*/
-
- uInt good_match;
- /* Use a faster search when the previous match is longer than this */
-
- int nice_match; /* Stop searching when current match exceeds this */
-
- /* used by trees.c: */
- /* Didn't use ct_data typedef below to suppress compiler warning */
- struct ct_data_s dyn_ltree[HEAP_SIZE]; /* literal and length tree */
- struct ct_data_s dyn_dtree[2*D_CODES+1]; /* distance tree */
- struct ct_data_s bl_tree[2*BL_CODES+1]; /* Huffman tree for bit lengths */
-
- struct tree_desc_s l_desc; /* desc. for literal tree */
- struct tree_desc_s d_desc; /* desc. for distance tree */
- struct tree_desc_s bl_desc; /* desc. for bit length tree */
-
- ush bl_count[MAX_BITS+1];
- /* number of codes at each bit length for an optimal tree */
-
- int heap[2*L_CODES+1]; /* heap used to build the Huffman trees */
- int heap_len; /* number of elements in the heap */
- int heap_max; /* element of largest frequency */
- /* The sons of heap[n] are heap[2*n] and heap[2*n+1]. heap[0] is not used.
- * The same heap array is used to build all trees.
- */
-
- uch depth[2*L_CODES+1];
- /* Depth of each subtree used as tie breaker for trees of equal frequency
- */
-
- uchf *l_buf; /* buffer for literals or lengths */
-
- uInt lit_bufsize;
- /* Size of match buffer for literals/lengths. There are 4 reasons for
- * limiting lit_bufsize to 64K:
- * - frequencies can be kept in 16 bit counters
- * - if compression is not successful for the first block, all input
- * data is still in the window so we can still emit a stored block even
- * when input comes from standard input. (This can also be done for
- * all blocks if lit_bufsize is not greater than 32K.)
- * - if compression is not successful for a file smaller than 64K, we can
- * even emit a stored file instead of a stored block (saving 5 bytes).
- * This is applicable only for zip (not gzip or zlib).
- * - creating new Huffman trees less frequently may not provide fast
- * adaptation to changes in the input data statistics. (Take for
- * example a binary file with poorly compressible code followed by
- * a highly compressible string table.) Smaller buffer sizes give
- * fast adaptation but have of course the overhead of transmitting
- * trees more frequently.
- * - I can't count above 4
- */
-
- uInt last_lit; /* running index in l_buf */
-
- ushf *d_buf;
- /* Buffer for distances. To simplify the code, d_buf and l_buf have
- * the same number of elements. To use different lengths, an extra flag
- * array would be necessary.
- */
-
- ulg opt_len; /* bit length of current block with optimal trees */
- ulg static_len; /* bit length of current block with static trees */
- uInt matches; /* number of string matches in current block */
- uInt insert; /* bytes at end of window left to insert */
-
-#ifdef DEBUG
- ulg compressed_len; /* total bit length of compressed file mod 2^32 */
- ulg bits_sent; /* bit length of compressed data sent mod 2^32 */
-#endif
-
- ush bi_buf;
- /* Output buffer. bits are inserted starting at the bottom (least
- * significant bits).
- */
- int bi_valid;
- /* Number of valid bits in bi_buf. All bits above the last valid bit
- * are always zero.
- */
-
- ulg high_water;
- /* High water mark offset in window for initialized bytes -- bytes above
- * this are set to zero in order to avoid memory check warnings when
- * longest match routines access bytes past the input. This is then
- * updated to the new high water mark.
- */
-
-} FAR deflate_state;
-
-/* Output a byte on the stream.
- * IN assertion: there is enough room in pending_buf.
- */
-#define put_byte(s, c) {s->pending_buf[s->pending++] = (c);}
-
-
-#define MIN_LOOKAHEAD (MAX_MATCH+MIN_MATCH+1)
-/* Minimum amount of lookahead, except at the end of the input file.
- * See deflate.c for comments about the MIN_MATCH+1.
- */
-
-#define MAX_DIST(s) ((s)->w_size-MIN_LOOKAHEAD)
-/* In order to simplify the code, particularly on 16 bit machines, match
- * distances are limited to MAX_DIST instead of WSIZE.
- */
-
-#define WIN_INIT MAX_MATCH
-/* Number of bytes after end of data in window to initialize in order to avoid
- memory checker errors from longest match routines */
-
- /* in trees.c */
-void ZLIB_INTERNAL _tr_init OF((deflate_state *s));
-int ZLIB_INTERNAL _tr_tally OF((deflate_state *s, unsigned dist, unsigned lc));
-void ZLIB_INTERNAL _tr_flush_block OF((deflate_state *s, charf *buf,
- ulg stored_len, int last));
-void ZLIB_INTERNAL _tr_flush_bits OF((deflate_state *s));
-void ZLIB_INTERNAL _tr_align OF((deflate_state *s));
-void ZLIB_INTERNAL _tr_stored_block OF((deflate_state *s, charf *buf,
- ulg stored_len, int last));
-
-#define d_code(dist) \
- ((dist) < 256 ? _dist_code[dist] : _dist_code[256+((dist)>>7)])
-/* Mapping from a distance to a distance code. dist is the distance - 1 and
- * must not have side effects. _dist_code[256] and _dist_code[257] are never
- * used.
- */
-
-#ifndef DEBUG
-/* Inline versions of _tr_tally for speed: */
-
-#if defined(GEN_TREES_H) || !defined(STDC)
- extern uch ZLIB_INTERNAL _length_code[];
- extern uch ZLIB_INTERNAL _dist_code[];
-#else
- extern const uch ZLIB_INTERNAL _length_code[];
- extern const uch ZLIB_INTERNAL _dist_code[];
-#endif
-
-# define _tr_tally_lit(s, c, flush) \
- { uch cc = (c); \
- s->d_buf[s->last_lit] = 0; \
- s->l_buf[s->last_lit++] = cc; \
- s->dyn_ltree[cc].Freq++; \
- flush = (s->last_lit == s->lit_bufsize-1); \
- }
-# define _tr_tally_dist(s, distance, length, flush) \
- { uch len = (length); \
- ush dist = (distance); \
- s->d_buf[s->last_lit] = dist; \
- s->l_buf[s->last_lit++] = len; \
- dist--; \
- s->dyn_ltree[_length_code[len]+LITERALS+1].Freq++; \
- s->dyn_dtree[d_code(dist)].Freq++; \
- flush = (s->last_lit == s->lit_bufsize-1); \
- }
-#else
-# define _tr_tally_lit(s, c, flush) flush = _tr_tally(s, 0, c)
-# define _tr_tally_dist(s, distance, length, flush) \
- flush = _tr_tally(s, distance, length)
-#endif
-
-#endif /* DEFLATE_H */
diff --git a/third-party/zlib/doc/algorithm.txt b/third-party/zlib/doc/algorithm.txt
deleted file mode 100644
index c97f495..0000000
--- a/third-party/zlib/doc/algorithm.txt
+++ /dev/null
@@ -1,209 +0,0 @@
-1. Compression algorithm (deflate)
-
-The deflation algorithm used by gzip (also zip and zlib) is a variation of
-LZ77 (Lempel-Ziv 1977, see reference below). It finds duplicated strings in
-the input data. The second occurrence of a string is replaced by a
-pointer to the previous string, in the form of a pair (distance,
-length). Distances are limited to 32K bytes, and lengths are limited
-to 258 bytes. When a string does not occur anywhere in the previous
-32K bytes, it is emitted as a sequence of literal bytes. (In this
-description, `string' must be taken as an arbitrary sequence of bytes,
-and is not restricted to printable characters.)
-
-Literals or match lengths are compressed with one Huffman tree, and
-match distances are compressed with another tree. The trees are stored
-in a compact form at the start of each block. The blocks can have any
-size (except that the compressed data for one block must fit in
-available memory). A block is terminated when deflate() determines that
-it would be useful to start another block with fresh trees. (This is
-somewhat similar to the behavior of LZW-based _compress_.)
-
-Duplicated strings are found using a hash table. All input strings of
-length 3 are inserted in the hash table. A hash index is computed for
-the next 3 bytes. If the hash chain for this index is not empty, all
-strings in the chain are compared with the current input string, and
-the longest match is selected.
-
-The hash chains are searched starting with the most recent strings, to
-favor small distances and thus take advantage of the Huffman encoding.
-The hash chains are singly linked. There are no deletions from the
-hash chains, the algorithm simply discards matches that are too old.
-
-To avoid a worst-case situation, very long hash chains are arbitrarily
-truncated at a certain length, determined by a runtime option (level
-parameter of deflateInit). So deflate() does not always find the longest
-possible match but generally finds a match which is long enough.
-
-deflate() also defers the selection of matches with a lazy evaluation
-mechanism. After a match of length N has been found, deflate() searches for
-a longer match at the next input byte. If a longer match is found, the
-previous match is truncated to a length of one (thus producing a single
-literal byte) and the process of lazy evaluation begins again. Otherwise,
-the original match is kept, and the next match search is attempted only N
-steps later.
-
-The lazy match evaluation is also subject to a runtime parameter. If
-the current match is long enough, deflate() reduces the search for a longer
-match, thus speeding up the whole process. If compression ratio is more
-important than speed, deflate() attempts a complete second search even if
-the first match is already long enough.
-
-The lazy match evaluation is not performed for the fastest compression
-modes (level parameter 1 to 3). For these fast modes, new strings
-are inserted in the hash table only when no match was found, or
-when the match is not too long. This degrades the compression ratio
-but saves time since there are both fewer insertions and fewer searches.
-
-
-2. Decompression algorithm (inflate)
-
-2.1 Introduction
-
-The key question is how to represent a Huffman code (or any prefix code) so
-that you can decode fast. The most important characteristic is that shorter
-codes are much more common than longer codes, so pay attention to decoding the
-short codes fast, and let the long codes take longer to decode.
-
-inflate() sets up a first level table that covers some number of bits of
-input less than the length of longest code. It gets that many bits from the
-stream, and looks it up in the table. The table will tell if the next
-code is that many bits or less and how many, and if it is, it will tell
-the value, else it will point to the next level table for which inflate()
-grabs more bits and tries to decode a longer code.
-
-How many bits to make the first lookup is a tradeoff between the time it
-takes to decode and the time it takes to build the table. If building the
-table took no time (and if you had infinite memory), then there would only
-be a first level table to cover all the way to the longest code. However,
-building the table ends up taking a lot longer for more bits since short
-codes are replicated many times in such a table. What inflate() does is
-simply to make the number of bits in the first table a variable, and then
-to set that variable for the maximum speed.
-
-For inflate, which has 286 possible codes for the literal/length tree, the size
-of the first table is nine bits. Also the distance trees have 30 possible
-values, and the size of the first table is six bits. Note that for each of
-those cases, the table ended up one bit longer than the ``average'' code
-length, i.e. the code length of an approximately flat code which would be a
-little more than eight bits for 286 symbols and a little less than five bits
-for 30 symbols.
-
-
-2.2 More details on the inflate table lookup
-
-Ok, you want to know what this cleverly obfuscated inflate tree actually
-looks like. You are correct that it's not a Huffman tree. It is simply a
-lookup table for the first, let's say, nine bits of a Huffman symbol. The
-symbol could be as short as one bit or as long as 15 bits. If a particular
-symbol is shorter than nine bits, then that symbol's translation is duplicated
-in all those entries that start with that symbol's bits. For example, if the
-symbol is four bits, then it's duplicated 32 times in a nine-bit table. If a
-symbol is nine bits long, it appears in the table once.
-
-If the symbol is longer than nine bits, then that entry in the table points
-to another similar table for the remaining bits. Again, there are duplicated
-entries as needed. The idea is that most of the time the symbol will be short
-and there will only be one table look up. (That's whole idea behind data
-compression in the first place.) For the less frequent long symbols, there
-will be two lookups. If you had a compression method with really long
-symbols, you could have as many levels of lookups as is efficient. For
-inflate, two is enough.
-
-So a table entry either points to another table (in which case nine bits in
-the above example are gobbled), or it contains the translation for the symbol
-and the number of bits to gobble. Then you start again with the next
-ungobbled bit.
-
-You may wonder: why not just have one lookup table for how ever many bits the
-longest symbol is? The reason is that if you do that, you end up spending
-more time filling in duplicate symbol entries than you do actually decoding.
-At least for deflate's output that generates new trees every several 10's of
-kbytes. You can imagine that filling in a 2^15 entry table for a 15-bit code
-would take too long if you're only decoding several thousand symbols. At the
-other extreme, you could make a new table for every bit in the code. In fact,
-that's essentially a Huffman tree. But then you spend too much time
-traversing the tree while decoding, even for short symbols.
-
-So the number of bits for the first lookup table is a trade of the time to
-fill out the table vs. the time spent looking at the second level and above of
-the table.
-
-Here is an example, scaled down:
-
-The code being decoded, with 10 symbols, from 1 to 6 bits long:
-
-A: 0
-B: 10
-C: 1100
-D: 11010
-E: 11011
-F: 11100
-G: 11101
-H: 11110
-I: 111110
-J: 111111
-
-Let's make the first table three bits long (eight entries):
-
-000: A,1
-001: A,1
-010: A,1
-011: A,1
-100: B,2
-101: B,2
-110: -> table X (gobble 3 bits)
-111: -> table Y (gobble 3 bits)
-
-Each entry is what the bits decode as and how many bits that is, i.e. how
-many bits to gobble. Or the entry points to another table, with the number of
-bits to gobble implicit in the size of the table.
-
-Table X is two bits long since the longest code starting with 110 is five bits
-long:
-
-00: C,1
-01: C,1
-10: D,2
-11: E,2
-
-Table Y is three bits long since the longest code starting with 111 is six
-bits long:
-
-000: F,2
-001: F,2
-010: G,2
-011: G,2
-100: H,2
-101: H,2
-110: I,3
-111: J,3
-
-So what we have here are three tables with a total of 20 entries that had to
-be constructed. That's compared to 64 entries for a single table. Or
-compared to 16 entries for a Huffman tree (six two entry tables and one four
-entry table). Assuming that the code ideally represents the probability of
-the symbols, it takes on the average 1.25 lookups per symbol. That's compared
-to one lookup for the single table, or 1.66 lookups per symbol for the
-Huffman tree.
-
-There, I think that gives you a picture of what's going on. For inflate, the
-meaning of a particular symbol is often more than just a letter. It can be a
-byte (a "literal"), or it can be either a length or a distance which
-indicates a base value and a number of bits to fetch after the code that is
-added to the base value. Or it might be the special end-of-block code. The
-data structures created in inftrees.c try to encode all that information
-compactly in the tables.
-
-
-Jean-loup Gailly Mark Adler
-jloup at gzip.org madler at alumni.caltech.edu
-
-
-References:
-
-[LZ77] Ziv J., Lempel A., ``A Universal Algorithm for Sequential Data
-Compression,'' IEEE Transactions on Information Theory, Vol. 23, No. 3,
-pp. 337-343.
-
-``DEFLATE Compressed Data Format Specification'' available in
-http://tools.ietf.org/html/rfc1951
diff --git a/third-party/zlib/doc/rfc1950.txt b/third-party/zlib/doc/rfc1950.txt
deleted file mode 100644
index ce6428a..0000000
--- a/third-party/zlib/doc/rfc1950.txt
+++ /dev/null
@@ -1,619 +0,0 @@
-
-
-
-
-
-
-Network Working Group P. Deutsch
-Request for Comments: 1950 Aladdin Enterprises
-Category: Informational J-L. Gailly
- Info-ZIP
- May 1996
-
-
- ZLIB Compressed Data Format Specification version 3.3
-
-Status of This Memo
-
- This memo provides information for the Internet community. This memo
- does not specify an Internet standard of any kind. Distribution of
- this memo is unlimited.
-
-IESG Note:
-
- The IESG takes no position on the validity of any Intellectual
- Property Rights statements contained in this document.
-
-Notices
-
- Copyright (c) 1996 L. Peter Deutsch and Jean-Loup Gailly
-
- Permission is granted to copy and distribute this document for any
- purpose and without charge, including translations into other
- languages and incorporation into compilations, provided that the
- copyright notice and this notice are preserved, and that any
- substantive changes or deletions from the original are clearly
- marked.
-
- A pointer to the latest version of this and related documentation in
- HTML format can be found at the URL
- <ftp://ftp.uu.net/graphics/png/documents/zlib/zdoc-index.html>.
-
-Abstract
-
- This specification defines a lossless compressed data format. The
- data can be produced or consumed, even for an arbitrarily long
- sequentially presented input data stream, using only an a priori
- bounded amount of intermediate storage. The format presently uses
- the DEFLATE compression method but can be easily extended to use
- other compression methods. It can be implemented readily in a manner
- not covered by patents. This specification also defines the ADLER-32
- checksum (an extension and improvement of the Fletcher checksum),
- used for detection of data corruption, and provides an algorithm for
- computing it.
-
-
-
-
-Deutsch & Gailly Informational [Page 1]
-
-RFC 1950 ZLIB Compressed Data Format Specification May 1996
-
-
-Table of Contents
-
- 1. Introduction ................................................... 2
- 1.1. Purpose ................................................... 2
- 1.2. Intended audience ......................................... 3
- 1.3. Scope ..................................................... 3
- 1.4. Compliance ................................................ 3
- 1.5. Definitions of terms and conventions used ................ 3
- 1.6. Changes from previous versions ............................ 3
- 2. Detailed specification ......................................... 3
- 2.1. Overall conventions ....................................... 3
- 2.2. Data format ............................................... 4
- 2.3. Compliance ................................................ 7
- 3. References ..................................................... 7
- 4. Source code .................................................... 8
- 5. Security Considerations ........................................ 8
- 6. Acknowledgements ............................................... 8
- 7. Authors' Addresses ............................................. 8
- 8. Appendix: Rationale ............................................ 9
- 9. Appendix: Sample code ..........................................10
-
-1. Introduction
-
- 1.1. Purpose
-
- The purpose of this specification is to define a lossless
- compressed data format that:
-
- * Is independent of CPU type, operating system, file system,
- and character set, and hence can be used for interchange;
-
- * Can be produced or consumed, even for an arbitrarily long
- sequentially presented input data stream, using only an a
- priori bounded amount of intermediate storage, and hence can
- be used in data communications or similar structures such as
- Unix filters;
-
- * Can use a number of different compression methods;
-
- * Can be implemented readily in a manner not covered by
- patents, and hence can be practiced freely.
-
- The data format defined by this specification does not attempt to
- allow random access to compressed data.
-
-
-
-
-
-
-
-Deutsch & Gailly Informational [Page 2]
-
-RFC 1950 ZLIB Compressed Data Format Specification May 1996
-
-
- 1.2. Intended audience
-
- This specification is intended for use by implementors of software
- to compress data into zlib format and/or decompress data from zlib
- format.
-
- The text of the specification assumes a basic background in
- programming at the level of bits and other primitive data
- representations.
-
- 1.3. Scope
-
- The specification specifies a compressed data format that can be
- used for in-memory compression of a sequence of arbitrary bytes.
-
- 1.4. Compliance
-
- Unless otherwise indicated below, a compliant decompressor must be
- able to accept and decompress any data set that conforms to all
- the specifications presented here; a compliant compressor must
- produce data sets that conform to all the specifications presented
- here.
-
- 1.5. Definitions of terms and conventions used
-
- byte: 8 bits stored or transmitted as a unit (same as an octet).
- (For this specification, a byte is exactly 8 bits, even on
- machines which store a character on a number of bits different
- from 8.) See below, for the numbering of bits within a byte.
-
- 1.6. Changes from previous versions
-
- Version 3.1 was the first public release of this specification.
- In version 3.2, some terminology was changed and the Adler-32
- sample code was rewritten for clarity. In version 3.3, the
- support for a preset dictionary was introduced, and the
- specification was converted to RFC style.
-
-2. Detailed specification
-
- 2.1. Overall conventions
-
- In the diagrams below, a box like this:
-
- +---+
- | | <-- the vertical bars might be missing
- +---+
-
-
-
-
-Deutsch & Gailly Informational [Page 3]
-
-RFC 1950 ZLIB Compressed Data Format Specification May 1996
-
-
- represents one byte; a box like this:
-
- +==============+
- | |
- +==============+
-
- represents a variable number of bytes.
-
- Bytes stored within a computer do not have a "bit order", since
- they are always treated as a unit. However, a byte considered as
- an integer between 0 and 255 does have a most- and least-
- significant bit, and since we write numbers with the most-
- significant digit on the left, we also write bytes with the most-
- significant bit on the left. In the diagrams below, we number the
- bits of a byte so that bit 0 is the least-significant bit, i.e.,
- the bits are numbered:
-
- +--------+
- |76543210|
- +--------+
-
- Within a computer, a number may occupy multiple bytes. All
- multi-byte numbers in the format described here are stored with
- the MOST-significant byte first (at the lower memory address).
- For example, the decimal number 520 is stored as:
-
- 0 1
- +--------+--------+
- |00000010|00001000|
- +--------+--------+
- ^ ^
- | |
- | + less significant byte = 8
- + more significant byte = 2 x 256
-
- 2.2. Data format
-
- A zlib stream has the following structure:
-
- 0 1
- +---+---+
- |CMF|FLG| (more-->)
- +---+---+
-
-
-
-
-
-
-
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-Deutsch & Gailly Informational [Page 4]
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-RFC 1950 ZLIB Compressed Data Format Specification May 1996
-
-
- (if FLG.FDICT set)
-
- 0 1 2 3
- +---+---+---+---+
- | DICTID | (more-->)
- +---+---+---+---+
-
- +=====================+---+---+---+---+
- |...compressed data...| ADLER32 |
- +=====================+---+---+---+---+
-
- Any data which may appear after ADLER32 are not part of the zlib
- stream.
-
- CMF (Compression Method and flags)
- This byte is divided into a 4-bit compression method and a 4-
- bit information field depending on the compression method.
-
- bits 0 to 3 CM Compression method
- bits 4 to 7 CINFO Compression info
-
- CM (Compression method)
- This identifies the compression method used in the file. CM = 8
- denotes the "deflate" compression method with a window size up
- to 32K. This is the method used by gzip and PNG (see
- references [1] and [2] in Chapter 3, below, for the reference
- documents). CM = 15 is reserved. It might be used in a future
- version of this specification to indicate the presence of an
- extra field before the compressed data.
-
- CINFO (Compression info)
- For CM = 8, CINFO is the base-2 logarithm of the LZ77 window
- size, minus eight (CINFO=7 indicates a 32K window size). Values
- of CINFO above 7 are not allowed in this version of the
- specification. CINFO is not defined in this specification for
- CM not equal to 8.
-
- FLG (FLaGs)
- This flag byte is divided as follows:
-
- bits 0 to 4 FCHECK (check bits for CMF and FLG)
- bit 5 FDICT (preset dictionary)
- bits 6 to 7 FLEVEL (compression level)
-
- The FCHECK value must be such that CMF and FLG, when viewed as
- a 16-bit unsigned integer stored in MSB order (CMF*256 + FLG),
- is a multiple of 31.
-
-
-
-
-Deutsch & Gailly Informational [Page 5]
-
-RFC 1950 ZLIB Compressed Data Format Specification May 1996
-
-
- FDICT (Preset dictionary)
- If FDICT is set, a DICT dictionary identifier is present
- immediately after the FLG byte. The dictionary is a sequence of
- bytes which are initially fed to the compressor without
- producing any compressed output. DICT is the Adler-32 checksum
- of this sequence of bytes (see the definition of ADLER32
- below). The decompressor can use this identifier to determine
- which dictionary has been used by the compressor.
-
- FLEVEL (Compression level)
- These flags are available for use by specific compression
- methods. The "deflate" method (CM = 8) sets these flags as
- follows:
-
- 0 - compressor used fastest algorithm
- 1 - compressor used fast algorithm
- 2 - compressor used default algorithm
- 3 - compressor used maximum compression, slowest algorithm
-
- The information in FLEVEL is not needed for decompression; it
- is there to indicate if recompression might be worthwhile.
-
- compressed data
- For compression method 8, the compressed data is stored in the
- deflate compressed data format as described in the document
- "DEFLATE Compressed Data Format Specification" by L. Peter
- Deutsch. (See reference [3] in Chapter 3, below)
-
- Other compressed data formats are not specified in this version
- of the zlib specification.
-
- ADLER32 (Adler-32 checksum)
- This contains a checksum value of the uncompressed data
- (excluding any dictionary data) computed according to Adler-32
- algorithm. This algorithm is a 32-bit extension and improvement
- of the Fletcher algorithm, used in the ITU-T X.224 / ISO 8073
- standard. See references [4] and [5] in Chapter 3, below)
-
- Adler-32 is composed of two sums accumulated per byte: s1 is
- the sum of all bytes, s2 is the sum of all s1 values. Both sums
- are done modulo 65521. s1 is initialized to 1, s2 to zero. The
- Adler-32 checksum is stored as s2*65536 + s1 in most-
- significant-byte first (network) order.
-
-
-
-
-
-
-
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-Deutsch & Gailly Informational [Page 6]
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-RFC 1950 ZLIB Compressed Data Format Specification May 1996
-
-
- 2.3. Compliance
-
- A compliant compressor must produce streams with correct CMF, FLG
- and ADLER32, but need not support preset dictionaries. When the
- zlib data format is used as part of another standard data format,
- the compressor may use only preset dictionaries that are specified
- by this other data format. If this other format does not use the
- preset dictionary feature, the compressor must not set the FDICT
- flag.
-
- A compliant decompressor must check CMF, FLG, and ADLER32, and
- provide an error indication if any of these have incorrect values.
- A compliant decompressor must give an error indication if CM is
- not one of the values defined in this specification (only the
- value 8 is permitted in this version), since another value could
- indicate the presence of new features that would cause subsequent
- data to be interpreted incorrectly. A compliant decompressor must
- give an error indication if FDICT is set and DICTID is not the
- identifier of a known preset dictionary. A decompressor may
- ignore FLEVEL and still be compliant. When the zlib data format
- is being used as a part of another standard format, a compliant
- decompressor must support all the preset dictionaries specified by
- the other format. When the other format does not use the preset
- dictionary feature, a compliant decompressor must reject any
- stream in which the FDICT flag is set.
-
-3. References
-
- [1] Deutsch, L.P.,"GZIP Compressed Data Format Specification",
- available in ftp://ftp.uu.net/pub/archiving/zip/doc/
-
- [2] Thomas Boutell, "PNG (Portable Network Graphics) specification",
- available in ftp://ftp.uu.net/graphics/png/documents/
-
- [3] Deutsch, L.P.,"DEFLATE Compressed Data Format Specification",
- available in ftp://ftp.uu.net/pub/archiving/zip/doc/
-
- [4] Fletcher, J. G., "An Arithmetic Checksum for Serial
- Transmissions," IEEE Transactions on Communications, Vol. COM-30,
- No. 1, January 1982, pp. 247-252.
-
- [5] ITU-T Recommendation X.224, Annex D, "Checksum Algorithms,"
- November, 1993, pp. 144, 145. (Available from
- gopher://info.itu.ch). ITU-T X.244 is also the same as ISO 8073.
-
-
-
-
-
-
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-RFC 1950 ZLIB Compressed Data Format Specification May 1996
-
-
-4. Source code
-
- Source code for a C language implementation of a "zlib" compliant
- library is available at ftp://ftp.uu.net/pub/archiving/zip/zlib/.
-
-5. Security Considerations
-
- A decoder that fails to check the ADLER32 checksum value may be
- subject to undetected data corruption.
-
-6. Acknowledgements
-
- Trademarks cited in this document are the property of their
- respective owners.
-
- Jean-Loup Gailly and Mark Adler designed the zlib format and wrote
- the related software described in this specification. Glenn
- Randers-Pehrson converted this document to RFC and HTML format.
-
-7. Authors' Addresses
-
- L. Peter Deutsch
- Aladdin Enterprises
- 203 Santa Margarita Ave.
- Menlo Park, CA 94025
-
- Phone: (415) 322-0103 (AM only)
- FAX: (415) 322-1734
- EMail: <ghost at aladdin.com>
-
-
- Jean-Loup Gailly
-
- EMail: <gzip at prep.ai.mit.edu>
-
- Questions about the technical content of this specification can be
- sent by email to
-
- Jean-Loup Gailly <gzip at prep.ai.mit.edu> and
- Mark Adler <madler at alumni.caltech.edu>
-
- Editorial comments on this specification can be sent by email to
-
- L. Peter Deutsch <ghost at aladdin.com> and
- Glenn Randers-Pehrson <randeg at alumni.rpi.edu>
-
-
-
-
-
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-RFC 1950 ZLIB Compressed Data Format Specification May 1996
-
-
-8. Appendix: Rationale
-
- 8.1. Preset dictionaries
-
- A preset dictionary is specially useful to compress short input
- sequences. The compressor can take advantage of the dictionary
- context to encode the input in a more compact manner. The
- decompressor can be initialized with the appropriate context by
- virtually decompressing a compressed version of the dictionary
- without producing any output. However for certain compression
- algorithms such as the deflate algorithm this operation can be
- achieved without actually performing any decompression.
-
- The compressor and the decompressor must use exactly the same
- dictionary. The dictionary may be fixed or may be chosen among a
- certain number of predefined dictionaries, according to the kind
- of input data. The decompressor can determine which dictionary has
- been chosen by the compressor by checking the dictionary
- identifier. This document does not specify the contents of
- predefined dictionaries, since the optimal dictionaries are
- application specific. Standard data formats using this feature of
- the zlib specification must precisely define the allowed
- dictionaries.
-
- 8.2. The Adler-32 algorithm
-
- The Adler-32 algorithm is much faster than the CRC32 algorithm yet
- still provides an extremely low probability of undetected errors.
-
- The modulo on unsigned long accumulators can be delayed for 5552
- bytes, so the modulo operation time is negligible. If the bytes
- are a, b, c, the second sum is 3a + 2b + c + 3, and so is position
- and order sensitive, unlike the first sum, which is just a
- checksum. That 65521 is prime is important to avoid a possible
- large class of two-byte errors that leave the check unchanged.
- (The Fletcher checksum uses 255, which is not prime and which also
- makes the Fletcher check insensitive to single byte changes 0 <->
- 255.)
-
- The sum s1 is initialized to 1 instead of zero to make the length
- of the sequence part of s2, so that the length does not have to be
- checked separately. (Any sequence of zeroes has a Fletcher
- checksum of zero.)
-
-
-
-
-
-
-
-
-Deutsch & Gailly Informational [Page 9]
-
-RFC 1950 ZLIB Compressed Data Format Specification May 1996
-
-
-9. Appendix: Sample code
-
- The following C code computes the Adler-32 checksum of a data buffer.
- It is written for clarity, not for speed. The sample code is in the
- ANSI C programming language. Non C users may find it easier to read
- with these hints:
-
- & Bitwise AND operator.
- >> Bitwise right shift operator. When applied to an
- unsigned quantity, as here, right shift inserts zero bit(s)
- at the left.
- << Bitwise left shift operator. Left shift inserts zero
- bit(s) at the right.
- ++ "n++" increments the variable n.
- % modulo operator: a % b is the remainder of a divided by b.
-
- #define BASE 65521 /* largest prime smaller than 65536 */
-
- /*
- Update a running Adler-32 checksum with the bytes buf[0..len-1]
- and return the updated checksum. The Adler-32 checksum should be
- initialized to 1.
-
- Usage example:
-
- unsigned long adler = 1L;
-
- while (read_buffer(buffer, length) != EOF) {
- adler = update_adler32(adler, buffer, length);
- }
- if (adler != original_adler) error();
- */
- unsigned long update_adler32(unsigned long adler,
- unsigned char *buf, int len)
- {
- unsigned long s1 = adler & 0xffff;
- unsigned long s2 = (adler >> 16) & 0xffff;
- int n;
-
- for (n = 0; n < len; n++) {
- s1 = (s1 + buf[n]) % BASE;
- s2 = (s2 + s1) % BASE;
- }
- return (s2 << 16) + s1;
- }
-
- /* Return the adler32 of the bytes buf[0..len-1] */
-
-
-
-
-Deutsch & Gailly Informational [Page 10]
-
-RFC 1950 ZLIB Compressed Data Format Specification May 1996
-
-
- unsigned long adler32(unsigned char *buf, int len)
- {
- return update_adler32(1L, buf, len);
- }
-
-
-
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-
-
-
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-
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diff --git a/third-party/zlib/doc/rfc1951.txt b/third-party/zlib/doc/rfc1951.txt
deleted file mode 100644
index 403c8c7..0000000
--- a/third-party/zlib/doc/rfc1951.txt
+++ /dev/null
@@ -1,955 +0,0 @@
-
-
-
-
-
-
-Network Working Group P. Deutsch
-Request for Comments: 1951 Aladdin Enterprises
-Category: Informational May 1996
-
-
- DEFLATE Compressed Data Format Specification version 1.3
-
-Status of This Memo
-
- This memo provides information for the Internet community. This memo
- does not specify an Internet standard of any kind. Distribution of
- this memo is unlimited.
-
-IESG Note:
-
- The IESG takes no position on the validity of any Intellectual
- Property Rights statements contained in this document.
-
-Notices
-
- Copyright (c) 1996 L. Peter Deutsch
-
- Permission is granted to copy and distribute this document for any
- purpose and without charge, including translations into other
- languages and incorporation into compilations, provided that the
- copyright notice and this notice are preserved, and that any
- substantive changes or deletions from the original are clearly
- marked.
-
- A pointer to the latest version of this and related documentation in
- HTML format can be found at the URL
- <ftp://ftp.uu.net/graphics/png/documents/zlib/zdoc-index.html>.
-
-Abstract
-
- This specification defines a lossless compressed data format that
- compresses data using a combination of the LZ77 algorithm and Huffman
- coding, with efficiency comparable to the best currently available
- general-purpose compression methods. The data can be produced or
- consumed, even for an arbitrarily long sequentially presented input
- data stream, using only an a priori bounded amount of intermediate
- storage. The format can be implemented readily in a manner not
- covered by patents.
-
-
-
-
-
-
-
-
-Deutsch Informational [Page 1]
-
-RFC 1951 DEFLATE Compressed Data Format Specification May 1996
-
-
-Table of Contents
-
- 1. Introduction ................................................... 2
- 1.1. Purpose ................................................... 2
- 1.2. Intended audience ......................................... 3
- 1.3. Scope ..................................................... 3
- 1.4. Compliance ................................................ 3
- 1.5. Definitions of terms and conventions used ................ 3
- 1.6. Changes from previous versions ............................ 4
- 2. Compressed representation overview ............................. 4
- 3. Detailed specification ......................................... 5
- 3.1. Overall conventions ....................................... 5
- 3.1.1. Packing into bytes .................................. 5
- 3.2. Compressed block format ................................... 6
- 3.2.1. Synopsis of prefix and Huffman coding ............... 6
- 3.2.2. Use of Huffman coding in the "deflate" format ....... 7
- 3.2.3. Details of block format ............................. 9
- 3.2.4. Non-compressed blocks (BTYPE=00) ................... 11
- 3.2.5. Compressed blocks (length and distance codes) ...... 11
- 3.2.6. Compression with fixed Huffman codes (BTYPE=01) .... 12
- 3.2.7. Compression with dynamic Huffman codes (BTYPE=10) .. 13
- 3.3. Compliance ............................................... 14
- 4. Compression algorithm details ................................. 14
- 5. References .................................................... 16
- 6. Security Considerations ....................................... 16
- 7. Source code ................................................... 16
- 8. Acknowledgements .............................................. 16
- 9. Author's Address .............................................. 17
-
-1. Introduction
-
- 1.1. Purpose
-
- The purpose of this specification is to define a lossless
- compressed data format that:
- * Is independent of CPU type, operating system, file system,
- and character set, and hence can be used for interchange;
- * Can be produced or consumed, even for an arbitrarily long
- sequentially presented input data stream, using only an a
- priori bounded amount of intermediate storage, and hence
- can be used in data communications or similar structures
- such as Unix filters;
- * Compresses data with efficiency comparable to the best
- currently available general-purpose compression methods,
- and in particular considerably better than the "compress"
- program;
- * Can be implemented readily in a manner not covered by
- patents, and hence can be practiced freely;
-
-
-
-Deutsch Informational [Page 2]
-
-RFC 1951 DEFLATE Compressed Data Format Specification May 1996
-
-
- * Is compatible with the file format produced by the current
- widely used gzip utility, in that conforming decompressors
- will be able to read data produced by the existing gzip
- compressor.
-
- The data format defined by this specification does not attempt to:
-
- * Allow random access to compressed data;
- * Compress specialized data (e.g., raster graphics) as well
- as the best currently available specialized algorithms.
-
- A simple counting argument shows that no lossless compression
- algorithm can compress every possible input data set. For the
- format defined here, the worst case expansion is 5 bytes per 32K-
- byte block, i.e., a size increase of 0.015% for large data sets.
- English text usually compresses by a factor of 2.5 to 3;
- executable files usually compress somewhat less; graphical data
- such as raster images may compress much more.
-
- 1.2. Intended audience
-
- This specification is intended for use by implementors of software
- to compress data into "deflate" format and/or decompress data from
- "deflate" format.
-
- The text of the specification assumes a basic background in
- programming at the level of bits and other primitive data
- representations. Familiarity with the technique of Huffman coding
- is helpful but not required.
-
- 1.3. Scope
-
- The specification specifies a method for representing a sequence
- of bytes as a (usually shorter) sequence of bits, and a method for
- packing the latter bit sequence into bytes.
-
- 1.4. Compliance
-
- Unless otherwise indicated below, a compliant decompressor must be
- able to accept and decompress any data set that conforms to all
- the specifications presented here; a compliant compressor must
- produce data sets that conform to all the specifications presented
- here.
-
- 1.5. Definitions of terms and conventions used
-
- Byte: 8 bits stored or transmitted as a unit (same as an octet).
- For this specification, a byte is exactly 8 bits, even on machines
-
-
-
-Deutsch Informational [Page 3]
-
-RFC 1951 DEFLATE Compressed Data Format Specification May 1996
-
-
- which store a character on a number of bits different from eight.
- See below, for the numbering of bits within a byte.
-
- String: a sequence of arbitrary bytes.
-
- 1.6. Changes from previous versions
-
- There have been no technical changes to the deflate format since
- version 1.1 of this specification. In version 1.2, some
- terminology was changed. Version 1.3 is a conversion of the
- specification to RFC style.
-
-2. Compressed representation overview
-
- A compressed data set consists of a series of blocks, corresponding
- to successive blocks of input data. The block sizes are arbitrary,
- except that non-compressible blocks are limited to 65,535 bytes.
-
- Each block is compressed using a combination of the LZ77 algorithm
- and Huffman coding. The Huffman trees for each block are independent
- of those for previous or subsequent blocks; the LZ77 algorithm may
- use a reference to a duplicated string occurring in a previous block,
- up to 32K input bytes before.
-
- Each block consists of two parts: a pair of Huffman code trees that
- describe the representation of the compressed data part, and a
- compressed data part. (The Huffman trees themselves are compressed
- using Huffman encoding.) The compressed data consists of a series of
- elements of two types: literal bytes (of strings that have not been
- detected as duplicated within the previous 32K input bytes), and
- pointers to duplicated strings, where a pointer is represented as a
- pair <length, backward distance>. The representation used in the
- "deflate" format limits distances to 32K bytes and lengths to 258
- bytes, but does not limit the size of a block, except for
- uncompressible blocks, which are limited as noted above.
-
- Each type of value (literals, distances, and lengths) in the
- compressed data is represented using a Huffman code, using one code
- tree for literals and lengths and a separate code tree for distances.
- The code trees for each block appear in a compact form just before
- the compressed data for that block.
-
-
-
-
-
-
-
-
-
-
-Deutsch Informational [Page 4]
-
-RFC 1951 DEFLATE Compressed Data Format Specification May 1996
-
-
-3. Detailed specification
-
- 3.1. Overall conventions In the diagrams below, a box like this:
-
- +---+
- | | <-- the vertical bars might be missing
- +---+
-
- represents one byte; a box like this:
-
- +==============+
- | |
- +==============+
-
- represents a variable number of bytes.
-
- Bytes stored within a computer do not have a "bit order", since
- they are always treated as a unit. However, a byte considered as
- an integer between 0 and 255 does have a most- and least-
- significant bit, and since we write numbers with the most-
- significant digit on the left, we also write bytes with the most-
- significant bit on the left. In the diagrams below, we number the
- bits of a byte so that bit 0 is the least-significant bit, i.e.,
- the bits are numbered:
-
- +--------+
- |76543210|
- +--------+
-
- Within a computer, a number may occupy multiple bytes. All
- multi-byte numbers in the format described here are stored with
- the least-significant byte first (at the lower memory address).
- For example, the decimal number 520 is stored as:
-
- 0 1
- +--------+--------+
- |00001000|00000010|
- +--------+--------+
- ^ ^
- | |
- | + more significant byte = 2 x 256
- + less significant byte = 8
-
- 3.1.1. Packing into bytes
-
- This document does not address the issue of the order in which
- bits of a byte are transmitted on a bit-sequential medium,
- since the final data format described here is byte- rather than
-
-
-
-Deutsch Informational [Page 5]
-
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-
-
- bit-oriented. However, we describe the compressed block format
- in below, as a sequence of data elements of various bit
- lengths, not a sequence of bytes. We must therefore specify
- how to pack these data elements into bytes to form the final
- compressed byte sequence:
-
- * Data elements are packed into bytes in order of
- increasing bit number within the byte, i.e., starting
- with the least-significant bit of the byte.
- * Data elements other than Huffman codes are packed
- starting with the least-significant bit of the data
- element.
- * Huffman codes are packed starting with the most-
- significant bit of the code.
-
- In other words, if one were to print out the compressed data as
- a sequence of bytes, starting with the first byte at the
- *right* margin and proceeding to the *left*, with the most-
- significant bit of each byte on the left as usual, one would be
- able to parse the result from right to left, with fixed-width
- elements in the correct MSB-to-LSB order and Huffman codes in
- bit-reversed order (i.e., with the first bit of the code in the
- relative LSB position).
-
- 3.2. Compressed block format
-
- 3.2.1. Synopsis of prefix and Huffman coding
-
- Prefix coding represents symbols from an a priori known
- alphabet by bit sequences (codes), one code for each symbol, in
- a manner such that different symbols may be represented by bit
- sequences of different lengths, but a parser can always parse
- an encoded string unambiguously symbol-by-symbol.
-
- We define a prefix code in terms of a binary tree in which the
- two edges descending from each non-leaf node are labeled 0 and
- 1 and in which the leaf nodes correspond one-for-one with (are
- labeled with) the symbols of the alphabet; then the code for a
- symbol is the sequence of 0's and 1's on the edges leading from
- the root to the leaf labeled with that symbol. For example:
-
-
-
-
-
-
-
-
-
-
-
-Deutsch Informational [Page 6]
-
-RFC 1951 DEFLATE Compressed Data Format Specification May 1996
-
-
- /\ Symbol Code
- 0 1 ------ ----
- / \ A 00
- /\ B B 1
- 0 1 C 011
- / \ D 010
- A /\
- 0 1
- / \
- D C
-
- A parser can decode the next symbol from an encoded input
- stream by walking down the tree from the root, at each step
- choosing the edge corresponding to the next input bit.
-
- Given an alphabet with known symbol frequencies, the Huffman
- algorithm allows the construction of an optimal prefix code
- (one which represents strings with those symbol frequencies
- using the fewest bits of any possible prefix codes for that
- alphabet). Such a code is called a Huffman code. (See
- reference [1] in Chapter 5, references for additional
- information on Huffman codes.)
-
- Note that in the "deflate" format, the Huffman codes for the
- various alphabets must not exceed certain maximum code lengths.
- This constraint complicates the algorithm for computing code
- lengths from symbol frequencies. Again, see Chapter 5,
- references for details.
-
- 3.2.2. Use of Huffman coding in the "deflate" format
-
- The Huffman codes used for each alphabet in the "deflate"
- format have two additional rules:
-
- * All codes of a given bit length have lexicographically
- consecutive values, in the same order as the symbols
- they represent;
-
- * Shorter codes lexicographically precede longer codes.
-
-
-
-
-
-
-
-
-
-
-
-
-Deutsch Informational [Page 7]
-
-RFC 1951 DEFLATE Compressed Data Format Specification May 1996
-
-
- We could recode the example above to follow this rule as
- follows, assuming that the order of the alphabet is ABCD:
-
- Symbol Code
- ------ ----
- A 10
- B 0
- C 110
- D 111
-
- I.e., 0 precedes 10 which precedes 11x, and 110 and 111 are
- lexicographically consecutive.
-
- Given this rule, we can define the Huffman code for an alphabet
- just by giving the bit lengths of the codes for each symbol of
- the alphabet in order; this is sufficient to determine the
- actual codes. In our example, the code is completely defined
- by the sequence of bit lengths (2, 1, 3, 3). The following
- algorithm generates the codes as integers, intended to be read
- from most- to least-significant bit. The code lengths are
- initially in tree[I].Len; the codes are produced in
- tree[I].Code.
-
- 1) Count the number of codes for each code length. Let
- bl_count[N] be the number of codes of length N, N >= 1.
-
- 2) Find the numerical value of the smallest code for each
- code length:
-
- code = 0;
- bl_count[0] = 0;
- for (bits = 1; bits <= MAX_BITS; bits++) {
- code = (code + bl_count[bits-1]) << 1;
- next_code[bits] = code;
- }
-
- 3) Assign numerical values to all codes, using consecutive
- values for all codes of the same length with the base
- values determined at step 2. Codes that are never used
- (which have a bit length of zero) must not be assigned a
- value.
-
- for (n = 0; n <= max_code; n++) {
- len = tree[n].Len;
- if (len != 0) {
- tree[n].Code = next_code[len];
- next_code[len]++;
- }
-
-
-
-Deutsch Informational [Page 8]
-
-RFC 1951 DEFLATE Compressed Data Format Specification May 1996
-
-
- }
-
- Example:
-
- Consider the alphabet ABCDEFGH, with bit lengths (3, 3, 3, 3,
- 3, 2, 4, 4). After step 1, we have:
-
- N bl_count[N]
- - -----------
- 2 1
- 3 5
- 4 2
-
- Step 2 computes the following next_code values:
-
- N next_code[N]
- - ------------
- 1 0
- 2 0
- 3 2
- 4 14
-
- Step 3 produces the following code values:
-
- Symbol Length Code
- ------ ------ ----
- A 3 010
- B 3 011
- C 3 100
- D 3 101
- E 3 110
- F 2 00
- G 4 1110
- H 4 1111
-
- 3.2.3. Details of block format
-
- Each block of compressed data begins with 3 header bits
- containing the following data:
-
- first bit BFINAL
- next 2 bits BTYPE
-
- Note that the header bits do not necessarily begin on a byte
- boundary, since a block does not necessarily occupy an integral
- number of bytes.
-
-
-
-
-
-Deutsch Informational [Page 9]
-
-RFC 1951 DEFLATE Compressed Data Format Specification May 1996
-
-
- BFINAL is set if and only if this is the last block of the data
- set.
-
- BTYPE specifies how the data are compressed, as follows:
-
- 00 - no compression
- 01 - compressed with fixed Huffman codes
- 10 - compressed with dynamic Huffman codes
- 11 - reserved (error)
-
- The only difference between the two compressed cases is how the
- Huffman codes for the literal/length and distance alphabets are
- defined.
-
- In all cases, the decoding algorithm for the actual data is as
- follows:
-
- do
- read block header from input stream.
- if stored with no compression
- skip any remaining bits in current partially
- processed byte
- read LEN and NLEN (see next section)
- copy LEN bytes of data to output
- otherwise
- if compressed with dynamic Huffman codes
- read representation of code trees (see
- subsection below)
- loop (until end of block code recognized)
- decode literal/length value from input stream
- if value < 256
- copy value (literal byte) to output stream
- otherwise
- if value = end of block (256)
- break from loop
- otherwise (value = 257..285)
- decode distance from input stream
-
- move backwards distance bytes in the output
- stream, and copy length bytes from this
- position to the output stream.
- end loop
- while not last block
-
- Note that a duplicated string reference may refer to a string
- in a previous block; i.e., the backward distance may cross one
- or more block boundaries. However a distance cannot refer past
- the beginning of the output stream. (An application using a
-
-
-
-Deutsch Informational [Page 10]
-
-RFC 1951 DEFLATE Compressed Data Format Specification May 1996
-
-
- preset dictionary might discard part of the output stream; a
- distance can refer to that part of the output stream anyway)
- Note also that the referenced string may overlap the current
- position; for example, if the last 2 bytes decoded have values
- X and Y, a string reference with <length = 5, distance = 2>
- adds X,Y,X,Y,X to the output stream.
-
- We now specify each compression method in turn.
-
- 3.2.4. Non-compressed blocks (BTYPE=00)
-
- Any bits of input up to the next byte boundary are ignored.
- The rest of the block consists of the following information:
-
- 0 1 2 3 4...
- +---+---+---+---+================================+
- | LEN | NLEN |... LEN bytes of literal data...|
- +---+---+---+---+================================+
-
- LEN is the number of data bytes in the block. NLEN is the
- one's complement of LEN.
-
- 3.2.5. Compressed blocks (length and distance codes)
-
- As noted above, encoded data blocks in the "deflate" format
- consist of sequences of symbols drawn from three conceptually
- distinct alphabets: either literal bytes, from the alphabet of
- byte values (0..255), or <length, backward distance> pairs,
- where the length is drawn from (3..258) and the distance is
- drawn from (1..32,768). In fact, the literal and length
- alphabets are merged into a single alphabet (0..285), where
- values 0..255 represent literal bytes, the value 256 indicates
- end-of-block, and values 257..285 represent length codes
- (possibly in conjunction with extra bits following the symbol
- code) as follows:
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-Deutsch Informational [Page 11]
-
-RFC 1951 DEFLATE Compressed Data Format Specification May 1996
-
-
- Extra Extra Extra
- Code Bits Length(s) Code Bits Lengths Code Bits Length(s)
- ---- ---- ------ ---- ---- ------- ---- ---- -------
- 257 0 3 267 1 15,16 277 4 67-82
- 258 0 4 268 1 17,18 278 4 83-98
- 259 0 5 269 2 19-22 279 4 99-114
- 260 0 6 270 2 23-26 280 4 115-130
- 261 0 7 271 2 27-30 281 5 131-162
- 262 0 8 272 2 31-34 282 5 163-194
- 263 0 9 273 3 35-42 283 5 195-226
- 264 0 10 274 3 43-50 284 5 227-257
- 265 1 11,12 275 3 51-58 285 0 258
- 266 1 13,14 276 3 59-66
-
- The extra bits should be interpreted as a machine integer
- stored with the most-significant bit first, e.g., bits 1110
- represent the value 14.
-
- Extra Extra Extra
- Code Bits Dist Code Bits Dist Code Bits Distance
- ---- ---- ---- ---- ---- ------ ---- ---- --------
- 0 0 1 10 4 33-48 20 9 1025-1536
- 1 0 2 11 4 49-64 21 9 1537-2048
- 2 0 3 12 5 65-96 22 10 2049-3072
- 3 0 4 13 5 97-128 23 10 3073-4096
- 4 1 5,6 14 6 129-192 24 11 4097-6144
- 5 1 7,8 15 6 193-256 25 11 6145-8192
- 6 2 9-12 16 7 257-384 26 12 8193-12288
- 7 2 13-16 17 7 385-512 27 12 12289-16384
- 8 3 17-24 18 8 513-768 28 13 16385-24576
- 9 3 25-32 19 8 769-1024 29 13 24577-32768
-
- 3.2.6. Compression with fixed Huffman codes (BTYPE=01)
-
- The Huffman codes for the two alphabets are fixed, and are not
- represented explicitly in the data. The Huffman code lengths
- for the literal/length alphabet are:
-
- Lit Value Bits Codes
- --------- ---- -----
- 0 - 143 8 00110000 through
- 10111111
- 144 - 255 9 110010000 through
- 111111111
- 256 - 279 7 0000000 through
- 0010111
- 280 - 287 8 11000000 through
- 11000111
-
-
-
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-
-RFC 1951 DEFLATE Compressed Data Format Specification May 1996
-
-
- The code lengths are sufficient to generate the actual codes,
- as described above; we show the codes in the table for added
- clarity. Literal/length values 286-287 will never actually
- occur in the compressed data, but participate in the code
- construction.
-
- Distance codes 0-31 are represented by (fixed-length) 5-bit
- codes, with possible additional bits as shown in the table
- shown in Paragraph 3.2.5, above. Note that distance codes 30-
- 31 will never actually occur in the compressed data.
-
- 3.2.7. Compression with dynamic Huffman codes (BTYPE=10)
-
- The Huffman codes for the two alphabets appear in the block
- immediately after the header bits and before the actual
- compressed data, first the literal/length code and then the
- distance code. Each code is defined by a sequence of code
- lengths, as discussed in Paragraph 3.2.2, above. For even
- greater compactness, the code length sequences themselves are
- compressed using a Huffman code. The alphabet for code lengths
- is as follows:
-
- 0 - 15: Represent code lengths of 0 - 15
- 16: Copy the previous code length 3 - 6 times.
- The next 2 bits indicate repeat length
- (0 = 3, ... , 3 = 6)
- Example: Codes 8, 16 (+2 bits 11),
- 16 (+2 bits 10) will expand to
- 12 code lengths of 8 (1 + 6 + 5)
- 17: Repeat a code length of 0 for 3 - 10 times.
- (3 bits of length)
- 18: Repeat a code length of 0 for 11 - 138 times
- (7 bits of length)
-
- A code length of 0 indicates that the corresponding symbol in
- the literal/length or distance alphabet will not occur in the
- block, and should not participate in the Huffman code
- construction algorithm given earlier. If only one distance
- code is used, it is encoded using one bit, not zero bits; in
- this case there is a single code length of one, with one unused
- code. One distance code of zero bits means that there are no
- distance codes used at all (the data is all literals).
-
- We can now define the format of the block:
-
- 5 Bits: HLIT, # of Literal/Length codes - 257 (257 - 286)
- 5 Bits: HDIST, # of Distance codes - 1 (1 - 32)
- 4 Bits: HCLEN, # of Code Length codes - 4 (4 - 19)
-
-
-
-Deutsch Informational [Page 13]
-
-RFC 1951 DEFLATE Compressed Data Format Specification May 1996
-
-
- (HCLEN + 4) x 3 bits: code lengths for the code length
- alphabet given just above, in the order: 16, 17, 18,
- 0, 8, 7, 9, 6, 10, 5, 11, 4, 12, 3, 13, 2, 14, 1, 15
-
- These code lengths are interpreted as 3-bit integers
- (0-7); as above, a code length of 0 means the
- corresponding symbol (literal/length or distance code
- length) is not used.
-
- HLIT + 257 code lengths for the literal/length alphabet,
- encoded using the code length Huffman code
-
- HDIST + 1 code lengths for the distance alphabet,
- encoded using the code length Huffman code
-
- The actual compressed data of the block,
- encoded using the literal/length and distance Huffman
- codes
-
- The literal/length symbol 256 (end of data),
- encoded using the literal/length Huffman code
-
- The code length repeat codes can cross from HLIT + 257 to the
- HDIST + 1 code lengths. In other words, all code lengths form
- a single sequence of HLIT + HDIST + 258 values.
-
- 3.3. Compliance
-
- A compressor may limit further the ranges of values specified in
- the previous section and still be compliant; for example, it may
- limit the range of backward pointers to some value smaller than
- 32K. Similarly, a compressor may limit the size of blocks so that
- a compressible block fits in memory.
-
- A compliant decompressor must accept the full range of possible
- values defined in the previous section, and must accept blocks of
- arbitrary size.
-
-4. Compression algorithm details
-
- While it is the intent of this document to define the "deflate"
- compressed data format without reference to any particular
- compression algorithm, the format is related to the compressed
- formats produced by LZ77 (Lempel-Ziv 1977, see reference [2] below);
- since many variations of LZ77 are patented, it is strongly
- recommended that the implementor of a compressor follow the general
- algorithm presented here, which is known not to be patented per se.
- The material in this section is not part of the definition of the
-
-
-
-Deutsch Informational [Page 14]
-
-RFC 1951 DEFLATE Compressed Data Format Specification May 1996
-
-
- specification per se, and a compressor need not follow it in order to
- be compliant.
-
- The compressor terminates a block when it determines that starting a
- new block with fresh trees would be useful, or when the block size
- fills up the compressor's block buffer.
-
- The compressor uses a chained hash table to find duplicated strings,
- using a hash function that operates on 3-byte sequences. At any
- given point during compression, let XYZ be the next 3 input bytes to
- be examined (not necessarily all different, of course). First, the
- compressor examines the hash chain for XYZ. If the chain is empty,
- the compressor simply writes out X as a literal byte and advances one
- byte in the input. If the hash chain is not empty, indicating that
- the sequence XYZ (or, if we are unlucky, some other 3 bytes with the
- same hash function value) has occurred recently, the compressor
- compares all strings on the XYZ hash chain with the actual input data
- sequence starting at the current point, and selects the longest
- match.
-
- The compressor searches the hash chains starting with the most recent
- strings, to favor small distances and thus take advantage of the
- Huffman encoding. The hash chains are singly linked. There are no
- deletions from the hash chains; the algorithm simply discards matches
- that are too old. To avoid a worst-case situation, very long hash
- chains are arbitrarily truncated at a certain length, determined by a
- run-time parameter.
-
- To improve overall compression, the compressor optionally defers the
- selection of matches ("lazy matching"): after a match of length N has
- been found, the compressor searches for a longer match starting at
- the next input byte. If it finds a longer match, it truncates the
- previous match to a length of one (thus producing a single literal
- byte) and then emits the longer match. Otherwise, it emits the
- original match, and, as described above, advances N bytes before
- continuing.
-
- Run-time parameters also control this "lazy match" procedure. If
- compression ratio is most important, the compressor attempts a
- complete second search regardless of the length of the first match.
- In the normal case, if the current match is "long enough", the
- compressor reduces the search for a longer match, thus speeding up
- the process. If speed is most important, the compressor inserts new
- strings in the hash table only when no match was found, or when the
- match is not "too long". This degrades the compression ratio but
- saves time since there are both fewer insertions and fewer searches.
-
-
-
-
-
-Deutsch Informational [Page 15]
-
-RFC 1951 DEFLATE Compressed Data Format Specification May 1996
-
-
-5. References
-
- [1] Huffman, D. A., "A Method for the Construction of Minimum
- Redundancy Codes", Proceedings of the Institute of Radio
- Engineers, September 1952, Volume 40, Number 9, pp. 1098-1101.
-
- [2] Ziv J., Lempel A., "A Universal Algorithm for Sequential Data
- Compression", IEEE Transactions on Information Theory, Vol. 23,
- No. 3, pp. 337-343.
-
- [3] Gailly, J.-L., and Adler, M., ZLIB documentation and sources,
- available in ftp://ftp.uu.net/pub/archiving/zip/doc/
-
- [4] Gailly, J.-L., and Adler, M., GZIP documentation and sources,
- available as gzip-*.tar in ftp://prep.ai.mit.edu/pub/gnu/
-
- [5] Schwartz, E. S., and Kallick, B. "Generating a canonical prefix
- encoding." Comm. ACM, 7,3 (Mar. 1964), pp. 166-169.
-
- [6] Hirschberg and Lelewer, "Efficient decoding of prefix codes,"
- Comm. ACM, 33,4, April 1990, pp. 449-459.
-
-6. Security Considerations
-
- Any data compression method involves the reduction of redundancy in
- the data. Consequently, any corruption of the data is likely to have
- severe effects and be difficult to correct. Uncompressed text, on
- the other hand, will probably still be readable despite the presence
- of some corrupted bytes.
-
- It is recommended that systems using this data format provide some
- means of validating the integrity of the compressed data. See
- reference [3], for example.
-
-7. Source code
-
- Source code for a C language implementation of a "deflate" compliant
- compressor and decompressor is available within the zlib package at
- ftp://ftp.uu.net/pub/archiving/zip/zlib/.
-
-8. Acknowledgements
-
- Trademarks cited in this document are the property of their
- respective owners.
-
- Phil Katz designed the deflate format. Jean-Loup Gailly and Mark
- Adler wrote the related software described in this specification.
- Glenn Randers-Pehrson converted this document to RFC and HTML format.
-
-
-
-Deutsch Informational [Page 16]
-
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-
-
-9. Author's Address
-
- L. Peter Deutsch
- Aladdin Enterprises
- 203 Santa Margarita Ave.
- Menlo Park, CA 94025
-
- Phone: (415) 322-0103 (AM only)
- FAX: (415) 322-1734
- EMail: <ghost at aladdin.com>
-
- Questions about the technical content of this specification can be
- sent by email to:
-
- Jean-Loup Gailly <gzip at prep.ai.mit.edu> and
- Mark Adler <madler at alumni.caltech.edu>
-
- Editorial comments on this specification can be sent by email to:
-
- L. Peter Deutsch <ghost at aladdin.com> and
- Glenn Randers-Pehrson <randeg at alumni.rpi.edu>
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-Deutsch Informational [Page 17]
-
diff --git a/third-party/zlib/doc/rfc1952.txt b/third-party/zlib/doc/rfc1952.txt
deleted file mode 100644
index a8e51b4..0000000
--- a/third-party/zlib/doc/rfc1952.txt
+++ /dev/null
@@ -1,675 +0,0 @@
-
-
-
-
-
-
-Network Working Group P. Deutsch
-Request for Comments: 1952 Aladdin Enterprises
-Category: Informational May 1996
-
-
- GZIP file format specification version 4.3
-
-Status of This Memo
-
- This memo provides information for the Internet community. This memo
- does not specify an Internet standard of any kind. Distribution of
- this memo is unlimited.
-
-IESG Note:
-
- The IESG takes no position on the validity of any Intellectual
- Property Rights statements contained in this document.
-
-Notices
-
- Copyright (c) 1996 L. Peter Deutsch
-
- Permission is granted to copy and distribute this document for any
- purpose and without charge, including translations into other
- languages and incorporation into compilations, provided that the
- copyright notice and this notice are preserved, and that any
- substantive changes or deletions from the original are clearly
- marked.
-
- A pointer to the latest version of this and related documentation in
- HTML format can be found at the URL
- <ftp://ftp.uu.net/graphics/png/documents/zlib/zdoc-index.html>.
-
-Abstract
-
- This specification defines a lossless compressed data format that is
- compatible with the widely used GZIP utility. The format includes a
- cyclic redundancy check value for detecting data corruption. The
- format presently uses the DEFLATE method of compression but can be
- easily extended to use other compression methods. The format can be
- implemented readily in a manner not covered by patents.
-
-
-
-
-
-
-
-
-
-
-Deutsch Informational [Page 1]
-
-RFC 1952 GZIP File Format Specification May 1996
-
-
-Table of Contents
-
- 1. Introduction ................................................... 2
- 1.1. Purpose ................................................... 2
- 1.2. Intended audience ......................................... 3
- 1.3. Scope ..................................................... 3
- 1.4. Compliance ................................................ 3
- 1.5. Definitions of terms and conventions used ................. 3
- 1.6. Changes from previous versions ............................ 3
- 2. Detailed specification ......................................... 4
- 2.1. Overall conventions ....................................... 4
- 2.2. File format ............................................... 5
- 2.3. Member format ............................................. 5
- 2.3.1. Member header and trailer ........................... 6
- 2.3.1.1. Extra field ................................... 8
- 2.3.1.2. Compliance .................................... 9
- 3. References .................................................. 9
- 4. Security Considerations .................................... 10
- 5. Acknowledgements ........................................... 10
- 6. Author's Address ........................................... 10
- 7. Appendix: Jean-Loup Gailly's gzip utility .................. 11
- 8. Appendix: Sample CRC Code .................................. 11
-
-1. Introduction
-
- 1.1. Purpose
-
- The purpose of this specification is to define a lossless
- compressed data format that:
-
- * Is independent of CPU type, operating system, file system,
- and character set, and hence can be used for interchange;
- * Can compress or decompress a data stream (as opposed to a
- randomly accessible file) to produce another data stream,
- using only an a priori bounded amount of intermediate
- storage, and hence can be used in data communications or
- similar structures such as Unix filters;
- * Compresses data with efficiency comparable to the best
- currently available general-purpose compression methods,
- and in particular considerably better than the "compress"
- program;
- * Can be implemented readily in a manner not covered by
- patents, and hence can be practiced freely;
- * Is compatible with the file format produced by the current
- widely used gzip utility, in that conforming decompressors
- will be able to read data produced by the existing gzip
- compressor.
-
-
-
-
-Deutsch Informational [Page 2]
-
-RFC 1952 GZIP File Format Specification May 1996
-
-
- The data format defined by this specification does not attempt to:
-
- * Provide random access to compressed data;
- * Compress specialized data (e.g., raster graphics) as well as
- the best currently available specialized algorithms.
-
- 1.2. Intended audience
-
- This specification is intended for use by implementors of software
- to compress data into gzip format and/or decompress data from gzip
- format.
-
- The text of the specification assumes a basic background in
- programming at the level of bits and other primitive data
- representations.
-
- 1.3. Scope
-
- The specification specifies a compression method and a file format
- (the latter assuming only that a file can store a sequence of
- arbitrary bytes). It does not specify any particular interface to
- a file system or anything about character sets or encodings
- (except for file names and comments, which are optional).
-
- 1.4. Compliance
-
- Unless otherwise indicated below, a compliant decompressor must be
- able to accept and decompress any file that conforms to all the
- specifications presented here; a compliant compressor must produce
- files that conform to all the specifications presented here. The
- material in the appendices is not part of the specification per se
- and is not relevant to compliance.
-
- 1.5. Definitions of terms and conventions used
-
- byte: 8 bits stored or transmitted as a unit (same as an octet).
- (For this specification, a byte is exactly 8 bits, even on
- machines which store a character on a number of bits different
- from 8.) See below for the numbering of bits within a byte.
-
- 1.6. Changes from previous versions
-
- There have been no technical changes to the gzip format since
- version 4.1 of this specification. In version 4.2, some
- terminology was changed, and the sample CRC code was rewritten for
- clarity and to eliminate the requirement for the caller to do pre-
- and post-conditioning. Version 4.3 is a conversion of the
- specification to RFC style.
-
-
-
-Deutsch Informational [Page 3]
-
-RFC 1952 GZIP File Format Specification May 1996
-
-
-2. Detailed specification
-
- 2.1. Overall conventions
-
- In the diagrams below, a box like this:
-
- +---+
- | | <-- the vertical bars might be missing
- +---+
-
- represents one byte; a box like this:
-
- +==============+
- | |
- +==============+
-
- represents a variable number of bytes.
-
- Bytes stored within a computer do not have a "bit order", since
- they are always treated as a unit. However, a byte considered as
- an integer between 0 and 255 does have a most- and least-
- significant bit, and since we write numbers with the most-
- significant digit on the left, we also write bytes with the most-
- significant bit on the left. In the diagrams below, we number the
- bits of a byte so that bit 0 is the least-significant bit, i.e.,
- the bits are numbered:
-
- +--------+
- |76543210|
- +--------+
-
- This document does not address the issue of the order in which
- bits of a byte are transmitted on a bit-sequential medium, since
- the data format described here is byte- rather than bit-oriented.
-
- Within a computer, a number may occupy multiple bytes. All
- multi-byte numbers in the format described here are stored with
- the least-significant byte first (at the lower memory address).
- For example, the decimal number 520 is stored as:
-
- 0 1
- +--------+--------+
- |00001000|00000010|
- +--------+--------+
- ^ ^
- | |
- | + more significant byte = 2 x 256
- + less significant byte = 8
-
-
-
-Deutsch Informational [Page 4]
-
-RFC 1952 GZIP File Format Specification May 1996
-
-
- 2.2. File format
-
- A gzip file consists of a series of "members" (compressed data
- sets). The format of each member is specified in the following
- section. The members simply appear one after another in the file,
- with no additional information before, between, or after them.
-
- 2.3. Member format
-
- Each member has the following structure:
-
- +---+---+---+---+---+---+---+---+---+---+
- |ID1|ID2|CM |FLG| MTIME |XFL|OS | (more-->)
- +---+---+---+---+---+---+---+---+---+---+
-
- (if FLG.FEXTRA set)
-
- +---+---+=================================+
- | XLEN |...XLEN bytes of "extra field"...| (more-->)
- +---+---+=================================+
-
- (if FLG.FNAME set)
-
- +=========================================+
- |...original file name, zero-terminated...| (more-->)
- +=========================================+
-
- (if FLG.FCOMMENT set)
-
- +===================================+
- |...file comment, zero-terminated...| (more-->)
- +===================================+
-
- (if FLG.FHCRC set)
-
- +---+---+
- | CRC16 |
- +---+---+
-
- +=======================+
- |...compressed blocks...| (more-->)
- +=======================+
-
- 0 1 2 3 4 5 6 7
- +---+---+---+---+---+---+---+---+
- | CRC32 | ISIZE |
- +---+---+---+---+---+---+---+---+
-
-
-
-
-Deutsch Informational [Page 5]
-
-RFC 1952 GZIP File Format Specification May 1996
-
-
- 2.3.1. Member header and trailer
-
- ID1 (IDentification 1)
- ID2 (IDentification 2)
- These have the fixed values ID1 = 31 (0x1f, \037), ID2 = 139
- (0x8b, \213), to identify the file as being in gzip format.
-
- CM (Compression Method)
- This identifies the compression method used in the file. CM
- = 0-7 are reserved. CM = 8 denotes the "deflate"
- compression method, which is the one customarily used by
- gzip and which is documented elsewhere.
-
- FLG (FLaGs)
- This flag byte is divided into individual bits as follows:
-
- bit 0 FTEXT
- bit 1 FHCRC
- bit 2 FEXTRA
- bit 3 FNAME
- bit 4 FCOMMENT
- bit 5 reserved
- bit 6 reserved
- bit 7 reserved
-
- If FTEXT is set, the file is probably ASCII text. This is
- an optional indication, which the compressor may set by
- checking a small amount of the input data to see whether any
- non-ASCII characters are present. In case of doubt, FTEXT
- is cleared, indicating binary data. For systems which have
- different file formats for ascii text and binary data, the
- decompressor can use FTEXT to choose the appropriate format.
- We deliberately do not specify the algorithm used to set
- this bit, since a compressor always has the option of
- leaving it cleared and a decompressor always has the option
- of ignoring it and letting some other program handle issues
- of data conversion.
-
- If FHCRC is set, a CRC16 for the gzip header is present,
- immediately before the compressed data. The CRC16 consists
- of the two least significant bytes of the CRC32 for all
- bytes of the gzip header up to and not including the CRC16.
- [The FHCRC bit was never set by versions of gzip up to
- 1.2.4, even though it was documented with a different
- meaning in gzip 1.2.4.]
-
- If FEXTRA is set, optional extra fields are present, as
- described in a following section.
-
-
-
-Deutsch Informational [Page 6]
-
-RFC 1952 GZIP File Format Specification May 1996
-
-
- If FNAME is set, an original file name is present,
- terminated by a zero byte. The name must consist of ISO
- 8859-1 (LATIN-1) characters; on operating systems using
- EBCDIC or any other character set for file names, the name
- must be translated to the ISO LATIN-1 character set. This
- is the original name of the file being compressed, with any
- directory components removed, and, if the file being
- compressed is on a file system with case insensitive names,
- forced to lower case. There is no original file name if the
- data was compressed from a source other than a named file;
- for example, if the source was stdin on a Unix system, there
- is no file name.
-
- If FCOMMENT is set, a zero-terminated file comment is
- present. This comment is not interpreted; it is only
- intended for human consumption. The comment must consist of
- ISO 8859-1 (LATIN-1) characters. Line breaks should be
- denoted by a single line feed character (10 decimal).
-
- Reserved FLG bits must be zero.
-
- MTIME (Modification TIME)
- This gives the most recent modification time of the original
- file being compressed. The time is in Unix format, i.e.,
- seconds since 00:00:00 GMT, Jan. 1, 1970. (Note that this
- may cause problems for MS-DOS and other systems that use
- local rather than Universal time.) If the compressed data
- did not come from a file, MTIME is set to the time at which
- compression started. MTIME = 0 means no time stamp is
- available.
-
- XFL (eXtra FLags)
- These flags are available for use by specific compression
- methods. The "deflate" method (CM = 8) sets these flags as
- follows:
-
- XFL = 2 - compressor used maximum compression,
- slowest algorithm
- XFL = 4 - compressor used fastest algorithm
-
- OS (Operating System)
- This identifies the type of file system on which compression
- took place. This may be useful in determining end-of-line
- convention for text files. The currently defined values are
- as follows:
-
-
-
-
-
-
-Deutsch Informational [Page 7]
-
-RFC 1952 GZIP File Format Specification May 1996
-
-
- 0 - FAT filesystem (MS-DOS, OS/2, NT/Win32)
- 1 - Amiga
- 2 - VMS (or OpenVMS)
- 3 - Unix
- 4 - VM/CMS
- 5 - Atari TOS
- 6 - HPFS filesystem (OS/2, NT)
- 7 - Macintosh
- 8 - Z-System
- 9 - CP/M
- 10 - TOPS-20
- 11 - NTFS filesystem (NT)
- 12 - QDOS
- 13 - Acorn RISCOS
- 255 - unknown
-
- XLEN (eXtra LENgth)
- If FLG.FEXTRA is set, this gives the length of the optional
- extra field. See below for details.
-
- CRC32 (CRC-32)
- This contains a Cyclic Redundancy Check value of the
- uncompressed data computed according to CRC-32 algorithm
- used in the ISO 3309 standard and in section 8.1.1.6.2 of
- ITU-T recommendation V.42. (See http://www.iso.ch for
- ordering ISO documents. See gopher://info.itu.ch for an
- online version of ITU-T V.42.)
-
- ISIZE (Input SIZE)
- This contains the size of the original (uncompressed) input
- data modulo 2^32.
-
- 2.3.1.1. Extra field
-
- If the FLG.FEXTRA bit is set, an "extra field" is present in
- the header, with total length XLEN bytes. It consists of a
- series of subfields, each of the form:
-
- +---+---+---+---+==================================+
- |SI1|SI2| LEN |... LEN bytes of subfield data ...|
- +---+---+---+---+==================================+
-
- SI1 and SI2 provide a subfield ID, typically two ASCII letters
- with some mnemonic value. Jean-Loup Gailly
- <gzip at prep.ai.mit.edu> is maintaining a registry of subfield
- IDs; please send him any subfield ID you wish to use. Subfield
- IDs with SI2 = 0 are reserved for future use. The following
- IDs are currently defined:
-
-
-
-Deutsch Informational [Page 8]
-
-RFC 1952 GZIP File Format Specification May 1996
-
-
- SI1 SI2 Data
- ---------- ---------- ----
- 0x41 ('A') 0x70 ('P') Apollo file type information
-
- LEN gives the length of the subfield data, excluding the 4
- initial bytes.
-
- 2.3.1.2. Compliance
-
- A compliant compressor must produce files with correct ID1,
- ID2, CM, CRC32, and ISIZE, but may set all the other fields in
- the fixed-length part of the header to default values (255 for
- OS, 0 for all others). The compressor must set all reserved
- bits to zero.
-
- A compliant decompressor must check ID1, ID2, and CM, and
- provide an error indication if any of these have incorrect
- values. It must examine FEXTRA/XLEN, FNAME, FCOMMENT and FHCRC
- at least so it can skip over the optional fields if they are
- present. It need not examine any other part of the header or
- trailer; in particular, a decompressor may ignore FTEXT and OS
- and always produce binary output, and still be compliant. A
- compliant decompressor must give an error indication if any
- reserved bit is non-zero, since such a bit could indicate the
- presence of a new field that would cause subsequent data to be
- interpreted incorrectly.
-
-3. References
-
- [1] "Information Processing - 8-bit single-byte coded graphic
- character sets - Part 1: Latin alphabet No.1" (ISO 8859-1:1987).
- The ISO 8859-1 (Latin-1) character set is a superset of 7-bit
- ASCII. Files defining this character set are available as
- iso_8859-1.* in ftp://ftp.uu.net/graphics/png/documents/
-
- [2] ISO 3309
-
- [3] ITU-T recommendation V.42
-
- [4] Deutsch, L.P.,"DEFLATE Compressed Data Format Specification",
- available in ftp://ftp.uu.net/pub/archiving/zip/doc/
-
- [5] Gailly, J.-L., GZIP documentation, available as gzip-*.tar in
- ftp://prep.ai.mit.edu/pub/gnu/
-
- [6] Sarwate, D.V., "Computation of Cyclic Redundancy Checks via Table
- Look-Up", Communications of the ACM, 31(8), pp.1008-1013.
-
-
-
-
-Deutsch Informational [Page 9]
-
-RFC 1952 GZIP File Format Specification May 1996
-
-
- [7] Schwaderer, W.D., "CRC Calculation", April 85 PC Tech Journal,
- pp.118-133.
-
- [8] ftp://ftp.adelaide.edu.au/pub/rocksoft/papers/crc_v3.txt,
- describing the CRC concept.
-
-4. Security Considerations
-
- Any data compression method involves the reduction of redundancy in
- the data. Consequently, any corruption of the data is likely to have
- severe effects and be difficult to correct. Uncompressed text, on
- the other hand, will probably still be readable despite the presence
- of some corrupted bytes.
-
- It is recommended that systems using this data format provide some
- means of validating the integrity of the compressed data, such as by
- setting and checking the CRC-32 check value.
-
-5. Acknowledgements
-
- Trademarks cited in this document are the property of their
- respective owners.
-
- Jean-Loup Gailly designed the gzip format and wrote, with Mark Adler,
- the related software described in this specification. Glenn
- Randers-Pehrson converted this document to RFC and HTML format.
-
-6. Author's Address
-
- L. Peter Deutsch
- Aladdin Enterprises
- 203 Santa Margarita Ave.
- Menlo Park, CA 94025
-
- Phone: (415) 322-0103 (AM only)
- FAX: (415) 322-1734
- EMail: <ghost at aladdin.com>
-
- Questions about the technical content of this specification can be
- sent by email to:
-
- Jean-Loup Gailly <gzip at prep.ai.mit.edu> and
- Mark Adler <madler at alumni.caltech.edu>
-
- Editorial comments on this specification can be sent by email to:
-
- L. Peter Deutsch <ghost at aladdin.com> and
- Glenn Randers-Pehrson <randeg at alumni.rpi.edu>
-
-
-
-Deutsch Informational [Page 10]
-
-RFC 1952 GZIP File Format Specification May 1996
-
-
-7. Appendix: Jean-Loup Gailly's gzip utility
-
- The most widely used implementation of gzip compression, and the
- original documentation on which this specification is based, were
- created by Jean-Loup Gailly <gzip at prep.ai.mit.edu>. Since this
- implementation is a de facto standard, we mention some more of its
- features here. Again, the material in this section is not part of
- the specification per se, and implementations need not follow it to
- be compliant.
-
- When compressing or decompressing a file, gzip preserves the
- protection, ownership, and modification time attributes on the local
- file system, since there is no provision for representing protection
- attributes in the gzip file format itself. Since the file format
- includes a modification time, the gzip decompressor provides a
- command line switch that assigns the modification time from the file,
- rather than the local modification time of the compressed input, to
- the decompressed output.
-
-8. Appendix: Sample CRC Code
-
- The following sample code represents a practical implementation of
- the CRC (Cyclic Redundancy Check). (See also ISO 3309 and ITU-T V.42
- for a formal specification.)
-
- The sample code is in the ANSI C programming language. Non C users
- may find it easier to read with these hints:
-
- & Bitwise AND operator.
- ^ Bitwise exclusive-OR operator.
- >> Bitwise right shift operator. When applied to an
- unsigned quantity, as here, right shift inserts zero
- bit(s) at the left.
- ! Logical NOT operator.
- ++ "n++" increments the variable n.
- 0xNNN 0x introduces a hexadecimal (base 16) constant.
- Suffix L indicates a long value (at least 32 bits).
-
- /* Table of CRCs of all 8-bit messages. */
- unsigned long crc_table[256];
-
- /* Flag: has the table been computed? Initially false. */
- int crc_table_computed = 0;
-
- /* Make the table for a fast CRC. */
- void make_crc_table(void)
- {
- unsigned long c;
-
-
-
-Deutsch Informational [Page 11]
-
-RFC 1952 GZIP File Format Specification May 1996
-
-
- int n, k;
- for (n = 0; n < 256; n++) {
- c = (unsigned long) n;
- for (k = 0; k < 8; k++) {
- if (c & 1) {
- c = 0xedb88320L ^ (c >> 1);
- } else {
- c = c >> 1;
- }
- }
- crc_table[n] = c;
- }
- crc_table_computed = 1;
- }
-
- /*
- Update a running crc with the bytes buf[0..len-1] and return
- the updated crc. The crc should be initialized to zero. Pre- and
- post-conditioning (one's complement) is performed within this
- function so it shouldn't be done by the caller. Usage example:
-
- unsigned long crc = 0L;
-
- while (read_buffer(buffer, length) != EOF) {
- crc = update_crc(crc, buffer, length);
- }
- if (crc != original_crc) error();
- */
- unsigned long update_crc(unsigned long crc,
- unsigned char *buf, int len)
- {
- unsigned long c = crc ^ 0xffffffffL;
- int n;
-
- if (!crc_table_computed)
- make_crc_table();
- for (n = 0; n < len; n++) {
- c = crc_table[(c ^ buf[n]) & 0xff] ^ (c >> 8);
- }
- return c ^ 0xffffffffL;
- }
-
- /* Return the CRC of the bytes buf[0..len-1]. */
- unsigned long crc(unsigned char *buf, int len)
- {
- return update_crc(0L, buf, len);
- }
-
-
-
-
-Deutsch Informational [Page 12]
-
diff --git a/third-party/zlib/doc/txtvsbin.txt b/third-party/zlib/doc/txtvsbin.txt
deleted file mode 100644
index 3d0f063..0000000
--- a/third-party/zlib/doc/txtvsbin.txt
+++ /dev/null
@@ -1,107 +0,0 @@
-A Fast Method for Identifying Plain Text Files
-==============================================
-
-
-Introduction
-------------
-
-Given a file coming from an unknown source, it is sometimes desirable
-to find out whether the format of that file is plain text. Although
-this may appear like a simple task, a fully accurate detection of the
-file type requires heavy-duty semantic analysis on the file contents.
-It is, however, possible to obtain satisfactory results by employing
-various heuristics.
-
-Previous versions of PKZip and other zip-compatible compression tools
-were using a crude detection scheme: if more than 80% (4/5) of the bytes
-found in a certain buffer are within the range [7..127], the file is
-labeled as plain text, otherwise it is labeled as binary. A prominent
-limitation of this scheme is the restriction to Latin-based alphabets.
-Other alphabets, like Greek, Cyrillic or Asian, make extensive use of
-the bytes within the range [128..255], and texts using these alphabets
-are most often misidentified by this scheme; in other words, the rate
-of false negatives is sometimes too high, which means that the recall
-is low. Another weakness of this scheme is a reduced precision, due to
-the false positives that may occur when binary files containing large
-amounts of textual characters are misidentified as plain text.
-
-In this article we propose a new, simple detection scheme that features
-a much increased precision and a near-100% recall. This scheme is
-designed to work on ASCII, Unicode and other ASCII-derived alphabets,
-and it handles single-byte encodings (ISO-8859, MacRoman, KOI8, etc.)
-and variable-sized encodings (ISO-2022, UTF-8, etc.). Wider encodings
-(UCS-2/UTF-16 and UCS-4/UTF-32) are not handled, however.
-
-
-The Algorithm
--------------
-
-The algorithm works by dividing the set of bytecodes [0..255] into three
-categories:
-- The white list of textual bytecodes:
- 9 (TAB), 10 (LF), 13 (CR), 32 (SPACE) to 255.
-- The gray list of tolerated bytecodes:
- 7 (BEL), 8 (BS), 11 (VT), 12 (FF), 26 (SUB), 27 (ESC).
-- The black list of undesired, non-textual bytecodes:
- 0 (NUL) to 6, 14 to 31.
-
-If a file contains at least one byte that belongs to the white list and
-no byte that belongs to the black list, then the file is categorized as
-plain text; otherwise, it is categorized as binary. (The boundary case,
-when the file is empty, automatically falls into the latter category.)
-
-
-Rationale
----------
-
-The idea behind this algorithm relies on two observations.
-
-The first observation is that, although the full range of 7-bit codes
-[0..127] is properly specified by the ASCII standard, most control
-characters in the range [0..31] are not used in practice. The only
-widely-used, almost universally-portable control codes are 9 (TAB),
-10 (LF) and 13 (CR). There are a few more control codes that are
-recognized on a reduced range of platforms and text viewers/editors:
-7 (BEL), 8 (BS), 11 (VT), 12 (FF), 26 (SUB) and 27 (ESC); but these
-codes are rarely (if ever) used alone, without being accompanied by
-some printable text. Even the newer, portable text formats such as
-XML avoid using control characters outside the list mentioned here.
-
-The second observation is that most of the binary files tend to contain
-control characters, especially 0 (NUL). Even though the older text
-detection schemes observe the presence of non-ASCII codes from the range
-[128..255], the precision rarely has to suffer if this upper range is
-labeled as textual, because the files that are genuinely binary tend to
-contain both control characters and codes from the upper range. On the
-other hand, the upper range needs to be labeled as textual, because it
-is used by virtually all ASCII extensions. In particular, this range is
-used for encoding non-Latin scripts.
-
-Since there is no counting involved, other than simply observing the
-presence or the absence of some byte values, the algorithm produces
-consistent results, regardless what alphabet encoding is being used.
-(If counting were involved, it could be possible to obtain different
-results on a text encoded, say, using ISO-8859-16 versus UTF-8.)
-
-There is an extra category of plain text files that are "polluted" with
-one or more black-listed codes, either by mistake or by peculiar design
-considerations. In such cases, a scheme that tolerates a small fraction
-of black-listed codes would provide an increased recall (i.e. more true
-positives). This, however, incurs a reduced precision overall, since
-false positives are more likely to appear in binary files that contain
-large chunks of textual data. Furthermore, "polluted" plain text should
-be regarded as binary by general-purpose text detection schemes, because
-general-purpose text processing algorithms might not be applicable.
-Under this premise, it is safe to say that our detection method provides
-a near-100% recall.
-
-Experiments have been run on many files coming from various platforms
-and applications. We tried plain text files, system logs, source code,
-formatted office documents, compiled object code, etc. The results
-confirm the optimistic assumptions about the capabilities of this
-algorithm.
-
-
---
-Cosmin Truta
-Last updated: 2006-May-28
diff --git a/third-party/zlib/examples/README.examples b/third-party/zlib/examples/README.examples
deleted file mode 100644
index 56a3171..0000000
--- a/third-party/zlib/examples/README.examples
+++ /dev/null
@@ -1,49 +0,0 @@
-This directory contains examples of the use of zlib and other relevant
-programs and documentation.
-
-enough.c
- calculation and justification of ENOUGH parameter in inftrees.h
- - calculates the maximum table space used in inflate tree
- construction over all possible Huffman codes
-
-fitblk.c
- compress just enough input to nearly fill a requested output size
- - zlib isn't designed to do this, but fitblk does it anyway
-
-gun.c
- uncompress a gzip file
- - illustrates the use of inflateBack() for high speed file-to-file
- decompression using call-back functions
- - is approximately twice as fast as gzip -d
- - also provides Unix uncompress functionality, again twice as fast
-
-gzappend.c
- append to a gzip file
- - illustrates the use of the Z_BLOCK flush parameter for inflate()
- - illustrates the use of deflatePrime() to start at any bit
-
-gzjoin.c
- join gzip files without recalculating the crc or recompressing
- - illustrates the use of the Z_BLOCK flush parameter for inflate()
- - illustrates the use of crc32_combine()
-
-gzlog.c
-gzlog.h
- efficiently and robustly maintain a message log file in gzip format
- - illustrates use of raw deflate, Z_PARTIAL_FLUSH, deflatePrime(),
- and deflateSetDictionary()
- - illustrates use of a gzip header extra field
-
-zlib_how.html
- painfully comprehensive description of zpipe.c (see below)
- - describes in excruciating detail the use of deflate() and inflate()
-
-zpipe.c
- reads and writes zlib streams from stdin to stdout
- - illustrates the proper use of deflate() and inflate()
- - deeply commented in zlib_how.html (see above)
-
-zran.c
- index a zlib or gzip stream and randomly access it
- - illustrates the use of Z_BLOCK, inflatePrime(), and
- inflateSetDictionary() to provide random access
diff --git a/third-party/zlib/examples/enough.c b/third-party/zlib/examples/enough.c
deleted file mode 100644
index b991144..0000000
--- a/third-party/zlib/examples/enough.c
+++ /dev/null
@@ -1,572 +0,0 @@
-/* enough.c -- determine the maximum size of inflate's Huffman code tables over
- * all possible valid and complete Huffman codes, subject to a length limit.
- * Copyright (C) 2007, 2008, 2012 Mark Adler
- * Version 1.4 18 August 2012 Mark Adler
- */
-
-/* Version history:
- 1.0 3 Jan 2007 First version (derived from codecount.c version 1.4)
- 1.1 4 Jan 2007 Use faster incremental table usage computation
- Prune examine() search on previously visited states
- 1.2 5 Jan 2007 Comments clean up
- As inflate does, decrease root for short codes
- Refuse cases where inflate would increase root
- 1.3 17 Feb 2008 Add argument for initial root table size
- Fix bug for initial root table size == max - 1
- Use a macro to compute the history index
- 1.4 18 Aug 2012 Avoid shifts more than bits in type (caused endless loop!)
- Clean up comparisons of different types
- Clean up code indentation
- */
-
-/*
- Examine all possible Huffman codes for a given number of symbols and a
- maximum code length in bits to determine the maximum table size for zilb's
- inflate. Only complete Huffman codes are counted.
-
- Two codes are considered distinct if the vectors of the number of codes per
- length are not identical. So permutations of the symbol assignments result
- in the same code for the counting, as do permutations of the assignments of
- the bit values to the codes (i.e. only canonical codes are counted).
-
- We build a code from shorter to longer lengths, determining how many symbols
- are coded at each length. At each step, we have how many symbols remain to
- be coded, what the last code length used was, and how many bit patterns of
- that length remain unused. Then we add one to the code length and double the
- number of unused patterns to graduate to the next code length. We then
- assign all portions of the remaining symbols to that code length that
- preserve the properties of a correct and eventually complete code. Those
- properties are: we cannot use more bit patterns than are available; and when
- all the symbols are used, there are exactly zero possible bit patterns
- remaining.
-
- The inflate Huffman decoding algorithm uses two-level lookup tables for
- speed. There is a single first-level table to decode codes up to root bits
- in length (root == 9 in the current inflate implementation). The table
- has 1 << root entries and is indexed by the next root bits of input. Codes
- shorter than root bits have replicated table entries, so that the correct
- entry is pointed to regardless of the bits that follow the short code. If
- the code is longer than root bits, then the table entry points to a second-
- level table. The size of that table is determined by the longest code with
- that root-bit prefix. If that longest code has length len, then the table
- has size 1 << (len - root), to index the remaining bits in that set of
- codes. Each subsequent root-bit prefix then has its own sub-table. The
- total number of table entries required by the code is calculated
- incrementally as the number of codes at each bit length is populated. When
- all of the codes are shorter than root bits, then root is reduced to the
- longest code length, resulting in a single, smaller, one-level table.
-
- The inflate algorithm also provides for small values of root (relative to
- the log2 of the number of symbols), where the shortest code has more bits
- than root. In that case, root is increased to the length of the shortest
- code. This program, by design, does not handle that case, so it is verified
- that the number of symbols is less than 2^(root + 1).
-
- In order to speed up the examination (by about ten orders of magnitude for
- the default arguments), the intermediate states in the build-up of a code
- are remembered and previously visited branches are pruned. The memory
- required for this will increase rapidly with the total number of symbols and
- the maximum code length in bits. However this is a very small price to pay
- for the vast speedup.
-
- First, all of the possible Huffman codes are counted, and reachable
- intermediate states are noted by a non-zero count in a saved-results array.
- Second, the intermediate states that lead to (root + 1) bit or longer codes
- are used to look at all sub-codes from those junctures for their inflate
- memory usage. (The amount of memory used is not affected by the number of
- codes of root bits or less in length.) Third, the visited states in the
- construction of those sub-codes and the associated calculation of the table
- size is recalled in order to avoid recalculating from the same juncture.
- Beginning the code examination at (root + 1) bit codes, which is enabled by
- identifying the reachable nodes, accounts for about six of the orders of
- magnitude of improvement for the default arguments. About another four
- orders of magnitude come from not revisiting previous states. Out of
- approximately 2x10^16 possible Huffman codes, only about 2x10^6 sub-codes
- need to be examined to cover all of the possible table memory usage cases
- for the default arguments of 286 symbols limited to 15-bit codes.
-
- Note that an unsigned long long type is used for counting. It is quite easy
- to exceed the capacity of an eight-byte integer with a large number of
- symbols and a large maximum code length, so multiple-precision arithmetic
- would need to replace the unsigned long long arithmetic in that case. This
- program will abort if an overflow occurs. The big_t type identifies where
- the counting takes place.
-
- An unsigned long long type is also used for calculating the number of
- possible codes remaining at the maximum length. This limits the maximum
- code length to the number of bits in a long long minus the number of bits
- needed to represent the symbols in a flat code. The code_t type identifies
- where the bit pattern counting takes place.
- */
-
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
-#include <assert.h>
-
-#define local static
-
-/* special data types */
-typedef unsigned long long big_t; /* type for code counting */
-typedef unsigned long long code_t; /* type for bit pattern counting */
-struct tab { /* type for been here check */
- size_t len; /* length of bit vector in char's */
- char *vec; /* allocated bit vector */
-};
-
-/* The array for saving results, num[], is indexed with this triplet:
-
- syms: number of symbols remaining to code
- left: number of available bit patterns at length len
- len: number of bits in the codes currently being assigned
-
- Those indices are constrained thusly when saving results:
-
- syms: 3..totsym (totsym == total symbols to code)
- left: 2..syms - 1, but only the evens (so syms == 8 -> 2, 4, 6)
- len: 1..max - 1 (max == maximum code length in bits)
-
- syms == 2 is not saved since that immediately leads to a single code. left
- must be even, since it represents the number of available bit patterns at
- the current length, which is double the number at the previous length.
- left ends at syms-1 since left == syms immediately results in a single code.
- (left > sym is not allowed since that would result in an incomplete code.)
- len is less than max, since the code completes immediately when len == max.
-
- The offset into the array is calculated for the three indices with the
- first one (syms) being outermost, and the last one (len) being innermost.
- We build the array with length max-1 lists for the len index, with syms-3
- of those for each symbol. There are totsym-2 of those, with each one
- varying in length as a function of sym. See the calculation of index in
- count() for the index, and the calculation of size in main() for the size
- of the array.
-
- For the deflate example of 286 symbols limited to 15-bit codes, the array
- has 284,284 entries, taking up 2.17 MB for an 8-byte big_t. More than
- half of the space allocated for saved results is actually used -- not all
- possible triplets are reached in the generation of valid Huffman codes.
- */
-
-/* The array for tracking visited states, done[], is itself indexed identically
- to the num[] array as described above for the (syms, left, len) triplet.
- Each element in the array is further indexed by the (mem, rem) doublet,
- where mem is the amount of inflate table space used so far, and rem is the
- remaining unused entries in the current inflate sub-table. Each indexed
- element is simply one bit indicating whether the state has been visited or
- not. Since the ranges for mem and rem are not known a priori, each bit
- vector is of a variable size, and grows as needed to accommodate the visited
- states. mem and rem are used to calculate a single index in a triangular
- array. Since the range of mem is expected in the default case to be about
- ten times larger than the range of rem, the array is skewed to reduce the
- memory usage, with eight times the range for mem than for rem. See the
- calculations for offset and bit in beenhere() for the details.
-
- For the deflate example of 286 symbols limited to 15-bit codes, the bit
- vectors grow to total approximately 21 MB, in addition to the 4.3 MB done[]
- array itself.
- */
-
-/* Globals to avoid propagating constants or constant pointers recursively */
-local int max; /* maximum allowed bit length for the codes */
-local int root; /* size of base code table in bits */
-local int large; /* largest code table so far */
-local size_t size; /* number of elements in num and done */
-local int *code; /* number of symbols assigned to each bit length */
-local big_t *num; /* saved results array for code counting */
-local struct tab *done; /* states already evaluated array */
-
-/* Index function for num[] and done[] */
-#define INDEX(i,j,k) (((size_t)((i-1)>>1)*((i-2)>>1)+(j>>1)-1)*(max-1)+k-1)
-
-/* Free allocated space. Uses globals code, num, and done. */
-local void cleanup(void)
-{
- size_t n;
-
- if (done != NULL) {
- for (n = 0; n < size; n++)
- if (done[n].len)
- free(done[n].vec);
- free(done);
- }
- if (num != NULL)
- free(num);
- if (code != NULL)
- free(code);
-}
-
-/* Return the number of possible Huffman codes using bit patterns of lengths
- len through max inclusive, coding syms symbols, with left bit patterns of
- length len unused -- return -1 if there is an overflow in the counting.
- Keep a record of previous results in num to prevent repeating the same
- calculation. Uses the globals max and num. */
-local big_t count(int syms, int len, int left)
-{
- big_t sum; /* number of possible codes from this juncture */
- big_t got; /* value returned from count() */
- int least; /* least number of syms to use at this juncture */
- int most; /* most number of syms to use at this juncture */
- int use; /* number of bit patterns to use in next call */
- size_t index; /* index of this case in *num */
-
- /* see if only one possible code */
- if (syms == left)
- return 1;
-
- /* note and verify the expected state */
- assert(syms > left && left > 0 && len < max);
-
- /* see if we've done this one already */
- index = INDEX(syms, left, len);
- got = num[index];
- if (got)
- return got; /* we have -- return the saved result */
-
- /* we need to use at least this many bit patterns so that the code won't be
- incomplete at the next length (more bit patterns than symbols) */
- least = (left << 1) - syms;
- if (least < 0)
- least = 0;
-
- /* we can use at most this many bit patterns, lest there not be enough
- available for the remaining symbols at the maximum length (if there were
- no limit to the code length, this would become: most = left - 1) */
- most = (((code_t)left << (max - len)) - syms) /
- (((code_t)1 << (max - len)) - 1);
-
- /* count all possible codes from this juncture and add them up */
- sum = 0;
- for (use = least; use <= most; use++) {
- got = count(syms - use, len + 1, (left - use) << 1);
- sum += got;
- if (got == (big_t)0 - 1 || sum < got) /* overflow */
- return (big_t)0 - 1;
- }
-
- /* verify that all recursive calls are productive */
- assert(sum != 0);
-
- /* save the result and return it */
- num[index] = sum;
- return sum;
-}
-
-/* Return true if we've been here before, set to true if not. Set a bit in a
- bit vector to indicate visiting this state. Each (syms,len,left) state
- has a variable size bit vector indexed by (mem,rem). The bit vector is
- lengthened if needed to allow setting the (mem,rem) bit. */
-local int beenhere(int syms, int len, int left, int mem, int rem)
-{
- size_t index; /* index for this state's bit vector */
- size_t offset; /* offset in this state's bit vector */
- int bit; /* mask for this state's bit */
- size_t length; /* length of the bit vector in bytes */
- char *vector; /* new or enlarged bit vector */
-
- /* point to vector for (syms,left,len), bit in vector for (mem,rem) */
- index = INDEX(syms, left, len);
- mem -= 1 << root;
- offset = (mem >> 3) + rem;
- offset = ((offset * (offset + 1)) >> 1) + rem;
- bit = 1 << (mem & 7);
-
- /* see if we've been here */
- length = done[index].len;
- if (offset < length && (done[index].vec[offset] & bit) != 0)
- return 1; /* done this! */
-
- /* we haven't been here before -- set the bit to show we have now */
-
- /* see if we need to lengthen the vector in order to set the bit */
- if (length <= offset) {
- /* if we have one already, enlarge it, zero out the appended space */
- if (length) {
- do {
- length <<= 1;
- } while (length <= offset);
- vector = realloc(done[index].vec, length);
- if (vector != NULL)
- memset(vector + done[index].len, 0, length - done[index].len);
- }
-
- /* otherwise we need to make a new vector and zero it out */
- else {
- length = 1 << (len - root);
- while (length <= offset)
- length <<= 1;
- vector = calloc(length, sizeof(char));
- }
-
- /* in either case, bail if we can't get the memory */
- if (vector == NULL) {
- fputs("abort: unable to allocate enough memory\n", stderr);
- cleanup();
- exit(1);
- }
-
- /* install the new vector */
- done[index].len = length;
- done[index].vec = vector;
- }
-
- /* set the bit */
- done[index].vec[offset] |= bit;
- return 0;
-}
-
-/* Examine all possible codes from the given node (syms, len, left). Compute
- the amount of memory required to build inflate's decoding tables, where the
- number of code structures used so far is mem, and the number remaining in
- the current sub-table is rem. Uses the globals max, code, root, large, and
- done. */
-local void examine(int syms, int len, int left, int mem, int rem)
-{
- int least; /* least number of syms to use at this juncture */
- int most; /* most number of syms to use at this juncture */
- int use; /* number of bit patterns to use in next call */
-
- /* see if we have a complete code */
- if (syms == left) {
- /* set the last code entry */
- code[len] = left;
-
- /* complete computation of memory used by this code */
- while (rem < left) {
- left -= rem;
- rem = 1 << (len - root);
- mem += rem;
- }
- assert(rem == left);
-
- /* if this is a new maximum, show the entries used and the sub-code */
- if (mem > large) {
- large = mem;
- printf("max %d: ", mem);
- for (use = root + 1; use <= max; use++)
- if (code[use])
- printf("%d[%d] ", code[use], use);
- putchar('\n');
- fflush(stdout);
- }
-
- /* remove entries as we drop back down in the recursion */
- code[len] = 0;
- return;
- }
-
- /* prune the tree if we can */
- if (beenhere(syms, len, left, mem, rem))
- return;
-
- /* we need to use at least this many bit patterns so that the code won't be
- incomplete at the next length (more bit patterns than symbols) */
- least = (left << 1) - syms;
- if (least < 0)
- least = 0;
-
- /* we can use at most this many bit patterns, lest there not be enough
- available for the remaining symbols at the maximum length (if there were
- no limit to the code length, this would become: most = left - 1) */
- most = (((code_t)left << (max - len)) - syms) /
- (((code_t)1 << (max - len)) - 1);
-
- /* occupy least table spaces, creating new sub-tables as needed */
- use = least;
- while (rem < use) {
- use -= rem;
- rem = 1 << (len - root);
- mem += rem;
- }
- rem -= use;
-
- /* examine codes from here, updating table space as we go */
- for (use = least; use <= most; use++) {
- code[len] = use;
- examine(syms - use, len + 1, (left - use) << 1,
- mem + (rem ? 1 << (len - root) : 0), rem << 1);
- if (rem == 0) {
- rem = 1 << (len - root);
- mem += rem;
- }
- rem--;
- }
-
- /* remove entries as we drop back down in the recursion */
- code[len] = 0;
-}
-
-/* Look at all sub-codes starting with root + 1 bits. Look at only the valid
- intermediate code states (syms, left, len). For each completed code,
- calculate the amount of memory required by inflate to build the decoding
- tables. Find the maximum amount of memory required and show the code that
- requires that maximum. Uses the globals max, root, and num. */
-local void enough(int syms)
-{
- int n; /* number of remaing symbols for this node */
- int left; /* number of unused bit patterns at this length */
- size_t index; /* index of this case in *num */
-
- /* clear code */
- for (n = 0; n <= max; n++)
- code[n] = 0;
-
- /* look at all (root + 1) bit and longer codes */
- large = 1 << root; /* base table */
- if (root < max) /* otherwise, there's only a base table */
- for (n = 3; n <= syms; n++)
- for (left = 2; left < n; left += 2)
- {
- /* look at all reachable (root + 1) bit nodes, and the
- resulting codes (complete at root + 2 or more) */
- index = INDEX(n, left, root + 1);
- if (root + 1 < max && num[index]) /* reachable node */
- examine(n, root + 1, left, 1 << root, 0);
-
- /* also look at root bit codes with completions at root + 1
- bits (not saved in num, since complete), just in case */
- if (num[index - 1] && n <= left << 1)
- examine((n - left) << 1, root + 1, (n - left) << 1,
- 1 << root, 0);
- }
-
- /* done */
- printf("done: maximum of %d table entries\n", large);
-}
-
-/*
- Examine and show the total number of possible Huffman codes for a given
- maximum number of symbols, initial root table size, and maximum code length
- in bits -- those are the command arguments in that order. The default
- values are 286, 9, and 15 respectively, for the deflate literal/length code.
- The possible codes are counted for each number of coded symbols from two to
- the maximum. The counts for each of those and the total number of codes are
- shown. The maximum number of inflate table entires is then calculated
- across all possible codes. Each new maximum number of table entries and the
- associated sub-code (starting at root + 1 == 10 bits) is shown.
-
- To count and examine Huffman codes that are not length-limited, provide a
- maximum length equal to the number of symbols minus one.
-
- For the deflate literal/length code, use "enough". For the deflate distance
- code, use "enough 30 6".
-
- This uses the %llu printf format to print big_t numbers, which assumes that
- big_t is an unsigned long long. If the big_t type is changed (for example
- to a multiple precision type), the method of printing will also need to be
- updated.
- */
-int main(int argc, char **argv)
-{
- int syms; /* total number of symbols to code */
- int n; /* number of symbols to code for this run */
- big_t got; /* return value of count() */
- big_t sum; /* accumulated number of codes over n */
- code_t word; /* for counting bits in code_t */
-
- /* set up globals for cleanup() */
- code = NULL;
- num = NULL;
- done = NULL;
-
- /* get arguments -- default to the deflate literal/length code */
- syms = 286;
- root = 9;
- max = 15;
- if (argc > 1) {
- syms = atoi(argv[1]);
- if (argc > 2) {
- root = atoi(argv[2]);
- if (argc > 3)
- max = atoi(argv[3]);
- }
- }
- if (argc > 4 || syms < 2 || root < 1 || max < 1) {
- fputs("invalid arguments, need: [sym >= 2 [root >= 1 [max >= 1]]]\n",
- stderr);
- return 1;
- }
-
- /* if not restricting the code length, the longest is syms - 1 */
- if (max > syms - 1)
- max = syms - 1;
-
- /* determine the number of bits in a code_t */
- for (n = 0, word = 1; word; n++, word <<= 1)
- ;
-
- /* make sure that the calculation of most will not overflow */
- if (max > n || (code_t)(syms - 2) >= (((code_t)0 - 1) >> (max - 1))) {
- fputs("abort: code length too long for internal types\n", stderr);
- return 1;
- }
-
- /* reject impossible code requests */
- if ((code_t)(syms - 1) > ((code_t)1 << max) - 1) {
- fprintf(stderr, "%d symbols cannot be coded in %d bits\n",
- syms, max);
- return 1;
- }
-
- /* allocate code vector */
- code = calloc(max + 1, sizeof(int));
- if (code == NULL) {
- fputs("abort: unable to allocate enough memory\n", stderr);
- return 1;
- }
-
- /* determine size of saved results array, checking for overflows,
- allocate and clear the array (set all to zero with calloc()) */
- if (syms == 2) /* iff max == 1 */
- num = NULL; /* won't be saving any results */
- else {
- size = syms >> 1;
- if (size > ((size_t)0 - 1) / (n = (syms - 1) >> 1) ||
- (size *= n, size > ((size_t)0 - 1) / (n = max - 1)) ||
- (size *= n, size > ((size_t)0 - 1) / sizeof(big_t)) ||
- (num = calloc(size, sizeof(big_t))) == NULL) {
- fputs("abort: unable to allocate enough memory\n", stderr);
- cleanup();
- return 1;
- }
- }
-
- /* count possible codes for all numbers of symbols, add up counts */
- sum = 0;
- for (n = 2; n <= syms; n++) {
- got = count(n, 1, 2);
- sum += got;
- if (got == (big_t)0 - 1 || sum < got) { /* overflow */
- fputs("abort: can't count that high!\n", stderr);
- cleanup();
- return 1;
- }
- printf("%llu %d-codes\n", got, n);
- }
- printf("%llu total codes for 2 to %d symbols", sum, syms);
- if (max < syms - 1)
- printf(" (%d-bit length limit)\n", max);
- else
- puts(" (no length limit)");
-
- /* allocate and clear done array for beenhere() */
- if (syms == 2)
- done = NULL;
- else if (size > ((size_t)0 - 1) / sizeof(struct tab) ||
- (done = calloc(size, sizeof(struct tab))) == NULL) {
- fputs("abort: unable to allocate enough memory\n", stderr);
- cleanup();
- return 1;
- }
-
- /* find and show maximum inflate table usage */
- if (root > max) /* reduce root to max length */
- root = max;
- if ((code_t)syms < ((code_t)1 << (root + 1)))
- enough(syms);
- else
- puts("cannot handle minimum code lengths > root");
-
- /* done */
- cleanup();
- return 0;
-}
diff --git a/third-party/zlib/examples/fitblk.c b/third-party/zlib/examples/fitblk.c
deleted file mode 100644
index c61de5c..0000000
--- a/third-party/zlib/examples/fitblk.c
+++ /dev/null
@@ -1,233 +0,0 @@
-/* fitblk.c: example of fitting compressed output to a specified size
- Not copyrighted -- provided to the public domain
- Version 1.1 25 November 2004 Mark Adler */
-
-/* Version history:
- 1.0 24 Nov 2004 First version
- 1.1 25 Nov 2004 Change deflateInit2() to deflateInit()
- Use fixed-size, stack-allocated raw buffers
- Simplify code moving compression to subroutines
- Use assert() for internal errors
- Add detailed description of approach
- */
-
-/* Approach to just fitting a requested compressed size:
-
- fitblk performs three compression passes on a portion of the input
- data in order to determine how much of that input will compress to
- nearly the requested output block size. The first pass generates
- enough deflate blocks to produce output to fill the requested
- output size plus a specfied excess amount (see the EXCESS define
- below). The last deflate block may go quite a bit past that, but
- is discarded. The second pass decompresses and recompresses just
- the compressed data that fit in the requested plus excess sized
- buffer. The deflate process is terminated after that amount of
- input, which is less than the amount consumed on the first pass.
- The last deflate block of the result will be of a comparable size
- to the final product, so that the header for that deflate block and
- the compression ratio for that block will be about the same as in
- the final product. The third compression pass decompresses the
- result of the second step, but only the compressed data up to the
- requested size minus an amount to allow the compressed stream to
- complete (see the MARGIN define below). That will result in a
- final compressed stream whose length is less than or equal to the
- requested size. Assuming sufficient input and a requested size
- greater than a few hundred bytes, the shortfall will typically be
- less than ten bytes.
-
- If the input is short enough that the first compression completes
- before filling the requested output size, then that compressed
- stream is return with no recompression.
-
- EXCESS is chosen to be just greater than the shortfall seen in a
- two pass approach similar to the above. That shortfall is due to
- the last deflate block compressing more efficiently with a smaller
- header on the second pass. EXCESS is set to be large enough so
- that there is enough uncompressed data for the second pass to fill
- out the requested size, and small enough so that the final deflate
- block of the second pass will be close in size to the final deflate
- block of the third and final pass. MARGIN is chosen to be just
- large enough to assure that the final compression has enough room
- to complete in all cases.
- */
-
-#include <stdio.h>
-#include <stdlib.h>
-#include <assert.h>
-#include "zlib.h"
-
-#define local static
-
-/* print nastygram and leave */
-local void quit(char *why)
-{
- fprintf(stderr, "fitblk abort: %s\n", why);
- exit(1);
-}
-
-#define RAWLEN 4096 /* intermediate uncompressed buffer size */
-
-/* compress from file to def until provided buffer is full or end of
- input reached; return last deflate() return value, or Z_ERRNO if
- there was read error on the file */
-local int partcompress(FILE *in, z_streamp def)
-{
- int ret, flush;
- unsigned char raw[RAWLEN];
-
- flush = Z_NO_FLUSH;
- do {
- def->avail_in = fread(raw, 1, RAWLEN, in);
- if (ferror(in))
- return Z_ERRNO;
- def->next_in = raw;
- if (feof(in))
- flush = Z_FINISH;
- ret = deflate(def, flush);
- assert(ret != Z_STREAM_ERROR);
- } while (def->avail_out != 0 && flush == Z_NO_FLUSH);
- return ret;
-}
-
-/* recompress from inf's input to def's output; the input for inf and
- the output for def are set in those structures before calling;
- return last deflate() return value, or Z_MEM_ERROR if inflate()
- was not able to allocate enough memory when it needed to */
-local int recompress(z_streamp inf, z_streamp def)
-{
- int ret, flush;
- unsigned char raw[RAWLEN];
-
- flush = Z_NO_FLUSH;
- do {
- /* decompress */
- inf->avail_out = RAWLEN;
- inf->next_out = raw;
- ret = inflate(inf, Z_NO_FLUSH);
- assert(ret != Z_STREAM_ERROR && ret != Z_DATA_ERROR &&
- ret != Z_NEED_DICT);
- if (ret == Z_MEM_ERROR)
- return ret;
-
- /* compress what was decompresed until done or no room */
- def->avail_in = RAWLEN - inf->avail_out;
- def->next_in = raw;
- if (inf->avail_out != 0)
- flush = Z_FINISH;
- ret = deflate(def, flush);
- assert(ret != Z_STREAM_ERROR);
- } while (ret != Z_STREAM_END && def->avail_out != 0);
- return ret;
-}
-
-#define EXCESS 256 /* empirically determined stream overage */
-#define MARGIN 8 /* amount to back off for completion */
-
-/* compress from stdin to fixed-size block on stdout */
-int main(int argc, char **argv)
-{
- int ret; /* return code */
- unsigned size; /* requested fixed output block size */
- unsigned have; /* bytes written by deflate() call */
- unsigned char *blk; /* intermediate and final stream */
- unsigned char *tmp; /* close to desired size stream */
- z_stream def, inf; /* zlib deflate and inflate states */
-
- /* get requested output size */
- if (argc != 2)
- quit("need one argument: size of output block");
- ret = strtol(argv[1], argv + 1, 10);
- if (argv[1][0] != 0)
- quit("argument must be a number");
- if (ret < 8) /* 8 is minimum zlib stream size */
- quit("need positive size of 8 or greater");
- size = (unsigned)ret;
-
- /* allocate memory for buffers and compression engine */
- blk = malloc(size + EXCESS);
- def.zalloc = Z_NULL;
- def.zfree = Z_NULL;
- def.opaque = Z_NULL;
- ret = deflateInit(&def, Z_DEFAULT_COMPRESSION);
- if (ret != Z_OK || blk == NULL)
- quit("out of memory");
-
- /* compress from stdin until output full, or no more input */
- def.avail_out = size + EXCESS;
- def.next_out = blk;
- ret = partcompress(stdin, &def);
- if (ret == Z_ERRNO)
- quit("error reading input");
-
- /* if it all fit, then size was undersubscribed -- done! */
- if (ret == Z_STREAM_END && def.avail_out >= EXCESS) {
- /* write block to stdout */
- have = size + EXCESS - def.avail_out;
- if (fwrite(blk, 1, have, stdout) != have || ferror(stdout))
- quit("error writing output");
-
- /* clean up and print results to stderr */
- ret = deflateEnd(&def);
- assert(ret != Z_STREAM_ERROR);
- free(blk);
- fprintf(stderr,
- "%u bytes unused out of %u requested (all input)\n",
- size - have, size);
- return 0;
- }
-
- /* it didn't all fit -- set up for recompression */
- inf.zalloc = Z_NULL;
- inf.zfree = Z_NULL;
- inf.opaque = Z_NULL;
- inf.avail_in = 0;
- inf.next_in = Z_NULL;
- ret = inflateInit(&inf);
- tmp = malloc(size + EXCESS);
- if (ret != Z_OK || tmp == NULL)
- quit("out of memory");
- ret = deflateReset(&def);
- assert(ret != Z_STREAM_ERROR);
-
- /* do first recompression close to the right amount */
- inf.avail_in = size + EXCESS;
- inf.next_in = blk;
- def.avail_out = size + EXCESS;
- def.next_out = tmp;
- ret = recompress(&inf, &def);
- if (ret == Z_MEM_ERROR)
- quit("out of memory");
-
- /* set up for next reocmpression */
- ret = inflateReset(&inf);
- assert(ret != Z_STREAM_ERROR);
- ret = deflateReset(&def);
- assert(ret != Z_STREAM_ERROR);
-
- /* do second and final recompression (third compression) */
- inf.avail_in = size - MARGIN; /* assure stream will complete */
- inf.next_in = tmp;
- def.avail_out = size;
- def.next_out = blk;
- ret = recompress(&inf, &def);
- if (ret == Z_MEM_ERROR)
- quit("out of memory");
- assert(ret == Z_STREAM_END); /* otherwise MARGIN too small */
-
- /* done -- write block to stdout */
- have = size - def.avail_out;
- if (fwrite(blk, 1, have, stdout) != have || ferror(stdout))
- quit("error writing output");
-
- /* clean up and print results to stderr */
- free(tmp);
- ret = inflateEnd(&inf);
- assert(ret != Z_STREAM_ERROR);
- ret = deflateEnd(&def);
- assert(ret != Z_STREAM_ERROR);
- free(blk);
- fprintf(stderr,
- "%u bytes unused out of %u requested (%lu input)\n",
- size - have, size, def.total_in);
- return 0;
-}
diff --git a/third-party/zlib/examples/gun.c b/third-party/zlib/examples/gun.c
deleted file mode 100644
index 89e484f..0000000
--- a/third-party/zlib/examples/gun.c
+++ /dev/null
@@ -1,702 +0,0 @@
-/* gun.c -- simple gunzip to give an example of the use of inflateBack()
- * Copyright (C) 2003, 2005, 2008, 2010, 2012 Mark Adler
- * For conditions of distribution and use, see copyright notice in zlib.h
- Version 1.7 12 August 2012 Mark Adler */
-
-/* Version history:
- 1.0 16 Feb 2003 First version for testing of inflateBack()
- 1.1 21 Feb 2005 Decompress concatenated gzip streams
- Remove use of "this" variable (C++ keyword)
- Fix return value for in()
- Improve allocation failure checking
- Add typecasting for void * structures
- Add -h option for command version and usage
- Add a bunch of comments
- 1.2 20 Mar 2005 Add Unix compress (LZW) decompression
- Copy file attributes from input file to output file
- 1.3 12 Jun 2005 Add casts for error messages [Oberhumer]
- 1.4 8 Dec 2006 LZW decompression speed improvements
- 1.5 9 Feb 2008 Avoid warning in latest version of gcc
- 1.6 17 Jan 2010 Avoid signed/unsigned comparison warnings
- 1.7 12 Aug 2012 Update for z_const usage in zlib 1.2.8
- */
-
-/*
- gun [ -t ] [ name ... ]
-
- decompresses the data in the named gzip files. If no arguments are given,
- gun will decompress from stdin to stdout. The names must end in .gz, -gz,
- .z, -z, _z, or .Z. The uncompressed data will be written to a file name
- with the suffix stripped. On success, the original file is deleted. On
- failure, the output file is deleted. For most failures, the command will
- continue to process the remaining names on the command line. A memory
- allocation failure will abort the command. If -t is specified, then the
- listed files or stdin will be tested as gzip files for integrity (without
- checking for a proper suffix), no output will be written, and no files
- will be deleted.
-
- Like gzip, gun allows concatenated gzip streams and will decompress them,
- writing all of the uncompressed data to the output. Unlike gzip, gun allows
- an empty file on input, and will produce no error writing an empty output
- file.
-
- gun will also decompress files made by Unix compress, which uses LZW
- compression. These files are automatically detected by virtue of their
- magic header bytes. Since the end of Unix compress stream is marked by the
- end-of-file, they cannot be concantenated. If a Unix compress stream is
- encountered in an input file, it is the last stream in that file.
-
- Like gunzip and uncompress, the file attributes of the orignal compressed
- file are maintained in the final uncompressed file, to the extent that the
- user permissions allow it.
-
- On my Mac OS X PowerPC G4, gun is almost twice as fast as gunzip (version
- 1.2.4) is on the same file, when gun is linked with zlib 1.2.2. Also the
- LZW decompression provided by gun is about twice as fast as the standard
- Unix uncompress command.
- */
-
-/* external functions and related types and constants */
-#include <stdio.h> /* fprintf() */
-#include <stdlib.h> /* malloc(), free() */
-#include <string.h> /* strerror(), strcmp(), strlen(), memcpy() */
-#include <errno.h> /* errno */
-#include <fcntl.h> /* open() */
-#include <unistd.h> /* read(), write(), close(), chown(), unlink() */
-#include <sys/types.h>
-#include <sys/stat.h> /* stat(), chmod() */
-#include <utime.h> /* utime() */
-#include "zlib.h" /* inflateBackInit(), inflateBack(), */
- /* inflateBackEnd(), crc32() */
-
-/* function declaration */
-#define local static
-
-/* buffer constants */
-#define SIZE 32768U /* input and output buffer sizes */
-#define PIECE 16384 /* limits i/o chunks for 16-bit int case */
-
-/* structure for infback() to pass to input function in() -- it maintains the
- input file and a buffer of size SIZE */
-struct ind {
- int infile;
- unsigned char *inbuf;
-};
-
-/* Load input buffer, assumed to be empty, and return bytes loaded and a
- pointer to them. read() is called until the buffer is full, or until it
- returns end-of-file or error. Return 0 on error. */
-local unsigned in(void *in_desc, z_const unsigned char **buf)
-{
- int ret;
- unsigned len;
- unsigned char *next;
- struct ind *me = (struct ind *)in_desc;
-
- next = me->inbuf;
- *buf = next;
- len = 0;
- do {
- ret = PIECE;
- if ((unsigned)ret > SIZE - len)
- ret = (int)(SIZE - len);
- ret = (int)read(me->infile, next, ret);
- if (ret == -1) {
- len = 0;
- break;
- }
- next += ret;
- len += ret;
- } while (ret != 0 && len < SIZE);
- return len;
-}
-
-/* structure for infback() to pass to output function out() -- it maintains the
- output file, a running CRC-32 check on the output and the total number of
- bytes output, both for checking against the gzip trailer. (The length in
- the gzip trailer is stored modulo 2^32, so it's ok if a long is 32 bits and
- the output is greater than 4 GB.) */
-struct outd {
- int outfile;
- int check; /* true if checking crc and total */
- unsigned long crc;
- unsigned long total;
-};
-
-/* Write output buffer and update the CRC-32 and total bytes written. write()
- is called until all of the output is written or an error is encountered.
- On success out() returns 0. For a write failure, out() returns 1. If the
- output file descriptor is -1, then nothing is written.
- */
-local int out(void *out_desc, unsigned char *buf, unsigned len)
-{
- int ret;
- struct outd *me = (struct outd *)out_desc;
-
- if (me->check) {
- me->crc = crc32(me->crc, buf, len);
- me->total += len;
- }
- if (me->outfile != -1)
- do {
- ret = PIECE;
- if ((unsigned)ret > len)
- ret = (int)len;
- ret = (int)write(me->outfile, buf, ret);
- if (ret == -1)
- return 1;
- buf += ret;
- len -= ret;
- } while (len != 0);
- return 0;
-}
-
-/* next input byte macro for use inside lunpipe() and gunpipe() */
-#define NEXT() (have ? 0 : (have = in(indp, &next)), \
- last = have ? (have--, (int)(*next++)) : -1)
-
-/* memory for gunpipe() and lunpipe() --
- the first 256 entries of prefix[] and suffix[] are never used, could
- have offset the index, but it's faster to waste the memory */
-unsigned char inbuf[SIZE]; /* input buffer */
-unsigned char outbuf[SIZE]; /* output buffer */
-unsigned short prefix[65536]; /* index to LZW prefix string */
-unsigned char suffix[65536]; /* one-character LZW suffix */
-unsigned char match[65280 + 2]; /* buffer for reversed match or gzip
- 32K sliding window */
-
-/* throw out what's left in the current bits byte buffer (this is a vestigial
- aspect of the compressed data format derived from an implementation that
- made use of a special VAX machine instruction!) */
-#define FLUSHCODE() \
- do { \
- left = 0; \
- rem = 0; \
- if (chunk > have) { \
- chunk -= have; \
- have = 0; \
- if (NEXT() == -1) \
- break; \
- chunk--; \
- if (chunk > have) { \
- chunk = have = 0; \
- break; \
- } \
- } \
- have -= chunk; \
- next += chunk; \
- chunk = 0; \
- } while (0)
-
-/* Decompress a compress (LZW) file from indp to outfile. The compress magic
- header (two bytes) has already been read and verified. There are have bytes
- of buffered input at next. strm is used for passing error information back
- to gunpipe().
-
- lunpipe() will return Z_OK on success, Z_BUF_ERROR for an unexpected end of
- file, read error, or write error (a write error indicated by strm->next_in
- not equal to Z_NULL), or Z_DATA_ERROR for invalid input.
- */
-local int lunpipe(unsigned have, z_const unsigned char *next, struct ind *indp,
- int outfile, z_stream *strm)
-{
- int last; /* last byte read by NEXT(), or -1 if EOF */
- unsigned chunk; /* bytes left in current chunk */
- int left; /* bits left in rem */
- unsigned rem; /* unused bits from input */
- int bits; /* current bits per code */
- unsigned code; /* code, table traversal index */
- unsigned mask; /* mask for current bits codes */
- int max; /* maximum bits per code for this stream */
- unsigned flags; /* compress flags, then block compress flag */
- unsigned end; /* last valid entry in prefix/suffix tables */
- unsigned temp; /* current code */
- unsigned prev; /* previous code */
- unsigned final; /* last character written for previous code */
- unsigned stack; /* next position for reversed string */
- unsigned outcnt; /* bytes in output buffer */
- struct outd outd; /* output structure */
- unsigned char *p;
-
- /* set up output */
- outd.outfile = outfile;
- outd.check = 0;
-
- /* process remainder of compress header -- a flags byte */
- flags = NEXT();
- if (last == -1)
- return Z_BUF_ERROR;
- if (flags & 0x60) {
- strm->msg = (char *)"unknown lzw flags set";
- return Z_DATA_ERROR;
- }
- max = flags & 0x1f;
- if (max < 9 || max > 16) {
- strm->msg = (char *)"lzw bits out of range";
- return Z_DATA_ERROR;
- }
- if (max == 9) /* 9 doesn't really mean 9 */
- max = 10;
- flags &= 0x80; /* true if block compress */
-
- /* clear table */
- bits = 9;
- mask = 0x1ff;
- end = flags ? 256 : 255;
-
- /* set up: get first 9-bit code, which is the first decompressed byte, but
- don't create a table entry until the next code */
- if (NEXT() == -1) /* no compressed data is ok */
- return Z_OK;
- final = prev = (unsigned)last; /* low 8 bits of code */
- if (NEXT() == -1) /* missing a bit */
- return Z_BUF_ERROR;
- if (last & 1) { /* code must be < 256 */
- strm->msg = (char *)"invalid lzw code";
- return Z_DATA_ERROR;
- }
- rem = (unsigned)last >> 1; /* remaining 7 bits */
- left = 7;
- chunk = bits - 2; /* 7 bytes left in this chunk */
- outbuf[0] = (unsigned char)final; /* write first decompressed byte */
- outcnt = 1;
-
- /* decode codes */
- stack = 0;
- for (;;) {
- /* if the table will be full after this, increment the code size */
- if (end >= mask && bits < max) {
- FLUSHCODE();
- bits++;
- mask <<= 1;
- mask++;
- }
-
- /* get a code of length bits */
- if (chunk == 0) /* decrement chunk modulo bits */
- chunk = bits;
- code = rem; /* low bits of code */
- if (NEXT() == -1) { /* EOF is end of compressed data */
- /* write remaining buffered output */
- if (outcnt && out(&outd, outbuf, outcnt)) {
- strm->next_in = outbuf; /* signal write error */
- return Z_BUF_ERROR;
- }
- return Z_OK;
- }
- code += (unsigned)last << left; /* middle (or high) bits of code */
- left += 8;
- chunk--;
- if (bits > left) { /* need more bits */
- if (NEXT() == -1) /* can't end in middle of code */
- return Z_BUF_ERROR;
- code += (unsigned)last << left; /* high bits of code */
- left += 8;
- chunk--;
- }
- code &= mask; /* mask to current code length */
- left -= bits; /* number of unused bits */
- rem = (unsigned)last >> (8 - left); /* unused bits from last byte */
-
- /* process clear code (256) */
- if (code == 256 && flags) {
- FLUSHCODE();
- bits = 9; /* initialize bits and mask */
- mask = 0x1ff;
- end = 255; /* empty table */
- continue; /* get next code */
- }
-
- /* special code to reuse last match */
- temp = code; /* save the current code */
- if (code > end) {
- /* Be picky on the allowed code here, and make sure that the code
- we drop through (prev) will be a valid index so that random
- input does not cause an exception. The code != end + 1 check is
- empirically derived, and not checked in the original uncompress
- code. If this ever causes a problem, that check could be safely
- removed. Leaving this check in greatly improves gun's ability
- to detect random or corrupted input after a compress header.
- In any case, the prev > end check must be retained. */
- if (code != end + 1 || prev > end) {
- strm->msg = (char *)"invalid lzw code";
- return Z_DATA_ERROR;
- }
- match[stack++] = (unsigned char)final;
- code = prev;
- }
-
- /* walk through linked list to generate output in reverse order */
- p = match + stack;
- while (code >= 256) {
- *p++ = suffix[code];
- code = prefix[code];
- }
- stack = p - match;
- match[stack++] = (unsigned char)code;
- final = code;
-
- /* link new table entry */
- if (end < mask) {
- end++;
- prefix[end] = (unsigned short)prev;
- suffix[end] = (unsigned char)final;
- }
-
- /* set previous code for next iteration */
- prev = temp;
-
- /* write output in forward order */
- while (stack > SIZE - outcnt) {
- while (outcnt < SIZE)
- outbuf[outcnt++] = match[--stack];
- if (out(&outd, outbuf, outcnt)) {
- strm->next_in = outbuf; /* signal write error */
- return Z_BUF_ERROR;
- }
- outcnt = 0;
- }
- p = match + stack;
- do {
- outbuf[outcnt++] = *--p;
- } while (p > match);
- stack = 0;
-
- /* loop for next code with final and prev as the last match, rem and
- left provide the first 0..7 bits of the next code, end is the last
- valid table entry */
- }
-}
-
-/* Decompress a gzip file from infile to outfile. strm is assumed to have been
- successfully initialized with inflateBackInit(). The input file may consist
- of a series of gzip streams, in which case all of them will be decompressed
- to the output file. If outfile is -1, then the gzip stream(s) integrity is
- checked and nothing is written.
-
- The return value is a zlib error code: Z_MEM_ERROR if out of memory,
- Z_DATA_ERROR if the header or the compressed data is invalid, or if the
- trailer CRC-32 check or length doesn't match, Z_BUF_ERROR if the input ends
- prematurely or a write error occurs, or Z_ERRNO if junk (not a another gzip
- stream) follows a valid gzip stream.
- */
-local int gunpipe(z_stream *strm, int infile, int outfile)
-{
- int ret, first, last;
- unsigned have, flags, len;
- z_const unsigned char *next = NULL;
- struct ind ind, *indp;
- struct outd outd;
-
- /* setup input buffer */
- ind.infile = infile;
- ind.inbuf = inbuf;
- indp = &ind;
-
- /* decompress concatenated gzip streams */
- have = 0; /* no input data read in yet */
- first = 1; /* looking for first gzip header */
- strm->next_in = Z_NULL; /* so Z_BUF_ERROR means EOF */
- for (;;) {
- /* look for the two magic header bytes for a gzip stream */
- if (NEXT() == -1) {
- ret = Z_OK;
- break; /* empty gzip stream is ok */
- }
- if (last != 31 || (NEXT() != 139 && last != 157)) {
- strm->msg = (char *)"incorrect header check";
- ret = first ? Z_DATA_ERROR : Z_ERRNO;
- break; /* not a gzip or compress header */
- }
- first = 0; /* next non-header is junk */
-
- /* process a compress (LZW) file -- can't be concatenated after this */
- if (last == 157) {
- ret = lunpipe(have, next, indp, outfile, strm);
- break;
- }
-
- /* process remainder of gzip header */
- ret = Z_BUF_ERROR;
- if (NEXT() != 8) { /* only deflate method allowed */
- if (last == -1) break;
- strm->msg = (char *)"unknown compression method";
- ret = Z_DATA_ERROR;
- break;
- }
- flags = NEXT(); /* header flags */
- NEXT(); /* discard mod time, xflgs, os */
- NEXT();
- NEXT();
- NEXT();
- NEXT();
- NEXT();
- if (last == -1) break;
- if (flags & 0xe0) {
- strm->msg = (char *)"unknown header flags set";
- ret = Z_DATA_ERROR;
- break;
- }
- if (flags & 4) { /* extra field */
- len = NEXT();
- len += (unsigned)(NEXT()) << 8;
- if (last == -1) break;
- while (len > have) {
- len -= have;
- have = 0;
- if (NEXT() == -1) break;
- len--;
- }
- if (last == -1) break;
- have -= len;
- next += len;
- }
- if (flags & 8) /* file name */
- while (NEXT() != 0 && last != -1)
- ;
- if (flags & 16) /* comment */
- while (NEXT() != 0 && last != -1)
- ;
- if (flags & 2) { /* header crc */
- NEXT();
- NEXT();
- }
- if (last == -1) break;
-
- /* set up output */
- outd.outfile = outfile;
- outd.check = 1;
- outd.crc = crc32(0L, Z_NULL, 0);
- outd.total = 0;
-
- /* decompress data to output */
- strm->next_in = next;
- strm->avail_in = have;
- ret = inflateBack(strm, in, indp, out, &outd);
- if (ret != Z_STREAM_END) break;
- next = strm->next_in;
- have = strm->avail_in;
- strm->next_in = Z_NULL; /* so Z_BUF_ERROR means EOF */
-
- /* check trailer */
- ret = Z_BUF_ERROR;
- if (NEXT() != (int)(outd.crc & 0xff) ||
- NEXT() != (int)((outd.crc >> 8) & 0xff) ||
- NEXT() != (int)((outd.crc >> 16) & 0xff) ||
- NEXT() != (int)((outd.crc >> 24) & 0xff)) {
- /* crc error */
- if (last != -1) {
- strm->msg = (char *)"incorrect data check";
- ret = Z_DATA_ERROR;
- }
- break;
- }
- if (NEXT() != (int)(outd.total & 0xff) ||
- NEXT() != (int)((outd.total >> 8) & 0xff) ||
- NEXT() != (int)((outd.total >> 16) & 0xff) ||
- NEXT() != (int)((outd.total >> 24) & 0xff)) {
- /* length error */
- if (last != -1) {
- strm->msg = (char *)"incorrect length check";
- ret = Z_DATA_ERROR;
- }
- break;
- }
-
- /* go back and look for another gzip stream */
- }
-
- /* clean up and return */
- return ret;
-}
-
-/* Copy file attributes, from -> to, as best we can. This is best effort, so
- no errors are reported. The mode bits, including suid, sgid, and the sticky
- bit are copied (if allowed), the owner's user id and group id are copied
- (again if allowed), and the access and modify times are copied. */
-local void copymeta(char *from, char *to)
-{
- struct stat was;
- struct utimbuf when;
-
- /* get all of from's Unix meta data, return if not a regular file */
- if (stat(from, &was) != 0 || (was.st_mode & S_IFMT) != S_IFREG)
- return;
-
- /* set to's mode bits, ignore errors */
- (void)chmod(to, was.st_mode & 07777);
-
- /* copy owner's user and group, ignore errors */
- (void)chown(to, was.st_uid, was.st_gid);
-
- /* copy access and modify times, ignore errors */
- when.actime = was.st_atime;
- when.modtime = was.st_mtime;
- (void)utime(to, &when);
-}
-
-/* Decompress the file inname to the file outnname, of if test is true, just
- decompress without writing and check the gzip trailer for integrity. If
- inname is NULL or an empty string, read from stdin. If outname is NULL or
- an empty string, write to stdout. strm is a pre-initialized inflateBack
- structure. When appropriate, copy the file attributes from inname to
- outname.
-
- gunzip() returns 1 if there is an out-of-memory error or an unexpected
- return code from gunpipe(). Otherwise it returns 0.
- */
-local int gunzip(z_stream *strm, char *inname, char *outname, int test)
-{
- int ret;
- int infile, outfile;
-
- /* open files */
- if (inname == NULL || *inname == 0) {
- inname = "-";
- infile = 0; /* stdin */
- }
- else {
- infile = open(inname, O_RDONLY, 0);
- if (infile == -1) {
- fprintf(stderr, "gun cannot open %s\n", inname);
- return 0;
- }
- }
- if (test)
- outfile = -1;
- else if (outname == NULL || *outname == 0) {
- outname = "-";
- outfile = 1; /* stdout */
- }
- else {
- outfile = open(outname, O_CREAT | O_TRUNC | O_WRONLY, 0666);
- if (outfile == -1) {
- close(infile);
- fprintf(stderr, "gun cannot create %s\n", outname);
- return 0;
- }
- }
- errno = 0;
-
- /* decompress */
- ret = gunpipe(strm, infile, outfile);
- if (outfile > 2) close(outfile);
- if (infile > 2) close(infile);
-
- /* interpret result */
- switch (ret) {
- case Z_OK:
- case Z_ERRNO:
- if (infile > 2 && outfile > 2) {
- copymeta(inname, outname); /* copy attributes */
- unlink(inname);
- }
- if (ret == Z_ERRNO)
- fprintf(stderr, "gun warning: trailing garbage ignored in %s\n",
- inname);
- break;
- case Z_DATA_ERROR:
- if (outfile > 2) unlink(outname);
- fprintf(stderr, "gun data error on %s: %s\n", inname, strm->msg);
- break;
- case Z_MEM_ERROR:
- if (outfile > 2) unlink(outname);
- fprintf(stderr, "gun out of memory error--aborting\n");
- return 1;
- case Z_BUF_ERROR:
- if (outfile > 2) unlink(outname);
- if (strm->next_in != Z_NULL) {
- fprintf(stderr, "gun write error on %s: %s\n",
- outname, strerror(errno));
- }
- else if (errno) {
- fprintf(stderr, "gun read error on %s: %s\n",
- inname, strerror(errno));
- }
- else {
- fprintf(stderr, "gun unexpected end of file on %s\n",
- inname);
- }
- break;
- default:
- if (outfile > 2) unlink(outname);
- fprintf(stderr, "gun internal error--aborting\n");
- return 1;
- }
- return 0;
-}
-
-/* Process the gun command line arguments. See the command syntax near the
- beginning of this source file. */
-int main(int argc, char **argv)
-{
- int ret, len, test;
- char *outname;
- unsigned char *window;
- z_stream strm;
-
- /* initialize inflateBack state for repeated use */
- window = match; /* reuse LZW match buffer */
- strm.zalloc = Z_NULL;
- strm.zfree = Z_NULL;
- strm.opaque = Z_NULL;
- ret = inflateBackInit(&strm, 15, window);
- if (ret != Z_OK) {
- fprintf(stderr, "gun out of memory error--aborting\n");
- return 1;
- }
-
- /* decompress each file to the same name with the suffix removed */
- argc--;
- argv++;
- test = 0;
- if (argc && strcmp(*argv, "-h") == 0) {
- fprintf(stderr, "gun 1.6 (17 Jan 2010)\n");
- fprintf(stderr, "Copyright (C) 2003-2010 Mark Adler\n");
- fprintf(stderr, "usage: gun [-t] [file1.gz [file2.Z ...]]\n");
- return 0;
- }
- if (argc && strcmp(*argv, "-t") == 0) {
- test = 1;
- argc--;
- argv++;
- }
- if (argc)
- do {
- if (test)
- outname = NULL;
- else {
- len = (int)strlen(*argv);
- if (strcmp(*argv + len - 3, ".gz") == 0 ||
- strcmp(*argv + len - 3, "-gz") == 0)
- len -= 3;
- else if (strcmp(*argv + len - 2, ".z") == 0 ||
- strcmp(*argv + len - 2, "-z") == 0 ||
- strcmp(*argv + len - 2, "_z") == 0 ||
- strcmp(*argv + len - 2, ".Z") == 0)
- len -= 2;
- else {
- fprintf(stderr, "gun error: no gz type on %s--skipping\n",
- *argv);
- continue;
- }
- outname = malloc(len + 1);
- if (outname == NULL) {
- fprintf(stderr, "gun out of memory error--aborting\n");
- ret = 1;
- break;
- }
- memcpy(outname, *argv, len);
- outname[len] = 0;
- }
- ret = gunzip(&strm, *argv, outname, test);
- if (outname != NULL) free(outname);
- if (ret) break;
- } while (argv++, --argc);
- else
- ret = gunzip(&strm, NULL, NULL, test);
-
- /* clean up */
- inflateBackEnd(&strm);
- return ret;
-}
diff --git a/third-party/zlib/examples/gzappend.c b/third-party/zlib/examples/gzappend.c
deleted file mode 100644
index 662dec3..0000000
--- a/third-party/zlib/examples/gzappend.c
+++ /dev/null
@@ -1,504 +0,0 @@
-/* gzappend -- command to append to a gzip file
-
- Copyright (C) 2003, 2012 Mark Adler, all rights reserved
- version 1.2, 11 Oct 2012
-
- This software is provided 'as-is', without any express or implied
- warranty. In no event will the author be held liable for any damages
- arising from the use of this software.
-
- Permission is granted to anyone to use this software for any purpose,
- including commercial applications, and to alter it and redistribute it
- freely, subject to the following restrictions:
-
- 1. The origin of this software must not be misrepresented; you must not
- claim that you wrote the original software. If you use this software
- in a product, an acknowledgment in the product documentation would be
- appreciated but is not required.
- 2. Altered source versions must be plainly marked as such, and must not be
- misrepresented as being the original software.
- 3. This notice may not be removed or altered from any source distribution.
-
- Mark Adler madler at alumni.caltech.edu
- */
-
-/*
- * Change history:
- *
- * 1.0 19 Oct 2003 - First version
- * 1.1 4 Nov 2003 - Expand and clarify some comments and notes
- * - Add version and copyright to help
- * - Send help to stdout instead of stderr
- * - Add some preemptive typecasts
- * - Add L to constants in lseek() calls
- * - Remove some debugging information in error messages
- * - Use new data_type definition for zlib 1.2.1
- * - Simplfy and unify file operations
- * - Finish off gzip file in gztack()
- * - Use deflatePrime() instead of adding empty blocks
- * - Keep gzip file clean on appended file read errors
- * - Use in-place rotate instead of auxiliary buffer
- * (Why you ask? Because it was fun to write!)
- * 1.2 11 Oct 2012 - Fix for proper z_const usage
- * - Check for input buffer malloc failure
- */
-
-/*
- gzappend takes a gzip file and appends to it, compressing files from the
- command line or data from stdin. The gzip file is written to directly, to
- avoid copying that file, in case it's large. Note that this results in the
- unfriendly behavior that if gzappend fails, the gzip file is corrupted.
-
- This program was written to illustrate the use of the new Z_BLOCK option of
- zlib 1.2.x's inflate() function. This option returns from inflate() at each
- block boundary to facilitate locating and modifying the last block bit at
- the start of the final deflate block. Also whether using Z_BLOCK or not,
- another required feature of zlib 1.2.x is that inflate() now provides the
- number of unusued bits in the last input byte used. gzappend will not work
- with versions of zlib earlier than 1.2.1.
-
- gzappend first decompresses the gzip file internally, discarding all but
- the last 32K of uncompressed data, and noting the location of the last block
- bit and the number of unused bits in the last byte of the compressed data.
- The gzip trailer containing the CRC-32 and length of the uncompressed data
- is verified. This trailer will be later overwritten.
-
- Then the last block bit is cleared by seeking back in the file and rewriting
- the byte that contains it. Seeking forward, the last byte of the compressed
- data is saved along with the number of unused bits to initialize deflate.
-
- A deflate process is initialized, using the last 32K of the uncompressed
- data from the gzip file to initialize the dictionary. If the total
- uncompressed data was less than 32K, then all of it is used to initialize
- the dictionary. The deflate output bit buffer is also initialized with the
- last bits from the original deflate stream. From here on, the data to
- append is simply compressed using deflate, and written to the gzip file.
- When that is complete, the new CRC-32 and uncompressed length are written
- as the trailer of the gzip file.
- */
-
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
-#include <fcntl.h>
-#include <unistd.h>
-#include "zlib.h"
-
-#define local static
-#define LGCHUNK 14
-#define CHUNK (1U << LGCHUNK)
-#define DSIZE 32768U
-
-/* print an error message and terminate with extreme prejudice */
-local void bye(char *msg1, char *msg2)
-{
- fprintf(stderr, "gzappend error: %s%s\n", msg1, msg2);
- exit(1);
-}
-
-/* return the greatest common divisor of a and b using Euclid's algorithm,
- modified to be fast when one argument much greater than the other, and
- coded to avoid unnecessary swapping */
-local unsigned gcd(unsigned a, unsigned b)
-{
- unsigned c;
-
- while (a && b)
- if (a > b) {
- c = b;
- while (a - c >= c)
- c <<= 1;
- a -= c;
- }
- else {
- c = a;
- while (b - c >= c)
- c <<= 1;
- b -= c;
- }
- return a + b;
-}
-
-/* rotate list[0..len-1] left by rot positions, in place */
-local void rotate(unsigned char *list, unsigned len, unsigned rot)
-{
- unsigned char tmp;
- unsigned cycles;
- unsigned char *start, *last, *to, *from;
-
- /* normalize rot and handle degenerate cases */
- if (len < 2) return;
- if (rot >= len) rot %= len;
- if (rot == 0) return;
-
- /* pointer to last entry in list */
- last = list + (len - 1);
-
- /* do simple left shift by one */
- if (rot == 1) {
- tmp = *list;
- memcpy(list, list + 1, len - 1);
- *last = tmp;
- return;
- }
-
- /* do simple right shift by one */
- if (rot == len - 1) {
- tmp = *last;
- memmove(list + 1, list, len - 1);
- *list = tmp;
- return;
- }
-
- /* otherwise do rotate as a set of cycles in place */
- cycles = gcd(len, rot); /* number of cycles */
- do {
- start = from = list + cycles; /* start index is arbitrary */
- tmp = *from; /* save entry to be overwritten */
- for (;;) {
- to = from; /* next step in cycle */
- from += rot; /* go right rot positions */
- if (from > last) from -= len; /* (pointer better not wrap) */
- if (from == start) break; /* all but one shifted */
- *to = *from; /* shift left */
- }
- *to = tmp; /* complete the circle */
- } while (--cycles);
-}
-
-/* structure for gzip file read operations */
-typedef struct {
- int fd; /* file descriptor */
- int size; /* 1 << size is bytes in buf */
- unsigned left; /* bytes available at next */
- unsigned char *buf; /* buffer */
- z_const unsigned char *next; /* next byte in buffer */
- char *name; /* file name for error messages */
-} file;
-
-/* reload buffer */
-local int readin(file *in)
-{
- int len;
-
- len = read(in->fd, in->buf, 1 << in->size);
- if (len == -1) bye("error reading ", in->name);
- in->left = (unsigned)len;
- in->next = in->buf;
- return len;
-}
-
-/* read from file in, exit if end-of-file */
-local int readmore(file *in)
-{
- if (readin(in) == 0) bye("unexpected end of ", in->name);
- return 0;
-}
-
-#define read1(in) (in->left == 0 ? readmore(in) : 0, \
- in->left--, *(in->next)++)
-
-/* skip over n bytes of in */
-local void skip(file *in, unsigned n)
-{
- unsigned bypass;
-
- if (n > in->left) {
- n -= in->left;
- bypass = n & ~((1U << in->size) - 1);
- if (bypass) {
- if (lseek(in->fd, (off_t)bypass, SEEK_CUR) == -1)
- bye("seeking ", in->name);
- n -= bypass;
- }
- readmore(in);
- if (n > in->left)
- bye("unexpected end of ", in->name);
- }
- in->left -= n;
- in->next += n;
-}
-
-/* read a four-byte unsigned integer, little-endian, from in */
-unsigned long read4(file *in)
-{
- unsigned long val;
-
- val = read1(in);
- val += (unsigned)read1(in) << 8;
- val += (unsigned long)read1(in) << 16;
- val += (unsigned long)read1(in) << 24;
- return val;
-}
-
-/* skip over gzip header */
-local void gzheader(file *in)
-{
- int flags;
- unsigned n;
-
- if (read1(in) != 31 || read1(in) != 139) bye(in->name, " not a gzip file");
- if (read1(in) != 8) bye("unknown compression method in", in->name);
- flags = read1(in);
- if (flags & 0xe0) bye("unknown header flags set in", in->name);
- skip(in, 6);
- if (flags & 4) {
- n = read1(in);
- n += (unsigned)(read1(in)) << 8;
- skip(in, n);
- }
- if (flags & 8) while (read1(in) != 0) ;
- if (flags & 16) while (read1(in) != 0) ;
- if (flags & 2) skip(in, 2);
-}
-
-/* decompress gzip file "name", return strm with a deflate stream ready to
- continue compression of the data in the gzip file, and return a file
- descriptor pointing to where to write the compressed data -- the deflate
- stream is initialized to compress using level "level" */
-local int gzscan(char *name, z_stream *strm, int level)
-{
- int ret, lastbit, left, full;
- unsigned have;
- unsigned long crc, tot;
- unsigned char *window;
- off_t lastoff, end;
- file gz;
-
- /* open gzip file */
- gz.name = name;
- gz.fd = open(name, O_RDWR, 0);
- if (gz.fd == -1) bye("cannot open ", name);
- gz.buf = malloc(CHUNK);
- if (gz.buf == NULL) bye("out of memory", "");
- gz.size = LGCHUNK;
- gz.left = 0;
-
- /* skip gzip header */
- gzheader(&gz);
-
- /* prepare to decompress */
- window = malloc(DSIZE);
- if (window == NULL) bye("out of memory", "");
- strm->zalloc = Z_NULL;
- strm->zfree = Z_NULL;
- strm->opaque = Z_NULL;
- ret = inflateInit2(strm, -15);
- if (ret != Z_OK) bye("out of memory", " or library mismatch");
-
- /* decompress the deflate stream, saving append information */
- lastbit = 0;
- lastoff = lseek(gz.fd, 0L, SEEK_CUR) - gz.left;
- left = 0;
- strm->avail_in = gz.left;
- strm->next_in = gz.next;
- crc = crc32(0L, Z_NULL, 0);
- have = full = 0;
- do {
- /* if needed, get more input */
- if (strm->avail_in == 0) {
- readmore(&gz);
- strm->avail_in = gz.left;
- strm->next_in = gz.next;
- }
-
- /* set up output to next available section of sliding window */
- strm->avail_out = DSIZE - have;
- strm->next_out = window + have;
-
- /* inflate and check for errors */
- ret = inflate(strm, Z_BLOCK);
- if (ret == Z_STREAM_ERROR) bye("internal stream error!", "");
- if (ret == Z_MEM_ERROR) bye("out of memory", "");
- if (ret == Z_DATA_ERROR)
- bye("invalid compressed data--format violated in", name);
-
- /* update crc and sliding window pointer */
- crc = crc32(crc, window + have, DSIZE - have - strm->avail_out);
- if (strm->avail_out)
- have = DSIZE - strm->avail_out;
- else {
- have = 0;
- full = 1;
- }
-
- /* process end of block */
- if (strm->data_type & 128) {
- if (strm->data_type & 64)
- left = strm->data_type & 0x1f;
- else {
- lastbit = strm->data_type & 0x1f;
- lastoff = lseek(gz.fd, 0L, SEEK_CUR) - strm->avail_in;
- }
- }
- } while (ret != Z_STREAM_END);
- inflateEnd(strm);
- gz.left = strm->avail_in;
- gz.next = strm->next_in;
-
- /* save the location of the end of the compressed data */
- end = lseek(gz.fd, 0L, SEEK_CUR) - gz.left;
-
- /* check gzip trailer and save total for deflate */
- if (crc != read4(&gz))
- bye("invalid compressed data--crc mismatch in ", name);
- tot = strm->total_out;
- if ((tot & 0xffffffffUL) != read4(&gz))
- bye("invalid compressed data--length mismatch in", name);
-
- /* if not at end of file, warn */
- if (gz.left || readin(&gz))
- fprintf(stderr,
- "gzappend warning: junk at end of gzip file overwritten\n");
-
- /* clear last block bit */
- lseek(gz.fd, lastoff - (lastbit != 0), SEEK_SET);
- if (read(gz.fd, gz.buf, 1) != 1) bye("reading after seek on ", name);
- *gz.buf = (unsigned char)(*gz.buf ^ (1 << ((8 - lastbit) & 7)));
- lseek(gz.fd, -1L, SEEK_CUR);
- if (write(gz.fd, gz.buf, 1) != 1) bye("writing after seek to ", name);
-
- /* if window wrapped, build dictionary from window by rotating */
- if (full) {
- rotate(window, DSIZE, have);
- have = DSIZE;
- }
-
- /* set up deflate stream with window, crc, total_in, and leftover bits */
- ret = deflateInit2(strm, level, Z_DEFLATED, -15, 8, Z_DEFAULT_STRATEGY);
- if (ret != Z_OK) bye("out of memory", "");
- deflateSetDictionary(strm, window, have);
- strm->adler = crc;
- strm->total_in = tot;
- if (left) {
- lseek(gz.fd, --end, SEEK_SET);
- if (read(gz.fd, gz.buf, 1) != 1) bye("reading after seek on ", name);
- deflatePrime(strm, 8 - left, *gz.buf);
- }
- lseek(gz.fd, end, SEEK_SET);
-
- /* clean up and return */
- free(window);
- free(gz.buf);
- return gz.fd;
-}
-
-/* append file "name" to gzip file gd using deflate stream strm -- if last
- is true, then finish off the deflate stream at the end */
-local void gztack(char *name, int gd, z_stream *strm, int last)
-{
- int fd, len, ret;
- unsigned left;
- unsigned char *in, *out;
-
- /* open file to compress and append */
- fd = 0;
- if (name != NULL) {
- fd = open(name, O_RDONLY, 0);
- if (fd == -1)
- fprintf(stderr, "gzappend warning: %s not found, skipping ...\n",
- name);
- }
-
- /* allocate buffers */
- in = malloc(CHUNK);
- out = malloc(CHUNK);
- if (in == NULL || out == NULL) bye("out of memory", "");
-
- /* compress input file and append to gzip file */
- do {
- /* get more input */
- len = read(fd, in, CHUNK);
- if (len == -1) {
- fprintf(stderr,
- "gzappend warning: error reading %s, skipping rest ...\n",
- name);
- len = 0;
- }
- strm->avail_in = (unsigned)len;
- strm->next_in = in;
- if (len) strm->adler = crc32(strm->adler, in, (unsigned)len);
-
- /* compress and write all available output */
- do {
- strm->avail_out = CHUNK;
- strm->next_out = out;
- ret = deflate(strm, last && len == 0 ? Z_FINISH : Z_NO_FLUSH);
- left = CHUNK - strm->avail_out;
- while (left) {
- len = write(gd, out + CHUNK - strm->avail_out - left, left);
- if (len == -1) bye("writing gzip file", "");
- left -= (unsigned)len;
- }
- } while (strm->avail_out == 0 && ret != Z_STREAM_END);
- } while (len != 0);
-
- /* write trailer after last entry */
- if (last) {
- deflateEnd(strm);
- out[0] = (unsigned char)(strm->adler);
- out[1] = (unsigned char)(strm->adler >> 8);
- out[2] = (unsigned char)(strm->adler >> 16);
- out[3] = (unsigned char)(strm->adler >> 24);
- out[4] = (unsigned char)(strm->total_in);
- out[5] = (unsigned char)(strm->total_in >> 8);
- out[6] = (unsigned char)(strm->total_in >> 16);
- out[7] = (unsigned char)(strm->total_in >> 24);
- len = 8;
- do {
- ret = write(gd, out + 8 - len, len);
- if (ret == -1) bye("writing gzip file", "");
- len -= ret;
- } while (len);
- close(gd);
- }
-
- /* clean up and return */
- free(out);
- free(in);
- if (fd > 0) close(fd);
-}
-
-/* process the compression level option if present, scan the gzip file, and
- append the specified files, or append the data from stdin if no other file
- names are provided on the command line -- the gzip file must be writable
- and seekable */
-int main(int argc, char **argv)
-{
- int gd, level;
- z_stream strm;
-
- /* ignore command name */
- argc--; argv++;
-
- /* provide usage if no arguments */
- if (*argv == NULL) {
- printf(
- "gzappend 1.2 (11 Oct 2012) Copyright (C) 2003, 2012 Mark Adler\n"
- );
- printf(
- "usage: gzappend [-level] file.gz [ addthis [ andthis ... ]]\n");
- return 0;
- }
-
- /* set compression level */
- level = Z_DEFAULT_COMPRESSION;
- if (argv[0][0] == '-') {
- if (argv[0][1] < '0' || argv[0][1] > '9' || argv[0][2] != 0)
- bye("invalid compression level", "");
- level = argv[0][1] - '0';
- if (*++argv == NULL) bye("no gzip file name after options", "");
- }
-
- /* prepare to append to gzip file */
- gd = gzscan(*argv++, &strm, level);
-
- /* append files on command line, or from stdin if none */
- if (*argv == NULL)
- gztack(NULL, gd, &strm, 1);
- else
- do {
- gztack(*argv, gd, &strm, argv[1] == NULL);
- } while (*++argv != NULL);
- return 0;
-}
diff --git a/third-party/zlib/examples/gzjoin.c b/third-party/zlib/examples/gzjoin.c
deleted file mode 100644
index 89e8098..0000000
--- a/third-party/zlib/examples/gzjoin.c
+++ /dev/null
@@ -1,449 +0,0 @@
-/* gzjoin -- command to join gzip files into one gzip file
-
- Copyright (C) 2004, 2005, 2012 Mark Adler, all rights reserved
- version 1.2, 14 Aug 2012
-
- This software is provided 'as-is', without any express or implied
- warranty. In no event will the author be held liable for any damages
- arising from the use of this software.
-
- Permission is granted to anyone to use this software for any purpose,
- including commercial applications, and to alter it and redistribute it
- freely, subject to the following restrictions:
-
- 1. The origin of this software must not be misrepresented; you must not
- claim that you wrote the original software. If you use this software
- in a product, an acknowledgment in the product documentation would be
- appreciated but is not required.
- 2. Altered source versions must be plainly marked as such, and must not be
- misrepresented as being the original software.
- 3. This notice may not be removed or altered from any source distribution.
-
- Mark Adler madler at alumni.caltech.edu
- */
-
-/*
- * Change history:
- *
- * 1.0 11 Dec 2004 - First version
- * 1.1 12 Jun 2005 - Changed ssize_t to long for portability
- * 1.2 14 Aug 2012 - Clean up for z_const usage
- */
-
-/*
- gzjoin takes one or more gzip files on the command line and writes out a
- single gzip file that will uncompress to the concatenation of the
- uncompressed data from the individual gzip files. gzjoin does this without
- having to recompress any of the data and without having to calculate a new
- crc32 for the concatenated uncompressed data. gzjoin does however have to
- decompress all of the input data in order to find the bits in the compressed
- data that need to be modified to concatenate the streams.
-
- gzjoin does not do an integrity check on the input gzip files other than
- checking the gzip header and decompressing the compressed data. They are
- otherwise assumed to be complete and correct.
-
- Each joint between gzip files removes at least 18 bytes of previous trailer
- and subsequent header, and inserts an average of about three bytes to the
- compressed data in order to connect the streams. The output gzip file
- has a minimal ten-byte gzip header with no file name or modification time.
-
- This program was written to illustrate the use of the Z_BLOCK option of
- inflate() and the crc32_combine() function. gzjoin will not compile with
- versions of zlib earlier than 1.2.3.
- */
-
-#include <stdio.h> /* fputs(), fprintf(), fwrite(), putc() */
-#include <stdlib.h> /* exit(), malloc(), free() */
-#include <fcntl.h> /* open() */
-#include <unistd.h> /* close(), read(), lseek() */
-#include "zlib.h"
- /* crc32(), crc32_combine(), inflateInit2(), inflate(), inflateEnd() */
-
-#define local static
-
-/* exit with an error (return a value to allow use in an expression) */
-local int bail(char *why1, char *why2)
-{
- fprintf(stderr, "gzjoin error: %s%s, output incomplete\n", why1, why2);
- exit(1);
- return 0;
-}
-
-/* -- simple buffered file input with access to the buffer -- */
-
-#define CHUNK 32768 /* must be a power of two and fit in unsigned */
-
-/* bin buffered input file type */
-typedef struct {
- char *name; /* name of file for error messages */
- int fd; /* file descriptor */
- unsigned left; /* bytes remaining at next */
- unsigned char *next; /* next byte to read */
- unsigned char *buf; /* allocated buffer of length CHUNK */
-} bin;
-
-/* close a buffered file and free allocated memory */
-local void bclose(bin *in)
-{
- if (in != NULL) {
- if (in->fd != -1)
- close(in->fd);
- if (in->buf != NULL)
- free(in->buf);
- free(in);
- }
-}
-
-/* open a buffered file for input, return a pointer to type bin, or NULL on
- failure */
-local bin *bopen(char *name)
-{
- bin *in;
-
- in = malloc(sizeof(bin));
- if (in == NULL)
- return NULL;
- in->buf = malloc(CHUNK);
- in->fd = open(name, O_RDONLY, 0);
- if (in->buf == NULL || in->fd == -1) {
- bclose(in);
- return NULL;
- }
- in->left = 0;
- in->next = in->buf;
- in->name = name;
- return in;
-}
-
-/* load buffer from file, return -1 on read error, 0 or 1 on success, with
- 1 indicating that end-of-file was reached */
-local int bload(bin *in)
-{
- long len;
-
- if (in == NULL)
- return -1;
- if (in->left != 0)
- return 0;
- in->next = in->buf;
- do {
- len = (long)read(in->fd, in->buf + in->left, CHUNK - in->left);
- if (len < 0)
- return -1;
- in->left += (unsigned)len;
- } while (len != 0 && in->left < CHUNK);
- return len == 0 ? 1 : 0;
-}
-
-/* get a byte from the file, bail if end of file */
-#define bget(in) (in->left ? 0 : bload(in), \
- in->left ? (in->left--, *(in->next)++) : \
- bail("unexpected end of file on ", in->name))
-
-/* get a four-byte little-endian unsigned integer from file */
-local unsigned long bget4(bin *in)
-{
- unsigned long val;
-
- val = bget(in);
- val += (unsigned long)(bget(in)) << 8;
- val += (unsigned long)(bget(in)) << 16;
- val += (unsigned long)(bget(in)) << 24;
- return val;
-}
-
-/* skip bytes in file */
-local void bskip(bin *in, unsigned skip)
-{
- /* check pointer */
- if (in == NULL)
- return;
-
- /* easy case -- skip bytes in buffer */
- if (skip <= in->left) {
- in->left -= skip;
- in->next += skip;
- return;
- }
-
- /* skip what's in buffer, discard buffer contents */
- skip -= in->left;
- in->left = 0;
-
- /* seek past multiples of CHUNK bytes */
- if (skip > CHUNK) {
- unsigned left;
-
- left = skip & (CHUNK - 1);
- if (left == 0) {
- /* exact number of chunks: seek all the way minus one byte to check
- for end-of-file with a read */
- lseek(in->fd, skip - 1, SEEK_CUR);
- if (read(in->fd, in->buf, 1) != 1)
- bail("unexpected end of file on ", in->name);
- return;
- }
-
- /* skip the integral chunks, update skip with remainder */
- lseek(in->fd, skip - left, SEEK_CUR);
- skip = left;
- }
-
- /* read more input and skip remainder */
- bload(in);
- if (skip > in->left)
- bail("unexpected end of file on ", in->name);
- in->left -= skip;
- in->next += skip;
-}
-
-/* -- end of buffered input functions -- */
-
-/* skip the gzip header from file in */
-local void gzhead(bin *in)
-{
- int flags;
-
- /* verify gzip magic header and compression method */
- if (bget(in) != 0x1f || bget(in) != 0x8b || bget(in) != 8)
- bail(in->name, " is not a valid gzip file");
-
- /* get and verify flags */
- flags = bget(in);
- if ((flags & 0xe0) != 0)
- bail("unknown reserved bits set in ", in->name);
-
- /* skip modification time, extra flags, and os */
- bskip(in, 6);
-
- /* skip extra field if present */
- if (flags & 4) {
- unsigned len;
-
- len = bget(in);
- len += (unsigned)(bget(in)) << 8;
- bskip(in, len);
- }
-
- /* skip file name if present */
- if (flags & 8)
- while (bget(in) != 0)
- ;
-
- /* skip comment if present */
- if (flags & 16)
- while (bget(in) != 0)
- ;
-
- /* skip header crc if present */
- if (flags & 2)
- bskip(in, 2);
-}
-
-/* write a four-byte little-endian unsigned integer to out */
-local void put4(unsigned long val, FILE *out)
-{
- putc(val & 0xff, out);
- putc((val >> 8) & 0xff, out);
- putc((val >> 16) & 0xff, out);
- putc((val >> 24) & 0xff, out);
-}
-
-/* Load up zlib stream from buffered input, bail if end of file */
-local void zpull(z_streamp strm, bin *in)
-{
- if (in->left == 0)
- bload(in);
- if (in->left == 0)
- bail("unexpected end of file on ", in->name);
- strm->avail_in = in->left;
- strm->next_in = in->next;
-}
-
-/* Write header for gzip file to out and initialize trailer. */
-local void gzinit(unsigned long *crc, unsigned long *tot, FILE *out)
-{
- fwrite("\x1f\x8b\x08\0\0\0\0\0\0\xff", 1, 10, out);
- *crc = crc32(0L, Z_NULL, 0);
- *tot = 0;
-}
-
-/* Copy the compressed data from name, zeroing the last block bit of the last
- block if clr is true, and adding empty blocks as needed to get to a byte
- boundary. If clr is false, then the last block becomes the last block of
- the output, and the gzip trailer is written. crc and tot maintains the
- crc and length (modulo 2^32) of the output for the trailer. The resulting
- gzip file is written to out. gzinit() must be called before the first call
- of gzcopy() to write the gzip header and to initialize crc and tot. */
-local void gzcopy(char *name, int clr, unsigned long *crc, unsigned long *tot,
- FILE *out)
-{
- int ret; /* return value from zlib functions */
- int pos; /* where the "last block" bit is in byte */
- int last; /* true if processing the last block */
- bin *in; /* buffered input file */
- unsigned char *start; /* start of compressed data in buffer */
- unsigned char *junk; /* buffer for uncompressed data -- discarded */
- z_off_t len; /* length of uncompressed data (support > 4 GB) */
- z_stream strm; /* zlib inflate stream */
-
- /* open gzip file and skip header */
- in = bopen(name);
- if (in == NULL)
- bail("could not open ", name);
- gzhead(in);
-
- /* allocate buffer for uncompressed data and initialize raw inflate
- stream */
- junk = malloc(CHUNK);
- strm.zalloc = Z_NULL;
- strm.zfree = Z_NULL;
- strm.opaque = Z_NULL;
- strm.avail_in = 0;
- strm.next_in = Z_NULL;
- ret = inflateInit2(&strm, -15);
- if (junk == NULL || ret != Z_OK)
- bail("out of memory", "");
-
- /* inflate and copy compressed data, clear last-block bit if requested */
- len = 0;
- zpull(&strm, in);
- start = in->next;
- last = start[0] & 1;
- if (last && clr)
- start[0] &= ~1;
- strm.avail_out = 0;
- for (;;) {
- /* if input used and output done, write used input and get more */
- if (strm.avail_in == 0 && strm.avail_out != 0) {
- fwrite(start, 1, strm.next_in - start, out);
- start = in->buf;
- in->left = 0;
- zpull(&strm, in);
- }
-
- /* decompress -- return early when end-of-block reached */
- strm.avail_out = CHUNK;
- strm.next_out = junk;
- ret = inflate(&strm, Z_BLOCK);
- switch (ret) {
- case Z_MEM_ERROR:
- bail("out of memory", "");
- case Z_DATA_ERROR:
- bail("invalid compressed data in ", in->name);
- }
-
- /* update length of uncompressed data */
- len += CHUNK - strm.avail_out;
-
- /* check for block boundary (only get this when block copied out) */
- if (strm.data_type & 128) {
- /* if that was the last block, then done */
- if (last)
- break;
-
- /* number of unused bits in last byte */
- pos = strm.data_type & 7;
-
- /* find the next last-block bit */
- if (pos != 0) {
- /* next last-block bit is in last used byte */
- pos = 0x100 >> pos;
- last = strm.next_in[-1] & pos;
- if (last && clr)
- in->buf[strm.next_in - in->buf - 1] &= ~pos;
- }
- else {
- /* next last-block bit is in next unused byte */
- if (strm.avail_in == 0) {
- /* don't have that byte yet -- get it */
- fwrite(start, 1, strm.next_in - start, out);
- start = in->buf;
- in->left = 0;
- zpull(&strm, in);
- }
- last = strm.next_in[0] & 1;
- if (last && clr)
- in->buf[strm.next_in - in->buf] &= ~1;
- }
- }
- }
-
- /* update buffer with unused input */
- in->left = strm.avail_in;
- in->next = in->buf + (strm.next_in - in->buf);
-
- /* copy used input, write empty blocks to get to byte boundary */
- pos = strm.data_type & 7;
- fwrite(start, 1, in->next - start - 1, out);
- last = in->next[-1];
- if (pos == 0 || !clr)
- /* already at byte boundary, or last file: write last byte */
- putc(last, out);
- else {
- /* append empty blocks to last byte */
- last &= ((0x100 >> pos) - 1); /* assure unused bits are zero */
- if (pos & 1) {
- /* odd -- append an empty stored block */
- putc(last, out);
- if (pos == 1)
- putc(0, out); /* two more bits in block header */
- fwrite("\0\0\xff\xff", 1, 4, out);
- }
- else {
- /* even -- append 1, 2, or 3 empty fixed blocks */
- switch (pos) {
- case 6:
- putc(last | 8, out);
- last = 0;
- case 4:
- putc(last | 0x20, out);
- last = 0;
- case 2:
- putc(last | 0x80, out);
- putc(0, out);
- }
- }
- }
-
- /* update crc and tot */
- *crc = crc32_combine(*crc, bget4(in), len);
- *tot += (unsigned long)len;
-
- /* clean up */
- inflateEnd(&strm);
- free(junk);
- bclose(in);
-
- /* write trailer if this is the last gzip file */
- if (!clr) {
- put4(*crc, out);
- put4(*tot, out);
- }
-}
-
-/* join the gzip files on the command line, write result to stdout */
-int main(int argc, char **argv)
-{
- unsigned long crc, tot; /* running crc and total uncompressed length */
-
- /* skip command name */
- argc--;
- argv++;
-
- /* show usage if no arguments */
- if (argc == 0) {
- fputs("gzjoin usage: gzjoin f1.gz [f2.gz [f3.gz ...]] > fjoin.gz\n",
- stderr);
- return 0;
- }
-
- /* join gzip files on command line and write to stdout */
- gzinit(&crc, &tot, stdout);
- while (argc--)
- gzcopy(*argv++, argc, &crc, &tot, stdout);
-
- /* done */
- return 0;
-}
diff --git a/third-party/zlib/examples/gzlog.c b/third-party/zlib/examples/gzlog.c
deleted file mode 100644
index 922f878..0000000
--- a/third-party/zlib/examples/gzlog.c
+++ /dev/null
@@ -1,1059 +0,0 @@
-/*
- * gzlog.c
- * Copyright (C) 2004, 2008, 2012 Mark Adler, all rights reserved
- * For conditions of distribution and use, see copyright notice in gzlog.h
- * version 2.2, 14 Aug 2012
- */
-
-/*
- gzlog provides a mechanism for frequently appending short strings to a gzip
- file that is efficient both in execution time and compression ratio. The
- strategy is to write the short strings in an uncompressed form to the end of
- the gzip file, only compressing when the amount of uncompressed data has
- reached a given threshold.
-
- gzlog also provides protection against interruptions in the process due to
- system crashes. The status of the operation is recorded in an extra field
- in the gzip file, and is only updated once the gzip file is brought to a
- valid state. The last data to be appended or compressed is saved in an
- auxiliary file, so that if the operation is interrupted, it can be completed
- the next time an append operation is attempted.
-
- gzlog maintains another auxiliary file with the last 32K of data from the
- compressed portion, which is preloaded for the compression of the subsequent
- data. This minimizes the impact to the compression ratio of appending.
- */
-
-/*
- Operations Concept:
-
- Files (log name "foo"):
- foo.gz -- gzip file with the complete log
- foo.add -- last message to append or last data to compress
- foo.dict -- dictionary of the last 32K of data for next compression
- foo.temp -- temporary dictionary file for compression after this one
- foo.lock -- lock file for reading and writing the other files
- foo.repairs -- log file for log file recovery operations (not compressed)
-
- gzip file structure:
- - fixed-length (no file name) header with extra field (see below)
- - compressed data ending initially with empty stored block
- - uncompressed data filling out originally empty stored block and
- subsequent stored blocks as needed (16K max each)
- - gzip trailer
- - no junk at end (no other gzip streams)
-
- When appending data, the information in the first three items above plus the
- foo.add file are sufficient to recover an interrupted append operation. The
- extra field has the necessary information to restore the start of the last
- stored block and determine where to append the data in the foo.add file, as
- well as the crc and length of the gzip data before the append operation.
-
- The foo.add file is created before the gzip file is marked for append, and
- deleted after the gzip file is marked as complete. So if the append
- operation is interrupted, the data to add will still be there. If due to
- some external force, the foo.add file gets deleted between when the append
- operation was interrupted and when recovery is attempted, the gzip file will
- still be restored, but without the appended data.
-
- When compressing data, the information in the first two items above plus the
- foo.add file are sufficient to recover an interrupted compress operation.
- The extra field has the necessary information to find the end of the
- compressed data, and contains both the crc and length of just the compressed
- data and of the complete set of data including the contents of the foo.add
- file.
-
- Again, the foo.add file is maintained during the compress operation in case
- of an interruption. If in the unlikely event the foo.add file with the data
- to be compressed is missing due to some external force, a gzip file with
- just the previous compressed data will be reconstructed. In this case, all
- of the data that was to be compressed is lost (approximately one megabyte).
- This will not occur if all that happened was an interruption of the compress
- operation.
-
- The third state that is marked is the replacement of the old dictionary with
- the new dictionary after a compress operation. Once compression is
- complete, the gzip file is marked as being in the replace state. This
- completes the gzip file, so an interrupt after being so marked does not
- result in recompression. Then the dictionary file is replaced, and the gzip
- file is marked as completed. This state prevents the possibility of
- restarting compression with the wrong dictionary file.
-
- All three operations are wrapped by a lock/unlock procedure. In order to
- gain exclusive access to the log files, first a foo.lock file must be
- exclusively created. When all operations are complete, the lock is
- released by deleting the foo.lock file. If when attempting to create the
- lock file, it already exists and the modify time of the lock file is more
- than five minutes old (set by the PATIENCE define below), then the old
- lock file is considered stale and deleted, and the exclusive creation of
- the lock file is retried. To assure that there are no false assessments
- of the staleness of the lock file, the operations periodically touch the
- lock file to update the modified date.
-
- Following is the definition of the extra field with all of the information
- required to enable the above append and compress operations and their
- recovery if interrupted. Multi-byte values are stored little endian
- (consistent with the gzip format). File pointers are eight bytes long.
- The crc's and lengths for the gzip trailer are four bytes long. (Note that
- the length at the end of a gzip file is used for error checking only, and
- for large files is actually the length modulo 2^32.) The stored block
- length is two bytes long. The gzip extra field two-byte identification is
- "ap" for append. It is assumed that writing the extra field to the file is
- an "atomic" operation. That is, either all of the extra field is written
- to the file, or none of it is, if the operation is interrupted right at the
- point of updating the extra field. This is a reasonable assumption, since
- the extra field is within the first 52 bytes of the file, which is smaller
- than any expected block size for a mass storage device (usually 512 bytes or
- larger).
-
- Extra field (35 bytes):
- - Pointer to first stored block length -- this points to the two-byte length
- of the first stored block, which is followed by the two-byte, one's
- complement of that length. The stored block length is preceded by the
- three-bit header of the stored block, which is the actual start of the
- stored block in the deflate format. See the bit offset field below.
- - Pointer to the last stored block length. This is the same as above, but
- for the last stored block of the uncompressed data in the gzip file.
- Initially this is the same as the first stored block length pointer.
- When the stored block gets to 16K (see the MAX_STORE define), then a new
- stored block as added, at which point the last stored block length pointer
- is different from the first stored block length pointer. When they are
- different, the first bit of the last stored block header is eight bits, or
- one byte back from the block length.
- - Compressed data crc and length. This is the crc and length of the data
- that is in the compressed portion of the deflate stream. These are used
- only in the event that the foo.add file containing the data to compress is
- lost after a compress operation is interrupted.
- - Total data crc and length. This is the crc and length of all of the data
- stored in the gzip file, compressed and uncompressed. It is used to
- reconstruct the gzip trailer when compressing, as well as when recovering
- interrupted operations.
- - Final stored block length. This is used to quickly find where to append,
- and allows the restoration of the original final stored block state when
- an append operation is interrupted.
- - First stored block start as the number of bits back from the final stored
- block first length byte. This value is in the range of 3..10, and is
- stored as the low three bits of the final byte of the extra field after
- subtracting three (0..7). This allows the last-block bit of the stored
- block header to be updated when a new stored block is added, for the case
- when the first stored block and the last stored block are the same. (When
- they are different, the numbers of bits back is known to be eight.) This
- also allows for new compressed data to be appended to the old compressed
- data in the compress operation, overwriting the previous first stored
- block, or for the compressed data to be terminated and a valid gzip file
- reconstructed on the off chance that a compression operation was
- interrupted and the data to compress in the foo.add file was deleted.
- - The operation in process. This is the next two bits in the last byte (the
- bits under the mask 0x18). The are interpreted as 0: nothing in process,
- 1: append in process, 2: compress in process, 3: replace in process.
- - The top three bits of the last byte in the extra field are reserved and
- are currently set to zero.
-
- Main procedure:
- - Exclusively create the foo.lock file using the O_CREAT and O_EXCL modes of
- the system open() call. If the modify time of an existing lock file is
- more than PATIENCE seconds old, then the lock file is deleted and the
- exclusive create is retried.
- - Load the extra field from the foo.gz file, and see if an operation was in
- progress but not completed. If so, apply the recovery procedure below.
- - Perform the append procedure with the provided data.
- - If the uncompressed data in the foo.gz file is 1MB or more, apply the
- compress procedure.
- - Delete the foo.lock file.
-
- Append procedure:
- - Put what to append in the foo.add file so that the operation can be
- restarted if this procedure is interrupted.
- - Mark the foo.gz extra field with the append operation in progress.
- + Restore the original last-block bit and stored block length of the last
- stored block from the information in the extra field, in case a previous
- append operation was interrupted.
- - Append the provided data to the last stored block, creating new stored
- blocks as needed and updating the stored blocks last-block bits and
- lengths.
- - Update the crc and length with the new data, and write the gzip trailer.
- - Write over the extra field (with a single write operation) with the new
- pointers, lengths, and crc's, and mark the gzip file as not in process.
- Though there is still a foo.add file, it will be ignored since nothing
- is in process. If a foo.add file is leftover from a previously
- completed operation, it is truncated when writing new data to it.
- - Delete the foo.add file.
-
- Compress and replace procedures:
- - Read all of the uncompressed data in the stored blocks in foo.gz and write
- it to foo.add. Also write foo.temp with the last 32K of that data to
- provide a dictionary for the next invocation of this procedure.
- - Rewrite the extra field marking foo.gz with a compression in process.
- * If there is no data provided to compress (due to a missing foo.add file
- when recovering), reconstruct and truncate the foo.gz file to contain
- only the previous compressed data and proceed to the step after the next
- one. Otherwise ...
- - Compress the data with the dictionary in foo.dict, and write to the
- foo.gz file starting at the bit immediately following the last previously
- compressed block. If there is no foo.dict, proceed anyway with the
- compression at slightly reduced efficiency. (For the foo.dict file to be
- missing requires some external failure beyond simply the interruption of
- a compress operation.) During this process, the foo.lock file is
- periodically touched to assure that that file is not considered stale by
- another process before we're done. The deflation is terminated with a
- non-last empty static block (10 bits long), that is then located and
- written over by a last-bit-set empty stored block.
- - Append the crc and length of the data in the gzip file (previously
- calculated during the append operations).
- - Write over the extra field with the updated stored block offsets, bits
- back, crc's, and lengths, and mark foo.gz as in process for a replacement
- of the dictionary.
- @ Delete the foo.add file.
- - Replace foo.dict with foo.temp.
- - Write over the extra field, marking foo.gz as complete.
-
- Recovery procedure:
- - If not a replace recovery, read in the foo.add file, and provide that data
- to the appropriate recovery below. If there is no foo.add file, provide
- a zero data length to the recovery. In that case, the append recovery
- restores the foo.gz to the previous compressed + uncompressed data state.
- For the the compress recovery, a missing foo.add file results in foo.gz
- being restored to the previous compressed-only data state.
- - Append recovery:
- - Pick up append at + step above
- - Compress recovery:
- - Pick up compress at * step above
- - Replace recovery:
- - Pick up compress at @ step above
- - Log the repair with a date stamp in foo.repairs
- */
-
-#include <sys/types.h>
-#include <stdio.h> /* rename, fopen, fprintf, fclose */
-#include <stdlib.h> /* malloc, free */
-#include <string.h> /* strlen, strrchr, strcpy, strncpy, strcmp */
-#include <fcntl.h> /* open */
-#include <unistd.h> /* lseek, read, write, close, unlink, sleep, */
- /* ftruncate, fsync */
-#include <errno.h> /* errno */
-#include <time.h> /* time, ctime */
-#include <sys/stat.h> /* stat */
-#include <sys/time.h> /* utimes */
-#include "zlib.h" /* crc32 */
-
-#include "gzlog.h" /* header for external access */
-
-#define local static
-typedef unsigned int uint;
-typedef unsigned long ulong;
-
-/* Macro for debugging to deterministically force recovery operations */
-#ifdef DEBUG
- #include <setjmp.h> /* longjmp */
- jmp_buf gzlog_jump; /* where to go back to */
- int gzlog_bail = 0; /* which point to bail at (1..8) */
- int gzlog_count = -1; /* number of times through to wait */
-# define BAIL(n) do { if (n == gzlog_bail && gzlog_count-- == 0) \
- longjmp(gzlog_jump, gzlog_bail); } while (0)
-#else
-# define BAIL(n)
-#endif
-
-/* how old the lock file can be in seconds before considering it stale */
-#define PATIENCE 300
-
-/* maximum stored block size in Kbytes -- must be in 1..63 */
-#define MAX_STORE 16
-
-/* number of stored Kbytes to trigger compression (must be >= 32 to allow
- dictionary construction, and <= 204 * MAX_STORE, in order for >> 10 to
- discard the stored block headers contribution of five bytes each) */
-#define TRIGGER 1024
-
-/* size of a deflate dictionary (this cannot be changed) */
-#define DICT 32768U
-
-/* values for the operation (2 bits) */
-#define NO_OP 0
-#define APPEND_OP 1
-#define COMPRESS_OP 2
-#define REPLACE_OP 3
-
-/* macros to extract little-endian integers from an unsigned byte buffer */
-#define PULL2(p) ((p)[0]+((uint)((p)[1])<<8))
-#define PULL4(p) (PULL2(p)+((ulong)PULL2(p+2)<<16))
-#define PULL8(p) (PULL4(p)+((off_t)PULL4(p+4)<<32))
-
-/* macros to store integers into a byte buffer in little-endian order */
-#define PUT2(p,a) do {(p)[0]=a;(p)[1]=(a)>>8;} while(0)
-#define PUT4(p,a) do {PUT2(p,a);PUT2(p+2,a>>16);} while(0)
-#define PUT8(p,a) do {PUT4(p,a);PUT4(p+4,a>>32);} while(0)
-
-/* internal structure for log information */
-#define LOGID "\106\035\172" /* should be three non-zero characters */
-struct log {
- char id[4]; /* contains LOGID to detect inadvertent overwrites */
- int fd; /* file descriptor for .gz file, opened read/write */
- char *path; /* allocated path, e.g. "/var/log/foo" or "foo" */
- char *end; /* end of path, for appending suffices such as ".gz" */
- off_t first; /* offset of first stored block first length byte */
- int back; /* location of first block id in bits back from first */
- uint stored; /* bytes currently in last stored block */
- off_t last; /* offset of last stored block first length byte */
- ulong ccrc; /* crc of compressed data */
- ulong clen; /* length (modulo 2^32) of compressed data */
- ulong tcrc; /* crc of total data */
- ulong tlen; /* length (modulo 2^32) of total data */
- time_t lock; /* last modify time of our lock file */
-};
-
-/* gzip header for gzlog */
-local unsigned char log_gzhead[] = {
- 0x1f, 0x8b, /* magic gzip id */
- 8, /* compression method is deflate */
- 4, /* there is an extra field (no file name) */
- 0, 0, 0, 0, /* no modification time provided */
- 0, 0xff, /* no extra flags, no OS specified */
- 39, 0, 'a', 'p', 35, 0 /* extra field with "ap" subfield */
- /* 35 is EXTRA, 39 is EXTRA + 4 */
-};
-
-#define HEAD sizeof(log_gzhead) /* should be 16 */
-
-/* initial gzip extra field content (52 == HEAD + EXTRA + 1) */
-local unsigned char log_gzext[] = {
- 52, 0, 0, 0, 0, 0, 0, 0, /* offset of first stored block length */
- 52, 0, 0, 0, 0, 0, 0, 0, /* offset of last stored block length */
- 0, 0, 0, 0, 0, 0, 0, 0, /* compressed data crc and length */
- 0, 0, 0, 0, 0, 0, 0, 0, /* total data crc and length */
- 0, 0, /* final stored block data length */
- 5 /* op is NO_OP, last bit 8 bits back */
-};
-
-#define EXTRA sizeof(log_gzext) /* should be 35 */
-
-/* initial gzip data and trailer */
-local unsigned char log_gzbody[] = {
- 1, 0, 0, 0xff, 0xff, /* empty stored block (last) */
- 0, 0, 0, 0, /* crc */
- 0, 0, 0, 0 /* uncompressed length */
-};
-
-#define BODY sizeof(log_gzbody)
-
-/* Exclusively create foo.lock in order to negotiate exclusive access to the
- foo.* files. If the modify time of an existing lock file is greater than
- PATIENCE seconds in the past, then consider the lock file to have been
- abandoned, delete it, and try the exclusive create again. Save the lock
- file modify time for verification of ownership. Return 0 on success, or -1
- on failure, usually due to an access restriction or invalid path. Note that
- if stat() or unlink() fails, it may be due to another process noticing the
- abandoned lock file a smidge sooner and deleting it, so those are not
- flagged as an error. */
-local int log_lock(struct log *log)
-{
- int fd;
- struct stat st;
-
- strcpy(log->end, ".lock");
- while ((fd = open(log->path, O_CREAT | O_EXCL, 0644)) < 0) {
- if (errno != EEXIST)
- return -1;
- if (stat(log->path, &st) == 0 && time(NULL) - st.st_mtime > PATIENCE) {
- unlink(log->path);
- continue;
- }
- sleep(2); /* relinquish the CPU for two seconds while waiting */
- }
- close(fd);
- if (stat(log->path, &st) == 0)
- log->lock = st.st_mtime;
- return 0;
-}
-
-/* Update the modify time of the lock file to now, in order to prevent another
- task from thinking that the lock is stale. Save the lock file modify time
- for verification of ownership. */
-local void log_touch(struct log *log)
-{
- struct stat st;
-
- strcpy(log->end, ".lock");
- utimes(log->path, NULL);
- if (stat(log->path, &st) == 0)
- log->lock = st.st_mtime;
-}
-
-/* Check the log file modify time against what is expected. Return true if
- this is not our lock. If it is our lock, touch it to keep it. */
-local int log_check(struct log *log)
-{
- struct stat st;
-
- strcpy(log->end, ".lock");
- if (stat(log->path, &st) || st.st_mtime != log->lock)
- return 1;
- log_touch(log);
- return 0;
-}
-
-/* Unlock a previously acquired lock, but only if it's ours. */
-local void log_unlock(struct log *log)
-{
- if (log_check(log))
- return;
- strcpy(log->end, ".lock");
- unlink(log->path);
- log->lock = 0;
-}
-
-/* Check the gzip header and read in the extra field, filling in the values in
- the log structure. Return op on success or -1 if the gzip header was not as
- expected. op is the current operation in progress last written to the extra
- field. This assumes that the gzip file has already been opened, with the
- file descriptor log->fd. */
-local int log_head(struct log *log)
-{
- int op;
- unsigned char buf[HEAD + EXTRA];
-
- if (lseek(log->fd, 0, SEEK_SET) < 0 ||
- read(log->fd, buf, HEAD + EXTRA) != HEAD + EXTRA ||
- memcmp(buf, log_gzhead, HEAD)) {
- return -1;
- }
- log->first = PULL8(buf + HEAD);
- log->last = PULL8(buf + HEAD + 8);
- log->ccrc = PULL4(buf + HEAD + 16);
- log->clen = PULL4(buf + HEAD + 20);
- log->tcrc = PULL4(buf + HEAD + 24);
- log->tlen = PULL4(buf + HEAD + 28);
- log->stored = PULL2(buf + HEAD + 32);
- log->back = 3 + (buf[HEAD + 34] & 7);
- op = (buf[HEAD + 34] >> 3) & 3;
- return op;
-}
-
-/* Write over the extra field contents, marking the operation as op. Use fsync
- to assure that the device is written to, and in the requested order. This
- operation, and only this operation, is assumed to be atomic in order to
- assure that the log is recoverable in the event of an interruption at any
- point in the process. Return -1 if the write to foo.gz failed. */
-local int log_mark(struct log *log, int op)
-{
- int ret;
- unsigned char ext[EXTRA];
-
- PUT8(ext, log->first);
- PUT8(ext + 8, log->last);
- PUT4(ext + 16, log->ccrc);
- PUT4(ext + 20, log->clen);
- PUT4(ext + 24, log->tcrc);
- PUT4(ext + 28, log->tlen);
- PUT2(ext + 32, log->stored);
- ext[34] = log->back - 3 + (op << 3);
- fsync(log->fd);
- ret = lseek(log->fd, HEAD, SEEK_SET) < 0 ||
- write(log->fd, ext, EXTRA) != EXTRA ? -1 : 0;
- fsync(log->fd);
- return ret;
-}
-
-/* Rewrite the last block header bits and subsequent zero bits to get to a byte
- boundary, setting the last block bit if last is true, and then write the
- remainder of the stored block header (length and one's complement). Leave
- the file pointer after the end of the last stored block data. Return -1 if
- there is a read or write failure on the foo.gz file */
-local int log_last(struct log *log, int last)
-{
- int back, len, mask;
- unsigned char buf[6];
-
- /* determine the locations of the bytes and bits to modify */
- back = log->last == log->first ? log->back : 8;
- len = back > 8 ? 2 : 1; /* bytes back from log->last */
- mask = 0x80 >> ((back - 1) & 7); /* mask for block last-bit */
-
- /* get the byte to modify (one or two back) into buf[0] -- don't need to
- read the byte if the last-bit is eight bits back, since in that case
- the entire byte will be modified */
- buf[0] = 0;
- if (back != 8 && (lseek(log->fd, log->last - len, SEEK_SET) < 0 ||
- read(log->fd, buf, 1) != 1))
- return -1;
-
- /* change the last-bit of the last stored block as requested -- note
- that all bits above the last-bit are set to zero, per the type bits
- of a stored block being 00 and per the convention that the bits to
- bring the stream to a byte boundary are also zeros */
- buf[1] = 0;
- buf[2 - len] = (*buf & (mask - 1)) + (last ? mask : 0);
-
- /* write the modified stored block header and lengths, move the file
- pointer to after the last stored block data */
- PUT2(buf + 2, log->stored);
- PUT2(buf + 4, log->stored ^ 0xffff);
- return lseek(log->fd, log->last - len, SEEK_SET) < 0 ||
- write(log->fd, buf + 2 - len, len + 4) != len + 4 ||
- lseek(log->fd, log->stored, SEEK_CUR) < 0 ? -1 : 0;
-}
-
-/* Append len bytes from data to the locked and open log file. len may be zero
- if recovering and no .add file was found. In that case, the previous state
- of the foo.gz file is restored. The data is appended uncompressed in
- deflate stored blocks. Return -1 if there was an error reading or writing
- the foo.gz file. */
-local int log_append(struct log *log, unsigned char *data, size_t len)
-{
- uint put;
- off_t end;
- unsigned char buf[8];
-
- /* set the last block last-bit and length, in case recovering an
- interrupted append, then position the file pointer to append to the
- block */
- if (log_last(log, 1))
- return -1;
-
- /* append, adding stored blocks and updating the offset of the last stored
- block as needed, and update the total crc and length */
- while (len) {
- /* append as much as we can to the last block */
- put = (MAX_STORE << 10) - log->stored;
- if (put > len)
- put = (uint)len;
- if (put) {
- if (write(log->fd, data, put) != put)
- return -1;
- BAIL(1);
- log->tcrc = crc32(log->tcrc, data, put);
- log->tlen += put;
- log->stored += put;
- data += put;
- len -= put;
- }
-
- /* if we need to, add a new empty stored block */
- if (len) {
- /* mark current block as not last */
- if (log_last(log, 0))
- return -1;
-
- /* point to new, empty stored block */
- log->last += 4 + log->stored + 1;
- log->stored = 0;
- }
-
- /* mark last block as last, update its length */
- if (log_last(log, 1))
- return -1;
- BAIL(2);
- }
-
- /* write the new crc and length trailer, and truncate just in case (could
- be recovering from partial append with a missing foo.add file) */
- PUT4(buf, log->tcrc);
- PUT4(buf + 4, log->tlen);
- if (write(log->fd, buf, 8) != 8 ||
- (end = lseek(log->fd, 0, SEEK_CUR)) < 0 || ftruncate(log->fd, end))
- return -1;
-
- /* write the extra field, marking the log file as done, delete .add file */
- if (log_mark(log, NO_OP))
- return -1;
- strcpy(log->end, ".add");
- unlink(log->path); /* ignore error, since may not exist */
- return 0;
-}
-
-/* Replace the foo.dict file with the foo.temp file. Also delete the foo.add
- file, since the compress operation may have been interrupted before that was
- done. Returns 1 if memory could not be allocated, or -1 if reading or
- writing foo.gz fails, or if the rename fails for some reason other than
- foo.temp not existing. foo.temp not existing is a permitted error, since
- the replace operation may have been interrupted after the rename is done,
- but before foo.gz is marked as complete. */
-local int log_replace(struct log *log)
-{
- int ret;
- char *dest;
-
- /* delete foo.add file */
- strcpy(log->end, ".add");
- unlink(log->path); /* ignore error, since may not exist */
- BAIL(3);
-
- /* rename foo.name to foo.dict, replacing foo.dict if it exists */
- strcpy(log->end, ".dict");
- dest = malloc(strlen(log->path) + 1);
- if (dest == NULL)
- return -2;
- strcpy(dest, log->path);
- strcpy(log->end, ".temp");
- ret = rename(log->path, dest);
- free(dest);
- if (ret && errno != ENOENT)
- return -1;
- BAIL(4);
-
- /* mark the foo.gz file as done */
- return log_mark(log, NO_OP);
-}
-
-/* Compress the len bytes at data and append the compressed data to the
- foo.gz deflate data immediately after the previous compressed data. This
- overwrites the previous uncompressed data, which was stored in foo.add
- and is the data provided in data[0..len-1]. If this operation is
- interrupted, it picks up at the start of this routine, with the foo.add
- file read in again. If there is no data to compress (len == 0), then we
- simply terminate the foo.gz file after the previously compressed data,
- appending a final empty stored block and the gzip trailer. Return -1 if
- reading or writing the log.gz file failed, or -2 if there was a memory
- allocation failure. */
-local int log_compress(struct log *log, unsigned char *data, size_t len)
-{
- int fd;
- uint got, max;
- ssize_t dict;
- off_t end;
- z_stream strm;
- unsigned char buf[DICT];
-
- /* compress and append compressed data */
- if (len) {
- /* set up for deflate, allocating memory */
- strm.zalloc = Z_NULL;
- strm.zfree = Z_NULL;
- strm.opaque = Z_NULL;
- if (deflateInit2(&strm, Z_DEFAULT_COMPRESSION, Z_DEFLATED, -15, 8,
- Z_DEFAULT_STRATEGY) != Z_OK)
- return -2;
-
- /* read in dictionary (last 32K of data that was compressed) */
- strcpy(log->end, ".dict");
- fd = open(log->path, O_RDONLY, 0);
- if (fd >= 0) {
- dict = read(fd, buf, DICT);
- close(fd);
- if (dict < 0) {
- deflateEnd(&strm);
- return -1;
- }
- if (dict)
- deflateSetDictionary(&strm, buf, (uint)dict);
- }
- log_touch(log);
-
- /* prime deflate with last bits of previous block, position write
- pointer to write those bits and overwrite what follows */
- if (lseek(log->fd, log->first - (log->back > 8 ? 2 : 1),
- SEEK_SET) < 0 ||
- read(log->fd, buf, 1) != 1 || lseek(log->fd, -1, SEEK_CUR) < 0) {
- deflateEnd(&strm);
- return -1;
- }
- deflatePrime(&strm, (8 - log->back) & 7, *buf);
-
- /* compress, finishing with a partial non-last empty static block */
- strm.next_in = data;
- max = (((uint)0 - 1) >> 1) + 1; /* in case int smaller than size_t */
- do {
- strm.avail_in = len > max ? max : (uint)len;
- len -= strm.avail_in;
- do {
- strm.avail_out = DICT;
- strm.next_out = buf;
- deflate(&strm, len ? Z_NO_FLUSH : Z_PARTIAL_FLUSH);
- got = DICT - strm.avail_out;
- if (got && write(log->fd, buf, got) != got) {
- deflateEnd(&strm);
- return -1;
- }
- log_touch(log);
- } while (strm.avail_out == 0);
- } while (len);
- deflateEnd(&strm);
- BAIL(5);
-
- /* find start of empty static block -- scanning backwards the first one
- bit is the second bit of the block, if the last byte is zero, then
- we know the byte before that has a one in the top bit, since an
- empty static block is ten bits long */
- if ((log->first = lseek(log->fd, -1, SEEK_CUR)) < 0 ||
- read(log->fd, buf, 1) != 1)
- return -1;
- log->first++;
- if (*buf) {
- log->back = 1;
- while ((*buf & ((uint)1 << (8 - log->back++))) == 0)
- ; /* guaranteed to terminate, since *buf != 0 */
- }
- else
- log->back = 10;
-
- /* update compressed crc and length */
- log->ccrc = log->tcrc;
- log->clen = log->tlen;
- }
- else {
- /* no data to compress -- fix up existing gzip stream */
- log->tcrc = log->ccrc;
- log->tlen = log->clen;
- }
-
- /* complete and truncate gzip stream */
- log->last = log->first;
- log->stored = 0;
- PUT4(buf, log->tcrc);
- PUT4(buf + 4, log->tlen);
- if (log_last(log, 1) || write(log->fd, buf, 8) != 8 ||
- (end = lseek(log->fd, 0, SEEK_CUR)) < 0 || ftruncate(log->fd, end))
- return -1;
- BAIL(6);
-
- /* mark as being in the replace operation */
- if (log_mark(log, REPLACE_OP))
- return -1;
-
- /* execute the replace operation and mark the file as done */
- return log_replace(log);
-}
-
-/* log a repair record to the .repairs file */
-local void log_log(struct log *log, int op, char *record)
-{
- time_t now;
- FILE *rec;
-
- now = time(NULL);
- strcpy(log->end, ".repairs");
- rec = fopen(log->path, "a");
- if (rec == NULL)
- return;
- fprintf(rec, "%.24s %s recovery: %s\n", ctime(&now), op == APPEND_OP ?
- "append" : (op == COMPRESS_OP ? "compress" : "replace"), record);
- fclose(rec);
- return;
-}
-
-/* Recover the interrupted operation op. First read foo.add for recovering an
- append or compress operation. Return -1 if there was an error reading or
- writing foo.gz or reading an existing foo.add, or -2 if there was a memory
- allocation failure. */
-local int log_recover(struct log *log, int op)
-{
- int fd, ret = 0;
- unsigned char *data = NULL;
- size_t len = 0;
- struct stat st;
-
- /* log recovery */
- log_log(log, op, "start");
-
- /* load foo.add file if expected and present */
- if (op == APPEND_OP || op == COMPRESS_OP) {
- strcpy(log->end, ".add");
- if (stat(log->path, &st) == 0 && st.st_size) {
- len = (size_t)(st.st_size);
- if ((off_t)len != st.st_size ||
- (data = malloc(st.st_size)) == NULL) {
- log_log(log, op, "allocation failure");
- return -2;
- }
- if ((fd = open(log->path, O_RDONLY, 0)) < 0) {
- log_log(log, op, ".add file read failure");
- return -1;
- }
- ret = (size_t)read(fd, data, len) != len;
- close(fd);
- if (ret) {
- log_log(log, op, ".add file read failure");
- return -1;
- }
- log_log(log, op, "loaded .add file");
- }
- else
- log_log(log, op, "missing .add file!");
- }
-
- /* recover the interrupted operation */
- switch (op) {
- case APPEND_OP:
- ret = log_append(log, data, len);
- break;
- case COMPRESS_OP:
- ret = log_compress(log, data, len);
- break;
- case REPLACE_OP:
- ret = log_replace(log);
- }
-
- /* log status */
- log_log(log, op, ret ? "failure" : "complete");
-
- /* clean up */
- if (data != NULL)
- free(data);
- return ret;
-}
-
-/* Close the foo.gz file (if open) and release the lock. */
-local void log_close(struct log *log)
-{
- if (log->fd >= 0)
- close(log->fd);
- log->fd = -1;
- log_unlock(log);
-}
-
-/* Open foo.gz, verify the header, and load the extra field contents, after
- first creating the foo.lock file to gain exclusive access to the foo.*
- files. If foo.gz does not exist or is empty, then write the initial header,
- extra, and body content of an empty foo.gz log file. If there is an error
- creating the lock file due to access restrictions, or an error reading or
- writing the foo.gz file, or if the foo.gz file is not a proper log file for
- this object (e.g. not a gzip file or does not contain the expected extra
- field), then return true. If there is an error, the lock is released.
- Otherwise, the lock is left in place. */
-local int log_open(struct log *log)
-{
- int op;
-
- /* release open file resource if left over -- can occur if lock lost
- between gzlog_open() and gzlog_write() */
- if (log->fd >= 0)
- close(log->fd);
- log->fd = -1;
-
- /* negotiate exclusive access */
- if (log_lock(log) < 0)
- return -1;
-
- /* open the log file, foo.gz */
- strcpy(log->end, ".gz");
- log->fd = open(log->path, O_RDWR | O_CREAT, 0644);
- if (log->fd < 0) {
- log_close(log);
- return -1;
- }
-
- /* if new, initialize foo.gz with an empty log, delete old dictionary */
- if (lseek(log->fd, 0, SEEK_END) == 0) {
- if (write(log->fd, log_gzhead, HEAD) != HEAD ||
- write(log->fd, log_gzext, EXTRA) != EXTRA ||
- write(log->fd, log_gzbody, BODY) != BODY) {
- log_close(log);
- return -1;
- }
- strcpy(log->end, ".dict");
- unlink(log->path);
- }
-
- /* verify log file and load extra field information */
- if ((op = log_head(log)) < 0) {
- log_close(log);
- return -1;
- }
-
- /* check for interrupted process and if so, recover */
- if (op != NO_OP && log_recover(log, op)) {
- log_close(log);
- return -1;
- }
-
- /* touch the lock file to prevent another process from grabbing it */
- log_touch(log);
- return 0;
-}
-
-/* See gzlog.h for the description of the external methods below */
-gzlog *gzlog_open(char *path)
-{
- size_t n;
- struct log *log;
-
- /* check arguments */
- if (path == NULL || *path == 0)
- return NULL;
-
- /* allocate and initialize log structure */
- log = malloc(sizeof(struct log));
- if (log == NULL)
- return NULL;
- strcpy(log->id, LOGID);
- log->fd = -1;
-
- /* save path and end of path for name construction */
- n = strlen(path);
- log->path = malloc(n + 9); /* allow for ".repairs" */
- if (log->path == NULL) {
- free(log);
- return NULL;
- }
- strcpy(log->path, path);
- log->end = log->path + n;
-
- /* gain exclusive access and verify log file -- may perform a
- recovery operation if needed */
- if (log_open(log)) {
- free(log->path);
- free(log);
- return NULL;
- }
-
- /* return pointer to log structure */
- return log;
-}
-
-/* gzlog_compress() return values:
- 0: all good
- -1: file i/o error (usually access issue)
- -2: memory allocation failure
- -3: invalid log pointer argument */
-int gzlog_compress(gzlog *logd)
-{
- int fd, ret;
- uint block;
- size_t len, next;
- unsigned char *data, buf[5];
- struct log *log = logd;
-
- /* check arguments */
- if (log == NULL || strcmp(log->id, LOGID))
- return -3;
-
- /* see if we lost the lock -- if so get it again and reload the extra
- field information (it probably changed), recover last operation if
- necessary */
- if (log_check(log) && log_open(log))
- return -1;
-
- /* create space for uncompressed data */
- len = ((size_t)(log->last - log->first) & ~(((size_t)1 << 10) - 1)) +
- log->stored;
- if ((data = malloc(len)) == NULL)
- return -2;
-
- /* do statement here is just a cheap trick for error handling */
- do {
- /* read in the uncompressed data */
- if (lseek(log->fd, log->first - 1, SEEK_SET) < 0)
- break;
- next = 0;
- while (next < len) {
- if (read(log->fd, buf, 5) != 5)
- break;
- block = PULL2(buf + 1);
- if (next + block > len ||
- read(log->fd, (char *)data + next, block) != block)
- break;
- next += block;
- }
- if (lseek(log->fd, 0, SEEK_CUR) != log->last + 4 + log->stored)
- break;
- log_touch(log);
-
- /* write the uncompressed data to the .add file */
- strcpy(log->end, ".add");
- fd = open(log->path, O_WRONLY | O_CREAT | O_TRUNC, 0644);
- if (fd < 0)
- break;
- ret = (size_t)write(fd, data, len) != len;
- if (ret | close(fd))
- break;
- log_touch(log);
-
- /* write the dictionary for the next compress to the .temp file */
- strcpy(log->end, ".temp");
- fd = open(log->path, O_WRONLY | O_CREAT | O_TRUNC, 0644);
- if (fd < 0)
- break;
- next = DICT > len ? len : DICT;
- ret = (size_t)write(fd, (char *)data + len - next, next) != next;
- if (ret | close(fd))
- break;
- log_touch(log);
-
- /* roll back to compressed data, mark the compress in progress */
- log->last = log->first;
- log->stored = 0;
- if (log_mark(log, COMPRESS_OP))
- break;
- BAIL(7);
-
- /* compress and append the data (clears mark) */
- ret = log_compress(log, data, len);
- free(data);
- return ret;
- } while (0);
-
- /* broke out of do above on i/o error */
- free(data);
- return -1;
-}
-
-/* gzlog_write() return values:
- 0: all good
- -1: file i/o error (usually access issue)
- -2: memory allocation failure
- -3: invalid log pointer argument */
-int gzlog_write(gzlog *logd, void *data, size_t len)
-{
- int fd, ret;
- struct log *log = logd;
-
- /* check arguments */
- if (log == NULL || strcmp(log->id, LOGID))
- return -3;
- if (data == NULL || len <= 0)
- return 0;
-
- /* see if we lost the lock -- if so get it again and reload the extra
- field information (it probably changed), recover last operation if
- necessary */
- if (log_check(log) && log_open(log))
- return -1;
-
- /* create and write .add file */
- strcpy(log->end, ".add");
- fd = open(log->path, O_WRONLY | O_CREAT | O_TRUNC, 0644);
- if (fd < 0)
- return -1;
- ret = (size_t)write(fd, data, len) != len;
- if (ret | close(fd))
- return -1;
- log_touch(log);
-
- /* mark log file with append in progress */
- if (log_mark(log, APPEND_OP))
- return -1;
- BAIL(8);
-
- /* append data (clears mark) */
- if (log_append(log, data, len))
- return -1;
-
- /* check to see if it's time to compress -- if not, then done */
- if (((log->last - log->first) >> 10) + (log->stored >> 10) < TRIGGER)
- return 0;
-
- /* time to compress */
- return gzlog_compress(log);
-}
-
-/* gzlog_close() return values:
- 0: ok
- -3: invalid log pointer argument */
-int gzlog_close(gzlog *logd)
-{
- struct log *log = logd;
-
- /* check arguments */
- if (log == NULL || strcmp(log->id, LOGID))
- return -3;
-
- /* close the log file and release the lock */
- log_close(log);
-
- /* free structure and return */
- if (log->path != NULL)
- free(log->path);
- strcpy(log->id, "bad");
- free(log);
- return 0;
-}
diff --git a/third-party/zlib/examples/gzlog.h b/third-party/zlib/examples/gzlog.h
deleted file mode 100644
index 86f0cec..0000000
--- a/third-party/zlib/examples/gzlog.h
+++ /dev/null
@@ -1,91 +0,0 @@
-/* gzlog.h
- Copyright (C) 2004, 2008, 2012 Mark Adler, all rights reserved
- version 2.2, 14 Aug 2012
-
- This software is provided 'as-is', without any express or implied
- warranty. In no event will the author be held liable for any damages
- arising from the use of this software.
-
- Permission is granted to anyone to use this software for any purpose,
- including commercial applications, and to alter it and redistribute it
- freely, subject to the following restrictions:
-
- 1. The origin of this software must not be misrepresented; you must not
- claim that you wrote the original software. If you use this software
- in a product, an acknowledgment in the product documentation would be
- appreciated but is not required.
- 2. Altered source versions must be plainly marked as such, and must not be
- misrepresented as being the original software.
- 3. This notice may not be removed or altered from any source distribution.
-
- Mark Adler madler at alumni.caltech.edu
- */
-
-/* Version History:
- 1.0 26 Nov 2004 First version
- 2.0 25 Apr 2008 Complete redesign for recovery of interrupted operations
- Interface changed slightly in that now path is a prefix
- Compression now occurs as needed during gzlog_write()
- gzlog_write() now always leaves the log file as valid gzip
- 2.1 8 Jul 2012 Fix argument checks in gzlog_compress() and gzlog_write()
- 2.2 14 Aug 2012 Clean up signed comparisons
- */
-
-/*
- The gzlog object allows writing short messages to a gzipped log file,
- opening the log file locked for small bursts, and then closing it. The log
- object works by appending stored (uncompressed) data to the gzip file until
- 1 MB has been accumulated. At that time, the stored data is compressed, and
- replaces the uncompressed data in the file. The log file is truncated to
- its new size at that time. After each write operation, the log file is a
- valid gzip file that can decompressed to recover what was written.
-
- The gzlog operations can be interupted at any point due to an application or
- system crash, and the log file will be recovered the next time the log is
- opened with gzlog_open().
- */
-
-#ifndef GZLOG_H
-#define GZLOG_H
-
-/* gzlog object type */
-typedef void gzlog;
-
-/* Open a gzlog object, creating the log file if it does not exist. Return
- NULL on error. Note that gzlog_open() could take a while to complete if it
- has to wait to verify that a lock is stale (possibly for five minutes), or
- if there is significant contention with other instantiations of this object
- when locking the resource. path is the prefix of the file names created by
- this object. If path is "foo", then the log file will be "foo.gz", and
- other auxiliary files will be created and destroyed during the process:
- "foo.dict" for a compression dictionary, "foo.temp" for a temporary (next)
- dictionary, "foo.add" for data being added or compressed, "foo.lock" for the
- lock file, and "foo.repairs" to log recovery operations performed due to
- interrupted gzlog operations. A gzlog_open() followed by a gzlog_close()
- will recover a previously interrupted operation, if any. */
-gzlog *gzlog_open(char *path);
-
-/* Write to a gzlog object. Return zero on success, -1 if there is a file i/o
- error on any of the gzlog files (this should not happen if gzlog_open()
- succeeded, unless the device has run out of space or leftover auxiliary
- files have permissions or ownership that prevent their use), -2 if there is
- a memory allocation failure, or -3 if the log argument is invalid (e.g. if
- it was not created by gzlog_open()). This function will write data to the
- file uncompressed, until 1 MB has been accumulated, at which time that data
- will be compressed. The log file will be a valid gzip file upon successful
- return. */
-int gzlog_write(gzlog *log, void *data, size_t len);
-
-/* Force compression of any uncompressed data in the log. This should be used
- sparingly, if at all. The main application would be when a log file will
- not be appended to again. If this is used to compress frequently while
- appending, it will both significantly increase the execution time and
- reduce the compression ratio. The return codes are the same as for
- gzlog_write(). */
-int gzlog_compress(gzlog *log);
-
-/* Close a gzlog object. Return zero on success, -3 if the log argument is
- invalid. The log object is freed, and so cannot be referenced again. */
-int gzlog_close(gzlog *log);
-
-#endif
diff --git a/third-party/zlib/examples/zlib_how.html b/third-party/zlib/examples/zlib_how.html
deleted file mode 100644
index 444ff1c..0000000
--- a/third-party/zlib/examples/zlib_how.html
+++ /dev/null
@@ -1,545 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN"
- "http://www.w3.org/TR/REC-html40/loose.dtd">
-<html>
-<head>
-<meta http-equiv="Content-Type" content="text/html; charset=ISO-8859-1">
-<title>zlib Usage Example</title>
-<!-- Copyright (c) 2004, 2005 Mark Adler. -->
-</head>
-<body bgcolor="#FFFFFF" text="#000000" link="#0000FF" vlink="#00A000">
-<h2 align="center"> zlib Usage Example </h2>
-We often get questions about how the <tt>deflate()</tt> and <tt>inflate()</tt> functions should be used.
-Users wonder when they should provide more input, when they should use more output,
-what to do with a <tt>Z_BUF_ERROR</tt>, how to make sure the process terminates properly, and
-so on. So for those who have read <tt>zlib.h</tt> (a few times), and
-would like further edification, below is an annotated example in C of simple routines to compress and decompress
-from an input file to an output file using <tt>deflate()</tt> and <tt>inflate()</tt> respectively. The
-annotations are interspersed between lines of the code. So please read between the lines.
-We hope this helps explain some of the intricacies of <em>zlib</em>.
-<p>
-Without further adieu, here is the program <a href="zpipe.c"><tt>zpipe.c</tt></a>:
-<pre><b>
-/* zpipe.c: example of proper use of zlib's inflate() and deflate()
- Not copyrighted -- provided to the public domain
- Version 1.4 11 December 2005 Mark Adler */
-
-/* Version history:
- 1.0 30 Oct 2004 First version
- 1.1 8 Nov 2004 Add void casting for unused return values
- Use switch statement for inflate() return values
- 1.2 9 Nov 2004 Add assertions to document zlib guarantees
- 1.3 6 Apr 2005 Remove incorrect assertion in inf()
- 1.4 11 Dec 2005 Add hack to avoid MSDOS end-of-line conversions
- Avoid some compiler warnings for input and output buffers
- */
-</b></pre><!-- -->
-We now include the header files for the required definitions. From
-<tt>stdio.h</tt> we use <tt>fopen()</tt>, <tt>fread()</tt>, <tt>fwrite()</tt>,
-<tt>feof()</tt>, <tt>ferror()</tt>, and <tt>fclose()</tt> for file i/o, and
-<tt>fputs()</tt> for error messages. From <tt>string.h</tt> we use
-<tt>strcmp()</tt> for command line argument processing.
-From <tt>assert.h</tt> we use the <tt>assert()</tt> macro.
-From <tt>zlib.h</tt>
-we use the basic compression functions <tt>deflateInit()</tt>,
-<tt>deflate()</tt>, and <tt>deflateEnd()</tt>, and the basic decompression
-functions <tt>inflateInit()</tt>, <tt>inflate()</tt>, and
-<tt>inflateEnd()</tt>.
-<pre><b>
-#include <stdio.h>
-#include <string.h>
-#include <assert.h>
-#include "zlib.h"
-</b></pre><!-- -->
-This is an ugly hack required to avoid corruption of the input and output data on
-Windows/MS-DOS systems. Without this, those systems would assume that the input and output
-files are text, and try to convert the end-of-line characters from one standard to
-another. That would corrupt binary data, and in particular would render the compressed data unusable.
-This sets the input and output to binary which suppresses the end-of-line conversions.
-<tt>SET_BINARY_MODE()</tt> will be used later on <tt>stdin</tt> and <tt>stdout</tt>, at the beginning of <tt>main()</tt>.
-<pre><b>
-#if defined(MSDOS) || defined(OS2) || defined(WIN32) || defined(__CYGWIN__)
-# include <fcntl.h>
-# include <io.h>
-# define SET_BINARY_MODE(file) setmode(fileno(file), O_BINARY)
-#else
-# define SET_BINARY_MODE(file)
-#endif
-</b></pre><!-- -->
-<tt>CHUNK</tt> is simply the buffer size for feeding data to and pulling data
-from the <em>zlib</em> routines. Larger buffer sizes would be more efficient,
-especially for <tt>inflate()</tt>. If the memory is available, buffers sizes
-on the order of 128K or 256K bytes should be used.
-<pre><b>
-#define CHUNK 16384
-</b></pre><!-- -->
-The <tt>def()</tt> routine compresses data from an input file to an output file. The output data
-will be in the <em>zlib</em> format, which is different from the <em>gzip</em> or <em>zip</em>
-formats. The <em>zlib</em> format has a very small header of only two bytes to identify it as
-a <em>zlib</em> stream and to provide decoding information, and a four-byte trailer with a fast
-check value to verify the integrity of the uncompressed data after decoding.
-<pre><b>
-/* Compress from file source to file dest until EOF on source.
- def() returns Z_OK on success, Z_MEM_ERROR if memory could not be
- allocated for processing, Z_STREAM_ERROR if an invalid compression
- level is supplied, Z_VERSION_ERROR if the version of zlib.h and the
- version of the library linked do not match, or Z_ERRNO if there is
- an error reading or writing the files. */
-int def(FILE *source, FILE *dest, int level)
-{
-</b></pre>
-Here are the local variables for <tt>def()</tt>. <tt>ret</tt> will be used for <em>zlib</em>
-return codes. <tt>flush</tt> will keep track of the current flushing state for <tt>deflate()</tt>,
-which is either no flushing, or flush to completion after the end of the input file is reached.
-<tt>have</tt> is the amount of data returned from <tt>deflate()</tt>. The <tt>strm</tt> structure
-is used to pass information to and from the <em>zlib</em> routines, and to maintain the
-<tt>deflate()</tt> state. <tt>in</tt> and <tt>out</tt> are the input and output buffers for
-<tt>deflate()</tt>.
-<pre><b>
- int ret, flush;
- unsigned have;
- z_stream strm;
- unsigned char in[CHUNK];
- unsigned char out[CHUNK];
-</b></pre><!-- -->
-The first thing we do is to initialize the <em>zlib</em> state for compression using
-<tt>deflateInit()</tt>. This must be done before the first use of <tt>deflate()</tt>.
-The <tt>zalloc</tt>, <tt>zfree</tt>, and <tt>opaque</tt> fields in the <tt>strm</tt>
-structure must be initialized before calling <tt>deflateInit()</tt>. Here they are
-set to the <em>zlib</em> constant <tt>Z_NULL</tt> to request that <em>zlib</em> use
-the default memory allocation routines. An application may also choose to provide
-custom memory allocation routines here. <tt>deflateInit()</tt> will allocate on the
-order of 256K bytes for the internal state.
-(See <a href="zlib_tech.html"><em>zlib Technical Details</em></a>.)
-<p>
-<tt>deflateInit()</tt> is called with a pointer to the structure to be initialized and
-the compression level, which is an integer in the range of -1 to 9. Lower compression
-levels result in faster execution, but less compression. Higher levels result in
-greater compression, but slower execution. The <em>zlib</em> constant Z_DEFAULT_COMPRESSION,
-equal to -1,
-provides a good compromise between compression and speed and is equivalent to level 6.
-Level 0 actually does no compression at all, and in fact expands the data slightly to produce
-the <em>zlib</em> format (it is not a byte-for-byte copy of the input).
-More advanced applications of <em>zlib</em>
-may use <tt>deflateInit2()</tt> here instead. Such an application may want to reduce how
-much memory will be used, at some price in compression. Or it may need to request a
-<em>gzip</em> header and trailer instead of a <em>zlib</em> header and trailer, or raw
-encoding with no header or trailer at all.
-<p>
-We must check the return value of <tt>deflateInit()</tt> against the <em>zlib</em> constant
-<tt>Z_OK</tt> to make sure that it was able to
-allocate memory for the internal state, and that the provided arguments were valid.
-<tt>deflateInit()</tt> will also check that the version of <em>zlib</em> that the <tt>zlib.h</tt>
-file came from matches the version of <em>zlib</em> actually linked with the program. This
-is especially important for environments in which <em>zlib</em> is a shared library.
-<p>
-Note that an application can initialize multiple, independent <em>zlib</em> streams, which can
-operate in parallel. The state information maintained in the structure allows the <em>zlib</em>
-routines to be reentrant.
-<pre><b>
- /* allocate deflate state */
- strm.zalloc = Z_NULL;
- strm.zfree = Z_NULL;
- strm.opaque = Z_NULL;
- ret = deflateInit(&strm, level);
- if (ret != Z_OK)
- return ret;
-</b></pre><!-- -->
-With the pleasantries out of the way, now we can get down to business. The outer <tt>do</tt>-loop
-reads all of the input file and exits at the bottom of the loop once end-of-file is reached.
-This loop contains the only call of <tt>deflate()</tt>. So we must make sure that all of the
-input data has been processed and that all of the output data has been generated and consumed
-before we fall out of the loop at the bottom.
-<pre><b>
- /* compress until end of file */
- do {
-</b></pre>
-We start off by reading data from the input file. The number of bytes read is put directly
-into <tt>avail_in</tt>, and a pointer to those bytes is put into <tt>next_in</tt>. We also
-check to see if end-of-file on the input has been reached. If we are at the end of file, then <tt>flush</tt> is set to the
-<em>zlib</em> constant <tt>Z_FINISH</tt>, which is later passed to <tt>deflate()</tt> to
-indicate that this is the last chunk of input data to compress. We need to use <tt>feof()</tt>
-to check for end-of-file as opposed to seeing if fewer than <tt>CHUNK</tt> bytes have been read. The
-reason is that if the input file length is an exact multiple of <tt>CHUNK</tt>, we will miss
-the fact that we got to the end-of-file, and not know to tell <tt>deflate()</tt> to finish
-up the compressed stream. If we are not yet at the end of the input, then the <em>zlib</em>
-constant <tt>Z_NO_FLUSH</tt> will be passed to <tt>deflate</tt> to indicate that we are still
-in the middle of the uncompressed data.
-<p>
-If there is an error in reading from the input file, the process is aborted with
-<tt>deflateEnd()</tt> being called to free the allocated <em>zlib</em> state before returning
-the error. We wouldn't want a memory leak, now would we? <tt>deflateEnd()</tt> can be called
-at any time after the state has been initialized. Once that's done, <tt>deflateInit()</tt> (or
-<tt>deflateInit2()</tt>) would have to be called to start a new compression process. There is
-no point here in checking the <tt>deflateEnd()</tt> return code. The deallocation can't fail.
-<pre><b>
- strm.avail_in = fread(in, 1, CHUNK, source);
- if (ferror(source)) {
- (void)deflateEnd(&strm);
- return Z_ERRNO;
- }
- flush = feof(source) ? Z_FINISH : Z_NO_FLUSH;
- strm.next_in = in;
-</b></pre><!-- -->
-The inner <tt>do</tt>-loop passes our chunk of input data to <tt>deflate()</tt>, and then
-keeps calling <tt>deflate()</tt> until it is done producing output. Once there is no more
-new output, <tt>deflate()</tt> is guaranteed to have consumed all of the input, i.e.,
-<tt>avail_in</tt> will be zero.
-<pre><b>
- /* run deflate() on input until output buffer not full, finish
- compression if all of source has been read in */
- do {
-</b></pre>
-Output space is provided to <tt>deflate()</tt> by setting <tt>avail_out</tt> to the number
-of available output bytes and <tt>next_out</tt> to a pointer to that space.
-<pre><b>
- strm.avail_out = CHUNK;
- strm.next_out = out;
-</b></pre>
-Now we call the compression engine itself, <tt>deflate()</tt>. It takes as many of the
-<tt>avail_in</tt> bytes at <tt>next_in</tt> as it can process, and writes as many as
-<tt>avail_out</tt> bytes to <tt>next_out</tt>. Those counters and pointers are then
-updated past the input data consumed and the output data written. It is the amount of
-output space available that may limit how much input is consumed.
-Hence the inner loop to make sure that
-all of the input is consumed by providing more output space each time. Since <tt>avail_in</tt>
-and <tt>next_in</tt> are updated by <tt>deflate()</tt>, we don't have to mess with those
-between <tt>deflate()</tt> calls until it's all used up.
-<p>
-The parameters to <tt>deflate()</tt> are a pointer to the <tt>strm</tt> structure containing
-the input and output information and the internal compression engine state, and a parameter
-indicating whether and how to flush data to the output. Normally <tt>deflate</tt> will consume
-several K bytes of input data before producing any output (except for the header), in order
-to accumulate statistics on the data for optimum compression. It will then put out a burst of
-compressed data, and proceed to consume more input before the next burst. Eventually,
-<tt>deflate()</tt>
-must be told to terminate the stream, complete the compression with provided input data, and
-write out the trailer check value. <tt>deflate()</tt> will continue to compress normally as long
-as the flush parameter is <tt>Z_NO_FLUSH</tt>. Once the <tt>Z_FINISH</tt> parameter is provided,
-<tt>deflate()</tt> will begin to complete the compressed output stream. However depending on how
-much output space is provided, <tt>deflate()</tt> may have to be called several times until it
-has provided the complete compressed stream, even after it has consumed all of the input. The flush
-parameter must continue to be <tt>Z_FINISH</tt> for those subsequent calls.
-<p>
-There are other values of the flush parameter that are used in more advanced applications. You can
-force <tt>deflate()</tt> to produce a burst of output that encodes all of the input data provided
-so far, even if it wouldn't have otherwise, for example to control data latency on a link with
-compressed data. You can also ask that <tt>deflate()</tt> do that as well as erase any history up to
-that point so that what follows can be decompressed independently, for example for random access
-applications. Both requests will degrade compression by an amount depending on how often such
-requests are made.
-<p>
-<tt>deflate()</tt> has a return value that can indicate errors, yet we do not check it here. Why
-not? Well, it turns out that <tt>deflate()</tt> can do no wrong here. Let's go through
-<tt>deflate()</tt>'s return values and dispense with them one by one. The possible values are
-<tt>Z_OK</tt>, <tt>Z_STREAM_END</tt>, <tt>Z_STREAM_ERROR</tt>, or <tt>Z_BUF_ERROR</tt>. <tt>Z_OK</tt>
-is, well, ok. <tt>Z_STREAM_END</tt> is also ok and will be returned for the last call of
-<tt>deflate()</tt>. This is already guaranteed by calling <tt>deflate()</tt> with <tt>Z_FINISH</tt>
-until it has no more output. <tt>Z_STREAM_ERROR</tt> is only possible if the stream is not
-initialized properly, but we did initialize it properly. There is no harm in checking for
-<tt>Z_STREAM_ERROR</tt> here, for example to check for the possibility that some
-other part of the application inadvertently clobbered the memory containing the <em>zlib</em> state.
-<tt>Z_BUF_ERROR</tt> will be explained further below, but
-suffice it to say that this is simply an indication that <tt>deflate()</tt> could not consume
-more input or produce more output. <tt>deflate()</tt> can be called again with more output space
-or more available input, which it will be in this code.
-<pre><b>
- ret = deflate(&strm, flush); /* no bad return value */
- assert(ret != Z_STREAM_ERROR); /* state not clobbered */
-</b></pre>
-Now we compute how much output <tt>deflate()</tt> provided on the last call, which is the
-difference between how much space was provided before the call, and how much output space
-is still available after the call. Then that data, if any, is written to the output file.
-We can then reuse the output buffer for the next call of <tt>deflate()</tt>. Again if there
-is a file i/o error, we call <tt>deflateEnd()</tt> before returning to avoid a memory leak.
-<pre><b>
- have = CHUNK - strm.avail_out;
- if (fwrite(out, 1, have, dest) != have || ferror(dest)) {
- (void)deflateEnd(&strm);
- return Z_ERRNO;
- }
-</b></pre>
-The inner <tt>do</tt>-loop is repeated until the last <tt>deflate()</tt> call fails to fill the
-provided output buffer. Then we know that <tt>deflate()</tt> has done as much as it can with
-the provided input, and that all of that input has been consumed. We can then fall out of this
-loop and reuse the input buffer.
-<p>
-The way we tell that <tt>deflate()</tt> has no more output is by seeing that it did not fill
-the output buffer, leaving <tt>avail_out</tt> greater than zero. However suppose that
-<tt>deflate()</tt> has no more output, but just so happened to exactly fill the output buffer!
-<tt>avail_out</tt> is zero, and we can't tell that <tt>deflate()</tt> has done all it can.
-As far as we know, <tt>deflate()</tt>
-has more output for us. So we call it again. But now <tt>deflate()</tt> produces no output
-at all, and <tt>avail_out</tt> remains unchanged as <tt>CHUNK</tt>. That <tt>deflate()</tt> call
-wasn't able to do anything, either consume input or produce output, and so it returns
-<tt>Z_BUF_ERROR</tt>. (See, I told you I'd cover this later.) However this is not a problem at
-all. Now we finally have the desired indication that <tt>deflate()</tt> is really done,
-and so we drop out of the inner loop to provide more input to <tt>deflate()</tt>.
-<p>
-With <tt>flush</tt> set to <tt>Z_FINISH</tt>, this final set of <tt>deflate()</tt> calls will
-complete the output stream. Once that is done, subsequent calls of <tt>deflate()</tt> would return
-<tt>Z_STREAM_ERROR</tt> if the flush parameter is not <tt>Z_FINISH</tt>, and do no more processing
-until the state is reinitialized.
-<p>
-Some applications of <em>zlib</em> have two loops that call <tt>deflate()</tt>
-instead of the single inner loop we have here. The first loop would call
-without flushing and feed all of the data to <tt>deflate()</tt>. The second loop would call
-<tt>deflate()</tt> with no more
-data and the <tt>Z_FINISH</tt> parameter to complete the process. As you can see from this
-example, that can be avoided by simply keeping track of the current flush state.
-<pre><b>
- } while (strm.avail_out == 0);
- assert(strm.avail_in == 0); /* all input will be used */
-</b></pre><!-- -->
-Now we check to see if we have already processed all of the input file. That information was
-saved in the <tt>flush</tt> variable, so we see if that was set to <tt>Z_FINISH</tt>. If so,
-then we're done and we fall out of the outer loop. We're guaranteed to get <tt>Z_STREAM_END</tt>
-from the last <tt>deflate()</tt> call, since we ran it until the last chunk of input was
-consumed and all of the output was generated.
-<pre><b>
- /* done when last data in file processed */
- } while (flush != Z_FINISH);
- assert(ret == Z_STREAM_END); /* stream will be complete */
-</b></pre><!-- -->
-The process is complete, but we still need to deallocate the state to avoid a memory leak
-(or rather more like a memory hemorrhage if you didn't do this). Then
-finally we can return with a happy return value.
-<pre><b>
- /* clean up and return */
- (void)deflateEnd(&strm);
- return Z_OK;
-}
-</b></pre><!-- -->
-Now we do the same thing for decompression in the <tt>inf()</tt> routine. <tt>inf()</tt>
-decompresses what is hopefully a valid <em>zlib</em> stream from the input file and writes the
-uncompressed data to the output file. Much of the discussion above for <tt>def()</tt>
-applies to <tt>inf()</tt> as well, so the discussion here will focus on the differences between
-the two.
-<pre><b>
-/* Decompress from file source to file dest until stream ends or EOF.
- inf() returns Z_OK on success, Z_MEM_ERROR if memory could not be
- allocated for processing, Z_DATA_ERROR if the deflate data is
- invalid or incomplete, Z_VERSION_ERROR if the version of zlib.h and
- the version of the library linked do not match, or Z_ERRNO if there
- is an error reading or writing the files. */
-int inf(FILE *source, FILE *dest)
-{
-</b></pre>
-The local variables have the same functionality as they do for <tt>def()</tt>. The
-only difference is that there is no <tt>flush</tt> variable, since <tt>inflate()</tt>
-can tell from the <em>zlib</em> stream itself when the stream is complete.
-<pre><b>
- int ret;
- unsigned have;
- z_stream strm;
- unsigned char in[CHUNK];
- unsigned char out[CHUNK];
-</b></pre><!-- -->
-The initialization of the state is the same, except that there is no compression level,
-of course, and two more elements of the structure are initialized. <tt>avail_in</tt>
-and <tt>next_in</tt> must be initialized before calling <tt>inflateInit()</tt>. This
-is because the application has the option to provide the start of the zlib stream in
-order for <tt>inflateInit()</tt> to have access to information about the compression
-method to aid in memory allocation. In the current implementation of <em>zlib</em>
-(up through versions 1.2.x), the method-dependent memory allocations are deferred to the first call of
-<tt>inflate()</tt> anyway. However those fields must be initialized since later versions
-of <em>zlib</em> that provide more compression methods may take advantage of this interface.
-In any case, no decompression is performed by <tt>inflateInit()</tt>, so the
-<tt>avail_out</tt> and <tt>next_out</tt> fields do not need to be initialized before calling.
-<p>
-Here <tt>avail_in</tt> is set to zero and <tt>next_in</tt> is set to <tt>Z_NULL</tt> to
-indicate that no input data is being provided.
-<pre><b>
- /* allocate inflate state */
- strm.zalloc = Z_NULL;
- strm.zfree = Z_NULL;
- strm.opaque = Z_NULL;
- strm.avail_in = 0;
- strm.next_in = Z_NULL;
- ret = inflateInit(&strm);
- if (ret != Z_OK)
- return ret;
-</b></pre><!-- -->
-The outer <tt>do</tt>-loop decompresses input until <tt>inflate()</tt> indicates
-that it has reached the end of the compressed data and has produced all of the uncompressed
-output. This is in contrast to <tt>def()</tt> which processes all of the input file.
-If end-of-file is reached before the compressed data self-terminates, then the compressed
-data is incomplete and an error is returned.
-<pre><b>
- /* decompress until deflate stream ends or end of file */
- do {
-</b></pre>
-We read input data and set the <tt>strm</tt> structure accordingly. If we've reached the
-end of the input file, then we leave the outer loop and report an error, since the
-compressed data is incomplete. Note that we may read more data than is eventually consumed
-by <tt>inflate()</tt>, if the input file continues past the <em>zlib</em> stream.
-For applications where <em>zlib</em> streams are embedded in other data, this routine would
-need to be modified to return the unused data, or at least indicate how much of the input
-data was not used, so the application would know where to pick up after the <em>zlib</em> stream.
-<pre><b>
- strm.avail_in = fread(in, 1, CHUNK, source);
- if (ferror(source)) {
- (void)inflateEnd(&strm);
- return Z_ERRNO;
- }
- if (strm.avail_in == 0)
- break;
- strm.next_in = in;
-</b></pre><!-- -->
-The inner <tt>do</tt>-loop has the same function it did in <tt>def()</tt>, which is to
-keep calling <tt>inflate()</tt> until has generated all of the output it can with the
-provided input.
-<pre><b>
- /* run inflate() on input until output buffer not full */
- do {
-</b></pre>
-Just like in <tt>def()</tt>, the same output space is provided for each call of <tt>inflate()</tt>.
-<pre><b>
- strm.avail_out = CHUNK;
- strm.next_out = out;
-</b></pre>
-Now we run the decompression engine itself. There is no need to adjust the flush parameter, since
-the <em>zlib</em> format is self-terminating. The main difference here is that there are
-return values that we need to pay attention to. <tt>Z_DATA_ERROR</tt>
-indicates that <tt>inflate()</tt> detected an error in the <em>zlib</em> compressed data format,
-which means that either the data is not a <em>zlib</em> stream to begin with, or that the data was
-corrupted somewhere along the way since it was compressed. The other error to be processed is
-<tt>Z_MEM_ERROR</tt>, which can occur since memory allocation is deferred until <tt>inflate()</tt>
-needs it, unlike <tt>deflate()</tt>, whose memory is allocated at the start by <tt>deflateInit()</tt>.
-<p>
-Advanced applications may use
-<tt>deflateSetDictionary()</tt> to prime <tt>deflate()</tt> with a set of likely data to improve the
-first 32K or so of compression. This is noted in the <em>zlib</em> header, so <tt>inflate()</tt>
-requests that that dictionary be provided before it can start to decompress. Without the dictionary,
-correct decompression is not possible. For this routine, we have no idea what the dictionary is,
-so the <tt>Z_NEED_DICT</tt> indication is converted to a <tt>Z_DATA_ERROR</tt>.
-<p>
-<tt>inflate()</tt> can also return <tt>Z_STREAM_ERROR</tt>, which should not be possible here,
-but could be checked for as noted above for <tt>def()</tt>. <tt>Z_BUF_ERROR</tt> does not need to be
-checked for here, for the same reasons noted for <tt>def()</tt>. <tt>Z_STREAM_END</tt> will be
-checked for later.
-<pre><b>
- ret = inflate(&strm, Z_NO_FLUSH);
- assert(ret != Z_STREAM_ERROR); /* state not clobbered */
- switch (ret) {
- case Z_NEED_DICT:
- ret = Z_DATA_ERROR; /* and fall through */
- case Z_DATA_ERROR:
- case Z_MEM_ERROR:
- (void)inflateEnd(&strm);
- return ret;
- }
-</b></pre>
-The output of <tt>inflate()</tt> is handled identically to that of <tt>deflate()</tt>.
-<pre><b>
- have = CHUNK - strm.avail_out;
- if (fwrite(out, 1, have, dest) != have || ferror(dest)) {
- (void)inflateEnd(&strm);
- return Z_ERRNO;
- }
-</b></pre>
-The inner <tt>do</tt>-loop ends when <tt>inflate()</tt> has no more output as indicated
-by not filling the output buffer, just as for <tt>deflate()</tt>. In this case, we cannot
-assert that <tt>strm.avail_in</tt> will be zero, since the deflate stream may end before the file
-does.
-<pre><b>
- } while (strm.avail_out == 0);
-</b></pre><!-- -->
-The outer <tt>do</tt>-loop ends when <tt>inflate()</tt> reports that it has reached the
-end of the input <em>zlib</em> stream, has completed the decompression and integrity
-check, and has provided all of the output. This is indicated by the <tt>inflate()</tt>
-return value <tt>Z_STREAM_END</tt>. The inner loop is guaranteed to leave <tt>ret</tt>
-equal to <tt>Z_STREAM_END</tt> if the last chunk of the input file read contained the end
-of the <em>zlib</em> stream. So if the return value is not <tt>Z_STREAM_END</tt>, the
-loop continues to read more input.
-<pre><b>
- /* done when inflate() says it's done */
- } while (ret != Z_STREAM_END);
-</b></pre><!-- -->
-At this point, decompression successfully completed, or we broke out of the loop due to no
-more data being available from the input file. If the last <tt>inflate()</tt> return value
-is not <tt>Z_STREAM_END</tt>, then the <em>zlib</em> stream was incomplete and a data error
-is returned. Otherwise, we return with a happy return value. Of course, <tt>inflateEnd()</tt>
-is called first to avoid a memory leak.
-<pre><b>
- /* clean up and return */
- (void)inflateEnd(&strm);
- return ret == Z_STREAM_END ? Z_OK : Z_DATA_ERROR;
-}
-</b></pre><!-- -->
-That ends the routines that directly use <em>zlib</em>. The following routines make this
-a command-line program by running data through the above routines from <tt>stdin</tt> to
-<tt>stdout</tt>, and handling any errors reported by <tt>def()</tt> or <tt>inf()</tt>.
-<p>
-<tt>zerr()</tt> is used to interpret the possible error codes from <tt>def()</tt>
-and <tt>inf()</tt>, as detailed in their comments above, and print out an error message.
-Note that these are only a subset of the possible return values from <tt>deflate()</tt>
-and <tt>inflate()</tt>.
-<pre><b>
-/* report a zlib or i/o error */
-void zerr(int ret)
-{
- fputs("zpipe: ", stderr);
- switch (ret) {
- case Z_ERRNO:
- if (ferror(stdin))
- fputs("error reading stdin\n", stderr);
- if (ferror(stdout))
- fputs("error writing stdout\n", stderr);
- break;
- case Z_STREAM_ERROR:
- fputs("invalid compression level\n", stderr);
- break;
- case Z_DATA_ERROR:
- fputs("invalid or incomplete deflate data\n", stderr);
- break;
- case Z_MEM_ERROR:
- fputs("out of memory\n", stderr);
- break;
- case Z_VERSION_ERROR:
- fputs("zlib version mismatch!\n", stderr);
- }
-}
-</b></pre><!-- -->
-Here is the <tt>main()</tt> routine used to test <tt>def()</tt> and <tt>inf()</tt>. The
-<tt>zpipe</tt> command is simply a compression pipe from <tt>stdin</tt> to <tt>stdout</tt>, if
-no arguments are given, or it is a decompression pipe if <tt>zpipe -d</tt> is used. If any other
-arguments are provided, no compression or decompression is performed. Instead a usage
-message is displayed. Examples are <tt>zpipe < foo.txt > foo.txt.z</tt> to compress, and
-<tt>zpipe -d < foo.txt.z > foo.txt</tt> to decompress.
-<pre><b>
-/* compress or decompress from stdin to stdout */
-int main(int argc, char **argv)
-{
- int ret;
-
- /* avoid end-of-line conversions */
- SET_BINARY_MODE(stdin);
- SET_BINARY_MODE(stdout);
-
- /* do compression if no arguments */
- if (argc == 1) {
- ret = def(stdin, stdout, Z_DEFAULT_COMPRESSION);
- if (ret != Z_OK)
- zerr(ret);
- return ret;
- }
-
- /* do decompression if -d specified */
- else if (argc == 2 && strcmp(argv[1], "-d") == 0) {
- ret = inf(stdin, stdout);
- if (ret != Z_OK)
- zerr(ret);
- return ret;
- }
-
- /* otherwise, report usage */
- else {
- fputs("zpipe usage: zpipe [-d] < source > dest\n", stderr);
- return 1;
- }
-}
-</b></pre>
-<hr>
-<i>Copyright (c) 2004, 2005 by Mark Adler<br>Last modified 11 December 2005</i>
-</body>
-</html>
diff --git a/third-party/zlib/examples/zpipe.c b/third-party/zlib/examples/zpipe.c
deleted file mode 100644
index 83535d1..0000000
--- a/third-party/zlib/examples/zpipe.c
+++ /dev/null
@@ -1,205 +0,0 @@
-/* zpipe.c: example of proper use of zlib's inflate() and deflate()
- Not copyrighted -- provided to the public domain
- Version 1.4 11 December 2005 Mark Adler */
-
-/* Version history:
- 1.0 30 Oct 2004 First version
- 1.1 8 Nov 2004 Add void casting for unused return values
- Use switch statement for inflate() return values
- 1.2 9 Nov 2004 Add assertions to document zlib guarantees
- 1.3 6 Apr 2005 Remove incorrect assertion in inf()
- 1.4 11 Dec 2005 Add hack to avoid MSDOS end-of-line conversions
- Avoid some compiler warnings for input and output buffers
- */
-
-#include <stdio.h>
-#include <string.h>
-#include <assert.h>
-#include "zlib.h"
-
-#if defined(MSDOS) || defined(OS2) || defined(WIN32) || defined(__CYGWIN__)
-# include <fcntl.h>
-# include <io.h>
-# define SET_BINARY_MODE(file) setmode(fileno(file), O_BINARY)
-#else
-# define SET_BINARY_MODE(file)
-#endif
-
-#define CHUNK 16384
-
-/* Compress from file source to file dest until EOF on source.
- def() returns Z_OK on success, Z_MEM_ERROR if memory could not be
- allocated for processing, Z_STREAM_ERROR if an invalid compression
- level is supplied, Z_VERSION_ERROR if the version of zlib.h and the
- version of the library linked do not match, or Z_ERRNO if there is
- an error reading or writing the files. */
-int def(FILE *source, FILE *dest, int level)
-{
- int ret, flush;
- unsigned have;
- z_stream strm;
- unsigned char in[CHUNK];
- unsigned char out[CHUNK];
-
- /* allocate deflate state */
- strm.zalloc = Z_NULL;
- strm.zfree = Z_NULL;
- strm.opaque = Z_NULL;
- ret = deflateInit(&strm, level);
- if (ret != Z_OK)
- return ret;
-
- /* compress until end of file */
- do {
- strm.avail_in = fread(in, 1, CHUNK, source);
- if (ferror(source)) {
- (void)deflateEnd(&strm);
- return Z_ERRNO;
- }
- flush = feof(source) ? Z_FINISH : Z_NO_FLUSH;
- strm.next_in = in;
-
- /* run deflate() on input until output buffer not full, finish
- compression if all of source has been read in */
- do {
- strm.avail_out = CHUNK;
- strm.next_out = out;
- ret = deflate(&strm, flush); /* no bad return value */
- assert(ret != Z_STREAM_ERROR); /* state not clobbered */
- have = CHUNK - strm.avail_out;
- if (fwrite(out, 1, have, dest) != have || ferror(dest)) {
- (void)deflateEnd(&strm);
- return Z_ERRNO;
- }
- } while (strm.avail_out == 0);
- assert(strm.avail_in == 0); /* all input will be used */
-
- /* done when last data in file processed */
- } while (flush != Z_FINISH);
- assert(ret == Z_STREAM_END); /* stream will be complete */
-
- /* clean up and return */
- (void)deflateEnd(&strm);
- return Z_OK;
-}
-
-/* Decompress from file source to file dest until stream ends or EOF.
- inf() returns Z_OK on success, Z_MEM_ERROR if memory could not be
- allocated for processing, Z_DATA_ERROR if the deflate data is
- invalid or incomplete, Z_VERSION_ERROR if the version of zlib.h and
- the version of the library linked do not match, or Z_ERRNO if there
- is an error reading or writing the files. */
-int inf(FILE *source, FILE *dest)
-{
- int ret;
- unsigned have;
- z_stream strm;
- unsigned char in[CHUNK];
- unsigned char out[CHUNK];
-
- /* allocate inflate state */
- strm.zalloc = Z_NULL;
- strm.zfree = Z_NULL;
- strm.opaque = Z_NULL;
- strm.avail_in = 0;
- strm.next_in = Z_NULL;
- ret = inflateInit(&strm);
- if (ret != Z_OK)
- return ret;
-
- /* decompress until deflate stream ends or end of file */
- do {
- strm.avail_in = fread(in, 1, CHUNK, source);
- if (ferror(source)) {
- (void)inflateEnd(&strm);
- return Z_ERRNO;
- }
- if (strm.avail_in == 0)
- break;
- strm.next_in = in;
-
- /* run inflate() on input until output buffer not full */
- do {
- strm.avail_out = CHUNK;
- strm.next_out = out;
- ret = inflate(&strm, Z_NO_FLUSH);
- assert(ret != Z_STREAM_ERROR); /* state not clobbered */
- switch (ret) {
- case Z_NEED_DICT:
- ret = Z_DATA_ERROR; /* and fall through */
- case Z_DATA_ERROR:
- case Z_MEM_ERROR:
- (void)inflateEnd(&strm);
- return ret;
- }
- have = CHUNK - strm.avail_out;
- if (fwrite(out, 1, have, dest) != have || ferror(dest)) {
- (void)inflateEnd(&strm);
- return Z_ERRNO;
- }
- } while (strm.avail_out == 0);
-
- /* done when inflate() says it's done */
- } while (ret != Z_STREAM_END);
-
- /* clean up and return */
- (void)inflateEnd(&strm);
- return ret == Z_STREAM_END ? Z_OK : Z_DATA_ERROR;
-}
-
-/* report a zlib or i/o error */
-void zerr(int ret)
-{
- fputs("zpipe: ", stderr);
- switch (ret) {
- case Z_ERRNO:
- if (ferror(stdin))
- fputs("error reading stdin\n", stderr);
- if (ferror(stdout))
- fputs("error writing stdout\n", stderr);
- break;
- case Z_STREAM_ERROR:
- fputs("invalid compression level\n", stderr);
- break;
- case Z_DATA_ERROR:
- fputs("invalid or incomplete deflate data\n", stderr);
- break;
- case Z_MEM_ERROR:
- fputs("out of memory\n", stderr);
- break;
- case Z_VERSION_ERROR:
- fputs("zlib version mismatch!\n", stderr);
- }
-}
-
-/* compress or decompress from stdin to stdout */
-int main(int argc, char **argv)
-{
- int ret;
-
- /* avoid end-of-line conversions */
- SET_BINARY_MODE(stdin);
- SET_BINARY_MODE(stdout);
-
- /* do compression if no arguments */
- if (argc == 1) {
- ret = def(stdin, stdout, Z_DEFAULT_COMPRESSION);
- if (ret != Z_OK)
- zerr(ret);
- return ret;
- }
-
- /* do decompression if -d specified */
- else if (argc == 2 && strcmp(argv[1], "-d") == 0) {
- ret = inf(stdin, stdout);
- if (ret != Z_OK)
- zerr(ret);
- return ret;
- }
-
- /* otherwise, report usage */
- else {
- fputs("zpipe usage: zpipe [-d] < source > dest\n", stderr);
- return 1;
- }
-}
diff --git a/third-party/zlib/examples/zran.c b/third-party/zlib/examples/zran.c
deleted file mode 100644
index 278f9ad..0000000
--- a/third-party/zlib/examples/zran.c
+++ /dev/null
@@ -1,409 +0,0 @@
-/* zran.c -- example of zlib/gzip stream indexing and random access
- * Copyright (C) 2005, 2012 Mark Adler
- * For conditions of distribution and use, see copyright notice in zlib.h
- Version 1.1 29 Sep 2012 Mark Adler */
-
-/* Version History:
- 1.0 29 May 2005 First version
- 1.1 29 Sep 2012 Fix memory reallocation error
- */
-
-/* Illustrate the use of Z_BLOCK, inflatePrime(), and inflateSetDictionary()
- for random access of a compressed file. A file containing a zlib or gzip
- stream is provided on the command line. The compressed stream is decoded in
- its entirety, and an index built with access points about every SPAN bytes
- in the uncompressed output. The compressed file is left open, and can then
- be read randomly, having to decompress on the average SPAN/2 uncompressed
- bytes before getting to the desired block of data.
-
- An access point can be created at the start of any deflate block, by saving
- the starting file offset and bit of that block, and the 32K bytes of
- uncompressed data that precede that block. Also the uncompressed offset of
- that block is saved to provide a referece for locating a desired starting
- point in the uncompressed stream. build_index() works by decompressing the
- input zlib or gzip stream a block at a time, and at the end of each block
- deciding if enough uncompressed data has gone by to justify the creation of
- a new access point. If so, that point is saved in a data structure that
- grows as needed to accommodate the points.
-
- To use the index, an offset in the uncompressed data is provided, for which
- the latest accees point at or preceding that offset is located in the index.
- The input file is positioned to the specified location in the index, and if
- necessary the first few bits of the compressed data is read from the file.
- inflate is initialized with those bits and the 32K of uncompressed data, and
- the decompression then proceeds until the desired offset in the file is
- reached. Then the decompression continues to read the desired uncompressed
- data from the file.
-
- Another approach would be to generate the index on demand. In that case,
- requests for random access reads from the compressed data would try to use
- the index, but if a read far enough past the end of the index is required,
- then further index entries would be generated and added.
-
- There is some fair bit of overhead to starting inflation for the random
- access, mainly copying the 32K byte dictionary. So if small pieces of the
- file are being accessed, it would make sense to implement a cache to hold
- some lookahead and avoid many calls to extract() for small lengths.
-
- Another way to build an index would be to use inflateCopy(). That would
- not be constrained to have access points at block boundaries, but requires
- more memory per access point, and also cannot be saved to file due to the
- use of pointers in the state. The approach here allows for storage of the
- index in a file.
- */
-
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
-#include "zlib.h"
-
-#define local static
-
-#define SPAN 1048576L /* desired distance between access points */
-#define WINSIZE 32768U /* sliding window size */
-#define CHUNK 16384 /* file input buffer size */
-
-/* access point entry */
-struct point {
- off_t out; /* corresponding offset in uncompressed data */
- off_t in; /* offset in input file of first full byte */
- int bits; /* number of bits (1-7) from byte at in - 1, or 0 */
- unsigned char window[WINSIZE]; /* preceding 32K of uncompressed data */
-};
-
-/* access point list */
-struct access {
- int have; /* number of list entries filled in */
- int size; /* number of list entries allocated */
- struct point *list; /* allocated list */
-};
-
-/* Deallocate an index built by build_index() */
-local void free_index(struct access *index)
-{
- if (index != NULL) {
- free(index->list);
- free(index);
- }
-}
-
-/* Add an entry to the access point list. If out of memory, deallocate the
- existing list and return NULL. */
-local struct access *addpoint(struct access *index, int bits,
- off_t in, off_t out, unsigned left, unsigned char *window)
-{
- struct point *next;
-
- /* if list is empty, create it (start with eight points) */
- if (index == NULL) {
- index = malloc(sizeof(struct access));
- if (index == NULL) return NULL;
- index->list = malloc(sizeof(struct point) << 3);
- if (index->list == NULL) {
- free(index);
- return NULL;
- }
- index->size = 8;
- index->have = 0;
- }
-
- /* if list is full, make it bigger */
- else if (index->have == index->size) {
- index->size <<= 1;
- next = realloc(index->list, sizeof(struct point) * index->size);
- if (next == NULL) {
- free_index(index);
- return NULL;
- }
- index->list = next;
- }
-
- /* fill in entry and increment how many we have */
- next = index->list + index->have;
- next->bits = bits;
- next->in = in;
- next->out = out;
- if (left)
- memcpy(next->window, window + WINSIZE - left, left);
- if (left < WINSIZE)
- memcpy(next->window + left, window, WINSIZE - left);
- index->have++;
-
- /* return list, possibly reallocated */
- return index;
-}
-
-/* Make one entire pass through the compressed stream and build an index, with
- access points about every span bytes of uncompressed output -- span is
- chosen to balance the speed of random access against the memory requirements
- of the list, about 32K bytes per access point. Note that data after the end
- of the first zlib or gzip stream in the file is ignored. build_index()
- returns the number of access points on success (>= 1), Z_MEM_ERROR for out
- of memory, Z_DATA_ERROR for an error in the input file, or Z_ERRNO for a
- file read error. On success, *built points to the resulting index. */
-local int build_index(FILE *in, off_t span, struct access **built)
-{
- int ret;
- off_t totin, totout; /* our own total counters to avoid 4GB limit */
- off_t last; /* totout value of last access point */
- struct access *index; /* access points being generated */
- z_stream strm;
- unsigned char input[CHUNK];
- unsigned char window[WINSIZE];
-
- /* initialize inflate */
- strm.zalloc = Z_NULL;
- strm.zfree = Z_NULL;
- strm.opaque = Z_NULL;
- strm.avail_in = 0;
- strm.next_in = Z_NULL;
- ret = inflateInit2(&strm, 47); /* automatic zlib or gzip decoding */
- if (ret != Z_OK)
- return ret;
-
- /* inflate the input, maintain a sliding window, and build an index -- this
- also validates the integrity of the compressed data using the check
- information at the end of the gzip or zlib stream */
- totin = totout = last = 0;
- index = NULL; /* will be allocated by first addpoint() */
- strm.avail_out = 0;
- do {
- /* get some compressed data from input file */
- strm.avail_in = fread(input, 1, CHUNK, in);
- if (ferror(in)) {
- ret = Z_ERRNO;
- goto build_index_error;
- }
- if (strm.avail_in == 0) {
- ret = Z_DATA_ERROR;
- goto build_index_error;
- }
- strm.next_in = input;
-
- /* process all of that, or until end of stream */
- do {
- /* reset sliding window if necessary */
- if (strm.avail_out == 0) {
- strm.avail_out = WINSIZE;
- strm.next_out = window;
- }
-
- /* inflate until out of input, output, or at end of block --
- update the total input and output counters */
- totin += strm.avail_in;
- totout += strm.avail_out;
- ret = inflate(&strm, Z_BLOCK); /* return at end of block */
- totin -= strm.avail_in;
- totout -= strm.avail_out;
- if (ret == Z_NEED_DICT)
- ret = Z_DATA_ERROR;
- if (ret == Z_MEM_ERROR || ret == Z_DATA_ERROR)
- goto build_index_error;
- if (ret == Z_STREAM_END)
- break;
-
- /* if at end of block, consider adding an index entry (note that if
- data_type indicates an end-of-block, then all of the
- uncompressed data from that block has been delivered, and none
- of the compressed data after that block has been consumed,
- except for up to seven bits) -- the totout == 0 provides an
- entry point after the zlib or gzip header, and assures that the
- index always has at least one access point; we avoid creating an
- access point after the last block by checking bit 6 of data_type
- */
- if ((strm.data_type & 128) && !(strm.data_type & 64) &&
- (totout == 0 || totout - last > span)) {
- index = addpoint(index, strm.data_type & 7, totin,
- totout, strm.avail_out, window);
- if (index == NULL) {
- ret = Z_MEM_ERROR;
- goto build_index_error;
- }
- last = totout;
- }
- } while (strm.avail_in != 0);
- } while (ret != Z_STREAM_END);
-
- /* clean up and return index (release unused entries in list) */
- (void)inflateEnd(&strm);
- index->list = realloc(index->list, sizeof(struct point) * index->have);
- index->size = index->have;
- *built = index;
- return index->size;
-
- /* return error */
- build_index_error:
- (void)inflateEnd(&strm);
- if (index != NULL)
- free_index(index);
- return ret;
-}
-
-/* Use the index to read len bytes from offset into buf, return bytes read or
- negative for error (Z_DATA_ERROR or Z_MEM_ERROR). If data is requested past
- the end of the uncompressed data, then extract() will return a value less
- than len, indicating how much as actually read into buf. This function
- should not return a data error unless the file was modified since the index
- was generated. extract() may also return Z_ERRNO if there is an error on
- reading or seeking the input file. */
-local int extract(FILE *in, struct access *index, off_t offset,
- unsigned char *buf, int len)
-{
- int ret, skip;
- z_stream strm;
- struct point *here;
- unsigned char input[CHUNK];
- unsigned char discard[WINSIZE];
-
- /* proceed only if something reasonable to do */
- if (len < 0)
- return 0;
-
- /* find where in stream to start */
- here = index->list;
- ret = index->have;
- while (--ret && here[1].out <= offset)
- here++;
-
- /* initialize file and inflate state to start there */
- strm.zalloc = Z_NULL;
- strm.zfree = Z_NULL;
- strm.opaque = Z_NULL;
- strm.avail_in = 0;
- strm.next_in = Z_NULL;
- ret = inflateInit2(&strm, -15); /* raw inflate */
- if (ret != Z_OK)
- return ret;
- ret = fseeko(in, here->in - (here->bits ? 1 : 0), SEEK_SET);
- if (ret == -1)
- goto extract_ret;
- if (here->bits) {
- ret = getc(in);
- if (ret == -1) {
- ret = ferror(in) ? Z_ERRNO : Z_DATA_ERROR;
- goto extract_ret;
- }
- (void)inflatePrime(&strm, here->bits, ret >> (8 - here->bits));
- }
- (void)inflateSetDictionary(&strm, here->window, WINSIZE);
-
- /* skip uncompressed bytes until offset reached, then satisfy request */
- offset -= here->out;
- strm.avail_in = 0;
- skip = 1; /* while skipping to offset */
- do {
- /* define where to put uncompressed data, and how much */
- if (offset == 0 && skip) { /* at offset now */
- strm.avail_out = len;
- strm.next_out = buf;
- skip = 0; /* only do this once */
- }
- if (offset > WINSIZE) { /* skip WINSIZE bytes */
- strm.avail_out = WINSIZE;
- strm.next_out = discard;
- offset -= WINSIZE;
- }
- else if (offset != 0) { /* last skip */
- strm.avail_out = (unsigned)offset;
- strm.next_out = discard;
- offset = 0;
- }
-
- /* uncompress until avail_out filled, or end of stream */
- do {
- if (strm.avail_in == 0) {
- strm.avail_in = fread(input, 1, CHUNK, in);
- if (ferror(in)) {
- ret = Z_ERRNO;
- goto extract_ret;
- }
- if (strm.avail_in == 0) {
- ret = Z_DATA_ERROR;
- goto extract_ret;
- }
- strm.next_in = input;
- }
- ret = inflate(&strm, Z_NO_FLUSH); /* normal inflate */
- if (ret == Z_NEED_DICT)
- ret = Z_DATA_ERROR;
- if (ret == Z_MEM_ERROR || ret == Z_DATA_ERROR)
- goto extract_ret;
- if (ret == Z_STREAM_END)
- break;
- } while (strm.avail_out != 0);
-
- /* if reach end of stream, then don't keep trying to get more */
- if (ret == Z_STREAM_END)
- break;
-
- /* do until offset reached and requested data read, or stream ends */
- } while (skip);
-
- /* compute number of uncompressed bytes read after offset */
- ret = skip ? 0 : len - strm.avail_out;
-
- /* clean up and return bytes read or error */
- extract_ret:
- (void)inflateEnd(&strm);
- return ret;
-}
-
-/* Demonstrate the use of build_index() and extract() by processing the file
- provided on the command line, and the extracting 16K from about 2/3rds of
- the way through the uncompressed output, and writing that to stdout. */
-int main(int argc, char **argv)
-{
- int len;
- off_t offset;
- FILE *in;
- struct access *index = NULL;
- unsigned char buf[CHUNK];
-
- /* open input file */
- if (argc != 2) {
- fprintf(stderr, "usage: zran file.gz\n");
- return 1;
- }
- in = fopen(argv[1], "rb");
- if (in == NULL) {
- fprintf(stderr, "zran: could not open %s for reading\n", argv[1]);
- return 1;
- }
-
- /* build index */
- len = build_index(in, SPAN, &index);
- if (len < 0) {
- fclose(in);
- switch (len) {
- case Z_MEM_ERROR:
- fprintf(stderr, "zran: out of memory\n");
- break;
- case Z_DATA_ERROR:
- fprintf(stderr, "zran: compressed data error in %s\n", argv[1]);
- break;
- case Z_ERRNO:
- fprintf(stderr, "zran: read error on %s\n", argv[1]);
- break;
- default:
- fprintf(stderr, "zran: error %d while building index\n", len);
- }
- return 1;
- }
- fprintf(stderr, "zran: built index with %d access points\n", len);
-
- /* use index by reading some bytes from an arbitrary offset */
- offset = (index->list[index->have - 1].out << 1) / 3;
- len = extract(in, index, offset, buf, CHUNK);
- if (len < 0)
- fprintf(stderr, "zran: extraction failed: %s error\n",
- len == Z_MEM_ERROR ? "out of memory" : "input corrupted");
- else {
- fwrite(buf, 1, len, stdout);
- fprintf(stderr, "zran: extracted %d bytes at %llu\n", len, offset);
- }
-
- /* clean up and exit */
- free_index(index);
- fclose(in);
- return 0;
-}
diff --git a/third-party/zlib/gzclose.c b/third-party/zlib/gzclose.c
deleted file mode 100644
index caeb99a..0000000
--- a/third-party/zlib/gzclose.c
+++ /dev/null
@@ -1,25 +0,0 @@
-/* gzclose.c -- zlib gzclose() function
- * Copyright (C) 2004, 2010 Mark Adler
- * For conditions of distribution and use, see copyright notice in zlib.h
- */
-
-#include "gzguts.h"
-
-/* gzclose() is in a separate file so that it is linked in only if it is used.
- That way the other gzclose functions can be used instead to avoid linking in
- unneeded compression or decompression routines. */
-int ZEXPORT gzclose(file)
- gzFile file;
-{
-#ifndef NO_GZCOMPRESS
- gz_statep state;
-
- if (file == NULL)
- return Z_STREAM_ERROR;
- state = (gz_statep)file;
-
- return state->mode == GZ_READ ? gzclose_r(file) : gzclose_w(file);
-#else
- return gzclose_r(file);
-#endif
-}
diff --git a/third-party/zlib/gzguts.h b/third-party/zlib/gzguts.h
deleted file mode 100644
index d87659d..0000000
--- a/third-party/zlib/gzguts.h
+++ /dev/null
@@ -1,209 +0,0 @@
-/* gzguts.h -- zlib internal header definitions for gz* operations
- * Copyright (C) 2004, 2005, 2010, 2011, 2012, 2013 Mark Adler
- * For conditions of distribution and use, see copyright notice in zlib.h
- */
-
-#ifdef _LARGEFILE64_SOURCE
-# ifndef _LARGEFILE_SOURCE
-# define _LARGEFILE_SOURCE 1
-# endif
-# ifdef _FILE_OFFSET_BITS
-# undef _FILE_OFFSET_BITS
-# endif
-#endif
-
-#ifdef HAVE_HIDDEN
-# define ZLIB_INTERNAL __attribute__((visibility ("hidden")))
-#else
-# define ZLIB_INTERNAL
-#endif
-
-#include <stdio.h>
-#include "zlib.h"
-#ifdef STDC
-# include <string.h>
-# include <stdlib.h>
-# include <limits.h>
-#endif
-#include <fcntl.h>
-
-#ifdef _WIN32
-# include <stddef.h>
-#endif
-
-#if defined(__TURBOC__) || defined(_MSC_VER) || defined(_WIN32)
-# include <io.h>
-#endif
-
-#ifdef WINAPI_FAMILY
-# define open _open
-# define read _read
-# define write _write
-# define close _close
-#endif
-
-#ifdef NO_DEFLATE /* for compatibility with old definition */
-# define NO_GZCOMPRESS
-#endif
-
-#if defined(STDC99) || (defined(__TURBOC__) && __TURBOC__ >= 0x550)
-# ifndef HAVE_VSNPRINTF
-# define HAVE_VSNPRINTF
-# endif
-#endif
-
-#if defined(__CYGWIN__)
-# ifndef HAVE_VSNPRINTF
-# define HAVE_VSNPRINTF
-# endif
-#endif
-
-#if defined(MSDOS) && defined(__BORLANDC__) && (BORLANDC > 0x410)
-# ifndef HAVE_VSNPRINTF
-# define HAVE_VSNPRINTF
-# endif
-#endif
-
-#ifndef HAVE_VSNPRINTF
-# ifdef MSDOS
-/* vsnprintf may exist on some MS-DOS compilers (DJGPP?),
- but for now we just assume it doesn't. */
-# define NO_vsnprintf
-# endif
-# ifdef __TURBOC__
-# define NO_vsnprintf
-# endif
-# ifdef WIN32
-/* In Win32, vsnprintf is available as the "non-ANSI" _vsnprintf. */
-# if !defined(vsnprintf) && !defined(NO_vsnprintf)
-# if !defined(_MSC_VER) || ( defined(_MSC_VER) && _MSC_VER < 1500 )
-# define vsnprintf _vsnprintf
-# endif
-# endif
-# endif
-# ifdef __SASC
-# define NO_vsnprintf
-# endif
-# ifdef VMS
-# define NO_vsnprintf
-# endif
-# ifdef __OS400__
-# define NO_vsnprintf
-# endif
-# ifdef __MVS__
-# define NO_vsnprintf
-# endif
-#endif
-
-/* unlike snprintf (which is required in C99, yet still not supported by
- Microsoft more than a decade later!), _snprintf does not guarantee null
- termination of the result -- however this is only used in gzlib.c where
- the result is assured to fit in the space provided */
-#ifdef _MSC_VER
-# define snprintf _snprintf
-#endif
-
-#ifndef local
-# define local static
-#endif
-/* compile with -Dlocal if your debugger can't find static symbols */
-
-/* gz* functions always use library allocation functions */
-#ifndef STDC
- extern voidp malloc OF((uInt size));
- extern void free OF((voidpf ptr));
-#endif
-
-/* get errno and strerror definition */
-#if defined UNDER_CE
-# include <windows.h>
-# define zstrerror() gz_strwinerror((DWORD)GetLastError())
-#else
-# ifndef NO_STRERROR
-# include <errno.h>
-# define zstrerror() strerror(errno)
-# else
-# define zstrerror() "stdio error (consult errno)"
-# endif
-#endif
-
-/* provide prototypes for these when building zlib without LFS */
-#if !defined(_LARGEFILE64_SOURCE) || _LFS64_LARGEFILE-0 == 0
- ZEXTERN gzFile ZEXPORT gzopen64 OF((const char *, const char *));
- ZEXTERN z_off64_t ZEXPORT gzseek64 OF((gzFile, z_off64_t, int));
- ZEXTERN z_off64_t ZEXPORT gztell64 OF((gzFile));
- ZEXTERN z_off64_t ZEXPORT gzoffset64 OF((gzFile));
-#endif
-
-/* default memLevel */
-#if MAX_MEM_LEVEL >= 8
-# define DEF_MEM_LEVEL 8
-#else
-# define DEF_MEM_LEVEL MAX_MEM_LEVEL
-#endif
-
-/* default i/o buffer size -- double this for output when reading (this and
- twice this must be able to fit in an unsigned type) */
-#define GZBUFSIZE 8192
-
-/* gzip modes, also provide a little integrity check on the passed structure */
-#define GZ_NONE 0
-#define GZ_READ 7247
-#define GZ_WRITE 31153
-#define GZ_APPEND 1 /* mode set to GZ_WRITE after the file is opened */
-
-/* values for gz_state how */
-#define LOOK 0 /* look for a gzip header */
-#define COPY 1 /* copy input directly */
-#define GZIP 2 /* decompress a gzip stream */
-
-/* internal gzip file state data structure */
-typedef struct {
- /* exposed contents for gzgetc() macro */
- struct gzFile_s x; /* "x" for exposed */
- /* x.have: number of bytes available at x.next */
- /* x.next: next output data to deliver or write */
- /* x.pos: current position in uncompressed data */
- /* used for both reading and writing */
- int mode; /* see gzip modes above */
- int fd; /* file descriptor */
- char *path; /* path or fd for error messages */
- unsigned size; /* buffer size, zero if not allocated yet */
- unsigned want; /* requested buffer size, default is GZBUFSIZE */
- unsigned char *in; /* input buffer */
- unsigned char *out; /* output buffer (double-sized when reading) */
- int direct; /* 0 if processing gzip, 1 if transparent */
- /* just for reading */
- int how; /* 0: get header, 1: copy, 2: decompress */
- z_off64_t start; /* where the gzip data started, for rewinding */
- int eof; /* true if end of input file reached */
- int past; /* true if read requested past end */
- /* just for writing */
- int level; /* compression level */
- int strategy; /* compression strategy */
- /* seek request */
- z_off64_t skip; /* amount to skip (already rewound if backwards) */
- int seek; /* true if seek request pending */
- /* error information */
- int err; /* error code */
- char *msg; /* error message */
- /* zlib inflate or deflate stream */
- z_stream strm; /* stream structure in-place (not a pointer) */
-} gz_state;
-typedef gz_state FAR *gz_statep;
-
-/* shared functions */
-void ZLIB_INTERNAL gz_error OF((gz_statep, int, const char *));
-#if defined UNDER_CE
-char ZLIB_INTERNAL *gz_strwinerror OF((DWORD error));
-#endif
-
-/* GT_OFF(x), where x is an unsigned value, is true if x > maximum z_off64_t
- value -- needed when comparing unsigned to z_off64_t, which is signed
- (possible z_off64_t types off_t, off64_t, and long are all signed) */
-#ifdef INT_MAX
-# define GT_OFF(x) (sizeof(int) == sizeof(z_off64_t) && (x) > INT_MAX)
-#else
-unsigned ZLIB_INTERNAL gz_intmax OF((void));
-# define GT_OFF(x) (sizeof(int) == sizeof(z_off64_t) && (x) > gz_intmax())
-#endif
diff --git a/third-party/zlib/gzlib.c b/third-party/zlib/gzlib.c
deleted file mode 100644
index fae202e..0000000
--- a/third-party/zlib/gzlib.c
+++ /dev/null
@@ -1,634 +0,0 @@
-/* gzlib.c -- zlib functions common to reading and writing gzip files
- * Copyright (C) 2004, 2010, 2011, 2012, 2013 Mark Adler
- * For conditions of distribution and use, see copyright notice in zlib.h
- */
-
-#include "gzguts.h"
-
-#if defined(_WIN32) && !defined(__BORLANDC__)
-# define LSEEK _lseeki64
-#else
-#if defined(_LARGEFILE64_SOURCE) && _LFS64_LARGEFILE-0
-# define LSEEK lseek64
-#else
-# define LSEEK lseek
-#endif
-#endif
-
-/* Local functions */
-local void gz_reset OF((gz_statep));
-local gzFile gz_open OF((const void *, int, const char *));
-
-#if defined UNDER_CE
-
-/* Map the Windows error number in ERROR to a locale-dependent error message
- string and return a pointer to it. Typically, the values for ERROR come
- from GetLastError.
-
- The string pointed to shall not be modified by the application, but may be
- overwritten by a subsequent call to gz_strwinerror
-
- The gz_strwinerror function does not change the current setting of
- GetLastError. */
-char ZLIB_INTERNAL *gz_strwinerror (error)
- DWORD error;
-{
- static char buf[1024];
-
- wchar_t *msgbuf;
- DWORD lasterr = GetLastError();
- DWORD chars = FormatMessage(FORMAT_MESSAGE_FROM_SYSTEM
- | FORMAT_MESSAGE_ALLOCATE_BUFFER,
- NULL,
- error,
- 0, /* Default language */
- (LPVOID)&msgbuf,
- 0,
- NULL);
- if (chars != 0) {
- /* If there is an \r\n appended, zap it. */
- if (chars >= 2
- && msgbuf[chars - 2] == '\r' && msgbuf[chars - 1] == '\n') {
- chars -= 2;
- msgbuf[chars] = 0;
- }
-
- if (chars > sizeof (buf) - 1) {
- chars = sizeof (buf) - 1;
- msgbuf[chars] = 0;
- }
-
- wcstombs(buf, msgbuf, chars + 1);
- LocalFree(msgbuf);
- }
- else {
- sprintf(buf, "unknown win32 error (%ld)", error);
- }
-
- SetLastError(lasterr);
- return buf;
-}
-
-#endif /* UNDER_CE */
-
-/* Reset gzip file state */
-local void gz_reset(state)
- gz_statep state;
-{
- state->x.have = 0; /* no output data available */
- if (state->mode == GZ_READ) { /* for reading ... */
- state->eof = 0; /* not at end of file */
- state->past = 0; /* have not read past end yet */
- state->how = LOOK; /* look for gzip header */
- }
- state->seek = 0; /* no seek request pending */
- gz_error(state, Z_OK, NULL); /* clear error */
- state->x.pos = 0; /* no uncompressed data yet */
- state->strm.avail_in = 0; /* no input data yet */
-}
-
-/* Open a gzip file either by name or file descriptor. */
-local gzFile gz_open(path, fd, mode)
- const void *path;
- int fd;
- const char *mode;
-{
- gz_statep state;
- size_t len;
- int oflag;
-#ifdef O_CLOEXEC
- int cloexec = 0;
-#endif
-#ifdef O_EXCL
- int exclusive = 0;
-#endif
-
- /* check input */
- if (path == NULL)
- return NULL;
-
- /* allocate gzFile structure to return */
- state = (gz_statep)malloc(sizeof(gz_state));
- if (state == NULL)
- return NULL;
- state->size = 0; /* no buffers allocated yet */
- state->want = GZBUFSIZE; /* requested buffer size */
- state->msg = NULL; /* no error message yet */
-
- /* interpret mode */
- state->mode = GZ_NONE;
- state->level = Z_DEFAULT_COMPRESSION;
- state->strategy = Z_DEFAULT_STRATEGY;
- state->direct = 0;
- while (*mode) {
- if (*mode >= '0' && *mode <= '9')
- state->level = *mode - '0';
- else
- switch (*mode) {
- case 'r':
- state->mode = GZ_READ;
- break;
-#ifndef NO_GZCOMPRESS
- case 'w':
- state->mode = GZ_WRITE;
- break;
- case 'a':
- state->mode = GZ_APPEND;
- break;
-#endif
- case '+': /* can't read and write at the same time */
- free(state);
- return NULL;
- case 'b': /* ignore -- will request binary anyway */
- break;
-#ifdef O_CLOEXEC
- case 'e':
- cloexec = 1;
- break;
-#endif
-#ifdef O_EXCL
- case 'x':
- exclusive = 1;
- break;
-#endif
- case 'f':
- state->strategy = Z_FILTERED;
- break;
- case 'h':
- state->strategy = Z_HUFFMAN_ONLY;
- break;
- case 'R':
- state->strategy = Z_RLE;
- break;
- case 'F':
- state->strategy = Z_FIXED;
- break;
- case 'T':
- state->direct = 1;
- break;
- default: /* could consider as an error, but just ignore */
- ;
- }
- mode++;
- }
-
- /* must provide an "r", "w", or "a" */
- if (state->mode == GZ_NONE) {
- free(state);
- return NULL;
- }
-
- /* can't force transparent read */
- if (state->mode == GZ_READ) {
- if (state->direct) {
- free(state);
- return NULL;
- }
- state->direct = 1; /* for empty file */
- }
-
- /* save the path name for error messages */
-#ifdef _WIN32
- if (fd == -2) {
- len = wcstombs(NULL, path, 0);
- if (len == (size_t)-1)
- len = 0;
- }
- else
-#endif
- len = strlen((const char *)path);
- state->path = (char *)malloc(len + 1);
- if (state->path == NULL) {
- free(state);
- return NULL;
- }
-#ifdef _WIN32
- if (fd == -2)
- if (len)
- wcstombs(state->path, path, len + 1);
- else
- *(state->path) = 0;
- else
-#endif
-#if !defined(NO_snprintf) && !defined(NO_vsnprintf)
- snprintf(state->path, len + 1, "%s", (const char *)path);
-#else
- strcpy(state->path, path);
-#endif
-
- /* compute the flags for open() */
- oflag =
-#ifdef O_LARGEFILE
- O_LARGEFILE |
-#endif
-#ifdef O_BINARY
- O_BINARY |
-#endif
-#ifdef O_CLOEXEC
- (cloexec ? O_CLOEXEC : 0) |
-#endif
- (state->mode == GZ_READ ?
- O_RDONLY :
- (O_WRONLY | O_CREAT |
-#ifdef O_EXCL
- (exclusive ? O_EXCL : 0) |
-#endif
- (state->mode == GZ_WRITE ?
- O_TRUNC :
- O_APPEND)));
-
- /* open the file with the appropriate flags (or just use fd) */
- state->fd = fd > -1 ? fd : (
-#ifdef _WIN32
- fd == -2 ? _wopen(path, oflag, 0666) :
-#endif
- open((const char *)path, oflag, 0666));
- if (state->fd == -1) {
- free(state->path);
- free(state);
- return NULL;
- }
- if (state->mode == GZ_APPEND)
- state->mode = GZ_WRITE; /* simplify later checks */
-
- /* save the current position for rewinding (only if reading) */
- if (state->mode == GZ_READ) {
- state->start = LSEEK(state->fd, 0, SEEK_CUR);
- if (state->start == -1) state->start = 0;
- }
-
- /* initialize stream */
- gz_reset(state);
-
- /* return stream */
- return (gzFile)state;
-}
-
-/* -- see zlib.h -- */
-gzFile ZEXPORT gzopen(path, mode)
- const char *path;
- const char *mode;
-{
- return gz_open(path, -1, mode);
-}
-
-/* -- see zlib.h -- */
-gzFile ZEXPORT gzopen64(path, mode)
- const char *path;
- const char *mode;
-{
- return gz_open(path, -1, mode);
-}
-
-/* -- see zlib.h -- */
-gzFile ZEXPORT gzdopen(fd, mode)
- int fd;
- const char *mode;
-{
- char *path; /* identifier for error messages */
- gzFile gz;
-
- if (fd == -1 || (path = (char *)malloc(7 + 3 * sizeof(int))) == NULL)
- return NULL;
-#if !defined(NO_snprintf) && !defined(NO_vsnprintf)
- snprintf(path, 7 + 3 * sizeof(int), "<fd:%d>", fd); /* for debugging */
-#else
- sprintf(path, "<fd:%d>", fd); /* for debugging */
-#endif
- gz = gz_open(path, fd, mode);
- free(path);
- return gz;
-}
-
-/* -- see zlib.h -- */
-#ifdef _WIN32
-gzFile ZEXPORT gzopen_w(path, mode)
- const wchar_t *path;
- const char *mode;
-{
- return gz_open(path, -2, mode);
-}
-#endif
-
-/* -- see zlib.h -- */
-int ZEXPORT gzbuffer(file, size)
- gzFile file;
- unsigned size;
-{
- gz_statep state;
-
- /* get internal structure and check integrity */
- if (file == NULL)
- return -1;
- state = (gz_statep)file;
- if (state->mode != GZ_READ && state->mode != GZ_WRITE)
- return -1;
-
- /* make sure we haven't already allocated memory */
- if (state->size != 0)
- return -1;
-
- /* check and set requested size */
- if (size < 2)
- size = 2; /* need two bytes to check magic header */
- state->want = size;
- return 0;
-}
-
-/* -- see zlib.h -- */
-int ZEXPORT gzrewind(file)
- gzFile file;
-{
- gz_statep state;
-
- /* get internal structure */
- if (file == NULL)
- return -1;
- state = (gz_statep)file;
-
- /* check that we're reading and that there's no error */
- if (state->mode != GZ_READ ||
- (state->err != Z_OK && state->err != Z_BUF_ERROR))
- return -1;
-
- /* back up and start over */
- if (LSEEK(state->fd, state->start, SEEK_SET) == -1)
- return -1;
- gz_reset(state);
- return 0;
-}
-
-/* -- see zlib.h -- */
-z_off64_t ZEXPORT gzseek64(file, offset, whence)
- gzFile file;
- z_off64_t offset;
- int whence;
-{
- unsigned n;
- z_off64_t ret;
- gz_statep state;
-
- /* get internal structure and check integrity */
- if (file == NULL)
- return -1;
- state = (gz_statep)file;
- if (state->mode != GZ_READ && state->mode != GZ_WRITE)
- return -1;
-
- /* check that there's no error */
- if (state->err != Z_OK && state->err != Z_BUF_ERROR)
- return -1;
-
- /* can only seek from start or relative to current position */
- if (whence != SEEK_SET && whence != SEEK_CUR)
- return -1;
-
- /* normalize offset to a SEEK_CUR specification */
- if (whence == SEEK_SET)
- offset -= state->x.pos;
- else if (state->seek)
- offset += state->skip;
- state->seek = 0;
-
- /* if within raw area while reading, just go there */
- if (state->mode == GZ_READ && state->how == COPY &&
- state->x.pos + offset >= 0) {
- ret = LSEEK(state->fd, offset - state->x.have, SEEK_CUR);
- if (ret == -1)
- return -1;
- state->x.have = 0;
- state->eof = 0;
- state->past = 0;
- state->seek = 0;
- gz_error(state, Z_OK, NULL);
- state->strm.avail_in = 0;
- state->x.pos += offset;
- return state->x.pos;
- }
-
- /* calculate skip amount, rewinding if needed for back seek when reading */
- if (offset < 0) {
- if (state->mode != GZ_READ) /* writing -- can't go backwards */
- return -1;
- offset += state->x.pos;
- if (offset < 0) /* before start of file! */
- return -1;
- if (gzrewind(file) == -1) /* rewind, then skip to offset */
- return -1;
- }
-
- /* if reading, skip what's in output buffer (one less gzgetc() check) */
- if (state->mode == GZ_READ) {
- n = GT_OFF(state->x.have) || (z_off64_t)state->x.have > offset ?
- (unsigned)offset : state->x.have;
- state->x.have -= n;
- state->x.next += n;
- state->x.pos += n;
- offset -= n;
- }
-
- /* request skip (if not zero) */
- if (offset) {
- state->seek = 1;
- state->skip = offset;
- }
- return state->x.pos + offset;
-}
-
-/* -- see zlib.h -- */
-z_off_t ZEXPORT gzseek(file, offset, whence)
- gzFile file;
- z_off_t offset;
- int whence;
-{
- z_off64_t ret;
-
- ret = gzseek64(file, (z_off64_t)offset, whence);
- return ret == (z_off_t)ret ? (z_off_t)ret : -1;
-}
-
-/* -- see zlib.h -- */
-z_off64_t ZEXPORT gztell64(file)
- gzFile file;
-{
- gz_statep state;
-
- /* get internal structure and check integrity */
- if (file == NULL)
- return -1;
- state = (gz_statep)file;
- if (state->mode != GZ_READ && state->mode != GZ_WRITE)
- return -1;
-
- /* return position */
- return state->x.pos + (state->seek ? state->skip : 0);
-}
-
-/* -- see zlib.h -- */
-z_off_t ZEXPORT gztell(file)
- gzFile file;
-{
- z_off64_t ret;
-
- ret = gztell64(file);
- return ret == (z_off_t)ret ? (z_off_t)ret : -1;
-}
-
-/* -- see zlib.h -- */
-z_off64_t ZEXPORT gzoffset64(file)
- gzFile file;
-{
- z_off64_t offset;
- gz_statep state;
-
- /* get internal structure and check integrity */
- if (file == NULL)
- return -1;
- state = (gz_statep)file;
- if (state->mode != GZ_READ && state->mode != GZ_WRITE)
- return -1;
-
- /* compute and return effective offset in file */
- offset = LSEEK(state->fd, 0, SEEK_CUR);
- if (offset == -1)
- return -1;
- if (state->mode == GZ_READ) /* reading */
- offset -= state->strm.avail_in; /* don't count buffered input */
- return offset;
-}
-
-/* -- see zlib.h -- */
-z_off_t ZEXPORT gzoffset(file)
- gzFile file;
-{
- z_off64_t ret;
-
- ret = gzoffset64(file);
- return ret == (z_off_t)ret ? (z_off_t)ret : -1;
-}
-
-/* -- see zlib.h -- */
-int ZEXPORT gzeof(file)
- gzFile file;
-{
- gz_statep state;
-
- /* get internal structure and check integrity */
- if (file == NULL)
- return 0;
- state = (gz_statep)file;
- if (state->mode != GZ_READ && state->mode != GZ_WRITE)
- return 0;
-
- /* return end-of-file state */
- return state->mode == GZ_READ ? state->past : 0;
-}
-
-/* -- see zlib.h -- */
-const char * ZEXPORT gzerror(file, errnum)
- gzFile file;
- int *errnum;
-{
- gz_statep state;
-
- /* get internal structure and check integrity */
- if (file == NULL)
- return NULL;
- state = (gz_statep)file;
- if (state->mode != GZ_READ && state->mode != GZ_WRITE)
- return NULL;
-
- /* return error information */
- if (errnum != NULL)
- *errnum = state->err;
- return state->err == Z_MEM_ERROR ? "out of memory" :
- (state->msg == NULL ? "" : state->msg);
-}
-
-/* -- see zlib.h -- */
-void ZEXPORT gzclearerr(file)
- gzFile file;
-{
- gz_statep state;
-
- /* get internal structure and check integrity */
- if (file == NULL)
- return;
- state = (gz_statep)file;
- if (state->mode != GZ_READ && state->mode != GZ_WRITE)
- return;
-
- /* clear error and end-of-file */
- if (state->mode == GZ_READ) {
- state->eof = 0;
- state->past = 0;
- }
- gz_error(state, Z_OK, NULL);
-}
-
-/* Create an error message in allocated memory and set state->err and
- state->msg accordingly. Free any previous error message already there. Do
- not try to free or allocate space if the error is Z_MEM_ERROR (out of
- memory). Simply save the error message as a static string. If there is an
- allocation failure constructing the error message, then convert the error to
- out of memory. */
-void ZLIB_INTERNAL gz_error(state, err, msg)
- gz_statep state;
- int err;
- const char *msg;
-{
- /* free previously allocated message and clear */
- if (state->msg != NULL) {
- if (state->err != Z_MEM_ERROR)
- free(state->msg);
- state->msg = NULL;
- }
-
- /* if fatal, set state->x.have to 0 so that the gzgetc() macro fails */
- if (err != Z_OK && err != Z_BUF_ERROR)
- state->x.have = 0;
-
- /* set error code, and if no message, then done */
- state->err = err;
- if (msg == NULL)
- return;
-
- /* for an out of memory error, return literal string when requested */
- if (err == Z_MEM_ERROR)
- return;
-
- /* construct error message with path */
- if ((state->msg = (char *)malloc(strlen(state->path) + strlen(msg) + 3)) ==
- NULL) {
- state->err = Z_MEM_ERROR;
- return;
- }
-#if !defined(NO_snprintf) && !defined(NO_vsnprintf)
- snprintf(state->msg, strlen(state->path) + strlen(msg) + 3,
- "%s%s%s", state->path, ": ", msg);
-#else
- strcpy(state->msg, state->path);
- strcat(state->msg, ": ");
- strcat(state->msg, msg);
-#endif
- return;
-}
-
-#ifndef INT_MAX
-/* portably return maximum value for an int (when limits.h presumed not
- available) -- we need to do this to cover cases where 2's complement not
- used, since C standard permits 1's complement and sign-bit representations,
- otherwise we could just use ((unsigned)-1) >> 1 */
-unsigned ZLIB_INTERNAL gz_intmax()
-{
- unsigned p, q;
-
- p = 1;
- do {
- q = p;
- p <<= 1;
- p++;
- } while (p > q);
- return q >> 1;
-}
-#endif
diff --git a/third-party/zlib/gzread.c b/third-party/zlib/gzread.c
deleted file mode 100644
index bf4538e..0000000
--- a/third-party/zlib/gzread.c
+++ /dev/null
@@ -1,594 +0,0 @@
-/* gzread.c -- zlib functions for reading gzip files
- * Copyright (C) 2004, 2005, 2010, 2011, 2012, 2013 Mark Adler
- * For conditions of distribution and use, see copyright notice in zlib.h
- */
-
-#include "gzguts.h"
-
-/* Local functions */
-local int gz_load OF((gz_statep, unsigned char *, unsigned, unsigned *));
-local int gz_avail OF((gz_statep));
-local int gz_look OF((gz_statep));
-local int gz_decomp OF((gz_statep));
-local int gz_fetch OF((gz_statep));
-local int gz_skip OF((gz_statep, z_off64_t));
-
-/* Use read() to load a buffer -- return -1 on error, otherwise 0. Read from
- state->fd, and update state->eof, state->err, and state->msg as appropriate.
- This function needs to loop on read(), since read() is not guaranteed to
- read the number of bytes requested, depending on the type of descriptor. */
-local int gz_load(state, buf, len, have)
- gz_statep state;
- unsigned char *buf;
- unsigned len;
- unsigned *have;
-{
- int ret;
-
- *have = 0;
- do {
- ret = read(state->fd, buf + *have, len - *have);
- if (ret <= 0)
- break;
- *have += ret;
- } while (*have < len);
- if (ret < 0) {
- gz_error(state, Z_ERRNO, zstrerror());
- return -1;
- }
- if (ret == 0)
- state->eof = 1;
- return 0;
-}
-
-/* Load up input buffer and set eof flag if last data loaded -- return -1 on
- error, 0 otherwise. Note that the eof flag is set when the end of the input
- file is reached, even though there may be unused data in the buffer. Once
- that data has been used, no more attempts will be made to read the file.
- If strm->avail_in != 0, then the current data is moved to the beginning of
- the input buffer, and then the remainder of the buffer is loaded with the
- available data from the input file. */
-local int gz_avail(state)
- gz_statep state;
-{
- unsigned got;
- z_streamp strm = &(state->strm);
-
- if (state->err != Z_OK && state->err != Z_BUF_ERROR)
- return -1;
- if (state->eof == 0) {
- if (strm->avail_in) { /* copy what's there to the start */
- unsigned char *p = state->in;
- unsigned const char *q = strm->next_in;
- unsigned n = strm->avail_in;
- do {
- *p++ = *q++;
- } while (--n);
- }
- if (gz_load(state, state->in + strm->avail_in,
- state->size - strm->avail_in, &got) == -1)
- return -1;
- strm->avail_in += got;
- strm->next_in = state->in;
- }
- return 0;
-}
-
-/* Look for gzip header, set up for inflate or copy. state->x.have must be 0.
- If this is the first time in, allocate required memory. state->how will be
- left unchanged if there is no more input data available, will be set to COPY
- if there is no gzip header and direct copying will be performed, or it will
- be set to GZIP for decompression. If direct copying, then leftover input
- data from the input buffer will be copied to the output buffer. In that
- case, all further file reads will be directly to either the output buffer or
- a user buffer. If decompressing, the inflate state will be initialized.
- gz_look() will return 0 on success or -1 on failure. */
-local int gz_look(state)
- gz_statep state;
-{
- z_streamp strm = &(state->strm);
-
- /* allocate read buffers and inflate memory */
- if (state->size == 0) {
- /* allocate buffers */
- state->in = (unsigned char *)malloc(state->want);
- state->out = (unsigned char *)malloc(state->want << 1);
- if (state->in == NULL || state->out == NULL) {
- if (state->out != NULL)
- free(state->out);
- if (state->in != NULL)
- free(state->in);
- gz_error(state, Z_MEM_ERROR, "out of memory");
- return -1;
- }
- state->size = state->want;
-
- /* allocate inflate memory */
- state->strm.zalloc = Z_NULL;
- state->strm.zfree = Z_NULL;
- state->strm.opaque = Z_NULL;
- state->strm.avail_in = 0;
- state->strm.next_in = Z_NULL;
- if (inflateInit2(&(state->strm), 15 + 16) != Z_OK) { /* gunzip */
- free(state->out);
- free(state->in);
- state->size = 0;
- gz_error(state, Z_MEM_ERROR, "out of memory");
- return -1;
- }
- }
-
- /* get at least the magic bytes in the input buffer */
- if (strm->avail_in < 2) {
- if (gz_avail(state) == -1)
- return -1;
- if (strm->avail_in == 0)
- return 0;
- }
-
- /* look for gzip magic bytes -- if there, do gzip decoding (note: there is
- a logical dilemma here when considering the case of a partially written
- gzip file, to wit, if a single 31 byte is written, then we cannot tell
- whether this is a single-byte file, or just a partially written gzip
- file -- for here we assume that if a gzip file is being written, then
- the header will be written in a single operation, so that reading a
- single byte is sufficient indication that it is not a gzip file) */
- if (strm->avail_in > 1 &&
- strm->next_in[0] == 31 && strm->next_in[1] == 139) {
- inflateReset(strm);
- state->how = GZIP;
- state->direct = 0;
- return 0;
- }
-
- /* no gzip header -- if we were decoding gzip before, then this is trailing
- garbage. Ignore the trailing garbage and finish. */
- if (state->direct == 0) {
- strm->avail_in = 0;
- state->eof = 1;
- state->x.have = 0;
- return 0;
- }
-
- /* doing raw i/o, copy any leftover input to output -- this assumes that
- the output buffer is larger than the input buffer, which also assures
- space for gzungetc() */
- state->x.next = state->out;
- if (strm->avail_in) {
- memcpy(state->x.next, strm->next_in, strm->avail_in);
- state->x.have = strm->avail_in;
- strm->avail_in = 0;
- }
- state->how = COPY;
- state->direct = 1;
- return 0;
-}
-
-/* Decompress from input to the provided next_out and avail_out in the state.
- On return, state->x.have and state->x.next point to the just decompressed
- data. If the gzip stream completes, state->how is reset to LOOK to look for
- the next gzip stream or raw data, once state->x.have is depleted. Returns 0
- on success, -1 on failure. */
-local int gz_decomp(state)
- gz_statep state;
-{
- int ret = Z_OK;
- unsigned had;
- z_streamp strm = &(state->strm);
-
- /* fill output buffer up to end of deflate stream */
- had = strm->avail_out;
- do {
- /* get more input for inflate() */
- if (strm->avail_in == 0 && gz_avail(state) == -1)
- return -1;
- if (strm->avail_in == 0) {
- gz_error(state, Z_BUF_ERROR, "unexpected end of file");
- break;
- }
-
- /* decompress and handle errors */
- ret = inflate(strm, Z_NO_FLUSH);
- if (ret == Z_STREAM_ERROR || ret == Z_NEED_DICT) {
- gz_error(state, Z_STREAM_ERROR,
- "internal error: inflate stream corrupt");
- return -1;
- }
- if (ret == Z_MEM_ERROR) {
- gz_error(state, Z_MEM_ERROR, "out of memory");
- return -1;
- }
- if (ret == Z_DATA_ERROR) { /* deflate stream invalid */
- gz_error(state, Z_DATA_ERROR,
- strm->msg == NULL ? "compressed data error" : strm->msg);
- return -1;
- }
- } while (strm->avail_out && ret != Z_STREAM_END);
-
- /* update available output */
- state->x.have = had - strm->avail_out;
- state->x.next = strm->next_out - state->x.have;
-
- /* if the gzip stream completed successfully, look for another */
- if (ret == Z_STREAM_END)
- state->how = LOOK;
-
- /* good decompression */
- return 0;
-}
-
-/* Fetch data and put it in the output buffer. Assumes state->x.have is 0.
- Data is either copied from the input file or decompressed from the input
- file depending on state->how. If state->how is LOOK, then a gzip header is
- looked for to determine whether to copy or decompress. Returns -1 on error,
- otherwise 0. gz_fetch() will leave state->how as COPY or GZIP unless the
- end of the input file has been reached and all data has been processed. */
-local int gz_fetch(state)
- gz_statep state;
-{
- z_streamp strm = &(state->strm);
-
- do {
- switch(state->how) {
- case LOOK: /* -> LOOK, COPY (only if never GZIP), or GZIP */
- if (gz_look(state) == -1)
- return -1;
- if (state->how == LOOK)
- return 0;
- break;
- case COPY: /* -> COPY */
- if (gz_load(state, state->out, state->size << 1, &(state->x.have))
- == -1)
- return -1;
- state->x.next = state->out;
- return 0;
- case GZIP: /* -> GZIP or LOOK (if end of gzip stream) */
- strm->avail_out = state->size << 1;
- strm->next_out = state->out;
- if (gz_decomp(state) == -1)
- return -1;
- }
- } while (state->x.have == 0 && (!state->eof || strm->avail_in));
- return 0;
-}
-
-/* Skip len uncompressed bytes of output. Return -1 on error, 0 on success. */
-local int gz_skip(state, len)
- gz_statep state;
- z_off64_t len;
-{
- unsigned n;
-
- /* skip over len bytes or reach end-of-file, whichever comes first */
- while (len)
- /* skip over whatever is in output buffer */
- if (state->x.have) {
- n = GT_OFF(state->x.have) || (z_off64_t)state->x.have > len ?
- (unsigned)len : state->x.have;
- state->x.have -= n;
- state->x.next += n;
- state->x.pos += n;
- len -= n;
- }
-
- /* output buffer empty -- return if we're at the end of the input */
- else if (state->eof && state->strm.avail_in == 0)
- break;
-
- /* need more data to skip -- load up output buffer */
- else {
- /* get more output, looking for header if required */
- if (gz_fetch(state) == -1)
- return -1;
- }
- return 0;
-}
-
-/* -- see zlib.h -- */
-int ZEXPORT gzread(file, buf, len)
- gzFile file;
- voidp buf;
- unsigned len;
-{
- unsigned got, n;
- gz_statep state;
- z_streamp strm;
-
- /* get internal structure */
- if (file == NULL)
- return -1;
- state = (gz_statep)file;
- strm = &(state->strm);
-
- /* check that we're reading and that there's no (serious) error */
- if (state->mode != GZ_READ ||
- (state->err != Z_OK && state->err != Z_BUF_ERROR))
- return -1;
-
- /* since an int is returned, make sure len fits in one, otherwise return
- with an error (this avoids the flaw in the interface) */
- if ((int)len < 0) {
- gz_error(state, Z_DATA_ERROR, "requested length does not fit in int");
- return -1;
- }
-
- /* if len is zero, avoid unnecessary operations */
- if (len == 0)
- return 0;
-
- /* process a skip request */
- if (state->seek) {
- state->seek = 0;
- if (gz_skip(state, state->skip) == -1)
- return -1;
- }
-
- /* get len bytes to buf, or less than len if at the end */
- got = 0;
- do {
- /* first just try copying data from the output buffer */
- if (state->x.have) {
- n = state->x.have > len ? len : state->x.have;
- memcpy(buf, state->x.next, n);
- state->x.next += n;
- state->x.have -= n;
- }
-
- /* output buffer empty -- return if we're at the end of the input */
- else if (state->eof && strm->avail_in == 0) {
- state->past = 1; /* tried to read past end */
- break;
- }
-
- /* need output data -- for small len or new stream load up our output
- buffer */
- else if (state->how == LOOK || len < (state->size << 1)) {
- /* get more output, looking for header if required */
- if (gz_fetch(state) == -1)
- return -1;
- continue; /* no progress yet -- go back to copy above */
- /* the copy above assures that we will leave with space in the
- output buffer, allowing at least one gzungetc() to succeed */
- }
-
- /* large len -- read directly into user buffer */
- else if (state->how == COPY) { /* read directly */
- if (gz_load(state, (unsigned char *)buf, len, &n) == -1)
- return -1;
- }
-
- /* large len -- decompress directly into user buffer */
- else { /* state->how == GZIP */
- strm->avail_out = len;
- strm->next_out = (unsigned char *)buf;
- if (gz_decomp(state) == -1)
- return -1;
- n = state->x.have;
- state->x.have = 0;
- }
-
- /* update progress */
- len -= n;
- buf = (char *)buf + n;
- got += n;
- state->x.pos += n;
- } while (len);
-
- /* return number of bytes read into user buffer (will fit in int) */
- return (int)got;
-}
-
-/* -- see zlib.h -- */
-#ifdef Z_PREFIX_SET
-# undef z_gzgetc
-#else
-# undef gzgetc
-#endif
-int ZEXPORT gzgetc(file)
- gzFile file;
-{
- int ret;
- unsigned char buf[1];
- gz_statep state;
-
- /* get internal structure */
- if (file == NULL)
- return -1;
- state = (gz_statep)file;
-
- /* check that we're reading and that there's no (serious) error */
- if (state->mode != GZ_READ ||
- (state->err != Z_OK && state->err != Z_BUF_ERROR))
- return -1;
-
- /* try output buffer (no need to check for skip request) */
- if (state->x.have) {
- state->x.have--;
- state->x.pos++;
- return *(state->x.next)++;
- }
-
- /* nothing there -- try gzread() */
- ret = gzread(file, buf, 1);
- return ret < 1 ? -1 : buf[0];
-}
-
-int ZEXPORT gzgetc_(file)
-gzFile file;
-{
- return gzgetc(file);
-}
-
-/* -- see zlib.h -- */
-int ZEXPORT gzungetc(c, file)
- int c;
- gzFile file;
-{
- gz_statep state;
-
- /* get internal structure */
- if (file == NULL)
- return -1;
- state = (gz_statep)file;
-
- /* check that we're reading and that there's no (serious) error */
- if (state->mode != GZ_READ ||
- (state->err != Z_OK && state->err != Z_BUF_ERROR))
- return -1;
-
- /* process a skip request */
- if (state->seek) {
- state->seek = 0;
- if (gz_skip(state, state->skip) == -1)
- return -1;
- }
-
- /* can't push EOF */
- if (c < 0)
- return -1;
-
- /* if output buffer empty, put byte at end (allows more pushing) */
- if (state->x.have == 0) {
- state->x.have = 1;
- state->x.next = state->out + (state->size << 1) - 1;
- state->x.next[0] = c;
- state->x.pos--;
- state->past = 0;
- return c;
- }
-
- /* if no room, give up (must have already done a gzungetc()) */
- if (state->x.have == (state->size << 1)) {
- gz_error(state, Z_DATA_ERROR, "out of room to push characters");
- return -1;
- }
-
- /* slide output data if needed and insert byte before existing data */
- if (state->x.next == state->out) {
- unsigned char *src = state->out + state->x.have;
- unsigned char *dest = state->out + (state->size << 1);
- while (src > state->out)
- *--dest = *--src;
- state->x.next = dest;
- }
- state->x.have++;
- state->x.next--;
- state->x.next[0] = c;
- state->x.pos--;
- state->past = 0;
- return c;
-}
-
-/* -- see zlib.h -- */
-char * ZEXPORT gzgets(file, buf, len)
- gzFile file;
- char *buf;
- int len;
-{
- unsigned left, n;
- char *str;
- unsigned char *eol;
- gz_statep state;
-
- /* check parameters and get internal structure */
- if (file == NULL || buf == NULL || len < 1)
- return NULL;
- state = (gz_statep)file;
-
- /* check that we're reading and that there's no (serious) error */
- if (state->mode != GZ_READ ||
- (state->err != Z_OK && state->err != Z_BUF_ERROR))
- return NULL;
-
- /* process a skip request */
- if (state->seek) {
- state->seek = 0;
- if (gz_skip(state, state->skip) == -1)
- return NULL;
- }
-
- /* copy output bytes up to new line or len - 1, whichever comes first --
- append a terminating zero to the string (we don't check for a zero in
- the contents, let the user worry about that) */
- str = buf;
- left = (unsigned)len - 1;
- if (left) do {
- /* assure that something is in the output buffer */
- if (state->x.have == 0 && gz_fetch(state) == -1)
- return NULL; /* error */
- if (state->x.have == 0) { /* end of file */
- state->past = 1; /* read past end */
- break; /* return what we have */
- }
-
- /* look for end-of-line in current output buffer */
- n = state->x.have > left ? left : state->x.have;
- eol = (unsigned char *)memchr(state->x.next, '\n', n);
- if (eol != NULL)
- n = (unsigned)(eol - state->x.next) + 1;
-
- /* copy through end-of-line, or remainder if not found */
- memcpy(buf, state->x.next, n);
- state->x.have -= n;
- state->x.next += n;
- state->x.pos += n;
- left -= n;
- buf += n;
- } while (left && eol == NULL);
-
- /* return terminated string, or if nothing, end of file */
- if (buf == str)
- return NULL;
- buf[0] = 0;
- return str;
-}
-
-/* -- see zlib.h -- */
-int ZEXPORT gzdirect(file)
- gzFile file;
-{
- gz_statep state;
-
- /* get internal structure */
- if (file == NULL)
- return 0;
- state = (gz_statep)file;
-
- /* if the state is not known, but we can find out, then do so (this is
- mainly for right after a gzopen() or gzdopen()) */
- if (state->mode == GZ_READ && state->how == LOOK && state->x.have == 0)
- (void)gz_look(state);
-
- /* return 1 if transparent, 0 if processing a gzip stream */
- return state->direct;
-}
-
-/* -- see zlib.h -- */
-int ZEXPORT gzclose_r(file)
- gzFile file;
-{
- int ret, err;
- gz_statep state;
-
- /* get internal structure */
- if (file == NULL)
- return Z_STREAM_ERROR;
- state = (gz_statep)file;
-
- /* check that we're reading */
- if (state->mode != GZ_READ)
- return Z_STREAM_ERROR;
-
- /* free memory and close file */
- if (state->size) {
- inflateEnd(&(state->strm));
- free(state->out);
- free(state->in);
- }
- err = state->err == Z_BUF_ERROR ? Z_BUF_ERROR : Z_OK;
- gz_error(state, Z_OK, NULL);
- free(state->path);
- ret = close(state->fd);
- free(state);
- return ret ? Z_ERRNO : err;
-}
diff --git a/third-party/zlib/gzwrite.c b/third-party/zlib/gzwrite.c
deleted file mode 100644
index aa767fb..0000000
--- a/third-party/zlib/gzwrite.c
+++ /dev/null
@@ -1,577 +0,0 @@
-/* gzwrite.c -- zlib functions for writing gzip files
- * Copyright (C) 2004, 2005, 2010, 2011, 2012, 2013 Mark Adler
- * For conditions of distribution and use, see copyright notice in zlib.h
- */
-
-#include "gzguts.h"
-
-/* Local functions */
-local int gz_init OF((gz_statep));
-local int gz_comp OF((gz_statep, int));
-local int gz_zero OF((gz_statep, z_off64_t));
-
-/* Initialize state for writing a gzip file. Mark initialization by setting
- state->size to non-zero. Return -1 on failure or 0 on success. */
-local int gz_init(state)
- gz_statep state;
-{
- int ret;
- z_streamp strm = &(state->strm);
-
- /* allocate input buffer */
- state->in = (unsigned char *)malloc(state->want);
- if (state->in == NULL) {
- gz_error(state, Z_MEM_ERROR, "out of memory");
- return -1;
- }
-
- /* only need output buffer and deflate state if compressing */
- if (!state->direct) {
- /* allocate output buffer */
- state->out = (unsigned char *)malloc(state->want);
- if (state->out == NULL) {
- free(state->in);
- gz_error(state, Z_MEM_ERROR, "out of memory");
- return -1;
- }
-
- /* allocate deflate memory, set up for gzip compression */
- strm->zalloc = Z_NULL;
- strm->zfree = Z_NULL;
- strm->opaque = Z_NULL;
- ret = deflateInit2(strm, state->level, Z_DEFLATED,
- MAX_WBITS + 16, DEF_MEM_LEVEL, state->strategy);
- if (ret != Z_OK) {
- free(state->out);
- free(state->in);
- gz_error(state, Z_MEM_ERROR, "out of memory");
- return -1;
- }
- }
-
- /* mark state as initialized */
- state->size = state->want;
-
- /* initialize write buffer if compressing */
- if (!state->direct) {
- strm->avail_out = state->size;
- strm->next_out = state->out;
- state->x.next = strm->next_out;
- }
- return 0;
-}
-
-/* Compress whatever is at avail_in and next_in and write to the output file.
- Return -1 if there is an error writing to the output file, otherwise 0.
- flush is assumed to be a valid deflate() flush value. If flush is Z_FINISH,
- then the deflate() state is reset to start a new gzip stream. If gz->direct
- is true, then simply write to the output file without compressing, and
- ignore flush. */
-local int gz_comp(state, flush)
- gz_statep state;
- int flush;
-{
- int ret, got;
- unsigned have;
- z_streamp strm = &(state->strm);
-
- /* allocate memory if this is the first time through */
- if (state->size == 0 && gz_init(state) == -1)
- return -1;
-
- /* write directly if requested */
- if (state->direct) {
- got = write(state->fd, strm->next_in, strm->avail_in);
- if (got < 0 || (unsigned)got != strm->avail_in) {
- gz_error(state, Z_ERRNO, zstrerror());
- return -1;
- }
- strm->avail_in = 0;
- return 0;
- }
-
- /* run deflate() on provided input until it produces no more output */
- ret = Z_OK;
- do {
- /* write out current buffer contents if full, or if flushing, but if
- doing Z_FINISH then don't write until we get to Z_STREAM_END */
- if (strm->avail_out == 0 || (flush != Z_NO_FLUSH &&
- (flush != Z_FINISH || ret == Z_STREAM_END))) {
- have = (unsigned)(strm->next_out - state->x.next);
- if (have && ((got = write(state->fd, state->x.next, have)) < 0 ||
- (unsigned)got != have)) {
- gz_error(state, Z_ERRNO, zstrerror());
- return -1;
- }
- if (strm->avail_out == 0) {
- strm->avail_out = state->size;
- strm->next_out = state->out;
- }
- state->x.next = strm->next_out;
- }
-
- /* compress */
- have = strm->avail_out;
- ret = deflate(strm, flush);
- if (ret == Z_STREAM_ERROR) {
- gz_error(state, Z_STREAM_ERROR,
- "internal error: deflate stream corrupt");
- return -1;
- }
- have -= strm->avail_out;
- } while (have);
-
- /* if that completed a deflate stream, allow another to start */
- if (flush == Z_FINISH)
- deflateReset(strm);
-
- /* all done, no errors */
- return 0;
-}
-
-/* Compress len zeros to output. Return -1 on error, 0 on success. */
-local int gz_zero(state, len)
- gz_statep state;
- z_off64_t len;
-{
- int first;
- unsigned n;
- z_streamp strm = &(state->strm);
-
- /* consume whatever's left in the input buffer */
- if (strm->avail_in && gz_comp(state, Z_NO_FLUSH) == -1)
- return -1;
-
- /* compress len zeros (len guaranteed > 0) */
- first = 1;
- while (len) {
- n = GT_OFF(state->size) || (z_off64_t)state->size > len ?
- (unsigned)len : state->size;
- if (first) {
- memset(state->in, 0, n);
- first = 0;
- }
- strm->avail_in = n;
- strm->next_in = state->in;
- state->x.pos += n;
- if (gz_comp(state, Z_NO_FLUSH) == -1)
- return -1;
- len -= n;
- }
- return 0;
-}
-
-/* -- see zlib.h -- */
-int ZEXPORT gzwrite(file, buf, len)
- gzFile file;
- voidpc buf;
- unsigned len;
-{
- unsigned put = len;
- gz_statep state;
- z_streamp strm;
-
- /* get internal structure */
- if (file == NULL)
- return 0;
- state = (gz_statep)file;
- strm = &(state->strm);
-
- /* check that we're writing and that there's no error */
- if (state->mode != GZ_WRITE || state->err != Z_OK)
- return 0;
-
- /* since an int is returned, make sure len fits in one, otherwise return
- with an error (this avoids the flaw in the interface) */
- if ((int)len < 0) {
- gz_error(state, Z_DATA_ERROR, "requested length does not fit in int");
- return 0;
- }
-
- /* if len is zero, avoid unnecessary operations */
- if (len == 0)
- return 0;
-
- /* allocate memory if this is the first time through */
- if (state->size == 0 && gz_init(state) == -1)
- return 0;
-
- /* check for seek request */
- if (state->seek) {
- state->seek = 0;
- if (gz_zero(state, state->skip) == -1)
- return 0;
- }
-
- /* for small len, copy to input buffer, otherwise compress directly */
- if (len < state->size) {
- /* copy to input buffer, compress when full */
- do {
- unsigned have, copy;
-
- if (strm->avail_in == 0)
- strm->next_in = state->in;
- have = (unsigned)((strm->next_in + strm->avail_in) - state->in);
- copy = state->size - have;
- if (copy > len)
- copy = len;
- memcpy(state->in + have, buf, copy);
- strm->avail_in += copy;
- state->x.pos += copy;
- buf = (const char *)buf + copy;
- len -= copy;
- if (len && gz_comp(state, Z_NO_FLUSH) == -1)
- return 0;
- } while (len);
- }
- else {
- /* consume whatever's left in the input buffer */
- if (strm->avail_in && gz_comp(state, Z_NO_FLUSH) == -1)
- return 0;
-
- /* directly compress user buffer to file */
- strm->avail_in = len;
- strm->next_in = (z_const Bytef *)buf;
- state->x.pos += len;
- if (gz_comp(state, Z_NO_FLUSH) == -1)
- return 0;
- }
-
- /* input was all buffered or compressed (put will fit in int) */
- return (int)put;
-}
-
-/* -- see zlib.h -- */
-int ZEXPORT gzputc(file, c)
- gzFile file;
- int c;
-{
- unsigned have;
- unsigned char buf[1];
- gz_statep state;
- z_streamp strm;
-
- /* get internal structure */
- if (file == NULL)
- return -1;
- state = (gz_statep)file;
- strm = &(state->strm);
-
- /* check that we're writing and that there's no error */
- if (state->mode != GZ_WRITE || state->err != Z_OK)
- return -1;
-
- /* check for seek request */
- if (state->seek) {
- state->seek = 0;
- if (gz_zero(state, state->skip) == -1)
- return -1;
- }
-
- /* try writing to input buffer for speed (state->size == 0 if buffer not
- initialized) */
- if (state->size) {
- if (strm->avail_in == 0)
- strm->next_in = state->in;
- have = (unsigned)((strm->next_in + strm->avail_in) - state->in);
- if (have < state->size) {
- state->in[have] = c;
- strm->avail_in++;
- state->x.pos++;
- return c & 0xff;
- }
- }
-
- /* no room in buffer or not initialized, use gz_write() */
- buf[0] = c;
- if (gzwrite(file, buf, 1) != 1)
- return -1;
- return c & 0xff;
-}
-
-/* -- see zlib.h -- */
-int ZEXPORT gzputs(file, str)
- gzFile file;
- const char *str;
-{
- int ret;
- unsigned len;
-
- /* write string */
- len = (unsigned)strlen(str);
- ret = gzwrite(file, str, len);
- return ret == 0 && len != 0 ? -1 : ret;
-}
-
-#if defined(STDC) || defined(Z_HAVE_STDARG_H)
-#include <stdarg.h>
-
-/* -- see zlib.h -- */
-int ZEXPORTVA gzvprintf(gzFile file, const char *format, va_list va)
-{
- int size, len;
- gz_statep state;
- z_streamp strm;
-
- /* get internal structure */
- if (file == NULL)
- return -1;
- state = (gz_statep)file;
- strm = &(state->strm);
-
- /* check that we're writing and that there's no error */
- if (state->mode != GZ_WRITE || state->err != Z_OK)
- return 0;
-
- /* make sure we have some buffer space */
- if (state->size == 0 && gz_init(state) == -1)
- return 0;
-
- /* check for seek request */
- if (state->seek) {
- state->seek = 0;
- if (gz_zero(state, state->skip) == -1)
- return 0;
- }
-
- /* consume whatever's left in the input buffer */
- if (strm->avail_in && gz_comp(state, Z_NO_FLUSH) == -1)
- return 0;
-
- /* do the printf() into the input buffer, put length in len */
- size = (int)(state->size);
- state->in[size - 1] = 0;
-#ifdef NO_vsnprintf
-# ifdef HAS_vsprintf_void
- (void)vsprintf((char *)(state->in), format, va);
- for (len = 0; len < size; len++)
- if (state->in[len] == 0) break;
-# else
- len = vsprintf((char *)(state->in), format, va);
-# endif
-#else
-# ifdef HAS_vsnprintf_void
- (void)vsnprintf((char *)(state->in), size, format, va);
- len = strlen((char *)(state->in));
-# else
- len = vsnprintf((char *)(state->in), size, format, va);
-# endif
-#endif
-
- /* check that printf() results fit in buffer */
- if (len <= 0 || len >= (int)size || state->in[size - 1] != 0)
- return 0;
-
- /* update buffer and position, defer compression until needed */
- strm->avail_in = (unsigned)len;
- strm->next_in = state->in;
- state->x.pos += len;
- return len;
-}
-
-int ZEXPORTVA gzprintf(gzFile file, const char *format, ...)
-{
- va_list va;
- int ret;
-
- va_start(va, format);
- ret = gzvprintf(file, format, va);
- va_end(va);
- return ret;
-}
-
-#else /* !STDC && !Z_HAVE_STDARG_H */
-
-/* -- see zlib.h -- */
-int ZEXPORTVA gzprintf (file, format, a1, a2, a3, a4, a5, a6, a7, a8, a9, a10,
- a11, a12, a13, a14, a15, a16, a17, a18, a19, a20)
- gzFile file;
- const char *format;
- int a1, a2, a3, a4, a5, a6, a7, a8, a9, a10,
- a11, a12, a13, a14, a15, a16, a17, a18, a19, a20;
-{
- int size, len;
- gz_statep state;
- z_streamp strm;
-
- /* get internal structure */
- if (file == NULL)
- return -1;
- state = (gz_statep)file;
- strm = &(state->strm);
-
- /* check that can really pass pointer in ints */
- if (sizeof(int) != sizeof(void *))
- return 0;
-
- /* check that we're writing and that there's no error */
- if (state->mode != GZ_WRITE || state->err != Z_OK)
- return 0;
-
- /* make sure we have some buffer space */
- if (state->size == 0 && gz_init(state) == -1)
- return 0;
-
- /* check for seek request */
- if (state->seek) {
- state->seek = 0;
- if (gz_zero(state, state->skip) == -1)
- return 0;
- }
-
- /* consume whatever's left in the input buffer */
- if (strm->avail_in && gz_comp(state, Z_NO_FLUSH) == -1)
- return 0;
-
- /* do the printf() into the input buffer, put length in len */
- size = (int)(state->size);
- state->in[size - 1] = 0;
-#ifdef NO_snprintf
-# ifdef HAS_sprintf_void
- sprintf((char *)(state->in), format, a1, a2, a3, a4, a5, a6, a7, a8,
- a9, a10, a11, a12, a13, a14, a15, a16, a17, a18, a19, a20);
- for (len = 0; len < size; len++)
- if (state->in[len] == 0) break;
-# else
- len = sprintf((char *)(state->in), format, a1, a2, a3, a4, a5, a6, a7, a8,
- a9, a10, a11, a12, a13, a14, a15, a16, a17, a18, a19, a20);
-# endif
-#else
-# ifdef HAS_snprintf_void
- snprintf((char *)(state->in), size, format, a1, a2, a3, a4, a5, a6, a7, a8,
- a9, a10, a11, a12, a13, a14, a15, a16, a17, a18, a19, a20);
- len = strlen((char *)(state->in));
-# else
- len = snprintf((char *)(state->in), size, format, a1, a2, a3, a4, a5, a6,
- a7, a8, a9, a10, a11, a12, a13, a14, a15, a16, a17, a18,
- a19, a20);
-# endif
-#endif
-
- /* check that printf() results fit in buffer */
- if (len <= 0 || len >= (int)size || state->in[size - 1] != 0)
- return 0;
-
- /* update buffer and position, defer compression until needed */
- strm->avail_in = (unsigned)len;
- strm->next_in = state->in;
- state->x.pos += len;
- return len;
-}
-
-#endif
-
-/* -- see zlib.h -- */
-int ZEXPORT gzflush(file, flush)
- gzFile file;
- int flush;
-{
- gz_statep state;
-
- /* get internal structure */
- if (file == NULL)
- return -1;
- state = (gz_statep)file;
-
- /* check that we're writing and that there's no error */
- if (state->mode != GZ_WRITE || state->err != Z_OK)
- return Z_STREAM_ERROR;
-
- /* check flush parameter */
- if (flush < 0 || flush > Z_FINISH)
- return Z_STREAM_ERROR;
-
- /* check for seek request */
- if (state->seek) {
- state->seek = 0;
- if (gz_zero(state, state->skip) == -1)
- return -1;
- }
-
- /* compress remaining data with requested flush */
- gz_comp(state, flush);
- return state->err;
-}
-
-/* -- see zlib.h -- */
-int ZEXPORT gzsetparams(file, level, strategy)
- gzFile file;
- int level;
- int strategy;
-{
- gz_statep state;
- z_streamp strm;
-
- /* get internal structure */
- if (file == NULL)
- return Z_STREAM_ERROR;
- state = (gz_statep)file;
- strm = &(state->strm);
-
- /* check that we're writing and that there's no error */
- if (state->mode != GZ_WRITE || state->err != Z_OK)
- return Z_STREAM_ERROR;
-
- /* if no change is requested, then do nothing */
- if (level == state->level && strategy == state->strategy)
- return Z_OK;
-
- /* check for seek request */
- if (state->seek) {
- state->seek = 0;
- if (gz_zero(state, state->skip) == -1)
- return -1;
- }
-
- /* change compression parameters for subsequent input */
- if (state->size) {
- /* flush previous input with previous parameters before changing */
- if (strm->avail_in && gz_comp(state, Z_PARTIAL_FLUSH) == -1)
- return state->err;
- deflateParams(strm, level, strategy);
- }
- state->level = level;
- state->strategy = strategy;
- return Z_OK;
-}
-
-/* -- see zlib.h -- */
-int ZEXPORT gzclose_w(file)
- gzFile file;
-{
- int ret = Z_OK;
- gz_statep state;
-
- /* get internal structure */
- if (file == NULL)
- return Z_STREAM_ERROR;
- state = (gz_statep)file;
-
- /* check that we're writing */
- if (state->mode != GZ_WRITE)
- return Z_STREAM_ERROR;
-
- /* check for seek request */
- if (state->seek) {
- state->seek = 0;
- if (gz_zero(state, state->skip) == -1)
- ret = state->err;
- }
-
- /* flush, free memory, and close file */
- if (gz_comp(state, Z_FINISH) == -1)
- ret = state->err;
- if (state->size) {
- if (!state->direct) {
- (void)deflateEnd(&(state->strm));
- free(state->out);
- }
- free(state->in);
- }
- gz_error(state, Z_OK, NULL);
- free(state->path);
- if (close(state->fd) == -1)
- ret = Z_ERRNO;
- free(state);
- return ret;
-}
diff --git a/third-party/zlib/infback.c b/third-party/zlib/infback.c
deleted file mode 100644
index f3833c2..0000000
--- a/third-party/zlib/infback.c
+++ /dev/null
@@ -1,640 +0,0 @@
-/* infback.c -- inflate using a call-back interface
- * Copyright (C) 1995-2011 Mark Adler
- * For conditions of distribution and use, see copyright notice in zlib.h
- */
-
-/*
- This code is largely copied from inflate.c. Normally either infback.o or
- inflate.o would be linked into an application--not both. The interface
- with inffast.c is retained so that optimized assembler-coded versions of
- inflate_fast() can be used with either inflate.c or infback.c.
- */
-
-#include "zutil.h"
-#include "inftrees.h"
-#include "inflate.h"
-#include "inffast.h"
-
-/* function prototypes */
-local void fixedtables OF((struct inflate_state FAR *state));
-
-/*
- strm provides memory allocation functions in zalloc and zfree, or
- Z_NULL to use the library memory allocation functions.
-
- windowBits is in the range 8..15, and window is a user-supplied
- window and output buffer that is 2**windowBits bytes.
- */
-int ZEXPORT inflateBackInit_(strm, windowBits, window, version, stream_size)
-z_streamp strm;
-int windowBits;
-unsigned char FAR *window;
-const char *version;
-int stream_size;
-{
- struct inflate_state FAR *state;
-
- if (version == Z_NULL || version[0] != ZLIB_VERSION[0] ||
- stream_size != (int)(sizeof(z_stream)))
- return Z_VERSION_ERROR;
- if (strm == Z_NULL || window == Z_NULL ||
- windowBits < 8 || windowBits > 15)
- return Z_STREAM_ERROR;
- strm->msg = Z_NULL; /* in case we return an error */
- if (strm->zalloc == (alloc_func)0) {
-#ifdef Z_SOLO
- return Z_STREAM_ERROR;
-#else
- strm->zalloc = zcalloc;
- strm->opaque = (voidpf)0;
-#endif
- }
- if (strm->zfree == (free_func)0)
-#ifdef Z_SOLO
- return Z_STREAM_ERROR;
-#else
- strm->zfree = zcfree;
-#endif
- state = (struct inflate_state FAR *)ZALLOC(strm, 1,
- sizeof(struct inflate_state));
- if (state == Z_NULL) return Z_MEM_ERROR;
- Tracev((stderr, "inflate: allocated\n"));
- strm->state = (struct internal_state FAR *)state;
- state->dmax = 32768U;
- state->wbits = windowBits;
- state->wsize = 1U << windowBits;
- state->window = window;
- state->wnext = 0;
- state->whave = 0;
- return Z_OK;
-}
-
-/*
- Return state with length and distance decoding tables and index sizes set to
- fixed code decoding. Normally this returns fixed tables from inffixed.h.
- If BUILDFIXED is defined, then instead this routine builds the tables the
- first time it's called, and returns those tables the first time and
- thereafter. This reduces the size of the code by about 2K bytes, in
- exchange for a little execution time. However, BUILDFIXED should not be
- used for threaded applications, since the rewriting of the tables and virgin
- may not be thread-safe.
- */
-local void fixedtables(state)
-struct inflate_state FAR *state;
-{
-#ifdef BUILDFIXED
- static int virgin = 1;
- static code *lenfix, *distfix;
- static code fixed[544];
-
- /* build fixed huffman tables if first call (may not be thread safe) */
- if (virgin) {
- unsigned sym, bits;
- static code *next;
-
- /* literal/length table */
- sym = 0;
- while (sym < 144) state->lens[sym++] = 8;
- while (sym < 256) state->lens[sym++] = 9;
- while (sym < 280) state->lens[sym++] = 7;
- while (sym < 288) state->lens[sym++] = 8;
- next = fixed;
- lenfix = next;
- bits = 9;
- inflate_table(LENS, state->lens, 288, &(next), &(bits), state->work);
-
- /* distance table */
- sym = 0;
- while (sym < 32) state->lens[sym++] = 5;
- distfix = next;
- bits = 5;
- inflate_table(DISTS, state->lens, 32, &(next), &(bits), state->work);
-
- /* do this just once */
- virgin = 0;
- }
-#else /* !BUILDFIXED */
-# include "inffixed.h"
-#endif /* BUILDFIXED */
- state->lencode = lenfix;
- state->lenbits = 9;
- state->distcode = distfix;
- state->distbits = 5;
-}
-
-/* Macros for inflateBack(): */
-
-/* Load returned state from inflate_fast() */
-#define LOAD() \
- do { \
- put = strm->next_out; \
- left = strm->avail_out; \
- next = strm->next_in; \
- have = strm->avail_in; \
- hold = state->hold; \
- bits = state->bits; \
- } while (0)
-
-/* Set state from registers for inflate_fast() */
-#define RESTORE() \
- do { \
- strm->next_out = put; \
- strm->avail_out = left; \
- strm->next_in = next; \
- strm->avail_in = have; \
- state->hold = hold; \
- state->bits = bits; \
- } while (0)
-
-/* Clear the input bit accumulator */
-#define INITBITS() \
- do { \
- hold = 0; \
- bits = 0; \
- } while (0)
-
-/* Assure that some input is available. If input is requested, but denied,
- then return a Z_BUF_ERROR from inflateBack(). */
-#define PULL() \
- do { \
- if (have == 0) { \
- have = in(in_desc, &next); \
- if (have == 0) { \
- next = Z_NULL; \
- ret = Z_BUF_ERROR; \
- goto inf_leave; \
- } \
- } \
- } while (0)
-
-/* Get a byte of input into the bit accumulator, or return from inflateBack()
- with an error if there is no input available. */
-#define PULLBYTE() \
- do { \
- PULL(); \
- have--; \
- hold += (unsigned long)(*next++) << bits; \
- bits += 8; \
- } while (0)
-
-/* Assure that there are at least n bits in the bit accumulator. If there is
- not enough available input to do that, then return from inflateBack() with
- an error. */
-#define NEEDBITS(n) \
- do { \
- while (bits < (unsigned)(n)) \
- PULLBYTE(); \
- } while (0)
-
-/* Return the low n bits of the bit accumulator (n < 16) */
-#define BITS(n) \
- ((unsigned)hold & ((1U << (n)) - 1))
-
-/* Remove n bits from the bit accumulator */
-#define DROPBITS(n) \
- do { \
- hold >>= (n); \
- bits -= (unsigned)(n); \
- } while (0)
-
-/* Remove zero to seven bits as needed to go to a byte boundary */
-#define BYTEBITS() \
- do { \
- hold >>= bits & 7; \
- bits -= bits & 7; \
- } while (0)
-
-/* Assure that some output space is available, by writing out the window
- if it's full. If the write fails, return from inflateBack() with a
- Z_BUF_ERROR. */
-#define ROOM() \
- do { \
- if (left == 0) { \
- put = state->window; \
- left = state->wsize; \
- state->whave = left; \
- if (out(out_desc, put, left)) { \
- ret = Z_BUF_ERROR; \
- goto inf_leave; \
- } \
- } \
- } while (0)
-
-/*
- strm provides the memory allocation functions and window buffer on input,
- and provides information on the unused input on return. For Z_DATA_ERROR
- returns, strm will also provide an error message.
-
- in() and out() are the call-back input and output functions. When
- inflateBack() needs more input, it calls in(). When inflateBack() has
- filled the window with output, or when it completes with data in the
- window, it calls out() to write out the data. The application must not
- change the provided input until in() is called again or inflateBack()
- returns. The application must not change the window/output buffer until
- inflateBack() returns.
-
- in() and out() are called with a descriptor parameter provided in the
- inflateBack() call. This parameter can be a structure that provides the
- information required to do the read or write, as well as accumulated
- information on the input and output such as totals and check values.
-
- in() should return zero on failure. out() should return non-zero on
- failure. If either in() or out() fails, than inflateBack() returns a
- Z_BUF_ERROR. strm->next_in can be checked for Z_NULL to see whether it
- was in() or out() that caused in the error. Otherwise, inflateBack()
- returns Z_STREAM_END on success, Z_DATA_ERROR for an deflate format
- error, or Z_MEM_ERROR if it could not allocate memory for the state.
- inflateBack() can also return Z_STREAM_ERROR if the input parameters
- are not correct, i.e. strm is Z_NULL or the state was not initialized.
- */
-int ZEXPORT inflateBack(strm, in, in_desc, out, out_desc)
-z_streamp strm;
-in_func in;
-void FAR *in_desc;
-out_func out;
-void FAR *out_desc;
-{
- struct inflate_state FAR *state;
- z_const unsigned char FAR *next; /* next input */
- unsigned char FAR *put; /* next output */
- unsigned have, left; /* available input and output */
- unsigned long hold; /* bit buffer */
- unsigned bits; /* bits in bit buffer */
- unsigned copy; /* number of stored or match bytes to copy */
- unsigned char FAR *from; /* where to copy match bytes from */
- code here; /* current decoding table entry */
- code last; /* parent table entry */
- unsigned len; /* length to copy for repeats, bits to drop */
- int ret; /* return code */
- static const unsigned short order[19] = /* permutation of code lengths */
- {16, 17, 18, 0, 8, 7, 9, 6, 10, 5, 11, 4, 12, 3, 13, 2, 14, 1, 15};
-
- /* Check that the strm exists and that the state was initialized */
- if (strm == Z_NULL || strm->state == Z_NULL)
- return Z_STREAM_ERROR;
- state = (struct inflate_state FAR *)strm->state;
-
- /* Reset the state */
- strm->msg = Z_NULL;
- state->mode = TYPE;
- state->last = 0;
- state->whave = 0;
- next = strm->next_in;
- have = next != Z_NULL ? strm->avail_in : 0;
- hold = 0;
- bits = 0;
- put = state->window;
- left = state->wsize;
-
- /* Inflate until end of block marked as last */
- for (;;)
- switch (state->mode) {
- case TYPE:
- /* determine and dispatch block type */
- if (state->last) {
- BYTEBITS();
- state->mode = DONE;
- break;
- }
- NEEDBITS(3);
- state->last = BITS(1);
- DROPBITS(1);
- switch (BITS(2)) {
- case 0: /* stored block */
- Tracev((stderr, "inflate: stored block%s\n",
- state->last ? " (last)" : ""));
- state->mode = STORED;
- break;
- case 1: /* fixed block */
- fixedtables(state);
- Tracev((stderr, "inflate: fixed codes block%s\n",
- state->last ? " (last)" : ""));
- state->mode = LEN; /* decode codes */
- break;
- case 2: /* dynamic block */
- Tracev((stderr, "inflate: dynamic codes block%s\n",
- state->last ? " (last)" : ""));
- state->mode = TABLE;
- break;
- case 3:
- strm->msg = (char *)"invalid block type";
- state->mode = BAD;
- }
- DROPBITS(2);
- break;
-
- case STORED:
- /* get and verify stored block length */
- BYTEBITS(); /* go to byte boundary */
- NEEDBITS(32);
- if ((hold & 0xffff) != ((hold >> 16) ^ 0xffff)) {
- strm->msg = (char *)"invalid stored block lengths";
- state->mode = BAD;
- break;
- }
- state->length = (unsigned)hold & 0xffff;
- Tracev((stderr, "inflate: stored length %u\n",
- state->length));
- INITBITS();
-
- /* copy stored block from input to output */
- while (state->length != 0) {
- copy = state->length;
- PULL();
- ROOM();
- if (copy > have) copy = have;
- if (copy > left) copy = left;
- zmemcpy(put, next, copy);
- have -= copy;
- next += copy;
- left -= copy;
- put += copy;
- state->length -= copy;
- }
- Tracev((stderr, "inflate: stored end\n"));
- state->mode = TYPE;
- break;
-
- case TABLE:
- /* get dynamic table entries descriptor */
- NEEDBITS(14);
- state->nlen = BITS(5) + 257;
- DROPBITS(5);
- state->ndist = BITS(5) + 1;
- DROPBITS(5);
- state->ncode = BITS(4) + 4;
- DROPBITS(4);
-#ifndef PKZIP_BUG_WORKAROUND
- if (state->nlen > 286 || state->ndist > 30) {
- strm->msg = (char *)"too many length or distance symbols";
- state->mode = BAD;
- break;
- }
-#endif
- Tracev((stderr, "inflate: table sizes ok\n"));
-
- /* get code length code lengths (not a typo) */
- state->have = 0;
- while (state->have < state->ncode) {
- NEEDBITS(3);
- state->lens[order[state->have++]] = (unsigned short)BITS(3);
- DROPBITS(3);
- }
- while (state->have < 19)
- state->lens[order[state->have++]] = 0;
- state->next = state->codes;
- state->lencode = (code const FAR *)(state->next);
- state->lenbits = 7;
- ret = inflate_table(CODES, state->lens, 19, &(state->next),
- &(state->lenbits), state->work);
- if (ret) {
- strm->msg = (char *)"invalid code lengths set";
- state->mode = BAD;
- break;
- }
- Tracev((stderr, "inflate: code lengths ok\n"));
-
- /* get length and distance code code lengths */
- state->have = 0;
- while (state->have < state->nlen + state->ndist) {
- for (;;) {
- here = state->lencode[BITS(state->lenbits)];
- if ((unsigned)(here.bits) <= bits) break;
- PULLBYTE();
- }
- if (here.val < 16) {
- DROPBITS(here.bits);
- state->lens[state->have++] = here.val;
- }
- else {
- if (here.val == 16) {
- NEEDBITS(here.bits + 2);
- DROPBITS(here.bits);
- if (state->have == 0) {
- strm->msg = (char *)"invalid bit length repeat";
- state->mode = BAD;
- break;
- }
- len = (unsigned)(state->lens[state->have - 1]);
- copy = 3 + BITS(2);
- DROPBITS(2);
- }
- else if (here.val == 17) {
- NEEDBITS(here.bits + 3);
- DROPBITS(here.bits);
- len = 0;
- copy = 3 + BITS(3);
- DROPBITS(3);
- }
- else {
- NEEDBITS(here.bits + 7);
- DROPBITS(here.bits);
- len = 0;
- copy = 11 + BITS(7);
- DROPBITS(7);
- }
- if (state->have + copy > state->nlen + state->ndist) {
- strm->msg = (char *)"invalid bit length repeat";
- state->mode = BAD;
- break;
- }
- while (copy--)
- state->lens[state->have++] = (unsigned short)len;
- }
- }
-
- /* handle error breaks in while */
- if (state->mode == BAD) break;
-
- /* check for end-of-block code (better have one) */
- if (state->lens[256] == 0) {
- strm->msg = (char *)"invalid code -- missing end-of-block";
- state->mode = BAD;
- break;
- }
-
- /* build code tables -- note: do not change the lenbits or distbits
- values here (9 and 6) without reading the comments in inftrees.h
- concerning the ENOUGH constants, which depend on those values */
- state->next = state->codes;
- state->lencode = (code const FAR *)(state->next);
- state->lenbits = 9;
- ret = inflate_table(LENS, state->lens, state->nlen, &(state->next),
- &(state->lenbits), state->work);
- if (ret) {
- strm->msg = (char *)"invalid literal/lengths set";
- state->mode = BAD;
- break;
- }
- state->distcode = (code const FAR *)(state->next);
- state->distbits = 6;
- ret = inflate_table(DISTS, state->lens + state->nlen, state->ndist,
- &(state->next), &(state->distbits), state->work);
- if (ret) {
- strm->msg = (char *)"invalid distances set";
- state->mode = BAD;
- break;
- }
- Tracev((stderr, "inflate: codes ok\n"));
- state->mode = LEN;
-
- case LEN:
- /* use inflate_fast() if we have enough input and output */
- if (have >= 6 && left >= 258) {
- RESTORE();
- if (state->whave < state->wsize)
- state->whave = state->wsize - left;
- inflate_fast(strm, state->wsize);
- LOAD();
- break;
- }
-
- /* get a literal, length, or end-of-block code */
- for (;;) {
- here = state->lencode[BITS(state->lenbits)];
- if ((unsigned)(here.bits) <= bits) break;
- PULLBYTE();
- }
- if (here.op && (here.op & 0xf0) == 0) {
- last = here;
- for (;;) {
- here = state->lencode[last.val +
- (BITS(last.bits + last.op) >> last.bits)];
- if ((unsigned)(last.bits + here.bits) <= bits) break;
- PULLBYTE();
- }
- DROPBITS(last.bits);
- }
- DROPBITS(here.bits);
- state->length = (unsigned)here.val;
-
- /* process literal */
- if (here.op == 0) {
- Tracevv((stderr, here.val >= 0x20 && here.val < 0x7f ?
- "inflate: literal '%c'\n" :
- "inflate: literal 0x%02x\n", here.val));
- ROOM();
- *put++ = (unsigned char)(state->length);
- left--;
- state->mode = LEN;
- break;
- }
-
- /* process end of block */
- if (here.op & 32) {
- Tracevv((stderr, "inflate: end of block\n"));
- state->mode = TYPE;
- break;
- }
-
- /* invalid code */
- if (here.op & 64) {
- strm->msg = (char *)"invalid literal/length code";
- state->mode = BAD;
- break;
- }
-
- /* length code -- get extra bits, if any */
- state->extra = (unsigned)(here.op) & 15;
- if (state->extra != 0) {
- NEEDBITS(state->extra);
- state->length += BITS(state->extra);
- DROPBITS(state->extra);
- }
- Tracevv((stderr, "inflate: length %u\n", state->length));
-
- /* get distance code */
- for (;;) {
- here = state->distcode[BITS(state->distbits)];
- if ((unsigned)(here.bits) <= bits) break;
- PULLBYTE();
- }
- if ((here.op & 0xf0) == 0) {
- last = here;
- for (;;) {
- here = state->distcode[last.val +
- (BITS(last.bits + last.op) >> last.bits)];
- if ((unsigned)(last.bits + here.bits) <= bits) break;
- PULLBYTE();
- }
- DROPBITS(last.bits);
- }
- DROPBITS(here.bits);
- if (here.op & 64) {
- strm->msg = (char *)"invalid distance code";
- state->mode = BAD;
- break;
- }
- state->offset = (unsigned)here.val;
-
- /* get distance extra bits, if any */
- state->extra = (unsigned)(here.op) & 15;
- if (state->extra != 0) {
- NEEDBITS(state->extra);
- state->offset += BITS(state->extra);
- DROPBITS(state->extra);
- }
- if (state->offset > state->wsize - (state->whave < state->wsize ?
- left : 0)) {
- strm->msg = (char *)"invalid distance too far back";
- state->mode = BAD;
- break;
- }
- Tracevv((stderr, "inflate: distance %u\n", state->offset));
-
- /* copy match from window to output */
- do {
- ROOM();
- copy = state->wsize - state->offset;
- if (copy < left) {
- from = put + copy;
- copy = left - copy;
- }
- else {
- from = put - state->offset;
- copy = left;
- }
- if (copy > state->length) copy = state->length;
- state->length -= copy;
- left -= copy;
- do {
- *put++ = *from++;
- } while (--copy);
- } while (state->length != 0);
- break;
-
- case DONE:
- /* inflate stream terminated properly -- write leftover output */
- ret = Z_STREAM_END;
- if (left < state->wsize) {
- if (out(out_desc, state->window, state->wsize - left))
- ret = Z_BUF_ERROR;
- }
- goto inf_leave;
-
- case BAD:
- ret = Z_DATA_ERROR;
- goto inf_leave;
-
- default: /* can't happen, but makes compilers happy */
- ret = Z_STREAM_ERROR;
- goto inf_leave;
- }
-
- /* Return unused input */
- inf_leave:
- strm->next_in = next;
- strm->avail_in = have;
- return ret;
-}
-
-int ZEXPORT inflateBackEnd(strm)
-z_streamp strm;
-{
- if (strm == Z_NULL || strm->state == Z_NULL || strm->zfree == (free_func)0)
- return Z_STREAM_ERROR;
- ZFREE(strm, strm->state);
- strm->state = Z_NULL;
- Tracev((stderr, "inflate: end\n"));
- return Z_OK;
-}
diff --git a/third-party/zlib/inffast.c b/third-party/zlib/inffast.c
deleted file mode 100644
index bda59ce..0000000
--- a/third-party/zlib/inffast.c
+++ /dev/null
@@ -1,340 +0,0 @@
-/* inffast.c -- fast decoding
- * Copyright (C) 1995-2008, 2010, 2013 Mark Adler
- * For conditions of distribution and use, see copyright notice in zlib.h
- */
-
-#include "zutil.h"
-#include "inftrees.h"
-#include "inflate.h"
-#include "inffast.h"
-
-#ifndef ASMINF
-
-/* Allow machine dependent optimization for post-increment or pre-increment.
- Based on testing to date,
- Pre-increment preferred for:
- - PowerPC G3 (Adler)
- - MIPS R5000 (Randers-Pehrson)
- Post-increment preferred for:
- - none
- No measurable difference:
- - Pentium III (Anderson)
- - M68060 (Nikl)
- */
-#ifdef POSTINC
-# define OFF 0
-# define PUP(a) *(a)++
-#else
-# define OFF 1
-# define PUP(a) *++(a)
-#endif
-
-/*
- Decode literal, length, and distance codes and write out the resulting
- literal and match bytes until either not enough input or output is
- available, an end-of-block is encountered, or a data error is encountered.
- When large enough input and output buffers are supplied to inflate(), for
- example, a 16K input buffer and a 64K output buffer, more than 95% of the
- inflate execution time is spent in this routine.
-
- Entry assumptions:
-
- state->mode == LEN
- strm->avail_in >= 6
- strm->avail_out >= 258
- start >= strm->avail_out
- state->bits < 8
-
- On return, state->mode is one of:
-
- LEN -- ran out of enough output space or enough available input
- TYPE -- reached end of block code, inflate() to interpret next block
- BAD -- error in block data
-
- Notes:
-
- - The maximum input bits used by a length/distance pair is 15 bits for the
- length code, 5 bits for the length extra, 15 bits for the distance code,
- and 13 bits for the distance extra. This totals 48 bits, or six bytes.
- Therefore if strm->avail_in >= 6, then there is enough input to avoid
- checking for available input while decoding.
-
- - The maximum bytes that a single length/distance pair can output is 258
- bytes, which is the maximum length that can be coded. inflate_fast()
- requires strm->avail_out >= 258 for each loop to avoid checking for
- output space.
- */
-void ZLIB_INTERNAL inflate_fast(strm, start)
-z_streamp strm;
-unsigned start; /* inflate()'s starting value for strm->avail_out */
-{
- struct inflate_state FAR *state;
- z_const unsigned char FAR *in; /* local strm->next_in */
- z_const unsigned char FAR *last; /* have enough input while in < last */
- unsigned char FAR *out; /* local strm->next_out */
- unsigned char FAR *beg; /* inflate()'s initial strm->next_out */
- unsigned char FAR *end; /* while out < end, enough space available */
-#ifdef INFLATE_STRICT
- unsigned dmax; /* maximum distance from zlib header */
-#endif
- unsigned wsize; /* window size or zero if not using window */
- unsigned whave; /* valid bytes in the window */
- unsigned wnext; /* window write index */
- unsigned char FAR *window; /* allocated sliding window, if wsize != 0 */
- unsigned long hold; /* local strm->hold */
- unsigned bits; /* local strm->bits */
- code const FAR *lcode; /* local strm->lencode */
- code const FAR *dcode; /* local strm->distcode */
- unsigned lmask; /* mask for first level of length codes */
- unsigned dmask; /* mask for first level of distance codes */
- code here; /* retrieved table entry */
- unsigned op; /* code bits, operation, extra bits, or */
- /* window position, window bytes to copy */
- unsigned len; /* match length, unused bytes */
- unsigned dist; /* match distance */
- unsigned char FAR *from; /* where to copy match from */
-
- /* copy state to local variables */
- state = (struct inflate_state FAR *)strm->state;
- in = strm->next_in - OFF;
- last = in + (strm->avail_in - 5);
- out = strm->next_out - OFF;
- beg = out - (start - strm->avail_out);
- end = out + (strm->avail_out - 257);
-#ifdef INFLATE_STRICT
- dmax = state->dmax;
-#endif
- wsize = state->wsize;
- whave = state->whave;
- wnext = state->wnext;
- window = state->window;
- hold = state->hold;
- bits = state->bits;
- lcode = state->lencode;
- dcode = state->distcode;
- lmask = (1U << state->lenbits) - 1;
- dmask = (1U << state->distbits) - 1;
-
- /* decode literals and length/distances until end-of-block or not enough
- input data or output space */
- do {
- if (bits < 15) {
- hold += (unsigned long)(PUP(in)) << bits;
- bits += 8;
- hold += (unsigned long)(PUP(in)) << bits;
- bits += 8;
- }
- here = lcode[hold & lmask];
- dolen:
- op = (unsigned)(here.bits);
- hold >>= op;
- bits -= op;
- op = (unsigned)(here.op);
- if (op == 0) { /* literal */
- Tracevv((stderr, here.val >= 0x20 && here.val < 0x7f ?
- "inflate: literal '%c'\n" :
- "inflate: literal 0x%02x\n", here.val));
- PUP(out) = (unsigned char)(here.val);
- }
- else if (op & 16) { /* length base */
- len = (unsigned)(here.val);
- op &= 15; /* number of extra bits */
- if (op) {
- if (bits < op) {
- hold += (unsigned long)(PUP(in)) << bits;
- bits += 8;
- }
- len += (unsigned)hold & ((1U << op) - 1);
- hold >>= op;
- bits -= op;
- }
- Tracevv((stderr, "inflate: length %u\n", len));
- if (bits < 15) {
- hold += (unsigned long)(PUP(in)) << bits;
- bits += 8;
- hold += (unsigned long)(PUP(in)) << bits;
- bits += 8;
- }
- here = dcode[hold & dmask];
- dodist:
- op = (unsigned)(here.bits);
- hold >>= op;
- bits -= op;
- op = (unsigned)(here.op);
- if (op & 16) { /* distance base */
- dist = (unsigned)(here.val);
- op &= 15; /* number of extra bits */
- if (bits < op) {
- hold += (unsigned long)(PUP(in)) << bits;
- bits += 8;
- if (bits < op) {
- hold += (unsigned long)(PUP(in)) << bits;
- bits += 8;
- }
- }
- dist += (unsigned)hold & ((1U << op) - 1);
-#ifdef INFLATE_STRICT
- if (dist > dmax) {
- strm->msg = (char *)"invalid distance too far back";
- state->mode = BAD;
- break;
- }
-#endif
- hold >>= op;
- bits -= op;
- Tracevv((stderr, "inflate: distance %u\n", dist));
- op = (unsigned)(out - beg); /* max distance in output */
- if (dist > op) { /* see if copy from window */
- op = dist - op; /* distance back in window */
- if (op > whave) {
- if (state->sane) {
- strm->msg =
- (char *)"invalid distance too far back";
- state->mode = BAD;
- break;
- }
-#ifdef INFLATE_ALLOW_INVALID_DISTANCE_TOOFAR_ARRR
- if (len <= op - whave) {
- do {
- PUP(out) = 0;
- } while (--len);
- continue;
- }
- len -= op - whave;
- do {
- PUP(out) = 0;
- } while (--op > whave);
- if (op == 0) {
- from = out - dist;
- do {
- PUP(out) = PUP(from);
- } while (--len);
- continue;
- }
-#endif
- }
- from = window - OFF;
- if (wnext == 0) { /* very common case */
- from += wsize - op;
- if (op < len) { /* some from window */
- len -= op;
- do {
- PUP(out) = PUP(from);
- } while (--op);
- from = out - dist; /* rest from output */
- }
- }
- else if (wnext < op) { /* wrap around window */
- from += wsize + wnext - op;
- op -= wnext;
- if (op < len) { /* some from end of window */
- len -= op;
- do {
- PUP(out) = PUP(from);
- } while (--op);
- from = window - OFF;
- if (wnext < len) { /* some from start of window */
- op = wnext;
- len -= op;
- do {
- PUP(out) = PUP(from);
- } while (--op);
- from = out - dist; /* rest from output */
- }
- }
- }
- else { /* contiguous in window */
- from += wnext - op;
- if (op < len) { /* some from window */
- len -= op;
- do {
- PUP(out) = PUP(from);
- } while (--op);
- from = out - dist; /* rest from output */
- }
- }
- while (len > 2) {
- PUP(out) = PUP(from);
- PUP(out) = PUP(from);
- PUP(out) = PUP(from);
- len -= 3;
- }
- if (len) {
- PUP(out) = PUP(from);
- if (len > 1)
- PUP(out) = PUP(from);
- }
- }
- else {
- from = out - dist; /* copy direct from output */
- do { /* minimum length is three */
- PUP(out) = PUP(from);
- PUP(out) = PUP(from);
- PUP(out) = PUP(from);
- len -= 3;
- } while (len > 2);
- if (len) {
- PUP(out) = PUP(from);
- if (len > 1)
- PUP(out) = PUP(from);
- }
- }
- }
- else if ((op & 64) == 0) { /* 2nd level distance code */
- here = dcode[here.val + (hold & ((1U << op) - 1))];
- goto dodist;
- }
- else {
- strm->msg = (char *)"invalid distance code";
- state->mode = BAD;
- break;
- }
- }
- else if ((op & 64) == 0) { /* 2nd level length code */
- here = lcode[here.val + (hold & ((1U << op) - 1))];
- goto dolen;
- }
- else if (op & 32) { /* end-of-block */
- Tracevv((stderr, "inflate: end of block\n"));
- state->mode = TYPE;
- break;
- }
- else {
- strm->msg = (char *)"invalid literal/length code";
- state->mode = BAD;
- break;
- }
- } while (in < last && out < end);
-
- /* return unused bytes (on entry, bits < 8, so in won't go too far back) */
- len = bits >> 3;
- in -= len;
- bits -= len << 3;
- hold &= (1U << bits) - 1;
-
- /* update state and return */
- strm->next_in = in + OFF;
- strm->next_out = out + OFF;
- strm->avail_in = (unsigned)(in < last ? 5 + (last - in) : 5 - (in - last));
- strm->avail_out = (unsigned)(out < end ?
- 257 + (end - out) : 257 - (out - end));
- state->hold = hold;
- state->bits = bits;
- return;
-}
-
-/*
- inflate_fast() speedups that turned out slower (on a PowerPC G3 750CXe):
- - Using bit fields for code structure
- - Different op definition to avoid & for extra bits (do & for table bits)
- - Three separate decoding do-loops for direct, window, and wnext == 0
- - Special case for distance > 1 copies to do overlapped load and store copy
- - Explicit branch predictions (based on measured branch probabilities)
- - Deferring match copy and interspersed it with decoding subsequent codes
- - Swapping literal/length else
- - Swapping window/direct else
- - Larger unrolled copy loops (three is about right)
- - Moving len -= 3 statement into middle of loop
- */
-
-#endif /* !ASMINF */
diff --git a/third-party/zlib/inffast.h b/third-party/zlib/inffast.h
deleted file mode 100644
index e5c1aa4..0000000
--- a/third-party/zlib/inffast.h
+++ /dev/null
@@ -1,11 +0,0 @@
-/* inffast.h -- header to use inffast.c
- * Copyright (C) 1995-2003, 2010 Mark Adler
- * For conditions of distribution and use, see copyright notice in zlib.h
- */
-
-/* WARNING: this file should *not* be used by applications. It is
- part of the implementation of the compression library and is
- subject to change. Applications should only use zlib.h.
- */
-
-void ZLIB_INTERNAL inflate_fast OF((z_streamp strm, unsigned start));
diff --git a/third-party/zlib/inffixed.h b/third-party/zlib/inffixed.h
deleted file mode 100644
index d628327..0000000
--- a/third-party/zlib/inffixed.h
+++ /dev/null
@@ -1,94 +0,0 @@
- /* inffixed.h -- table for decoding fixed codes
- * Generated automatically by makefixed().
- */
-
- /* WARNING: this file should *not* be used by applications.
- It is part of the implementation of this library and is
- subject to change. Applications should only use zlib.h.
- */
-
- static const code lenfix[512] = {
- {96,7,0},{0,8,80},{0,8,16},{20,8,115},{18,7,31},{0,8,112},{0,8,48},
- {0,9,192},{16,7,10},{0,8,96},{0,8,32},{0,9,160},{0,8,0},{0,8,128},
- {0,8,64},{0,9,224},{16,7,6},{0,8,88},{0,8,24},{0,9,144},{19,7,59},
- {0,8,120},{0,8,56},{0,9,208},{17,7,17},{0,8,104},{0,8,40},{0,9,176},
- {0,8,8},{0,8,136},{0,8,72},{0,9,240},{16,7,4},{0,8,84},{0,8,20},
- {21,8,227},{19,7,43},{0,8,116},{0,8,52},{0,9,200},{17,7,13},{0,8,100},
- {0,8,36},{0,9,168},{0,8,4},{0,8,132},{0,8,68},{0,9,232},{16,7,8},
- {0,8,92},{0,8,28},{0,9,152},{20,7,83},{0,8,124},{0,8,60},{0,9,216},
- {18,7,23},{0,8,108},{0,8,44},{0,9,184},{0,8,12},{0,8,140},{0,8,76},
- {0,9,248},{16,7,3},{0,8,82},{0,8,18},{21,8,163},{19,7,35},{0,8,114},
- {0,8,50},{0,9,196},{17,7,11},{0,8,98},{0,8,34},{0,9,164},{0,8,2},
- {0,8,130},{0,8,66},{0,9,228},{16,7,7},{0,8,90},{0,8,26},{0,9,148},
- {20,7,67},{0,8,122},{0,8,58},{0,9,212},{18,7,19},{0,8,106},{0,8,42},
- {0,9,180},{0,8,10},{0,8,138},{0,8,74},{0,9,244},{16,7,5},{0,8,86},
- {0,8,22},{64,8,0},{19,7,51},{0,8,118},{0,8,54},{0,9,204},{17,7,15},
- {0,8,102},{0,8,38},{0,9,172},{0,8,6},{0,8,134},{0,8,70},{0,9,236},
- {16,7,9},{0,8,94},{0,8,30},{0,9,156},{20,7,99},{0,8,126},{0,8,62},
- {0,9,220},{18,7,27},{0,8,110},{0,8,46},{0,9,188},{0,8,14},{0,8,142},
- {0,8,78},{0,9,252},{96,7,0},{0,8,81},{0,8,17},{21,8,131},{18,7,31},
- {0,8,113},{0,8,49},{0,9,194},{16,7,10},{0,8,97},{0,8,33},{0,9,162},
- {0,8,1},{0,8,129},{0,8,65},{0,9,226},{16,7,6},{0,8,89},{0,8,25},
- {0,9,146},{19,7,59},{0,8,121},{0,8,57},{0,9,210},{17,7,17},{0,8,105},
- {0,8,41},{0,9,178},{0,8,9},{0,8,137},{0,8,73},{0,9,242},{16,7,4},
- {0,8,85},{0,8,21},{16,8,258},{19,7,43},{0,8,117},{0,8,53},{0,9,202},
- {17,7,13},{0,8,101},{0,8,37},{0,9,170},{0,8,5},{0,8,133},{0,8,69},
- {0,9,234},{16,7,8},{0,8,93},{0,8,29},{0,9,154},{20,7,83},{0,8,125},
- {0,8,61},{0,9,218},{18,7,23},{0,8,109},{0,8,45},{0,9,186},{0,8,13},
- {0,8,141},{0,8,77},{0,9,250},{16,7,3},{0,8,83},{0,8,19},{21,8,195},
- {19,7,35},{0,8,115},{0,8,51},{0,9,198},{17,7,11},{0,8,99},{0,8,35},
- {0,9,166},{0,8,3},{0,8,131},{0,8,67},{0,9,230},{16,7,7},{0,8,91},
- {0,8,27},{0,9,150},{20,7,67},{0,8,123},{0,8,59},{0,9,214},{18,7,19},
- {0,8,107},{0,8,43},{0,9,182},{0,8,11},{0,8,139},{0,8,75},{0,9,246},
- {16,7,5},{0,8,87},{0,8,23},{64,8,0},{19,7,51},{0,8,119},{0,8,55},
- {0,9,206},{17,7,15},{0,8,103},{0,8,39},{0,9,174},{0,8,7},{0,8,135},
- {0,8,71},{0,9,238},{16,7,9},{0,8,95},{0,8,31},{0,9,158},{20,7,99},
- {0,8,127},{0,8,63},{0,9,222},{18,7,27},{0,8,111},{0,8,47},{0,9,190},
- {0,8,15},{0,8,143},{0,8,79},{0,9,254},{96,7,0},{0,8,80},{0,8,16},
- {20,8,115},{18,7,31},{0,8,112},{0,8,48},{0,9,193},{16,7,10},{0,8,96},
- {0,8,32},{0,9,161},{0,8,0},{0,8,128},{0,8,64},{0,9,225},{16,7,6},
- {0,8,88},{0,8,24},{0,9,145},{19,7,59},{0,8,120},{0,8,56},{0,9,209},
- {17,7,17},{0,8,104},{0,8,40},{0,9,177},{0,8,8},{0,8,136},{0,8,72},
- {0,9,241},{16,7,4},{0,8,84},{0,8,20},{21,8,227},{19,7,43},{0,8,116},
- {0,8,52},{0,9,201},{17,7,13},{0,8,100},{0,8,36},{0,9,169},{0,8,4},
- {0,8,132},{0,8,68},{0,9,233},{16,7,8},{0,8,92},{0,8,28},{0,9,153},
- {20,7,83},{0,8,124},{0,8,60},{0,9,217},{18,7,23},{0,8,108},{0,8,44},
- {0,9,185},{0,8,12},{0,8,140},{0,8,76},{0,9,249},{16,7,3},{0,8,82},
- {0,8,18},{21,8,163},{19,7,35},{0,8,114},{0,8,50},{0,9,197},{17,7,11},
- {0,8,98},{0,8,34},{0,9,165},{0,8,2},{0,8,130},{0,8,66},{0,9,229},
- {16,7,7},{0,8,90},{0,8,26},{0,9,149},{20,7,67},{0,8,122},{0,8,58},
- {0,9,213},{18,7,19},{0,8,106},{0,8,42},{0,9,181},{0,8,10},{0,8,138},
- {0,8,74},{0,9,245},{16,7,5},{0,8,86},{0,8,22},{64,8,0},{19,7,51},
- {0,8,118},{0,8,54},{0,9,205},{17,7,15},{0,8,102},{0,8,38},{0,9,173},
- {0,8,6},{0,8,134},{0,8,70},{0,9,237},{16,7,9},{0,8,94},{0,8,30},
- {0,9,157},{20,7,99},{0,8,126},{0,8,62},{0,9,221},{18,7,27},{0,8,110},
- {0,8,46},{0,9,189},{0,8,14},{0,8,142},{0,8,78},{0,9,253},{96,7,0},
- {0,8,81},{0,8,17},{21,8,131},{18,7,31},{0,8,113},{0,8,49},{0,9,195},
- {16,7,10},{0,8,97},{0,8,33},{0,9,163},{0,8,1},{0,8,129},{0,8,65},
- {0,9,227},{16,7,6},{0,8,89},{0,8,25},{0,9,147},{19,7,59},{0,8,121},
- {0,8,57},{0,9,211},{17,7,17},{0,8,105},{0,8,41},{0,9,179},{0,8,9},
- {0,8,137},{0,8,73},{0,9,243},{16,7,4},{0,8,85},{0,8,21},{16,8,258},
- {19,7,43},{0,8,117},{0,8,53},{0,9,203},{17,7,13},{0,8,101},{0,8,37},
- {0,9,171},{0,8,5},{0,8,133},{0,8,69},{0,9,235},{16,7,8},{0,8,93},
- {0,8,29},{0,9,155},{20,7,83},{0,8,125},{0,8,61},{0,9,219},{18,7,23},
- {0,8,109},{0,8,45},{0,9,187},{0,8,13},{0,8,141},{0,8,77},{0,9,251},
- {16,7,3},{0,8,83},{0,8,19},{21,8,195},{19,7,35},{0,8,115},{0,8,51},
- {0,9,199},{17,7,11},{0,8,99},{0,8,35},{0,9,167},{0,8,3},{0,8,131},
- {0,8,67},{0,9,231},{16,7,7},{0,8,91},{0,8,27},{0,9,151},{20,7,67},
- {0,8,123},{0,8,59},{0,9,215},{18,7,19},{0,8,107},{0,8,43},{0,9,183},
- {0,8,11},{0,8,139},{0,8,75},{0,9,247},{16,7,5},{0,8,87},{0,8,23},
- {64,8,0},{19,7,51},{0,8,119},{0,8,55},{0,9,207},{17,7,15},{0,8,103},
- {0,8,39},{0,9,175},{0,8,7},{0,8,135},{0,8,71},{0,9,239},{16,7,9},
- {0,8,95},{0,8,31},{0,9,159},{20,7,99},{0,8,127},{0,8,63},{0,9,223},
- {18,7,27},{0,8,111},{0,8,47},{0,9,191},{0,8,15},{0,8,143},{0,8,79},
- {0,9,255}
- };
-
- static const code distfix[32] = {
- {16,5,1},{23,5,257},{19,5,17},{27,5,4097},{17,5,5},{25,5,1025},
- {21,5,65},{29,5,16385},{16,5,3},{24,5,513},{20,5,33},{28,5,8193},
- {18,5,9},{26,5,2049},{22,5,129},{64,5,0},{16,5,2},{23,5,385},
- {19,5,25},{27,5,6145},{17,5,7},{25,5,1537},{21,5,97},{29,5,24577},
- {16,5,4},{24,5,769},{20,5,49},{28,5,12289},{18,5,13},{26,5,3073},
- {22,5,193},{64,5,0}
- };
diff --git a/third-party/zlib/inflate.c b/third-party/zlib/inflate.c
deleted file mode 100644
index 870f89b..0000000
--- a/third-party/zlib/inflate.c
+++ /dev/null
@@ -1,1512 +0,0 @@
-/* inflate.c -- zlib decompression
- * Copyright (C) 1995-2012 Mark Adler
- * For conditions of distribution and use, see copyright notice in zlib.h
- */
-
-/*
- * Change history:
- *
- * 1.2.beta0 24 Nov 2002
- * - First version -- complete rewrite of inflate to simplify code, avoid
- * creation of window when not needed, minimize use of window when it is
- * needed, make inffast.c even faster, implement gzip decoding, and to
- * improve code readability and style over the previous zlib inflate code
- *
- * 1.2.beta1 25 Nov 2002
- * - Use pointers for available input and output checking in inffast.c
- * - Remove input and output counters in inffast.c
- * - Change inffast.c entry and loop from avail_in >= 7 to >= 6
- * - Remove unnecessary second byte pull from length extra in inffast.c
- * - Unroll direct copy to three copies per loop in inffast.c
- *
- * 1.2.beta2 4 Dec 2002
- * - Change external routine names to reduce potential conflicts
- * - Correct filename to inffixed.h for fixed tables in inflate.c
- * - Make hbuf[] unsigned char to match parameter type in inflate.c
- * - Change strm->next_out[-state->offset] to *(strm->next_out - state->offset)
- * to avoid negation problem on Alphas (64 bit) in inflate.c
- *
- * 1.2.beta3 22 Dec 2002
- * - Add comments on state->bits assertion in inffast.c
- * - Add comments on op field in inftrees.h
- * - Fix bug in reuse of allocated window after inflateReset()
- * - Remove bit fields--back to byte structure for speed
- * - Remove distance extra == 0 check in inflate_fast()--only helps for lengths
- * - Change post-increments to pre-increments in inflate_fast(), PPC biased?
- * - Add compile time option, POSTINC, to use post-increments instead (Intel?)
- * - Make MATCH copy in inflate() much faster for when inflate_fast() not used
- * - Use local copies of stream next and avail values, as well as local bit
- * buffer and bit count in inflate()--for speed when inflate_fast() not used
- *
- * 1.2.beta4 1 Jan 2003
- * - Split ptr - 257 statements in inflate_table() to avoid compiler warnings
- * - Move a comment on output buffer sizes from inffast.c to inflate.c
- * - Add comments in inffast.c to introduce the inflate_fast() routine
- * - Rearrange window copies in inflate_fast() for speed and simplification
- * - Unroll last copy for window match in inflate_fast()
- * - Use local copies of window variables in inflate_fast() for speed
- * - Pull out common wnext == 0 case for speed in inflate_fast()
- * - Make op and len in inflate_fast() unsigned for consistency
- * - Add FAR to lcode and dcode declarations in inflate_fast()
- * - Simplified bad distance check in inflate_fast()
- * - Added inflateBackInit(), inflateBack(), and inflateBackEnd() in new
- * source file infback.c to provide a call-back interface to inflate for
- * programs like gzip and unzip -- uses window as output buffer to avoid
- * window copying
- *
- * 1.2.beta5 1 Jan 2003
- * - Improved inflateBack() interface to allow the caller to provide initial
- * input in strm.
- * - Fixed stored blocks bug in inflateBack()
- *
- * 1.2.beta6 4 Jan 2003
- * - Added comments in inffast.c on effectiveness of POSTINC
- * - Typecasting all around to reduce compiler warnings
- * - Changed loops from while (1) or do {} while (1) to for (;;), again to
- * make compilers happy
- * - Changed type of window in inflateBackInit() to unsigned char *
- *
- * 1.2.beta7 27 Jan 2003
- * - Changed many types to unsigned or unsigned short to avoid warnings
- * - Added inflateCopy() function
- *
- * 1.2.0 9 Mar 2003
- * - Changed inflateBack() interface to provide separate opaque descriptors
- * for the in() and out() functions
- * - Changed inflateBack() argument and in_func typedef to swap the length
- * and buffer address return values for the input function
- * - Check next_in and next_out for Z_NULL on entry to inflate()
- *
- * The history for versions after 1.2.0 are in ChangeLog in zlib distribution.
- */
-
-#include "zutil.h"
-#include "inftrees.h"
-#include "inflate.h"
-#include "inffast.h"
-
-#ifdef MAKEFIXED
-# ifndef BUILDFIXED
-# define BUILDFIXED
-# endif
-#endif
-
-/* function prototypes */
-local void fixedtables OF((struct inflate_state FAR *state));
-local int updatewindow OF((z_streamp strm, const unsigned char FAR *end,
- unsigned copy));
-#ifdef BUILDFIXED
- void makefixed OF((void));
-#endif
-local unsigned syncsearch OF((unsigned FAR *have, const unsigned char FAR *buf,
- unsigned len));
-
-int ZEXPORT inflateResetKeep(strm)
-z_streamp strm;
-{
- struct inflate_state FAR *state;
-
- if (strm == Z_NULL || strm->state == Z_NULL) return Z_STREAM_ERROR;
- state = (struct inflate_state FAR *)strm->state;
- strm->total_in = strm->total_out = state->total = 0;
- strm->msg = Z_NULL;
- if (state->wrap) /* to support ill-conceived Java test suite */
- strm->adler = state->wrap & 1;
- state->mode = HEAD;
- state->last = 0;
- state->havedict = 0;
- state->dmax = 32768U;
- state->head = Z_NULL;
- state->hold = 0;
- state->bits = 0;
- state->lencode = state->distcode = state->next = state->codes;
- state->sane = 1;
- state->back = -1;
- Tracev((stderr, "inflate: reset\n"));
- return Z_OK;
-}
-
-int ZEXPORT inflateReset(strm)
-z_streamp strm;
-{
- struct inflate_state FAR *state;
-
- if (strm == Z_NULL || strm->state == Z_NULL) return Z_STREAM_ERROR;
- state = (struct inflate_state FAR *)strm->state;
- state->wsize = 0;
- state->whave = 0;
- state->wnext = 0;
- return inflateResetKeep(strm);
-}
-
-int ZEXPORT inflateReset2(strm, windowBits)
-z_streamp strm;
-int windowBits;
-{
- int wrap;
- struct inflate_state FAR *state;
-
- /* get the state */
- if (strm == Z_NULL || strm->state == Z_NULL) return Z_STREAM_ERROR;
- state = (struct inflate_state FAR *)strm->state;
-
- /* extract wrap request from windowBits parameter */
- if (windowBits < 0) {
- wrap = 0;
- windowBits = -windowBits;
- }
- else {
- wrap = (windowBits >> 4) + 1;
-#ifdef GUNZIP
- if (windowBits < 48)
- windowBits &= 15;
-#endif
- }
-
- /* set number of window bits, free window if different */
- if (windowBits && (windowBits < 8 || windowBits > 15))
- return Z_STREAM_ERROR;
- if (state->window != Z_NULL && state->wbits != (unsigned)windowBits) {
- ZFREE(strm, state->window);
- state->window = Z_NULL;
- }
-
- /* update state and reset the rest of it */
- state->wrap = wrap;
- state->wbits = (unsigned)windowBits;
- return inflateReset(strm);
-}
-
-int ZEXPORT inflateInit2_(strm, windowBits, version, stream_size)
-z_streamp strm;
-int windowBits;
-const char *version;
-int stream_size;
-{
- int ret;
- struct inflate_state FAR *state;
-
- if (version == Z_NULL || version[0] != ZLIB_VERSION[0] ||
- stream_size != (int)(sizeof(z_stream)))
- return Z_VERSION_ERROR;
- if (strm == Z_NULL) return Z_STREAM_ERROR;
- strm->msg = Z_NULL; /* in case we return an error */
- if (strm->zalloc == (alloc_func)0) {
-#ifdef Z_SOLO
- return Z_STREAM_ERROR;
-#else
- strm->zalloc = zcalloc;
- strm->opaque = (voidpf)0;
-#endif
- }
- if (strm->zfree == (free_func)0)
-#ifdef Z_SOLO
- return Z_STREAM_ERROR;
-#else
- strm->zfree = zcfree;
-#endif
- state = (struct inflate_state FAR *)
- ZALLOC(strm, 1, sizeof(struct inflate_state));
- if (state == Z_NULL) return Z_MEM_ERROR;
- Tracev((stderr, "inflate: allocated\n"));
- strm->state = (struct internal_state FAR *)state;
- state->window = Z_NULL;
- ret = inflateReset2(strm, windowBits);
- if (ret != Z_OK) {
- ZFREE(strm, state);
- strm->state = Z_NULL;
- }
- return ret;
-}
-
-int ZEXPORT inflateInit_(strm, version, stream_size)
-z_streamp strm;
-const char *version;
-int stream_size;
-{
- return inflateInit2_(strm, DEF_WBITS, version, stream_size);
-}
-
-int ZEXPORT inflatePrime(strm, bits, value)
-z_streamp strm;
-int bits;
-int value;
-{
- struct inflate_state FAR *state;
-
- if (strm == Z_NULL || strm->state == Z_NULL) return Z_STREAM_ERROR;
- state = (struct inflate_state FAR *)strm->state;
- if (bits < 0) {
- state->hold = 0;
- state->bits = 0;
- return Z_OK;
- }
- if (bits > 16 || state->bits + bits > 32) return Z_STREAM_ERROR;
- value &= (1L << bits) - 1;
- state->hold += value << state->bits;
- state->bits += bits;
- return Z_OK;
-}
-
-/*
- Return state with length and distance decoding tables and index sizes set to
- fixed code decoding. Normally this returns fixed tables from inffixed.h.
- If BUILDFIXED is defined, then instead this routine builds the tables the
- first time it's called, and returns those tables the first time and
- thereafter. This reduces the size of the code by about 2K bytes, in
- exchange for a little execution time. However, BUILDFIXED should not be
- used for threaded applications, since the rewriting of the tables and virgin
- may not be thread-safe.
- */
-local void fixedtables(state)
-struct inflate_state FAR *state;
-{
-#ifdef BUILDFIXED
- static int virgin = 1;
- static code *lenfix, *distfix;
- static code fixed[544];
-
- /* build fixed huffman tables if first call (may not be thread safe) */
- if (virgin) {
- unsigned sym, bits;
- static code *next;
-
- /* literal/length table */
- sym = 0;
- while (sym < 144) state->lens[sym++] = 8;
- while (sym < 256) state->lens[sym++] = 9;
- while (sym < 280) state->lens[sym++] = 7;
- while (sym < 288) state->lens[sym++] = 8;
- next = fixed;
- lenfix = next;
- bits = 9;
- inflate_table(LENS, state->lens, 288, &(next), &(bits), state->work);
-
- /* distance table */
- sym = 0;
- while (sym < 32) state->lens[sym++] = 5;
- distfix = next;
- bits = 5;
- inflate_table(DISTS, state->lens, 32, &(next), &(bits), state->work);
-
- /* do this just once */
- virgin = 0;
- }
-#else /* !BUILDFIXED */
-# include "inffixed.h"
-#endif /* BUILDFIXED */
- state->lencode = lenfix;
- state->lenbits = 9;
- state->distcode = distfix;
- state->distbits = 5;
-}
-
-#ifdef MAKEFIXED
-#include <stdio.h>
-
-/*
- Write out the inffixed.h that is #include'd above. Defining MAKEFIXED also
- defines BUILDFIXED, so the tables are built on the fly. makefixed() writes
- those tables to stdout, which would be piped to inffixed.h. A small program
- can simply call makefixed to do this:
-
- void makefixed(void);
-
- int main(void)
- {
- makefixed();
- return 0;
- }
-
- Then that can be linked with zlib built with MAKEFIXED defined and run:
-
- a.out > inffixed.h
- */
-void makefixed()
-{
- unsigned low, size;
- struct inflate_state state;
-
- fixedtables(&state);
- puts(" /* inffixed.h -- table for decoding fixed codes");
- puts(" * Generated automatically by makefixed().");
- puts(" */");
- puts("");
- puts(" /* WARNING: this file should *not* be used by applications.");
- puts(" It is part of the implementation of this library and is");
- puts(" subject to change. Applications should only use zlib.h.");
- puts(" */");
- puts("");
- size = 1U << 9;
- printf(" static const code lenfix[%u] = {", size);
- low = 0;
- for (;;) {
- if ((low % 7) == 0) printf("\n ");
- printf("{%u,%u,%d}", (low & 127) == 99 ? 64 : state.lencode[low].op,
- state.lencode[low].bits, state.lencode[low].val);
- if (++low == size) break;
- putchar(',');
- }
- puts("\n };");
- size = 1U << 5;
- printf("\n static const code distfix[%u] = {", size);
- low = 0;
- for (;;) {
- if ((low % 6) == 0) printf("\n ");
- printf("{%u,%u,%d}", state.distcode[low].op, state.distcode[low].bits,
- state.distcode[low].val);
- if (++low == size) break;
- putchar(',');
- }
- puts("\n };");
-}
-#endif /* MAKEFIXED */
-
-/*
- Update the window with the last wsize (normally 32K) bytes written before
- returning. If window does not exist yet, create it. This is only called
- when a window is already in use, or when output has been written during this
- inflate call, but the end of the deflate stream has not been reached yet.
- It is also called to create a window for dictionary data when a dictionary
- is loaded.
-
- Providing output buffers larger than 32K to inflate() should provide a speed
- advantage, since only the last 32K of output is copied to the sliding window
- upon return from inflate(), and since all distances after the first 32K of
- output will fall in the output data, making match copies simpler and faster.
- The advantage may be dependent on the size of the processor's data caches.
- */
-local int updatewindow(strm, end, copy)
-z_streamp strm;
-const Bytef *end;
-unsigned copy;
-{
- struct inflate_state FAR *state;
- unsigned dist;
-
- state = (struct inflate_state FAR *)strm->state;
-
- /* if it hasn't been done already, allocate space for the window */
- if (state->window == Z_NULL) {
- state->window = (unsigned char FAR *)
- ZALLOC(strm, 1U << state->wbits,
- sizeof(unsigned char));
- if (state->window == Z_NULL) return 1;
- }
-
- /* if window not in use yet, initialize */
- if (state->wsize == 0) {
- state->wsize = 1U << state->wbits;
- state->wnext = 0;
- state->whave = 0;
- }
-
- /* copy state->wsize or less output bytes into the circular window */
- if (copy >= state->wsize) {
- zmemcpy(state->window, end - state->wsize, state->wsize);
- state->wnext = 0;
- state->whave = state->wsize;
- }
- else {
- dist = state->wsize - state->wnext;
- if (dist > copy) dist = copy;
- zmemcpy(state->window + state->wnext, end - copy, dist);
- copy -= dist;
- if (copy) {
- zmemcpy(state->window, end - copy, copy);
- state->wnext = copy;
- state->whave = state->wsize;
- }
- else {
- state->wnext += dist;
- if (state->wnext == state->wsize) state->wnext = 0;
- if (state->whave < state->wsize) state->whave += dist;
- }
- }
- return 0;
-}
-
-/* Macros for inflate(): */
-
-/* check function to use adler32() for zlib or crc32() for gzip */
-#ifdef GUNZIP
-# define UPDATE(check, buf, len) \
- (state->flags ? crc32(check, buf, len) : adler32(check, buf, len))
-#else
-# define UPDATE(check, buf, len) adler32(check, buf, len)
-#endif
-
-/* check macros for header crc */
-#ifdef GUNZIP
-# define CRC2(check, word) \
- do { \
- hbuf[0] = (unsigned char)(word); \
- hbuf[1] = (unsigned char)((word) >> 8); \
- check = crc32(check, hbuf, 2); \
- } while (0)
-
-# define CRC4(check, word) \
- do { \
- hbuf[0] = (unsigned char)(word); \
- hbuf[1] = (unsigned char)((word) >> 8); \
- hbuf[2] = (unsigned char)((word) >> 16); \
- hbuf[3] = (unsigned char)((word) >> 24); \
- check = crc32(check, hbuf, 4); \
- } while (0)
-#endif
-
-/* Load registers with state in inflate() for speed */
-#define LOAD() \
- do { \
- put = strm->next_out; \
- left = strm->avail_out; \
- next = strm->next_in; \
- have = strm->avail_in; \
- hold = state->hold; \
- bits = state->bits; \
- } while (0)
-
-/* Restore state from registers in inflate() */
-#define RESTORE() \
- do { \
- strm->next_out = put; \
- strm->avail_out = left; \
- strm->next_in = next; \
- strm->avail_in = have; \
- state->hold = hold; \
- state->bits = bits; \
- } while (0)
-
-/* Clear the input bit accumulator */
-#define INITBITS() \
- do { \
- hold = 0; \
- bits = 0; \
- } while (0)
-
-/* Get a byte of input into the bit accumulator, or return from inflate()
- if there is no input available. */
-#define PULLBYTE() \
- do { \
- if (have == 0) goto inf_leave; \
- have--; \
- hold += (unsigned long)(*next++) << bits; \
- bits += 8; \
- } while (0)
-
-/* Assure that there are at least n bits in the bit accumulator. If there is
- not enough available input to do that, then return from inflate(). */
-#define NEEDBITS(n) \
- do { \
- while (bits < (unsigned)(n)) \
- PULLBYTE(); \
- } while (0)
-
-/* Return the low n bits of the bit accumulator (n < 16) */
-#define BITS(n) \
- ((unsigned)hold & ((1U << (n)) - 1))
-
-/* Remove n bits from the bit accumulator */
-#define DROPBITS(n) \
- do { \
- hold >>= (n); \
- bits -= (unsigned)(n); \
- } while (0)
-
-/* Remove zero to seven bits as needed to go to a byte boundary */
-#define BYTEBITS() \
- do { \
- hold >>= bits & 7; \
- bits -= bits & 7; \
- } while (0)
-
-/*
- inflate() uses a state machine to process as much input data and generate as
- much output data as possible before returning. The state machine is
- structured roughly as follows:
-
- for (;;) switch (state) {
- ...
- case STATEn:
- if (not enough input data or output space to make progress)
- return;
- ... make progress ...
- state = STATEm;
- break;
- ...
- }
-
- so when inflate() is called again, the same case is attempted again, and
- if the appropriate resources are provided, the machine proceeds to the
- next state. The NEEDBITS() macro is usually the way the state evaluates
- whether it can proceed or should return. NEEDBITS() does the return if
- the requested bits are not available. The typical use of the BITS macros
- is:
-
- NEEDBITS(n);
- ... do something with BITS(n) ...
- DROPBITS(n);
-
- where NEEDBITS(n) either returns from inflate() if there isn't enough
- input left to load n bits into the accumulator, or it continues. BITS(n)
- gives the low n bits in the accumulator. When done, DROPBITS(n) drops
- the low n bits off the accumulator. INITBITS() clears the accumulator
- and sets the number of available bits to zero. BYTEBITS() discards just
- enough bits to put the accumulator on a byte boundary. After BYTEBITS()
- and a NEEDBITS(8), then BITS(8) would return the next byte in the stream.
-
- NEEDBITS(n) uses PULLBYTE() to get an available byte of input, or to return
- if there is no input available. The decoding of variable length codes uses
- PULLBYTE() directly in order to pull just enough bytes to decode the next
- code, and no more.
-
- Some states loop until they get enough input, making sure that enough
- state information is maintained to continue the loop where it left off
- if NEEDBITS() returns in the loop. For example, want, need, and keep
- would all have to actually be part of the saved state in case NEEDBITS()
- returns:
-
- case STATEw:
- while (want < need) {
- NEEDBITS(n);
- keep[want++] = BITS(n);
- DROPBITS(n);
- }
- state = STATEx;
- case STATEx:
-
- As shown above, if the next state is also the next case, then the break
- is omitted.
-
- A state may also return if there is not enough output space available to
- complete that state. Those states are copying stored data, writing a
- literal byte, and copying a matching string.
-
- When returning, a "goto inf_leave" is used to update the total counters,
- update the check value, and determine whether any progress has been made
- during that inflate() call in order to return the proper return code.
- Progress is defined as a change in either strm->avail_in or strm->avail_out.
- When there is a window, goto inf_leave will update the window with the last
- output written. If a goto inf_leave occurs in the middle of decompression
- and there is no window currently, goto inf_leave will create one and copy
- output to the window for the next call of inflate().
-
- In this implementation, the flush parameter of inflate() only affects the
- return code (per zlib.h). inflate() always writes as much as possible to
- strm->next_out, given the space available and the provided input--the effect
- documented in zlib.h of Z_SYNC_FLUSH. Furthermore, inflate() always defers
- the allocation of and copying into a sliding window until necessary, which
- provides the effect documented in zlib.h for Z_FINISH when the entire input
- stream available. So the only thing the flush parameter actually does is:
- when flush is set to Z_FINISH, inflate() cannot return Z_OK. Instead it
- will return Z_BUF_ERROR if it has not reached the end of the stream.
- */
-
-int ZEXPORT inflate(strm, flush)
-z_streamp strm;
-int flush;
-{
- struct inflate_state FAR *state;
- z_const unsigned char FAR *next; /* next input */
- unsigned char FAR *put; /* next output */
- unsigned have, left; /* available input and output */
- unsigned long hold; /* bit buffer */
- unsigned bits; /* bits in bit buffer */
- unsigned in, out; /* save starting available input and output */
- unsigned copy; /* number of stored or match bytes to copy */
- unsigned char FAR *from; /* where to copy match bytes from */
- code here; /* current decoding table entry */
- code last; /* parent table entry */
- unsigned len; /* length to copy for repeats, bits to drop */
- int ret; /* return code */
-#ifdef GUNZIP
- unsigned char hbuf[4]; /* buffer for gzip header crc calculation */
-#endif
- static const unsigned short order[19] = /* permutation of code lengths */
- {16, 17, 18, 0, 8, 7, 9, 6, 10, 5, 11, 4, 12, 3, 13, 2, 14, 1, 15};
-
- if (strm == Z_NULL || strm->state == Z_NULL || strm->next_out == Z_NULL ||
- (strm->next_in == Z_NULL && strm->avail_in != 0))
- return Z_STREAM_ERROR;
-
- state = (struct inflate_state FAR *)strm->state;
- if (state->mode == TYPE) state->mode = TYPEDO; /* skip check */
- LOAD();
- in = have;
- out = left;
- ret = Z_OK;
- for (;;)
- switch (state->mode) {
- case HEAD:
- if (state->wrap == 0) {
- state->mode = TYPEDO;
- break;
- }
- NEEDBITS(16);
-#ifdef GUNZIP
- if ((state->wrap & 2) && hold == 0x8b1f) { /* gzip header */
- state->check = crc32(0L, Z_NULL, 0);
- CRC2(state->check, hold);
- INITBITS();
- state->mode = FLAGS;
- break;
- }
- state->flags = 0; /* expect zlib header */
- if (state->head != Z_NULL)
- state->head->done = -1;
- if (!(state->wrap & 1) || /* check if zlib header allowed */
-#else
- if (
-#endif
- ((BITS(8) << 8) + (hold >> 8)) % 31) {
- strm->msg = (char *)"incorrect header check";
- state->mode = BAD;
- break;
- }
- if (BITS(4) != Z_DEFLATED) {
- strm->msg = (char *)"unknown compression method";
- state->mode = BAD;
- break;
- }
- DROPBITS(4);
- len = BITS(4) + 8;
- if (state->wbits == 0)
- state->wbits = len;
- else if (len > state->wbits) {
- strm->msg = (char *)"invalid window size";
- state->mode = BAD;
- break;
- }
- state->dmax = 1U << len;
- Tracev((stderr, "inflate: zlib header ok\n"));
- strm->adler = state->check = adler32(0L, Z_NULL, 0);
- state->mode = hold & 0x200 ? DICTID : TYPE;
- INITBITS();
- break;
-#ifdef GUNZIP
- case FLAGS:
- NEEDBITS(16);
- state->flags = (int)(hold);
- if ((state->flags & 0xff) != Z_DEFLATED) {
- strm->msg = (char *)"unknown compression method";
- state->mode = BAD;
- break;
- }
- if (state->flags & 0xe000) {
- strm->msg = (char *)"unknown header flags set";
- state->mode = BAD;
- break;
- }
- if (state->head != Z_NULL)
- state->head->text = (int)((hold >> 8) & 1);
- if (state->flags & 0x0200) CRC2(state->check, hold);
- INITBITS();
- state->mode = TIME;
- case TIME:
- NEEDBITS(32);
- if (state->head != Z_NULL)
- state->head->time = hold;
- if (state->flags & 0x0200) CRC4(state->check, hold);
- INITBITS();
- state->mode = OS;
- case OS:
- NEEDBITS(16);
- if (state->head != Z_NULL) {
- state->head->xflags = (int)(hold & 0xff);
- state->head->os = (int)(hold >> 8);
- }
- if (state->flags & 0x0200) CRC2(state->check, hold);
- INITBITS();
- state->mode = EXLEN;
- case EXLEN:
- if (state->flags & 0x0400) {
- NEEDBITS(16);
- state->length = (unsigned)(hold);
- if (state->head != Z_NULL)
- state->head->extra_len = (unsigned)hold;
- if (state->flags & 0x0200) CRC2(state->check, hold);
- INITBITS();
- }
- else if (state->head != Z_NULL)
- state->head->extra = Z_NULL;
- state->mode = EXTRA;
- case EXTRA:
- if (state->flags & 0x0400) {
- copy = state->length;
- if (copy > have) copy = have;
- if (copy) {
- if (state->head != Z_NULL &&
- state->head->extra != Z_NULL) {
- len = state->head->extra_len - state->length;
- zmemcpy(state->head->extra + len, next,
- len + copy > state->head->extra_max ?
- state->head->extra_max - len : copy);
- }
- if (state->flags & 0x0200)
- state->check = crc32(state->check, next, copy);
- have -= copy;
- next += copy;
- state->length -= copy;
- }
- if (state->length) goto inf_leave;
- }
- state->length = 0;
- state->mode = NAME;
- case NAME:
- if (state->flags & 0x0800) {
- if (have == 0) goto inf_leave;
- copy = 0;
- do {
- len = (unsigned)(next[copy++]);
- if (state->head != Z_NULL &&
- state->head->name != Z_NULL &&
- state->length < state->head->name_max)
- state->head->name[state->length++] = len;
- } while (len && copy < have);
- if (state->flags & 0x0200)
- state->check = crc32(state->check, next, copy);
- have -= copy;
- next += copy;
- if (len) goto inf_leave;
- }
- else if (state->head != Z_NULL)
- state->head->name = Z_NULL;
- state->length = 0;
- state->mode = COMMENT;
- case COMMENT:
- if (state->flags & 0x1000) {
- if (have == 0) goto inf_leave;
- copy = 0;
- do {
- len = (unsigned)(next[copy++]);
- if (state->head != Z_NULL &&
- state->head->comment != Z_NULL &&
- state->length < state->head->comm_max)
- state->head->comment[state->length++] = len;
- } while (len && copy < have);
- if (state->flags & 0x0200)
- state->check = crc32(state->check, next, copy);
- have -= copy;
- next += copy;
- if (len) goto inf_leave;
- }
- else if (state->head != Z_NULL)
- state->head->comment = Z_NULL;
- state->mode = HCRC;
- case HCRC:
- if (state->flags & 0x0200) {
- NEEDBITS(16);
- if (hold != (state->check & 0xffff)) {
- strm->msg = (char *)"header crc mismatch";
- state->mode = BAD;
- break;
- }
- INITBITS();
- }
- if (state->head != Z_NULL) {
- state->head->hcrc = (int)((state->flags >> 9) & 1);
- state->head->done = 1;
- }
- strm->adler = state->check = crc32(0L, Z_NULL, 0);
- state->mode = TYPE;
- break;
-#endif
- case DICTID:
- NEEDBITS(32);
- strm->adler = state->check = ZSWAP32(hold);
- INITBITS();
- state->mode = DICT;
- case DICT:
- if (state->havedict == 0) {
- RESTORE();
- return Z_NEED_DICT;
- }
- strm->adler = state->check = adler32(0L, Z_NULL, 0);
- state->mode = TYPE;
- case TYPE:
- if (flush == Z_BLOCK || flush == Z_TREES) goto inf_leave;
- case TYPEDO:
- if (state->last) {
- BYTEBITS();
- state->mode = CHECK;
- break;
- }
- NEEDBITS(3);
- state->last = BITS(1);
- DROPBITS(1);
- switch (BITS(2)) {
- case 0: /* stored block */
- Tracev((stderr, "inflate: stored block%s\n",
- state->last ? " (last)" : ""));
- state->mode = STORED;
- break;
- case 1: /* fixed block */
- fixedtables(state);
- Tracev((stderr, "inflate: fixed codes block%s\n",
- state->last ? " (last)" : ""));
- state->mode = LEN_; /* decode codes */
- if (flush == Z_TREES) {
- DROPBITS(2);
- goto inf_leave;
- }
- break;
- case 2: /* dynamic block */
- Tracev((stderr, "inflate: dynamic codes block%s\n",
- state->last ? " (last)" : ""));
- state->mode = TABLE;
- break;
- case 3:
- strm->msg = (char *)"invalid block type";
- state->mode = BAD;
- }
- DROPBITS(2);
- break;
- case STORED:
- BYTEBITS(); /* go to byte boundary */
- NEEDBITS(32);
- if ((hold & 0xffff) != ((hold >> 16) ^ 0xffff)) {
- strm->msg = (char *)"invalid stored block lengths";
- state->mode = BAD;
- break;
- }
- state->length = (unsigned)hold & 0xffff;
- Tracev((stderr, "inflate: stored length %u\n",
- state->length));
- INITBITS();
- state->mode = COPY_;
- if (flush == Z_TREES) goto inf_leave;
- case COPY_:
- state->mode = COPY;
- case COPY:
- copy = state->length;
- if (copy) {
- if (copy > have) copy = have;
- if (copy > left) copy = left;
- if (copy == 0) goto inf_leave;
- zmemcpy(put, next, copy);
- have -= copy;
- next += copy;
- left -= copy;
- put += copy;
- state->length -= copy;
- break;
- }
- Tracev((stderr, "inflate: stored end\n"));
- state->mode = TYPE;
- break;
- case TABLE:
- NEEDBITS(14);
- state->nlen = BITS(5) + 257;
- DROPBITS(5);
- state->ndist = BITS(5) + 1;
- DROPBITS(5);
- state->ncode = BITS(4) + 4;
- DROPBITS(4);
-#ifndef PKZIP_BUG_WORKAROUND
- if (state->nlen > 286 || state->ndist > 30) {
- strm->msg = (char *)"too many length or distance symbols";
- state->mode = BAD;
- break;
- }
-#endif
- Tracev((stderr, "inflate: table sizes ok\n"));
- state->have = 0;
- state->mode = LENLENS;
- case LENLENS:
- while (state->have < state->ncode) {
- NEEDBITS(3);
- state->lens[order[state->have++]] = (unsigned short)BITS(3);
- DROPBITS(3);
- }
- while (state->have < 19)
- state->lens[order[state->have++]] = 0;
- state->next = state->codes;
- state->lencode = (const code FAR *)(state->next);
- state->lenbits = 7;
- ret = inflate_table(CODES, state->lens, 19, &(state->next),
- &(state->lenbits), state->work);
- if (ret) {
- strm->msg = (char *)"invalid code lengths set";
- state->mode = BAD;
- break;
- }
- Tracev((stderr, "inflate: code lengths ok\n"));
- state->have = 0;
- state->mode = CODELENS;
- case CODELENS:
- while (state->have < state->nlen + state->ndist) {
- for (;;) {
- here = state->lencode[BITS(state->lenbits)];
- if ((unsigned)(here.bits) <= bits) break;
- PULLBYTE();
- }
- if (here.val < 16) {
- DROPBITS(here.bits);
- state->lens[state->have++] = here.val;
- }
- else {
- if (here.val == 16) {
- NEEDBITS(here.bits + 2);
- DROPBITS(here.bits);
- if (state->have == 0) {
- strm->msg = (char *)"invalid bit length repeat";
- state->mode = BAD;
- break;
- }
- len = state->lens[state->have - 1];
- copy = 3 + BITS(2);
- DROPBITS(2);
- }
- else if (here.val == 17) {
- NEEDBITS(here.bits + 3);
- DROPBITS(here.bits);
- len = 0;
- copy = 3 + BITS(3);
- DROPBITS(3);
- }
- else {
- NEEDBITS(here.bits + 7);
- DROPBITS(here.bits);
- len = 0;
- copy = 11 + BITS(7);
- DROPBITS(7);
- }
- if (state->have + copy > state->nlen + state->ndist) {
- strm->msg = (char *)"invalid bit length repeat";
- state->mode = BAD;
- break;
- }
- while (copy--)
- state->lens[state->have++] = (unsigned short)len;
- }
- }
-
- /* handle error breaks in while */
- if (state->mode == BAD) break;
-
- /* check for end-of-block code (better have one) */
- if (state->lens[256] == 0) {
- strm->msg = (char *)"invalid code -- missing end-of-block";
- state->mode = BAD;
- break;
- }
-
- /* build code tables -- note: do not change the lenbits or distbits
- values here (9 and 6) without reading the comments in inftrees.h
- concerning the ENOUGH constants, which depend on those values */
- state->next = state->codes;
- state->lencode = (const code FAR *)(state->next);
- state->lenbits = 9;
- ret = inflate_table(LENS, state->lens, state->nlen, &(state->next),
- &(state->lenbits), state->work);
- if (ret) {
- strm->msg = (char *)"invalid literal/lengths set";
- state->mode = BAD;
- break;
- }
- state->distcode = (const code FAR *)(state->next);
- state->distbits = 6;
- ret = inflate_table(DISTS, state->lens + state->nlen, state->ndist,
- &(state->next), &(state->distbits), state->work);
- if (ret) {
- strm->msg = (char *)"invalid distances set";
- state->mode = BAD;
- break;
- }
- Tracev((stderr, "inflate: codes ok\n"));
- state->mode = LEN_;
- if (flush == Z_TREES) goto inf_leave;
- case LEN_:
- state->mode = LEN;
- case LEN:
- if (have >= 6 && left >= 258) {
- RESTORE();
- inflate_fast(strm, out);
- LOAD();
- if (state->mode == TYPE)
- state->back = -1;
- break;
- }
- state->back = 0;
- for (;;) {
- here = state->lencode[BITS(state->lenbits)];
- if ((unsigned)(here.bits) <= bits) break;
- PULLBYTE();
- }
- if (here.op && (here.op & 0xf0) == 0) {
- last = here;
- for (;;) {
- here = state->lencode[last.val +
- (BITS(last.bits + last.op) >> last.bits)];
- if ((unsigned)(last.bits + here.bits) <= bits) break;
- PULLBYTE();
- }
- DROPBITS(last.bits);
- state->back += last.bits;
- }
- DROPBITS(here.bits);
- state->back += here.bits;
- state->length = (unsigned)here.val;
- if ((int)(here.op) == 0) {
- Tracevv((stderr, here.val >= 0x20 && here.val < 0x7f ?
- "inflate: literal '%c'\n" :
- "inflate: literal 0x%02x\n", here.val));
- state->mode = LIT;
- break;
- }
- if (here.op & 32) {
- Tracevv((stderr, "inflate: end of block\n"));
- state->back = -1;
- state->mode = TYPE;
- break;
- }
- if (here.op & 64) {
- strm->msg = (char *)"invalid literal/length code";
- state->mode = BAD;
- break;
- }
- state->extra = (unsigned)(here.op) & 15;
- state->mode = LENEXT;
- case LENEXT:
- if (state->extra) {
- NEEDBITS(state->extra);
- state->length += BITS(state->extra);
- DROPBITS(state->extra);
- state->back += state->extra;
- }
- Tracevv((stderr, "inflate: length %u\n", state->length));
- state->was = state->length;
- state->mode = DIST;
- case DIST:
- for (;;) {
- here = state->distcode[BITS(state->distbits)];
- if ((unsigned)(here.bits) <= bits) break;
- PULLBYTE();
- }
- if ((here.op & 0xf0) == 0) {
- last = here;
- for (;;) {
- here = state->distcode[last.val +
- (BITS(last.bits + last.op) >> last.bits)];
- if ((unsigned)(last.bits + here.bits) <= bits) break;
- PULLBYTE();
- }
- DROPBITS(last.bits);
- state->back += last.bits;
- }
- DROPBITS(here.bits);
- state->back += here.bits;
- if (here.op & 64) {
- strm->msg = (char *)"invalid distance code";
- state->mode = BAD;
- break;
- }
- state->offset = (unsigned)here.val;
- state->extra = (unsigned)(here.op) & 15;
- state->mode = DISTEXT;
- case DISTEXT:
- if (state->extra) {
- NEEDBITS(state->extra);
- state->offset += BITS(state->extra);
- DROPBITS(state->extra);
- state->back += state->extra;
- }
-#ifdef INFLATE_STRICT
- if (state->offset > state->dmax) {
- strm->msg = (char *)"invalid distance too far back";
- state->mode = BAD;
- break;
- }
-#endif
- Tracevv((stderr, "inflate: distance %u\n", state->offset));
- state->mode = MATCH;
- case MATCH:
- if (left == 0) goto inf_leave;
- copy = out - left;
- if (state->offset > copy) { /* copy from window */
- copy = state->offset - copy;
- if (copy > state->whave) {
- if (state->sane) {
- strm->msg = (char *)"invalid distance too far back";
- state->mode = BAD;
- break;
- }
-#ifdef INFLATE_ALLOW_INVALID_DISTANCE_TOOFAR_ARRR
- Trace((stderr, "inflate.c too far\n"));
- copy -= state->whave;
- if (copy > state->length) copy = state->length;
- if (copy > left) copy = left;
- left -= copy;
- state->length -= copy;
- do {
- *put++ = 0;
- } while (--copy);
- if (state->length == 0) state->mode = LEN;
- break;
-#endif
- }
- if (copy > state->wnext) {
- copy -= state->wnext;
- from = state->window + (state->wsize - copy);
- }
- else
- from = state->window + (state->wnext - copy);
- if (copy > state->length) copy = state->length;
- }
- else { /* copy from output */
- from = put - state->offset;
- copy = state->length;
- }
- if (copy > left) copy = left;
- left -= copy;
- state->length -= copy;
- do {
- *put++ = *from++;
- } while (--copy);
- if (state->length == 0) state->mode = LEN;
- break;
- case LIT:
- if (left == 0) goto inf_leave;
- *put++ = (unsigned char)(state->length);
- left--;
- state->mode = LEN;
- break;
- case CHECK:
- if (state->wrap) {
- NEEDBITS(32);
- out -= left;
- strm->total_out += out;
- state->total += out;
- if (out)
- strm->adler = state->check =
- UPDATE(state->check, put - out, out);
- out = left;
- if ((
-#ifdef GUNZIP
- state->flags ? hold :
-#endif
- ZSWAP32(hold)) != state->check) {
- strm->msg = (char *)"incorrect data check";
- state->mode = BAD;
- break;
- }
- INITBITS();
- Tracev((stderr, "inflate: check matches trailer\n"));
- }
-#ifdef GUNZIP
- state->mode = LENGTH;
- case LENGTH:
- if (state->wrap && state->flags) {
- NEEDBITS(32);
- if (hold != (state->total & 0xffffffffUL)) {
- strm->msg = (char *)"incorrect length check";
- state->mode = BAD;
- break;
- }
- INITBITS();
- Tracev((stderr, "inflate: length matches trailer\n"));
- }
-#endif
- state->mode = DONE;
- case DONE:
- ret = Z_STREAM_END;
- goto inf_leave;
- case BAD:
- ret = Z_DATA_ERROR;
- goto inf_leave;
- case MEM:
- return Z_MEM_ERROR;
- case SYNC:
- default:
- return Z_STREAM_ERROR;
- }
-
- /*
- Return from inflate(), updating the total counts and the check value.
- If there was no progress during the inflate() call, return a buffer
- error. Call updatewindow() to create and/or update the window state.
- Note: a memory error from inflate() is non-recoverable.
- */
- inf_leave:
- RESTORE();
- if (state->wsize || (out != strm->avail_out && state->mode < BAD &&
- (state->mode < CHECK || flush != Z_FINISH)))
- if (updatewindow(strm, strm->next_out, out - strm->avail_out)) {
- state->mode = MEM;
- return Z_MEM_ERROR;
- }
- in -= strm->avail_in;
- out -= strm->avail_out;
- strm->total_in += in;
- strm->total_out += out;
- state->total += out;
- if (state->wrap && out)
- strm->adler = state->check =
- UPDATE(state->check, strm->next_out - out, out);
- strm->data_type = state->bits + (state->last ? 64 : 0) +
- (state->mode == TYPE ? 128 : 0) +
- (state->mode == LEN_ || state->mode == COPY_ ? 256 : 0);
- if (((in == 0 && out == 0) || flush == Z_FINISH) && ret == Z_OK)
- ret = Z_BUF_ERROR;
- return ret;
-}
-
-int ZEXPORT inflateEnd(strm)
-z_streamp strm;
-{
- struct inflate_state FAR *state;
- if (strm == Z_NULL || strm->state == Z_NULL || strm->zfree == (free_func)0)
- return Z_STREAM_ERROR;
- state = (struct inflate_state FAR *)strm->state;
- if (state->window != Z_NULL) ZFREE(strm, state->window);
- ZFREE(strm, strm->state);
- strm->state = Z_NULL;
- Tracev((stderr, "inflate: end\n"));
- return Z_OK;
-}
-
-int ZEXPORT inflateGetDictionary(strm, dictionary, dictLength)
-z_streamp strm;
-Bytef *dictionary;
-uInt *dictLength;
-{
- struct inflate_state FAR *state;
-
- /* check state */
- if (strm == Z_NULL || strm->state == Z_NULL) return Z_STREAM_ERROR;
- state = (struct inflate_state FAR *)strm->state;
-
- /* copy dictionary */
- if (state->whave && dictionary != Z_NULL) {
- zmemcpy(dictionary, state->window + state->wnext,
- state->whave - state->wnext);
- zmemcpy(dictionary + state->whave - state->wnext,
- state->window, state->wnext);
- }
- if (dictLength != Z_NULL)
- *dictLength = state->whave;
- return Z_OK;
-}
-
-int ZEXPORT inflateSetDictionary(strm, dictionary, dictLength)
-z_streamp strm;
-const Bytef *dictionary;
-uInt dictLength;
-{
- struct inflate_state FAR *state;
- unsigned long dictid;
- int ret;
-
- /* check state */
- if (strm == Z_NULL || strm->state == Z_NULL) return Z_STREAM_ERROR;
- state = (struct inflate_state FAR *)strm->state;
- if (state->wrap != 0 && state->mode != DICT)
- return Z_STREAM_ERROR;
-
- /* check for correct dictionary identifier */
- if (state->mode == DICT) {
- dictid = adler32(0L, Z_NULL, 0);
- dictid = adler32(dictid, dictionary, dictLength);
- if (dictid != state->check)
- return Z_DATA_ERROR;
- }
-
- /* copy dictionary to window using updatewindow(), which will amend the
- existing dictionary if appropriate */
- ret = updatewindow(strm, dictionary + dictLength, dictLength);
- if (ret) {
- state->mode = MEM;
- return Z_MEM_ERROR;
- }
- state->havedict = 1;
- Tracev((stderr, "inflate: dictionary set\n"));
- return Z_OK;
-}
-
-int ZEXPORT inflateGetHeader(strm, head)
-z_streamp strm;
-gz_headerp head;
-{
- struct inflate_state FAR *state;
-
- /* check state */
- if (strm == Z_NULL || strm->state == Z_NULL) return Z_STREAM_ERROR;
- state = (struct inflate_state FAR *)strm->state;
- if ((state->wrap & 2) == 0) return Z_STREAM_ERROR;
-
- /* save header structure */
- state->head = head;
- head->done = 0;
- return Z_OK;
-}
-
-/*
- Search buf[0..len-1] for the pattern: 0, 0, 0xff, 0xff. Return when found
- or when out of input. When called, *have is the number of pattern bytes
- found in order so far, in 0..3. On return *have is updated to the new
- state. If on return *have equals four, then the pattern was found and the
- return value is how many bytes were read including the last byte of the
- pattern. If *have is less than four, then the pattern has not been found
- yet and the return value is len. In the latter case, syncsearch() can be
- called again with more data and the *have state. *have is initialized to
- zero for the first call.
- */
-local unsigned syncsearch(have, buf, len)
-unsigned FAR *have;
-const unsigned char FAR *buf;
-unsigned len;
-{
- unsigned got;
- unsigned next;
-
- got = *have;
- next = 0;
- while (next < len && got < 4) {
- if ((int)(buf[next]) == (got < 2 ? 0 : 0xff))
- got++;
- else if (buf[next])
- got = 0;
- else
- got = 4 - got;
- next++;
- }
- *have = got;
- return next;
-}
-
-int ZEXPORT inflateSync(strm)
-z_streamp strm;
-{
- unsigned len; /* number of bytes to look at or looked at */
- unsigned long in, out; /* temporary to save total_in and total_out */
- unsigned char buf[4]; /* to restore bit buffer to byte string */
- struct inflate_state FAR *state;
-
- /* check parameters */
- if (strm == Z_NULL || strm->state == Z_NULL) return Z_STREAM_ERROR;
- state = (struct inflate_state FAR *)strm->state;
- if (strm->avail_in == 0 && state->bits < 8) return Z_BUF_ERROR;
-
- /* if first time, start search in bit buffer */
- if (state->mode != SYNC) {
- state->mode = SYNC;
- state->hold <<= state->bits & 7;
- state->bits -= state->bits & 7;
- len = 0;
- while (state->bits >= 8) {
- buf[len++] = (unsigned char)(state->hold);
- state->hold >>= 8;
- state->bits -= 8;
- }
- state->have = 0;
- syncsearch(&(state->have), buf, len);
- }
-
- /* search available input */
- len = syncsearch(&(state->have), strm->next_in, strm->avail_in);
- strm->avail_in -= len;
- strm->next_in += len;
- strm->total_in += len;
-
- /* return no joy or set up to restart inflate() on a new block */
- if (state->have != 4) return Z_DATA_ERROR;
- in = strm->total_in; out = strm->total_out;
- inflateReset(strm);
- strm->total_in = in; strm->total_out = out;
- state->mode = TYPE;
- return Z_OK;
-}
-
-/*
- Returns true if inflate is currently at the end of a block generated by
- Z_SYNC_FLUSH or Z_FULL_FLUSH. This function is used by one PPP
- implementation to provide an additional safety check. PPP uses
- Z_SYNC_FLUSH but removes the length bytes of the resulting empty stored
- block. When decompressing, PPP checks that at the end of input packet,
- inflate is waiting for these length bytes.
- */
-int ZEXPORT inflateSyncPoint(strm)
-z_streamp strm;
-{
- struct inflate_state FAR *state;
-
- if (strm == Z_NULL || strm->state == Z_NULL) return Z_STREAM_ERROR;
- state = (struct inflate_state FAR *)strm->state;
- return state->mode == STORED && state->bits == 0;
-}
-
-int ZEXPORT inflateCopy(dest, source)
-z_streamp dest;
-z_streamp source;
-{
- struct inflate_state FAR *state;
- struct inflate_state FAR *copy;
- unsigned char FAR *window;
- unsigned wsize;
-
- /* check input */
- if (dest == Z_NULL || source == Z_NULL || source->state == Z_NULL ||
- source->zalloc == (alloc_func)0 || source->zfree == (free_func)0)
- return Z_STREAM_ERROR;
- state = (struct inflate_state FAR *)source->state;
-
- /* allocate space */
- copy = (struct inflate_state FAR *)
- ZALLOC(source, 1, sizeof(struct inflate_state));
- if (copy == Z_NULL) return Z_MEM_ERROR;
- window = Z_NULL;
- if (state->window != Z_NULL) {
- window = (unsigned char FAR *)
- ZALLOC(source, 1U << state->wbits, sizeof(unsigned char));
- if (window == Z_NULL) {
- ZFREE(source, copy);
- return Z_MEM_ERROR;
- }
- }
-
- /* copy state */
- zmemcpy((voidpf)dest, (voidpf)source, sizeof(z_stream));
- zmemcpy((voidpf)copy, (voidpf)state, sizeof(struct inflate_state));
- if (state->lencode >= state->codes &&
- state->lencode <= state->codes + ENOUGH - 1) {
- copy->lencode = copy->codes + (state->lencode - state->codes);
- copy->distcode = copy->codes + (state->distcode - state->codes);
- }
- copy->next = copy->codes + (state->next - state->codes);
- if (window != Z_NULL) {
- wsize = 1U << state->wbits;
- zmemcpy(window, state->window, wsize);
- }
- copy->window = window;
- dest->state = (struct internal_state FAR *)copy;
- return Z_OK;
-}
-
-int ZEXPORT inflateUndermine(strm, subvert)
-z_streamp strm;
-int subvert;
-{
- struct inflate_state FAR *state;
-
- if (strm == Z_NULL || strm->state == Z_NULL) return Z_STREAM_ERROR;
- state = (struct inflate_state FAR *)strm->state;
- state->sane = !subvert;
-#ifdef INFLATE_ALLOW_INVALID_DISTANCE_TOOFAR_ARRR
- return Z_OK;
-#else
- state->sane = 1;
- return Z_DATA_ERROR;
-#endif
-}
-
-long ZEXPORT inflateMark(strm)
-z_streamp strm;
-{
- struct inflate_state FAR *state;
-
- if (strm == Z_NULL || strm->state == Z_NULL) return -1L << 16;
- state = (struct inflate_state FAR *)strm->state;
- return ((long)(state->back) << 16) +
- (state->mode == COPY ? state->length :
- (state->mode == MATCH ? state->was - state->length : 0));
-}
diff --git a/third-party/zlib/inflate.h b/third-party/zlib/inflate.h
deleted file mode 100644
index 95f4986..0000000
--- a/third-party/zlib/inflate.h
+++ /dev/null
@@ -1,122 +0,0 @@
-/* inflate.h -- internal inflate state definition
- * Copyright (C) 1995-2009 Mark Adler
- * For conditions of distribution and use, see copyright notice in zlib.h
- */
-
-/* WARNING: this file should *not* be used by applications. It is
- part of the implementation of the compression library and is
- subject to change. Applications should only use zlib.h.
- */
-
-/* define NO_GZIP when compiling if you want to disable gzip header and
- trailer decoding by inflate(). NO_GZIP would be used to avoid linking in
- the crc code when it is not needed. For shared libraries, gzip decoding
- should be left enabled. */
-#ifndef NO_GZIP
-# define GUNZIP
-#endif
-
-/* Possible inflate modes between inflate() calls */
-typedef enum {
- HEAD, /* i: waiting for magic header */
- FLAGS, /* i: waiting for method and flags (gzip) */
- TIME, /* i: waiting for modification time (gzip) */
- OS, /* i: waiting for extra flags and operating system (gzip) */
- EXLEN, /* i: waiting for extra length (gzip) */
- EXTRA, /* i: waiting for extra bytes (gzip) */
- NAME, /* i: waiting for end of file name (gzip) */
- COMMENT, /* i: waiting for end of comment (gzip) */
- HCRC, /* i: waiting for header crc (gzip) */
- DICTID, /* i: waiting for dictionary check value */
- DICT, /* waiting for inflateSetDictionary() call */
- TYPE, /* i: waiting for type bits, including last-flag bit */
- TYPEDO, /* i: same, but skip check to exit inflate on new block */
- STORED, /* i: waiting for stored size (length and complement) */
- COPY_, /* i/o: same as COPY below, but only first time in */
- COPY, /* i/o: waiting for input or output to copy stored block */
- TABLE, /* i: waiting for dynamic block table lengths */
- LENLENS, /* i: waiting for code length code lengths */
- CODELENS, /* i: waiting for length/lit and distance code lengths */
- LEN_, /* i: same as LEN below, but only first time in */
- LEN, /* i: waiting for length/lit/eob code */
- LENEXT, /* i: waiting for length extra bits */
- DIST, /* i: waiting for distance code */
- DISTEXT, /* i: waiting for distance extra bits */
- MATCH, /* o: waiting for output space to copy string */
- LIT, /* o: waiting for output space to write literal */
- CHECK, /* i: waiting for 32-bit check value */
- LENGTH, /* i: waiting for 32-bit length (gzip) */
- DONE, /* finished check, done -- remain here until reset */
- BAD, /* got a data error -- remain here until reset */
- MEM, /* got an inflate() memory error -- remain here until reset */
- SYNC /* looking for synchronization bytes to restart inflate() */
-} inflate_mode;
-
-/*
- State transitions between above modes -
-
- (most modes can go to BAD or MEM on error -- not shown for clarity)
-
- Process header:
- HEAD -> (gzip) or (zlib) or (raw)
- (gzip) -> FLAGS -> TIME -> OS -> EXLEN -> EXTRA -> NAME -> COMMENT ->
- HCRC -> TYPE
- (zlib) -> DICTID or TYPE
- DICTID -> DICT -> TYPE
- (raw) -> TYPEDO
- Read deflate blocks:
- TYPE -> TYPEDO -> STORED or TABLE or LEN_ or CHECK
- STORED -> COPY_ -> COPY -> TYPE
- TABLE -> LENLENS -> CODELENS -> LEN_
- LEN_ -> LEN
- Read deflate codes in fixed or dynamic block:
- LEN -> LENEXT or LIT or TYPE
- LENEXT -> DIST -> DISTEXT -> MATCH -> LEN
- LIT -> LEN
- Process trailer:
- CHECK -> LENGTH -> DONE
- */
-
-/* state maintained between inflate() calls. Approximately 10K bytes. */
-struct inflate_state {
- inflate_mode mode; /* current inflate mode */
- int last; /* true if processing last block */
- int wrap; /* bit 0 true for zlib, bit 1 true for gzip */
- int havedict; /* true if dictionary provided */
- int flags; /* gzip header method and flags (0 if zlib) */
- unsigned dmax; /* zlib header max distance (INFLATE_STRICT) */
- unsigned long check; /* protected copy of check value */
- unsigned long total; /* protected copy of output count */
- gz_headerp head; /* where to save gzip header information */
- /* sliding window */
- unsigned wbits; /* log base 2 of requested window size */
- unsigned wsize; /* window size or zero if not using window */
- unsigned whave; /* valid bytes in the window */
- unsigned wnext; /* window write index */
- unsigned char FAR *window; /* allocated sliding window, if needed */
- /* bit accumulator */
- unsigned long hold; /* input bit accumulator */
- unsigned bits; /* number of bits in "in" */
- /* for string and stored block copying */
- unsigned length; /* literal or length of data to copy */
- unsigned offset; /* distance back to copy string from */
- /* for table and code decoding */
- unsigned extra; /* extra bits needed */
- /* fixed and dynamic code tables */
- code const FAR *lencode; /* starting table for length/literal codes */
- code const FAR *distcode; /* starting table for distance codes */
- unsigned lenbits; /* index bits for lencode */
- unsigned distbits; /* index bits for distcode */
- /* dynamic table building */
- unsigned ncode; /* number of code length code lengths */
- unsigned nlen; /* number of length code lengths */
- unsigned ndist; /* number of distance code lengths */
- unsigned have; /* number of code lengths in lens[] */
- code FAR *next; /* next available space in codes[] */
- unsigned short lens[320]; /* temporary storage for code lengths */
- unsigned short work[288]; /* work area for code table building */
- code codes[ENOUGH]; /* space for code tables */
- int sane; /* if false, allow invalid distance too far */
- int back; /* bits back of last unprocessed length/lit */
- unsigned was; /* initial length of match */
-};
diff --git a/third-party/zlib/inftrees.c b/third-party/zlib/inftrees.c
deleted file mode 100644
index 44d89cf..0000000
--- a/third-party/zlib/inftrees.c
+++ /dev/null
@@ -1,306 +0,0 @@
-/* inftrees.c -- generate Huffman trees for efficient decoding
- * Copyright (C) 1995-2013 Mark Adler
- * For conditions of distribution and use, see copyright notice in zlib.h
- */
-
-#include "zutil.h"
-#include "inftrees.h"
-
-#define MAXBITS 15
-
-const char inflate_copyright[] =
- " inflate 1.2.8 Copyright 1995-2013 Mark Adler ";
-/*
- If you use the zlib library in a product, an acknowledgment is welcome
- in the documentation of your product. If for some reason you cannot
- include such an acknowledgment, I would appreciate that you keep this
- copyright string in the executable of your product.
- */
-
-/*
- Build a set of tables to decode the provided canonical Huffman code.
- The code lengths are lens[0..codes-1]. The result starts at *table,
- whose indices are 0..2^bits-1. work is a writable array of at least
- lens shorts, which is used as a work area. type is the type of code
- to be generated, CODES, LENS, or DISTS. On return, zero is success,
- -1 is an invalid code, and +1 means that ENOUGH isn't enough. table
- on return points to the next available entry's address. bits is the
- requested root table index bits, and on return it is the actual root
- table index bits. It will differ if the request is greater than the
- longest code or if it is less than the shortest code.
- */
-int ZLIB_INTERNAL inflate_table(type, lens, codes, table, bits, work)
-codetype type;
-unsigned short FAR *lens;
-unsigned codes;
-code FAR * FAR *table;
-unsigned FAR *bits;
-unsigned short FAR *work;
-{
- unsigned len; /* a code's length in bits */
- unsigned sym; /* index of code symbols */
- unsigned min, max; /* minimum and maximum code lengths */
- unsigned root; /* number of index bits for root table */
- unsigned curr; /* number of index bits for current table */
- unsigned drop; /* code bits to drop for sub-table */
- int left; /* number of prefix codes available */
- unsigned used; /* code entries in table used */
- unsigned huff; /* Huffman code */
- unsigned incr; /* for incrementing code, index */
- unsigned fill; /* index for replicating entries */
- unsigned low; /* low bits for current root entry */
- unsigned mask; /* mask for low root bits */
- code here; /* table entry for duplication */
- code FAR *next; /* next available space in table */
- const unsigned short FAR *base; /* base value table to use */
- const unsigned short FAR *extra; /* extra bits table to use */
- int end; /* use base and extra for symbol > end */
- unsigned short count[MAXBITS+1]; /* number of codes of each length */
- unsigned short offs[MAXBITS+1]; /* offsets in table for each length */
- static const unsigned short lbase[31] = { /* Length codes 257..285 base */
- 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 15, 17, 19, 23, 27, 31,
- 35, 43, 51, 59, 67, 83, 99, 115, 131, 163, 195, 227, 258, 0, 0};
- static const unsigned short lext[31] = { /* Length codes 257..285 extra */
- 16, 16, 16, 16, 16, 16, 16, 16, 17, 17, 17, 17, 18, 18, 18, 18,
- 19, 19, 19, 19, 20, 20, 20, 20, 21, 21, 21, 21, 16, 72, 78};
- static const unsigned short dbase[32] = { /* Distance codes 0..29 base */
- 1, 2, 3, 4, 5, 7, 9, 13, 17, 25, 33, 49, 65, 97, 129, 193,
- 257, 385, 513, 769, 1025, 1537, 2049, 3073, 4097, 6145,
- 8193, 12289, 16385, 24577, 0, 0};
- static const unsigned short dext[32] = { /* Distance codes 0..29 extra */
- 16, 16, 16, 16, 17, 17, 18, 18, 19, 19, 20, 20, 21, 21, 22, 22,
- 23, 23, 24, 24, 25, 25, 26, 26, 27, 27,
- 28, 28, 29, 29, 64, 64};
-
- /*
- Process a set of code lengths to create a canonical Huffman code. The
- code lengths are lens[0..codes-1]. Each length corresponds to the
- symbols 0..codes-1. The Huffman code is generated by first sorting the
- symbols by length from short to long, and retaining the symbol order
- for codes with equal lengths. Then the code starts with all zero bits
- for the first code of the shortest length, and the codes are integer
- increments for the same length, and zeros are appended as the length
- increases. For the deflate format, these bits are stored backwards
- from their more natural integer increment ordering, and so when the
- decoding tables are built in the large loop below, the integer codes
- are incremented backwards.
-
- This routine assumes, but does not check, that all of the entries in
- lens[] are in the range 0..MAXBITS. The caller must assure this.
- 1..MAXBITS is interpreted as that code length. zero means that that
- symbol does not occur in this code.
-
- The codes are sorted by computing a count of codes for each length,
- creating from that a table of starting indices for each length in the
- sorted table, and then entering the symbols in order in the sorted
- table. The sorted table is work[], with that space being provided by
- the caller.
-
- The length counts are used for other purposes as well, i.e. finding
- the minimum and maximum length codes, determining if there are any
- codes at all, checking for a valid set of lengths, and looking ahead
- at length counts to determine sub-table sizes when building the
- decoding tables.
- */
-
- /* accumulate lengths for codes (assumes lens[] all in 0..MAXBITS) */
- for (len = 0; len <= MAXBITS; len++)
- count[len] = 0;
- for (sym = 0; sym < codes; sym++)
- count[lens[sym]]++;
-
- /* bound code lengths, force root to be within code lengths */
- root = *bits;
- for (max = MAXBITS; max >= 1; max--)
- if (count[max] != 0) break;
- if (root > max) root = max;
- if (max == 0) { /* no symbols to code at all */
- here.op = (unsigned char)64; /* invalid code marker */
- here.bits = (unsigned char)1;
- here.val = (unsigned short)0;
- *(*table)++ = here; /* make a table to force an error */
- *(*table)++ = here;
- *bits = 1;
- return 0; /* no symbols, but wait for decoding to report error */
- }
- for (min = 1; min < max; min++)
- if (count[min] != 0) break;
- if (root < min) root = min;
-
- /* check for an over-subscribed or incomplete set of lengths */
- left = 1;
- for (len = 1; len <= MAXBITS; len++) {
- left <<= 1;
- left -= count[len];
- if (left < 0) return -1; /* over-subscribed */
- }
- if (left > 0 && (type == CODES || max != 1))
- return -1; /* incomplete set */
-
- /* generate offsets into symbol table for each length for sorting */
- offs[1] = 0;
- for (len = 1; len < MAXBITS; len++)
- offs[len + 1] = offs[len] + count[len];
-
- /* sort symbols by length, by symbol order within each length */
- for (sym = 0; sym < codes; sym++)
- if (lens[sym] != 0) work[offs[lens[sym]]++] = (unsigned short)sym;
-
- /*
- Create and fill in decoding tables. In this loop, the table being
- filled is at next and has curr index bits. The code being used is huff
- with length len. That code is converted to an index by dropping drop
- bits off of the bottom. For codes where len is less than drop + curr,
- those top drop + curr - len bits are incremented through all values to
- fill the table with replicated entries.
-
- root is the number of index bits for the root table. When len exceeds
- root, sub-tables are created pointed to by the root entry with an index
- of the low root bits of huff. This is saved in low to check for when a
- new sub-table should be started. drop is zero when the root table is
- being filled, and drop is root when sub-tables are being filled.
-
- When a new sub-table is needed, it is necessary to look ahead in the
- code lengths to determine what size sub-table is needed. The length
- counts are used for this, and so count[] is decremented as codes are
- entered in the tables.
-
- used keeps track of how many table entries have been allocated from the
- provided *table space. It is checked for LENS and DIST tables against
- the constants ENOUGH_LENS and ENOUGH_DISTS to guard against changes in
- the initial root table size constants. See the comments in inftrees.h
- for more information.
-
- sym increments through all symbols, and the loop terminates when
- all codes of length max, i.e. all codes, have been processed. This
- routine permits incomplete codes, so another loop after this one fills
- in the rest of the decoding tables with invalid code markers.
- */
-
- /* set up for code type */
- switch (type) {
- case CODES:
- base = extra = work; /* dummy value--not used */
- end = 19;
- break;
- case LENS:
- base = lbase;
- base -= 257;
- extra = lext;
- extra -= 257;
- end = 256;
- break;
- default: /* DISTS */
- base = dbase;
- extra = dext;
- end = -1;
- }
-
- /* initialize state for loop */
- huff = 0; /* starting code */
- sym = 0; /* starting code symbol */
- len = min; /* starting code length */
- next = *table; /* current table to fill in */
- curr = root; /* current table index bits */
- drop = 0; /* current bits to drop from code for index */
- low = (unsigned)(-1); /* trigger new sub-table when len > root */
- used = 1U << root; /* use root table entries */
- mask = used - 1; /* mask for comparing low */
-
- /* check available table space */
- if ((type == LENS && used > ENOUGH_LENS) ||
- (type == DISTS && used > ENOUGH_DISTS))
- return 1;
-
- /* process all codes and make table entries */
- for (;;) {
- /* create table entry */
- here.bits = (unsigned char)(len - drop);
- if ((int)(work[sym]) < end) {
- here.op = (unsigned char)0;
- here.val = work[sym];
- }
- else if ((int)(work[sym]) > end) {
- here.op = (unsigned char)(extra[work[sym]]);
- here.val = base[work[sym]];
- }
- else {
- here.op = (unsigned char)(32 + 64); /* end of block */
- here.val = 0;
- }
-
- /* replicate for those indices with low len bits equal to huff */
- incr = 1U << (len - drop);
- fill = 1U << curr;
- min = fill; /* save offset to next table */
- do {
- fill -= incr;
- next[(huff >> drop) + fill] = here;
- } while (fill != 0);
-
- /* backwards increment the len-bit code huff */
- incr = 1U << (len - 1);
- while (huff & incr)
- incr >>= 1;
- if (incr != 0) {
- huff &= incr - 1;
- huff += incr;
- }
- else
- huff = 0;
-
- /* go to next symbol, update count, len */
- sym++;
- if (--(count[len]) == 0) {
- if (len == max) break;
- len = lens[work[sym]];
- }
-
- /* create new sub-table if needed */
- if (len > root && (huff & mask) != low) {
- /* if first time, transition to sub-tables */
- if (drop == 0)
- drop = root;
-
- /* increment past last table */
- next += min; /* here min is 1 << curr */
-
- /* determine length of next table */
- curr = len - drop;
- left = (int)(1 << curr);
- while (curr + drop < max) {
- left -= count[curr + drop];
- if (left <= 0) break;
- curr++;
- left <<= 1;
- }
-
- /* check for enough space */
- used += 1U << curr;
- if ((type == LENS && used > ENOUGH_LENS) ||
- (type == DISTS && used > ENOUGH_DISTS))
- return 1;
-
- /* point entry in root table to sub-table */
- low = huff & mask;
- (*table)[low].op = (unsigned char)curr;
- (*table)[low].bits = (unsigned char)root;
- (*table)[low].val = (unsigned short)(next - *table);
- }
- }
-
- /* fill in remaining table entry if code is incomplete (guaranteed to have
- at most one remaining entry, since if the code is incomplete, the
- maximum code length that was allowed to get this far is one bit) */
- if (huff != 0) {
- here.op = (unsigned char)64; /* invalid code marker */
- here.bits = (unsigned char)(len - drop);
- here.val = (unsigned short)0;
- next[huff] = here;
- }
-
- /* set return parameters */
- *table += used;
- *bits = root;
- return 0;
-}
diff --git a/third-party/zlib/inftrees.h b/third-party/zlib/inftrees.h
deleted file mode 100644
index baa53a0..0000000
--- a/third-party/zlib/inftrees.h
+++ /dev/null
@@ -1,62 +0,0 @@
-/* inftrees.h -- header to use inftrees.c
- * Copyright (C) 1995-2005, 2010 Mark Adler
- * For conditions of distribution and use, see copyright notice in zlib.h
- */
-
-/* WARNING: this file should *not* be used by applications. It is
- part of the implementation of the compression library and is
- subject to change. Applications should only use zlib.h.
- */
-
-/* Structure for decoding tables. Each entry provides either the
- information needed to do the operation requested by the code that
- indexed that table entry, or it provides a pointer to another
- table that indexes more bits of the code. op indicates whether
- the entry is a pointer to another table, a literal, a length or
- distance, an end-of-block, or an invalid code. For a table
- pointer, the low four bits of op is the number of index bits of
- that table. For a length or distance, the low four bits of op
- is the number of extra bits to get after the code. bits is
- the number of bits in this code or part of the code to drop off
- of the bit buffer. val is the actual byte to output in the case
- of a literal, the base length or distance, or the offset from
- the current table to the next table. Each entry is four bytes. */
-typedef struct {
- unsigned char op; /* operation, extra bits, table bits */
- unsigned char bits; /* bits in this part of the code */
- unsigned short val; /* offset in table or code value */
-} code;
-
-/* op values as set by inflate_table():
- 00000000 - literal
- 0000tttt - table link, tttt != 0 is the number of table index bits
- 0001eeee - length or distance, eeee is the number of extra bits
- 01100000 - end of block
- 01000000 - invalid code
- */
-
-/* Maximum size of the dynamic table. The maximum number of code structures is
- 1444, which is the sum of 852 for literal/length codes and 592 for distance
- codes. These values were found by exhaustive searches using the program
- examples/enough.c found in the zlib distribtution. The arguments to that
- program are the number of symbols, the initial root table size, and the
- maximum bit length of a code. "enough 286 9 15" for literal/length codes
- returns returns 852, and "enough 30 6 15" for distance codes returns 592.
- The initial root table size (9 or 6) is found in the fifth argument of the
- inflate_table() calls in inflate.c and infback.c. If the root table size is
- changed, then these maximum sizes would be need to be recalculated and
- updated. */
-#define ENOUGH_LENS 852
-#define ENOUGH_DISTS 592
-#define ENOUGH (ENOUGH_LENS+ENOUGH_DISTS)
-
-/* Type of code to build for inflate_table() */
-typedef enum {
- CODES,
- LENS,
- DISTS
-} codetype;
-
-int ZLIB_INTERNAL inflate_table OF((codetype type, unsigned short FAR *lens,
- unsigned codes, code FAR * FAR *table,
- unsigned FAR *bits, unsigned short FAR *work));
diff --git a/third-party/zlib/make_vms.com b/third-party/zlib/make_vms.com
deleted file mode 100644
index 65e9d0c..0000000
--- a/third-party/zlib/make_vms.com
+++ /dev/null
@@ -1,867 +0,0 @@
-$! make libz under VMS written by
-$! Martin P.J. Zinser
-$!
-$! In case of problems with the install you might contact me at
-$! zinser at zinser.no-ip.info(preferred) or
-$! martin.zinser at eurexchange.com (work)
-$!
-$! Make procedure history for Zlib
-$!
-$!------------------------------------------------------------------------------
-$! Version history
-$! 0.01 20060120 First version to receive a number
-$! 0.02 20061008 Adapt to new Makefile.in
-$! 0.03 20091224 Add support for large file check
-$! 0.04 20100110 Add new gzclose, gzlib, gzread, gzwrite
-$! 0.05 20100221 Exchange zlibdefs.h by zconf.h.in
-$! 0.06 20120111 Fix missing amiss_err, update zconf_h.in, fix new exmples
-$! subdir path, update module search in makefile.in
-$! 0.07 20120115 Triggered by work done by Alexey Chupahin completly redesigned
-$! shared image creation
-$! 0.08 20120219 Make it work on VAX again, pre-load missing symbols to shared
-$! image
-$! 0.09 20120305 SMS. P1 sets builder ("MMK", "MMS", " " (built-in)).
-$! "" -> automatic, preference: MMK, MMS, built-in.
-$!
-$ on error then goto err_exit
-$!
-$ true = 1
-$ false = 0
-$ tmpnam = "temp_" + f$getjpi("","pid")
-$ tt = tmpnam + ".txt"
-$ tc = tmpnam + ".c"
-$ th = tmpnam + ".h"
-$ define/nolog tconfig 'th'
-$ its_decc = false
-$ its_vaxc = false
-$ its_gnuc = false
-$ s_case = False
-$!
-$! Setup variables holding "config" information
-$!
-$ Make = "''p1'"
-$ name = "Zlib"
-$ version = "?.?.?"
-$ v_string = "ZLIB_VERSION"
-$ v_file = "zlib.h"
-$ ccopt = "/include = []"
-$ lopts = ""
-$ dnsrl = ""
-$ aconf_in_file = "zconf.h.in#zconf.h_in#zconf_h.in"
-$ conf_check_string = ""
-$ linkonly = false
-$ optfile = name + ".opt"
-$ mapfile = name + ".map"
-$ libdefs = ""
-$ vax = f$getsyi("HW_MODEL").lt.1024
-$ axp = f$getsyi("HW_MODEL").ge.1024 .and. f$getsyi("HW_MODEL").lt.4096
-$ ia64 = f$getsyi("HW_MODEL").ge.4096
-$!
-$! 2012-03-05 SMS.
-$! Why is this needed? And if it is needed, why not simply ".not. vax"?
-$!
-$!!! if axp .or. ia64 then set proc/parse=extended
-$!
-$ whoami = f$parse(f$environment("Procedure"),,,,"NO_CONCEAL")
-$ mydef = F$parse(whoami,,,"DEVICE")
-$ mydir = f$parse(whoami,,,"DIRECTORY") - "]["
-$ myproc = f$parse(whoami,,,"Name") + f$parse(whoami,,,"type")
-$!
-$! Check for MMK/MMS
-$!
-$ if (Make .eqs. "")
-$ then
-$ If F$Search ("Sys$System:MMS.EXE") .nes. "" Then Make = "MMS"
-$ If F$Type (MMK) .eqs. "STRING" Then Make = "MMK"
-$ else
-$ Make = f$edit( Make, "trim")
-$ endif
-$!
-$ gosub find_version
-$!
-$ open/write topt tmp.opt
-$ open/write optf 'optfile'
-$!
-$ gosub check_opts
-$!
-$! Look for the compiler used
-$!
-$ gosub check_compiler
-$ close topt
-$ close optf
-$!
-$ if its_decc
-$ then
-$ ccopt = "/prefix=all" + ccopt
-$ if f$trnlnm("SYS") .eqs. ""
-$ then
-$ if axp
-$ then
-$ define sys sys$library:
-$ else
-$ ccopt = "/decc" + ccopt
-$ define sys decc$library_include:
-$ endif
-$ endif
-$!
-$! 2012-03-05 SMS.
-$! Why /NAMES = AS_IS? Why not simply ".not. vax"? And why not on VAX?
-$!
-$ if axp .or. ia64
-$ then
-$ ccopt = ccopt + "/name=as_is/opt=(inline=speed)"
-$ s_case = true
-$ endif
-$ endif
-$ if its_vaxc .or. its_gnuc
-$ then
-$ if f$trnlnm("SYS").eqs."" then define sys sys$library:
-$ endif
-$!
-$! Build a fake configure input header
-$!
-$ open/write conf_hin config.hin
-$ write conf_hin "#undef _LARGEFILE64_SOURCE"
-$ close conf_hin
-$!
-$!
-$ i = 0
-$FIND_ACONF:
-$ fname = f$element(i,"#",aconf_in_file)
-$ if fname .eqs. "#" then goto AMISS_ERR
-$ if f$search(fname) .eqs. ""
-$ then
-$ i = i + 1
-$ goto find_aconf
-$ endif
-$ open/read/err=aconf_err aconf_in 'fname'
-$ open/write aconf zconf.h
-$ACONF_LOOP:
-$ read/end_of_file=aconf_exit aconf_in line
-$ work = f$edit(line, "compress,trim")
-$ if f$extract(0,6,work) .nes. "#undef"
-$ then
-$ if f$extract(0,12,work) .nes. "#cmakedefine"
-$ then
-$ write aconf line
-$ endif
-$ else
-$ cdef = f$element(1," ",work)
-$ gosub check_config
-$ endif
-$ goto aconf_loop
-$ACONF_EXIT:
-$ write aconf ""
-$ write aconf "/* VMS specifics added by make_vms.com: */"
-$ write aconf "#define VMS 1"
-$ write aconf "#include <unistd.h>"
-$ write aconf "#include <unixio.h>"
-$ write aconf "#ifdef _LARGEFILE"
-$ write aconf "# define off64_t __off64_t"
-$ write aconf "# define fopen64 fopen"
-$ write aconf "# define fseeko64 fseeko"
-$ write aconf "# define lseek64 lseek"
-$ write aconf "# define ftello64 ftell"
-$ write aconf "#endif"
-$ write aconf "#if !defined( __VAX) && (__CRTL_VER >= 70312000)"
-$ write aconf "# define HAVE_VSNPRINTF"
-$ write aconf "#endif"
-$ close aconf_in
-$ close aconf
-$ if f$search("''th'") .nes. "" then delete 'th';*
-$! Build the thing plain or with mms
-$!
-$ write sys$output "Compiling Zlib sources ..."
-$ if make.eqs.""
-$ then
-$ if (f$search( "example.obj;*") .nes. "") then delete example.obj;*
-$ if (f$search( "minigzip.obj;*") .nes. "") then delete minigzip.obj;*
-$ CALL MAKE adler32.OBJ "CC ''CCOPT' adler32" -
- adler32.c zlib.h zconf.h
-$ CALL MAKE compress.OBJ "CC ''CCOPT' compress" -
- compress.c zlib.h zconf.h
-$ CALL MAKE crc32.OBJ "CC ''CCOPT' crc32" -
- crc32.c zlib.h zconf.h
-$ CALL MAKE deflate.OBJ "CC ''CCOPT' deflate" -
- deflate.c deflate.h zutil.h zlib.h zconf.h
-$ CALL MAKE gzclose.OBJ "CC ''CCOPT' gzclose" -
- gzclose.c zutil.h zlib.h zconf.h
-$ CALL MAKE gzlib.OBJ "CC ''CCOPT' gzlib" -
- gzlib.c zutil.h zlib.h zconf.h
-$ CALL MAKE gzread.OBJ "CC ''CCOPT' gzread" -
- gzread.c zutil.h zlib.h zconf.h
-$ CALL MAKE gzwrite.OBJ "CC ''CCOPT' gzwrite" -
- gzwrite.c zutil.h zlib.h zconf.h
-$ CALL MAKE infback.OBJ "CC ''CCOPT' infback" -
- infback.c zutil.h inftrees.h inflate.h inffast.h inffixed.h
-$ CALL MAKE inffast.OBJ "CC ''CCOPT' inffast" -
- inffast.c zutil.h zlib.h zconf.h inffast.h
-$ CALL MAKE inflate.OBJ "CC ''CCOPT' inflate" -
- inflate.c zutil.h zlib.h zconf.h infblock.h
-$ CALL MAKE inftrees.OBJ "CC ''CCOPT' inftrees" -
- inftrees.c zutil.h zlib.h zconf.h inftrees.h
-$ CALL MAKE trees.OBJ "CC ''CCOPT' trees" -
- trees.c deflate.h zutil.h zlib.h zconf.h
-$ CALL MAKE uncompr.OBJ "CC ''CCOPT' uncompr" -
- uncompr.c zlib.h zconf.h
-$ CALL MAKE zutil.OBJ "CC ''CCOPT' zutil" -
- zutil.c zutil.h zlib.h zconf.h
-$ write sys$output "Building Zlib ..."
-$ CALL MAKE libz.OLB "lib/crea libz.olb *.obj" *.OBJ
-$ write sys$output "Building example..."
-$ CALL MAKE example.OBJ "CC ''CCOPT' [.test]example" -
- [.test]example.c zlib.h zconf.h
-$ call make example.exe "LINK example,libz.olb/lib" example.obj libz.olb
-$ write sys$output "Building minigzip..."
-$ CALL MAKE minigzip.OBJ "CC ''CCOPT' [.test]minigzip" -
- [.test]minigzip.c zlib.h zconf.h
-$ call make minigzip.exe -
- "LINK minigzip,libz.olb/lib" -
- minigzip.obj libz.olb
-$ else
-$ gosub crea_mms
-$ write sys$output "Make ''name' ''version' with ''Make' "
-$ 'make'
-$ endif
-$!
-$! Create shareable image
-$!
-$ gosub crea_olist
-$ write sys$output "Creating libzshr.exe"
-$ call map_2_shopt 'mapfile' 'optfile'
-$ LINK_'lopts'/SHARE=libzshr.exe modules.opt/opt,'optfile'/opt
-$ write sys$output "Zlib build completed"
-$ delete/nolog tmp.opt;*
-$ exit
-$AMISS_ERR:
-$ write sys$output "No source for config.hin found."
-$ write sys$output "Tried any of ''aconf_in_file'"
-$ goto err_exit
-$CC_ERR:
-$ write sys$output "C compiler required to build ''name'"
-$ goto err_exit
-$ERR_EXIT:
-$ set message/facil/ident/sever/text
-$ close/nolog optf
-$ close/nolog topt
-$ close/nolog aconf_in
-$ close/nolog aconf
-$ close/nolog out
-$ close/nolog min
-$ close/nolog mod
-$ close/nolog h_in
-$ write sys$output "Exiting..."
-$ exit 2
-$!
-$!
-$MAKE: SUBROUTINE !SUBROUTINE TO CHECK DEPENDENCIES
-$ V = 'F$Verify(0)
-$! P1 = What we are trying to make
-$! P2 = Command to make it
-$! P3 - P8 What it depends on
-$
-$ If F$Search(P1) .Eqs. "" Then Goto Makeit
-$ Time = F$CvTime(F$File(P1,"RDT"))
-$arg=3
-$Loop:
-$ Argument = P'arg
-$ If Argument .Eqs. "" Then Goto Exit
-$ El=0
-$Loop2:
-$ File = F$Element(El," ",Argument)
-$ If File .Eqs. " " Then Goto Endl
-$ AFile = ""
-$Loop3:
-$ OFile = AFile
-$ AFile = F$Search(File)
-$ If AFile .Eqs. "" .Or. AFile .Eqs. OFile Then Goto NextEl
-$ If F$CvTime(F$File(AFile,"RDT")) .Ges. Time Then Goto Makeit
-$ Goto Loop3
-$NextEL:
-$ El = El + 1
-$ Goto Loop2
-$EndL:
-$ arg=arg+1
-$ If arg .Le. 8 Then Goto Loop
-$ Goto Exit
-$
-$Makeit:
-$ VV=F$VERIFY(0)
-$ write sys$output P2
-$ 'P2
-$ VV='F$Verify(VV)
-$Exit:
-$ If V Then Set Verify
-$ENDSUBROUTINE
-$!------------------------------------------------------------------------------
-$!
-$! Check command line options and set symbols accordingly
-$!
-$!------------------------------------------------------------------------------
-$! Version history
-$! 0.01 20041206 First version to receive a number
-$! 0.02 20060126 Add new "HELP" target
-$ CHECK_OPTS:
-$ i = 1
-$ OPT_LOOP:
-$ if i .lt. 9
-$ then
-$ cparm = f$edit(p'i',"upcase")
-$!
-$! Check if parameter actually contains something
-$!
-$ if f$edit(cparm,"trim") .nes. ""
-$ then
-$ if cparm .eqs. "DEBUG"
-$ then
-$ ccopt = ccopt + "/noopt/deb"
-$ lopts = lopts + "/deb"
-$ endif
-$ if f$locate("CCOPT=",cparm) .lt. f$length(cparm)
-$ then
-$ start = f$locate("=",cparm) + 1
-$ len = f$length(cparm) - start
-$ ccopt = ccopt + f$extract(start,len,cparm)
-$ if f$locate("AS_IS",f$edit(ccopt,"UPCASE")) .lt. f$length(ccopt) -
- then s_case = true
-$ endif
-$ if cparm .eqs. "LINK" then linkonly = true
-$ if f$locate("LOPTS=",cparm) .lt. f$length(cparm)
-$ then
-$ start = f$locate("=",cparm) + 1
-$ len = f$length(cparm) - start
-$ lopts = lopts + f$extract(start,len,cparm)
-$ endif
-$ if f$locate("CC=",cparm) .lt. f$length(cparm)
-$ then
-$ start = f$locate("=",cparm) + 1
-$ len = f$length(cparm) - start
-$ cc_com = f$extract(start,len,cparm)
- if (cc_com .nes. "DECC") .and. -
- (cc_com .nes. "VAXC") .and. -
- (cc_com .nes. "GNUC")
-$ then
-$ write sys$output "Unsupported compiler choice ''cc_com' ignored"
-$ write sys$output "Use DECC, VAXC, or GNUC instead"
-$ else
-$ if cc_com .eqs. "DECC" then its_decc = true
-$ if cc_com .eqs. "VAXC" then its_vaxc = true
-$ if cc_com .eqs. "GNUC" then its_gnuc = true
-$ endif
-$ endif
-$ if f$locate("MAKE=",cparm) .lt. f$length(cparm)
-$ then
-$ start = f$locate("=",cparm) + 1
-$ len = f$length(cparm) - start
-$ mmks = f$extract(start,len,cparm)
-$ if (mmks .eqs. "MMK") .or. (mmks .eqs. "MMS")
-$ then
-$ make = mmks
-$ else
-$ write sys$output "Unsupported make choice ''mmks' ignored"
-$ write sys$output "Use MMK or MMS instead"
-$ endif
-$ endif
-$ if cparm .eqs. "HELP" then gosub bhelp
-$ endif
-$ i = i + 1
-$ goto opt_loop
-$ endif
-$ return
-$!------------------------------------------------------------------------------
-$!
-$! Look for the compiler used
-$!
-$! Version history
-$! 0.01 20040223 First version to receive a number
-$! 0.02 20040229 Save/set value of decc$no_rooted_search_lists
-$! 0.03 20060202 Extend handling of GNU C
-$! 0.04 20090402 Compaq -> hp
-$CHECK_COMPILER:
-$ if (.not. (its_decc .or. its_vaxc .or. its_gnuc))
-$ then
-$ its_decc = (f$search("SYS$SYSTEM:DECC$COMPILER.EXE") .nes. "")
-$ its_vaxc = .not. its_decc .and. (F$Search("SYS$System:VAXC.Exe") .nes. "")
-$ its_gnuc = .not. (its_decc .or. its_vaxc) .and. (f$trnlnm("gnu_cc") .nes. "")
-$ endif
-$!
-$! Exit if no compiler available
-$!
-$ if (.not. (its_decc .or. its_vaxc .or. its_gnuc))
-$ then goto CC_ERR
-$ else
-$ if its_decc
-$ then
-$ write sys$output "CC compiler check ... hp C"
-$ if f$trnlnm("decc$no_rooted_search_lists") .nes. ""
-$ then
-$ dnrsl = f$trnlnm("decc$no_rooted_search_lists")
-$ endif
-$ define/nolog decc$no_rooted_search_lists 1
-$ else
-$ if its_vaxc then write sys$output "CC compiler check ... VAX C"
-$ if its_gnuc
-$ then
-$ write sys$output "CC compiler check ... GNU C"
-$ if f$trnlnm(topt) then write topt "gnu_cc:[000000]gcclib.olb/lib"
-$ if f$trnlnm(optf) then write optf "gnu_cc:[000000]gcclib.olb/lib"
-$ cc = "gcc"
-$ endif
-$ if f$trnlnm(topt) then write topt "sys$share:vaxcrtl.exe/share"
-$ if f$trnlnm(optf) then write optf "sys$share:vaxcrtl.exe/share"
-$ endif
-$ endif
-$ return
-$!------------------------------------------------------------------------------
-$!
-$! If MMS/MMK are available dump out the descrip.mms if required
-$!
-$CREA_MMS:
-$ write sys$output "Creating descrip.mms..."
-$ create descrip.mms
-$ open/append out descrip.mms
-$ copy sys$input: out
-$ deck
-# descrip.mms: MMS description file for building zlib on VMS
-# written by Martin P.J. Zinser
-# <zinser at zinser.no-ip.info or martin.zinser at eurexchange.com>
-
-OBJS = adler32.obj, compress.obj, crc32.obj, gzclose.obj, gzlib.obj\
- gzread.obj, gzwrite.obj, uncompr.obj, infback.obj\
- deflate.obj, trees.obj, zutil.obj, inflate.obj, \
- inftrees.obj, inffast.obj
-
-$ eod
-$ write out "CFLAGS=", ccopt
-$ write out "LOPTS=", lopts
-$ write out "all : example.exe minigzip.exe libz.olb"
-$ copy sys$input: out
-$ deck
- @ write sys$output " Example applications available"
-
-libz.olb : libz.olb($(OBJS))
- @ write sys$output " libz available"
-
-example.exe : example.obj libz.olb
- link $(LOPTS) example,libz.olb/lib
-
-minigzip.exe : minigzip.obj libz.olb
- link $(LOPTS) minigzip,libz.olb/lib
-
-clean :
- delete *.obj;*,libz.olb;*,*.opt;*,*.exe;*
-
-
-# Other dependencies.
-adler32.obj : adler32.c zutil.h zlib.h zconf.h
-compress.obj : compress.c zlib.h zconf.h
-crc32.obj : crc32.c zutil.h zlib.h zconf.h
-deflate.obj : deflate.c deflate.h zutil.h zlib.h zconf.h
-example.obj : [.test]example.c zlib.h zconf.h
-gzclose.obj : gzclose.c zutil.h zlib.h zconf.h
-gzlib.obj : gzlib.c zutil.h zlib.h zconf.h
-gzread.obj : gzread.c zutil.h zlib.h zconf.h
-gzwrite.obj : gzwrite.c zutil.h zlib.h zconf.h
-inffast.obj : inffast.c zutil.h zlib.h zconf.h inftrees.h inffast.h
-inflate.obj : inflate.c zutil.h zlib.h zconf.h
-inftrees.obj : inftrees.c zutil.h zlib.h zconf.h inftrees.h
-minigzip.obj : [.test]minigzip.c zlib.h zconf.h
-trees.obj : trees.c deflate.h zutil.h zlib.h zconf.h
-uncompr.obj : uncompr.c zlib.h zconf.h
-zutil.obj : zutil.c zutil.h zlib.h zconf.h
-infback.obj : infback.c zutil.h inftrees.h inflate.h inffast.h inffixed.h
-$ eod
-$ close out
-$ return
-$!------------------------------------------------------------------------------
-$!
-$! Read list of core library sources from makefile.in and create options
-$! needed to build shareable image
-$!
-$CREA_OLIST:
-$ open/read min makefile.in
-$ open/write mod modules.opt
-$ src_check_list = "OBJZ =#OBJG ="
-$MRLOOP:
-$ read/end=mrdone min rec
-$ i = 0
-$SRC_CHECK_LOOP:
-$ src_check = f$element(i, "#", src_check_list)
-$ i = i+1
-$ if src_check .eqs. "#" then goto mrloop
-$ if (f$extract(0,6,rec) .nes. src_check) then goto src_check_loop
-$ rec = rec - src_check
-$ gosub extra_filnam
-$ if (f$element(1,"\",rec) .eqs. "\") then goto mrloop
-$MRSLOOP:
-$ read/end=mrdone min rec
-$ gosub extra_filnam
-$ if (f$element(1,"\",rec) .nes. "\") then goto mrsloop
-$MRDONE:
-$ close min
-$ close mod
-$ return
-$!------------------------------------------------------------------------------
-$!
-$! Take record extracted in crea_olist and split it into single filenames
-$!
-$EXTRA_FILNAM:
-$ myrec = f$edit(rec - "\", "trim,compress")
-$ i = 0
-$FELOOP:
-$ srcfil = f$element(i," ", myrec)
-$ if (srcfil .nes. " ")
-$ then
-$ write mod f$parse(srcfil,,,"NAME"), ".obj"
-$ i = i + 1
-$ goto feloop
-$ endif
-$ return
-$!------------------------------------------------------------------------------
-$!
-$! Find current Zlib version number
-$!
-$FIND_VERSION:
-$ open/read h_in 'v_file'
-$hloop:
-$ read/end=hdone h_in rec
-$ rec = f$edit(rec,"TRIM")
-$ if (f$extract(0,1,rec) .nes. "#") then goto hloop
-$ rec = f$edit(rec - "#", "TRIM")
-$ if f$element(0," ",rec) .nes. "define" then goto hloop
-$ if f$element(1," ",rec) .eqs. v_string
-$ then
-$ version = 'f$element(2," ",rec)'
-$ goto hdone
-$ endif
-$ goto hloop
-$hdone:
-$ close h_in
-$ return
-$!------------------------------------------------------------------------------
-$!
-$CHECK_CONFIG:
-$!
-$ in_ldef = f$locate(cdef,libdefs)
-$ if (in_ldef .lt. f$length(libdefs))
-$ then
-$ write aconf "#define ''cdef' 1"
-$ libdefs = f$extract(0,in_ldef,libdefs) + -
- f$extract(in_ldef + f$length(cdef) + 1, -
- f$length(libdefs) - in_ldef - f$length(cdef) - 1, -
- libdefs)
-$ else
-$ if (f$type('cdef') .eqs. "INTEGER")
-$ then
-$ write aconf "#define ''cdef' ", 'cdef'
-$ else
-$ if (f$type('cdef') .eqs. "STRING")
-$ then
-$ write aconf "#define ''cdef' ", """", '''cdef'', """"
-$ else
-$ gosub check_cc_def
-$ endif
-$ endif
-$ endif
-$ return
-$!------------------------------------------------------------------------------
-$!
-$! Check if this is a define relating to the properties of the C/C++
-$! compiler
-$!
-$ CHECK_CC_DEF:
-$ if (cdef .eqs. "_LARGEFILE64_SOURCE")
-$ then
-$ copy sys$input: 'tc'
-$ deck
-#include "tconfig"
-#define _LARGEFILE
-#include <stdio.h>
-
-int main(){
-FILE *fp;
- fp = fopen("temp.txt","r");
- fseeko(fp,1,SEEK_SET);
- fclose(fp);
-}
-
-$ eod
-$ test_inv = false
-$ comm_h = false
-$ gosub cc_prop_check
-$ return
-$ endif
-$ write aconf "/* ", line, " */"
-$ return
-$!------------------------------------------------------------------------------
-$!
-$! Check for properties of C/C++ compiler
-$!
-$! Version history
-$! 0.01 20031020 First version to receive a number
-$! 0.02 20031022 Added logic for defines with value
-$! 0.03 20040309 Make sure local config file gets not deleted
-$! 0.04 20041230 Also write include for configure run
-$! 0.05 20050103 Add processing of "comment defines"
-$CC_PROP_CHECK:
-$ cc_prop = true
-$ is_need = false
-$ is_need = (f$extract(0,4,cdef) .eqs. "NEED") .or. (test_inv .eq. true)
-$ if f$search(th) .eqs. "" then create 'th'
-$ set message/nofac/noident/nosever/notext
-$ on error then continue
-$ cc 'tmpnam'
-$ if .not. ($status) then cc_prop = false
-$ on error then continue
-$! The headers might lie about the capabilities of the RTL
-$ link 'tmpnam',tmp.opt/opt
-$ if .not. ($status) then cc_prop = false
-$ set message/fac/ident/sever/text
-$ on error then goto err_exit
-$ delete/nolog 'tmpnam'.*;*/exclude='th'
-$ if (cc_prop .and. .not. is_need) .or. -
- (.not. cc_prop .and. is_need)
-$ then
-$ write sys$output "Checking for ''cdef'... yes"
-$ if f$type('cdef_val'_yes) .nes. ""
-$ then
-$ if f$type('cdef_val'_yes) .eqs. "INTEGER" -
- then call write_config f$fao("#define !AS !UL",cdef,'cdef_val'_yes)
-$ if f$type('cdef_val'_yes) .eqs. "STRING" -
- then call write_config f$fao("#define !AS !AS",cdef,'cdef_val'_yes)
-$ else
-$ call write_config f$fao("#define !AS 1",cdef)
-$ endif
-$ if (cdef .eqs. "HAVE_FSEEKO") .or. (cdef .eqs. "_LARGE_FILES") .or. -
- (cdef .eqs. "_LARGEFILE64_SOURCE") then -
- call write_config f$string("#define _LARGEFILE 1")
-$ else
-$ write sys$output "Checking for ''cdef'... no"
-$ if (comm_h)
-$ then
- call write_config f$fao("/* !AS */",line)
-$ else
-$ if f$type('cdef_val'_no) .nes. ""
-$ then
-$ if f$type('cdef_val'_no) .eqs. "INTEGER" -
- then call write_config f$fao("#define !AS !UL",cdef,'cdef_val'_no)
-$ if f$type('cdef_val'_no) .eqs. "STRING" -
- then call write_config f$fao("#define !AS !AS",cdef,'cdef_val'_no)
-$ else
-$ call write_config f$fao("#undef !AS",cdef)
-$ endif
-$ endif
-$ endif
-$ return
-$!------------------------------------------------------------------------------
-$!
-$! Check for properties of C/C++ compiler with multiple result values
-$!
-$! Version history
-$! 0.01 20040127 First version
-$! 0.02 20050103 Reconcile changes from cc_prop up to version 0.05
-$CC_MPROP_CHECK:
-$ cc_prop = true
-$ i = 1
-$ idel = 1
-$ MT_LOOP:
-$ if f$type(result_'i') .eqs. "STRING"
-$ then
-$ set message/nofac/noident/nosever/notext
-$ on error then continue
-$ cc 'tmpnam'_'i'
-$ if .not. ($status) then cc_prop = false
-$ on error then continue
-$! The headers might lie about the capabilities of the RTL
-$ link 'tmpnam'_'i',tmp.opt/opt
-$ if .not. ($status) then cc_prop = false
-$ set message/fac/ident/sever/text
-$ on error then goto err_exit
-$ delete/nolog 'tmpnam'_'i'.*;*
-$ if (cc_prop)
-$ then
-$ write sys$output "Checking for ''cdef'... ", mdef_'i'
-$ if f$type(mdef_'i') .eqs. "INTEGER" -
- then call write_config f$fao("#define !AS !UL",cdef,mdef_'i')
-$ if f$type('cdef_val'_yes) .eqs. "STRING" -
- then call write_config f$fao("#define !AS !AS",cdef,mdef_'i')
-$ goto msym_clean
-$ else
-$ i = i + 1
-$ goto mt_loop
-$ endif
-$ endif
-$ write sys$output "Checking for ''cdef'... no"
-$ call write_config f$fao("#undef !AS",cdef)
-$ MSYM_CLEAN:
-$ if (idel .le. msym_max)
-$ then
-$ delete/sym mdef_'idel'
-$ idel = idel + 1
-$ goto msym_clean
-$ endif
-$ return
-$!------------------------------------------------------------------------------
-$!
-$! Write configuration to both permanent and temporary config file
-$!
-$! Version history
-$! 0.01 20031029 First version to receive a number
-$!
-$WRITE_CONFIG: SUBROUTINE
-$ write aconf 'p1'
-$ open/append confh 'th'
-$ write confh 'p1'
-$ close confh
-$ENDSUBROUTINE
-$!------------------------------------------------------------------------------
-$!
-$! Analyze the project map file and create the symbol vector for a shareable
-$! image from it
-$!
-$! Version history
-$! 0.01 20120128 First version
-$! 0.02 20120226 Add pre-load logic
-$!
-$ MAP_2_SHOPT: Subroutine
-$!
-$ SAY := "WRITE_ SYS$OUTPUT"
-$!
-$ IF F$SEARCH("''P1'") .EQS. ""
-$ THEN
-$ SAY "MAP_2_SHOPT-E-NOSUCHFILE: Error, inputfile ''p1' not available"
-$ goto exit_m2s
-$ ENDIF
-$ IF "''P2'" .EQS. ""
-$ THEN
-$ SAY "MAP_2_SHOPT: Error, no output file provided"
-$ goto exit_m2s
-$ ENDIF
-$!
-$ module1 = "deflate#deflateEnd#deflateInit_#deflateParams#deflateSetDictionary"
-$ module2 = "gzclose#gzerror#gzgetc#gzgets#gzopen#gzprintf#gzputc#gzputs#gzread"
-$ module3 = "gzseek#gztell#inflate#inflateEnd#inflateInit_#inflateSetDictionary"
-$ module4 = "inflateSync#uncompress#zlibVersion#compress"
-$ open/read map 'p1
-$ if axp .or. ia64
-$ then
-$ open/write aopt a.opt
-$ open/write bopt b.opt
-$ write aopt " CASE_SENSITIVE=YES"
-$ write bopt "SYMBOL_VECTOR= (-"
-$ mod_sym_num = 1
-$ MOD_SYM_LOOP:
-$ if f$type(module'mod_sym_num') .nes. ""
-$ then
-$ mod_in = 0
-$ MOD_SYM_IN:
-$ shared_proc = f$element(mod_in, "#", module'mod_sym_num')
-$ if shared_proc .nes. "#"
-$ then
-$ write aopt f$fao(" symbol_vector=(!AS/!AS=PROCEDURE)",-
- f$edit(shared_proc,"upcase"),shared_proc)
-$ write bopt f$fao("!AS=PROCEDURE,-",shared_proc)
-$ mod_in = mod_in + 1
-$ goto mod_sym_in
-$ endif
-$ mod_sym_num = mod_sym_num + 1
-$ goto mod_sym_loop
-$ endif
-$MAP_LOOP:
-$ read/end=map_end map line
-$ if (f$locate("{",line).lt. f$length(line)) .or. -
- (f$locate("global:", line) .lt. f$length(line))
-$ then
-$ proc = true
-$ goto map_loop
-$ endif
-$ if f$locate("}",line).lt. f$length(line) then proc = false
-$ if f$locate("local:", line) .lt. f$length(line) then proc = false
-$ if proc
-$ then
-$ shared_proc = f$edit(line,"collapse")
-$ chop_semi = f$locate(";", shared_proc)
-$ if chop_semi .lt. f$length(shared_proc) then -
- shared_proc = f$extract(0, chop_semi, shared_proc)
-$ write aopt f$fao(" symbol_vector=(!AS/!AS=PROCEDURE)",-
- f$edit(shared_proc,"upcase"),shared_proc)
-$ write bopt f$fao("!AS=PROCEDURE,-",shared_proc)
-$ endif
-$ goto map_loop
-$MAP_END:
-$ close/nolog aopt
-$ close/nolog bopt
-$ open/append libopt 'p2'
-$ open/read aopt a.opt
-$ open/read bopt b.opt
-$ALOOP:
-$ read/end=aloop_end aopt line
-$ write libopt line
-$ goto aloop
-$ALOOP_END:
-$ close/nolog aopt
-$ sv = ""
-$BLOOP:
-$ read/end=bloop_end bopt svn
-$ if (svn.nes."")
-$ then
-$ if (sv.nes."") then write libopt sv
-$ sv = svn
-$ endif
-$ goto bloop
-$BLOOP_END:
-$ write libopt f$extract(0,f$length(sv)-2,sv), "-"
-$ write libopt ")"
-$ close/nolog bopt
-$ delete/nolog/noconf a.opt;*,b.opt;*
-$ else
-$ if vax
-$ then
-$ open/append libopt 'p2'
-$ mod_sym_num = 1
-$ VMOD_SYM_LOOP:
-$ if f$type(module'mod_sym_num') .nes. ""
-$ then
-$ mod_in = 0
-$ VMOD_SYM_IN:
-$ shared_proc = f$element(mod_in, "#", module'mod_sym_num')
-$ if shared_proc .nes. "#"
-$ then
-$ write libopt f$fao("UNIVERSAL=!AS",-
- f$edit(shared_proc,"upcase"))
-$ mod_in = mod_in + 1
-$ goto vmod_sym_in
-$ endif
-$ mod_sym_num = mod_sym_num + 1
-$ goto vmod_sym_loop
-$ endif
-$VMAP_LOOP:
-$ read/end=vmap_end map line
-$ if (f$locate("{",line).lt. f$length(line)) .or. -
- (f$locate("global:", line) .lt. f$length(line))
-$ then
-$ proc = true
-$ goto vmap_loop
-$ endif
-$ if f$locate("}",line).lt. f$length(line) then proc = false
-$ if f$locate("local:", line) .lt. f$length(line) then proc = false
-$ if proc
-$ then
-$ shared_proc = f$edit(line,"collapse")
-$ chop_semi = f$locate(";", shared_proc)
-$ if chop_semi .lt. f$length(shared_proc) then -
- shared_proc = f$extract(0, chop_semi, shared_proc)
-$ write libopt f$fao("UNIVERSAL=!AS",-
- f$edit(shared_proc,"upcase"))
-$ endif
-$ goto vmap_loop
-$VMAP_END:
-$ else
-$ write sys$output "Unknown Architecture (Not VAX, AXP, or IA64)"
-$ write sys$output "No options file created"
-$ endif
-$ endif
-$ EXIT_M2S:
-$ close/nolog map
-$ close/nolog libopt
-$ endsubroutine
diff --git a/third-party/zlib/msdos/Makefile.bor b/third-party/zlib/msdos/Makefile.bor
deleted file mode 100644
index 3d12a2c..0000000
--- a/third-party/zlib/msdos/Makefile.bor
+++ /dev/null
@@ -1,115 +0,0 @@
-# Makefile for zlib
-# Borland C++
-# Last updated: 15-Mar-2003
-
-# To use, do "make -fmakefile.bor"
-# To compile in small model, set below: MODEL=s
-
-# WARNING: the small model is supported but only for small values of
-# MAX_WBITS and MAX_MEM_LEVEL. For example:
-# -DMAX_WBITS=11 -DDEF_WBITS=11 -DMAX_MEM_LEVEL=3
-# If you wish to reduce the memory requirements (default 256K for big
-# objects plus a few K), you can add to the LOC macro below:
-# -DMAX_MEM_LEVEL=7 -DMAX_WBITS=14
-# See zconf.h for details about the memory requirements.
-
-# ------------ Turbo C++, Borland C++ ------------
-
-# Optional nonstandard preprocessor flags (e.g. -DMAX_MEM_LEVEL=7)
-# should be added to the environment via "set LOCAL_ZLIB=-DFOO" or added
-# to the declaration of LOC here:
-LOC = $(LOCAL_ZLIB)
-
-# type for CPU required: 0: 8086, 1: 80186, 2: 80286, 3: 80386, etc.
-CPU_TYP = 0
-
-# memory model: one of s, m, c, l (small, medium, compact, large)
-MODEL=l
-
-# replace bcc with tcc for Turbo C++ 1.0, with bcc32 for the 32 bit version
-CC=bcc
-LD=bcc
-AR=tlib
-
-# compiler flags
-# replace "-O2" by "-O -G -a -d" for Turbo C++ 1.0
-CFLAGS=-O2 -Z -m$(MODEL) $(LOC)
-
-LDFLAGS=-m$(MODEL) -f-
-
-
-# variables
-ZLIB_LIB = zlib_$(MODEL).lib
-
-OBJ1 = adler32.obj compress.obj crc32.obj deflate.obj gzclose.obj gzlib.obj gzread.obj
-OBJ2 = gzwrite.obj infback.obj inffast.obj inflate.obj inftrees.obj trees.obj uncompr.obj zutil.obj
-OBJP1 = +adler32.obj+compress.obj+crc32.obj+deflate.obj+gzclose.obj+gzlib.obj+gzread.obj
-OBJP2 = +gzwrite.obj+infback.obj+inffast.obj+inflate.obj+inftrees.obj+trees.obj+uncompr.obj+zutil.obj
-
-
-# targets
-all: $(ZLIB_LIB) example.exe minigzip.exe
-
-.c.obj:
- $(CC) -c $(CFLAGS) $*.c
-
-adler32.obj: adler32.c zlib.h zconf.h
-
-compress.obj: compress.c zlib.h zconf.h
-
-crc32.obj: crc32.c zlib.h zconf.h crc32.h
-
-deflate.obj: deflate.c deflate.h zutil.h zlib.h zconf.h
-
-gzclose.obj: gzclose.c zlib.h zconf.h gzguts.h
-
-gzlib.obj: gzlib.c zlib.h zconf.h gzguts.h
-
-gzread.obj: gzread.c zlib.h zconf.h gzguts.h
-
-gzwrite.obj: gzwrite.c zlib.h zconf.h gzguts.h
-
-infback.obj: infback.c zutil.h zlib.h zconf.h inftrees.h inflate.h \
- inffast.h inffixed.h
-
-inffast.obj: inffast.c zutil.h zlib.h zconf.h inftrees.h inflate.h \
- inffast.h
-
-inflate.obj: inflate.c zutil.h zlib.h zconf.h inftrees.h inflate.h \
- inffast.h inffixed.h
-
-inftrees.obj: inftrees.c zutil.h zlib.h zconf.h inftrees.h
-
-trees.obj: trees.c zutil.h zlib.h zconf.h deflate.h trees.h
-
-uncompr.obj: uncompr.c zlib.h zconf.h
-
-zutil.obj: zutil.c zutil.h zlib.h zconf.h
-
-example.obj: test/example.c zlib.h zconf.h
-
-minigzip.obj: test/minigzip.c zlib.h zconf.h
-
-
-# the command line is cut to fit in the MS-DOS 128 byte limit:
-$(ZLIB_LIB): $(OBJ1) $(OBJ2)
- -del $(ZLIB_LIB)
- $(AR) $(ZLIB_LIB) $(OBJP1)
- $(AR) $(ZLIB_LIB) $(OBJP2)
-
-example.exe: example.obj $(ZLIB_LIB)
- $(LD) $(LDFLAGS) example.obj $(ZLIB_LIB)
-
-minigzip.exe: minigzip.obj $(ZLIB_LIB)
- $(LD) $(LDFLAGS) minigzip.obj $(ZLIB_LIB)
-
-test: example.exe minigzip.exe
- example
- echo hello world | minigzip | minigzip -d
-
-clean:
- -del *.obj
- -del *.lib
- -del *.exe
- -del zlib_*.bak
- -del foo.gz
diff --git a/third-party/zlib/msdos/Makefile.dj2 b/third-party/zlib/msdos/Makefile.dj2
deleted file mode 100644
index 29b0395..0000000
--- a/third-party/zlib/msdos/Makefile.dj2
+++ /dev/null
@@ -1,104 +0,0 @@
-# Makefile for zlib. Modified for djgpp v2.0 by F. J. Donahoe, 3/15/96.
-# Copyright (C) 1995-1998 Jean-loup Gailly.
-# For conditions of distribution and use, see copyright notice in zlib.h
-
-# To compile, or to compile and test, type:
-#
-# make -fmakefile.dj2; make test -fmakefile.dj2
-#
-# To install libz.a, zconf.h and zlib.h in the djgpp directories, type:
-#
-# make install -fmakefile.dj2
-#
-# after first defining LIBRARY_PATH and INCLUDE_PATH in djgpp.env as
-# in the sample below if the pattern of the DJGPP distribution is to
-# be followed. Remember that, while <sp>'es around <=> are ignored in
-# makefiles, they are *not* in batch files or in djgpp.env.
-# - - - - -
-# [make]
-# INCLUDE_PATH=%\>;INCLUDE_PATH%%\DJDIR%\include
-# LIBRARY_PATH=%\>;LIBRARY_PATH%%\DJDIR%\lib
-# BUTT=-m486
-# - - - - -
-# Alternately, these variables may be defined below, overriding the values
-# in djgpp.env, as
-# INCLUDE_PATH=c:\usr\include
-# LIBRARY_PATH=c:\usr\lib
-
-CC=gcc
-
-#CFLAGS=-MMD -O
-#CFLAGS=-O -DMAX_WBITS=14 -DMAX_MEM_LEVEL=7
-#CFLAGS=-MMD -g -DDEBUG
-CFLAGS=-MMD -O3 $(BUTT) -Wall -Wwrite-strings -Wpointer-arith -Wconversion \
- -Wstrict-prototypes -Wmissing-prototypes
-
-# If cp.exe is available, replace "copy /Y" with "cp -fp" .
-CP=copy /Y
-# If gnu install.exe is available, replace $(CP) with ginstall.
-INSTALL=$(CP)
-# The default value of RM is "rm -f." If "rm.exe" is found, comment out:
-RM=del
-LDLIBS=-L. -lz
-LD=$(CC) -s -o
-LDSHARED=$(CC)
-
-INCL=zlib.h zconf.h
-LIBS=libz.a
-
-AR=ar rcs
-
-prefix=/usr/local
-exec_prefix = $(prefix)
-
-OBJS = adler32.o compress.o crc32.o gzclose.o gzlib.o gzread.o gzwrite.o \
- uncompr.o deflate.o trees.o zutil.o inflate.o infback.o inftrees.o inffast.o
-
-OBJA =
-# to use the asm code: make OBJA=match.o
-
-TEST_OBJS = example.o minigzip.o
-
-all: example.exe minigzip.exe
-
-check: test
-test: all
- ./example
- echo hello world | .\minigzip | .\minigzip -d
-
-%.o : %.c
- $(CC) $(CFLAGS) -c $< -o $@
-
-libz.a: $(OBJS) $(OBJA)
- $(AR) $@ $(OBJS) $(OBJA)
-
-%.exe : %.o $(LIBS)
- $(LD) $@ $< $(LDLIBS)
-
-# INCLUDE_PATH and LIBRARY_PATH were set for [make] in djgpp.env .
-
-.PHONY : uninstall clean
-
-install: $(INCL) $(LIBS)
- - at if not exist $(INCLUDE_PATH)\nul mkdir $(INCLUDE_PATH)
- - at if not exist $(LIBRARY_PATH)\nul mkdir $(LIBRARY_PATH)
- $(INSTALL) zlib.h $(INCLUDE_PATH)
- $(INSTALL) zconf.h $(INCLUDE_PATH)
- $(INSTALL) libz.a $(LIBRARY_PATH)
-
-uninstall:
- $(RM) $(INCLUDE_PATH)\zlib.h
- $(RM) $(INCLUDE_PATH)\zconf.h
- $(RM) $(LIBRARY_PATH)\libz.a
-
-clean:
- $(RM) *.d
- $(RM) *.o
- $(RM) *.exe
- $(RM) libz.a
- $(RM) foo.gz
-
-DEPS := $(wildcard *.d)
-ifneq ($(DEPS),)
-include $(DEPS)
-endif
diff --git a/third-party/zlib/msdos/Makefile.emx b/third-party/zlib/msdos/Makefile.emx
deleted file mode 100644
index 9c1b57a..0000000
--- a/third-party/zlib/msdos/Makefile.emx
+++ /dev/null
@@ -1,69 +0,0 @@
-# Makefile for zlib. Modified for emx 0.9c by Chr. Spieler, 6/17/98.
-# Copyright (C) 1995-1998 Jean-loup Gailly.
-# For conditions of distribution and use, see copyright notice in zlib.h
-
-# To compile, or to compile and test, type:
-#
-# make -fmakefile.emx; make test -fmakefile.emx
-#
-
-CC=gcc
-
-#CFLAGS=-MMD -O
-#CFLAGS=-O -DMAX_WBITS=14 -DMAX_MEM_LEVEL=7
-#CFLAGS=-MMD -g -DDEBUG
-CFLAGS=-MMD -O3 $(BUTT) -Wall -Wwrite-strings -Wpointer-arith -Wconversion \
- -Wstrict-prototypes -Wmissing-prototypes
-
-# If cp.exe is available, replace "copy /Y" with "cp -fp" .
-CP=copy /Y
-# If gnu install.exe is available, replace $(CP) with ginstall.
-INSTALL=$(CP)
-# The default value of RM is "rm -f." If "rm.exe" is found, comment out:
-RM=del
-LDLIBS=-L. -lzlib
-LD=$(CC) -s -o
-LDSHARED=$(CC)
-
-INCL=zlib.h zconf.h
-LIBS=zlib.a
-
-AR=ar rcs
-
-prefix=/usr/local
-exec_prefix = $(prefix)
-
-OBJS = adler32.o compress.o crc32.o gzclose.o gzlib.o gzread.o gzwrite.o \
- uncompr.o deflate.o trees.o zutil.o inflate.o infback.o inftrees.o inffast.o
-
-TEST_OBJS = example.o minigzip.o
-
-all: example.exe minigzip.exe
-
-test: all
- ./example
- echo hello world | .\minigzip | .\minigzip -d
-
-%.o : %.c
- $(CC) $(CFLAGS) -c $< -o $@
-
-zlib.a: $(OBJS)
- $(AR) $@ $(OBJS)
-
-%.exe : %.o $(LIBS)
- $(LD) $@ $< $(LDLIBS)
-
-
-.PHONY : clean
-
-clean:
- $(RM) *.d
- $(RM) *.o
- $(RM) *.exe
- $(RM) zlib.a
- $(RM) foo.gz
-
-DEPS := $(wildcard *.d)
-ifneq ($(DEPS),)
-include $(DEPS)
-endif
diff --git a/third-party/zlib/msdos/Makefile.msc b/third-party/zlib/msdos/Makefile.msc
deleted file mode 100644
index ae83786..0000000
--- a/third-party/zlib/msdos/Makefile.msc
+++ /dev/null
@@ -1,112 +0,0 @@
-# Makefile for zlib
-# Microsoft C 5.1 or later
-# Last updated: 19-Mar-2003
-
-# To use, do "make makefile.msc"
-# To compile in small model, set below: MODEL=S
-
-# If you wish to reduce the memory requirements (default 256K for big
-# objects plus a few K), you can add to the LOC macro below:
-# -DMAX_MEM_LEVEL=7 -DMAX_WBITS=14
-# See zconf.h for details about the memory requirements.
-
-# ------------- Microsoft C 5.1 and later -------------
-
-# Optional nonstandard preprocessor flags (e.g. -DMAX_MEM_LEVEL=7)
-# should be added to the environment via "set LOCAL_ZLIB=-DFOO" or added
-# to the declaration of LOC here:
-LOC = $(LOCAL_ZLIB)
-
-# Type for CPU required: 0: 8086, 1: 80186, 2: 80286, 3: 80386, etc.
-CPU_TYP = 0
-
-# Memory model: one of S, M, C, L (small, medium, compact, large)
-MODEL=L
-
-CC=cl
-CFLAGS=-nologo -A$(MODEL) -G$(CPU_TYP) -W3 -Oait -Gs $(LOC)
-#-Ox generates bad code with MSC 5.1
-LIB_CFLAGS=-Zl $(CFLAGS)
-
-LD=link
-LDFLAGS=/noi/e/st:0x1500/noe/farcall/packcode
-# "/farcall/packcode" are only useful for `large code' memory models
-# but should be a "no-op" for small code models.
-
-
-# variables
-ZLIB_LIB = zlib_$(MODEL).lib
-
-OBJ1 = adler32.obj compress.obj crc32.obj deflate.obj gzclose.obj gzlib.obj gzread.obj
-OBJ2 = gzwrite.obj infback.obj inffast.obj inflate.obj inftrees.obj trees.obj uncompr.obj zutil.obj
-
-
-# targets
-all: $(ZLIB_LIB) example.exe minigzip.exe
-
-.c.obj:
- $(CC) -c $(LIB_CFLAGS) $*.c
-
-adler32.obj: adler32.c zlib.h zconf.h
-
-compress.obj: compress.c zlib.h zconf.h
-
-crc32.obj: crc32.c zlib.h zconf.h crc32.h
-
-deflate.obj: deflate.c deflate.h zutil.h zlib.h zconf.h
-
-gzclose.obj: gzclose.c zlib.h zconf.h gzguts.h
-
-gzlib.obj: gzlib.c zlib.h zconf.h gzguts.h
-
-gzread.obj: gzread.c zlib.h zconf.h gzguts.h
-
-gzwrite.obj: gzwrite.c zlib.h zconf.h gzguts.h
-
-infback.obj: infback.c zutil.h zlib.h zconf.h inftrees.h inflate.h \
- inffast.h inffixed.h
-
-inffast.obj: inffast.c zutil.h zlib.h zconf.h inftrees.h inflate.h \
- inffast.h
-
-inflate.obj: inflate.c zutil.h zlib.h zconf.h inftrees.h inflate.h \
- inffast.h inffixed.h
-
-inftrees.obj: inftrees.c zutil.h zlib.h zconf.h inftrees.h
-
-trees.obj: trees.c zutil.h zlib.h zconf.h deflate.h trees.h
-
-uncompr.obj: uncompr.c zlib.h zconf.h
-
-zutil.obj: zutil.c zutil.h zlib.h zconf.h
-
-example.obj: test/example.c zlib.h zconf.h
- $(CC) -c $(CFLAGS) $*.c
-
-minigzip.obj: test/minigzip.c zlib.h zconf.h
- $(CC) -c $(CFLAGS) $*.c
-
-
-# the command line is cut to fit in the MS-DOS 128 byte limit:
-$(ZLIB_LIB): $(OBJ1) $(OBJ2)
- if exist $(ZLIB_LIB) del $(ZLIB_LIB)
- lib $(ZLIB_LIB) $(OBJ1);
- lib $(ZLIB_LIB) $(OBJ2);
-
-example.exe: example.obj $(ZLIB_LIB)
- $(LD) $(LDFLAGS) example.obj,,,$(ZLIB_LIB);
-
-minigzip.exe: minigzip.obj $(ZLIB_LIB)
- $(LD) $(LDFLAGS) minigzip.obj,,,$(ZLIB_LIB);
-
-test: example.exe minigzip.exe
- example
- echo hello world | minigzip | minigzip -d
-
-clean:
- -del *.obj
- -del *.lib
- -del *.exe
- -del *.map
- -del zlib_*.bak
- -del foo.gz
diff --git a/third-party/zlib/msdos/Makefile.tc b/third-party/zlib/msdos/Makefile.tc
deleted file mode 100644
index 5aec82a..0000000
--- a/third-party/zlib/msdos/Makefile.tc
+++ /dev/null
@@ -1,100 +0,0 @@
-# Makefile for zlib
-# Turbo C 2.01, Turbo C++ 1.01
-# Last updated: 15-Mar-2003
-
-# To use, do "make -fmakefile.tc"
-# To compile in small model, set below: MODEL=s
-
-# WARNING: the small model is supported but only for small values of
-# MAX_WBITS and MAX_MEM_LEVEL. For example:
-# -DMAX_WBITS=11 -DMAX_MEM_LEVEL=3
-# If you wish to reduce the memory requirements (default 256K for big
-# objects plus a few K), you can add to CFLAGS below:
-# -DMAX_MEM_LEVEL=7 -DMAX_WBITS=14
-# See zconf.h for details about the memory requirements.
-
-# ------------ Turbo C 2.01, Turbo C++ 1.01 ------------
-MODEL=l
-CC=tcc
-LD=tcc
-AR=tlib
-# CFLAGS=-O2 -G -Z -m$(MODEL) -DMAX_WBITS=11 -DMAX_MEM_LEVEL=3
-CFLAGS=-O2 -G -Z -m$(MODEL)
-LDFLAGS=-m$(MODEL) -f-
-
-
-# variables
-ZLIB_LIB = zlib_$(MODEL).lib
-
-OBJ1 = adler32.obj compress.obj crc32.obj deflate.obj gzclose.obj gzlib.obj gzread.obj
-OBJ2 = gzwrite.obj infback.obj inffast.obj inflate.obj inftrees.obj trees.obj uncompr.obj zutil.obj
-OBJP1 = +adler32.obj+compress.obj+crc32.obj+deflate.obj+gzclose.obj+gzlib.obj+gzread.obj
-OBJP2 = +gzwrite.obj+infback.obj+inffast.obj+inflate.obj+inftrees.obj+trees.obj+uncompr.obj+zutil.obj
-
-
-# targets
-all: $(ZLIB_LIB) example.exe minigzip.exe
-
-.c.obj:
- $(CC) -c $(CFLAGS) $*.c
-
-adler32.obj: adler32.c zlib.h zconf.h
-
-compress.obj: compress.c zlib.h zconf.h
-
-crc32.obj: crc32.c zlib.h zconf.h crc32.h
-
-deflate.obj: deflate.c deflate.h zutil.h zlib.h zconf.h
-
-gzclose.obj: gzclose.c zlib.h zconf.h gzguts.h
-
-gzlib.obj: gzlib.c zlib.h zconf.h gzguts.h
-
-gzread.obj: gzread.c zlib.h zconf.h gzguts.h
-
-gzwrite.obj: gzwrite.c zlib.h zconf.h gzguts.h
-
-infback.obj: infback.c zutil.h zlib.h zconf.h inftrees.h inflate.h \
- inffast.h inffixed.h
-
-inffast.obj: inffast.c zutil.h zlib.h zconf.h inftrees.h inflate.h \
- inffast.h
-
-inflate.obj: inflate.c zutil.h zlib.h zconf.h inftrees.h inflate.h \
- inffast.h inffixed.h
-
-inftrees.obj: inftrees.c zutil.h zlib.h zconf.h inftrees.h
-
-trees.obj: trees.c zutil.h zlib.h zconf.h deflate.h trees.h
-
-uncompr.obj: uncompr.c zlib.h zconf.h
-
-zutil.obj: zutil.c zutil.h zlib.h zconf.h
-
-example.obj: test/example.c zlib.h zconf.h
-
-minigzip.obj: test/minigzip.c zlib.h zconf.h
-
-
-# the command line is cut to fit in the MS-DOS 128 byte limit:
-$(ZLIB_LIB): $(OBJ1) $(OBJ2)
- -del $(ZLIB_LIB)
- $(AR) $(ZLIB_LIB) $(OBJP1)
- $(AR) $(ZLIB_LIB) $(OBJP2)
-
-example.exe: example.obj $(ZLIB_LIB)
- $(LD) $(LDFLAGS) example.obj $(ZLIB_LIB)
-
-minigzip.exe: minigzip.obj $(ZLIB_LIB)
- $(LD) $(LDFLAGS) minigzip.obj $(ZLIB_LIB)
-
-test: example.exe minigzip.exe
- example
- echo hello world | minigzip | minigzip -d
-
-clean:
- -del *.obj
- -del *.lib
- -del *.exe
- -del zlib_*.bak
- -del foo.gz
diff --git a/third-party/zlib/nintendods/README b/third-party/zlib/nintendods/README
deleted file mode 100644
index ba7a37d..0000000
--- a/third-party/zlib/nintendods/README
+++ /dev/null
@@ -1,5 +0,0 @@
-This Makefile requires devkitARM (http://www.devkitpro.org/category/devkitarm/) and works inside "contrib/nds". It is based on a devkitARM template.
-
-Eduardo Costa <eduardo.m.costa at gmail.com>
-January 3, 2009
-
diff --git a/third-party/zlib/old/Makefile.emx b/third-party/zlib/old/Makefile.emx
deleted file mode 100644
index 4d6ab0e..0000000
--- a/third-party/zlib/old/Makefile.emx
+++ /dev/null
@@ -1,69 +0,0 @@
-# Makefile for zlib. Modified for emx/rsxnt by Chr. Spieler, 6/16/98.
-# Copyright (C) 1995-1998 Jean-loup Gailly.
-# For conditions of distribution and use, see copyright notice in zlib.h
-
-# To compile, or to compile and test, type:
-#
-# make -fmakefile.emx; make test -fmakefile.emx
-#
-
-CC=gcc -Zwin32
-
-#CFLAGS=-MMD -O
-#CFLAGS=-O -DMAX_WBITS=14 -DMAX_MEM_LEVEL=7
-#CFLAGS=-MMD -g -DDEBUG
-CFLAGS=-MMD -O3 $(BUTT) -Wall -Wwrite-strings -Wpointer-arith -Wconversion \
- -Wstrict-prototypes -Wmissing-prototypes
-
-# If cp.exe is available, replace "copy /Y" with "cp -fp" .
-CP=copy /Y
-# If gnu install.exe is available, replace $(CP) with ginstall.
-INSTALL=$(CP)
-# The default value of RM is "rm -f." If "rm.exe" is found, comment out:
-RM=del
-LDLIBS=-L. -lzlib
-LD=$(CC) -s -o
-LDSHARED=$(CC)
-
-INCL=zlib.h zconf.h
-LIBS=zlib.a
-
-AR=ar rcs
-
-prefix=/usr/local
-exec_prefix = $(prefix)
-
-OBJS = adler32.o compress.o crc32.o deflate.o gzclose.o gzlib.o gzread.o \
- gzwrite.o infback.o inffast.o inflate.o inftrees.o trees.o uncompr.o zutil.o
-
-TEST_OBJS = example.o minigzip.o
-
-all: example.exe minigzip.exe
-
-test: all
- ./example
- echo hello world | .\minigzip | .\minigzip -d
-
-%.o : %.c
- $(CC) $(CFLAGS) -c $< -o $@
-
-zlib.a: $(OBJS)
- $(AR) $@ $(OBJS)
-
-%.exe : %.o $(LIBS)
- $(LD) $@ $< $(LDLIBS)
-
-
-.PHONY : clean
-
-clean:
- $(RM) *.d
- $(RM) *.o
- $(RM) *.exe
- $(RM) zlib.a
- $(RM) foo.gz
-
-DEPS := $(wildcard *.d)
-ifneq ($(DEPS),)
-include $(DEPS)
-endif
diff --git a/third-party/zlib/old/Makefile.riscos b/third-party/zlib/old/Makefile.riscos
deleted file mode 100644
index 57e29d3..0000000
--- a/third-party/zlib/old/Makefile.riscos
+++ /dev/null
@@ -1,151 +0,0 @@
-# Project: zlib_1_03
-# Patched for zlib 1.1.2 rw at shadow.org.uk 19980430
-# test works out-of-the-box, installs `somewhere' on demand
-
-# Toolflags:
-CCflags = -c -depend !Depend -IC: -g -throwback -DRISCOS -fah
-C++flags = -c -depend !Depend -IC: -throwback
-Linkflags = -aif -c++ -o $@
-ObjAsmflags = -throwback -NoCache -depend !Depend
-CMHGflags =
-LibFileflags = -c -l -o $@
-Squeezeflags = -o $@
-
-# change the line below to where _you_ want the library installed.
-libdest = lib:zlib
-
-# Final targets:
- at .lib: @.o.adler32 @.o.compress @.o.crc32 @.o.deflate @.o.gzio \
- @.o.infblock @.o.infcodes @.o.inffast @.o.inflate @.o.inftrees @.o.infutil @.o.trees \
- @.o.uncompr @.o.zutil
- LibFile $(LibFileflags) @.o.adler32 @.o.compress @.o.crc32 @.o.deflate \
- @.o.gzio @.o.infblock @.o.infcodes @.o.inffast @.o.inflate @.o.inftrees @.o.infutil \
- @.o.trees @.o.uncompr @.o.zutil
-test: @.minigzip @.example @.lib
- @copy @.lib @.libc A~C~DF~L~N~P~Q~RS~TV
- @echo running tests: hang on.
- @/@.minigzip -f -9 libc
- @/@.minigzip -d libc-gz
- @/@.minigzip -f -1 libc
- @/@.minigzip -d libc-gz
- @/@.minigzip -h -9 libc
- @/@.minigzip -d libc-gz
- @/@.minigzip -h -1 libc
- @/@.minigzip -d libc-gz
- @/@.minigzip -9 libc
- @/@.minigzip -d libc-gz
- @/@.minigzip -1 libc
- @/@.minigzip -d libc-gz
- @diff @.lib @.libc
- @echo that should have reported '@.lib and @.libc identical' if you have diff.
- @/@.example @.fred @.fred
- @echo that will have given lots of hello!'s.
-
- at .minigzip: @.o.minigzip @.lib C:o.Stubs
- Link $(Linkflags) @.o.minigzip @.lib C:o.Stubs
- at .example: @.o.example @.lib C:o.Stubs
- Link $(Linkflags) @.o.example @.lib C:o.Stubs
-
-install: @.lib
- cdir $(libdest)
- cdir $(libdest).h
- @copy @.h.zlib $(libdest).h.zlib A~C~DF~L~N~P~Q~RS~TV
- @copy @.h.zconf $(libdest).h.zconf A~C~DF~L~N~P~Q~RS~TV
- @copy @.lib $(libdest).lib A~C~DF~L~N~P~Q~RS~TV
- @echo okay, installed zlib in $(libdest)
-
-clean:; remove @.minigzip
- remove @.example
- remove @.libc
- -wipe @.o.* F~r~cV
- remove @.fred
-
-# User-editable dependencies:
-.c.o:
- cc $(ccflags) -o $@ $<
-
-# Static dependencies:
-
-# Dynamic dependencies:
-o.example: c.example
-o.example: h.zlib
-o.example: h.zconf
-o.minigzip: c.minigzip
-o.minigzip: h.zlib
-o.minigzip: h.zconf
-o.adler32: c.adler32
-o.adler32: h.zlib
-o.adler32: h.zconf
-o.compress: c.compress
-o.compress: h.zlib
-o.compress: h.zconf
-o.crc32: c.crc32
-o.crc32: h.zlib
-o.crc32: h.zconf
-o.deflate: c.deflate
-o.deflate: h.deflate
-o.deflate: h.zutil
-o.deflate: h.zlib
-o.deflate: h.zconf
-o.gzio: c.gzio
-o.gzio: h.zutil
-o.gzio: h.zlib
-o.gzio: h.zconf
-o.infblock: c.infblock
-o.infblock: h.zutil
-o.infblock: h.zlib
-o.infblock: h.zconf
-o.infblock: h.infblock
-o.infblock: h.inftrees
-o.infblock: h.infcodes
-o.infblock: h.infutil
-o.infcodes: c.infcodes
-o.infcodes: h.zutil
-o.infcodes: h.zlib
-o.infcodes: h.zconf
-o.infcodes: h.inftrees
-o.infcodes: h.infblock
-o.infcodes: h.infcodes
-o.infcodes: h.infutil
-o.infcodes: h.inffast
-o.inffast: c.inffast
-o.inffast: h.zutil
-o.inffast: h.zlib
-o.inffast: h.zconf
-o.inffast: h.inftrees
-o.inffast: h.infblock
-o.inffast: h.infcodes
-o.inffast: h.infutil
-o.inffast: h.inffast
-o.inflate: c.inflate
-o.inflate: h.zutil
-o.inflate: h.zlib
-o.inflate: h.zconf
-o.inflate: h.infblock
-o.inftrees: c.inftrees
-o.inftrees: h.zutil
-o.inftrees: h.zlib
-o.inftrees: h.zconf
-o.inftrees: h.inftrees
-o.inftrees: h.inffixed
-o.infutil: c.infutil
-o.infutil: h.zutil
-o.infutil: h.zlib
-o.infutil: h.zconf
-o.infutil: h.infblock
-o.infutil: h.inftrees
-o.infutil: h.infcodes
-o.infutil: h.infutil
-o.trees: c.trees
-o.trees: h.deflate
-o.trees: h.zutil
-o.trees: h.zlib
-o.trees: h.zconf
-o.trees: h.trees
-o.uncompr: c.uncompr
-o.uncompr: h.zlib
-o.uncompr: h.zconf
-o.zutil: c.zutil
-o.zutil: h.zutil
-o.zutil: h.zlib
-o.zutil: h.zconf
diff --git a/third-party/zlib/old/README b/third-party/zlib/old/README
deleted file mode 100644
index 800bf07..0000000
--- a/third-party/zlib/old/README
+++ /dev/null
@@ -1,3 +0,0 @@
-This directory contains files that have not been updated for zlib 1.2.x
-
-(Volunteers are encouraged to help clean this up. Thanks.)
diff --git a/third-party/zlib/old/descrip.mms b/third-party/zlib/old/descrip.mms
deleted file mode 100644
index 7066da5..0000000
--- a/third-party/zlib/old/descrip.mms
+++ /dev/null
@@ -1,48 +0,0 @@
-# descrip.mms: MMS description file for building zlib on VMS
-# written by Martin P.J. Zinser <m.zinser at gsi.de>
-
-cc_defs =
-c_deb =
-
-.ifdef __DECC__
-pref = /prefix=all
-.endif
-
-OBJS = adler32.obj, compress.obj, crc32.obj, gzio.obj, uncompr.obj,\
- deflate.obj, trees.obj, zutil.obj, inflate.obj, infblock.obj,\
- inftrees.obj, infcodes.obj, infutil.obj, inffast.obj
-
-CFLAGS= $(C_DEB) $(CC_DEFS) $(PREF)
-
-all : example.exe minigzip.exe
- @ write sys$output " Example applications available"
-libz.olb : libz.olb($(OBJS))
- @ write sys$output " libz available"
-
-example.exe : example.obj libz.olb
- link example,libz.olb/lib
-
-minigzip.exe : minigzip.obj libz.olb
- link minigzip,libz.olb/lib,x11vms:xvmsutils.olb/lib
-
-clean :
- delete *.obj;*,libz.olb;*
-
-
-# Other dependencies.
-adler32.obj : zutil.h zlib.h zconf.h
-compress.obj : zlib.h zconf.h
-crc32.obj : zutil.h zlib.h zconf.h
-deflate.obj : deflate.h zutil.h zlib.h zconf.h
-example.obj : zlib.h zconf.h
-gzio.obj : zutil.h zlib.h zconf.h
-infblock.obj : zutil.h zlib.h zconf.h infblock.h inftrees.h infcodes.h infutil.h
-infcodes.obj : zutil.h zlib.h zconf.h inftrees.h infutil.h infcodes.h inffast.h
-inffast.obj : zutil.h zlib.h zconf.h inftrees.h infutil.h inffast.h
-inflate.obj : zutil.h zlib.h zconf.h infblock.h
-inftrees.obj : zutil.h zlib.h zconf.h inftrees.h
-infutil.obj : zutil.h zlib.h zconf.h inftrees.h infutil.h
-minigzip.obj : zlib.h zconf.h
-trees.obj : deflate.h zutil.h zlib.h zconf.h
-uncompr.obj : zlib.h zconf.h
-zutil.obj : zutil.h zlib.h zconf.h
diff --git a/third-party/zlib/old/os2/Makefile.os2 b/third-party/zlib/old/os2/Makefile.os2
deleted file mode 100644
index a105aaa..0000000
--- a/third-party/zlib/old/os2/Makefile.os2
+++ /dev/null
@@ -1,136 +0,0 @@
-# Makefile for zlib under OS/2 using GCC (PGCC)
-# For conditions of distribution and use, see copyright notice in zlib.h
-
-# To compile and test, type:
-# cp Makefile.os2 ..
-# cd ..
-# make -f Makefile.os2 test
-
-# This makefile will build a static library z.lib, a shared library
-# z.dll and a import library zdll.lib. You can use either z.lib or
-# zdll.lib by specifying either -lz or -lzdll on gcc's command line
-
-CC=gcc -Zomf -s
-
-CFLAGS=-O6 -Wall
-#CFLAGS=-O -DMAX_WBITS=14 -DMAX_MEM_LEVEL=7
-#CFLAGS=-g -DDEBUG
-#CFLAGS=-O3 -Wall -Wwrite-strings -Wpointer-arith -Wconversion \
-# -Wstrict-prototypes -Wmissing-prototypes
-
-#################### BUG WARNING: #####################
-## infcodes.c hits a bug in pgcc-1.0, so you have to use either
-## -O# where # <= 4 or one of (-fno-ommit-frame-pointer or -fno-force-mem)
-## This bug is reportedly fixed in pgcc >1.0, but this was not tested
-CFLAGS+=-fno-force-mem
-
-LDFLAGS=-s -L. -lzdll -Zcrtdll
-LDSHARED=$(CC) -s -Zomf -Zdll -Zcrtdll
-
-VER=1.1.0
-ZLIB=z.lib
-SHAREDLIB=z.dll
-SHAREDLIBIMP=zdll.lib
-LIBS=$(ZLIB) $(SHAREDLIB) $(SHAREDLIBIMP)
-
-AR=emxomfar cr
-IMPLIB=emximp
-RANLIB=echo
-TAR=tar
-SHELL=bash
-
-prefix=/usr/local
-exec_prefix = $(prefix)
-
-OBJS = adler32.o compress.o crc32.o gzio.o uncompr.o deflate.o trees.o \
- zutil.o inflate.o infblock.o inftrees.o infcodes.o infutil.o inffast.o
-
-TEST_OBJS = example.o minigzip.o
-
-DISTFILES = README INDEX ChangeLog configure Make*[a-z0-9] *.[ch] descrip.mms \
- algorithm.txt zlib.3 msdos/Make*[a-z0-9] msdos/zlib.def msdos/zlib.rc \
- nt/Makefile.nt nt/zlib.dnt contrib/README.contrib contrib/*.txt \
- contrib/asm386/*.asm contrib/asm386/*.c \
- contrib/asm386/*.bat contrib/asm386/zlibvc.d?? contrib/iostream/*.cpp \
- contrib/iostream/*.h contrib/iostream2/*.h contrib/iostream2/*.cpp \
- contrib/untgz/Makefile contrib/untgz/*.c contrib/untgz/*.w32
-
-all: example.exe minigzip.exe
-
-test: all
- @LD_LIBRARY_PATH=.:$(LD_LIBRARY_PATH) ; export LD_LIBRARY_PATH; \
- echo hello world | ./minigzip | ./minigzip -d || \
- echo ' *** minigzip test FAILED ***' ; \
- if ./example; then \
- echo ' *** zlib test OK ***'; \
- else \
- echo ' *** zlib test FAILED ***'; \
- fi
-
-$(ZLIB): $(OBJS)
- $(AR) $@ $(OBJS)
- -@ ($(RANLIB) $@ || true) >/dev/null 2>&1
-
-$(SHAREDLIB): $(OBJS) os2/z.def
- $(LDSHARED) -o $@ $^
-
-$(SHAREDLIBIMP): os2/z.def
- $(IMPLIB) -o $@ $^
-
-example.exe: example.o $(LIBS)
- $(CC) $(CFLAGS) -o $@ example.o $(LDFLAGS)
-
-minigzip.exe: minigzip.o $(LIBS)
- $(CC) $(CFLAGS) -o $@ minigzip.o $(LDFLAGS)
-
-clean:
- rm -f *.o *~ example minigzip libz.a libz.so* foo.gz
-
-distclean: clean
-
-zip:
- mv Makefile Makefile~; cp -p Makefile.in Makefile
- rm -f test.c ztest*.c
- v=`sed -n -e 's/\.//g' -e '/VERSION "/s/.*"\(.*\)".*/\1/p' < zlib.h`;\
- zip -ul9 zlib$$v $(DISTFILES)
- mv Makefile~ Makefile
-
-dist:
- mv Makefile Makefile~; cp -p Makefile.in Makefile
- rm -f test.c ztest*.c
- d=zlib-`sed -n '/VERSION "/s/.*"\(.*\)".*/\1/p' < zlib.h`;\
- rm -f $$d.tar.gz; \
- if test ! -d ../$$d; then rm -f ../$$d; ln -s `pwd` ../$$d; fi; \
- files=""; \
- for f in $(DISTFILES); do files="$$files $$d/$$f"; done; \
- cd ..; \
- GZIP=-9 $(TAR) chofz $$d/$$d.tar.gz $$files; \
- if test ! -d $$d; then rm -f $$d; fi
- mv Makefile~ Makefile
-
-tags:
- etags *.[ch]
-
-depend:
- makedepend -- $(CFLAGS) -- *.[ch]
-
-# DO NOT DELETE THIS LINE -- make depend depends on it.
-
-adler32.o: zlib.h zconf.h
-compress.o: zlib.h zconf.h
-crc32.o: zlib.h zconf.h
-deflate.o: deflate.h zutil.h zlib.h zconf.h
-example.o: zlib.h zconf.h
-gzio.o: zutil.h zlib.h zconf.h
-infblock.o: infblock.h inftrees.h infcodes.h infutil.h zutil.h zlib.h zconf.h
-infcodes.o: zutil.h zlib.h zconf.h
-infcodes.o: inftrees.h infblock.h infcodes.h infutil.h inffast.h
-inffast.o: zutil.h zlib.h zconf.h inftrees.h
-inffast.o: infblock.h infcodes.h infutil.h inffast.h
-inflate.o: zutil.h zlib.h zconf.h infblock.h
-inftrees.o: zutil.h zlib.h zconf.h inftrees.h
-infutil.o: zutil.h zlib.h zconf.h infblock.h inftrees.h infcodes.h infutil.h
-minigzip.o: zlib.h zconf.h
-trees.o: deflate.h zutil.h zlib.h zconf.h trees.h
-uncompr.o: zlib.h zconf.h
-zutil.o: zutil.h zlib.h zconf.h
diff --git a/third-party/zlib/old/os2/zlib.def b/third-party/zlib/old/os2/zlib.def
deleted file mode 100644
index 4c753f1..0000000
--- a/third-party/zlib/old/os2/zlib.def
+++ /dev/null
@@ -1,51 +0,0 @@
-;
-; Slightly modified version of ../nt/zlib.dnt :-)
-;
-
-LIBRARY Z
-DESCRIPTION "Zlib compression library for OS/2"
-CODE PRELOAD MOVEABLE DISCARDABLE
-DATA PRELOAD MOVEABLE MULTIPLE
-
-EXPORTS
- adler32
- compress
- crc32
- deflate
- deflateCopy
- deflateEnd
- deflateInit2_
- deflateInit_
- deflateParams
- deflateReset
- deflateSetDictionary
- gzclose
- gzdopen
- gzerror
- gzflush
- gzopen
- gzread
- gzwrite
- inflate
- inflateEnd
- inflateInit2_
- inflateInit_
- inflateReset
- inflateSetDictionary
- inflateSync
- uncompress
- zlibVersion
- gzprintf
- gzputc
- gzgetc
- gzseek
- gzrewind
- gztell
- gzeof
- gzsetparams
- zError
- inflateSyncPoint
- get_crc_table
- compress2
- gzputs
- gzgets
diff --git a/third-party/zlib/old/visual-basic.txt b/third-party/zlib/old/visual-basic.txt
deleted file mode 100644
index 57efe58..0000000
--- a/third-party/zlib/old/visual-basic.txt
+++ /dev/null
@@ -1,160 +0,0 @@
-See below some functions declarations for Visual Basic.
-
-Frequently Asked Question:
-
-Q: Each time I use the compress function I get the -5 error (not enough
- room in the output buffer).
-
-A: Make sure that the length of the compressed buffer is passed by
- reference ("as any"), not by value ("as long"). Also check that
- before the call of compress this length is equal to the total size of
- the compressed buffer and not zero.
-
-
-From: "Jon Caruana" <jon-net at usa.net>
-Subject: Re: How to port zlib declares to vb?
-Date: Mon, 28 Oct 1996 18:33:03 -0600
-
-Got the answer! (I haven't had time to check this but it's what I got, and
-looks correct):
-
-He has the following routines working:
- compress
- uncompress
- gzopen
- gzwrite
- gzread
- gzclose
-
-Declares follow: (Quoted from Carlos Rios <c_rios at sonda.cl>, in Vb4 form)
-
-#If Win16 Then 'Use Win16 calls.
-Declare Function compress Lib "ZLIB.DLL" (ByVal compr As
- String, comprLen As Any, ByVal buf As String, ByVal buflen
- As Long) As Integer
-Declare Function uncompress Lib "ZLIB.DLL" (ByVal uncompr
- As String, uncomprLen As Any, ByVal compr As String, ByVal
- lcompr As Long) As Integer
-Declare Function gzopen Lib "ZLIB.DLL" (ByVal filePath As
- String, ByVal mode As String) As Long
-Declare Function gzread Lib "ZLIB.DLL" (ByVal file As
- Long, ByVal uncompr As String, ByVal uncomprLen As Integer)
- As Integer
-Declare Function gzwrite Lib "ZLIB.DLL" (ByVal file As
- Long, ByVal uncompr As String, ByVal uncomprLen As Integer)
- As Integer
-Declare Function gzclose Lib "ZLIB.DLL" (ByVal file As
- Long) As Integer
-#Else
-Declare Function compress Lib "ZLIB32.DLL"
- (ByVal compr As String, comprLen As Any, ByVal buf As
- String, ByVal buflen As Long) As Integer
-Declare Function uncompress Lib "ZLIB32.DLL"
- (ByVal uncompr As String, uncomprLen As Any, ByVal compr As
- String, ByVal lcompr As Long) As Long
-Declare Function gzopen Lib "ZLIB32.DLL"
- (ByVal file As String, ByVal mode As String) As Long
-Declare Function gzread Lib "ZLIB32.DLL"
- (ByVal file As Long, ByVal uncompr As String, ByVal
- uncomprLen As Long) As Long
-Declare Function gzwrite Lib "ZLIB32.DLL"
- (ByVal file As Long, ByVal uncompr As String, ByVal
- uncomprLen As Long) As Long
-Declare Function gzclose Lib "ZLIB32.DLL"
- (ByVal file As Long) As Long
-#End If
-
--Jon Caruana
-jon-net at usa.net
-Microsoft Sitebuilder Network Level 1 Member - HTML Writer's Guild Member
-
-
-Here is another example from Michael <michael_borgsys at hotmail.com> that he
-says conforms to the VB guidelines, and that solves the problem of not
-knowing the uncompressed size by storing it at the end of the file:
-
-'Calling the functions:
-'bracket meaning: <parameter> [optional] {Range of possible values}
-'Call subCompressFile(<path with filename to compress> [, <path with
-filename to write to>, [level of compression {1..9}]])
-'Call subUncompressFile(<path with filename to compress>)
-
-Option Explicit
-Private lngpvtPcnSml As Long 'Stores value for 'lngPercentSmaller'
-Private Const SUCCESS As Long = 0
-Private Const strFilExt As String = ".cpr"
-Private Declare Function lngfncCpr Lib "zlib.dll" Alias "compress2" (ByRef
-dest As Any, ByRef destLen As Any, ByRef src As Any, ByVal srcLen As Long,
-ByVal level As Integer) As Long
-Private Declare Function lngfncUcp Lib "zlib.dll" Alias "uncompress" (ByRef
-dest As Any, ByRef destLen As Any, ByRef src As Any, ByVal srcLen As Long)
-As Long
-
-Public Sub subCompressFile(ByVal strargOriFilPth As String, Optional ByVal
-strargCprFilPth As String, Optional ByVal intLvl As Integer = 9)
- Dim strCprPth As String
- Dim lngOriSiz As Long
- Dim lngCprSiz As Long
- Dim bytaryOri() As Byte
- Dim bytaryCpr() As Byte
- lngOriSiz = FileLen(strargOriFilPth)
- ReDim bytaryOri(lngOriSiz - 1)
- Open strargOriFilPth For Binary Access Read As #1
- Get #1, , bytaryOri()
- Close #1
- strCprPth = IIf(strargCprFilPth = "", strargOriFilPth, strargCprFilPth)
-'Select file path and name
- strCprPth = strCprPth & IIf(Right(strCprPth, Len(strFilExt)) =
-strFilExt, "", strFilExt) 'Add file extension if not exists
- lngCprSiz = (lngOriSiz * 1.01) + 12 'Compression needs temporary a bit
-more space then original file size
- ReDim bytaryCpr(lngCprSiz - 1)
- If lngfncCpr(bytaryCpr(0), lngCprSiz, bytaryOri(0), lngOriSiz, intLvl) =
-SUCCESS Then
- lngpvtPcnSml = (1# - (lngCprSiz / lngOriSiz)) * 100
- ReDim Preserve bytaryCpr(lngCprSiz - 1)
- Open strCprPth For Binary Access Write As #1
- Put #1, , bytaryCpr()
- Put #1, , lngOriSiz 'Add the the original size value to the end
-(last 4 bytes)
- Close #1
- Else
- MsgBox "Compression error"
- End If
- Erase bytaryCpr
- Erase bytaryOri
-End Sub
-
-Public Sub subUncompressFile(ByVal strargFilPth As String)
- Dim bytaryCpr() As Byte
- Dim bytaryOri() As Byte
- Dim lngOriSiz As Long
- Dim lngCprSiz As Long
- Dim strOriPth As String
- lngCprSiz = FileLen(strargFilPth)
- ReDim bytaryCpr(lngCprSiz - 1)
- Open strargFilPth For Binary Access Read As #1
- Get #1, , bytaryCpr()
- Close #1
- 'Read the original file size value:
- lngOriSiz = bytaryCpr(lngCprSiz - 1) * (2 ^ 24) _
- + bytaryCpr(lngCprSiz - 2) * (2 ^ 16) _
- + bytaryCpr(lngCprSiz - 3) * (2 ^ 8) _
- + bytaryCpr(lngCprSiz - 4)
- ReDim Preserve bytaryCpr(lngCprSiz - 5) 'Cut of the original size value
- ReDim bytaryOri(lngOriSiz - 1)
- If lngfncUcp(bytaryOri(0), lngOriSiz, bytaryCpr(0), lngCprSiz) = SUCCESS
-Then
- strOriPth = Left(strargFilPth, Len(strargFilPth) - Len(strFilExt))
- Open strOriPth For Binary Access Write As #1
- Put #1, , bytaryOri()
- Close #1
- Else
- MsgBox "Uncompression error"
- End If
- Erase bytaryCpr
- Erase bytaryOri
-End Sub
-Public Property Get lngPercentSmaller() As Long
- lngPercentSmaller = lngpvtPcnSml
-End Property
diff --git a/third-party/zlib/qnx/package.qpg b/third-party/zlib/qnx/package.qpg
deleted file mode 100644
index aebf6e3..0000000
--- a/third-party/zlib/qnx/package.qpg
+++ /dev/null
@@ -1,141 +0,0 @@
-<QPG:Generation>
- <QPG:Options>
- <QPG:User unattended="no" verbosity="2" listfiles="yes"/>
- <QPG:Defaults type="qnx_package"/>
- <QPG:Source></QPG:Source>
- <QPG:Release number="+"/>
- <QPG:Build></QPG:Build>
- <QPG:FileSorting strip="yes"/>
- <QPG:Package targets="combine"/>
- <QPG:Repository generate="yes"/>
- <QPG:FinalDir></QPG:FinalDir>
- <QPG:Cleanup></QPG:Cleanup>
- </QPG:Options>
-
- <QPG:Responsible>
- <QPG:Company></QPG:Company>
- <QPG:Department></QPG:Department>
- <QPG:Group></QPG:Group>
- <QPG:Team></QPG:Team>
- <QPG:Employee></QPG:Employee>
- <QPG:EmailAddress></QPG:EmailAddress>
- </QPG:Responsible>
-
- <QPG:Values>
- <QPG:Files>
- <QPG:Add file="../zconf.h" install="/opt/include/" user="root:sys" permission="644"/>
- <QPG:Add file="../zlib.h" install="/opt/include/" user="root:sys" permission="644"/>
- <QPG:Add file="../libz.so.1.2.8" install="/opt/lib/" user="root:bin" permission="644"/>
- <QPG:Add file="libz.so" install="/opt/lib/" component="dev" filetype="symlink" linkto="libz.so.1.2.8"/>
- <QPG:Add file="libz.so.1" install="/opt/lib/" filetype="symlink" linkto="libz.so.1.2.8"/>
- <QPG:Add file="../libz.so.1.2.8" install="/opt/lib/" component="slib"/>
- </QPG:Files>
-
- <QPG:PackageFilter>
- <QPM:PackageManifest>
- <QPM:PackageDescription>
- <QPM:PackageType>Library</QPM:PackageType>
- <QPM:PackageReleaseNotes></QPM:PackageReleaseNotes>
- <QPM:PackageReleaseUrgency>Medium</QPM:PackageReleaseUrgency>
- <QPM:PackageRepository></QPM:PackageRepository>
- <QPM:FileVersion>2.0</QPM:FileVersion>
- </QPM:PackageDescription>
-
- <QPM:ProductDescription>
- <QPM:ProductName>zlib</QPM:ProductName>
- <QPM:ProductIdentifier>zlib</QPM:ProductIdentifier>
- <QPM:ProductEmail>alain.bonnefoy at icbt.com</QPM:ProductEmail>
- <QPM:VendorName>Public</QPM:VendorName>
- <QPM:VendorInstallName>public</QPM:VendorInstallName>
- <QPM:VendorURL>www.gzip.org/zlib</QPM:VendorURL>
- <QPM:VendorEmbedURL></QPM:VendorEmbedURL>
- <QPM:VendorEmail></QPM:VendorEmail>
- <QPM:AuthorName>Jean-Loup Gailly,Mark Adler</QPM:AuthorName>
- <QPM:AuthorURL>www.gzip.org/zlib</QPM:AuthorURL>
- <QPM:AuthorEmbedURL></QPM:AuthorEmbedURL>
- <QPM:AuthorEmail>zlib at gzip.org</QPM:AuthorEmail>
- <QPM:ProductIconSmall></QPM:ProductIconSmall>
- <QPM:ProductIconLarge></QPM:ProductIconLarge>
- <QPM:ProductDescriptionShort>A massively spiffy yet delicately unobtrusive compression library.</QPM:ProductDescriptionShort>
- <QPM:ProductDescriptionLong>zlib is designed to be a free, general-purpose, legally unencumbered, lossless data compression library for use on virtually any computer hardware and operating system.</QPM:ProductDescriptionLong>
- <QPM:ProductDescriptionURL>http://www.gzip.org/zlib</QPM:ProductDescriptionURL>
- <QPM:ProductDescriptionEmbedURL></QPM:ProductDescriptionEmbedURL>
- </QPM:ProductDescription>
-
- <QPM:ReleaseDescription>
- <QPM:ReleaseVersion>1.2.8</QPM:ReleaseVersion>
- <QPM:ReleaseUrgency>Medium</QPM:ReleaseUrgency>
- <QPM:ReleaseStability>Stable</QPM:ReleaseStability>
- <QPM:ReleaseNoteMinor></QPM:ReleaseNoteMinor>
- <QPM:ReleaseNoteMajor></QPM:ReleaseNoteMajor>
- <QPM:ExcludeCountries>
- <QPM:Country></QPM:Country>
- </QPM:ExcludeCountries>
-
- <QPM:ReleaseCopyright>No License</QPM:ReleaseCopyright>
- </QPM:ReleaseDescription>
-
- <QPM:ContentDescription>
- <QPM:ContentTopic xmlmultiple="true">Software Development/Libraries and Extensions/C Libraries</QPM:ContentTopic>
- <QPM:ContentKeyword>zlib,compression</QPM:ContentKeyword>
- <QPM:TargetOS>qnx6</QPM:TargetOS>
- <QPM:HostOS>qnx6</QPM:HostOS>
- <QPM:DisplayEnvironment xmlmultiple="true">None</QPM:DisplayEnvironment>
- <QPM:TargetAudience xmlmultiple="true">Developer</QPM:TargetAudience>
- </QPM:ContentDescription>
- </QPM:PackageManifest>
- </QPG:PackageFilter>
-
- <QPG:PackageFilter proc="none" target="none">
- <QPM:PackageManifest>
- <QPM:ProductInstallationDependencies>
- <QPM:ProductRequirements></QPM:ProductRequirements>
- </QPM:ProductInstallationDependencies>
-
- <QPM:ProductInstallationProcedure>
- <QPM:Script xmlmultiple="true">
- <QPM:ScriptName></QPM:ScriptName>
- <QPM:ScriptType>Install</QPM:ScriptType>
- <QPM:ScriptTiming>Post</QPM:ScriptTiming>
- <QPM:ScriptBlocking>No</QPM:ScriptBlocking>
- <QPM:ScriptResult>Ignore</QPM:ScriptResult>
- <QPM:ShortDescription></QPM:ShortDescription>
- <QPM:UseBinaries>No</QPM:UseBinaries>
- <QPM:Priority>Optional</QPM:Priority>
- </QPM:Script>
- </QPM:ProductInstallationProcedure>
- </QPM:PackageManifest>
-
- <QPM:Launch>
- </QPM:Launch>
- </QPG:PackageFilter>
-
- <QPG:PackageFilter type="core" component="none">
- <QPM:PackageManifest>
- <QPM:ProductInstallationProcedure>
- <QPM:OrderDependency xmlmultiple="true">
- <QPM:Order>InstallOver</QPM:Order>
- <QPM:Product>zlib</QPM:Product>
- </QPM:OrderDependency>
- </QPM:ProductInstallationProcedure>
- </QPM:PackageManifest>
-
- <QPM:Launch>
- </QPM:Launch>
- </QPG:PackageFilter>
-
- <QPG:PackageFilter type="core" component="dev">
- <QPM:PackageManifest>
- <QPM:ProductInstallationProcedure>
- <QPM:OrderDependency xmlmultiple="true">
- <QPM:Order>InstallOver</QPM:Order>
- <QPM:Product>zlib-dev</QPM:Product>
- </QPM:OrderDependency>
- </QPM:ProductInstallationProcedure>
- </QPM:PackageManifest>
-
- <QPM:Launch>
- </QPM:Launch>
- </QPG:PackageFilter>
- </QPG:Values>
-</QPG:Generation>
diff --git a/third-party/zlib/test/example.c b/third-party/zlib/test/example.c
deleted file mode 100644
index 138a699..0000000
--- a/third-party/zlib/test/example.c
+++ /dev/null
@@ -1,601 +0,0 @@
-/* example.c -- usage example of the zlib compression library
- * Copyright (C) 1995-2006, 2011 Jean-loup Gailly.
- * For conditions of distribution and use, see copyright notice in zlib.h
- */
-
-/* @(#) $Id$ */
-
-#include "zlib.h"
-#include <stdio.h>
-
-#ifdef STDC
-# include <string.h>
-# include <stdlib.h>
-#endif
-
-#if defined(VMS) || defined(RISCOS)
-# define TESTFILE "foo-gz"
-#else
-# define TESTFILE "foo.gz"
-#endif
-
-#define CHECK_ERR(err, msg) { \
- if (err != Z_OK) { \
- fprintf(stderr, "%s error: %d\n", msg, err); \
- exit(1); \
- } \
-}
-
-z_const char hello[] = "hello, hello!";
-/* "hello world" would be more standard, but the repeated "hello"
- * stresses the compression code better, sorry...
- */
-
-const char dictionary[] = "hello";
-uLong dictId; /* Adler32 value of the dictionary */
-
-void test_deflate OF((Byte *compr, uLong comprLen));
-void test_inflate OF((Byte *compr, uLong comprLen,
- Byte *uncompr, uLong uncomprLen));
-void test_large_deflate OF((Byte *compr, uLong comprLen,
- Byte *uncompr, uLong uncomprLen));
-void test_large_inflate OF((Byte *compr, uLong comprLen,
- Byte *uncompr, uLong uncomprLen));
-void test_flush OF((Byte *compr, uLong *comprLen));
-void test_sync OF((Byte *compr, uLong comprLen,
- Byte *uncompr, uLong uncomprLen));
-void test_dict_deflate OF((Byte *compr, uLong comprLen));
-void test_dict_inflate OF((Byte *compr, uLong comprLen,
- Byte *uncompr, uLong uncomprLen));
-int main OF((int argc, char *argv[]));
-
-
-#ifdef Z_SOLO
-
-void *myalloc OF((void *, unsigned, unsigned));
-void myfree OF((void *, void *));
-
-void *myalloc(q, n, m)
- void *q;
- unsigned n, m;
-{
- q = Z_NULL;
- return calloc(n, m);
-}
-
-void myfree(void *q, void *p)
-{
- q = Z_NULL;
- free(p);
-}
-
-static alloc_func zalloc = myalloc;
-static free_func zfree = myfree;
-
-#else /* !Z_SOLO */
-
-static alloc_func zalloc = (alloc_func)0;
-static free_func zfree = (free_func)0;
-
-void test_compress OF((Byte *compr, uLong comprLen,
- Byte *uncompr, uLong uncomprLen));
-void test_gzio OF((const char *fname,
- Byte *uncompr, uLong uncomprLen));
-
-/* ===========================================================================
- * Test compress() and uncompress()
- */
-void test_compress(compr, comprLen, uncompr, uncomprLen)
- Byte *compr, *uncompr;
- uLong comprLen, uncomprLen;
-{
- int err;
- uLong len = (uLong)strlen(hello)+1;
-
- err = compress(compr, &comprLen, (const Bytef*)hello, len);
- CHECK_ERR(err, "compress");
-
- strcpy((char*)uncompr, "garbage");
-
- err = uncompress(uncompr, &uncomprLen, compr, comprLen);
- CHECK_ERR(err, "uncompress");
-
- if (strcmp((char*)uncompr, hello)) {
- fprintf(stderr, "bad uncompress\n");
- exit(1);
- } else {
- printf("uncompress(): %s\n", (char *)uncompr);
- }
-}
-
-/* ===========================================================================
- * Test read/write of .gz files
- */
-void test_gzio(fname, uncompr, uncomprLen)
- const char *fname; /* compressed file name */
- Byte *uncompr;
- uLong uncomprLen;
-{
-#ifdef NO_GZCOMPRESS
- fprintf(stderr, "NO_GZCOMPRESS -- gz* functions cannot compress\n");
-#else
- int err;
- int len = (int)strlen(hello)+1;
- gzFile file;
- z_off_t pos;
-
- file = gzopen(fname, "wb");
- if (file == NULL) {
- fprintf(stderr, "gzopen error\n");
- exit(1);
- }
- gzputc(file, 'h');
- if (gzputs(file, "ello") != 4) {
- fprintf(stderr, "gzputs err: %s\n", gzerror(file, &err));
- exit(1);
- }
- if (gzprintf(file, ", %s!", "hello") != 8) {
- fprintf(stderr, "gzprintf err: %s\n", gzerror(file, &err));
- exit(1);
- }
- gzseek(file, 1L, SEEK_CUR); /* add one zero byte */
- gzclose(file);
-
- file = gzopen(fname, "rb");
- if (file == NULL) {
- fprintf(stderr, "gzopen error\n");
- exit(1);
- }
- strcpy((char*)uncompr, "garbage");
-
- if (gzread(file, uncompr, (unsigned)uncomprLen) != len) {
- fprintf(stderr, "gzread err: %s\n", gzerror(file, &err));
- exit(1);
- }
- if (strcmp((char*)uncompr, hello)) {
- fprintf(stderr, "bad gzread: %s\n", (char*)uncompr);
- exit(1);
- } else {
- printf("gzread(): %s\n", (char*)uncompr);
- }
-
- pos = gzseek(file, -8L, SEEK_CUR);
- if (pos != 6 || gztell(file) != pos) {
- fprintf(stderr, "gzseek error, pos=%ld, gztell=%ld\n",
- (long)pos, (long)gztell(file));
- exit(1);
- }
-
- if (gzgetc(file) != ' ') {
- fprintf(stderr, "gzgetc error\n");
- exit(1);
- }
-
- if (gzungetc(' ', file) != ' ') {
- fprintf(stderr, "gzungetc error\n");
- exit(1);
- }
-
- gzgets(file, (char*)uncompr, (int)uncomprLen);
- if (strlen((char*)uncompr) != 7) { /* " hello!" */
- fprintf(stderr, "gzgets err after gzseek: %s\n", gzerror(file, &err));
- exit(1);
- }
- if (strcmp((char*)uncompr, hello + 6)) {
- fprintf(stderr, "bad gzgets after gzseek\n");
- exit(1);
- } else {
- printf("gzgets() after gzseek: %s\n", (char*)uncompr);
- }
-
- gzclose(file);
-#endif
-}
-
-#endif /* Z_SOLO */
-
-/* ===========================================================================
- * Test deflate() with small buffers
- */
-void test_deflate(compr, comprLen)
- Byte *compr;
- uLong comprLen;
-{
- z_stream c_stream; /* compression stream */
- int err;
- uLong len = (uLong)strlen(hello)+1;
-
- c_stream.zalloc = zalloc;
- c_stream.zfree = zfree;
- c_stream.opaque = (voidpf)0;
-
- err = deflateInit(&c_stream, Z_DEFAULT_COMPRESSION);
- CHECK_ERR(err, "deflateInit");
-
- c_stream.next_in = (z_const unsigned char *)hello;
- c_stream.next_out = compr;
-
- while (c_stream.total_in != len && c_stream.total_out < comprLen) {
- c_stream.avail_in = c_stream.avail_out = 1; /* force small buffers */
- err = deflate(&c_stream, Z_NO_FLUSH);
- CHECK_ERR(err, "deflate");
- }
- /* Finish the stream, still forcing small buffers: */
- for (;;) {
- c_stream.avail_out = 1;
- err = deflate(&c_stream, Z_FINISH);
- if (err == Z_STREAM_END) break;
- CHECK_ERR(err, "deflate");
- }
-
- err = deflateEnd(&c_stream);
- CHECK_ERR(err, "deflateEnd");
-}
-
-/* ===========================================================================
- * Test inflate() with small buffers
- */
-void test_inflate(compr, comprLen, uncompr, uncomprLen)
- Byte *compr, *uncompr;
- uLong comprLen, uncomprLen;
-{
- int err;
- z_stream d_stream; /* decompression stream */
-
- strcpy((char*)uncompr, "garbage");
-
- d_stream.zalloc = zalloc;
- d_stream.zfree = zfree;
- d_stream.opaque = (voidpf)0;
-
- d_stream.next_in = compr;
- d_stream.avail_in = 0;
- d_stream.next_out = uncompr;
-
- err = inflateInit(&d_stream);
- CHECK_ERR(err, "inflateInit");
-
- while (d_stream.total_out < uncomprLen && d_stream.total_in < comprLen) {
- d_stream.avail_in = d_stream.avail_out = 1; /* force small buffers */
- err = inflate(&d_stream, Z_NO_FLUSH);
- if (err == Z_STREAM_END) break;
- CHECK_ERR(err, "inflate");
- }
-
- err = inflateEnd(&d_stream);
- CHECK_ERR(err, "inflateEnd");
-
- if (strcmp((char*)uncompr, hello)) {
- fprintf(stderr, "bad inflate\n");
- exit(1);
- } else {
- printf("inflate(): %s\n", (char *)uncompr);
- }
-}
-
-/* ===========================================================================
- * Test deflate() with large buffers and dynamic change of compression level
- */
-void test_large_deflate(compr, comprLen, uncompr, uncomprLen)
- Byte *compr, *uncompr;
- uLong comprLen, uncomprLen;
-{
- z_stream c_stream; /* compression stream */
- int err;
-
- c_stream.zalloc = zalloc;
- c_stream.zfree = zfree;
- c_stream.opaque = (voidpf)0;
-
- err = deflateInit(&c_stream, Z_BEST_SPEED);
- CHECK_ERR(err, "deflateInit");
-
- c_stream.next_out = compr;
- c_stream.avail_out = (uInt)comprLen;
-
- /* At this point, uncompr is still mostly zeroes, so it should compress
- * very well:
- */
- c_stream.next_in = uncompr;
- c_stream.avail_in = (uInt)uncomprLen;
- err = deflate(&c_stream, Z_NO_FLUSH);
- CHECK_ERR(err, "deflate");
- if (c_stream.avail_in != 0) {
- fprintf(stderr, "deflate not greedy\n");
- exit(1);
- }
-
- /* Feed in already compressed data and switch to no compression: */
- deflateParams(&c_stream, Z_NO_COMPRESSION, Z_DEFAULT_STRATEGY);
- c_stream.next_in = compr;
- c_stream.avail_in = (uInt)comprLen/2;
- err = deflate(&c_stream, Z_NO_FLUSH);
- CHECK_ERR(err, "deflate");
-
- /* Switch back to compressing mode: */
- deflateParams(&c_stream, Z_BEST_COMPRESSION, Z_FILTERED);
- c_stream.next_in = uncompr;
- c_stream.avail_in = (uInt)uncomprLen;
- err = deflate(&c_stream, Z_NO_FLUSH);
- CHECK_ERR(err, "deflate");
-
- err = deflate(&c_stream, Z_FINISH);
- if (err != Z_STREAM_END) {
- fprintf(stderr, "deflate should report Z_STREAM_END\n");
- exit(1);
- }
- err = deflateEnd(&c_stream);
- CHECK_ERR(err, "deflateEnd");
-}
-
-/* ===========================================================================
- * Test inflate() with large buffers
- */
-void test_large_inflate(compr, comprLen, uncompr, uncomprLen)
- Byte *compr, *uncompr;
- uLong comprLen, uncomprLen;
-{
- int err;
- z_stream d_stream; /* decompression stream */
-
- strcpy((char*)uncompr, "garbage");
-
- d_stream.zalloc = zalloc;
- d_stream.zfree = zfree;
- d_stream.opaque = (voidpf)0;
-
- d_stream.next_in = compr;
- d_stream.avail_in = (uInt)comprLen;
-
- err = inflateInit(&d_stream);
- CHECK_ERR(err, "inflateInit");
-
- for (;;) {
- d_stream.next_out = uncompr; /* discard the output */
- d_stream.avail_out = (uInt)uncomprLen;
- err = inflate(&d_stream, Z_NO_FLUSH);
- if (err == Z_STREAM_END) break;
- CHECK_ERR(err, "large inflate");
- }
-
- err = inflateEnd(&d_stream);
- CHECK_ERR(err, "inflateEnd");
-
- if (d_stream.total_out != 2*uncomprLen + comprLen/2) {
- fprintf(stderr, "bad large inflate: %ld\n", d_stream.total_out);
- exit(1);
- } else {
- printf("large_inflate(): OK\n");
- }
-}
-
-/* ===========================================================================
- * Test deflate() with full flush
- */
-void test_flush(compr, comprLen)
- Byte *compr;
- uLong *comprLen;
-{
- z_stream c_stream; /* compression stream */
- int err;
- uInt len = (uInt)strlen(hello)+1;
-
- c_stream.zalloc = zalloc;
- c_stream.zfree = zfree;
- c_stream.opaque = (voidpf)0;
-
- err = deflateInit(&c_stream, Z_DEFAULT_COMPRESSION);
- CHECK_ERR(err, "deflateInit");
-
- c_stream.next_in = (z_const unsigned char *)hello;
- c_stream.next_out = compr;
- c_stream.avail_in = 3;
- c_stream.avail_out = (uInt)*comprLen;
- err = deflate(&c_stream, Z_FULL_FLUSH);
- CHECK_ERR(err, "deflate");
-
- compr[3]++; /* force an error in first compressed block */
- c_stream.avail_in = len - 3;
-
- err = deflate(&c_stream, Z_FINISH);
- if (err != Z_STREAM_END) {
- CHECK_ERR(err, "deflate");
- }
- err = deflateEnd(&c_stream);
- CHECK_ERR(err, "deflateEnd");
-
- *comprLen = c_stream.total_out;
-}
-
-/* ===========================================================================
- * Test inflateSync()
- */
-void test_sync(compr, comprLen, uncompr, uncomprLen)
- Byte *compr, *uncompr;
- uLong comprLen, uncomprLen;
-{
- int err;
- z_stream d_stream; /* decompression stream */
-
- strcpy((char*)uncompr, "garbage");
-
- d_stream.zalloc = zalloc;
- d_stream.zfree = zfree;
- d_stream.opaque = (voidpf)0;
-
- d_stream.next_in = compr;
- d_stream.avail_in = 2; /* just read the zlib header */
-
- err = inflateInit(&d_stream);
- CHECK_ERR(err, "inflateInit");
-
- d_stream.next_out = uncompr;
- d_stream.avail_out = (uInt)uncomprLen;
-
- inflate(&d_stream, Z_NO_FLUSH);
- CHECK_ERR(err, "inflate");
-
- d_stream.avail_in = (uInt)comprLen-2; /* read all compressed data */
- err = inflateSync(&d_stream); /* but skip the damaged part */
- CHECK_ERR(err, "inflateSync");
-
- err = inflate(&d_stream, Z_FINISH);
- if (err != Z_DATA_ERROR) {
- fprintf(stderr, "inflate should report DATA_ERROR\n");
- /* Because of incorrect adler32 */
- exit(1);
- }
- err = inflateEnd(&d_stream);
- CHECK_ERR(err, "inflateEnd");
-
- printf("after inflateSync(): hel%s\n", (char *)uncompr);
-}
-
-/* ===========================================================================
- * Test deflate() with preset dictionary
- */
-void test_dict_deflate(compr, comprLen)
- Byte *compr;
- uLong comprLen;
-{
- z_stream c_stream; /* compression stream */
- int err;
-
- c_stream.zalloc = zalloc;
- c_stream.zfree = zfree;
- c_stream.opaque = (voidpf)0;
-
- err = deflateInit(&c_stream, Z_BEST_COMPRESSION);
- CHECK_ERR(err, "deflateInit");
-
- err = deflateSetDictionary(&c_stream,
- (const Bytef*)dictionary, (int)sizeof(dictionary));
- CHECK_ERR(err, "deflateSetDictionary");
-
- dictId = c_stream.adler;
- c_stream.next_out = compr;
- c_stream.avail_out = (uInt)comprLen;
-
- c_stream.next_in = (z_const unsigned char *)hello;
- c_stream.avail_in = (uInt)strlen(hello)+1;
-
- err = deflate(&c_stream, Z_FINISH);
- if (err != Z_STREAM_END) {
- fprintf(stderr, "deflate should report Z_STREAM_END\n");
- exit(1);
- }
- err = deflateEnd(&c_stream);
- CHECK_ERR(err, "deflateEnd");
-}
-
-/* ===========================================================================
- * Test inflate() with a preset dictionary
- */
-void test_dict_inflate(compr, comprLen, uncompr, uncomprLen)
- Byte *compr, *uncompr;
- uLong comprLen, uncomprLen;
-{
- int err;
- z_stream d_stream; /* decompression stream */
-
- strcpy((char*)uncompr, "garbage");
-
- d_stream.zalloc = zalloc;
- d_stream.zfree = zfree;
- d_stream.opaque = (voidpf)0;
-
- d_stream.next_in = compr;
- d_stream.avail_in = (uInt)comprLen;
-
- err = inflateInit(&d_stream);
- CHECK_ERR(err, "inflateInit");
-
- d_stream.next_out = uncompr;
- d_stream.avail_out = (uInt)uncomprLen;
-
- for (;;) {
- err = inflate(&d_stream, Z_NO_FLUSH);
- if (err == Z_STREAM_END) break;
- if (err == Z_NEED_DICT) {
- if (d_stream.adler != dictId) {
- fprintf(stderr, "unexpected dictionary");
- exit(1);
- }
- err = inflateSetDictionary(&d_stream, (const Bytef*)dictionary,
- (int)sizeof(dictionary));
- }
- CHECK_ERR(err, "inflate with dict");
- }
-
- err = inflateEnd(&d_stream);
- CHECK_ERR(err, "inflateEnd");
-
- if (strcmp((char*)uncompr, hello)) {
- fprintf(stderr, "bad inflate with dict\n");
- exit(1);
- } else {
- printf("inflate with dictionary: %s\n", (char *)uncompr);
- }
-}
-
-/* ===========================================================================
- * Usage: example [output.gz [input.gz]]
- */
-
-int main(argc, argv)
- int argc;
- char *argv[];
-{
- Byte *compr, *uncompr;
- uLong comprLen = 10000*sizeof(int); /* don't overflow on MSDOS */
- uLong uncomprLen = comprLen;
- static const char* myVersion = ZLIB_VERSION;
-
- if (zlibVersion()[0] != myVersion[0]) {
- fprintf(stderr, "incompatible zlib version\n");
- exit(1);
-
- } else if (strcmp(zlibVersion(), ZLIB_VERSION) != 0) {
- fprintf(stderr, "warning: different zlib version\n");
- }
-
- printf("zlib version %s = 0x%04x, compile flags = 0x%lx\n",
- ZLIB_VERSION, ZLIB_VERNUM, zlibCompileFlags());
-
- compr = (Byte*)calloc((uInt)comprLen, 1);
- uncompr = (Byte*)calloc((uInt)uncomprLen, 1);
- /* compr and uncompr are cleared to avoid reading uninitialized
- * data and to ensure that uncompr compresses well.
- */
- if (compr == Z_NULL || uncompr == Z_NULL) {
- printf("out of memory\n");
- exit(1);
- }
-
-#ifdef Z_SOLO
- argc = strlen(argv[0]);
-#else
- test_compress(compr, comprLen, uncompr, uncomprLen);
-
- test_gzio((argc > 1 ? argv[1] : TESTFILE),
- uncompr, uncomprLen);
-#endif
-
- test_deflate(compr, comprLen);
- test_inflate(compr, comprLen, uncompr, uncomprLen);
-
- test_large_deflate(compr, comprLen, uncompr, uncomprLen);
- test_large_inflate(compr, comprLen, uncompr, uncomprLen);
-
- test_flush(compr, &comprLen);
- test_sync(compr, comprLen, uncompr, uncomprLen);
- comprLen = uncomprLen;
-
- test_dict_deflate(compr, comprLen);
- test_dict_inflate(compr, comprLen, uncompr, uncomprLen);
-
- free(compr);
- free(uncompr);
-
- return 0;
-}
diff --git a/third-party/zlib/test/infcover.c b/third-party/zlib/test/infcover.c
deleted file mode 100644
index fe3d920..0000000
--- a/third-party/zlib/test/infcover.c
+++ /dev/null
@@ -1,671 +0,0 @@
-/* infcover.c -- test zlib's inflate routines with full code coverage
- * Copyright (C) 2011 Mark Adler
- * For conditions of distribution and use, see copyright notice in zlib.h
- */
-
-/* to use, do: ./configure --cover && make cover */
-
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
-#include <assert.h>
-#include "zlib.h"
-
-/* get definition of internal structure so we can mess with it (see pull()),
- and so we can call inflate_trees() (see cover5()) */
-#define ZLIB_INTERNAL
-#include "inftrees.h"
-#include "inflate.h"
-
-#define local static
-
-/* -- memory tracking routines -- */
-
-/*
- These memory tracking routines are provided to zlib and track all of zlib's
- allocations and deallocations, check for LIFO operations, keep a current
- and high water mark of total bytes requested, optionally set a limit on the
- total memory that can be allocated, and when done check for memory leaks.
-
- They are used as follows:
-
- z_stream strm;
- mem_setup(&strm) initializes the memory tracking and sets the
- zalloc, zfree, and opaque members of strm to use
- memory tracking for all zlib operations on strm
- mem_limit(&strm, limit) sets a limit on the total bytes requested -- a
- request that exceeds this limit will result in an
- allocation failure (returns NULL) -- setting the
- limit to zero means no limit, which is the default
- after mem_setup()
- mem_used(&strm, "msg") prints to stderr "msg" and the total bytes used
- mem_high(&strm, "msg") prints to stderr "msg" and the high water mark
- mem_done(&strm, "msg") ends memory tracking, releases all allocations
- for the tracking as well as leaked zlib blocks, if
- any. If there was anything unusual, such as leaked
- blocks, non-FIFO frees, or frees of addresses not
- allocated, then "msg" and information about the
- problem is printed to stderr. If everything is
- normal, nothing is printed. mem_done resets the
- strm members to Z_NULL to use the default memory
- allocation routines on the next zlib initialization
- using strm.
- */
-
-/* these items are strung together in a linked list, one for each allocation */
-struct mem_item {
- void *ptr; /* pointer to allocated memory */
- size_t size; /* requested size of allocation */
- struct mem_item *next; /* pointer to next item in list, or NULL */
-};
-
-/* this structure is at the root of the linked list, and tracks statistics */
-struct mem_zone {
- struct mem_item *first; /* pointer to first item in list, or NULL */
- size_t total, highwater; /* total allocations, and largest total */
- size_t limit; /* memory allocation limit, or 0 if no limit */
- int notlifo, rogue; /* counts of non-LIFO frees and rogue frees */
-};
-
-/* memory allocation routine to pass to zlib */
-local void *mem_alloc(void *mem, unsigned count, unsigned size)
-{
- void *ptr;
- struct mem_item *item;
- struct mem_zone *zone = mem;
- size_t len = count * (size_t)size;
-
- /* induced allocation failure */
- if (zone == NULL || (zone->limit && zone->total + len > zone->limit))
- return NULL;
-
- /* perform allocation using the standard library, fill memory with a
- non-zero value to make sure that the code isn't depending on zeros */
- ptr = malloc(len);
- if (ptr == NULL)
- return NULL;
- memset(ptr, 0xa5, len);
-
- /* create a new item for the list */
- item = malloc(sizeof(struct mem_item));
- if (item == NULL) {
- free(ptr);
- return NULL;
- }
- item->ptr = ptr;
- item->size = len;
-
- /* insert item at the beginning of the list */
- item->next = zone->first;
- zone->first = item;
-
- /* update the statistics */
- zone->total += item->size;
- if (zone->total > zone->highwater)
- zone->highwater = zone->total;
-
- /* return the allocated memory */
- return ptr;
-}
-
-/* memory free routine to pass to zlib */
-local void mem_free(void *mem, void *ptr)
-{
- struct mem_item *item, *next;
- struct mem_zone *zone = mem;
-
- /* if no zone, just do a free */
- if (zone == NULL) {
- free(ptr);
- return;
- }
-
- /* point next to the item that matches ptr, or NULL if not found -- remove
- the item from the linked list if found */
- next = zone->first;
- if (next) {
- if (next->ptr == ptr)
- zone->first = next->next; /* first one is it, remove from list */
- else {
- do { /* search the linked list */
- item = next;
- next = item->next;
- } while (next != NULL && next->ptr != ptr);
- if (next) { /* if found, remove from linked list */
- item->next = next->next;
- zone->notlifo++; /* not a LIFO free */
- }
-
- }
- }
-
- /* if found, update the statistics and free the item */
- if (next) {
- zone->total -= next->size;
- free(next);
- }
-
- /* if not found, update the rogue count */
- else
- zone->rogue++;
-
- /* in any case, do the requested free with the standard library function */
- free(ptr);
-}
-
-/* set up a controlled memory allocation space for monitoring, set the stream
- parameters to the controlled routines, with opaque pointing to the space */
-local void mem_setup(z_stream *strm)
-{
- struct mem_zone *zone;
-
- zone = malloc(sizeof(struct mem_zone));
- assert(zone != NULL);
- zone->first = NULL;
- zone->total = 0;
- zone->highwater = 0;
- zone->limit = 0;
- zone->notlifo = 0;
- zone->rogue = 0;
- strm->opaque = zone;
- strm->zalloc = mem_alloc;
- strm->zfree = mem_free;
-}
-
-/* set a limit on the total memory allocation, or 0 to remove the limit */
-local void mem_limit(z_stream *strm, size_t limit)
-{
- struct mem_zone *zone = strm->opaque;
-
- zone->limit = limit;
-}
-
-/* show the current total requested allocations in bytes */
-local void mem_used(z_stream *strm, char *prefix)
-{
- struct mem_zone *zone = strm->opaque;
-
- fprintf(stderr, "%s: %lu allocated\n", prefix, zone->total);
-}
-
-/* show the high water allocation in bytes */
-local void mem_high(z_stream *strm, char *prefix)
-{
- struct mem_zone *zone = strm->opaque;
-
- fprintf(stderr, "%s: %lu high water mark\n", prefix, zone->highwater);
-}
-
-/* release the memory allocation zone -- if there are any surprises, notify */
-local void mem_done(z_stream *strm, char *prefix)
-{
- int count = 0;
- struct mem_item *item, *next;
- struct mem_zone *zone = strm->opaque;
-
- /* show high water mark */
- mem_high(strm, prefix);
-
- /* free leftover allocations and item structures, if any */
- item = zone->first;
- while (item != NULL) {
- free(item->ptr);
- next = item->next;
- free(item);
- item = next;
- count++;
- }
-
- /* issue alerts about anything unexpected */
- if (count || zone->total)
- fprintf(stderr, "** %s: %lu bytes in %d blocks not freed\n",
- prefix, zone->total, count);
- if (zone->notlifo)
- fprintf(stderr, "** %s: %d frees not LIFO\n", prefix, zone->notlifo);
- if (zone->rogue)
- fprintf(stderr, "** %s: %d frees not recognized\n",
- prefix, zone->rogue);
-
- /* free the zone and delete from the stream */
- free(zone);
- strm->opaque = Z_NULL;
- strm->zalloc = Z_NULL;
- strm->zfree = Z_NULL;
-}
-
-/* -- inflate test routines -- */
-
-/* Decode a hexadecimal string, set *len to length, in[] to the bytes. This
- decodes liberally, in that hex digits can be adjacent, in which case two in
- a row writes a byte. Or they can delimited by any non-hex character, where
- the delimiters are ignored except when a single hex digit is followed by a
- delimiter in which case that single digit writes a byte. The returned
- data is allocated and must eventually be freed. NULL is returned if out of
- memory. If the length is not needed, then len can be NULL. */
-local unsigned char *h2b(const char *hex, unsigned *len)
-{
- unsigned char *in;
- unsigned next, val;
-
- in = malloc((strlen(hex) + 1) >> 1);
- if (in == NULL)
- return NULL;
- next = 0;
- val = 1;
- do {
- if (*hex >= '0' && *hex <= '9')
- val = (val << 4) + *hex - '0';
- else if (*hex >= 'A' && *hex <= 'F')
- val = (val << 4) + *hex - 'A' + 10;
- else if (*hex >= 'a' && *hex <= 'f')
- val = (val << 4) + *hex - 'a' + 10;
- else if (val != 1 && val < 32) /* one digit followed by delimiter */
- val += 240; /* make it look like two digits */
- if (val > 255) { /* have two digits */
- in[next++] = val & 0xff; /* save the decoded byte */
- val = 1; /* start over */
- }
- } while (*hex++); /* go through the loop with the terminating null */
- if (len != NULL)
- *len = next;
- in = reallocf(in, next);
- return in;
-}
-
-/* generic inflate() run, where hex is the hexadecimal input data, what is the
- text to include in an error message, step is how much input data to feed
- inflate() on each call, or zero to feed it all, win is the window bits
- parameter to inflateInit2(), len is the size of the output buffer, and err
- is the error code expected from the first inflate() call (the second
- inflate() call is expected to return Z_STREAM_END). If win is 47, then
- header information is collected with inflateGetHeader(). If a zlib stream
- is looking for a dictionary, then an empty dictionary is provided.
- inflate() is run until all of the input data is consumed. */
-local void inf(char *hex, char *what, unsigned step, int win, unsigned len,
- int err)
-{
- int ret;
- unsigned have;
- unsigned char *in, *out;
- z_stream strm, copy;
- gz_header head;
-
- mem_setup(&strm);
- strm.avail_in = 0;
- strm.next_in = Z_NULL;
- ret = inflateInit2(&strm, win);
- if (ret != Z_OK) {
- mem_done(&strm, what);
- return;
- }
- out = malloc(len); assert(out != NULL);
- if (win == 47) {
- head.extra = out;
- head.extra_max = len;
- head.name = out;
- head.name_max = len;
- head.comment = out;
- head.comm_max = len;
- ret = inflateGetHeader(&strm, &head); assert(ret == Z_OK);
- }
- in = h2b(hex, &have); assert(in != NULL);
- if (step == 0 || step > have)
- step = have;
- strm.avail_in = step;
- have -= step;
- strm.next_in = in;
- do {
- strm.avail_out = len;
- strm.next_out = out;
- ret = inflate(&strm, Z_NO_FLUSH); assert(err == 9 || ret == err);
- if (ret != Z_OK && ret != Z_BUF_ERROR && ret != Z_NEED_DICT)
- break;
- if (ret == Z_NEED_DICT) {
- ret = inflateSetDictionary(&strm, in, 1);
- assert(ret == Z_DATA_ERROR);
- mem_limit(&strm, 1);
- ret = inflateSetDictionary(&strm, out, 0);
- assert(ret == Z_MEM_ERROR);
- mem_limit(&strm, 0);
- ((struct inflate_state *)strm.state)->mode = DICT;
- ret = inflateSetDictionary(&strm, out, 0);
- assert(ret == Z_OK);
- ret = inflate(&strm, Z_NO_FLUSH); assert(ret == Z_BUF_ERROR);
- }
- ret = inflateCopy(©, &strm); assert(ret == Z_OK);
- ret = inflateEnd(©); assert(ret == Z_OK);
- err = 9; /* don't care next time around */
- have += strm.avail_in;
- strm.avail_in = step > have ? have : step;
- have -= strm.avail_in;
- } while (strm.avail_in);
- free(in);
- free(out);
- ret = inflateReset2(&strm, -8); assert(ret == Z_OK);
- ret = inflateEnd(&strm); assert(ret == Z_OK);
- mem_done(&strm, what);
-}
-
-/* cover all of the lines in inflate.c up to inflate() */
-local void cover_support(void)
-{
- int ret;
- z_stream strm;
-
- mem_setup(&strm);
- strm.avail_in = 0;
- strm.next_in = Z_NULL;
- ret = inflateInit(&strm); assert(ret == Z_OK);
- mem_used(&strm, "inflate init");
- ret = inflatePrime(&strm, 5, 31); assert(ret == Z_OK);
- ret = inflatePrime(&strm, -1, 0); assert(ret == Z_OK);
- ret = inflateSetDictionary(&strm, Z_NULL, 0);
- assert(ret == Z_STREAM_ERROR);
- ret = inflateEnd(&strm); assert(ret == Z_OK);
- mem_done(&strm, "prime");
-
- inf("63 0", "force window allocation", 0, -15, 1, Z_OK);
- inf("63 18 5", "force window replacement", 0, -8, 259, Z_OK);
- inf("63 18 68 30 d0 0 0", "force split window update", 4, -8, 259, Z_OK);
- inf("3 0", "use fixed blocks", 0, -15, 1, Z_STREAM_END);
- inf("", "bad window size", 0, 1, 0, Z_STREAM_ERROR);
-
- mem_setup(&strm);
- strm.avail_in = 0;
- strm.next_in = Z_NULL;
- ret = inflateInit_(&strm, ZLIB_VERSION - 1, (int)sizeof(z_stream));
- assert(ret == Z_VERSION_ERROR);
- mem_done(&strm, "wrong version");
-
- strm.avail_in = 0;
- strm.next_in = Z_NULL;
- ret = inflateInit(&strm); assert(ret == Z_OK);
- ret = inflateEnd(&strm); assert(ret == Z_OK);
- fputs("inflate built-in memory routines\n", stderr);
-}
-
-/* cover all inflate() header and trailer cases and code after inflate() */
-local void cover_wrap(void)
-{
- int ret;
- z_stream strm, copy;
- unsigned char dict[257];
-
- ret = inflate(Z_NULL, 0); assert(ret == Z_STREAM_ERROR);
- ret = inflateEnd(Z_NULL); assert(ret == Z_STREAM_ERROR);
- ret = inflateCopy(Z_NULL, Z_NULL); assert(ret == Z_STREAM_ERROR);
- fputs("inflate bad parameters\n", stderr);
-
- inf("1f 8b 0 0", "bad gzip method", 0, 31, 0, Z_DATA_ERROR);
- inf("1f 8b 8 80", "bad gzip flags", 0, 31, 0, Z_DATA_ERROR);
- inf("77 85", "bad zlib method", 0, 15, 0, Z_DATA_ERROR);
- inf("8 99", "set window size from header", 0, 0, 0, Z_OK);
- inf("78 9c", "bad zlib window size", 0, 8, 0, Z_DATA_ERROR);
- inf("78 9c 63 0 0 0 1 0 1", "check adler32", 0, 15, 1, Z_STREAM_END);
- inf("1f 8b 8 1e 0 0 0 0 0 0 1 0 0 0 0 0 0", "bad header crc", 0, 47, 1,
- Z_DATA_ERROR);
- inf("1f 8b 8 2 0 0 0 0 0 0 1d 26 3 0 0 0 0 0 0 0 0 0", "check gzip length",
- 0, 47, 0, Z_STREAM_END);
- inf("78 90", "bad zlib header check", 0, 47, 0, Z_DATA_ERROR);
- inf("8 b8 0 0 0 1", "need dictionary", 0, 8, 0, Z_NEED_DICT);
- inf("78 9c 63 0", "compute adler32", 0, 15, 1, Z_OK);
-
- mem_setup(&strm);
- strm.avail_in = 0;
- strm.next_in = Z_NULL;
- ret = inflateInit2(&strm, -8);
- strm.avail_in = 2;
- strm.next_in = (void *)"\x63";
- strm.avail_out = 1;
- strm.next_out = (void *)&ret;
- mem_limit(&strm, 1);
- ret = inflate(&strm, Z_NO_FLUSH); assert(ret == Z_MEM_ERROR);
- ret = inflate(&strm, Z_NO_FLUSH); assert(ret == Z_MEM_ERROR);
- mem_limit(&strm, 0);
- memset(dict, 0, 257);
- ret = inflateSetDictionary(&strm, dict, 257);
- assert(ret == Z_OK);
- mem_limit(&strm, (sizeof(struct inflate_state) << 1) + 256);
- ret = inflatePrime(&strm, 16, 0); assert(ret == Z_OK);
- strm.avail_in = 2;
- strm.next_in = (void *)"\x80";
- ret = inflateSync(&strm); assert(ret == Z_DATA_ERROR);
- ret = inflate(&strm, Z_NO_FLUSH); assert(ret == Z_STREAM_ERROR);
- strm.avail_in = 4;
- strm.next_in = (void *)"\0\0\xff\xff";
- ret = inflateSync(&strm); assert(ret == Z_OK);
- (void)inflateSyncPoint(&strm);
- ret = inflateCopy(©, &strm); assert(ret == Z_MEM_ERROR);
- mem_limit(&strm, 0);
- ret = inflateUndermine(&strm, 1); assert(ret == Z_DATA_ERROR);
- (void)inflateMark(&strm);
- ret = inflateEnd(&strm); assert(ret == Z_OK);
- mem_done(&strm, "miscellaneous, force memory errors");
-}
-
-/* input and output functions for inflateBack() */
-local unsigned pull(void *desc, unsigned char **buf)
-{
- static unsigned int next = 0;
- static unsigned char dat[] = {0x63, 0, 2, 0};
- struct inflate_state *state;
-
- if (desc == Z_NULL) {
- next = 0;
- return 0; /* no input (already provided at next_in) */
- }
- state = (void *)((z_stream *)desc)->state;
- if (state != Z_NULL)
- state->mode = SYNC; /* force an otherwise impossible situation */
- return next < sizeof(dat) ? (*buf = dat + next++, 1) : 0;
-}
-
-local int push(void *desc, unsigned char *buf, unsigned len)
-{
- buf += len;
- return desc != Z_NULL; /* force error if desc not null */
-}
-
-/* cover inflateBack() up to common deflate data cases and after those */
-local void cover_back(void)
-{
- int ret;
- z_stream strm;
- unsigned char win[32768];
-
- ret = inflateBackInit_(Z_NULL, 0, win, 0, 0);
- assert(ret == Z_VERSION_ERROR);
- ret = inflateBackInit(Z_NULL, 0, win); assert(ret == Z_STREAM_ERROR);
- ret = inflateBack(Z_NULL, Z_NULL, Z_NULL, Z_NULL, Z_NULL);
- assert(ret == Z_STREAM_ERROR);
- ret = inflateBackEnd(Z_NULL); assert(ret == Z_STREAM_ERROR);
- fputs("inflateBack bad parameters\n", stderr);
-
- mem_setup(&strm);
- ret = inflateBackInit(&strm, 15, win); assert(ret == Z_OK);
- strm.avail_in = 2;
- strm.next_in = (void *)"\x03";
- ret = inflateBack(&strm, pull, Z_NULL, push, Z_NULL);
- assert(ret == Z_STREAM_END);
- /* force output error */
- strm.avail_in = 3;
- strm.next_in = (void *)"\x63\x00";
- ret = inflateBack(&strm, pull, Z_NULL, push, &strm);
- assert(ret == Z_BUF_ERROR);
- /* force mode error by mucking with state */
- ret = inflateBack(&strm, pull, &strm, push, Z_NULL);
- assert(ret == Z_STREAM_ERROR);
- ret = inflateBackEnd(&strm); assert(ret == Z_OK);
- mem_done(&strm, "inflateBack bad state");
-
- ret = inflateBackInit(&strm, 15, win); assert(ret == Z_OK);
- ret = inflateBackEnd(&strm); assert(ret == Z_OK);
- fputs("inflateBack built-in memory routines\n", stderr);
-}
-
-/* do a raw inflate of data in hexadecimal with both inflate and inflateBack */
-local int try(char *hex, char *id, int err)
-{
- int ret;
- unsigned len, size;
- unsigned char *in, *out, *win;
- char *prefix;
- z_stream strm;
-
- /* convert to hex */
- in = h2b(hex, &len);
- assert(in != NULL);
-
- /* allocate work areas */
- size = len << 3;
- out = malloc(size);
- assert(out != NULL);
- win = malloc(32768);
- assert(win != NULL);
- prefix = malloc(strlen(id) + 6);
- assert(prefix != NULL);
-
- /* first with inflate */
- strcpy(prefix, id);
- strcat(prefix, "-late");
- mem_setup(&strm);
- strm.avail_in = 0;
- strm.next_in = Z_NULL;
- ret = inflateInit2(&strm, err < 0 ? 47 : -15);
- assert(ret == Z_OK);
- strm.avail_in = len;
- strm.next_in = in;
- do {
- strm.avail_out = size;
- strm.next_out = out;
- ret = inflate(&strm, Z_TREES);
- assert(ret != Z_STREAM_ERROR && ret != Z_MEM_ERROR);
- if (ret == Z_DATA_ERROR || ret == Z_NEED_DICT)
- break;
- } while (strm.avail_in || strm.avail_out == 0);
- if (err) {
- assert(ret == Z_DATA_ERROR);
- assert(strcmp(id, strm.msg) == 0);
- }
- inflateEnd(&strm);
- mem_done(&strm, prefix);
-
- /* then with inflateBack */
- if (err >= 0) {
- strcpy(prefix, id);
- strcat(prefix, "-back");
- mem_setup(&strm);
- ret = inflateBackInit(&strm, 15, win);
- assert(ret == Z_OK);
- strm.avail_in = len;
- strm.next_in = in;
- ret = inflateBack(&strm, pull, Z_NULL, push, Z_NULL);
- assert(ret != Z_STREAM_ERROR);
- if (err) {
- assert(ret == Z_DATA_ERROR);
- assert(strcmp(id, strm.msg) == 0);
- }
- inflateBackEnd(&strm);
- mem_done(&strm, prefix);
- }
-
- /* clean up */
- free(prefix);
- free(win);
- free(out);
- free(in);
- return ret;
-}
-
-/* cover deflate data cases in both inflate() and inflateBack() */
-local void cover_inflate(void)
-{
- try("0 0 0 0 0", "invalid stored block lengths", 1);
- try("3 0", "fixed", 0);
- try("6", "invalid block type", 1);
- try("1 1 0 fe ff 0", "stored", 0);
- try("fc 0 0", "too many length or distance symbols", 1);
- try("4 0 fe ff", "invalid code lengths set", 1);
- try("4 0 24 49 0", "invalid bit length repeat", 1);
- try("4 0 24 e9 ff ff", "invalid bit length repeat", 1);
- try("4 0 24 e9 ff 6d", "invalid code -- missing end-of-block", 1);
- try("4 80 49 92 24 49 92 24 71 ff ff 93 11 0",
- "invalid literal/lengths set", 1);
- try("4 80 49 92 24 49 92 24 f b4 ff ff c3 84", "invalid distances set", 1);
- try("4 c0 81 8 0 0 0 0 20 7f eb b 0 0", "invalid literal/length code", 1);
- try("2 7e ff ff", "invalid distance code", 1);
- try("c c0 81 0 0 0 0 0 90 ff 6b 4 0", "invalid distance too far back", 1);
-
- /* also trailer mismatch just in inflate() */
- try("1f 8b 8 0 0 0 0 0 0 0 3 0 0 0 0 1", "incorrect data check", -1);
- try("1f 8b 8 0 0 0 0 0 0 0 3 0 0 0 0 0 0 0 0 1",
- "incorrect length check", -1);
- try("5 c0 21 d 0 0 0 80 b0 fe 6d 2f 91 6c", "pull 17", 0);
- try("5 e0 81 91 24 cb b2 2c 49 e2 f 2e 8b 9a 47 56 9f fb fe ec d2 ff 1f",
- "long code", 0);
- try("ed c0 1 1 0 0 0 40 20 ff 57 1b 42 2c 4f", "length extra", 0);
- try("ed cf c1 b1 2c 47 10 c4 30 fa 6f 35 1d 1 82 59 3d fb be 2e 2a fc f c",
- "long distance and extra", 0);
- try("ed c0 81 0 0 0 0 80 a0 fd a9 17 a9 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 "
- "0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6", "window end", 0);
- inf("2 8 20 80 0 3 0", "inflate_fast TYPE return", 0, -15, 258,
- Z_STREAM_END);
- inf("63 18 5 40 c 0", "window wrap", 3, -8, 300, Z_OK);
-}
-
-/* cover remaining lines in inftrees.c */
-local void cover_trees(void)
-{
- int ret;
- unsigned bits;
- unsigned short lens[16], work[16];
- code *next, table[ENOUGH_DISTS];
-
- /* we need to call inflate_table() directly in order to manifest not-
- enough errors, since zlib insures that enough is always enough */
- for (bits = 0; bits < 15; bits++)
- lens[bits] = (unsigned short)(bits + 1);
- lens[15] = 15;
- next = table;
- bits = 15;
- ret = inflate_table(DISTS, lens, 16, &next, &bits, work);
- assert(ret == 1);
- next = table;
- bits = 1;
- ret = inflate_table(DISTS, lens, 16, &next, &bits, work);
- assert(ret == 1);
- fputs("inflate_table not enough errors\n", stderr);
-}
-
-/* cover remaining inffast.c decoding and window copying */
-local void cover_fast(void)
-{
- inf("e5 e0 81 ad 6d cb b2 2c c9 01 1e 59 63 ae 7d ee fb 4d fd b5 35 41 68"
- " ff 7f 0f 0 0 0", "fast length extra bits", 0, -8, 258, Z_DATA_ERROR);
- inf("25 fd 81 b5 6d 59 b6 6a 49 ea af 35 6 34 eb 8c b9 f6 b9 1e ef 67 49"
- " 50 fe ff ff 3f 0 0", "fast distance extra bits", 0, -8, 258,
- Z_DATA_ERROR);
- inf("3 7e 0 0 0 0 0", "fast invalid distance code", 0, -8, 258,
- Z_DATA_ERROR);
- inf("1b 7 0 0 0 0 0", "fast invalid literal/length code", 0, -8, 258,
- Z_DATA_ERROR);
- inf("d c7 1 ae eb 38 c 4 41 a0 87 72 de df fb 1f b8 36 b1 38 5d ff ff 0",
- "fast 2nd level codes and too far back", 0, -8, 258, Z_DATA_ERROR);
- inf("63 18 5 8c 10 8 0 0 0 0", "very common case", 0, -8, 259, Z_OK);
- inf("63 60 60 18 c9 0 8 18 18 18 26 c0 28 0 29 0 0 0",
- "contiguous and wrap around window", 6, -8, 259, Z_OK);
- inf("63 0 3 0 0 0 0 0", "copy direct from output", 0, -8, 259,
- Z_STREAM_END);
-}
-
-int main(void)
-{
- fprintf(stderr, "%s\n", zlibVersion());
- cover_support();
- cover_wrap();
- cover_back();
- cover_inflate();
- cover_trees();
- cover_fast();
- return 0;
-}
diff --git a/third-party/zlib/test/minigzip.c b/third-party/zlib/test/minigzip.c
deleted file mode 100644
index b3025a4..0000000
--- a/third-party/zlib/test/minigzip.c
+++ /dev/null
@@ -1,651 +0,0 @@
-/* minigzip.c -- simulate gzip using the zlib compression library
- * Copyright (C) 1995-2006, 2010, 2011 Jean-loup Gailly.
- * For conditions of distribution and use, see copyright notice in zlib.h
- */
-
-/*
- * minigzip is a minimal implementation of the gzip utility. This is
- * only an example of using zlib and isn't meant to replace the
- * full-featured gzip. No attempt is made to deal with file systems
- * limiting names to 14 or 8+3 characters, etc... Error checking is
- * very limited. So use minigzip only for testing; use gzip for the
- * real thing. On MSDOS, use only on file names without extension
- * or in pipe mode.
- */
-
-/* @(#) $Id$ */
-
-#include "zlib.h"
-#include <stdio.h>
-
-#ifdef STDC
-# include <string.h>
-# include <stdlib.h>
-#endif
-
-#ifdef USE_MMAP
-# include <sys/types.h>
-# include <sys/mman.h>
-# include <sys/stat.h>
-#endif
-
-#if defined(MSDOS) || defined(OS2) || defined(WIN32) || defined(__CYGWIN__)
-# include <fcntl.h>
-# include <io.h>
-# ifdef UNDER_CE
-# include <stdlib.h>
-# endif
-# define SET_BINARY_MODE(file) setmode(fileno(file), O_BINARY)
-#else
-# define SET_BINARY_MODE(file)
-#endif
-
-#ifdef _MSC_VER
-# define snprintf _snprintf
-#endif
-
-#ifdef VMS
-# define unlink delete
-# define GZ_SUFFIX "-gz"
-#endif
-#ifdef RISCOS
-# define unlink remove
-# define GZ_SUFFIX "-gz"
-# define fileno(file) file->__file
-#endif
-#if defined(__MWERKS__) && __dest_os != __be_os && __dest_os != __win32_os
-# include <unix.h> /* for fileno */
-#endif
-
-#if !defined(Z_HAVE_UNISTD_H) && !defined(_LARGEFILE64_SOURCE)
-#ifndef WIN32 /* unlink already in stdio.h for WIN32 */
- extern int unlink OF((const char *));
-#endif
-#endif
-
-#if defined(UNDER_CE)
-# include <windows.h>
-# define perror(s) pwinerror(s)
-
-/* Map the Windows error number in ERROR to a locale-dependent error
- message string and return a pointer to it. Typically, the values
- for ERROR come from GetLastError.
-
- The string pointed to shall not be modified by the application,
- but may be overwritten by a subsequent call to strwinerror
-
- The strwinerror function does not change the current setting
- of GetLastError. */
-
-static char *strwinerror (error)
- DWORD error;
-{
- static char buf[1024];
-
- wchar_t *msgbuf;
- DWORD lasterr = GetLastError();
- DWORD chars = FormatMessage(FORMAT_MESSAGE_FROM_SYSTEM
- | FORMAT_MESSAGE_ALLOCATE_BUFFER,
- NULL,
- error,
- 0, /* Default language */
- (LPVOID)&msgbuf,
- 0,
- NULL);
- if (chars != 0) {
- /* If there is an \r\n appended, zap it. */
- if (chars >= 2
- && msgbuf[chars - 2] == '\r' && msgbuf[chars - 1] == '\n') {
- chars -= 2;
- msgbuf[chars] = 0;
- }
-
- if (chars > sizeof (buf) - 1) {
- chars = sizeof (buf) - 1;
- msgbuf[chars] = 0;
- }
-
- wcstombs(buf, msgbuf, chars + 1);
- LocalFree(msgbuf);
- }
- else {
- sprintf(buf, "unknown win32 error (%ld)", error);
- }
-
- SetLastError(lasterr);
- return buf;
-}
-
-static void pwinerror (s)
- const char *s;
-{
- if (s && *s)
- fprintf(stderr, "%s: %s\n", s, strwinerror(GetLastError ()));
- else
- fprintf(stderr, "%s\n", strwinerror(GetLastError ()));
-}
-
-#endif /* UNDER_CE */
-
-#ifndef GZ_SUFFIX
-# define GZ_SUFFIX ".gz"
-#endif
-#define SUFFIX_LEN (sizeof(GZ_SUFFIX)-1)
-
-#define BUFLEN 16384
-#define MAX_NAME_LEN 1024
-
-#ifdef MAXSEG_64K
-# define local static
- /* Needed for systems with limitation on stack size. */
-#else
-# define local
-#endif
-
-#ifdef Z_SOLO
-/* for Z_SOLO, create simplified gz* functions using deflate and inflate */
-
-#if defined(Z_HAVE_UNISTD_H) || defined(Z_LARGE)
-# include <unistd.h> /* for unlink() */
-#endif
-
-void *myalloc OF((void *, unsigned, unsigned));
-void myfree OF((void *, void *));
-
-void *myalloc(q, n, m)
- void *q;
- unsigned n, m;
-{
- q = Z_NULL;
- return calloc(n, m);
-}
-
-void myfree(q, p)
- void *q, *p;
-{
- q = Z_NULL;
- free(p);
-}
-
-typedef struct gzFile_s {
- FILE *file;
- int write;
- int err;
- char *msg;
- z_stream strm;
-} *gzFile;
-
-gzFile gzopen OF((const char *, const char *));
-gzFile gzdopen OF((int, const char *));
-gzFile gz_open OF((const char *, int, const char *));
-
-gzFile gzopen(path, mode)
-const char *path;
-const char *mode;
-{
- return gz_open(path, -1, mode);
-}
-
-gzFile gzdopen(fd, mode)
-int fd;
-const char *mode;
-{
- return gz_open(NULL, fd, mode);
-}
-
-gzFile gz_open(path, fd, mode)
- const char *path;
- int fd;
- const char *mode;
-{
- gzFile gz;
- int ret;
-
- gz = malloc(sizeof(struct gzFile_s));
- if (gz == NULL)
- return NULL;
- gz->write = strchr(mode, 'w') != NULL;
- gz->strm.zalloc = myalloc;
- gz->strm.zfree = myfree;
- gz->strm.opaque = Z_NULL;
- if (gz->write)
- ret = deflateInit2(&(gz->strm), -1, 8, 15 + 16, 8, 0);
- else {
- gz->strm.next_in = 0;
- gz->strm.avail_in = Z_NULL;
- ret = inflateInit2(&(gz->strm), 15 + 16);
- }
- if (ret != Z_OK) {
- free(gz);
- return NULL;
- }
- gz->file = path == NULL ? fdopen(fd, gz->write ? "wb" : "rb") :
- fopen(path, gz->write ? "wb" : "rb");
- if (gz->file == NULL) {
- gz->write ? deflateEnd(&(gz->strm)) : inflateEnd(&(gz->strm));
- free(gz);
- return NULL;
- }
- gz->err = 0;
- gz->msg = "";
- return gz;
-}
-
-int gzwrite OF((gzFile, const void *, unsigned));
-
-int gzwrite(gz, buf, len)
- gzFile gz;
- const void *buf;
- unsigned len;
-{
- z_stream *strm;
- unsigned char out[BUFLEN];
-
- if (gz == NULL || !gz->write)
- return 0;
- strm = &(gz->strm);
- strm->next_in = (void *)buf;
- strm->avail_in = len;
- do {
- strm->next_out = out;
- strm->avail_out = BUFLEN;
- (void)deflate(strm, Z_NO_FLUSH);
- fwrite(out, 1, BUFLEN - strm->avail_out, gz->file);
- } while (strm->avail_out == 0);
- return len;
-}
-
-int gzread OF((gzFile, void *, unsigned));
-
-int gzread(gz, buf, len)
- gzFile gz;
- void *buf;
- unsigned len;
-{
- int ret;
- unsigned got;
- unsigned char in[1];
- z_stream *strm;
-
- if (gz == NULL || gz->write)
- return 0;
- if (gz->err)
- return 0;
- strm = &(gz->strm);
- strm->next_out = (void *)buf;
- strm->avail_out = len;
- do {
- got = fread(in, 1, 1, gz->file);
- if (got == 0)
- break;
- strm->next_in = in;
- strm->avail_in = 1;
- ret = inflate(strm, Z_NO_FLUSH);
- if (ret == Z_DATA_ERROR) {
- gz->err = Z_DATA_ERROR;
- gz->msg = strm->msg;
- return 0;
- }
- if (ret == Z_STREAM_END)
- inflateReset(strm);
- } while (strm->avail_out);
- return len - strm->avail_out;
-}
-
-int gzclose OF((gzFile));
-
-int gzclose(gz)
- gzFile gz;
-{
- z_stream *strm;
- unsigned char out[BUFLEN];
-
- if (gz == NULL)
- return Z_STREAM_ERROR;
- strm = &(gz->strm);
- if (gz->write) {
- strm->next_in = Z_NULL;
- strm->avail_in = 0;
- do {
- strm->next_out = out;
- strm->avail_out = BUFLEN;
- (void)deflate(strm, Z_FINISH);
- fwrite(out, 1, BUFLEN - strm->avail_out, gz->file);
- } while (strm->avail_out == 0);
- deflateEnd(strm);
- }
- else
- inflateEnd(strm);
- fclose(gz->file);
- free(gz);
- return Z_OK;
-}
-
-const char *gzerror OF((gzFile, int *));
-
-const char *gzerror(gz, err)
- gzFile gz;
- int *err;
-{
- *err = gz->err;
- return gz->msg;
-}
-
-#endif
-
-char *prog;
-
-void error OF((const char *msg));
-void gz_compress OF((FILE *in, gzFile out));
-#ifdef USE_MMAP
-int gz_compress_mmap OF((FILE *in, gzFile out));
-#endif
-void gz_uncompress OF((gzFile in, FILE *out));
-void file_compress OF((char *file, char *mode));
-void file_uncompress OF((char *file));
-int main OF((int argc, char *argv[]));
-
-/* ===========================================================================
- * Display error message and exit
- */
-void error(msg)
- const char *msg;
-{
- fprintf(stderr, "%s: %s\n", prog, msg);
- exit(1);
-}
-
-/* ===========================================================================
- * Compress input to output then close both files.
- */
-
-void gz_compress(in, out)
- FILE *in;
- gzFile out;
-{
- local char buf[BUFLEN];
- int len;
- int err;
-
-#ifdef USE_MMAP
- /* Try first compressing with mmap. If mmap fails (minigzip used in a
- * pipe), use the normal fread loop.
- */
- if (gz_compress_mmap(in, out) == Z_OK) return;
-#endif
- for (;;) {
- len = (int)fread(buf, 1, sizeof(buf), in);
- if (ferror(in)) {
- perror("fread");
- exit(1);
- }
- if (len == 0) break;
-
- if (gzwrite(out, buf, (unsigned)len) != len) error(gzerror(out, &err));
- }
- fclose(in);
- if (gzclose(out) != Z_OK) error("failed gzclose");
-}
-
-#ifdef USE_MMAP /* MMAP version, Miguel Albrecht <malbrech at eso.org> */
-
-/* Try compressing the input file at once using mmap. Return Z_OK if
- * if success, Z_ERRNO otherwise.
- */
-int gz_compress_mmap(in, out)
- FILE *in;
- gzFile out;
-{
- int len;
- int err;
- int ifd = fileno(in);
- caddr_t buf; /* mmap'ed buffer for the entire input file */
- off_t buf_len; /* length of the input file */
- struct stat sb;
-
- /* Determine the size of the file, needed for mmap: */
- if (fstat(ifd, &sb) < 0) return Z_ERRNO;
- buf_len = sb.st_size;
- if (buf_len <= 0) return Z_ERRNO;
-
- /* Now do the actual mmap: */
- buf = mmap((caddr_t) 0, buf_len, PROT_READ, MAP_SHARED, ifd, (off_t)0);
- if (buf == (caddr_t)(-1)) return Z_ERRNO;
-
- /* Compress the whole file at once: */
- len = gzwrite(out, (char *)buf, (unsigned)buf_len);
-
- if (len != (int)buf_len) error(gzerror(out, &err));
-
- munmap(buf, buf_len);
- fclose(in);
- if (gzclose(out) != Z_OK) error("failed gzclose");
- return Z_OK;
-}
-#endif /* USE_MMAP */
-
-/* ===========================================================================
- * Uncompress input to output then close both files.
- */
-void gz_uncompress(in, out)
- gzFile in;
- FILE *out;
-{
- local char buf[BUFLEN];
- int len;
- int err;
-
- for (;;) {
- len = gzread(in, buf, sizeof(buf));
- if (len < 0) error (gzerror(in, &err));
- if (len == 0) break;
-
- if ((int)fwrite(buf, 1, (unsigned)len, out) != len) {
- error("failed fwrite");
- }
- }
- if (fclose(out)) error("failed fclose");
-
- if (gzclose(in) != Z_OK) error("failed gzclose");
-}
-
-
-/* ===========================================================================
- * Compress the given file: create a corresponding .gz file and remove the
- * original.
- */
-void file_compress(file, mode)
- char *file;
- char *mode;
-{
- local char outfile[MAX_NAME_LEN];
- FILE *in;
- gzFile out;
-
- if (strlen(file) + strlen(GZ_SUFFIX) >= sizeof(outfile)) {
- fprintf(stderr, "%s: filename too long\n", prog);
- exit(1);
- }
-
-#if !defined(NO_snprintf) && !defined(NO_vsnprintf)
- snprintf(outfile, sizeof(outfile), "%s%s", file, GZ_SUFFIX);
-#else
- strcpy(outfile, file);
- strcat(outfile, GZ_SUFFIX);
-#endif
-
- in = fopen(file, "rb");
- if (in == NULL) {
- perror(file);
- exit(1);
- }
- out = gzopen(outfile, mode);
- if (out == NULL) {
- fprintf(stderr, "%s: can't gzopen %s\n", prog, outfile);
- exit(1);
- }
- gz_compress(in, out);
-
- unlink(file);
-}
-
-
-/* ===========================================================================
- * Uncompress the given file and remove the original.
- */
-void file_uncompress(file)
- char *file;
-{
- local char buf[MAX_NAME_LEN];
- char *infile, *outfile;
- FILE *out;
- gzFile in;
- size_t len = strlen(file);
-
- if (len + strlen(GZ_SUFFIX) >= sizeof(buf)) {
- fprintf(stderr, "%s: filename too long\n", prog);
- exit(1);
- }
-
-#if !defined(NO_snprintf) && !defined(NO_vsnprintf)
- snprintf(buf, sizeof(buf), "%s", file);
-#else
- strcpy(buf, file);
-#endif
-
- if (len > SUFFIX_LEN && strcmp(file+len-SUFFIX_LEN, GZ_SUFFIX) == 0) {
- infile = file;
- outfile = buf;
- outfile[len-3] = '\0';
- } else {
- outfile = file;
- infile = buf;
-#if !defined(NO_snprintf) && !defined(NO_vsnprintf)
- snprintf(buf + len, sizeof(buf) - len, "%s", GZ_SUFFIX);
-#else
- strcat(infile, GZ_SUFFIX);
-#endif
- }
- in = gzopen(infile, "rb");
- if (in == NULL) {
- fprintf(stderr, "%s: can't gzopen %s\n", prog, infile);
- exit(1);
- }
- out = fopen(outfile, "wb");
- if (out == NULL) {
- perror(file);
- exit(1);
- }
-
- gz_uncompress(in, out);
-
- unlink(infile);
-}
-
-
-/* ===========================================================================
- * Usage: minigzip [-c] [-d] [-f] [-h] [-r] [-1 to -9] [files...]
- * -c : write to standard output
- * -d : decompress
- * -f : compress with Z_FILTERED
- * -h : compress with Z_HUFFMAN_ONLY
- * -r : compress with Z_RLE
- * -1 to -9 : compression level
- */
-
-int main(argc, argv)
- int argc;
- char *argv[];
-{
- int copyout = 0;
- int uncompr = 0;
- gzFile file;
- char *bname, outmode[20];
-
-#if !defined(NO_snprintf) && !defined(NO_vsnprintf)
- snprintf(outmode, sizeof(outmode), "%s", "wb6 ");
-#else
- strcpy(outmode, "wb6 ");
-#endif
-
- prog = argv[0];
- bname = strrchr(argv[0], '/');
- if (bname)
- bname++;
- else
- bname = argv[0];
- argc--, argv++;
-
- if (!strcmp(bname, "gunzip"))
- uncompr = 1;
- else if (!strcmp(bname, "zcat"))
- copyout = uncompr = 1;
-
- while (argc > 0) {
- if (strcmp(*argv, "-c") == 0)
- copyout = 1;
- else if (strcmp(*argv, "-d") == 0)
- uncompr = 1;
- else if (strcmp(*argv, "-f") == 0)
- outmode[3] = 'f';
- else if (strcmp(*argv, "-h") == 0)
- outmode[3] = 'h';
- else if (strcmp(*argv, "-r") == 0)
- outmode[3] = 'R';
- else if ((*argv)[0] == '-' && (*argv)[1] >= '1' && (*argv)[1] <= '9' &&
- (*argv)[2] == 0)
- outmode[2] = (*argv)[1];
- else
- break;
- argc--, argv++;
- }
- if (outmode[3] == ' ')
- outmode[3] = 0;
- if (argc == 0) {
- SET_BINARY_MODE(stdin);
- SET_BINARY_MODE(stdout);
- if (uncompr) {
- file = gzdopen(fileno(stdin), "rb");
- if (file == NULL) error("can't gzdopen stdin");
- gz_uncompress(file, stdout);
- } else {
- file = gzdopen(fileno(stdout), outmode);
- if (file == NULL) error("can't gzdopen stdout");
- gz_compress(stdin, file);
- }
- } else {
- if (copyout) {
- SET_BINARY_MODE(stdout);
- }
- do {
- if (uncompr) {
- if (copyout) {
- file = gzopen(*argv, "rb");
- if (file == NULL)
- fprintf(stderr, "%s: can't gzopen %s\n", prog, *argv);
- else
- gz_uncompress(file, stdout);
- } else {
- file_uncompress(*argv);
- }
- } else {
- if (copyout) {
- FILE * in = fopen(*argv, "rb");
-
- if (in == NULL) {
- perror(*argv);
- } else {
- file = gzdopen(fileno(stdout), outmode);
- if (file == NULL) error("can't gzdopen stdout");
-
- gz_compress(in, file);
- }
-
- } else {
- file_compress(*argv, outmode);
- }
- }
- } while (argv++, --argc);
- }
- return 0;
-}
diff --git a/third-party/zlib/treebuild.xml b/third-party/zlib/treebuild.xml
deleted file mode 100644
index 38d29d7..0000000
--- a/third-party/zlib/treebuild.xml
+++ /dev/null
@@ -1,116 +0,0 @@
-<?xml version="1.0" ?>
-<package name="zlib" version="1.2.8">
- <library name="zlib" dlversion="1.2.8" dlname="z">
- <property name="description"> zip compression library </property>
- <property name="include-target-dir" value="$(@PACKAGE/install-includedir)" />
-
- <!-- fixme: not implemented yet -->
- <property name="compiler/c/inline" value="yes" />
-
- <include-file name="zlib.h" scope="public" mode="644" />
- <include-file name="zconf.h" scope="public" mode="644" />
-
- <source name="adler32.c">
- <depend name="zlib.h" />
- <depend name="zconf.h" />
- </source>
- <source name="compress.c">
- <depend name="zlib.h" />
- <depend name="zconf.h" />
- </source>
- <source name="crc32.c">
- <depend name="zlib.h" />
- <depend name="zconf.h" />
- <depend name="crc32.h" />
- </source>
- <source name="gzclose.c">
- <depend name="zlib.h" />
- <depend name="zconf.h" />
- <depend name="gzguts.h" />
- </source>
- <source name="gzlib.c">
- <depend name="zlib.h" />
- <depend name="zconf.h" />
- <depend name="gzguts.h" />
- </source>
- <source name="gzread.c">
- <depend name="zlib.h" />
- <depend name="zconf.h" />
- <depend name="gzguts.h" />
- </source>
- <source name="gzwrite.c">
- <depend name="zlib.h" />
- <depend name="zconf.h" />
- <depend name="gzguts.h" />
- </source>
- <source name="uncompr.c">
- <depend name="zlib.h" />
- <depend name="zconf.h" />
- </source>
- <source name="deflate.c">
- <depend name="zlib.h" />
- <depend name="zconf.h" />
- <depend name="zutil.h" />
- <depend name="deflate.h" />
- </source>
- <source name="trees.c">
- <depend name="zlib.h" />
- <depend name="zconf.h" />
- <depend name="zutil.h" />
- <depend name="deflate.h" />
- <depend name="trees.h" />
- </source>
- <source name="zutil.c">
- <depend name="zlib.h" />
- <depend name="zconf.h" />
- <depend name="zutil.h" />
- </source>
- <source name="inflate.c">
- <depend name="zlib.h" />
- <depend name="zconf.h" />
- <depend name="zutil.h" />
- <depend name="inftrees.h" />
- <depend name="inflate.h" />
- <depend name="inffast.h" />
- </source>
- <source name="infback.c">
- <depend name="zlib.h" />
- <depend name="zconf.h" />
- <depend name="zutil.h" />
- <depend name="inftrees.h" />
- <depend name="inflate.h" />
- <depend name="inffast.h" />
- </source>
- <source name="inftrees.c">
- <depend name="zlib.h" />
- <depend name="zconf.h" />
- <depend name="zutil.h" />
- <depend name="inftrees.h" />
- </source>
- <source name="inffast.c">
- <depend name="zlib.h" />
- <depend name="zconf.h" />
- <depend name="zutil.h" />
- <depend name="inftrees.h" />
- <depend name="inflate.h" />
- <depend name="inffast.h" />
- </source>
- </library>
-</package>
-
-<!--
-CFLAGS=-O
-#CFLAGS=-O -DMAX_WBITS=14 -DMAX_MEM_LEVEL=7
-#CFLAGS=-g -DDEBUG
-#CFLAGS=-O3 -Wall -Wwrite-strings -Wpointer-arith -Wconversion \
-# -Wstrict-prototypes -Wmissing-prototypes
-
-# OBJA =
-# to use the asm code: make OBJA=match.o
-#
-match.o: match.S
- $(CPP) match.S > _match.s
- $(CC) -c _match.s
- mv _match.o match.o
- rm -f _match.s
--->
diff --git a/third-party/zlib/trees.c b/third-party/zlib/trees.c
deleted file mode 100644
index 1fd7759..0000000
--- a/third-party/zlib/trees.c
+++ /dev/null
@@ -1,1226 +0,0 @@
-/* trees.c -- output deflated data using Huffman coding
- * Copyright (C) 1995-2012 Jean-loup Gailly
- * detect_data_type() function provided freely by Cosmin Truta, 2006
- * For conditions of distribution and use, see copyright notice in zlib.h
- */
-
-/*
- * ALGORITHM
- *
- * The "deflation" process uses several Huffman trees. The more
- * common source values are represented by shorter bit sequences.
- *
- * Each code tree is stored in a compressed form which is itself
- * a Huffman encoding of the lengths of all the code strings (in
- * ascending order by source values). The actual code strings are
- * reconstructed from the lengths in the inflate process, as described
- * in the deflate specification.
- *
- * REFERENCES
- *
- * Deutsch, L.P.,"'Deflate' Compressed Data Format Specification".
- * Available in ftp.uu.net:/pub/archiving/zip/doc/deflate-1.1.doc
- *
- * Storer, James A.
- * Data Compression: Methods and Theory, pp. 49-50.
- * Computer Science Press, 1988. ISBN 0-7167-8156-5.
- *
- * Sedgewick, R.
- * Algorithms, p290.
- * Addison-Wesley, 1983. ISBN 0-201-06672-6.
- */
-
-/* @(#) $Id$ */
-
-/* #define GEN_TREES_H */
-
-#include "deflate.h"
-
-#ifdef DEBUG
-# include <ctype.h>
-#endif
-
-/* ===========================================================================
- * Constants
- */
-
-#define MAX_BL_BITS 7
-/* Bit length codes must not exceed MAX_BL_BITS bits */
-
-#define END_BLOCK 256
-/* end of block literal code */
-
-#define REP_3_6 16
-/* repeat previous bit length 3-6 times (2 bits of repeat count) */
-
-#define REPZ_3_10 17
-/* repeat a zero length 3-10 times (3 bits of repeat count) */
-
-#define REPZ_11_138 18
-/* repeat a zero length 11-138 times (7 bits of repeat count) */
-
-local const int extra_lbits[LENGTH_CODES] /* extra bits for each length code */
- = {0,0,0,0,0,0,0,0,1,1,1,1,2,2,2,2,3,3,3,3,4,4,4,4,5,5,5,5,0};
-
-local const int extra_dbits[D_CODES] /* extra bits for each distance code */
- = {0,0,0,0,1,1,2,2,3,3,4,4,5,5,6,6,7,7,8,8,9,9,10,10,11,11,12,12,13,13};
-
-local const int extra_blbits[BL_CODES]/* extra bits for each bit length code */
- = {0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,2,3,7};
-
-local const uch bl_order[BL_CODES]
- = {16,17,18,0,8,7,9,6,10,5,11,4,12,3,13,2,14,1,15};
-/* The lengths of the bit length codes are sent in order of decreasing
- * probability, to avoid transmitting the lengths for unused bit length codes.
- */
-
-/* ===========================================================================
- * Local data. These are initialized only once.
- */
-
-#define DIST_CODE_LEN 512 /* see definition of array dist_code below */
-
-#if defined(GEN_TREES_H) || !defined(STDC)
-/* non ANSI compilers may not accept trees.h */
-
-local ct_data static_ltree[L_CODES+2];
-/* The static literal tree. Since the bit lengths are imposed, there is no
- * need for the L_CODES extra codes used during heap construction. However
- * The codes 286 and 287 are needed to build a canonical tree (see _tr_init
- * below).
- */
-
-local ct_data static_dtree[D_CODES];
-/* The static distance tree. (Actually a trivial tree since all codes use
- * 5 bits.)
- */
-
-uch _dist_code[DIST_CODE_LEN];
-/* Distance codes. The first 256 values correspond to the distances
- * 3 .. 258, the last 256 values correspond to the top 8 bits of
- * the 15 bit distances.
- */
-
-uch _length_code[MAX_MATCH-MIN_MATCH+1];
-/* length code for each normalized match length (0 == MIN_MATCH) */
-
-local int base_length[LENGTH_CODES];
-/* First normalized length for each code (0 = MIN_MATCH) */
-
-local int base_dist[D_CODES];
-/* First normalized distance for each code (0 = distance of 1) */
-
-#else
-# include "trees.h"
-#endif /* GEN_TREES_H */
-
-struct static_tree_desc_s {
- const ct_data *static_tree; /* static tree or NULL */
- const intf *extra_bits; /* extra bits for each code or NULL */
- int extra_base; /* base index for extra_bits */
- int elems; /* max number of elements in the tree */
- int max_length; /* max bit length for the codes */
-};
-
-local static_tree_desc static_l_desc =
-{static_ltree, extra_lbits, LITERALS+1, L_CODES, MAX_BITS};
-
-local static_tree_desc static_d_desc =
-{static_dtree, extra_dbits, 0, D_CODES, MAX_BITS};
-
-local static_tree_desc static_bl_desc =
-{(const ct_data *)0, extra_blbits, 0, BL_CODES, MAX_BL_BITS};
-
-/* ===========================================================================
- * Local (static) routines in this file.
- */
-
-local void tr_static_init OF((void));
-local void init_block OF((deflate_state *s));
-local void pqdownheap OF((deflate_state *s, ct_data *tree, int k));
-local void gen_bitlen OF((deflate_state *s, tree_desc *desc));
-local void gen_codes OF((ct_data *tree, int max_code, ushf *bl_count));
-local void build_tree OF((deflate_state *s, tree_desc *desc));
-local void scan_tree OF((deflate_state *s, ct_data *tree, int max_code));
-local void send_tree OF((deflate_state *s, ct_data *tree, int max_code));
-local int build_bl_tree OF((deflate_state *s));
-local void send_all_trees OF((deflate_state *s, int lcodes, int dcodes,
- int blcodes));
-local void compress_block OF((deflate_state *s, const ct_data *ltree,
- const ct_data *dtree));
-local int detect_data_type OF((deflate_state *s));
-local unsigned bi_reverse OF((unsigned value, int length));
-local void bi_windup OF((deflate_state *s));
-local void bi_flush OF((deflate_state *s));
-local void copy_block OF((deflate_state *s, charf *buf, unsigned len,
- int header));
-
-#ifdef GEN_TREES_H
-local void gen_trees_header OF((void));
-#endif
-
-#ifndef DEBUG
-# define send_code(s, c, tree) send_bits(s, tree[c].Code, tree[c].Len)
- /* Send a code of the given tree. c and tree must not have side effects */
-
-#else /* DEBUG */
-# define send_code(s, c, tree) \
- { if (z_verbose>2) fprintf(stderr,"\ncd %3d ",(c)); \
- send_bits(s, tree[c].Code, tree[c].Len); }
-#endif
-
-/* ===========================================================================
- * Output a short LSB first on the stream.
- * IN assertion: there is enough room in pendingBuf.
- */
-#define put_short(s, w) { \
- put_byte(s, (uch)((w) & 0xff)); \
- put_byte(s, (uch)((ush)(w) >> 8)); \
-}
-
-/* ===========================================================================
- * Send a value on a given number of bits.
- * IN assertion: length <= 16 and value fits in length bits.
- */
-#ifdef DEBUG
-local void send_bits OF((deflate_state *s, int value, int length));
-
-local void send_bits(s, value, length)
- deflate_state *s;
- int value; /* value to send */
- int length; /* number of bits */
-{
- Tracevv((stderr," l %2d v %4x ", length, value));
- Assert(length > 0 && length <= 15, "invalid length");
- s->bits_sent += (ulg)length;
-
- /* If not enough room in bi_buf, use (valid) bits from bi_buf and
- * (16 - bi_valid) bits from value, leaving (width - (16-bi_valid))
- * unused bits in value.
- */
- if (s->bi_valid > (int)Buf_size - length) {
- s->bi_buf |= (ush)value << s->bi_valid;
- put_short(s, s->bi_buf);
- s->bi_buf = (ush)value >> (Buf_size - s->bi_valid);
- s->bi_valid += length - Buf_size;
- } else {
- s->bi_buf |= (ush)value << s->bi_valid;
- s->bi_valid += length;
- }
-}
-#else /* !DEBUG */
-
-#define send_bits(s, value, length) \
-{ int len = length;\
- if (s->bi_valid > (int)Buf_size - len) {\
- int val = value;\
- s->bi_buf |= (ush)val << s->bi_valid;\
- put_short(s, s->bi_buf);\
- s->bi_buf = (ush)val >> (Buf_size - s->bi_valid);\
- s->bi_valid += len - Buf_size;\
- } else {\
- s->bi_buf |= (ush)(value) << s->bi_valid;\
- s->bi_valid += len;\
- }\
-}
-#endif /* DEBUG */
-
-
-/* the arguments must not have side effects */
-
-/* ===========================================================================
- * Initialize the various 'constant' tables.
- */
-local void tr_static_init()
-{
-#if defined(GEN_TREES_H) || !defined(STDC)
- static int static_init_done = 0;
- int n; /* iterates over tree elements */
- int bits; /* bit counter */
- int length; /* length value */
- int code; /* code value */
- int dist; /* distance index */
- ush bl_count[MAX_BITS+1];
- /* number of codes at each bit length for an optimal tree */
-
- if (static_init_done) return;
-
- /* For some embedded targets, global variables are not initialized: */
-#ifdef NO_INIT_GLOBAL_POINTERS
- static_l_desc.static_tree = static_ltree;
- static_l_desc.extra_bits = extra_lbits;
- static_d_desc.static_tree = static_dtree;
- static_d_desc.extra_bits = extra_dbits;
- static_bl_desc.extra_bits = extra_blbits;
-#endif
-
- /* Initialize the mapping length (0..255) -> length code (0..28) */
- length = 0;
- for (code = 0; code < LENGTH_CODES-1; code++) {
- base_length[code] = length;
- for (n = 0; n < (1<<extra_lbits[code]); n++) {
- _length_code[length++] = (uch)code;
- }
- }
- Assert (length == 256, "tr_static_init: length != 256");
- /* Note that the length 255 (match length 258) can be represented
- * in two different ways: code 284 + 5 bits or code 285, so we
- * overwrite length_code[255] to use the best encoding:
- */
- _length_code[length-1] = (uch)code;
-
- /* Initialize the mapping dist (0..32K) -> dist code (0..29) */
- dist = 0;
- for (code = 0 ; code < 16; code++) {
- base_dist[code] = dist;
- for (n = 0; n < (1<<extra_dbits[code]); n++) {
- _dist_code[dist++] = (uch)code;
- }
- }
- Assert (dist == 256, "tr_static_init: dist != 256");
- dist >>= 7; /* from now on, all distances are divided by 128 */
- for ( ; code < D_CODES; code++) {
- base_dist[code] = dist << 7;
- for (n = 0; n < (1<<(extra_dbits[code]-7)); n++) {
- _dist_code[256 + dist++] = (uch)code;
- }
- }
- Assert (dist == 256, "tr_static_init: 256+dist != 512");
-
- /* Construct the codes of the static literal tree */
- for (bits = 0; bits <= MAX_BITS; bits++) bl_count[bits] = 0;
- n = 0;
- while (n <= 143) static_ltree[n++].Len = 8, bl_count[8]++;
- while (n <= 255) static_ltree[n++].Len = 9, bl_count[9]++;
- while (n <= 279) static_ltree[n++].Len = 7, bl_count[7]++;
- while (n <= 287) static_ltree[n++].Len = 8, bl_count[8]++;
- /* Codes 286 and 287 do not exist, but we must include them in the
- * tree construction to get a canonical Huffman tree (longest code
- * all ones)
- */
- gen_codes((ct_data *)static_ltree, L_CODES+1, bl_count);
-
- /* The static distance tree is trivial: */
- for (n = 0; n < D_CODES; n++) {
- static_dtree[n].Len = 5;
- static_dtree[n].Code = bi_reverse((unsigned)n, 5);
- }
- static_init_done = 1;
-
-# ifdef GEN_TREES_H
- gen_trees_header();
-# endif
-#endif /* defined(GEN_TREES_H) || !defined(STDC) */
-}
-
-/* ===========================================================================
- * Genererate the file trees.h describing the static trees.
- */
-#ifdef GEN_TREES_H
-# ifndef DEBUG
-# include <stdio.h>
-# endif
-
-# define SEPARATOR(i, last, width) \
- ((i) == (last)? "\n};\n\n" : \
- ((i) % (width) == (width)-1 ? ",\n" : ", "))
-
-void gen_trees_header()
-{
- FILE *header = fopen("trees.h", "w");
- int i;
-
- Assert (header != NULL, "Can't open trees.h");
- fprintf(header,
- "/* header created automatically with -DGEN_TREES_H */\n\n");
-
- fprintf(header, "local const ct_data static_ltree[L_CODES+2] = {\n");
- for (i = 0; i < L_CODES+2; i++) {
- fprintf(header, "{{%3u},{%3u}}%s", static_ltree[i].Code,
- static_ltree[i].Len, SEPARATOR(i, L_CODES+1, 5));
- }
-
- fprintf(header, "local const ct_data static_dtree[D_CODES] = {\n");
- for (i = 0; i < D_CODES; i++) {
- fprintf(header, "{{%2u},{%2u}}%s", static_dtree[i].Code,
- static_dtree[i].Len, SEPARATOR(i, D_CODES-1, 5));
- }
-
- fprintf(header, "const uch ZLIB_INTERNAL _dist_code[DIST_CODE_LEN] = {\n");
- for (i = 0; i < DIST_CODE_LEN; i++) {
- fprintf(header, "%2u%s", _dist_code[i],
- SEPARATOR(i, DIST_CODE_LEN-1, 20));
- }
-
- fprintf(header,
- "const uch ZLIB_INTERNAL _length_code[MAX_MATCH-MIN_MATCH+1]= {\n");
- for (i = 0; i < MAX_MATCH-MIN_MATCH+1; i++) {
- fprintf(header, "%2u%s", _length_code[i],
- SEPARATOR(i, MAX_MATCH-MIN_MATCH, 20));
- }
-
- fprintf(header, "local const int base_length[LENGTH_CODES] = {\n");
- for (i = 0; i < LENGTH_CODES; i++) {
- fprintf(header, "%1u%s", base_length[i],
- SEPARATOR(i, LENGTH_CODES-1, 20));
- }
-
- fprintf(header, "local const int base_dist[D_CODES] = {\n");
- for (i = 0; i < D_CODES; i++) {
- fprintf(header, "%5u%s", base_dist[i],
- SEPARATOR(i, D_CODES-1, 10));
- }
-
- fclose(header);
-}
-#endif /* GEN_TREES_H */
-
-/* ===========================================================================
- * Initialize the tree data structures for a new zlib stream.
- */
-void ZLIB_INTERNAL _tr_init(s)
- deflate_state *s;
-{
- tr_static_init();
-
- s->l_desc.dyn_tree = s->dyn_ltree;
- s->l_desc.stat_desc = &static_l_desc;
-
- s->d_desc.dyn_tree = s->dyn_dtree;
- s->d_desc.stat_desc = &static_d_desc;
-
- s->bl_desc.dyn_tree = s->bl_tree;
- s->bl_desc.stat_desc = &static_bl_desc;
-
- s->bi_buf = 0;
- s->bi_valid = 0;
-#ifdef DEBUG
- s->compressed_len = 0L;
- s->bits_sent = 0L;
-#endif
-
- /* Initialize the first block of the first file: */
- init_block(s);
-}
-
-/* ===========================================================================
- * Initialize a new block.
- */
-local void init_block(s)
- deflate_state *s;
-{
- int n; /* iterates over tree elements */
-
- /* Initialize the trees. */
- for (n = 0; n < L_CODES; n++) s->dyn_ltree[n].Freq = 0;
- for (n = 0; n < D_CODES; n++) s->dyn_dtree[n].Freq = 0;
- for (n = 0; n < BL_CODES; n++) s->bl_tree[n].Freq = 0;
-
- s->dyn_ltree[END_BLOCK].Freq = 1;
- s->opt_len = s->static_len = 0L;
- s->last_lit = s->matches = 0;
-}
-
-#define SMALLEST 1
-/* Index within the heap array of least frequent node in the Huffman tree */
-
-
-/* ===========================================================================
- * Remove the smallest element from the heap and recreate the heap with
- * one less element. Updates heap and heap_len.
- */
-#define pqremove(s, tree, top) \
-{\
- top = s->heap[SMALLEST]; \
- s->heap[SMALLEST] = s->heap[s->heap_len--]; \
- pqdownheap(s, tree, SMALLEST); \
-}
-
-/* ===========================================================================
- * Compares to subtrees, using the tree depth as tie breaker when
- * the subtrees have equal frequency. This minimizes the worst case length.
- */
-#define smaller(tree, n, m, depth) \
- (tree[n].Freq < tree[m].Freq || \
- (tree[n].Freq == tree[m].Freq && depth[n] <= depth[m]))
-
-/* ===========================================================================
- * Restore the heap property by moving down the tree starting at node k,
- * exchanging a node with the smallest of its two sons if necessary, stopping
- * when the heap property is re-established (each father smaller than its
- * two sons).
- */
-local void pqdownheap(s, tree, k)
- deflate_state *s;
- ct_data *tree; /* the tree to restore */
- int k; /* node to move down */
-{
- int v = s->heap[k];
- int j = k << 1; /* left son of k */
- while (j <= s->heap_len) {
- /* Set j to the smallest of the two sons: */
- if (j < s->heap_len &&
- smaller(tree, s->heap[j+1], s->heap[j], s->depth)) {
- j++;
- }
- /* Exit if v is smaller than both sons */
- if (smaller(tree, v, s->heap[j], s->depth)) break;
-
- /* Exchange v with the smallest son */
- s->heap[k] = s->heap[j]; k = j;
-
- /* And continue down the tree, setting j to the left son of k */
- j <<= 1;
- }
- s->heap[k] = v;
-}
-
-/* ===========================================================================
- * Compute the optimal bit lengths for a tree and update the total bit length
- * for the current block.
- * IN assertion: the fields freq and dad are set, heap[heap_max] and
- * above are the tree nodes sorted by increasing frequency.
- * OUT assertions: the field len is set to the optimal bit length, the
- * array bl_count contains the frequencies for each bit length.
- * The length opt_len is updated; static_len is also updated if stree is
- * not null.
- */
-local void gen_bitlen(s, desc)
- deflate_state *s;
- tree_desc *desc; /* the tree descriptor */
-{
- ct_data *tree = desc->dyn_tree;
- int max_code = desc->max_code;
- const ct_data *stree = desc->stat_desc->static_tree;
- const intf *extra = desc->stat_desc->extra_bits;
- int base = desc->stat_desc->extra_base;
- int max_length = desc->stat_desc->max_length;
- int h; /* heap index */
- int n, m; /* iterate over the tree elements */
- int bits; /* bit length */
- int xbits; /* extra bits */
- ush f; /* frequency */
- int overflow = 0; /* number of elements with bit length too large */
-
- for (bits = 0; bits <= MAX_BITS; bits++) s->bl_count[bits] = 0;
-
- /* In a first pass, compute the optimal bit lengths (which may
- * overflow in the case of the bit length tree).
- */
- tree[s->heap[s->heap_max]].Len = 0; /* root of the heap */
-
- for (h = s->heap_max+1; h < HEAP_SIZE; h++) {
- n = s->heap[h];
- bits = tree[tree[n].Dad].Len + 1;
- if (bits > max_length) bits = max_length, overflow++;
- tree[n].Len = (ush)bits;
- /* We overwrite tree[n].Dad which is no longer needed */
-
- if (n > max_code) continue; /* not a leaf node */
-
- s->bl_count[bits]++;
- xbits = 0;
- if (n >= base) xbits = extra[n-base];
- f = tree[n].Freq;
- s->opt_len += (ulg)f * (bits + xbits);
- if (stree) s->static_len += (ulg)f * (stree[n].Len + xbits);
- }
- if (overflow == 0) return;
-
- Trace((stderr,"\nbit length overflow\n"));
- /* This happens for example on obj2 and pic of the Calgary corpus */
-
- /* Find the first bit length which could increase: */
- do {
- bits = max_length-1;
- while (s->bl_count[bits] == 0) bits--;
- s->bl_count[bits]--; /* move one leaf down the tree */
- s->bl_count[bits+1] += 2; /* move one overflow item as its brother */
- s->bl_count[max_length]--;
- /* The brother of the overflow item also moves one step up,
- * but this does not affect bl_count[max_length]
- */
- overflow -= 2;
- } while (overflow > 0);
-
- /* Now recompute all bit lengths, scanning in increasing frequency.
- * h is still equal to HEAP_SIZE. (It is simpler to reconstruct all
- * lengths instead of fixing only the wrong ones. This idea is taken
- * from 'ar' written by Haruhiko Okumura.)
- */
- for (bits = max_length; bits != 0; bits--) {
- n = s->bl_count[bits];
- while (n != 0) {
- m = s->heap[--h];
- if (m > max_code) continue;
- if ((unsigned) tree[m].Len != (unsigned) bits) {
- Trace((stderr,"code %d bits %d->%d\n", m, tree[m].Len, bits));
- s->opt_len += ((long)bits - (long)tree[m].Len)
- *(long)tree[m].Freq;
- tree[m].Len = (ush)bits;
- }
- n--;
- }
- }
-}
-
-/* ===========================================================================
- * Generate the codes for a given tree and bit counts (which need not be
- * optimal).
- * IN assertion: the array bl_count contains the bit length statistics for
- * the given tree and the field len is set for all tree elements.
- * OUT assertion: the field code is set for all tree elements of non
- * zero code length.
- */
-local void gen_codes (tree, max_code, bl_count)
- ct_data *tree; /* the tree to decorate */
- int max_code; /* largest code with non zero frequency */
- ushf *bl_count; /* number of codes at each bit length */
-{
- ush next_code[MAX_BITS+1]; /* next code value for each bit length */
- ush code = 0; /* running code value */
- int bits; /* bit index */
- int n; /* code index */
-
- /* The distribution counts are first used to generate the code values
- * without bit reversal.
- */
- for (bits = 1; bits <= MAX_BITS; bits++) {
- next_code[bits] = code = (code + bl_count[bits-1]) << 1;
- }
- /* Check that the bit counts in bl_count are consistent. The last code
- * must be all ones.
- */
- Assert (code + bl_count[MAX_BITS]-1 == (1<<MAX_BITS)-1,
- "inconsistent bit counts");
- Tracev((stderr,"\ngen_codes: max_code %d ", max_code));
-
- for (n = 0; n <= max_code; n++) {
- int len = tree[n].Len;
- if (len == 0) continue;
- /* Now reverse the bits */
- tree[n].Code = bi_reverse(next_code[len]++, len);
-
- Tracecv(tree != static_ltree, (stderr,"\nn %3d %c l %2d c %4x (%x) ",
- n, (isgraph(n) ? n : ' '), len, tree[n].Code, next_code[len]-1));
- }
-}
-
-/* ===========================================================================
- * Construct one Huffman tree and assigns the code bit strings and lengths.
- * Update the total bit length for the current block.
- * IN assertion: the field freq is set for all tree elements.
- * OUT assertions: the fields len and code are set to the optimal bit length
- * and corresponding code. The length opt_len is updated; static_len is
- * also updated if stree is not null. The field max_code is set.
- */
-local void build_tree(s, desc)
- deflate_state *s;
- tree_desc *desc; /* the tree descriptor */
-{
- ct_data *tree = desc->dyn_tree;
- const ct_data *stree = desc->stat_desc->static_tree;
- int elems = desc->stat_desc->elems;
- int n, m; /* iterate over heap elements */
- int max_code = -1; /* largest code with non zero frequency */
- int node; /* new node being created */
-
- /* Construct the initial heap, with least frequent element in
- * heap[SMALLEST]. The sons of heap[n] are heap[2*n] and heap[2*n+1].
- * heap[0] is not used.
- */
- s->heap_len = 0, s->heap_max = HEAP_SIZE;
-
- for (n = 0; n < elems; n++) {
- if (tree[n].Freq != 0) {
- s->heap[++(s->heap_len)] = max_code = n;
- s->depth[n] = 0;
- } else {
- tree[n].Len = 0;
- }
- }
-
- /* The pkzip format requires that at least one distance code exists,
- * and that at least one bit should be sent even if there is only one
- * possible code. So to avoid special checks later on we force at least
- * two codes of non zero frequency.
- */
- while (s->heap_len < 2) {
- node = s->heap[++(s->heap_len)] = (max_code < 2 ? ++max_code : 0);
- tree[node].Freq = 1;
- s->depth[node] = 0;
- s->opt_len--; if (stree) s->static_len -= stree[node].Len;
- /* node is 0 or 1 so it does not have extra bits */
- }
- desc->max_code = max_code;
-
- /* The elements heap[heap_len/2+1 .. heap_len] are leaves of the tree,
- * establish sub-heaps of increasing lengths:
- */
- for (n = s->heap_len/2; n >= 1; n--) pqdownheap(s, tree, n);
-
- /* Construct the Huffman tree by repeatedly combining the least two
- * frequent nodes.
- */
- node = elems; /* next internal node of the tree */
- do {
- pqremove(s, tree, n); /* n = node of least frequency */
- m = s->heap[SMALLEST]; /* m = node of next least frequency */
-
- s->heap[--(s->heap_max)] = n; /* keep the nodes sorted by frequency */
- s->heap[--(s->heap_max)] = m;
-
- /* Create a new node father of n and m */
- tree[node].Freq = tree[n].Freq + tree[m].Freq;
- s->depth[node] = (uch)((s->depth[n] >= s->depth[m] ?
- s->depth[n] : s->depth[m]) + 1);
- tree[n].Dad = tree[m].Dad = (ush)node;
-#ifdef DUMP_BL_TREE
- if (tree == s->bl_tree) {
- fprintf(stderr,"\nnode %d(%d), sons %d(%d) %d(%d)",
- node, tree[node].Freq, n, tree[n].Freq, m, tree[m].Freq);
- }
-#endif
- /* and insert the new node in the heap */
- s->heap[SMALLEST] = node++;
- pqdownheap(s, tree, SMALLEST);
-
- } while (s->heap_len >= 2);
-
- s->heap[--(s->heap_max)] = s->heap[SMALLEST];
-
- /* At this point, the fields freq and dad are set. We can now
- * generate the bit lengths.
- */
- gen_bitlen(s, (tree_desc *)desc);
-
- /* The field len is now set, we can generate the bit codes */
- gen_codes ((ct_data *)tree, max_code, s->bl_count);
-}
-
-/* ===========================================================================
- * Scan a literal or distance tree to determine the frequencies of the codes
- * in the bit length tree.
- */
-local void scan_tree (s, tree, max_code)
- deflate_state *s;
- ct_data *tree; /* the tree to be scanned */
- int max_code; /* and its largest code of non zero frequency */
-{
- int n; /* iterates over all tree elements */
- int prevlen = -1; /* last emitted length */
- int curlen; /* length of current code */
- int nextlen = tree[0].Len; /* length of next code */
- int count = 0; /* repeat count of the current code */
- int max_count = 7; /* max repeat count */
- int min_count = 4; /* min repeat count */
-
- if (nextlen == 0) max_count = 138, min_count = 3;
- tree[max_code+1].Len = (ush)0xffff; /* guard */
-
- for (n = 0; n <= max_code; n++) {
- curlen = nextlen; nextlen = tree[n+1].Len;
- if (++count < max_count && curlen == nextlen) {
- continue;
- } else if (count < min_count) {
- s->bl_tree[curlen].Freq += count;
- } else if (curlen != 0) {
- if (curlen != prevlen) s->bl_tree[curlen].Freq++;
- s->bl_tree[REP_3_6].Freq++;
- } else if (count <= 10) {
- s->bl_tree[REPZ_3_10].Freq++;
- } else {
- s->bl_tree[REPZ_11_138].Freq++;
- }
- count = 0; prevlen = curlen;
- if (nextlen == 0) {
- max_count = 138, min_count = 3;
- } else if (curlen == nextlen) {
- max_count = 6, min_count = 3;
- } else {
- max_count = 7, min_count = 4;
- }
- }
-}
-
-/* ===========================================================================
- * Send a literal or distance tree in compressed form, using the codes in
- * bl_tree.
- */
-local void send_tree (s, tree, max_code)
- deflate_state *s;
- ct_data *tree; /* the tree to be scanned */
- int max_code; /* and its largest code of non zero frequency */
-{
- int n; /* iterates over all tree elements */
- int prevlen = -1; /* last emitted length */
- int curlen; /* length of current code */
- int nextlen = tree[0].Len; /* length of next code */
- int count = 0; /* repeat count of the current code */
- int max_count = 7; /* max repeat count */
- int min_count = 4; /* min repeat count */
-
- /* tree[max_code+1].Len = -1; */ /* guard already set */
- if (nextlen == 0) max_count = 138, min_count = 3;
-
- for (n = 0; n <= max_code; n++) {
- curlen = nextlen; nextlen = tree[n+1].Len;
- if (++count < max_count && curlen == nextlen) {
- continue;
- } else if (count < min_count) {
- do { send_code(s, curlen, s->bl_tree); } while (--count != 0);
-
- } else if (curlen != 0) {
- if (curlen != prevlen) {
- send_code(s, curlen, s->bl_tree); count--;
- }
- Assert(count >= 3 && count <= 6, " 3_6?");
- send_code(s, REP_3_6, s->bl_tree); send_bits(s, count-3, 2);
-
- } else if (count <= 10) {
- send_code(s, REPZ_3_10, s->bl_tree); send_bits(s, count-3, 3);
-
- } else {
- send_code(s, REPZ_11_138, s->bl_tree); send_bits(s, count-11, 7);
- }
- count = 0; prevlen = curlen;
- if (nextlen == 0) {
- max_count = 138, min_count = 3;
- } else if (curlen == nextlen) {
- max_count = 6, min_count = 3;
- } else {
- max_count = 7, min_count = 4;
- }
- }
-}
-
-/* ===========================================================================
- * Construct the Huffman tree for the bit lengths and return the index in
- * bl_order of the last bit length code to send.
- */
-local int build_bl_tree(s)
- deflate_state *s;
-{
- int max_blindex; /* index of last bit length code of non zero freq */
-
- /* Determine the bit length frequencies for literal and distance trees */
- scan_tree(s, (ct_data *)s->dyn_ltree, s->l_desc.max_code);
- scan_tree(s, (ct_data *)s->dyn_dtree, s->d_desc.max_code);
-
- /* Build the bit length tree: */
- build_tree(s, (tree_desc *)(&(s->bl_desc)));
- /* opt_len now includes the length of the tree representations, except
- * the lengths of the bit lengths codes and the 5+5+4 bits for the counts.
- */
-
- /* Determine the number of bit length codes to send. The pkzip format
- * requires that at least 4 bit length codes be sent. (appnote.txt says
- * 3 but the actual value used is 4.)
- */
- for (max_blindex = BL_CODES-1; max_blindex >= 3; max_blindex--) {
- if (s->bl_tree[bl_order[max_blindex]].Len != 0) break;
- }
- /* Update opt_len to include the bit length tree and counts */
- s->opt_len += 3*(max_blindex+1) + 5+5+4;
- Tracev((stderr, "\ndyn trees: dyn %ld, stat %ld",
- s->opt_len, s->static_len));
-
- return max_blindex;
-}
-
-/* ===========================================================================
- * Send the header for a block using dynamic Huffman trees: the counts, the
- * lengths of the bit length codes, the literal tree and the distance tree.
- * IN assertion: lcodes >= 257, dcodes >= 1, blcodes >= 4.
- */
-local void send_all_trees(s, lcodes, dcodes, blcodes)
- deflate_state *s;
- int lcodes, dcodes, blcodes; /* number of codes for each tree */
-{
- int rank; /* index in bl_order */
-
- Assert (lcodes >= 257 && dcodes >= 1 && blcodes >= 4, "not enough codes");
- Assert (lcodes <= L_CODES && dcodes <= D_CODES && blcodes <= BL_CODES,
- "too many codes");
- Tracev((stderr, "\nbl counts: "));
- send_bits(s, lcodes-257, 5); /* not +255 as stated in appnote.txt */
- send_bits(s, dcodes-1, 5);
- send_bits(s, blcodes-4, 4); /* not -3 as stated in appnote.txt */
- for (rank = 0; rank < blcodes; rank++) {
- Tracev((stderr, "\nbl code %2d ", bl_order[rank]));
- send_bits(s, s->bl_tree[bl_order[rank]].Len, 3);
- }
- Tracev((stderr, "\nbl tree: sent %ld", s->bits_sent));
-
- send_tree(s, (ct_data *)s->dyn_ltree, lcodes-1); /* literal tree */
- Tracev((stderr, "\nlit tree: sent %ld", s->bits_sent));
-
- send_tree(s, (ct_data *)s->dyn_dtree, dcodes-1); /* distance tree */
- Tracev((stderr, "\ndist tree: sent %ld", s->bits_sent));
-}
-
-/* ===========================================================================
- * Send a stored block
- */
-void ZLIB_INTERNAL _tr_stored_block(s, buf, stored_len, last)
- deflate_state *s;
- charf *buf; /* input block */
- ulg stored_len; /* length of input block */
- int last; /* one if this is the last block for a file */
-{
- send_bits(s, (STORED_BLOCK<<1)+last, 3); /* send block type */
-#ifdef DEBUG
- s->compressed_len = (s->compressed_len + 3 + 7) & (ulg)~7L;
- s->compressed_len += (stored_len + 4) << 3;
-#endif
- copy_block(s, buf, (unsigned)stored_len, 1); /* with header */
-}
-
-/* ===========================================================================
- * Flush the bits in the bit buffer to pending output (leaves at most 7 bits)
- */
-void ZLIB_INTERNAL _tr_flush_bits(s)
- deflate_state *s;
-{
- bi_flush(s);
-}
-
-/* ===========================================================================
- * Send one empty static block to give enough lookahead for inflate.
- * This takes 10 bits, of which 7 may remain in the bit buffer.
- */
-void ZLIB_INTERNAL _tr_align(s)
- deflate_state *s;
-{
- send_bits(s, STATIC_TREES<<1, 3);
- send_code(s, END_BLOCK, static_ltree);
-#ifdef DEBUG
- s->compressed_len += 10L; /* 3 for block type, 7 for EOB */
-#endif
- bi_flush(s);
-}
-
-/* ===========================================================================
- * Determine the best encoding for the current block: dynamic trees, static
- * trees or store, and output the encoded block to the zip file.
- */
-void ZLIB_INTERNAL _tr_flush_block(s, buf, stored_len, last)
- deflate_state *s;
- charf *buf; /* input block, or NULL if too old */
- ulg stored_len; /* length of input block */
- int last; /* one if this is the last block for a file */
-{
- ulg opt_lenb, static_lenb; /* opt_len and static_len in bytes */
- int max_blindex = 0; /* index of last bit length code of non zero freq */
-
- /* Build the Huffman trees unless a stored block is forced */
- if (s->level > 0) {
-
- /* Check if the file is binary or text */
- if (s->strm->data_type == Z_UNKNOWN)
- s->strm->data_type = detect_data_type(s);
-
- /* Construct the literal and distance trees */
- build_tree(s, (tree_desc *)(&(s->l_desc)));
- Tracev((stderr, "\nlit data: dyn %ld, stat %ld", s->opt_len,
- s->static_len));
-
- build_tree(s, (tree_desc *)(&(s->d_desc)));
- Tracev((stderr, "\ndist data: dyn %ld, stat %ld", s->opt_len,
- s->static_len));
- /* At this point, opt_len and static_len are the total bit lengths of
- * the compressed block data, excluding the tree representations.
- */
-
- /* Build the bit length tree for the above two trees, and get the index
- * in bl_order of the last bit length code to send.
- */
- max_blindex = build_bl_tree(s);
-
- /* Determine the best encoding. Compute the block lengths in bytes. */
- opt_lenb = (s->opt_len+3+7)>>3;
- static_lenb = (s->static_len+3+7)>>3;
-
- Tracev((stderr, "\nopt %lu(%lu) stat %lu(%lu) stored %lu lit %u ",
- opt_lenb, s->opt_len, static_lenb, s->static_len, stored_len,
- s->last_lit));
-
- if (static_lenb <= opt_lenb) opt_lenb = static_lenb;
-
- } else {
- Assert(buf != (char*)0, "lost buf");
- opt_lenb = static_lenb = stored_len + 5; /* force a stored block */
- }
-
-#ifdef FORCE_STORED
- if (buf != (char*)0) { /* force stored block */
-#else
- if (stored_len+4 <= opt_lenb && buf != (char*)0) {
- /* 4: two words for the lengths */
-#endif
- /* The test buf != NULL is only necessary if LIT_BUFSIZE > WSIZE.
- * Otherwise we can't have processed more than WSIZE input bytes since
- * the last block flush, because compression would have been
- * successful. If LIT_BUFSIZE <= WSIZE, it is never too late to
- * transform a block into a stored block.
- */
- _tr_stored_block(s, buf, stored_len, last);
-
-#ifdef FORCE_STATIC
- } else if (static_lenb >= 0) { /* force static trees */
-#else
- } else if (s->strategy == Z_FIXED || static_lenb == opt_lenb) {
-#endif
- send_bits(s, (STATIC_TREES<<1)+last, 3);
- compress_block(s, (const ct_data *)static_ltree,
- (const ct_data *)static_dtree);
-#ifdef DEBUG
- s->compressed_len += 3 + s->static_len;
-#endif
- } else {
- send_bits(s, (DYN_TREES<<1)+last, 3);
- send_all_trees(s, s->l_desc.max_code+1, s->d_desc.max_code+1,
- max_blindex+1);
- compress_block(s, (const ct_data *)s->dyn_ltree,
- (const ct_data *)s->dyn_dtree);
-#ifdef DEBUG
- s->compressed_len += 3 + s->opt_len;
-#endif
- }
- Assert (s->compressed_len == s->bits_sent, "bad compressed size");
- /* The above check is made mod 2^32, for files larger than 512 MB
- * and uLong implemented on 32 bits.
- */
- init_block(s);
-
- if (last) {
- bi_windup(s);
-#ifdef DEBUG
- s->compressed_len += 7; /* align on byte boundary */
-#endif
- }
- Tracev((stderr,"\ncomprlen %lu(%lu) ", s->compressed_len>>3,
- s->compressed_len-7*last));
-}
-
-/* ===========================================================================
- * Save the match info and tally the frequency counts. Return true if
- * the current block must be flushed.
- */
-int ZLIB_INTERNAL _tr_tally (s, dist, lc)
- deflate_state *s;
- unsigned dist; /* distance of matched string */
- unsigned lc; /* match length-MIN_MATCH or unmatched char (if dist==0) */
-{
- s->d_buf[s->last_lit] = (ush)dist;
- s->l_buf[s->last_lit++] = (uch)lc;
- if (dist == 0) {
- /* lc is the unmatched char */
- s->dyn_ltree[lc].Freq++;
- } else {
- s->matches++;
- /* Here, lc is the match length - MIN_MATCH */
- dist--; /* dist = match distance - 1 */
- Assert((ush)dist < (ush)MAX_DIST(s) &&
- (ush)lc <= (ush)(MAX_MATCH-MIN_MATCH) &&
- (ush)d_code(dist) < (ush)D_CODES, "_tr_tally: bad match");
-
- s->dyn_ltree[_length_code[lc]+LITERALS+1].Freq++;
- s->dyn_dtree[d_code(dist)].Freq++;
- }
-
-#ifdef TRUNCATE_BLOCK
- /* Try to guess if it is profitable to stop the current block here */
- if ((s->last_lit & 0x1fff) == 0 && s->level > 2) {
- /* Compute an upper bound for the compressed length */
- ulg out_length = (ulg)s->last_lit*8L;
- ulg in_length = (ulg)((long)s->strstart - s->block_start);
- int dcode;
- for (dcode = 0; dcode < D_CODES; dcode++) {
- out_length += (ulg)s->dyn_dtree[dcode].Freq *
- (5L+extra_dbits[dcode]);
- }
- out_length >>= 3;
- Tracev((stderr,"\nlast_lit %u, in %ld, out ~%ld(%ld%%) ",
- s->last_lit, in_length, out_length,
- 100L - out_length*100L/in_length));
- if (s->matches < s->last_lit/2 && out_length < in_length/2) return 1;
- }
-#endif
- return (s->last_lit == s->lit_bufsize-1);
- /* We avoid equality with lit_bufsize because of wraparound at 64K
- * on 16 bit machines and because stored blocks are restricted to
- * 64K-1 bytes.
- */
-}
-
-/* ===========================================================================
- * Send the block data compressed using the given Huffman trees
- */
-local void compress_block(s, ltree, dtree)
- deflate_state *s;
- const ct_data *ltree; /* literal tree */
- const ct_data *dtree; /* distance tree */
-{
- unsigned dist; /* distance of matched string */
- int lc; /* match length or unmatched char (if dist == 0) */
- unsigned lx = 0; /* running index in l_buf */
- unsigned code; /* the code to send */
- int extra; /* number of extra bits to send */
-
- if (s->last_lit != 0) do {
- dist = s->d_buf[lx];
- lc = s->l_buf[lx++];
- if (dist == 0) {
- send_code(s, lc, ltree); /* send a literal byte */
- Tracecv(isgraph(lc), (stderr," '%c' ", lc));
- } else {
- /* Here, lc is the match length - MIN_MATCH */
- code = _length_code[lc];
- send_code(s, code+LITERALS+1, ltree); /* send the length code */
- extra = extra_lbits[code];
- if (extra != 0) {
- lc -= base_length[code];
- send_bits(s, lc, extra); /* send the extra length bits */
- }
- dist--; /* dist is now the match distance - 1 */
- code = d_code(dist);
- Assert (code < D_CODES, "bad d_code");
-
- send_code(s, code, dtree); /* send the distance code */
- extra = extra_dbits[code];
- if (extra != 0) {
- dist -= base_dist[code];
- send_bits(s, dist, extra); /* send the extra distance bits */
- }
- } /* literal or match pair ? */
-
- /* Check that the overlay between pending_buf and d_buf+l_buf is ok: */
- Assert((uInt)(s->pending) < s->lit_bufsize + 2*lx,
- "pendingBuf overflow");
-
- } while (lx < s->last_lit);
-
- send_code(s, END_BLOCK, ltree);
-}
-
-/* ===========================================================================
- * Check if the data type is TEXT or BINARY, using the following algorithm:
- * - TEXT if the two conditions below are satisfied:
- * a) There are no non-portable control characters belonging to the
- * "black list" (0..6, 14..25, 28..31).
- * b) There is at least one printable character belonging to the
- * "white list" (9 {TAB}, 10 {LF}, 13 {CR}, 32..255).
- * - BINARY otherwise.
- * - The following partially-portable control characters form a
- * "gray list" that is ignored in this detection algorithm:
- * (7 {BEL}, 8 {BS}, 11 {VT}, 12 {FF}, 26 {SUB}, 27 {ESC}).
- * IN assertion: the fields Freq of dyn_ltree are set.
- */
-local int detect_data_type(s)
- deflate_state *s;
-{
- /* black_mask is the bit mask of black-listed bytes
- * set bits 0..6, 14..25, and 28..31
- * 0xf3ffc07f = binary 11110011111111111100000001111111
- */
- unsigned long black_mask = 0xf3ffc07fUL;
- int n;
-
- /* Check for non-textual ("black-listed") bytes. */
- for (n = 0; n <= 31; n++, black_mask >>= 1)
- if ((black_mask & 1) && (s->dyn_ltree[n].Freq != 0))
- return Z_BINARY;
-
- /* Check for textual ("white-listed") bytes. */
- if (s->dyn_ltree[9].Freq != 0 || s->dyn_ltree[10].Freq != 0
- || s->dyn_ltree[13].Freq != 0)
- return Z_TEXT;
- for (n = 32; n < LITERALS; n++)
- if (s->dyn_ltree[n].Freq != 0)
- return Z_TEXT;
-
- /* There are no "black-listed" or "white-listed" bytes:
- * this stream either is empty or has tolerated ("gray-listed") bytes only.
- */
- return Z_BINARY;
-}
-
-/* ===========================================================================
- * Reverse the first len bits of a code, using straightforward code (a faster
- * method would use a table)
- * IN assertion: 1 <= len <= 15
- */
-local unsigned bi_reverse(code, len)
- unsigned code; /* the value to invert */
- int len; /* its bit length */
-{
- register unsigned res = 0;
- do {
- res |= code & 1;
- code >>= 1, res <<= 1;
- } while (--len > 0);
- return res >> 1;
-}
-
-/* ===========================================================================
- * Flush the bit buffer, keeping at most 7 bits in it.
- */
-local void bi_flush(s)
- deflate_state *s;
-{
- if (s->bi_valid == 16) {
- put_short(s, s->bi_buf);
- s->bi_buf = 0;
- s->bi_valid = 0;
- } else if (s->bi_valid >= 8) {
- put_byte(s, (Byte)s->bi_buf);
- s->bi_buf >>= 8;
- s->bi_valid -= 8;
- }
-}
-
-/* ===========================================================================
- * Flush the bit buffer and align the output on a byte boundary
- */
-local void bi_windup(s)
- deflate_state *s;
-{
- if (s->bi_valid > 8) {
- put_short(s, s->bi_buf);
- } else if (s->bi_valid > 0) {
- put_byte(s, (Byte)s->bi_buf);
- }
- s->bi_buf = 0;
- s->bi_valid = 0;
-#ifdef DEBUG
- s->bits_sent = (s->bits_sent+7) & ~7;
-#endif
-}
-
-/* ===========================================================================
- * Copy a stored block, storing first the length and its
- * one's complement if requested.
- */
-local void copy_block(s, buf, len, header)
- deflate_state *s;
- charf *buf; /* the input data */
- unsigned len; /* its length */
- int header; /* true if block header must be written */
-{
- bi_windup(s); /* align on byte boundary */
-
- if (header) {
- put_short(s, (ush)len);
- put_short(s, (ush)~len);
-#ifdef DEBUG
- s->bits_sent += 2*16;
-#endif
- }
-#ifdef DEBUG
- s->bits_sent += (ulg)len<<3;
-#endif
- while (len--) {
- put_byte(s, *buf++);
- }
-}
diff --git a/third-party/zlib/trees.h b/third-party/zlib/trees.h
deleted file mode 100644
index d35639d..0000000
--- a/third-party/zlib/trees.h
+++ /dev/null
@@ -1,128 +0,0 @@
-/* header created automatically with -DGEN_TREES_H */
-
-local const ct_data static_ltree[L_CODES+2] = {
-{{ 12},{ 8}}, {{140},{ 8}}, {{ 76},{ 8}}, {{204},{ 8}}, {{ 44},{ 8}},
-{{172},{ 8}}, {{108},{ 8}}, {{236},{ 8}}, {{ 28},{ 8}}, {{156},{ 8}},
-{{ 92},{ 8}}, {{220},{ 8}}, {{ 60},{ 8}}, {{188},{ 8}}, {{124},{ 8}},
-{{252},{ 8}}, {{ 2},{ 8}}, {{130},{ 8}}, {{ 66},{ 8}}, {{194},{ 8}},
-{{ 34},{ 8}}, {{162},{ 8}}, {{ 98},{ 8}}, {{226},{ 8}}, {{ 18},{ 8}},
-{{146},{ 8}}, {{ 82},{ 8}}, {{210},{ 8}}, {{ 50},{ 8}}, {{178},{ 8}},
-{{114},{ 8}}, {{242},{ 8}}, {{ 10},{ 8}}, {{138},{ 8}}, {{ 74},{ 8}},
-{{202},{ 8}}, {{ 42},{ 8}}, {{170},{ 8}}, {{106},{ 8}}, {{234},{ 8}},
-{{ 26},{ 8}}, {{154},{ 8}}, {{ 90},{ 8}}, {{218},{ 8}}, {{ 58},{ 8}},
-{{186},{ 8}}, {{122},{ 8}}, {{250},{ 8}}, {{ 6},{ 8}}, {{134},{ 8}},
-{{ 70},{ 8}}, {{198},{ 8}}, {{ 38},{ 8}}, {{166},{ 8}}, {{102},{ 8}},
-{{230},{ 8}}, {{ 22},{ 8}}, {{150},{ 8}}, {{ 86},{ 8}}, {{214},{ 8}},
-{{ 54},{ 8}}, {{182},{ 8}}, {{118},{ 8}}, {{246},{ 8}}, {{ 14},{ 8}},
-{{142},{ 8}}, {{ 78},{ 8}}, {{206},{ 8}}, {{ 46},{ 8}}, {{174},{ 8}},
-{{110},{ 8}}, {{238},{ 8}}, {{ 30},{ 8}}, {{158},{ 8}}, {{ 94},{ 8}},
-{{222},{ 8}}, {{ 62},{ 8}}, {{190},{ 8}}, {{126},{ 8}}, {{254},{ 8}},
-{{ 1},{ 8}}, {{129},{ 8}}, {{ 65},{ 8}}, {{193},{ 8}}, {{ 33},{ 8}},
-{{161},{ 8}}, {{ 97},{ 8}}, {{225},{ 8}}, {{ 17},{ 8}}, {{145},{ 8}},
-{{ 81},{ 8}}, {{209},{ 8}}, {{ 49},{ 8}}, {{177},{ 8}}, {{113},{ 8}},
-{{241},{ 8}}, {{ 9},{ 8}}, {{137},{ 8}}, {{ 73},{ 8}}, {{201},{ 8}},
-{{ 41},{ 8}}, {{169},{ 8}}, {{105},{ 8}}, {{233},{ 8}}, {{ 25},{ 8}},
-{{153},{ 8}}, {{ 89},{ 8}}, {{217},{ 8}}, {{ 57},{ 8}}, {{185},{ 8}},
-{{121},{ 8}}, {{249},{ 8}}, {{ 5},{ 8}}, {{133},{ 8}}, {{ 69},{ 8}},
-{{197},{ 8}}, {{ 37},{ 8}}, {{165},{ 8}}, {{101},{ 8}}, {{229},{ 8}},
-{{ 21},{ 8}}, {{149},{ 8}}, {{ 85},{ 8}}, {{213},{ 8}}, {{ 53},{ 8}},
-{{181},{ 8}}, {{117},{ 8}}, {{245},{ 8}}, {{ 13},{ 8}}, {{141},{ 8}},
-{{ 77},{ 8}}, {{205},{ 8}}, {{ 45},{ 8}}, {{173},{ 8}}, {{109},{ 8}},
-{{237},{ 8}}, {{ 29},{ 8}}, {{157},{ 8}}, {{ 93},{ 8}}, {{221},{ 8}},
-{{ 61},{ 8}}, {{189},{ 8}}, {{125},{ 8}}, {{253},{ 8}}, {{ 19},{ 9}},
-{{275},{ 9}}, {{147},{ 9}}, {{403},{ 9}}, {{ 83},{ 9}}, {{339},{ 9}},
-{{211},{ 9}}, {{467},{ 9}}, {{ 51},{ 9}}, {{307},{ 9}}, {{179},{ 9}},
-{{435},{ 9}}, {{115},{ 9}}, {{371},{ 9}}, {{243},{ 9}}, {{499},{ 9}},
-{{ 11},{ 9}}, {{267},{ 9}}, {{139},{ 9}}, {{395},{ 9}}, {{ 75},{ 9}},
-{{331},{ 9}}, {{203},{ 9}}, {{459},{ 9}}, {{ 43},{ 9}}, {{299},{ 9}},
-{{171},{ 9}}, {{427},{ 9}}, {{107},{ 9}}, {{363},{ 9}}, {{235},{ 9}},
-{{491},{ 9}}, {{ 27},{ 9}}, {{283},{ 9}}, {{155},{ 9}}, {{411},{ 9}},
-{{ 91},{ 9}}, {{347},{ 9}}, {{219},{ 9}}, {{475},{ 9}}, {{ 59},{ 9}},
-{{315},{ 9}}, {{187},{ 9}}, {{443},{ 9}}, {{123},{ 9}}, {{379},{ 9}},
-{{251},{ 9}}, {{507},{ 9}}, {{ 7},{ 9}}, {{263},{ 9}}, {{135},{ 9}},
-{{391},{ 9}}, {{ 71},{ 9}}, {{327},{ 9}}, {{199},{ 9}}, {{455},{ 9}},
-{{ 39},{ 9}}, {{295},{ 9}}, {{167},{ 9}}, {{423},{ 9}}, {{103},{ 9}},
-{{359},{ 9}}, {{231},{ 9}}, {{487},{ 9}}, {{ 23},{ 9}}, {{279},{ 9}},
-{{151},{ 9}}, {{407},{ 9}}, {{ 87},{ 9}}, {{343},{ 9}}, {{215},{ 9}},
-{{471},{ 9}}, {{ 55},{ 9}}, {{311},{ 9}}, {{183},{ 9}}, {{439},{ 9}},
-{{119},{ 9}}, {{375},{ 9}}, {{247},{ 9}}, {{503},{ 9}}, {{ 15},{ 9}},
-{{271},{ 9}}, {{143},{ 9}}, {{399},{ 9}}, {{ 79},{ 9}}, {{335},{ 9}},
-{{207},{ 9}}, {{463},{ 9}}, {{ 47},{ 9}}, {{303},{ 9}}, {{175},{ 9}},
-{{431},{ 9}}, {{111},{ 9}}, {{367},{ 9}}, {{239},{ 9}}, {{495},{ 9}},
-{{ 31},{ 9}}, {{287},{ 9}}, {{159},{ 9}}, {{415},{ 9}}, {{ 95},{ 9}},
-{{351},{ 9}}, {{223},{ 9}}, {{479},{ 9}}, {{ 63},{ 9}}, {{319},{ 9}},
-{{191},{ 9}}, {{447},{ 9}}, {{127},{ 9}}, {{383},{ 9}}, {{255},{ 9}},
-{{511},{ 9}}, {{ 0},{ 7}}, {{ 64},{ 7}}, {{ 32},{ 7}}, {{ 96},{ 7}},
-{{ 16},{ 7}}, {{ 80},{ 7}}, {{ 48},{ 7}}, {{112},{ 7}}, {{ 8},{ 7}},
-{{ 72},{ 7}}, {{ 40},{ 7}}, {{104},{ 7}}, {{ 24},{ 7}}, {{ 88},{ 7}},
-{{ 56},{ 7}}, {{120},{ 7}}, {{ 4},{ 7}}, {{ 68},{ 7}}, {{ 36},{ 7}},
-{{100},{ 7}}, {{ 20},{ 7}}, {{ 84},{ 7}}, {{ 52},{ 7}}, {{116},{ 7}},
-{{ 3},{ 8}}, {{131},{ 8}}, {{ 67},{ 8}}, {{195},{ 8}}, {{ 35},{ 8}},
-{{163},{ 8}}, {{ 99},{ 8}}, {{227},{ 8}}
-};
-
-local const ct_data static_dtree[D_CODES] = {
-{{ 0},{ 5}}, {{16},{ 5}}, {{ 8},{ 5}}, {{24},{ 5}}, {{ 4},{ 5}},
-{{20},{ 5}}, {{12},{ 5}}, {{28},{ 5}}, {{ 2},{ 5}}, {{18},{ 5}},
-{{10},{ 5}}, {{26},{ 5}}, {{ 6},{ 5}}, {{22},{ 5}}, {{14},{ 5}},
-{{30},{ 5}}, {{ 1},{ 5}}, {{17},{ 5}}, {{ 9},{ 5}}, {{25},{ 5}},
-{{ 5},{ 5}}, {{21},{ 5}}, {{13},{ 5}}, {{29},{ 5}}, {{ 3},{ 5}},
-{{19},{ 5}}, {{11},{ 5}}, {{27},{ 5}}, {{ 7},{ 5}}, {{23},{ 5}}
-};
-
-const uch ZLIB_INTERNAL _dist_code[DIST_CODE_LEN] = {
- 0, 1, 2, 3, 4, 4, 5, 5, 6, 6, 6, 6, 7, 7, 7, 7, 8, 8, 8, 8,
- 8, 8, 8, 8, 9, 9, 9, 9, 9, 9, 9, 9, 10, 10, 10, 10, 10, 10, 10, 10,
-10, 10, 10, 10, 10, 10, 10, 10, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11,
-11, 11, 11, 11, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12,
-12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 13, 13, 13, 13,
-13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13,
-13, 13, 13, 13, 13, 13, 13, 13, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14,
-14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14,
-14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14,
-14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 15, 15, 15, 15, 15, 15, 15, 15,
-15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15,
-15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15,
-15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 0, 0, 16, 17,
-18, 18, 19, 19, 20, 20, 20, 20, 21, 21, 21, 21, 22, 22, 22, 22, 22, 22, 22, 22,
-23, 23, 23, 23, 23, 23, 23, 23, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24,
-24, 24, 24, 24, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25,
-26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26,
-26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 27, 27, 27, 27, 27, 27, 27, 27,
-27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27,
-27, 27, 27, 27, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28,
-28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28,
-28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28,
-28, 28, 28, 28, 28, 28, 28, 28, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29,
-29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29,
-29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29,
-29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29
-};
-
-const uch ZLIB_INTERNAL _length_code[MAX_MATCH-MIN_MATCH+1]= {
- 0, 1, 2, 3, 4, 5, 6, 7, 8, 8, 9, 9, 10, 10, 11, 11, 12, 12, 12, 12,
-13, 13, 13, 13, 14, 14, 14, 14, 15, 15, 15, 15, 16, 16, 16, 16, 16, 16, 16, 16,
-17, 17, 17, 17, 17, 17, 17, 17, 18, 18, 18, 18, 18, 18, 18, 18, 19, 19, 19, 19,
-19, 19, 19, 19, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20,
-21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 22, 22, 22, 22,
-22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 23, 23, 23, 23, 23, 23, 23, 23,
-23, 23, 23, 23, 23, 23, 23, 23, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24,
-24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24,
-25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25,
-25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 26, 26, 26, 26, 26, 26, 26, 26,
-26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26,
-26, 26, 26, 26, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27,
-27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 28
-};
-
-local const int base_length[LENGTH_CODES] = {
-0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 12, 14, 16, 20, 24, 28, 32, 40, 48, 56,
-64, 80, 96, 112, 128, 160, 192, 224, 0
-};
-
-local const int base_dist[D_CODES] = {
- 0, 1, 2, 3, 4, 6, 8, 12, 16, 24,
- 32, 48, 64, 96, 128, 192, 256, 384, 512, 768,
- 1024, 1536, 2048, 3072, 4096, 6144, 8192, 12288, 16384, 24576
-};
-
diff --git a/third-party/zlib/uncompr.c b/third-party/zlib/uncompr.c
deleted file mode 100644
index 242e949..0000000
--- a/third-party/zlib/uncompr.c
+++ /dev/null
@@ -1,59 +0,0 @@
-/* uncompr.c -- decompress a memory buffer
- * Copyright (C) 1995-2003, 2010 Jean-loup Gailly.
- * For conditions of distribution and use, see copyright notice in zlib.h
- */
-
-/* @(#) $Id$ */
-
-#define ZLIB_INTERNAL
-#include "zlib.h"
-
-/* ===========================================================================
- Decompresses the source buffer into the destination buffer. sourceLen is
- the byte length of the source buffer. Upon entry, destLen is the total
- size of the destination buffer, which must be large enough to hold the
- entire uncompressed data. (The size of the uncompressed data must have
- been saved previously by the compressor and transmitted to the decompressor
- by some mechanism outside the scope of this compression library.)
- Upon exit, destLen is the actual size of the compressed buffer.
-
- uncompress returns Z_OK if success, Z_MEM_ERROR if there was not
- enough memory, Z_BUF_ERROR if there was not enough room in the output
- buffer, or Z_DATA_ERROR if the input data was corrupted.
-*/
-int ZEXPORT uncompress (dest, destLen, source, sourceLen)
- Bytef *dest;
- uLongf *destLen;
- const Bytef *source;
- uLong sourceLen;
-{
- z_stream stream;
- int err;
-
- stream.next_in = (z_const Bytef *)source;
- stream.avail_in = (uInt)sourceLen;
- /* Check for source > 64K on 16-bit machine: */
- if ((uLong)stream.avail_in != sourceLen) return Z_BUF_ERROR;
-
- stream.next_out = dest;
- stream.avail_out = (uInt)*destLen;
- if ((uLong)stream.avail_out != *destLen) return Z_BUF_ERROR;
-
- stream.zalloc = (alloc_func)0;
- stream.zfree = (free_func)0;
-
- err = inflateInit(&stream);
- if (err != Z_OK) return err;
-
- err = inflate(&stream, Z_FINISH);
- if (err != Z_STREAM_END) {
- inflateEnd(&stream);
- if (err == Z_NEED_DICT || (err == Z_BUF_ERROR && stream.avail_in == 0))
- return Z_DATA_ERROR;
- return err;
- }
- *destLen = stream.total_out;
-
- err = inflateEnd(&stream);
- return err;
-}
diff --git a/third-party/zlib/watcom/watcom_f.mak b/third-party/zlib/watcom/watcom_f.mak
deleted file mode 100644
index 37f4d74..0000000
--- a/third-party/zlib/watcom/watcom_f.mak
+++ /dev/null
@@ -1,43 +0,0 @@
-# Makefile for zlib
-# OpenWatcom flat model
-# Last updated: 28-Dec-2005
-
-# To use, do "wmake -f watcom_f.mak"
-
-C_SOURCE = adler32.c compress.c crc32.c deflate.c &
- gzclose.c gzlib.c gzread.c gzwrite.c &
- infback.c inffast.c inflate.c inftrees.c &
- trees.c uncompr.c zutil.c
-
-OBJS = adler32.obj compress.obj crc32.obj deflate.obj &
- gzclose.obj gzlib.obj gzread.obj gzwrite.obj &
- infback.obj inffast.obj inflate.obj inftrees.obj &
- trees.obj uncompr.obj zutil.obj
-
-CC = wcc386
-LINKER = wcl386
-CFLAGS = -zq -mf -3r -fp3 -s -bt=dos -oilrtfm -fr=nul -wx
-ZLIB_LIB = zlib_f.lib
-
-.C.OBJ:
- $(CC) $(CFLAGS) $[@
-
-all: $(ZLIB_LIB) example.exe minigzip.exe
-
-$(ZLIB_LIB): $(OBJS)
- wlib -b -c $(ZLIB_LIB) -+adler32.obj -+compress.obj -+crc32.obj
- wlib -b -c $(ZLIB_LIB) -+gzclose.obj -+gzlib.obj -+gzread.obj -+gzwrite.obj
- wlib -b -c $(ZLIB_LIB) -+deflate.obj -+infback.obj
- wlib -b -c $(ZLIB_LIB) -+inffast.obj -+inflate.obj -+inftrees.obj
- wlib -b -c $(ZLIB_LIB) -+trees.obj -+uncompr.obj -+zutil.obj
-
-example.exe: $(ZLIB_LIB) example.obj
- $(LINKER) -ldos32a -fe=example.exe example.obj $(ZLIB_LIB)
-
-minigzip.exe: $(ZLIB_LIB) minigzip.obj
- $(LINKER) -ldos32a -fe=minigzip.exe minigzip.obj $(ZLIB_LIB)
-
-clean: .SYMBOLIC
- del *.obj
- del $(ZLIB_LIB)
- @echo Cleaning done
diff --git a/third-party/zlib/watcom/watcom_l.mak b/third-party/zlib/watcom/watcom_l.mak
deleted file mode 100644
index 193eed7..0000000
--- a/third-party/zlib/watcom/watcom_l.mak
+++ /dev/null
@@ -1,43 +0,0 @@
-# Makefile for zlib
-# OpenWatcom large model
-# Last updated: 28-Dec-2005
-
-# To use, do "wmake -f watcom_l.mak"
-
-C_SOURCE = adler32.c compress.c crc32.c deflate.c &
- gzclose.c gzlib.c gzread.c gzwrite.c &
- infback.c inffast.c inflate.c inftrees.c &
- trees.c uncompr.c zutil.c
-
-OBJS = adler32.obj compress.obj crc32.obj deflate.obj &
- gzclose.obj gzlib.obj gzread.obj gzwrite.obj &
- infback.obj inffast.obj inflate.obj inftrees.obj &
- trees.obj uncompr.obj zutil.obj
-
-CC = wcc
-LINKER = wcl
-CFLAGS = -zq -ml -s -bt=dos -oilrtfm -fr=nul -wx
-ZLIB_LIB = zlib_l.lib
-
-.C.OBJ:
- $(CC) $(CFLAGS) $[@
-
-all: $(ZLIB_LIB) example.exe minigzip.exe
-
-$(ZLIB_LIB): $(OBJS)
- wlib -b -c $(ZLIB_LIB) -+adler32.obj -+compress.obj -+crc32.obj
- wlib -b -c $(ZLIB_LIB) -+gzclose.obj -+gzlib.obj -+gzread.obj -+gzwrite.obj
- wlib -b -c $(ZLIB_LIB) -+deflate.obj -+infback.obj
- wlib -b -c $(ZLIB_LIB) -+inffast.obj -+inflate.obj -+inftrees.obj
- wlib -b -c $(ZLIB_LIB) -+trees.obj -+uncompr.obj -+zutil.obj
-
-example.exe: $(ZLIB_LIB) example.obj
- $(LINKER) -fe=example.exe example.obj $(ZLIB_LIB)
-
-minigzip.exe: $(ZLIB_LIB) minigzip.obj
- $(LINKER) -fe=minigzip.exe minigzip.obj $(ZLIB_LIB)
-
-clean: .SYMBOLIC
- del *.obj
- del $(ZLIB_LIB)
- @echo Cleaning done
diff --git a/third-party/zlib/win32/DLL_FAQ.txt b/third-party/zlib/win32/DLL_FAQ.txt
deleted file mode 100644
index 12c0090..0000000
--- a/third-party/zlib/win32/DLL_FAQ.txt
+++ /dev/null
@@ -1,397 +0,0 @@
-
- Frequently Asked Questions about ZLIB1.DLL
-
-
-This document describes the design, the rationale, and the usage
-of the official DLL build of zlib, named ZLIB1.DLL. If you have
-general questions about zlib, you should see the file "FAQ" found
-in the zlib distribution, or at the following location:
- http://www.gzip.org/zlib/zlib_faq.html
-
-
- 1. What is ZLIB1.DLL, and how can I get it?
-
- - ZLIB1.DLL is the official build of zlib as a DLL.
- (Please remark the character '1' in the name.)
-
- Pointers to a precompiled ZLIB1.DLL can be found in the zlib
- web site at:
- http://www.zlib.net/
-
- Applications that link to ZLIB1.DLL can rely on the following
- specification:
-
- * The exported symbols are exclusively defined in the source
- files "zlib.h" and "zlib.def", found in an official zlib
- source distribution.
- * The symbols are exported by name, not by ordinal.
- * The exported names are undecorated.
- * The calling convention of functions is "C" (CDECL).
- * The ZLIB1.DLL binary is linked to MSVCRT.DLL.
-
- The archive in which ZLIB1.DLL is bundled contains compiled
- test programs that must run with a valid build of ZLIB1.DLL.
- It is recommended to download the prebuilt DLL from the zlib
- web site, instead of building it yourself, to avoid potential
- incompatibilities that could be introduced by your compiler
- and build settings. If you do build the DLL yourself, please
- make sure that it complies with all the above requirements,
- and it runs with the precompiled test programs, bundled with
- the original ZLIB1.DLL distribution.
-
- If, for any reason, you need to build an incompatible DLL,
- please use a different file name.
-
-
- 2. Why did you change the name of the DLL to ZLIB1.DLL?
- What happened to the old ZLIB.DLL?
-
- - The old ZLIB.DLL, built from zlib-1.1.4 or earlier, required
- compilation settings that were incompatible to those used by
- a static build. The DLL settings were supposed to be enabled
- by defining the macro ZLIB_DLL, before including "zlib.h".
- Incorrect handling of this macro was silently accepted at
- build time, resulting in two major problems:
-
- * ZLIB_DLL was missing from the old makefile. When building
- the DLL, not all people added it to the build options. In
- consequence, incompatible incarnations of ZLIB.DLL started
- to circulate around the net.
-
- * When switching from using the static library to using the
- DLL, applications had to define the ZLIB_DLL macro and
- to recompile all the sources that contained calls to zlib
- functions. Failure to do so resulted in creating binaries
- that were unable to run with the official ZLIB.DLL build.
-
- The only possible solution that we could foresee was to make
- a binary-incompatible change in the DLL interface, in order to
- remove the dependency on the ZLIB_DLL macro, and to release
- the new DLL under a different name.
-
- We chose the name ZLIB1.DLL, where '1' indicates the major
- zlib version number. We hope that we will not have to break
- the binary compatibility again, at least not as long as the
- zlib-1.x series will last.
-
- There is still a ZLIB_DLL macro, that can trigger a more
- efficient build and use of the DLL, but compatibility no
- longer dependents on it.
-
-
- 3. Can I build ZLIB.DLL from the new zlib sources, and replace
- an old ZLIB.DLL, that was built from zlib-1.1.4 or earlier?
-
- - In principle, you can do it by assigning calling convention
- keywords to the macros ZEXPORT and ZEXPORTVA. In practice,
- it depends on what you mean by "an old ZLIB.DLL", because the
- old DLL exists in several mutually-incompatible versions.
- You have to find out first what kind of calling convention is
- being used in your particular ZLIB.DLL build, and to use the
- same one in the new build. If you don't know what this is all
- about, you might be better off if you would just leave the old
- DLL intact.
-
-
- 4. Can I compile my application using the new zlib interface, and
- link it to an old ZLIB.DLL, that was built from zlib-1.1.4 or
- earlier?
-
- - The official answer is "no"; the real answer depends again on
- what kind of ZLIB.DLL you have. Even if you are lucky, this
- course of action is unreliable.
-
- If you rebuild your application and you intend to use a newer
- version of zlib (post- 1.1.4), it is strongly recommended to
- link it to the new ZLIB1.DLL.
-
-
- 5. Why are the zlib symbols exported by name, and not by ordinal?
-
- - Although exporting symbols by ordinal is a little faster, it
- is risky. Any single glitch in the maintenance or use of the
- DEF file that contains the ordinals can result in incompatible
- builds and frustrating crashes. Simply put, the benefits of
- exporting symbols by ordinal do not justify the risks.
-
- Technically, it should be possible to maintain ordinals in
- the DEF file, and still export the symbols by name. Ordinals
- exist in every DLL, and even if the dynamic linking performed
- at the DLL startup is searching for names, ordinals serve as
- hints, for a faster name lookup. However, if the DEF file
- contains ordinals, the Microsoft linker automatically builds
- an implib that will cause the executables linked to it to use
- those ordinals, and not the names. It is interesting to
- notice that the GNU linker for Win32 does not suffer from this
- problem.
-
- It is possible to avoid the DEF file if the exported symbols
- are accompanied by a "__declspec(dllexport)" attribute in the
- source files. You can do this in zlib by predefining the
- ZLIB_DLL macro.
-
-
- 6. I see that the ZLIB1.DLL functions use the "C" (CDECL) calling
- convention. Why not use the STDCALL convention?
- STDCALL is the standard convention in Win32, and I need it in
- my Visual Basic project!
-
- (For readability, we use CDECL to refer to the convention
- triggered by the "__cdecl" keyword, STDCALL to refer to
- the convention triggered by "__stdcall", and FASTCALL to
- refer to the convention triggered by "__fastcall".)
-
- - Most of the native Windows API functions (without varargs) use
- indeed the WINAPI convention (which translates to STDCALL in
- Win32), but the standard C functions use CDECL. If a user
- application is intrinsically tied to the Windows API (e.g.
- it calls native Windows API functions such as CreateFile()),
- sometimes it makes sense to decorate its own functions with
- WINAPI. But if ANSI C or POSIX portability is a goal (e.g.
- it calls standard C functions such as fopen()), it is not a
- sound decision to request the inclusion of <windows.h>, or to
- use non-ANSI constructs, for the sole purpose to make the user
- functions STDCALL-able.
-
- The functionality offered by zlib is not in the category of
- "Windows functionality", but is more like "C functionality".
-
- Technically, STDCALL is not bad; in fact, it is slightly
- faster than CDECL, and it works with variable-argument
- functions, just like CDECL. It is unfortunate that, in spite
- of using STDCALL in the Windows API, it is not the default
- convention used by the C compilers that run under Windows.
- The roots of the problem reside deep inside the unsafety of
- the K&R-style function prototypes, where the argument types
- are not specified; but that is another story for another day.
-
- The remaining fact is that CDECL is the default convention.
- Even if an explicit convention is hard-coded into the function
- prototypes inside C headers, problems may appear. The
- necessity to expose the convention in users' callbacks is one
- of these problems.
-
- The calling convention issues are also important when using
- zlib in other programming languages. Some of them, like Ada
- (GNAT) and Fortran (GNU G77), have C bindings implemented
- initially on Unix, and relying on the C calling convention.
- On the other hand, the pre- .NET versions of Microsoft Visual
- Basic require STDCALL, while Borland Delphi prefers, although
- it does not require, FASTCALL.
-
- In fairness to all possible uses of zlib outside the C
- programming language, we choose the default "C" convention.
- Anyone interested in different bindings or conventions is
- encouraged to maintain specialized projects. The "contrib/"
- directory from the zlib distribution already holds a couple
- of foreign bindings, such as Ada, C++, and Delphi.
-
-
- 7. I need a DLL for my Visual Basic project. What can I do?
-
- - Define the ZLIB_WINAPI macro before including "zlib.h", when
- building both the DLL and the user application (except that
- you don't need to define anything when using the DLL in Visual
- Basic). The ZLIB_WINAPI macro will switch on the WINAPI
- (STDCALL) convention. The name of this DLL must be different
- than the official ZLIB1.DLL.
-
- Gilles Vollant has contributed a build named ZLIBWAPI.DLL,
- with the ZLIB_WINAPI macro turned on, and with the minizip
- functionality built in. For more information, please read
- the notes inside "contrib/vstudio/readme.txt", found in the
- zlib distribution.
-
-
- 8. I need to use zlib in my Microsoft .NET project. What can I
- do?
-
- - Henrik Ravn has contributed a .NET wrapper around zlib. Look
- into contrib/dotzlib/, inside the zlib distribution.
-
-
- 9. If my application uses ZLIB1.DLL, should I link it to
- MSVCRT.DLL? Why?
-
- - It is not required, but it is recommended to link your
- application to MSVCRT.DLL, if it uses ZLIB1.DLL.
-
- The executables (.EXE, .DLL, etc.) that are involved in the
- same process and are using the C run-time library (i.e. they
- are calling standard C functions), must link to the same
- library. There are several libraries in the Win32 system:
- CRTDLL.DLL, MSVCRT.DLL, the static C libraries, etc.
- Since ZLIB1.DLL is linked to MSVCRT.DLL, the executables that
- depend on it should also be linked to MSVCRT.DLL.
-
-
-10. Why are you saying that ZLIB1.DLL and my application should
- be linked to the same C run-time (CRT) library? I linked my
- application and my DLLs to different C libraries (e.g. my
- application to a static library, and my DLLs to MSVCRT.DLL),
- and everything works fine.
-
- - If a user library invokes only pure Win32 API (accessible via
- <windows.h> and the related headers), its DLL build will work
- in any context. But if this library invokes standard C API,
- things get more complicated.
-
- There is a single Win32 library in a Win32 system. Every
- function in this library resides in a single DLL module, that
- is safe to call from anywhere. On the other hand, there are
- multiple versions of the C library, and each of them has its
- own separate internal state. Standalone executables and user
- DLLs that call standard C functions must link to a C run-time
- (CRT) library, be it static or shared (DLL). Intermixing
- occurs when an executable (not necessarily standalone) and a
- DLL are linked to different CRTs, and both are running in the
- same process.
-
- Intermixing multiple CRTs is possible, as long as their
- internal states are kept intact. The Microsoft Knowledge Base
- articles KB94248 "HOWTO: Use the C Run-Time" and KB140584
- "HOWTO: Link with the Correct C Run-Time (CRT) Library"
- mention the potential problems raised by intermixing.
-
- If intermixing works for you, it's because your application
- and DLLs are avoiding the corruption of each of the CRTs'
- internal states, maybe by careful design, or maybe by fortune.
-
- Also note that linking ZLIB1.DLL to non-Microsoft CRTs, such
- as those provided by Borland, raises similar problems.
-
-
-11. Why are you linking ZLIB1.DLL to MSVCRT.DLL?
-
- - MSVCRT.DLL exists on every Windows 95 with a new service pack
- installed, or with Microsoft Internet Explorer 4 or later, and
- on all other Windows 4.x or later (Windows 98, Windows NT 4,
- or later). It is freely distributable; if not present in the
- system, it can be downloaded from Microsoft or from other
- software provider for free.
-
- The fact that MSVCRT.DLL does not exist on a virgin Windows 95
- is not so problematic. Windows 95 is scarcely found nowadays,
- Microsoft ended its support a long time ago, and many recent
- applications from various vendors, including Microsoft, do not
- even run on it. Furthermore, no serious user should run
- Windows 95 without a proper update installed.
-
-
-12. Why are you not linking ZLIB1.DLL to
- <<my favorite C run-time library>> ?
-
- - We considered and abandoned the following alternatives:
-
- * Linking ZLIB1.DLL to a static C library (LIBC.LIB, or
- LIBCMT.LIB) is not a good option. People are using the DLL
- mainly to save disk space. If you are linking your program
- to a static C library, you may as well consider linking zlib
- in statically, too.
-
- * Linking ZLIB1.DLL to CRTDLL.DLL looks appealing, because
- CRTDLL.DLL is present on every Win32 installation.
- Unfortunately, it has a series of problems: it does not
- work properly with Microsoft's C++ libraries, it does not
- provide support for 64-bit file offsets, (and so on...),
- and Microsoft discontinued its support a long time ago.
-
- * Linking ZLIB1.DLL to MSVCR70.DLL or MSVCR71.DLL, supplied
- with the Microsoft .NET platform, and Visual C++ 7.0/7.1,
- raises problems related to the status of ZLIB1.DLL as a
- system component. According to the Microsoft Knowledge Base
- article KB326922 "INFO: Redistribution of the Shared C
- Runtime Component in Visual C++ .NET", MSVCR70.DLL and
- MSVCR71.DLL are not supposed to function as system DLLs,
- because they may clash with MSVCRT.DLL. Instead, the
- application's installer is supposed to put these DLLs
- (if needed) in the application's private directory.
- If ZLIB1.DLL depends on a non-system runtime, it cannot
- function as a redistributable system component.
-
- * Linking ZLIB1.DLL to non-Microsoft runtimes, such as
- Borland's, or Cygwin's, raises problems related to the
- reliable presence of these runtimes on Win32 systems.
- It's easier to let the DLL build of zlib up to the people
- who distribute these runtimes, and who may proceed as
- explained in the answer to Question 14.
-
-
-13. If ZLIB1.DLL cannot be linked to MSVCR70.DLL or MSVCR71.DLL,
- how can I build/use ZLIB1.DLL in Microsoft Visual C++ 7.0
- (Visual Studio .NET) or newer?
-
- - Due to the problems explained in the Microsoft Knowledge Base
- article KB326922 (see the previous answer), the C runtime that
- comes with the VC7 environment is no longer considered a
- system component. That is, it should not be assumed that this
- runtime exists, or may be installed in a system directory.
- Since ZLIB1.DLL is supposed to be a system component, it may
- not depend on a non-system component.
-
- In order to link ZLIB1.DLL and your application to MSVCRT.DLL
- in VC7, you need the library of Visual C++ 6.0 or older. If
- you don't have this library at hand, it's probably best not to
- use ZLIB1.DLL.
-
- We are hoping that, in the future, Microsoft will provide a
- way to build applications linked to a proper system runtime,
- from the Visual C++ environment. Until then, you have a
- couple of alternatives, such as linking zlib in statically.
- If your application requires dynamic linking, you may proceed
- as explained in the answer to Question 14.
-
-
-14. I need to link my own DLL build to a CRT different than
- MSVCRT.DLL. What can I do?
-
- - Feel free to rebuild the DLL from the zlib sources, and link
- it the way you want. You should, however, clearly state that
- your build is unofficial. You should give it a different file
- name, and/or install it in a private directory that can be
- accessed by your application only, and is not visible to the
- others (i.e. it's neither in the PATH, nor in the SYSTEM or
- SYSTEM32 directories). Otherwise, your build may clash with
- applications that link to the official build.
-
- For example, in Cygwin, zlib is linked to the Cygwin runtime
- CYGWIN1.DLL, and it is distributed under the name CYGZ.DLL.
-
-
-15. May I include additional pieces of code that I find useful,
- link them in ZLIB1.DLL, and export them?
-
- - No. A legitimate build of ZLIB1.DLL must not include code
- that does not originate from the official zlib source code.
- But you can make your own private DLL build, under a different
- file name, as suggested in the previous answer.
-
- For example, zlib is a part of the VCL library, distributed
- with Borland Delphi and C++ Builder. The DLL build of VCL
- is a redistributable file, named VCLxx.DLL.
-
-
-16. May I remove some functionality out of ZLIB1.DLL, by enabling
- macros like NO_GZCOMPRESS or NO_GZIP at compile time?
-
- - No. A legitimate build of ZLIB1.DLL must provide the complete
- zlib functionality, as implemented in the official zlib source
- code. But you can make your own private DLL build, under a
- different file name, as suggested in the previous answer.
-
-
-17. I made my own ZLIB1.DLL build. Can I test it for compliance?
-
- - We prefer that you download the official DLL from the zlib
- web site. If you need something peculiar from this DLL, you
- can send your suggestion to the zlib mailing list.
-
- However, in case you do rebuild the DLL yourself, you can run
- it with the test programs found in the DLL distribution.
- Running these test programs is not a guarantee of compliance,
- but a failure can imply a detected problem.
-
-**
-
-This document is written and maintained by
-Cosmin Truta <cosmint at cs.ubbcluj.ro>
diff --git a/third-party/zlib/win32/Makefile.bor b/third-party/zlib/win32/Makefile.bor
deleted file mode 100644
index d152bbb..0000000
--- a/third-party/zlib/win32/Makefile.bor
+++ /dev/null
@@ -1,110 +0,0 @@
-# Makefile for zlib
-# Borland C++ for Win32
-#
-# Usage:
-# make -f win32/Makefile.bor
-# make -f win32/Makefile.bor LOCAL_ZLIB=-DASMV OBJA=match.obj OBJPA=+match.obj
-
-# ------------ Borland C++ ------------
-
-# Optional nonstandard preprocessor flags (e.g. -DMAX_MEM_LEVEL=7)
-# should be added to the environment via "set LOCAL_ZLIB=-DFOO" or
-# added to the declaration of LOC here:
-LOC = $(LOCAL_ZLIB)
-
-CC = bcc32
-AS = bcc32
-LD = bcc32
-AR = tlib
-CFLAGS = -a -d -k- -O2 $(LOC)
-ASFLAGS = $(LOC)
-LDFLAGS = $(LOC)
-
-
-# variables
-ZLIB_LIB = zlib.lib
-
-OBJ1 = adler32.obj compress.obj crc32.obj deflate.obj gzclose.obj gzlib.obj gzread.obj
-OBJ2 = gzwrite.obj infback.obj inffast.obj inflate.obj inftrees.obj trees.obj uncompr.obj zutil.obj
-#OBJA =
-OBJP1 = +adler32.obj+compress.obj+crc32.obj+deflate.obj+gzclose.obj+gzlib.obj+gzread.obj
-OBJP2 = +gzwrite.obj+infback.obj+inffast.obj+inflate.obj+inftrees.obj+trees.obj+uncompr.obj+zutil.obj
-#OBJPA=
-
-
-# targets
-all: $(ZLIB_LIB) example.exe minigzip.exe
-
-.c.obj:
- $(CC) -c $(CFLAGS) $<
-
-.asm.obj:
- $(AS) -c $(ASFLAGS) $<
-
-adler32.obj: adler32.c zlib.h zconf.h
-
-compress.obj: compress.c zlib.h zconf.h
-
-crc32.obj: crc32.c zlib.h zconf.h crc32.h
-
-deflate.obj: deflate.c deflate.h zutil.h zlib.h zconf.h
-
-gzclose.obj: gzclose.c zlib.h zconf.h gzguts.h
-
-gzlib.obj: gzlib.c zlib.h zconf.h gzguts.h
-
-gzread.obj: gzread.c zlib.h zconf.h gzguts.h
-
-gzwrite.obj: gzwrite.c zlib.h zconf.h gzguts.h
-
-infback.obj: infback.c zutil.h zlib.h zconf.h inftrees.h inflate.h \
- inffast.h inffixed.h
-
-inffast.obj: inffast.c zutil.h zlib.h zconf.h inftrees.h inflate.h \
- inffast.h
-
-inflate.obj: inflate.c zutil.h zlib.h zconf.h inftrees.h inflate.h \
- inffast.h inffixed.h
-
-inftrees.obj: inftrees.c zutil.h zlib.h zconf.h inftrees.h
-
-trees.obj: trees.c zutil.h zlib.h zconf.h deflate.h trees.h
-
-uncompr.obj: uncompr.c zlib.h zconf.h
-
-zutil.obj: zutil.c zutil.h zlib.h zconf.h
-
-example.obj: test/example.c zlib.h zconf.h
-
-minigzip.obj: test/minigzip.c zlib.h zconf.h
-
-
-# For the sake of the old Borland make,
-# the command line is cut to fit in the MS-DOS 128 byte limit:
-$(ZLIB_LIB): $(OBJ1) $(OBJ2) $(OBJA)
- -del $(ZLIB_LIB)
- $(AR) $(ZLIB_LIB) $(OBJP1)
- $(AR) $(ZLIB_LIB) $(OBJP2)
- $(AR) $(ZLIB_LIB) $(OBJPA)
-
-
-# testing
-test: example.exe minigzip.exe
- example
- echo hello world | minigzip | minigzip -d
-
-example.exe: example.obj $(ZLIB_LIB)
- $(LD) $(LDFLAGS) example.obj $(ZLIB_LIB)
-
-minigzip.exe: minigzip.obj $(ZLIB_LIB)
- $(LD) $(LDFLAGS) minigzip.obj $(ZLIB_LIB)
-
-
-# cleanup
-clean:
- -del $(ZLIB_LIB)
- -del *.obj
- -del *.exe
- -del *.tds
- -del zlib.bak
- -del foo.gz
diff --git a/third-party/zlib/win32/Makefile.gcc b/third-party/zlib/win32/Makefile.gcc
deleted file mode 100644
index 6d1ded6..0000000
--- a/third-party/zlib/win32/Makefile.gcc
+++ /dev/null
@@ -1,182 +0,0 @@
-# Makefile for zlib, derived from Makefile.dj2.
-# Modified for mingw32 by C. Spieler, 6/16/98.
-# Updated for zlib 1.2.x by Christian Spieler and Cosmin Truta, Mar-2003.
-# Last updated: Mar 2012.
-# Tested under Cygwin and MinGW.
-
-# Copyright (C) 1995-2003 Jean-loup Gailly.
-# For conditions of distribution and use, see copyright notice in zlib.h
-
-# To compile, or to compile and test, type from the top level zlib directory:
-#
-# make -fwin32/Makefile.gcc; make test testdll -fwin32/Makefile.gcc
-#
-# To use the asm code, type:
-# cp contrib/asm?86/match.S ./match.S
-# make LOC=-DASMV OBJA=match.o -fwin32/Makefile.gcc
-#
-# To install libz.a, zconf.h and zlib.h in the system directories, type:
-#
-# make install -fwin32/Makefile.gcc
-#
-# BINARY_PATH, INCLUDE_PATH and LIBRARY_PATH must be set.
-#
-# To install the shared lib, append SHARED_MODE=1 to the make command :
-#
-# make install -fwin32/Makefile.gcc SHARED_MODE=1
-
-# Note:
-# If the platform is *not* MinGW (e.g. it is Cygwin or UWIN),
-# the DLL name should be changed from "zlib1.dll".
-
-STATICLIB = libz.a
-SHAREDLIB = zlib1.dll
-IMPLIB = libz.dll.a
-
-#
-# Set to 1 if shared object needs to be installed
-#
-SHARED_MODE=0
-
-#LOC = -DASMV
-#LOC = -DDEBUG -g
-
-PREFIX =
-CC = $(PREFIX)gcc
-CFLAGS = $(LOC) -O3 -Wall
-
-AS = $(CC)
-ASFLAGS = $(LOC) -Wall
-
-LD = $(CC)
-LDFLAGS = $(LOC)
-
-AR = $(PREFIX)ar
-ARFLAGS = rcs
-
-RC = $(PREFIX)windres
-RCFLAGS = --define GCC_WINDRES
-
-STRIP = $(PREFIX)strip
-
-CP = cp -fp
-# If GNU install is available, replace $(CP) with install.
-INSTALL = $(CP)
-RM = rm -f
-
-prefix ?= /usr/local
-exec_prefix = $(prefix)
-
-OBJS = adler32.o compress.o crc32.o deflate.o gzclose.o gzlib.o gzread.o \
- gzwrite.o infback.o inffast.o inflate.o inftrees.o trees.o uncompr.o zutil.o
-OBJA =
-
-all: $(STATICLIB) $(SHAREDLIB) $(IMPLIB) example.exe minigzip.exe example_d.exe minigzip_d.exe
-
-test: example.exe minigzip.exe
- ./example
- echo hello world | ./minigzip | ./minigzip -d
-
-testdll: example_d.exe minigzip_d.exe
- ./example_d
- echo hello world | ./minigzip_d | ./minigzip_d -d
-
-.c.o:
- $(CC) $(CFLAGS) -c -o $@ $<
-
-.S.o:
- $(AS) $(ASFLAGS) -c -o $@ $<
-
-$(STATICLIB): $(OBJS) $(OBJA)
- $(AR) $(ARFLAGS) $@ $(OBJS) $(OBJA)
-
-$(IMPLIB): $(SHAREDLIB)
-
-$(SHAREDLIB): win32/zlib.def $(OBJS) $(OBJA) zlibrc.o
- $(CC) -shared -Wl,--out-implib,$(IMPLIB) $(LDFLAGS) \
- -o $@ win32/zlib.def $(OBJS) $(OBJA) zlibrc.o
- $(STRIP) $@
-
-example.exe: example.o $(STATICLIB)
- $(LD) $(LDFLAGS) -o $@ example.o $(STATICLIB)
- $(STRIP) $@
-
-minigzip.exe: minigzip.o $(STATICLIB)
- $(LD) $(LDFLAGS) -o $@ minigzip.o $(STATICLIB)
- $(STRIP) $@
-
-example_d.exe: example.o $(IMPLIB)
- $(LD) $(LDFLAGS) -o $@ example.o $(IMPLIB)
- $(STRIP) $@
-
-minigzip_d.exe: minigzip.o $(IMPLIB)
- $(LD) $(LDFLAGS) -o $@ minigzip.o $(IMPLIB)
- $(STRIP) $@
-
-example.o: test/example.c zlib.h zconf.h
- $(CC) $(CFLAGS) -I. -c -o $@ test/example.c
-
-minigzip.o: test/minigzip.c zlib.h zconf.h
- $(CC) $(CFLAGS) -I. -c -o $@ test/minigzip.c
-
-zlibrc.o: win32/zlib1.rc
- $(RC) $(RCFLAGS) -o $@ win32/zlib1.rc
-
-.PHONY: install uninstall clean
-
-install: zlib.h zconf.h $(STATICLIB) $(IMPLIB)
- @if test -z "$(DESTDIR)$(INCLUDE_PATH)" -o -z "$(DESTDIR)$(LIBRARY_PATH)" -o -z "$(DESTDIR)$(BINARY_PATH)"; then \
- echo INCLUDE_PATH, LIBRARY_PATH, and BINARY_PATH must be specified; \
- exit 1; \
- fi
- - at mkdir -p '$(DESTDIR)$(INCLUDE_PATH)'
- - at mkdir -p '$(DESTDIR)$(LIBRARY_PATH)' '$(DESTDIR)$(LIBRARY_PATH)'/pkgconfig
- -if [ "$(SHARED_MODE)" = "1" ]; then \
- mkdir -p '$(DESTDIR)$(BINARY_PATH)'; \
- $(INSTALL) $(SHAREDLIB) '$(DESTDIR)$(BINARY_PATH)'; \
- $(INSTALL) $(IMPLIB) '$(DESTDIR)$(LIBRARY_PATH)'; \
- fi
- -$(INSTALL) zlib.h '$(DESTDIR)$(INCLUDE_PATH)'
- -$(INSTALL) zconf.h '$(DESTDIR)$(INCLUDE_PATH)'
- -$(INSTALL) $(STATICLIB) '$(DESTDIR)$(LIBRARY_PATH)'
- sed \
- -e 's|@prefix@|${prefix}|g' \
- -e 's|@exec_prefix@|${exec_prefix}|g' \
- -e 's|@libdir@|$(LIBRARY_PATH)|g' \
- -e 's|@sharedlibdir@|$(LIBRARY_PATH)|g' \
- -e 's|@includedir@|$(INCLUDE_PATH)|g' \
- -e 's|@VERSION@|'`sed -n -e '/VERSION "/s/.*"\(.*\)".*/\1/p' zlib.h`'|g' \
- zlib.pc.in > '$(DESTDIR)$(LIBRARY_PATH)'/pkgconfig/zlib.pc
-
-uninstall:
- -if [ "$(SHARED_MODE)" = "1" ]; then \
- $(RM) '$(DESTDIR)$(BINARY_PATH)'/$(SHAREDLIB); \
- $(RM) '$(DESTDIR)$(LIBRARY_PATH)'/$(IMPLIB); \
- fi
- -$(RM) '$(DESTDIR)$(INCLUDE_PATH)'/zlib.h
- -$(RM) '$(DESTDIR)$(INCLUDE_PATH)'/zconf.h
- -$(RM) '$(DESTDIR)$(LIBRARY_PATH)'/$(STATICLIB)
-
-clean:
- -$(RM) $(STATICLIB)
- -$(RM) $(SHAREDLIB)
- -$(RM) $(IMPLIB)
- -$(RM) *.o
- -$(RM) *.exe
- -$(RM) foo.gz
-
-adler32.o: zlib.h zconf.h
-compress.o: zlib.h zconf.h
-crc32.o: crc32.h zlib.h zconf.h
-deflate.o: deflate.h zutil.h zlib.h zconf.h
-gzclose.o: zlib.h zconf.h gzguts.h
-gzlib.o: zlib.h zconf.h gzguts.h
-gzread.o: zlib.h zconf.h gzguts.h
-gzwrite.o: zlib.h zconf.h gzguts.h
-inffast.o: zutil.h zlib.h zconf.h inftrees.h inflate.h inffast.h
-inflate.o: zutil.h zlib.h zconf.h inftrees.h inflate.h inffast.h
-infback.o: zutil.h zlib.h zconf.h inftrees.h inflate.h inffast.h
-inftrees.o: zutil.h zlib.h zconf.h inftrees.h
-trees.o: deflate.h zutil.h zlib.h zconf.h trees.h
-uncompr.o: zlib.h zconf.h
-zutil.o: zutil.h zlib.h zconf.h
diff --git a/third-party/zlib/win32/Makefile.msc b/third-party/zlib/win32/Makefile.msc
deleted file mode 100644
index 67b7731..0000000
--- a/third-party/zlib/win32/Makefile.msc
+++ /dev/null
@@ -1,163 +0,0 @@
-# Makefile for zlib using Microsoft (Visual) C
-# zlib is copyright (C) 1995-2006 Jean-loup Gailly and Mark Adler
-#
-# Usage:
-# nmake -f win32/Makefile.msc (standard build)
-# nmake -f win32/Makefile.msc LOC=-DFOO (nonstandard build)
-# nmake -f win32/Makefile.msc LOC="-DASMV -DASMINF" \
-# OBJA="inffas32.obj match686.obj" (use ASM code, x86)
-# nmake -f win32/Makefile.msc AS=ml64 LOC="-DASMV -DASMINF -I." \
-# OBJA="inffasx64.obj gvmat64.obj inffas8664.obj" (use ASM code, x64)
-
-# The toplevel directory of the source tree.
-#
-TOP = .
-
-# optional build flags
-LOC =
-
-# variables
-STATICLIB = zlib.lib
-SHAREDLIB = zlib1.dll
-IMPLIB = zdll.lib
-
-CC = cl
-AS = ml
-LD = link
-AR = lib
-RC = rc
-CFLAGS = -nologo -MD -W3 -O2 -Oy- -Zi -Fd"zlib" $(LOC)
-WFLAGS = -D_CRT_SECURE_NO_DEPRECATE -D_CRT_NONSTDC_NO_DEPRECATE
-ASFLAGS = -coff -Zi $(LOC)
-LDFLAGS = -nologo -debug -incremental:no -opt:ref
-ARFLAGS = -nologo
-RCFLAGS = /dWIN32 /r
-
-OBJS = adler32.obj compress.obj crc32.obj deflate.obj gzclose.obj gzlib.obj gzread.obj \
- gzwrite.obj infback.obj inflate.obj inftrees.obj inffast.obj trees.obj uncompr.obj zutil.obj
-OBJA =
-
-
-# targets
-all: $(STATICLIB) $(SHAREDLIB) $(IMPLIB) \
- example.exe minigzip.exe example_d.exe minigzip_d.exe
-
-$(STATICLIB): $(OBJS) $(OBJA)
- $(AR) $(ARFLAGS) -out:$@ $(OBJS) $(OBJA)
-
-$(IMPLIB): $(SHAREDLIB)
-
-$(SHAREDLIB): $(TOP)/win32/zlib.def $(OBJS) $(OBJA) zlib1.res
- $(LD) $(LDFLAGS) -def:$(TOP)/win32/zlib.def -dll -implib:$(IMPLIB) \
- -out:$@ -base:0x5A4C0000 $(OBJS) $(OBJA) zlib1.res
- if exist $@.manifest \
- mt -nologo -manifest $@.manifest -outputresource:$@;2
-
-example.exe: example.obj $(STATICLIB)
- $(LD) $(LDFLAGS) example.obj $(STATICLIB)
- if exist $@.manifest \
- mt -nologo -manifest $@.manifest -outputresource:$@;1
-
-minigzip.exe: minigzip.obj $(STATICLIB)
- $(LD) $(LDFLAGS) minigzip.obj $(STATICLIB)
- if exist $@.manifest \
- mt -nologo -manifest $@.manifest -outputresource:$@;1
-
-example_d.exe: example.obj $(IMPLIB)
- $(LD) $(LDFLAGS) -out:$@ example.obj $(IMPLIB)
- if exist $@.manifest \
- mt -nologo -manifest $@.manifest -outputresource:$@;1
-
-minigzip_d.exe: minigzip.obj $(IMPLIB)
- $(LD) $(LDFLAGS) -out:$@ minigzip.obj $(IMPLIB)
- if exist $@.manifest \
- mt -nologo -manifest $@.manifest -outputresource:$@;1
-
-{$(TOP)}.c.obj:
- $(CC) -c $(WFLAGS) $(CFLAGS) $<
-
-{$(TOP)/test}.c.obj:
- $(CC) -c -I$(TOP) $(WFLAGS) $(CFLAGS) $<
-
-{$(TOP)/contrib/masmx64}.c.obj:
- $(CC) -c $(WFLAGS) $(CFLAGS) $<
-
-{$(TOP)/contrib/masmx64}.asm.obj:
- $(AS) -c $(ASFLAGS) $<
-
-{$(TOP)/contrib/masmx86}.asm.obj:
- $(AS) -c $(ASFLAGS) $<
-
-adler32.obj: $(TOP)/adler32.c $(TOP)/zlib.h $(TOP)/zconf.h
-
-compress.obj: $(TOP)/compress.c $(TOP)/zlib.h $(TOP)/zconf.h
-
-crc32.obj: $(TOP)/crc32.c $(TOP)/zlib.h $(TOP)/zconf.h $(TOP)/crc32.h
-
-deflate.obj: $(TOP)/deflate.c $(TOP)/deflate.h $(TOP)/zutil.h $(TOP)/zlib.h $(TOP)/zconf.h
-
-gzclose.obj: $(TOP)/gzclose.c $(TOP)/zlib.h $(TOP)/zconf.h $(TOP)/gzguts.h
-
-gzlib.obj: $(TOP)/gzlib.c $(TOP)/zlib.h $(TOP)/zconf.h $(TOP)/gzguts.h
-
-gzread.obj: $(TOP)/gzread.c $(TOP)/zlib.h $(TOP)/zconf.h $(TOP)/gzguts.h
-
-gzwrite.obj: $(TOP)/gzwrite.c $(TOP)/zlib.h $(TOP)/zconf.h $(TOP)/gzguts.h
-
-infback.obj: $(TOP)/infback.c $(TOP)/zutil.h $(TOP)/zlib.h $(TOP)/zconf.h $(TOP)/inftrees.h $(TOP)/inflate.h \
- $(TOP)/inffast.h $(TOP)/inffixed.h
-
-inffast.obj: $(TOP)/inffast.c $(TOP)/zutil.h $(TOP)/zlib.h $(TOP)/zconf.h $(TOP)/inftrees.h $(TOP)/inflate.h \
- $(TOP)/inffast.h
-
-inflate.obj: $(TOP)/inflate.c $(TOP)/zutil.h $(TOP)/zlib.h $(TOP)/zconf.h $(TOP)/inftrees.h $(TOP)/inflate.h \
- $(TOP)/inffast.h $(TOP)/inffixed.h
-
-inftrees.obj: $(TOP)/inftrees.c $(TOP)/zutil.h $(TOP)/zlib.h $(TOP)/zconf.h $(TOP)/inftrees.h
-
-trees.obj: $(TOP)/trees.c $(TOP)/zutil.h $(TOP)/zlib.h $(TOP)/zconf.h $(TOP)/deflate.h $(TOP)/trees.h
-
-uncompr.obj: $(TOP)/uncompr.c $(TOP)/zlib.h $(TOP)/zconf.h
-
-zutil.obj: $(TOP)/zutil.c $(TOP)/zutil.h $(TOP)/zlib.h $(TOP)/zconf.h
-
-gvmat64.obj: $(TOP)/contrib\masmx64\gvmat64.asm
-
-inffasx64.obj: $(TOP)/contrib\masmx64\inffasx64.asm
-
-inffas8664.obj: $(TOP)/contrib\masmx64\inffas8664.c $(TOP)/zutil.h $(TOP)/zlib.h $(TOP)/zconf.h \
- $(TOP)/inftrees.h $(TOP)/inflate.h $(TOP)/inffast.h
-
-inffas32.obj: $(TOP)/contrib\masmx86\inffas32.asm
-
-match686.obj: $(TOP)/contrib\masmx86\match686.asm
-
-example.obj: $(TOP)/test/example.c $(TOP)/zlib.h $(TOP)/zconf.h
-
-minigzip.obj: $(TOP)/test/minigzip.c $(TOP)/zlib.h $(TOP)/zconf.h
-
-zlib1.res: $(TOP)/win32/zlib1.rc
- $(RC) $(RCFLAGS) /fo$@ $(TOP)/win32/zlib1.rc
-
-# testing
-test: example.exe minigzip.exe
- example
- echo hello world | minigzip | minigzip -d
-
-testdll: example_d.exe minigzip_d.exe
- example_d
- echo hello world | minigzip_d | minigzip_d -d
-
-
-# cleanup
-clean:
- -del $(STATICLIB)
- -del $(SHAREDLIB)
- -del $(IMPLIB)
- -del *.obj
- -del *.res
- -del *.exp
- -del *.exe
- -del *.pdb
- -del *.manifest
- -del foo.gz
diff --git a/third-party/zlib/win32/README-WIN32.txt b/third-party/zlib/win32/README-WIN32.txt
deleted file mode 100644
index 3d77d52..0000000
--- a/third-party/zlib/win32/README-WIN32.txt
+++ /dev/null
@@ -1,103 +0,0 @@
-ZLIB DATA COMPRESSION LIBRARY
-
-zlib 1.2.8 is a general purpose data compression library. All the code is
-thread safe. The data format used by the zlib library is described by RFCs
-(Request for Comments) 1950 to 1952 in the files
-http://www.ietf.org/rfc/rfc1950.txt (zlib format), rfc1951.txt (deflate format)
-and rfc1952.txt (gzip format).
-
-All functions of the compression library are documented in the file zlib.h
-(volunteer to write man pages welcome, contact zlib at gzip.org). Two compiled
-examples are distributed in this package, example and minigzip. The example_d
-and minigzip_d flavors validate that the zlib1.dll file is working correctly.
-
-Questions about zlib should be sent to <zlib at gzip.org>. The zlib home page
-is http://zlib.net/ . Before reporting a problem, please check this site to
-verify that you have the latest version of zlib; otherwise get the latest
-version and check whether the problem still exists or not.
-
-PLEASE read DLL_FAQ.txt, and the the zlib FAQ http://zlib.net/zlib_faq.html
-before asking for help.
-
-
-Manifest:
-
-The package zlib-1.2.8-win32-x86.zip will contain the following files:
-
- README-WIN32.txt This document
- ChangeLog Changes since previous zlib packages
- DLL_FAQ.txt Frequently asked questions about zlib1.dll
- zlib.3.pdf Documentation of this library in Adobe Acrobat format
-
- example.exe A statically-bound example (using zlib.lib, not the dll)
- example.pdb Symbolic information for debugging example.exe
-
- example_d.exe A zlib1.dll bound example (using zdll.lib)
- example_d.pdb Symbolic information for debugging example_d.exe
-
- minigzip.exe A statically-bound test program (using zlib.lib, not the dll)
- minigzip.pdb Symbolic information for debugging minigzip.exe
-
- minigzip_d.exe A zlib1.dll bound test program (using zdll.lib)
- minigzip_d.pdb Symbolic information for debugging minigzip_d.exe
-
- zlib.h Install these files into the compilers' INCLUDE path to
- zconf.h compile programs which use zlib.lib or zdll.lib
-
- zdll.lib Install these files into the compilers' LIB path if linking
- zdll.exp a compiled program to the zlib1.dll binary
-
- zlib.lib Install these files into the compilers' LIB path to link zlib
- zlib.pdb into compiled programs, without zlib1.dll runtime dependency
- (zlib.pdb provides debugging info to the compile time linker)
-
- zlib1.dll Install this binary shared library into the system PATH, or
- the program's runtime directory (where the .exe resides)
- zlib1.pdb Install in the same directory as zlib1.dll, in order to debug
- an application crash using WinDbg or similar tools.
-
-All .pdb files above are entirely optional, but are very useful to a developer
-attempting to diagnose program misbehavior or a crash. Many additional
-important files for developers can be found in the zlib127.zip source package
-available from http://zlib.net/ - review that package's README file for details.
-
-
-Acknowledgments:
-
-The deflate format used by zlib was defined by Phil Katz. The deflate and
-zlib specifications were written by L. Peter Deutsch. Thanks to all the
-people who reported problems and suggested various improvements in zlib; they
-are too numerous to cite here.
-
-
-Copyright notice:
-
- (C) 1995-2012 Jean-loup Gailly and Mark Adler
-
- This software is provided 'as-is', without any express or implied
- warranty. In no event will the authors be held liable for any damages
- arising from the use of this software.
-
- Permission is granted to anyone to use this software for any purpose,
- including commercial applications, and to alter it and redistribute it
- freely, subject to the following restrictions:
-
- 1. The origin of this software must not be misrepresented; you must not
- claim that you wrote the original software. If you use this software
- in a product, an acknowledgment in the product documentation would be
- appreciated but is not required.
- 2. Altered source versions must be plainly marked as such, and must not be
- misrepresented as being the original software.
- 3. This notice may not be removed or altered from any source distribution.
-
- Jean-loup Gailly Mark Adler
- jloup at gzip.org madler at alumni.caltech.edu
-
-If you use the zlib library in a product, we would appreciate *not* receiving
-lengthy legal documents to sign. The sources are provided for free but without
-warranty of any kind. The library has been entirely written by Jean-loup
-Gailly and Mark Adler; it does not include third-party code.
-
-If you redistribute modified sources, we would appreciate that you include in
-the file ChangeLog history information documenting your changes. Please read
-the FAQ for more information on the distribution of modified source versions.
diff --git a/third-party/zlib/win32/VisualC.txt b/third-party/zlib/win32/VisualC.txt
deleted file mode 100644
index 579a5fc..0000000
--- a/third-party/zlib/win32/VisualC.txt
+++ /dev/null
@@ -1,3 +0,0 @@
-
-To build zlib using the Microsoft Visual C++ environment,
-use the appropriate project from the projects/ directory.
diff --git a/third-party/zlib/win32/zlib.def b/third-party/zlib/win32/zlib.def
deleted file mode 100644
index face655..0000000
--- a/third-party/zlib/win32/zlib.def
+++ /dev/null
@@ -1,86 +0,0 @@
-; zlib data compression library
-EXPORTS
-; basic functions
- zlibVersion
- deflate
- deflateEnd
- inflate
- inflateEnd
-; advanced functions
- deflateSetDictionary
- deflateCopy
- deflateReset
- deflateParams
- deflateTune
- deflateBound
- deflatePending
- deflatePrime
- deflateSetHeader
- inflateSetDictionary
- inflateGetDictionary
- inflateSync
- inflateCopy
- inflateReset
- inflateReset2
- inflatePrime
- inflateMark
- inflateGetHeader
- inflateBack
- inflateBackEnd
- zlibCompileFlags
-; utility functions
- compress
- compress2
- compressBound
- uncompress
- gzopen
- gzdopen
- gzbuffer
- gzsetparams
- gzread
- gzwrite
- gzprintf
- gzvprintf
- gzputs
- gzgets
- gzputc
- gzgetc
- gzungetc
- gzflush
- gzseek
- gzrewind
- gztell
- gzoffset
- gzeof
- gzdirect
- gzclose
- gzclose_r
- gzclose_w
- gzerror
- gzclearerr
-; large file functions
- gzopen64
- gzseek64
- gztell64
- gzoffset64
- adler32_combine64
- crc32_combine64
-; checksum functions
- adler32
- crc32
- adler32_combine
- crc32_combine
-; various hacks, don't look :)
- deflateInit_
- deflateInit2_
- inflateInit_
- inflateInit2_
- inflateBackInit_
- gzgetc_
- zError
- inflateSyncPoint
- get_crc_table
- inflateUndermine
- inflateResetKeep
- deflateResetKeep
- gzopen_w
diff --git a/third-party/zlib/win32/zlib1.rc b/third-party/zlib/win32/zlib1.rc
deleted file mode 100644
index 5c0feed..0000000
--- a/third-party/zlib/win32/zlib1.rc
+++ /dev/null
@@ -1,40 +0,0 @@
-#include <winver.h>
-#include "../zlib.h"
-
-#ifdef GCC_WINDRES
-VS_VERSION_INFO VERSIONINFO
-#else
-VS_VERSION_INFO VERSIONINFO MOVEABLE IMPURE LOADONCALL DISCARDABLE
-#endif
- FILEVERSION ZLIB_VER_MAJOR,ZLIB_VER_MINOR,ZLIB_VER_REVISION,0
- PRODUCTVERSION ZLIB_VER_MAJOR,ZLIB_VER_MINOR,ZLIB_VER_REVISION,0
- FILEFLAGSMASK VS_FFI_FILEFLAGSMASK
-#ifdef _DEBUG
- FILEFLAGS 1
-#else
- FILEFLAGS 0
-#endif
- FILEOS VOS__WINDOWS32
- FILETYPE VFT_DLL
- FILESUBTYPE 0 // not used
-BEGIN
- BLOCK "StringFileInfo"
- BEGIN
- BLOCK "040904E4"
- //language ID = U.S. English, char set = Windows, Multilingual
- BEGIN
- VALUE "FileDescription", "zlib data compression library\0"
- VALUE "FileVersion", ZLIB_VERSION "\0"
- VALUE "InternalName", "zlib1.dll\0"
- VALUE "LegalCopyright", "(C) 1995-2013 Jean-loup Gailly & Mark Adler\0"
- VALUE "OriginalFilename", "zlib1.dll\0"
- VALUE "ProductName", "zlib\0"
- VALUE "ProductVersion", ZLIB_VERSION "\0"
- VALUE "Comments", "For more information visit http://www.zlib.net/\0"
- END
- END
- BLOCK "VarFileInfo"
- BEGIN
- VALUE "Translation", 0x0409, 1252
- END
-END
diff --git a/third-party/zlib/zconf.h.cmakein b/third-party/zlib/zconf.h.cmakein
deleted file mode 100644
index 043019c..0000000
--- a/third-party/zlib/zconf.h.cmakein
+++ /dev/null
@@ -1,513 +0,0 @@
-/* zconf.h -- configuration of the zlib compression library
- * Copyright (C) 1995-2013 Jean-loup Gailly.
- * For conditions of distribution and use, see copyright notice in zlib.h
- */
-
-/* @(#) $Id$ */
-
-#ifndef ZCONF_H
-#define ZCONF_H
-#cmakedefine Z_PREFIX
-#cmakedefine Z_HAVE_UNISTD_H
-
-/*
- * If you *really* need a unique prefix for all types and library functions,
- * compile with -DZ_PREFIX. The "standard" zlib should be compiled without it.
- * Even better than compiling with -DZ_PREFIX would be to use configure to set
- * this permanently in zconf.h using "./configure --zprefix".
- */
-#ifdef Z_PREFIX /* may be set to #if 1 by ./configure */
-# define Z_PREFIX_SET
-
-/* all linked symbols */
-# define _dist_code z__dist_code
-# define _length_code z__length_code
-# define _tr_align z__tr_align
-# define _tr_flush_bits z__tr_flush_bits
-# define _tr_flush_block z__tr_flush_block
-# define _tr_init z__tr_init
-# define _tr_stored_block z__tr_stored_block
-# define _tr_tally z__tr_tally
-# define adler32 z_adler32
-# define adler32_combine z_adler32_combine
-# define adler32_combine64 z_adler32_combine64
-# ifndef Z_SOLO
-# define compress z_compress
-# define compress2 z_compress2
-# define compressBound z_compressBound
-# endif
-# define crc32 z_crc32
-# define crc32_combine z_crc32_combine
-# define crc32_combine64 z_crc32_combine64
-# define deflate z_deflate
-# define deflateBound z_deflateBound
-# define deflateCopy z_deflateCopy
-# define deflateEnd z_deflateEnd
-# define deflateInit2_ z_deflateInit2_
-# define deflateInit_ z_deflateInit_
-# define deflateParams z_deflateParams
-# define deflatePending z_deflatePending
-# define deflatePrime z_deflatePrime
-# define deflateReset z_deflateReset
-# define deflateResetKeep z_deflateResetKeep
-# define deflateSetDictionary z_deflateSetDictionary
-# define deflateSetHeader z_deflateSetHeader
-# define deflateTune z_deflateTune
-# define deflate_copyright z_deflate_copyright
-# define get_crc_table z_get_crc_table
-# ifndef Z_SOLO
-# define gz_error z_gz_error
-# define gz_intmax z_gz_intmax
-# define gz_strwinerror z_gz_strwinerror
-# define gzbuffer z_gzbuffer
-# define gzclearerr z_gzclearerr
-# define gzclose z_gzclose
-# define gzclose_r z_gzclose_r
-# define gzclose_w z_gzclose_w
-# define gzdirect z_gzdirect
-# define gzdopen z_gzdopen
-# define gzeof z_gzeof
-# define gzerror z_gzerror
-# define gzflush z_gzflush
-# define gzgetc z_gzgetc
-# define gzgetc_ z_gzgetc_
-# define gzgets z_gzgets
-# define gzoffset z_gzoffset
-# define gzoffset64 z_gzoffset64
-# define gzopen z_gzopen
-# define gzopen64 z_gzopen64
-# ifdef _WIN32
-# define gzopen_w z_gzopen_w
-# endif
-# define gzprintf z_gzprintf
-# define gzvprintf z_gzvprintf
-# define gzputc z_gzputc
-# define gzputs z_gzputs
-# define gzread z_gzread
-# define gzrewind z_gzrewind
-# define gzseek z_gzseek
-# define gzseek64 z_gzseek64
-# define gzsetparams z_gzsetparams
-# define gztell z_gztell
-# define gztell64 z_gztell64
-# define gzungetc z_gzungetc
-# define gzwrite z_gzwrite
-# endif
-# define inflate z_inflate
-# define inflateBack z_inflateBack
-# define inflateBackEnd z_inflateBackEnd
-# define inflateBackInit_ z_inflateBackInit_
-# define inflateCopy z_inflateCopy
-# define inflateEnd z_inflateEnd
-# define inflateGetHeader z_inflateGetHeader
-# define inflateInit2_ z_inflateInit2_
-# define inflateInit_ z_inflateInit_
-# define inflateMark z_inflateMark
-# define inflatePrime z_inflatePrime
-# define inflateReset z_inflateReset
-# define inflateReset2 z_inflateReset2
-# define inflateSetDictionary z_inflateSetDictionary
-# define inflateGetDictionary z_inflateGetDictionary
-# define inflateSync z_inflateSync
-# define inflateSyncPoint z_inflateSyncPoint
-# define inflateUndermine z_inflateUndermine
-# define inflateResetKeep z_inflateResetKeep
-# define inflate_copyright z_inflate_copyright
-# define inflate_fast z_inflate_fast
-# define inflate_table z_inflate_table
-# ifndef Z_SOLO
-# define uncompress z_uncompress
-# endif
-# define zError z_zError
-# ifndef Z_SOLO
-# define zcalloc z_zcalloc
-# define zcfree z_zcfree
-# endif
-# define zlibCompileFlags z_zlibCompileFlags
-# define zlibVersion z_zlibVersion
-
-/* all zlib typedefs in zlib.h and zconf.h */
-# define Byte z_Byte
-# define Bytef z_Bytef
-# define alloc_func z_alloc_func
-# define charf z_charf
-# define free_func z_free_func
-# ifndef Z_SOLO
-# define gzFile z_gzFile
-# endif
-# define gz_header z_gz_header
-# define gz_headerp z_gz_headerp
-# define in_func z_in_func
-# define intf z_intf
-# define out_func z_out_func
-# define uInt z_uInt
-# define uIntf z_uIntf
-# define uLong z_uLong
-# define uLongf z_uLongf
-# define voidp z_voidp
-# define voidpc z_voidpc
-# define voidpf z_voidpf
-
-/* all zlib structs in zlib.h and zconf.h */
-# define gz_header_s z_gz_header_s
-# define internal_state z_internal_state
-
-#endif
-
-#if defined(__MSDOS__) && !defined(MSDOS)
-# define MSDOS
-#endif
-#if (defined(OS_2) || defined(__OS2__)) && !defined(OS2)
-# define OS2
-#endif
-#if defined(_WINDOWS) && !defined(WINDOWS)
-# define WINDOWS
-#endif
-#if defined(_WIN32) || defined(_WIN32_WCE) || defined(__WIN32__)
-# ifndef WIN32
-# define WIN32
-# endif
-#endif
-#if (defined(MSDOS) || defined(OS2) || defined(WINDOWS)) && !defined(WIN32)
-# if !defined(__GNUC__) && !defined(__FLAT__) && !defined(__386__)
-# ifndef SYS16BIT
-# define SYS16BIT
-# endif
-# endif
-#endif
-
-/*
- * Compile with -DMAXSEG_64K if the alloc function cannot allocate more
- * than 64k bytes at a time (needed on systems with 16-bit int).
- */
-#ifdef SYS16BIT
-# define MAXSEG_64K
-#endif
-#ifdef MSDOS
-# define UNALIGNED_OK
-#endif
-
-#ifdef __STDC_VERSION__
-# ifndef STDC
-# define STDC
-# endif
-# if __STDC_VERSION__ >= 199901L
-# ifndef STDC99
-# define STDC99
-# endif
-# endif
-#endif
-#if !defined(STDC) && (defined(__STDC__) || defined(__cplusplus))
-# define STDC
-#endif
-#if !defined(STDC) && (defined(__GNUC__) || defined(__BORLANDC__))
-# define STDC
-#endif
-#if !defined(STDC) && (defined(MSDOS) || defined(WINDOWS) || defined(WIN32))
-# define STDC
-#endif
-#if !defined(STDC) && (defined(OS2) || defined(__HOS_AIX__))
-# define STDC
-#endif
-
-#if defined(__OS400__) && !defined(STDC) /* iSeries (formerly AS/400). */
-# define STDC
-#endif
-
-#ifndef STDC
-# ifndef const /* cannot use !defined(STDC) && !defined(const) on Mac */
-# define const /* note: need a more gentle solution here */
-# endif
-#endif
-
-#if defined(ZLIB_CONST) && !defined(z_const)
-# define z_const const
-#else
-# define z_const
-#endif
-
-/* Some Mac compilers merge all .h files incorrectly: */
-#if defined(__MWERKS__)||defined(applec)||defined(THINK_C)||defined(__SC__)
-# define NO_DUMMY_DECL
-#endif
-
-/* Maximum value for memLevel in deflateInit2 */
-#ifndef MAX_MEM_LEVEL
-# ifdef MAXSEG_64K
-# define MAX_MEM_LEVEL 8
-# else
-# define MAX_MEM_LEVEL 9
-# endif
-#endif
-
-/* Maximum value for windowBits in deflateInit2 and inflateInit2.
- * WARNING: reducing MAX_WBITS makes minigzip unable to extract .gz files
- * created by gzip. (Files created by minigzip can still be extracted by
- * gzip.)
- */
-#ifndef MAX_WBITS
-# define MAX_WBITS 15 /* 32K LZ77 window */
-#endif
-
-/* The memory requirements for deflate are (in bytes):
- (1 << (windowBits+2)) + (1 << (memLevel+9))
- that is: 128K for windowBits=15 + 128K for memLevel = 8 (default values)
- plus a few kilobytes for small objects. For example, if you want to reduce
- the default memory requirements from 256K to 128K, compile with
- make CFLAGS="-O -DMAX_WBITS=14 -DMAX_MEM_LEVEL=7"
- Of course this will generally degrade compression (there's no free lunch).
-
- The memory requirements for inflate are (in bytes) 1 << windowBits
- that is, 32K for windowBits=15 (default value) plus a few kilobytes
- for small objects.
-*/
-
- /* Type declarations */
-
-#ifndef OF /* function prototypes */
-# ifdef STDC
-# define OF(args) args
-# else
-# define OF(args) ()
-# endif
-#endif
-
-#ifndef Z_ARG /* function prototypes for stdarg */
-# if defined(STDC) || defined(Z_HAVE_STDARG_H)
-# define Z_ARG(args) args
-# else
-# define Z_ARG(args) ()
-# endif
-#endif
-
-/* The following definitions for FAR are needed only for MSDOS mixed
- * model programming (small or medium model with some far allocations).
- * This was tested only with MSC; for other MSDOS compilers you may have
- * to define NO_MEMCPY in zutil.h. If you don't need the mixed model,
- * just define FAR to be empty.
- */
-#ifdef SYS16BIT
-# if defined(M_I86SM) || defined(M_I86MM)
- /* MSC small or medium model */
-# define SMALL_MEDIUM
-# ifdef _MSC_VER
-# define FAR _far
-# else
-# define FAR far
-# endif
-# endif
-# if (defined(__SMALL__) || defined(__MEDIUM__))
- /* Turbo C small or medium model */
-# define SMALL_MEDIUM
-# ifdef __BORLANDC__
-# define FAR _far
-# else
-# define FAR far
-# endif
-# endif
-#endif
-
-#if defined(WINDOWS) || defined(WIN32)
- /* If building or using zlib as a DLL, define ZLIB_DLL.
- * This is not mandatory, but it offers a little performance increase.
- */
-# ifdef ZLIB_DLL
-# if defined(WIN32) && (!defined(__BORLANDC__) || (__BORLANDC__ >= 0x500))
-# ifdef ZLIB_INTERNAL
-# define ZEXTERN extern __declspec(dllexport)
-# else
-# define ZEXTERN extern __declspec(dllimport)
-# endif
-# endif
-# endif /* ZLIB_DLL */
- /* If building or using zlib with the WINAPI/WINAPIV calling convention,
- * define ZLIB_WINAPI.
- * Caution: the standard ZLIB1.DLL is NOT compiled using ZLIB_WINAPI.
- */
-# ifdef ZLIB_WINAPI
-# ifdef FAR
-# undef FAR
-# endif
-# include <windows.h>
- /* No need for _export, use ZLIB.DEF instead. */
- /* For complete Windows compatibility, use WINAPI, not __stdcall. */
-# define ZEXPORT WINAPI
-# ifdef WIN32
-# define ZEXPORTVA WINAPIV
-# else
-# define ZEXPORTVA FAR CDECL
-# endif
-# endif
-#endif
-
-#if defined (__BEOS__)
-# ifdef ZLIB_DLL
-# ifdef ZLIB_INTERNAL
-# define ZEXPORT __declspec(dllexport)
-# define ZEXPORTVA __declspec(dllexport)
-# else
-# define ZEXPORT __declspec(dllimport)
-# define ZEXPORTVA __declspec(dllimport)
-# endif
-# endif
-#endif
-
-#ifndef ZEXTERN
-# define ZEXTERN extern
-#endif
-#ifndef ZEXPORT
-# define ZEXPORT
-#endif
-#ifndef ZEXPORTVA
-# define ZEXPORTVA
-#endif
-
-#ifndef FAR
-# define FAR
-#endif
-
-#if !defined(__MACTYPES__)
-typedef unsigned char Byte; /* 8 bits */
-#endif
-typedef unsigned int uInt; /* 16 bits or more */
-typedef unsigned long uLong; /* 32 bits or more */
-
-#ifdef SMALL_MEDIUM
- /* Borland C/C++ and some old MSC versions ignore FAR inside typedef */
-# define Bytef Byte FAR
-#else
- typedef Byte FAR Bytef;
-#endif
-typedef char FAR charf;
-typedef int FAR intf;
-typedef uInt FAR uIntf;
-typedef uLong FAR uLongf;
-
-#ifdef STDC
- typedef void const *voidpc;
- typedef void FAR *voidpf;
- typedef void *voidp;
-#else
- typedef Byte const *voidpc;
- typedef Byte FAR *voidpf;
- typedef Byte *voidp;
-#endif
-
-#if !defined(Z_U4) && !defined(Z_SOLO) && defined(STDC)
-# include <limits.h>
-# if (UINT_MAX == 0xffffffffUL)
-# define Z_U4 unsigned
-# elif (ULONG_MAX == 0xffffffffUL)
-# define Z_U4 unsigned long
-# elif (USHRT_MAX == 0xffffffffUL)
-# define Z_U4 unsigned short
-# endif
-#endif
-
-#ifdef Z_U4
- typedef Z_U4 z_crc_t;
-#else
- typedef unsigned long z_crc_t;
-#endif
-
-#ifdef HAVE_UNISTD_H /* may be set to #if 1 by ./configure */
-# define Z_HAVE_UNISTD_H
-#endif
-
-#ifdef HAVE_STDARG_H /* may be set to #if 1 by ./configure */
-# define Z_HAVE_STDARG_H
-#endif
-
-#ifdef STDC
-# ifndef Z_SOLO
-# include <sys/types.h> /* for off_t */
-# endif
-#endif
-
-#if defined(STDC) || defined(Z_HAVE_STDARG_H)
-# ifndef Z_SOLO
-# include <stdarg.h> /* for va_list */
-# endif
-#endif
-
-#ifdef _WIN32
-# ifndef Z_SOLO
-# include <stddef.h> /* for wchar_t */
-# endif
-#endif
-
-/* a little trick to accommodate both "#define _LARGEFILE64_SOURCE" and
- * "#define _LARGEFILE64_SOURCE 1" as requesting 64-bit operations, (even
- * though the former does not conform to the LFS document), but considering
- * both "#undef _LARGEFILE64_SOURCE" and "#define _LARGEFILE64_SOURCE 0" as
- * equivalently requesting no 64-bit operations
- */
-#if defined(_LARGEFILE64_SOURCE) && -_LARGEFILE64_SOURCE - -1 == 1
-# undef _LARGEFILE64_SOURCE
-#endif
-
-#if defined(__WATCOMC__) && !defined(Z_HAVE_UNISTD_H)
-# define Z_HAVE_UNISTD_H
-#endif
-#ifndef Z_SOLO
-# if defined(Z_HAVE_UNISTD_H) || defined(_LARGEFILE64_SOURCE)
-# include <unistd.h> /* for SEEK_*, off_t, and _LFS64_LARGEFILE */
-# ifdef VMS
-# include <unixio.h> /* for off_t */
-# endif
-# ifndef z_off_t
-# define z_off_t off_t
-# endif
-# endif
-#endif
-
-#if defined(_LFS64_LARGEFILE) && _LFS64_LARGEFILE-0
-# define Z_LFS64
-#endif
-
-#if defined(_LARGEFILE64_SOURCE) && defined(Z_LFS64)
-# define Z_LARGE64
-#endif
-
-#if defined(_FILE_OFFSET_BITS) && _FILE_OFFSET_BITS-0 == 64 && defined(Z_LFS64)
-# define Z_WANT64
-#endif
-
-#if !defined(SEEK_SET) && !defined(Z_SOLO)
-# define SEEK_SET 0 /* Seek from beginning of file. */
-# define SEEK_CUR 1 /* Seek from current position. */
-# define SEEK_END 2 /* Set file pointer to EOF plus "offset" */
-#endif
-
-#ifndef z_off_t
-# define z_off_t long
-#endif
-
-#if !defined(_WIN32) && defined(Z_LARGE64)
-# define z_off64_t off64_t
-#else
-# if defined(_WIN32) && !defined(__GNUC__) && !defined(Z_SOLO)
-# define z_off64_t __int64
-# else
-# define z_off64_t z_off_t
-# endif
-#endif
-
-/* MVS linker does not support external names larger than 8 bytes */
-#if defined(__MVS__)
- #pragma map(deflateInit_,"DEIN")
- #pragma map(deflateInit2_,"DEIN2")
- #pragma map(deflateEnd,"DEEND")
- #pragma map(deflateBound,"DEBND")
- #pragma map(inflateInit_,"ININ")
- #pragma map(inflateInit2_,"ININ2")
- #pragma map(inflateEnd,"INEND")
- #pragma map(inflateSync,"INSY")
- #pragma map(inflateSetDictionary,"INSEDI")
- #pragma map(compressBound,"CMBND")
- #pragma map(inflate_table,"INTABL")
- #pragma map(inflate_fast,"INFA")
- #pragma map(inflate_copyright,"INCOPY")
-#endif
-
-#endif /* ZCONF_H */
diff --git a/third-party/zlib/zconf.h.in b/third-party/zlib/zconf.h.in
deleted file mode 100644
index 9987a77..0000000
--- a/third-party/zlib/zconf.h.in
+++ /dev/null
@@ -1,511 +0,0 @@
-/* zconf.h -- configuration of the zlib compression library
- * Copyright (C) 1995-2013 Jean-loup Gailly.
- * For conditions of distribution and use, see copyright notice in zlib.h
- */
-
-/* @(#) $Id$ */
-
-#ifndef ZCONF_H
-#define ZCONF_H
-
-/*
- * If you *really* need a unique prefix for all types and library functions,
- * compile with -DZ_PREFIX. The "standard" zlib should be compiled without it.
- * Even better than compiling with -DZ_PREFIX would be to use configure to set
- * this permanently in zconf.h using "./configure --zprefix".
- */
-#ifdef Z_PREFIX /* may be set to #if 1 by ./configure */
-# define Z_PREFIX_SET
-
-/* all linked symbols */
-# define _dist_code z__dist_code
-# define _length_code z__length_code
-# define _tr_align z__tr_align
-# define _tr_flush_bits z__tr_flush_bits
-# define _tr_flush_block z__tr_flush_block
-# define _tr_init z__tr_init
-# define _tr_stored_block z__tr_stored_block
-# define _tr_tally z__tr_tally
-# define adler32 z_adler32
-# define adler32_combine z_adler32_combine
-# define adler32_combine64 z_adler32_combine64
-# ifndef Z_SOLO
-# define compress z_compress
-# define compress2 z_compress2
-# define compressBound z_compressBound
-# endif
-# define crc32 z_crc32
-# define crc32_combine z_crc32_combine
-# define crc32_combine64 z_crc32_combine64
-# define deflate z_deflate
-# define deflateBound z_deflateBound
-# define deflateCopy z_deflateCopy
-# define deflateEnd z_deflateEnd
-# define deflateInit2_ z_deflateInit2_
-# define deflateInit_ z_deflateInit_
-# define deflateParams z_deflateParams
-# define deflatePending z_deflatePending
-# define deflatePrime z_deflatePrime
-# define deflateReset z_deflateReset
-# define deflateResetKeep z_deflateResetKeep
-# define deflateSetDictionary z_deflateSetDictionary
-# define deflateSetHeader z_deflateSetHeader
-# define deflateTune z_deflateTune
-# define deflate_copyright z_deflate_copyright
-# define get_crc_table z_get_crc_table
-# ifndef Z_SOLO
-# define gz_error z_gz_error
-# define gz_intmax z_gz_intmax
-# define gz_strwinerror z_gz_strwinerror
-# define gzbuffer z_gzbuffer
-# define gzclearerr z_gzclearerr
-# define gzclose z_gzclose
-# define gzclose_r z_gzclose_r
-# define gzclose_w z_gzclose_w
-# define gzdirect z_gzdirect
-# define gzdopen z_gzdopen
-# define gzeof z_gzeof
-# define gzerror z_gzerror
-# define gzflush z_gzflush
-# define gzgetc z_gzgetc
-# define gzgetc_ z_gzgetc_
-# define gzgets z_gzgets
-# define gzoffset z_gzoffset
-# define gzoffset64 z_gzoffset64
-# define gzopen z_gzopen
-# define gzopen64 z_gzopen64
-# ifdef _WIN32
-# define gzopen_w z_gzopen_w
-# endif
-# define gzprintf z_gzprintf
-# define gzvprintf z_gzvprintf
-# define gzputc z_gzputc
-# define gzputs z_gzputs
-# define gzread z_gzread
-# define gzrewind z_gzrewind
-# define gzseek z_gzseek
-# define gzseek64 z_gzseek64
-# define gzsetparams z_gzsetparams
-# define gztell z_gztell
-# define gztell64 z_gztell64
-# define gzungetc z_gzungetc
-# define gzwrite z_gzwrite
-# endif
-# define inflate z_inflate
-# define inflateBack z_inflateBack
-# define inflateBackEnd z_inflateBackEnd
-# define inflateBackInit_ z_inflateBackInit_
-# define inflateCopy z_inflateCopy
-# define inflateEnd z_inflateEnd
-# define inflateGetHeader z_inflateGetHeader
-# define inflateInit2_ z_inflateInit2_
-# define inflateInit_ z_inflateInit_
-# define inflateMark z_inflateMark
-# define inflatePrime z_inflatePrime
-# define inflateReset z_inflateReset
-# define inflateReset2 z_inflateReset2
-# define inflateSetDictionary z_inflateSetDictionary
-# define inflateGetDictionary z_inflateGetDictionary
-# define inflateSync z_inflateSync
-# define inflateSyncPoint z_inflateSyncPoint
-# define inflateUndermine z_inflateUndermine
-# define inflateResetKeep z_inflateResetKeep
-# define inflate_copyright z_inflate_copyright
-# define inflate_fast z_inflate_fast
-# define inflate_table z_inflate_table
-# ifndef Z_SOLO
-# define uncompress z_uncompress
-# endif
-# define zError z_zError
-# ifndef Z_SOLO
-# define zcalloc z_zcalloc
-# define zcfree z_zcfree
-# endif
-# define zlibCompileFlags z_zlibCompileFlags
-# define zlibVersion z_zlibVersion
-
-/* all zlib typedefs in zlib.h and zconf.h */
-# define Byte z_Byte
-# define Bytef z_Bytef
-# define alloc_func z_alloc_func
-# define charf z_charf
-# define free_func z_free_func
-# ifndef Z_SOLO
-# define gzFile z_gzFile
-# endif
-# define gz_header z_gz_header
-# define gz_headerp z_gz_headerp
-# define in_func z_in_func
-# define intf z_intf
-# define out_func z_out_func
-# define uInt z_uInt
-# define uIntf z_uIntf
-# define uLong z_uLong
-# define uLongf z_uLongf
-# define voidp z_voidp
-# define voidpc z_voidpc
-# define voidpf z_voidpf
-
-/* all zlib structs in zlib.h and zconf.h */
-# define gz_header_s z_gz_header_s
-# define internal_state z_internal_state
-
-#endif
-
-#if defined(__MSDOS__) && !defined(MSDOS)
-# define MSDOS
-#endif
-#if (defined(OS_2) || defined(__OS2__)) && !defined(OS2)
-# define OS2
-#endif
-#if defined(_WINDOWS) && !defined(WINDOWS)
-# define WINDOWS
-#endif
-#if defined(_WIN32) || defined(_WIN32_WCE) || defined(__WIN32__)
-# ifndef WIN32
-# define WIN32
-# endif
-#endif
-#if (defined(MSDOS) || defined(OS2) || defined(WINDOWS)) && !defined(WIN32)
-# if !defined(__GNUC__) && !defined(__FLAT__) && !defined(__386__)
-# ifndef SYS16BIT
-# define SYS16BIT
-# endif
-# endif
-#endif
-
-/*
- * Compile with -DMAXSEG_64K if the alloc function cannot allocate more
- * than 64k bytes at a time (needed on systems with 16-bit int).
- */
-#ifdef SYS16BIT
-# define MAXSEG_64K
-#endif
-#ifdef MSDOS
-# define UNALIGNED_OK
-#endif
-
-#ifdef __STDC_VERSION__
-# ifndef STDC
-# define STDC
-# endif
-# if __STDC_VERSION__ >= 199901L
-# ifndef STDC99
-# define STDC99
-# endif
-# endif
-#endif
-#if !defined(STDC) && (defined(__STDC__) || defined(__cplusplus))
-# define STDC
-#endif
-#if !defined(STDC) && (defined(__GNUC__) || defined(__BORLANDC__))
-# define STDC
-#endif
-#if !defined(STDC) && (defined(MSDOS) || defined(WINDOWS) || defined(WIN32))
-# define STDC
-#endif
-#if !defined(STDC) && (defined(OS2) || defined(__HOS_AIX__))
-# define STDC
-#endif
-
-#if defined(__OS400__) && !defined(STDC) /* iSeries (formerly AS/400). */
-# define STDC
-#endif
-
-#ifndef STDC
-# ifndef const /* cannot use !defined(STDC) && !defined(const) on Mac */
-# define const /* note: need a more gentle solution here */
-# endif
-#endif
-
-#if defined(ZLIB_CONST) && !defined(z_const)
-# define z_const const
-#else
-# define z_const
-#endif
-
-/* Some Mac compilers merge all .h files incorrectly: */
-#if defined(__MWERKS__)||defined(applec)||defined(THINK_C)||defined(__SC__)
-# define NO_DUMMY_DECL
-#endif
-
-/* Maximum value for memLevel in deflateInit2 */
-#ifndef MAX_MEM_LEVEL
-# ifdef MAXSEG_64K
-# define MAX_MEM_LEVEL 8
-# else
-# define MAX_MEM_LEVEL 9
-# endif
-#endif
-
-/* Maximum value for windowBits in deflateInit2 and inflateInit2.
- * WARNING: reducing MAX_WBITS makes minigzip unable to extract .gz files
- * created by gzip. (Files created by minigzip can still be extracted by
- * gzip.)
- */
-#ifndef MAX_WBITS
-# define MAX_WBITS 15 /* 32K LZ77 window */
-#endif
-
-/* The memory requirements for deflate are (in bytes):
- (1 << (windowBits+2)) + (1 << (memLevel+9))
- that is: 128K for windowBits=15 + 128K for memLevel = 8 (default values)
- plus a few kilobytes for small objects. For example, if you want to reduce
- the default memory requirements from 256K to 128K, compile with
- make CFLAGS="-O -DMAX_WBITS=14 -DMAX_MEM_LEVEL=7"
- Of course this will generally degrade compression (there's no free lunch).
-
- The memory requirements for inflate are (in bytes) 1 << windowBits
- that is, 32K for windowBits=15 (default value) plus a few kilobytes
- for small objects.
-*/
-
- /* Type declarations */
-
-#ifndef OF /* function prototypes */
-# ifdef STDC
-# define OF(args) args
-# else
-# define OF(args) ()
-# endif
-#endif
-
-#ifndef Z_ARG /* function prototypes for stdarg */
-# if defined(STDC) || defined(Z_HAVE_STDARG_H)
-# define Z_ARG(args) args
-# else
-# define Z_ARG(args) ()
-# endif
-#endif
-
-/* The following definitions for FAR are needed only for MSDOS mixed
- * model programming (small or medium model with some far allocations).
- * This was tested only with MSC; for other MSDOS compilers you may have
- * to define NO_MEMCPY in zutil.h. If you don't need the mixed model,
- * just define FAR to be empty.
- */
-#ifdef SYS16BIT
-# if defined(M_I86SM) || defined(M_I86MM)
- /* MSC small or medium model */
-# define SMALL_MEDIUM
-# ifdef _MSC_VER
-# define FAR _far
-# else
-# define FAR far
-# endif
-# endif
-# if (defined(__SMALL__) || defined(__MEDIUM__))
- /* Turbo C small or medium model */
-# define SMALL_MEDIUM
-# ifdef __BORLANDC__
-# define FAR _far
-# else
-# define FAR far
-# endif
-# endif
-#endif
-
-#if defined(WINDOWS) || defined(WIN32)
- /* If building or using zlib as a DLL, define ZLIB_DLL.
- * This is not mandatory, but it offers a little performance increase.
- */
-# ifdef ZLIB_DLL
-# if defined(WIN32) && (!defined(__BORLANDC__) || (__BORLANDC__ >= 0x500))
-# ifdef ZLIB_INTERNAL
-# define ZEXTERN extern __declspec(dllexport)
-# else
-# define ZEXTERN extern __declspec(dllimport)
-# endif
-# endif
-# endif /* ZLIB_DLL */
- /* If building or using zlib with the WINAPI/WINAPIV calling convention,
- * define ZLIB_WINAPI.
- * Caution: the standard ZLIB1.DLL is NOT compiled using ZLIB_WINAPI.
- */
-# ifdef ZLIB_WINAPI
-# ifdef FAR
-# undef FAR
-# endif
-# include <windows.h>
- /* No need for _export, use ZLIB.DEF instead. */
- /* For complete Windows compatibility, use WINAPI, not __stdcall. */
-# define ZEXPORT WINAPI
-# ifdef WIN32
-# define ZEXPORTVA WINAPIV
-# else
-# define ZEXPORTVA FAR CDECL
-# endif
-# endif
-#endif
-
-#if defined (__BEOS__)
-# ifdef ZLIB_DLL
-# ifdef ZLIB_INTERNAL
-# define ZEXPORT __declspec(dllexport)
-# define ZEXPORTVA __declspec(dllexport)
-# else
-# define ZEXPORT __declspec(dllimport)
-# define ZEXPORTVA __declspec(dllimport)
-# endif
-# endif
-#endif
-
-#ifndef ZEXTERN
-# define ZEXTERN extern
-#endif
-#ifndef ZEXPORT
-# define ZEXPORT
-#endif
-#ifndef ZEXPORTVA
-# define ZEXPORTVA
-#endif
-
-#ifndef FAR
-# define FAR
-#endif
-
-#if !defined(__MACTYPES__)
-typedef unsigned char Byte; /* 8 bits */
-#endif
-typedef unsigned int uInt; /* 16 bits or more */
-typedef unsigned long uLong; /* 32 bits or more */
-
-#ifdef SMALL_MEDIUM
- /* Borland C/C++ and some old MSC versions ignore FAR inside typedef */
-# define Bytef Byte FAR
-#else
- typedef Byte FAR Bytef;
-#endif
-typedef char FAR charf;
-typedef int FAR intf;
-typedef uInt FAR uIntf;
-typedef uLong FAR uLongf;
-
-#ifdef STDC
- typedef void const *voidpc;
- typedef void FAR *voidpf;
- typedef void *voidp;
-#else
- typedef Byte const *voidpc;
- typedef Byte FAR *voidpf;
- typedef Byte *voidp;
-#endif
-
-#if !defined(Z_U4) && !defined(Z_SOLO) && defined(STDC)
-# include <limits.h>
-# if (UINT_MAX == 0xffffffffUL)
-# define Z_U4 unsigned
-# elif (ULONG_MAX == 0xffffffffUL)
-# define Z_U4 unsigned long
-# elif (USHRT_MAX == 0xffffffffUL)
-# define Z_U4 unsigned short
-# endif
-#endif
-
-#ifdef Z_U4
- typedef Z_U4 z_crc_t;
-#else
- typedef unsigned long z_crc_t;
-#endif
-
-#ifdef HAVE_UNISTD_H /* may be set to #if 1 by ./configure */
-# define Z_HAVE_UNISTD_H
-#endif
-
-#ifdef HAVE_STDARG_H /* may be set to #if 1 by ./configure */
-# define Z_HAVE_STDARG_H
-#endif
-
-#ifdef STDC
-# ifndef Z_SOLO
-# include <sys/types.h> /* for off_t */
-# endif
-#endif
-
-#if defined(STDC) || defined(Z_HAVE_STDARG_H)
-# ifndef Z_SOLO
-# include <stdarg.h> /* for va_list */
-# endif
-#endif
-
-#ifdef _WIN32
-# ifndef Z_SOLO
-# include <stddef.h> /* for wchar_t */
-# endif
-#endif
-
-/* a little trick to accommodate both "#define _LARGEFILE64_SOURCE" and
- * "#define _LARGEFILE64_SOURCE 1" as requesting 64-bit operations, (even
- * though the former does not conform to the LFS document), but considering
- * both "#undef _LARGEFILE64_SOURCE" and "#define _LARGEFILE64_SOURCE 0" as
- * equivalently requesting no 64-bit operations
- */
-#if defined(_LARGEFILE64_SOURCE) && -_LARGEFILE64_SOURCE - -1 == 1
-# undef _LARGEFILE64_SOURCE
-#endif
-
-#if defined(__WATCOMC__) && !defined(Z_HAVE_UNISTD_H)
-# define Z_HAVE_UNISTD_H
-#endif
-#ifndef Z_SOLO
-# if defined(Z_HAVE_UNISTD_H) || defined(_LARGEFILE64_SOURCE)
-# include <unistd.h> /* for SEEK_*, off_t, and _LFS64_LARGEFILE */
-# ifdef VMS
-# include <unixio.h> /* for off_t */
-# endif
-# ifndef z_off_t
-# define z_off_t off_t
-# endif
-# endif
-#endif
-
-#if defined(_LFS64_LARGEFILE) && _LFS64_LARGEFILE-0
-# define Z_LFS64
-#endif
-
-#if defined(_LARGEFILE64_SOURCE) && defined(Z_LFS64)
-# define Z_LARGE64
-#endif
-
-#if defined(_FILE_OFFSET_BITS) && _FILE_OFFSET_BITS-0 == 64 && defined(Z_LFS64)
-# define Z_WANT64
-#endif
-
-#if !defined(SEEK_SET) && !defined(Z_SOLO)
-# define SEEK_SET 0 /* Seek from beginning of file. */
-# define SEEK_CUR 1 /* Seek from current position. */
-# define SEEK_END 2 /* Set file pointer to EOF plus "offset" */
-#endif
-
-#ifndef z_off_t
-# define z_off_t long
-#endif
-
-#if !defined(_WIN32) && defined(Z_LARGE64)
-# define z_off64_t off64_t
-#else
-# if defined(_WIN32) && !defined(__GNUC__) && !defined(Z_SOLO)
-# define z_off64_t __int64
-# else
-# define z_off64_t z_off_t
-# endif
-#endif
-
-/* MVS linker does not support external names larger than 8 bytes */
-#if defined(__MVS__)
- #pragma map(deflateInit_,"DEIN")
- #pragma map(deflateInit2_,"DEIN2")
- #pragma map(deflateEnd,"DEEND")
- #pragma map(deflateBound,"DEBND")
- #pragma map(inflateInit_,"ININ")
- #pragma map(inflateInit2_,"ININ2")
- #pragma map(inflateEnd,"INEND")
- #pragma map(inflateSync,"INSY")
- #pragma map(inflateSetDictionary,"INSEDI")
- #pragma map(compressBound,"CMBND")
- #pragma map(inflate_table,"INTABL")
- #pragma map(inflate_fast,"INFA")
- #pragma map(inflate_copyright,"INCOPY")
-#endif
-
-#endif /* ZCONF_H */
diff --git a/third-party/zlib/zlib.3 b/third-party/zlib/zlib.3
deleted file mode 100644
index 0160e62..0000000
--- a/third-party/zlib/zlib.3
+++ /dev/null
@@ -1,151 +0,0 @@
-.TH ZLIB 3 "28 Apr 2013"
-.SH NAME
-zlib \- compression/decompression library
-.SH SYNOPSIS
-[see
-.I zlib.h
-for full description]
-.SH DESCRIPTION
-The
-.I zlib
-library is a general purpose data compression library.
-The code is thread safe, assuming that the standard library functions
-used are thread safe, such as memory allocation routines.
-It provides in-memory compression and decompression functions,
-including integrity checks of the uncompressed data.
-This version of the library supports only one compression method (deflation)
-but other algorithms may be added later
-with the same stream interface.
-.LP
-Compression can be done in a single step if the buffers are large enough
-or can be done by repeated calls of the compression function.
-In the latter case,
-the application must provide more input and/or consume the output
-(providing more output space) before each call.
-.LP
-The library also supports reading and writing files in
-.IR gzip (1)
-(.gz) format
-with an interface similar to that of stdio.
-.LP
-The library does not install any signal handler.
-The decoder checks the consistency of the compressed data,
-so the library should never crash even in the case of corrupted input.
-.LP
-All functions of the compression library are documented in the file
-.IR zlib.h .
-The distribution source includes examples of use of the library
-in the files
-.I test/example.c
-and
-.IR test/minigzip.c,
-as well as other examples in the
-.IR examples/
-directory.
-.LP
-Changes to this version are documented in the file
-.I ChangeLog
-that accompanies the source.
-.LP
-.I zlib
-is available in Java using the java.util.zip package:
-.IP
-http://java.sun.com/developer/technicalArticles/Programming/compression/
-.LP
-A Perl interface to
-.IR zlib ,
-written by Paul Marquess (pmqs at cpan.org),
-is available at CPAN (Comprehensive Perl Archive Network) sites,
-including:
-.IP
-http://search.cpan.org/~pmqs/IO-Compress-Zlib/
-.LP
-A Python interface to
-.IR zlib ,
-written by A.M. Kuchling (amk at magnet.com),
-is available in Python 1.5 and later versions:
-.IP
-http://docs.python.org/library/zlib.html
-.LP
-.I zlib
-is built into
-.IR tcl:
-.IP
-http://wiki.tcl.tk/4610
-.LP
-An experimental package to read and write files in .zip format,
-written on top of
-.I zlib
-by Gilles Vollant (info at winimage.com),
-is available at:
-.IP
-http://www.winimage.com/zLibDll/minizip.html
-and also in the
-.I contrib/minizip
-directory of the main
-.I zlib
-source distribution.
-.SH "SEE ALSO"
-The
-.I zlib
-web site can be found at:
-.IP
-http://zlib.net/
-.LP
-The data format used by the zlib library is described by RFC
-(Request for Comments) 1950 to 1952 in the files:
-.IP
-http://tools.ietf.org/html/rfc1950 (for the zlib header and trailer format)
-.br
-http://tools.ietf.org/html/rfc1951 (for the deflate compressed data format)
-.br
-http://tools.ietf.org/html/rfc1952 (for the gzip header and trailer format)
-.LP
-Mark Nelson wrote an article about
-.I zlib
-for the Jan. 1997 issue of Dr. Dobb's Journal;
-a copy of the article is available at:
-.IP
-http://marknelson.us/1997/01/01/zlib-engine/
-.SH "REPORTING PROBLEMS"
-Before reporting a problem,
-please check the
-.I zlib
-web site to verify that you have the latest version of
-.IR zlib ;
-otherwise,
-obtain the latest version and see if the problem still exists.
-Please read the
-.I zlib
-FAQ at:
-.IP
-http://zlib.net/zlib_faq.html
-.LP
-before asking for help.
-Send questions and/or comments to zlib at gzip.org,
-or (for the Windows DLL version) to Gilles Vollant (info at winimage.com).
-.SH AUTHORS
-Version 1.2.8
-Copyright (C) 1995-2013 Jean-loup Gailly (jloup at gzip.org)
-and Mark Adler (madler at alumni.caltech.edu).
-.LP
-This software is provided "as-is,"
-without any express or implied warranty.
-In no event will the authors be held liable for any damages
-arising from the use of this software.
-See the distribution directory with respect to requirements
-governing redistribution.
-The deflate format used by
-.I zlib
-was defined by Phil Katz.
-The deflate and
-.I zlib
-specifications were written by L. Peter Deutsch.
-Thanks to all the people who reported problems and suggested various
-improvements in
-.IR zlib ;
-who are too numerous to cite here.
-.LP
-UNIX manual page by R. P. C. Rodgers,
-U.S. National Library of Medicine (rodgers at nlm.nih.gov).
-.\" end of man page
diff --git a/third-party/zlib/zlib.3.pdf b/third-party/zlib/zlib.3.pdf
deleted file mode 100644
index a346b5d..0000000
Binary files a/third-party/zlib/zlib.3.pdf and /dev/null differ
diff --git a/third-party/zlib/zlib.h b/third-party/zlib/zlib.h
deleted file mode 100644
index 3e0c767..0000000
--- a/third-party/zlib/zlib.h
+++ /dev/null
@@ -1,1768 +0,0 @@
-/* zlib.h -- interface of the 'zlib' general purpose compression library
- version 1.2.8, April 28th, 2013
-
- Copyright (C) 1995-2013 Jean-loup Gailly and Mark Adler
-
- This software is provided 'as-is', without any express or implied
- warranty. In no event will the authors be held liable for any damages
- arising from the use of this software.
-
- Permission is granted to anyone to use this software for any purpose,
- including commercial applications, and to alter it and redistribute it
- freely, subject to the following restrictions:
-
- 1. The origin of this software must not be misrepresented; you must not
- claim that you wrote the original software. If you use this software
- in a product, an acknowledgment in the product documentation would be
- appreciated but is not required.
- 2. Altered source versions must be plainly marked as such, and must not be
- misrepresented as being the original software.
- 3. This notice may not be removed or altered from any source distribution.
-
- Jean-loup Gailly Mark Adler
- jloup at gzip.org madler at alumni.caltech.edu
-
-
- The data format used by the zlib library is described by RFCs (Request for
- Comments) 1950 to 1952 in the files http://tools.ietf.org/html/rfc1950
- (zlib format), rfc1951 (deflate format) and rfc1952 (gzip format).
-*/
-
-#ifndef ZLIB_H
-#define ZLIB_H
-
-#include "zconf.h"
-
-#ifdef __cplusplus
-extern "C" {
-#endif
-
-#define ZLIB_VERSION "1.2.8"
-#define ZLIB_VERNUM 0x1280
-#define ZLIB_VER_MAJOR 1
-#define ZLIB_VER_MINOR 2
-#define ZLIB_VER_REVISION 8
-#define ZLIB_VER_SUBREVISION 0
-
-/*
- The 'zlib' compression library provides in-memory compression and
- decompression functions, including integrity checks of the uncompressed data.
- This version of the library supports only one compression method (deflation)
- but other algorithms will be added later and will have the same stream
- interface.
-
- Compression can be done in a single step if the buffers are large enough,
- or can be done by repeated calls of the compression function. In the latter
- case, the application must provide more input and/or consume the output
- (providing more output space) before each call.
-
- The compressed data format used by default by the in-memory functions is
- the zlib format, which is a zlib wrapper documented in RFC 1950, wrapped
- around a deflate stream, which is itself documented in RFC 1951.
-
- The library also supports reading and writing files in gzip (.gz) format
- with an interface similar to that of stdio using the functions that start
- with "gz". The gzip format is different from the zlib format. gzip is a
- gzip wrapper, documented in RFC 1952, wrapped around a deflate stream.
-
- This library can optionally read and write gzip streams in memory as well.
-
- The zlib format was designed to be compact and fast for use in memory
- and on communications channels. The gzip format was designed for single-
- file compression on file systems, has a larger header than zlib to maintain
- directory information, and uses a different, slower check method than zlib.
-
- The library does not install any signal handler. The decoder checks
- the consistency of the compressed data, so the library should never crash
- even in case of corrupted input.
-*/
-
-typedef voidpf (*alloc_func) OF((voidpf opaque, uInt items, uInt size));
-typedef void (*free_func) OF((voidpf opaque, voidpf address));
-
-struct internal_state;
-
-typedef struct z_stream_s {
- z_const Bytef *next_in; /* next input byte */
- uInt avail_in; /* number of bytes available at next_in */
- uLong total_in; /* total number of input bytes read so far */
-
- Bytef *next_out; /* next output byte should be put there */
- uInt avail_out; /* remaining free space at next_out */
- uLong total_out; /* total number of bytes output so far */
-
- z_const char *msg; /* last error message, NULL if no error */
- struct internal_state FAR *state; /* not visible by applications */
-
- alloc_func zalloc; /* used to allocate the internal state */
- free_func zfree; /* used to free the internal state */
- voidpf opaque; /* private data object passed to zalloc and zfree */
-
- int data_type; /* best guess about the data type: binary or text */
- uLong adler; /* adler32 value of the uncompressed data */
- uLong reserved; /* reserved for future use */
-} z_stream;
-
-typedef z_stream FAR *z_streamp;
-
-/*
- gzip header information passed to and from zlib routines. See RFC 1952
- for more details on the meanings of these fields.
-*/
-typedef struct gz_header_s {
- int text; /* true if compressed data believed to be text */
- uLong time; /* modification time */
- int xflags; /* extra flags (not used when writing a gzip file) */
- int os; /* operating system */
- Bytef *extra; /* pointer to extra field or Z_NULL if none */
- uInt extra_len; /* extra field length (valid if extra != Z_NULL) */
- uInt extra_max; /* space at extra (only when reading header) */
- Bytef *name; /* pointer to zero-terminated file name or Z_NULL */
- uInt name_max; /* space at name (only when reading header) */
- Bytef *comment; /* pointer to zero-terminated comment or Z_NULL */
- uInt comm_max; /* space at comment (only when reading header) */
- int hcrc; /* true if there was or will be a header crc */
- int done; /* true when done reading gzip header (not used
- when writing a gzip file) */
-} gz_header;
-
-typedef gz_header FAR *gz_headerp;
-
-/*
- The application must update next_in and avail_in when avail_in has dropped
- to zero. It must update next_out and avail_out when avail_out has dropped
- to zero. The application must initialize zalloc, zfree and opaque before
- calling the init function. All other fields are set by the compression
- library and must not be updated by the application.
-
- The opaque value provided by the application will be passed as the first
- parameter for calls of zalloc and zfree. This can be useful for custom
- memory management. The compression library attaches no meaning to the
- opaque value.
-
- zalloc must return Z_NULL if there is not enough memory for the object.
- If zlib is used in a multi-threaded application, zalloc and zfree must be
- thread safe.
-
- On 16-bit systems, the functions zalloc and zfree must be able to allocate
- exactly 65536 bytes, but will not be required to allocate more than this if
- the symbol MAXSEG_64K is defined (see zconf.h). WARNING: On MSDOS, pointers
- returned by zalloc for objects of exactly 65536 bytes *must* have their
- offset normalized to zero. The default allocation function provided by this
- library ensures this (see zutil.c). To reduce memory requirements and avoid
- any allocation of 64K objects, at the expense of compression ratio, compile
- the library with -DMAX_WBITS=14 (see zconf.h).
-
- The fields total_in and total_out can be used for statistics or progress
- reports. After compression, total_in holds the total size of the
- uncompressed data and may be saved for use in the decompressor (particularly
- if the decompressor wants to decompress everything in a single step).
-*/
-
- /* constants */
-
-#define Z_NO_FLUSH 0
-#define Z_PARTIAL_FLUSH 1
-#define Z_SYNC_FLUSH 2
-#define Z_FULL_FLUSH 3
-#define Z_FINISH 4
-#define Z_BLOCK 5
-#define Z_TREES 6
-/* Allowed flush values; see deflate() and inflate() below for details */
-
-#define Z_OK 0
-#define Z_STREAM_END 1
-#define Z_NEED_DICT 2
-#define Z_ERRNO (-1)
-#define Z_STREAM_ERROR (-2)
-#define Z_DATA_ERROR (-3)
-#define Z_MEM_ERROR (-4)
-#define Z_BUF_ERROR (-5)
-#define Z_VERSION_ERROR (-6)
-/* Return codes for the compression/decompression functions. Negative values
- * are errors, positive values are used for special but normal events.
- */
-
-#define Z_NO_COMPRESSION 0
-#define Z_BEST_SPEED 1
-#define Z_BEST_COMPRESSION 9
-#define Z_DEFAULT_COMPRESSION (-1)
-/* compression levels */
-
-#define Z_FILTERED 1
-#define Z_HUFFMAN_ONLY 2
-#define Z_RLE 3
-#define Z_FIXED 4
-#define Z_DEFAULT_STRATEGY 0
-/* compression strategy; see deflateInit2() below for details */
-
-#define Z_BINARY 0
-#define Z_TEXT 1
-#define Z_ASCII Z_TEXT /* for compatibility with 1.2.2 and earlier */
-#define Z_UNKNOWN 2
-/* Possible values of the data_type field (though see inflate()) */
-
-#define Z_DEFLATED 8
-/* The deflate compression method (the only one supported in this version) */
-
-#define Z_NULL 0 /* for initializing zalloc, zfree, opaque */
-
-#define zlib_version zlibVersion()
-/* for compatibility with versions < 1.0.2 */
-
-
- /* basic functions */
-
-ZEXTERN const char * ZEXPORT zlibVersion OF((void));
-/* The application can compare zlibVersion and ZLIB_VERSION for consistency.
- If the first character differs, the library code actually used is not
- compatible with the zlib.h header file used by the application. This check
- is automatically made by deflateInit and inflateInit.
- */
-
-/*
-ZEXTERN int ZEXPORT deflateInit OF((z_streamp strm, int level));
-
- Initializes the internal stream state for compression. The fields
- zalloc, zfree and opaque must be initialized before by the caller. If
- zalloc and zfree are set to Z_NULL, deflateInit updates them to use default
- allocation functions.
-
- The compression level must be Z_DEFAULT_COMPRESSION, or between 0 and 9:
- 1 gives best speed, 9 gives best compression, 0 gives no compression at all
- (the input data is simply copied a block at a time). Z_DEFAULT_COMPRESSION
- requests a default compromise between speed and compression (currently
- equivalent to level 6).
-
- deflateInit returns Z_OK if success, Z_MEM_ERROR if there was not enough
- memory, Z_STREAM_ERROR if level is not a valid compression level, or
- Z_VERSION_ERROR if the zlib library version (zlib_version) is incompatible
- with the version assumed by the caller (ZLIB_VERSION). msg is set to null
- if there is no error message. deflateInit does not perform any compression:
- this will be done by deflate().
-*/
-
-
-ZEXTERN int ZEXPORT deflate OF((z_streamp strm, int flush));
-/*
- deflate compresses as much data as possible, and stops when the input
- buffer becomes empty or the output buffer becomes full. It may introduce
- some output latency (reading input without producing any output) except when
- forced to flush.
-
- The detailed semantics are as follows. deflate performs one or both of the
- following actions:
-
- - Compress more input starting at next_in and update next_in and avail_in
- accordingly. If not all input can be processed (because there is not
- enough room in the output buffer), next_in and avail_in are updated and
- processing will resume at this point for the next call of deflate().
-
- - Provide more output starting at next_out and update next_out and avail_out
- accordingly. This action is forced if the parameter flush is non zero.
- Forcing flush frequently degrades the compression ratio, so this parameter
- should be set only when necessary (in interactive applications). Some
- output may be provided even if flush is not set.
-
- Before the call of deflate(), the application should ensure that at least
- one of the actions is possible, by providing more input and/or consuming more
- output, and updating avail_in or avail_out accordingly; avail_out should
- never be zero before the call. The application can consume the compressed
- output when it wants, for example when the output buffer is full (avail_out
- == 0), or after each call of deflate(). If deflate returns Z_OK and with
- zero avail_out, it must be called again after making room in the output
- buffer because there might be more output pending.
-
- Normally the parameter flush is set to Z_NO_FLUSH, which allows deflate to
- decide how much data to accumulate before producing output, in order to
- maximize compression.
-
- If the parameter flush is set to Z_SYNC_FLUSH, all pending output is
- flushed to the output buffer and the output is aligned on a byte boundary, so
- that the decompressor can get all input data available so far. (In
- particular avail_in is zero after the call if enough output space has been
- provided before the call.) Flushing may degrade compression for some
- compression algorithms and so it should be used only when necessary. This
- completes the current deflate block and follows it with an empty stored block
- that is three bits plus filler bits to the next byte, followed by four bytes
- (00 00 ff ff).
-
- If flush is set to Z_PARTIAL_FLUSH, all pending output is flushed to the
- output buffer, but the output is not aligned to a byte boundary. All of the
- input data so far will be available to the decompressor, as for Z_SYNC_FLUSH.
- This completes the current deflate block and follows it with an empty fixed
- codes block that is 10 bits long. This assures that enough bytes are output
- in order for the decompressor to finish the block before the empty fixed code
- block.
-
- If flush is set to Z_BLOCK, a deflate block is completed and emitted, as
- for Z_SYNC_FLUSH, but the output is not aligned on a byte boundary, and up to
- seven bits of the current block are held to be written as the next byte after
- the next deflate block is completed. In this case, the decompressor may not
- be provided enough bits at this point in order to complete decompression of
- the data provided so far to the compressor. It may need to wait for the next
- block to be emitted. This is for advanced applications that need to control
- the emission of deflate blocks.
-
- If flush is set to Z_FULL_FLUSH, all output is flushed as with
- Z_SYNC_FLUSH, and the compression state is reset so that decompression can
- restart from this point if previous compressed data has been damaged or if
- random access is desired. Using Z_FULL_FLUSH too often can seriously degrade
- compression.
-
- If deflate returns with avail_out == 0, this function must be called again
- with the same value of the flush parameter and more output space (updated
- avail_out), until the flush is complete (deflate returns with non-zero
- avail_out). In the case of a Z_FULL_FLUSH or Z_SYNC_FLUSH, make sure that
- avail_out is greater than six to avoid repeated flush markers due to
- avail_out == 0 on return.
-
- If the parameter flush is set to Z_FINISH, pending input is processed,
- pending output is flushed and deflate returns with Z_STREAM_END if there was
- enough output space; if deflate returns with Z_OK, this function must be
- called again with Z_FINISH and more output space (updated avail_out) but no
- more input data, until it returns with Z_STREAM_END or an error. After
- deflate has returned Z_STREAM_END, the only possible operations on the stream
- are deflateReset or deflateEnd.
-
- Z_FINISH can be used immediately after deflateInit if all the compression
- is to be done in a single step. In this case, avail_out must be at least the
- value returned by deflateBound (see below). Then deflate is guaranteed to
- return Z_STREAM_END. If not enough output space is provided, deflate will
- not return Z_STREAM_END, and it must be called again as described above.
-
- deflate() sets strm->adler to the adler32 checksum of all input read
- so far (that is, total_in bytes).
-
- deflate() may update strm->data_type if it can make a good guess about
- the input data type (Z_BINARY or Z_TEXT). In doubt, the data is considered
- binary. This field is only for information purposes and does not affect the
- compression algorithm in any manner.
-
- deflate() returns Z_OK if some progress has been made (more input
- processed or more output produced), Z_STREAM_END if all input has been
- consumed and all output has been produced (only when flush is set to
- Z_FINISH), Z_STREAM_ERROR if the stream state was inconsistent (for example
- if next_in or next_out was Z_NULL), Z_BUF_ERROR if no progress is possible
- (for example avail_in or avail_out was zero). Note that Z_BUF_ERROR is not
- fatal, and deflate() can be called again with more input and more output
- space to continue compressing.
-*/
-
-
-ZEXTERN int ZEXPORT deflateEnd OF((z_streamp strm));
-/*
- All dynamically allocated data structures for this stream are freed.
- This function discards any unprocessed input and does not flush any pending
- output.
-
- deflateEnd returns Z_OK if success, Z_STREAM_ERROR if the
- stream state was inconsistent, Z_DATA_ERROR if the stream was freed
- prematurely (some input or output was discarded). In the error case, msg
- may be set but then points to a static string (which must not be
- deallocated).
-*/
-
-
-/*
-ZEXTERN int ZEXPORT inflateInit OF((z_streamp strm));
-
- Initializes the internal stream state for decompression. The fields
- next_in, avail_in, zalloc, zfree and opaque must be initialized before by
- the caller. If next_in is not Z_NULL and avail_in is large enough (the
- exact value depends on the compression method), inflateInit determines the
- compression method from the zlib header and allocates all data structures
- accordingly; otherwise the allocation will be deferred to the first call of
- inflate. If zalloc and zfree are set to Z_NULL, inflateInit updates them to
- use default allocation functions.
-
- inflateInit returns Z_OK if success, Z_MEM_ERROR if there was not enough
- memory, Z_VERSION_ERROR if the zlib library version is incompatible with the
- version assumed by the caller, or Z_STREAM_ERROR if the parameters are
- invalid, such as a null pointer to the structure. msg is set to null if
- there is no error message. inflateInit does not perform any decompression
- apart from possibly reading the zlib header if present: actual decompression
- will be done by inflate(). (So next_in and avail_in may be modified, but
- next_out and avail_out are unused and unchanged.) The current implementation
- of inflateInit() does not process any header information -- that is deferred
- until inflate() is called.
-*/
-
-
-ZEXTERN int ZEXPORT inflate OF((z_streamp strm, int flush));
-/*
- inflate decompresses as much data as possible, and stops when the input
- buffer becomes empty or the output buffer becomes full. It may introduce
- some output latency (reading input without producing any output) except when
- forced to flush.
-
- The detailed semantics are as follows. inflate performs one or both of the
- following actions:
-
- - Decompress more input starting at next_in and update next_in and avail_in
- accordingly. If not all input can be processed (because there is not
- enough room in the output buffer), next_in is updated and processing will
- resume at this point for the next call of inflate().
-
- - Provide more output starting at next_out and update next_out and avail_out
- accordingly. inflate() provides as much output as possible, until there is
- no more input data or no more space in the output buffer (see below about
- the flush parameter).
-
- Before the call of inflate(), the application should ensure that at least
- one of the actions is possible, by providing more input and/or consuming more
- output, and updating the next_* and avail_* values accordingly. The
- application can consume the uncompressed output when it wants, for example
- when the output buffer is full (avail_out == 0), or after each call of
- inflate(). If inflate returns Z_OK and with zero avail_out, it must be
- called again after making room in the output buffer because there might be
- more output pending.
-
- The flush parameter of inflate() can be Z_NO_FLUSH, Z_SYNC_FLUSH, Z_FINISH,
- Z_BLOCK, or Z_TREES. Z_SYNC_FLUSH requests that inflate() flush as much
- output as possible to the output buffer. Z_BLOCK requests that inflate()
- stop if and when it gets to the next deflate block boundary. When decoding
- the zlib or gzip format, this will cause inflate() to return immediately
- after the header and before the first block. When doing a raw inflate,
- inflate() will go ahead and process the first block, and will return when it
- gets to the end of that block, or when it runs out of data.
-
- The Z_BLOCK option assists in appending to or combining deflate streams.
- Also to assist in this, on return inflate() will set strm->data_type to the
- number of unused bits in the last byte taken from strm->next_in, plus 64 if
- inflate() is currently decoding the last block in the deflate stream, plus
- 128 if inflate() returned immediately after decoding an end-of-block code or
- decoding the complete header up to just before the first byte of the deflate
- stream. The end-of-block will not be indicated until all of the uncompressed
- data from that block has been written to strm->next_out. The number of
- unused bits may in general be greater than seven, except when bit 7 of
- data_type is set, in which case the number of unused bits will be less than
- eight. data_type is set as noted here every time inflate() returns for all
- flush options, and so can be used to determine the amount of currently
- consumed input in bits.
-
- The Z_TREES option behaves as Z_BLOCK does, but it also returns when the
- end of each deflate block header is reached, before any actual data in that
- block is decoded. This allows the caller to determine the length of the
- deflate block header for later use in random access within a deflate block.
- 256 is added to the value of strm->data_type when inflate() returns
- immediately after reaching the end of the deflate block header.
-
- inflate() should normally be called until it returns Z_STREAM_END or an
- error. However if all decompression is to be performed in a single step (a
- single call of inflate), the parameter flush should be set to Z_FINISH. In
- this case all pending input is processed and all pending output is flushed;
- avail_out must be large enough to hold all of the uncompressed data for the
- operation to complete. (The size of the uncompressed data may have been
- saved by the compressor for this purpose.) The use of Z_FINISH is not
- required to perform an inflation in one step. However it may be used to
- inform inflate that a faster approach can be used for the single inflate()
- call. Z_FINISH also informs inflate to not maintain a sliding window if the
- stream completes, which reduces inflate's memory footprint. If the stream
- does not complete, either because not all of the stream is provided or not
- enough output space is provided, then a sliding window will be allocated and
- inflate() can be called again to continue the operation as if Z_NO_FLUSH had
- been used.
-
- In this implementation, inflate() always flushes as much output as
- possible to the output buffer, and always uses the faster approach on the
- first call. So the effects of the flush parameter in this implementation are
- on the return value of inflate() as noted below, when inflate() returns early
- when Z_BLOCK or Z_TREES is used, and when inflate() avoids the allocation of
- memory for a sliding window when Z_FINISH is used.
-
- If a preset dictionary is needed after this call (see inflateSetDictionary
- below), inflate sets strm->adler to the Adler-32 checksum of the dictionary
- chosen by the compressor and returns Z_NEED_DICT; otherwise it sets
- strm->adler to the Adler-32 checksum of all output produced so far (that is,
- total_out bytes) and returns Z_OK, Z_STREAM_END or an error code as described
- below. At the end of the stream, inflate() checks that its computed adler32
- checksum is equal to that saved by the compressor and returns Z_STREAM_END
- only if the checksum is correct.
-
- inflate() can decompress and check either zlib-wrapped or gzip-wrapped
- deflate data. The header type is detected automatically, if requested when
- initializing with inflateInit2(). Any information contained in the gzip
- header is not retained, so applications that need that information should
- instead use raw inflate, see inflateInit2() below, or inflateBack() and
- perform their own processing of the gzip header and trailer. When processing
- gzip-wrapped deflate data, strm->adler32 is set to the CRC-32 of the output
- producted so far. The CRC-32 is checked against the gzip trailer.
-
- inflate() returns Z_OK if some progress has been made (more input processed
- or more output produced), Z_STREAM_END if the end of the compressed data has
- been reached and all uncompressed output has been produced, Z_NEED_DICT if a
- preset dictionary is needed at this point, Z_DATA_ERROR if the input data was
- corrupted (input stream not conforming to the zlib format or incorrect check
- value), Z_STREAM_ERROR if the stream structure was inconsistent (for example
- next_in or next_out was Z_NULL), Z_MEM_ERROR if there was not enough memory,
- Z_BUF_ERROR if no progress is possible or if there was not enough room in the
- output buffer when Z_FINISH is used. Note that Z_BUF_ERROR is not fatal, and
- inflate() can be called again with more input and more output space to
- continue decompressing. If Z_DATA_ERROR is returned, the application may
- then call inflateSync() to look for a good compression block if a partial
- recovery of the data is desired.
-*/
-
-
-ZEXTERN int ZEXPORT inflateEnd OF((z_streamp strm));
-/*
- All dynamically allocated data structures for this stream are freed.
- This function discards any unprocessed input and does not flush any pending
- output.
-
- inflateEnd returns Z_OK if success, Z_STREAM_ERROR if the stream state
- was inconsistent. In the error case, msg may be set but then points to a
- static string (which must not be deallocated).
-*/
-
-
- /* Advanced functions */
-
-/*
- The following functions are needed only in some special applications.
-*/
-
-/*
-ZEXTERN int ZEXPORT deflateInit2 OF((z_streamp strm,
- int level,
- int method,
- int windowBits,
- int memLevel,
- int strategy));
-
- This is another version of deflateInit with more compression options. The
- fields next_in, zalloc, zfree and opaque must be initialized before by the
- caller.
-
- The method parameter is the compression method. It must be Z_DEFLATED in
- this version of the library.
-
- The windowBits parameter is the base two logarithm of the window size
- (the size of the history buffer). It should be in the range 8..15 for this
- version of the library. Larger values of this parameter result in better
- compression at the expense of memory usage. The default value is 15 if
- deflateInit is used instead.
-
- windowBits can also be -8..-15 for raw deflate. In this case, -windowBits
- determines the window size. deflate() will then generate raw deflate data
- with no zlib header or trailer, and will not compute an adler32 check value.
-
- windowBits can also be greater than 15 for optional gzip encoding. Add
- 16 to windowBits to write a simple gzip header and trailer around the
- compressed data instead of a zlib wrapper. The gzip header will have no
- file name, no extra data, no comment, no modification time (set to zero), no
- header crc, and the operating system will be set to 255 (unknown). If a
- gzip stream is being written, strm->adler is a crc32 instead of an adler32.
-
- The memLevel parameter specifies how much memory should be allocated
- for the internal compression state. memLevel=1 uses minimum memory but is
- slow and reduces compression ratio; memLevel=9 uses maximum memory for
- optimal speed. The default value is 8. See zconf.h for total memory usage
- as a function of windowBits and memLevel.
-
- The strategy parameter is used to tune the compression algorithm. Use the
- value Z_DEFAULT_STRATEGY for normal data, Z_FILTERED for data produced by a
- filter (or predictor), Z_HUFFMAN_ONLY to force Huffman encoding only (no
- string match), or Z_RLE to limit match distances to one (run-length
- encoding). Filtered data consists mostly of small values with a somewhat
- random distribution. In this case, the compression algorithm is tuned to
- compress them better. The effect of Z_FILTERED is to force more Huffman
- coding and less string matching; it is somewhat intermediate between
- Z_DEFAULT_STRATEGY and Z_HUFFMAN_ONLY. Z_RLE is designed to be almost as
- fast as Z_HUFFMAN_ONLY, but give better compression for PNG image data. The
- strategy parameter only affects the compression ratio but not the
- correctness of the compressed output even if it is not set appropriately.
- Z_FIXED prevents the use of dynamic Huffman codes, allowing for a simpler
- decoder for special applications.
-
- deflateInit2 returns Z_OK if success, Z_MEM_ERROR if there was not enough
- memory, Z_STREAM_ERROR if any parameter is invalid (such as an invalid
- method), or Z_VERSION_ERROR if the zlib library version (zlib_version) is
- incompatible with the version assumed by the caller (ZLIB_VERSION). msg is
- set to null if there is no error message. deflateInit2 does not perform any
- compression: this will be done by deflate().
-*/
-
-ZEXTERN int ZEXPORT deflateSetDictionary OF((z_streamp strm,
- const Bytef *dictionary,
- uInt dictLength));
-/*
- Initializes the compression dictionary from the given byte sequence
- without producing any compressed output. When using the zlib format, this
- function must be called immediately after deflateInit, deflateInit2 or
- deflateReset, and before any call of deflate. When doing raw deflate, this
- function must be called either before any call of deflate, or immediately
- after the completion of a deflate block, i.e. after all input has been
- consumed and all output has been delivered when using any of the flush
- options Z_BLOCK, Z_PARTIAL_FLUSH, Z_SYNC_FLUSH, or Z_FULL_FLUSH. The
- compressor and decompressor must use exactly the same dictionary (see
- inflateSetDictionary).
-
- The dictionary should consist of strings (byte sequences) that are likely
- to be encountered later in the data to be compressed, with the most commonly
- used strings preferably put towards the end of the dictionary. Using a
- dictionary is most useful when the data to be compressed is short and can be
- predicted with good accuracy; the data can then be compressed better than
- with the default empty dictionary.
-
- Depending on the size of the compression data structures selected by
- deflateInit or deflateInit2, a part of the dictionary may in effect be
- discarded, for example if the dictionary is larger than the window size
- provided in deflateInit or deflateInit2. Thus the strings most likely to be
- useful should be put at the end of the dictionary, not at the front. In
- addition, the current implementation of deflate will use at most the window
- size minus 262 bytes of the provided dictionary.
-
- Upon return of this function, strm->adler is set to the adler32 value
- of the dictionary; the decompressor may later use this value to determine
- which dictionary has been used by the compressor. (The adler32 value
- applies to the whole dictionary even if only a subset of the dictionary is
- actually used by the compressor.) If a raw deflate was requested, then the
- adler32 value is not computed and strm->adler is not set.
-
- deflateSetDictionary returns Z_OK if success, or Z_STREAM_ERROR if a
- parameter is invalid (e.g. dictionary being Z_NULL) or the stream state is
- inconsistent (for example if deflate has already been called for this stream
- or if not at a block boundary for raw deflate). deflateSetDictionary does
- not perform any compression: this will be done by deflate().
-*/
-
-ZEXTERN int ZEXPORT deflateCopy OF((z_streamp dest,
- z_streamp source));
-/*
- Sets the destination stream as a complete copy of the source stream.
-
- This function can be useful when several compression strategies will be
- tried, for example when there are several ways of pre-processing the input
- data with a filter. The streams that will be discarded should then be freed
- by calling deflateEnd. Note that deflateCopy duplicates the internal
- compression state which can be quite large, so this strategy is slow and can
- consume lots of memory.
-
- deflateCopy returns Z_OK if success, Z_MEM_ERROR if there was not
- enough memory, Z_STREAM_ERROR if the source stream state was inconsistent
- (such as zalloc being Z_NULL). msg is left unchanged in both source and
- destination.
-*/
-
-ZEXTERN int ZEXPORT deflateReset OF((z_streamp strm));
-/*
- This function is equivalent to deflateEnd followed by deflateInit,
- but does not free and reallocate all the internal compression state. The
- stream will keep the same compression level and any other attributes that
- may have been set by deflateInit2.
-
- deflateReset returns Z_OK if success, or Z_STREAM_ERROR if the source
- stream state was inconsistent (such as zalloc or state being Z_NULL).
-*/
-
-ZEXTERN int ZEXPORT deflateParams OF((z_streamp strm,
- int level,
- int strategy));
-/*
- Dynamically update the compression level and compression strategy. The
- interpretation of level and strategy is as in deflateInit2. This can be
- used to switch between compression and straight copy of the input data, or
- to switch to a different kind of input data requiring a different strategy.
- If the compression level is changed, the input available so far is
- compressed with the old level (and may be flushed); the new level will take
- effect only at the next call of deflate().
-
- Before the call of deflateParams, the stream state must be set as for
- a call of deflate(), since the currently available input may have to be
- compressed and flushed. In particular, strm->avail_out must be non-zero.
-
- deflateParams returns Z_OK if success, Z_STREAM_ERROR if the source
- stream state was inconsistent or if a parameter was invalid, Z_BUF_ERROR if
- strm->avail_out was zero.
-*/
-
-ZEXTERN int ZEXPORT deflateTune OF((z_streamp strm,
- int good_length,
- int max_lazy,
- int nice_length,
- int max_chain));
-/*
- Fine tune deflate's internal compression parameters. This should only be
- used by someone who understands the algorithm used by zlib's deflate for
- searching for the best matching string, and even then only by the most
- fanatic optimizer trying to squeeze out the last compressed bit for their
- specific input data. Read the deflate.c source code for the meaning of the
- max_lazy, good_length, nice_length, and max_chain parameters.
-
- deflateTune() can be called after deflateInit() or deflateInit2(), and
- returns Z_OK on success, or Z_STREAM_ERROR for an invalid deflate stream.
- */
-
-ZEXTERN uLong ZEXPORT deflateBound OF((z_streamp strm,
- uLong sourceLen));
-/*
- deflateBound() returns an upper bound on the compressed size after
- deflation of sourceLen bytes. It must be called after deflateInit() or
- deflateInit2(), and after deflateSetHeader(), if used. This would be used
- to allocate an output buffer for deflation in a single pass, and so would be
- called before deflate(). If that first deflate() call is provided the
- sourceLen input bytes, an output buffer allocated to the size returned by
- deflateBound(), and the flush value Z_FINISH, then deflate() is guaranteed
- to return Z_STREAM_END. Note that it is possible for the compressed size to
- be larger than the value returned by deflateBound() if flush options other
- than Z_FINISH or Z_NO_FLUSH are used.
-*/
-
-ZEXTERN int ZEXPORT deflatePending OF((z_streamp strm,
- unsigned *pending,
- int *bits));
-/*
- deflatePending() returns the number of bytes and bits of output that have
- been generated, but not yet provided in the available output. The bytes not
- provided would be due to the available output space having being consumed.
- The number of bits of output not provided are between 0 and 7, where they
- await more bits to join them in order to fill out a full byte. If pending
- or bits are Z_NULL, then those values are not set.
-
- deflatePending returns Z_OK if success, or Z_STREAM_ERROR if the source
- stream state was inconsistent.
- */
-
-ZEXTERN int ZEXPORT deflatePrime OF((z_streamp strm,
- int bits,
- int value));
-/*
- deflatePrime() inserts bits in the deflate output stream. The intent
- is that this function is used to start off the deflate output with the bits
- leftover from a previous deflate stream when appending to it. As such, this
- function can only be used for raw deflate, and must be used before the first
- deflate() call after a deflateInit2() or deflateReset(). bits must be less
- than or equal to 16, and that many of the least significant bits of value
- will be inserted in the output.
-
- deflatePrime returns Z_OK if success, Z_BUF_ERROR if there was not enough
- room in the internal buffer to insert the bits, or Z_STREAM_ERROR if the
- source stream state was inconsistent.
-*/
-
-ZEXTERN int ZEXPORT deflateSetHeader OF((z_streamp strm,
- gz_headerp head));
-/*
- deflateSetHeader() provides gzip header information for when a gzip
- stream is requested by deflateInit2(). deflateSetHeader() may be called
- after deflateInit2() or deflateReset() and before the first call of
- deflate(). The text, time, os, extra field, name, and comment information
- in the provided gz_header structure are written to the gzip header (xflag is
- ignored -- the extra flags are set according to the compression level). The
- caller must assure that, if not Z_NULL, name and comment are terminated with
- a zero byte, and that if extra is not Z_NULL, that extra_len bytes are
- available there. If hcrc is true, a gzip header crc is included. Note that
- the current versions of the command-line version of gzip (up through version
- 1.3.x) do not support header crc's, and will report that it is a "multi-part
- gzip file" and give up.
-
- If deflateSetHeader is not used, the default gzip header has text false,
- the time set to zero, and os set to 255, with no extra, name, or comment
- fields. The gzip header is returned to the default state by deflateReset().
-
- deflateSetHeader returns Z_OK if success, or Z_STREAM_ERROR if the source
- stream state was inconsistent.
-*/
-
-/*
-ZEXTERN int ZEXPORT inflateInit2 OF((z_streamp strm,
- int windowBits));
-
- This is another version of inflateInit with an extra parameter. The
- fields next_in, avail_in, zalloc, zfree and opaque must be initialized
- before by the caller.
-
- The windowBits parameter is the base two logarithm of the maximum window
- size (the size of the history buffer). It should be in the range 8..15 for
- this version of the library. The default value is 15 if inflateInit is used
- instead. windowBits must be greater than or equal to the windowBits value
- provided to deflateInit2() while compressing, or it must be equal to 15 if
- deflateInit2() was not used. If a compressed stream with a larger window
- size is given as input, inflate() will return with the error code
- Z_DATA_ERROR instead of trying to allocate a larger window.
-
- windowBits can also be zero to request that inflate use the window size in
- the zlib header of the compressed stream.
-
- windowBits can also be -8..-15 for raw inflate. In this case, -windowBits
- determines the window size. inflate() will then process raw deflate data,
- not looking for a zlib or gzip header, not generating a check value, and not
- looking for any check values for comparison at the end of the stream. This
- is for use with other formats that use the deflate compressed data format
- such as zip. Those formats provide their own check values. If a custom
- format is developed using the raw deflate format for compressed data, it is
- recommended that a check value such as an adler32 or a crc32 be applied to
- the uncompressed data as is done in the zlib, gzip, and zip formats. For
- most applications, the zlib format should be used as is. Note that comments
- above on the use in deflateInit2() applies to the magnitude of windowBits.
-
- windowBits can also be greater than 15 for optional gzip decoding. Add
- 32 to windowBits to enable zlib and gzip decoding with automatic header
- detection, or add 16 to decode only the gzip format (the zlib format will
- return a Z_DATA_ERROR). If a gzip stream is being decoded, strm->adler is a
- crc32 instead of an adler32.
-
- inflateInit2 returns Z_OK if success, Z_MEM_ERROR if there was not enough
- memory, Z_VERSION_ERROR if the zlib library version is incompatible with the
- version assumed by the caller, or Z_STREAM_ERROR if the parameters are
- invalid, such as a null pointer to the structure. msg is set to null if
- there is no error message. inflateInit2 does not perform any decompression
- apart from possibly reading the zlib header if present: actual decompression
- will be done by inflate(). (So next_in and avail_in may be modified, but
- next_out and avail_out are unused and unchanged.) The current implementation
- of inflateInit2() does not process any header information -- that is
- deferred until inflate() is called.
-*/
-
-ZEXTERN int ZEXPORT inflateSetDictionary OF((z_streamp strm,
- const Bytef *dictionary,
- uInt dictLength));
-/*
- Initializes the decompression dictionary from the given uncompressed byte
- sequence. This function must be called immediately after a call of inflate,
- if that call returned Z_NEED_DICT. The dictionary chosen by the compressor
- can be determined from the adler32 value returned by that call of inflate.
- The compressor and decompressor must use exactly the same dictionary (see
- deflateSetDictionary). For raw inflate, this function can be called at any
- time to set the dictionary. If the provided dictionary is smaller than the
- window and there is already data in the window, then the provided dictionary
- will amend what's there. The application must insure that the dictionary
- that was used for compression is provided.
-
- inflateSetDictionary returns Z_OK if success, Z_STREAM_ERROR if a
- parameter is invalid (e.g. dictionary being Z_NULL) or the stream state is
- inconsistent, Z_DATA_ERROR if the given dictionary doesn't match the
- expected one (incorrect adler32 value). inflateSetDictionary does not
- perform any decompression: this will be done by subsequent calls of
- inflate().
-*/
-
-ZEXTERN int ZEXPORT inflateGetDictionary OF((z_streamp strm,
- Bytef *dictionary,
- uInt *dictLength));
-/*
- Returns the sliding dictionary being maintained by inflate. dictLength is
- set to the number of bytes in the dictionary, and that many bytes are copied
- to dictionary. dictionary must have enough space, where 32768 bytes is
- always enough. If inflateGetDictionary() is called with dictionary equal to
- Z_NULL, then only the dictionary length is returned, and nothing is copied.
- Similary, if dictLength is Z_NULL, then it is not set.
-
- inflateGetDictionary returns Z_OK on success, or Z_STREAM_ERROR if the
- stream state is inconsistent.
-*/
-
-ZEXTERN int ZEXPORT inflateSync OF((z_streamp strm));
-/*
- Skips invalid compressed data until a possible full flush point (see above
- for the description of deflate with Z_FULL_FLUSH) can be found, or until all
- available input is skipped. No output is provided.
-
- inflateSync searches for a 00 00 FF FF pattern in the compressed data.
- All full flush points have this pattern, but not all occurrences of this
- pattern are full flush points.
-
- inflateSync returns Z_OK if a possible full flush point has been found,
- Z_BUF_ERROR if no more input was provided, Z_DATA_ERROR if no flush point
- has been found, or Z_STREAM_ERROR if the stream structure was inconsistent.
- In the success case, the application may save the current current value of
- total_in which indicates where valid compressed data was found. In the
- error case, the application may repeatedly call inflateSync, providing more
- input each time, until success or end of the input data.
-*/
-
-ZEXTERN int ZEXPORT inflateCopy OF((z_streamp dest,
- z_streamp source));
-/*
- Sets the destination stream as a complete copy of the source stream.
-
- This function can be useful when randomly accessing a large stream. The
- first pass through the stream can periodically record the inflate state,
- allowing restarting inflate at those points when randomly accessing the
- stream.
-
- inflateCopy returns Z_OK if success, Z_MEM_ERROR if there was not
- enough memory, Z_STREAM_ERROR if the source stream state was inconsistent
- (such as zalloc being Z_NULL). msg is left unchanged in both source and
- destination.
-*/
-
-ZEXTERN int ZEXPORT inflateReset OF((z_streamp strm));
-/*
- This function is equivalent to inflateEnd followed by inflateInit,
- but does not free and reallocate all the internal decompression state. The
- stream will keep attributes that may have been set by inflateInit2.
-
- inflateReset returns Z_OK if success, or Z_STREAM_ERROR if the source
- stream state was inconsistent (such as zalloc or state being Z_NULL).
-*/
-
-ZEXTERN int ZEXPORT inflateReset2 OF((z_streamp strm,
- int windowBits));
-/*
- This function is the same as inflateReset, but it also permits changing
- the wrap and window size requests. The windowBits parameter is interpreted
- the same as it is for inflateInit2.
-
- inflateReset2 returns Z_OK if success, or Z_STREAM_ERROR if the source
- stream state was inconsistent (such as zalloc or state being Z_NULL), or if
- the windowBits parameter is invalid.
-*/
-
-ZEXTERN int ZEXPORT inflatePrime OF((z_streamp strm,
- int bits,
- int value));
-/*
- This function inserts bits in the inflate input stream. The intent is
- that this function is used to start inflating at a bit position in the
- middle of a byte. The provided bits will be used before any bytes are used
- from next_in. This function should only be used with raw inflate, and
- should be used before the first inflate() call after inflateInit2() or
- inflateReset(). bits must be less than or equal to 16, and that many of the
- least significant bits of value will be inserted in the input.
-
- If bits is negative, then the input stream bit buffer is emptied. Then
- inflatePrime() can be called again to put bits in the buffer. This is used
- to clear out bits leftover after feeding inflate a block description prior
- to feeding inflate codes.
-
- inflatePrime returns Z_OK if success, or Z_STREAM_ERROR if the source
- stream state was inconsistent.
-*/
-
-ZEXTERN long ZEXPORT inflateMark OF((z_streamp strm));
-/*
- This function returns two values, one in the lower 16 bits of the return
- value, and the other in the remaining upper bits, obtained by shifting the
- return value down 16 bits. If the upper value is -1 and the lower value is
- zero, then inflate() is currently decoding information outside of a block.
- If the upper value is -1 and the lower value is non-zero, then inflate is in
- the middle of a stored block, with the lower value equaling the number of
- bytes from the input remaining to copy. If the upper value is not -1, then
- it is the number of bits back from the current bit position in the input of
- the code (literal or length/distance pair) currently being processed. In
- that case the lower value is the number of bytes already emitted for that
- code.
-
- A code is being processed if inflate is waiting for more input to complete
- decoding of the code, or if it has completed decoding but is waiting for
- more output space to write the literal or match data.
-
- inflateMark() is used to mark locations in the input data for random
- access, which may be at bit positions, and to note those cases where the
- output of a code may span boundaries of random access blocks. The current
- location in the input stream can be determined from avail_in and data_type
- as noted in the description for the Z_BLOCK flush parameter for inflate.
-
- inflateMark returns the value noted above or -1 << 16 if the provided
- source stream state was inconsistent.
-*/
-
-ZEXTERN int ZEXPORT inflateGetHeader OF((z_streamp strm,
- gz_headerp head));
-/*
- inflateGetHeader() requests that gzip header information be stored in the
- provided gz_header structure. inflateGetHeader() may be called after
- inflateInit2() or inflateReset(), and before the first call of inflate().
- As inflate() processes the gzip stream, head->done is zero until the header
- is completed, at which time head->done is set to one. If a zlib stream is
- being decoded, then head->done is set to -1 to indicate that there will be
- no gzip header information forthcoming. Note that Z_BLOCK or Z_TREES can be
- used to force inflate() to return immediately after header processing is
- complete and before any actual data is decompressed.
-
- The text, time, xflags, and os fields are filled in with the gzip header
- contents. hcrc is set to true if there is a header CRC. (The header CRC
- was valid if done is set to one.) If extra is not Z_NULL, then extra_max
- contains the maximum number of bytes to write to extra. Once done is true,
- extra_len contains the actual extra field length, and extra contains the
- extra field, or that field truncated if extra_max is less than extra_len.
- If name is not Z_NULL, then up to name_max characters are written there,
- terminated with a zero unless the length is greater than name_max. If
- comment is not Z_NULL, then up to comm_max characters are written there,
- terminated with a zero unless the length is greater than comm_max. When any
- of extra, name, or comment are not Z_NULL and the respective field is not
- present in the header, then that field is set to Z_NULL to signal its
- absence. This allows the use of deflateSetHeader() with the returned
- structure to duplicate the header. However if those fields are set to
- allocated memory, then the application will need to save those pointers
- elsewhere so that they can be eventually freed.
-
- If inflateGetHeader is not used, then the header information is simply
- discarded. The header is always checked for validity, including the header
- CRC if present. inflateReset() will reset the process to discard the header
- information. The application would need to call inflateGetHeader() again to
- retrieve the header from the next gzip stream.
-
- inflateGetHeader returns Z_OK if success, or Z_STREAM_ERROR if the source
- stream state was inconsistent.
-*/
-
-/*
-ZEXTERN int ZEXPORT inflateBackInit OF((z_streamp strm, int windowBits,
- unsigned char FAR *window));
-
- Initialize the internal stream state for decompression using inflateBack()
- calls. The fields zalloc, zfree and opaque in strm must be initialized
- before the call. If zalloc and zfree are Z_NULL, then the default library-
- derived memory allocation routines are used. windowBits is the base two
- logarithm of the window size, in the range 8..15. window is a caller
- supplied buffer of that size. Except for special applications where it is
- assured that deflate was used with small window sizes, windowBits must be 15
- and a 32K byte window must be supplied to be able to decompress general
- deflate streams.
-
- See inflateBack() for the usage of these routines.
-
- inflateBackInit will return Z_OK on success, Z_STREAM_ERROR if any of
- the parameters are invalid, Z_MEM_ERROR if the internal state could not be
- allocated, or Z_VERSION_ERROR if the version of the library does not match
- the version of the header file.
-*/
-
-typedef unsigned (*in_func) OF((void FAR *,
- z_const unsigned char FAR * FAR *));
-typedef int (*out_func) OF((void FAR *, unsigned char FAR *, unsigned));
-
-ZEXTERN int ZEXPORT inflateBack OF((z_streamp strm,
- in_func in, void FAR *in_desc,
- out_func out, void FAR *out_desc));
-/*
- inflateBack() does a raw inflate with a single call using a call-back
- interface for input and output. This is potentially more efficient than
- inflate() for file i/o applications, in that it avoids copying between the
- output and the sliding window by simply making the window itself the output
- buffer. inflate() can be faster on modern CPUs when used with large
- buffers. inflateBack() trusts the application to not change the output
- buffer passed by the output function, at least until inflateBack() returns.
-
- inflateBackInit() must be called first to allocate the internal state
- and to initialize the state with the user-provided window buffer.
- inflateBack() may then be used multiple times to inflate a complete, raw
- deflate stream with each call. inflateBackEnd() is then called to free the
- allocated state.
-
- A raw deflate stream is one with no zlib or gzip header or trailer.
- This routine would normally be used in a utility that reads zip or gzip
- files and writes out uncompressed files. The utility would decode the
- header and process the trailer on its own, hence this routine expects only
- the raw deflate stream to decompress. This is different from the normal
- behavior of inflate(), which expects either a zlib or gzip header and
- trailer around the deflate stream.
-
- inflateBack() uses two subroutines supplied by the caller that are then
- called by inflateBack() for input and output. inflateBack() calls those
- routines until it reads a complete deflate stream and writes out all of the
- uncompressed data, or until it encounters an error. The function's
- parameters and return types are defined above in the in_func and out_func
- typedefs. inflateBack() will call in(in_desc, &buf) which should return the
- number of bytes of provided input, and a pointer to that input in buf. If
- there is no input available, in() must return zero--buf is ignored in that
- case--and inflateBack() will return a buffer error. inflateBack() will call
- out(out_desc, buf, len) to write the uncompressed data buf[0..len-1]. out()
- should return zero on success, or non-zero on failure. If out() returns
- non-zero, inflateBack() will return with an error. Neither in() nor out()
- are permitted to change the contents of the window provided to
- inflateBackInit(), which is also the buffer that out() uses to write from.
- The length written by out() will be at most the window size. Any non-zero
- amount of input may be provided by in().
-
- For convenience, inflateBack() can be provided input on the first call by
- setting strm->next_in and strm->avail_in. If that input is exhausted, then
- in() will be called. Therefore strm->next_in must be initialized before
- calling inflateBack(). If strm->next_in is Z_NULL, then in() will be called
- immediately for input. If strm->next_in is not Z_NULL, then strm->avail_in
- must also be initialized, and then if strm->avail_in is not zero, input will
- initially be taken from strm->next_in[0 .. strm->avail_in - 1].
-
- The in_desc and out_desc parameters of inflateBack() is passed as the
- first parameter of in() and out() respectively when they are called. These
- descriptors can be optionally used to pass any information that the caller-
- supplied in() and out() functions need to do their job.
-
- On return, inflateBack() will set strm->next_in and strm->avail_in to
- pass back any unused input that was provided by the last in() call. The
- return values of inflateBack() can be Z_STREAM_END on success, Z_BUF_ERROR
- if in() or out() returned an error, Z_DATA_ERROR if there was a format error
- in the deflate stream (in which case strm->msg is set to indicate the nature
- of the error), or Z_STREAM_ERROR if the stream was not properly initialized.
- In the case of Z_BUF_ERROR, an input or output error can be distinguished
- using strm->next_in which will be Z_NULL only if in() returned an error. If
- strm->next_in is not Z_NULL, then the Z_BUF_ERROR was due to out() returning
- non-zero. (in() will always be called before out(), so strm->next_in is
- assured to be defined if out() returns non-zero.) Note that inflateBack()
- cannot return Z_OK.
-*/
-
-ZEXTERN int ZEXPORT inflateBackEnd OF((z_streamp strm));
-/*
- All memory allocated by inflateBackInit() is freed.
-
- inflateBackEnd() returns Z_OK on success, or Z_STREAM_ERROR if the stream
- state was inconsistent.
-*/
-
-ZEXTERN uLong ZEXPORT zlibCompileFlags OF((void));
-/* Return flags indicating compile-time options.
-
- Type sizes, two bits each, 00 = 16 bits, 01 = 32, 10 = 64, 11 = other:
- 1.0: size of uInt
- 3.2: size of uLong
- 5.4: size of voidpf (pointer)
- 7.6: size of z_off_t
-
- Compiler, assembler, and debug options:
- 8: DEBUG
- 9: ASMV or ASMINF -- use ASM code
- 10: ZLIB_WINAPI -- exported functions use the WINAPI calling convention
- 11: 0 (reserved)
-
- One-time table building (smaller code, but not thread-safe if true):
- 12: BUILDFIXED -- build static block decoding tables when needed
- 13: DYNAMIC_CRC_TABLE -- build CRC calculation tables when needed
- 14,15: 0 (reserved)
-
- Library content (indicates missing functionality):
- 16: NO_GZCOMPRESS -- gz* functions cannot compress (to avoid linking
- deflate code when not needed)
- 17: NO_GZIP -- deflate can't write gzip streams, and inflate can't detect
- and decode gzip streams (to avoid linking crc code)
- 18-19: 0 (reserved)
-
- Operation variations (changes in library functionality):
- 20: PKZIP_BUG_WORKAROUND -- slightly more permissive inflate
- 21: FASTEST -- deflate algorithm with only one, lowest compression level
- 22,23: 0 (reserved)
-
- The sprintf variant used by gzprintf (zero is best):
- 24: 0 = vs*, 1 = s* -- 1 means limited to 20 arguments after the format
- 25: 0 = *nprintf, 1 = *printf -- 1 means gzprintf() not secure!
- 26: 0 = returns value, 1 = void -- 1 means inferred string length returned
-
- Remainder:
- 27-31: 0 (reserved)
- */
-
-#ifndef Z_SOLO
-
- /* utility functions */
-
-/*
- The following utility functions are implemented on top of the basic
- stream-oriented functions. To simplify the interface, some default options
- are assumed (compression level and memory usage, standard memory allocation
- functions). The source code of these utility functions can be modified if
- you need special options.
-*/
-
-ZEXTERN int ZEXPORT compress OF((Bytef *dest, uLongf *destLen,
- const Bytef *source, uLong sourceLen));
-/*
- Compresses the source buffer into the destination buffer. sourceLen is
- the byte length of the source buffer. Upon entry, destLen is the total size
- of the destination buffer, which must be at least the value returned by
- compressBound(sourceLen). Upon exit, destLen is the actual size of the
- compressed buffer.
-
- compress returns Z_OK if success, Z_MEM_ERROR if there was not
- enough memory, Z_BUF_ERROR if there was not enough room in the output
- buffer.
-*/
-
-ZEXTERN int ZEXPORT compress2 OF((Bytef *dest, uLongf *destLen,
- const Bytef *source, uLong sourceLen,
- int level));
-/*
- Compresses the source buffer into the destination buffer. The level
- parameter has the same meaning as in deflateInit. sourceLen is the byte
- length of the source buffer. Upon entry, destLen is the total size of the
- destination buffer, which must be at least the value returned by
- compressBound(sourceLen). Upon exit, destLen is the actual size of the
- compressed buffer.
-
- compress2 returns Z_OK if success, Z_MEM_ERROR if there was not enough
- memory, Z_BUF_ERROR if there was not enough room in the output buffer,
- Z_STREAM_ERROR if the level parameter is invalid.
-*/
-
-ZEXTERN uLong ZEXPORT compressBound OF((uLong sourceLen));
-/*
- compressBound() returns an upper bound on the compressed size after
- compress() or compress2() on sourceLen bytes. It would be used before a
- compress() or compress2() call to allocate the destination buffer.
-*/
-
-ZEXTERN int ZEXPORT uncompress OF((Bytef *dest, uLongf *destLen,
- const Bytef *source, uLong sourceLen));
-/*
- Decompresses the source buffer into the destination buffer. sourceLen is
- the byte length of the source buffer. Upon entry, destLen is the total size
- of the destination buffer, which must be large enough to hold the entire
- uncompressed data. (The size of the uncompressed data must have been saved
- previously by the compressor and transmitted to the decompressor by some
- mechanism outside the scope of this compression library.) Upon exit, destLen
- is the actual size of the uncompressed buffer.
-
- uncompress returns Z_OK if success, Z_MEM_ERROR if there was not
- enough memory, Z_BUF_ERROR if there was not enough room in the output
- buffer, or Z_DATA_ERROR if the input data was corrupted or incomplete. In
- the case where there is not enough room, uncompress() will fill the output
- buffer with the uncompressed data up to that point.
-*/
-
- /* gzip file access functions */
-
-/*
- This library supports reading and writing files in gzip (.gz) format with
- an interface similar to that of stdio, using the functions that start with
- "gz". The gzip format is different from the zlib format. gzip is a gzip
- wrapper, documented in RFC 1952, wrapped around a deflate stream.
-*/
-
-typedef struct gzFile_s *gzFile; /* semi-opaque gzip file descriptor */
-
-/*
-ZEXTERN gzFile ZEXPORT gzopen OF((const char *path, const char *mode));
-
- Opens a gzip (.gz) file for reading or writing. The mode parameter is as
- in fopen ("rb" or "wb") but can also include a compression level ("wb9") or
- a strategy: 'f' for filtered data as in "wb6f", 'h' for Huffman-only
- compression as in "wb1h", 'R' for run-length encoding as in "wb1R", or 'F'
- for fixed code compression as in "wb9F". (See the description of
- deflateInit2 for more information about the strategy parameter.) 'T' will
- request transparent writing or appending with no compression and not using
- the gzip format.
-
- "a" can be used instead of "w" to request that the gzip stream that will
- be written be appended to the file. "+" will result in an error, since
- reading and writing to the same gzip file is not supported. The addition of
- "x" when writing will create the file exclusively, which fails if the file
- already exists. On systems that support it, the addition of "e" when
- reading or writing will set the flag to close the file on an execve() call.
-
- These functions, as well as gzip, will read and decode a sequence of gzip
- streams in a file. The append function of gzopen() can be used to create
- such a file. (Also see gzflush() for another way to do this.) When
- appending, gzopen does not test whether the file begins with a gzip stream,
- nor does it look for the end of the gzip streams to begin appending. gzopen
- will simply append a gzip stream to the existing file.
-
- gzopen can be used to read a file which is not in gzip format; in this
- case gzread will directly read from the file without decompression. When
- reading, this will be detected automatically by looking for the magic two-
- byte gzip header.
-
- gzopen returns NULL if the file could not be opened, if there was
- insufficient memory to allocate the gzFile state, or if an invalid mode was
- specified (an 'r', 'w', or 'a' was not provided, or '+' was provided).
- errno can be checked to determine if the reason gzopen failed was that the
- file could not be opened.
-*/
-
-ZEXTERN gzFile ZEXPORT gzdopen OF((int fd, const char *mode));
-/*
- gzdopen associates a gzFile with the file descriptor fd. File descriptors
- are obtained from calls like open, dup, creat, pipe or fileno (if the file
- has been previously opened with fopen). The mode parameter is as in gzopen.
-
- The next call of gzclose on the returned gzFile will also close the file
- descriptor fd, just like fclose(fdopen(fd, mode)) closes the file descriptor
- fd. If you want to keep fd open, use fd = dup(fd_keep); gz = gzdopen(fd,
- mode);. The duplicated descriptor should be saved to avoid a leak, since
- gzdopen does not close fd if it fails. If you are using fileno() to get the
- file descriptor from a FILE *, then you will have to use dup() to avoid
- double-close()ing the file descriptor. Both gzclose() and fclose() will
- close the associated file descriptor, so they need to have different file
- descriptors.
-
- gzdopen returns NULL if there was insufficient memory to allocate the
- gzFile state, if an invalid mode was specified (an 'r', 'w', or 'a' was not
- provided, or '+' was provided), or if fd is -1. The file descriptor is not
- used until the next gz* read, write, seek, or close operation, so gzdopen
- will not detect if fd is invalid (unless fd is -1).
-*/
-
-ZEXTERN int ZEXPORT gzbuffer OF((gzFile file, unsigned size));
-/*
- Set the internal buffer size used by this library's functions. The
- default buffer size is 8192 bytes. This function must be called after
- gzopen() or gzdopen(), and before any other calls that read or write the
- file. The buffer memory allocation is always deferred to the first read or
- write. Two buffers are allocated, either both of the specified size when
- writing, or one of the specified size and the other twice that size when
- reading. A larger buffer size of, for example, 64K or 128K bytes will
- noticeably increase the speed of decompression (reading).
-
- The new buffer size also affects the maximum length for gzprintf().
-
- gzbuffer() returns 0 on success, or -1 on failure, such as being called
- too late.
-*/
-
-ZEXTERN int ZEXPORT gzsetparams OF((gzFile file, int level, int strategy));
-/*
- Dynamically update the compression level or strategy. See the description
- of deflateInit2 for the meaning of these parameters.
-
- gzsetparams returns Z_OK if success, or Z_STREAM_ERROR if the file was not
- opened for writing.
-*/
-
-ZEXTERN int ZEXPORT gzread OF((gzFile file, voidp buf, unsigned len));
-/*
- Reads the given number of uncompressed bytes from the compressed file. If
- the input file is not in gzip format, gzread copies the given number of
- bytes into the buffer directly from the file.
-
- After reaching the end of a gzip stream in the input, gzread will continue
- to read, looking for another gzip stream. Any number of gzip streams may be
- concatenated in the input file, and will all be decompressed by gzread().
- If something other than a gzip stream is encountered after a gzip stream,
- that remaining trailing garbage is ignored (and no error is returned).
-
- gzread can be used to read a gzip file that is being concurrently written.
- Upon reaching the end of the input, gzread will return with the available
- data. If the error code returned by gzerror is Z_OK or Z_BUF_ERROR, then
- gzclearerr can be used to clear the end of file indicator in order to permit
- gzread to be tried again. Z_OK indicates that a gzip stream was completed
- on the last gzread. Z_BUF_ERROR indicates that the input file ended in the
- middle of a gzip stream. Note that gzread does not return -1 in the event
- of an incomplete gzip stream. This error is deferred until gzclose(), which
- will return Z_BUF_ERROR if the last gzread ended in the middle of a gzip
- stream. Alternatively, gzerror can be used before gzclose to detect this
- case.
-
- gzread returns the number of uncompressed bytes actually read, less than
- len for end of file, or -1 for error.
-*/
-
-ZEXTERN int ZEXPORT gzwrite OF((gzFile file,
- voidpc buf, unsigned len));
-/*
- Writes the given number of uncompressed bytes into the compressed file.
- gzwrite returns the number of uncompressed bytes written or 0 in case of
- error.
-*/
-
-ZEXTERN int ZEXPORTVA gzprintf Z_ARG((gzFile file, const char *format, ...));
-/*
- Converts, formats, and writes the arguments to the compressed file under
- control of the format string, as in fprintf. gzprintf returns the number of
- uncompressed bytes actually written, or 0 in case of error. The number of
- uncompressed bytes written is limited to 8191, or one less than the buffer
- size given to gzbuffer(). The caller should assure that this limit is not
- exceeded. If it is exceeded, then gzprintf() will return an error (0) with
- nothing written. In this case, there may also be a buffer overflow with
- unpredictable consequences, which is possible only if zlib was compiled with
- the insecure functions sprintf() or vsprintf() because the secure snprintf()
- or vsnprintf() functions were not available. This can be determined using
- zlibCompileFlags().
-*/
-
-ZEXTERN int ZEXPORT gzputs OF((gzFile file, const char *s));
-/*
- Writes the given null-terminated string to the compressed file, excluding
- the terminating null character.
-
- gzputs returns the number of characters written, or -1 in case of error.
-*/
-
-ZEXTERN char * ZEXPORT gzgets OF((gzFile file, char *buf, int len));
-/*
- Reads bytes from the compressed file until len-1 characters are read, or a
- newline character is read and transferred to buf, or an end-of-file
- condition is encountered. If any characters are read or if len == 1, the
- string is terminated with a null character. If no characters are read due
- to an end-of-file or len < 1, then the buffer is left untouched.
-
- gzgets returns buf which is a null-terminated string, or it returns NULL
- for end-of-file or in case of error. If there was an error, the contents at
- buf are indeterminate.
-*/
-
-ZEXTERN int ZEXPORT gzputc OF((gzFile file, int c));
-/*
- Writes c, converted to an unsigned char, into the compressed file. gzputc
- returns the value that was written, or -1 in case of error.
-*/
-
-ZEXTERN int ZEXPORT gzgetc OF((gzFile file));
-/*
- Reads one byte from the compressed file. gzgetc returns this byte or -1
- in case of end of file or error. This is implemented as a macro for speed.
- As such, it does not do all of the checking the other functions do. I.e.
- it does not check to see if file is NULL, nor whether the structure file
- points to has been clobbered or not.
-*/
-
-ZEXTERN int ZEXPORT gzungetc OF((int c, gzFile file));
-/*
- Push one character back onto the stream to be read as the first character
- on the next read. At least one character of push-back is allowed.
- gzungetc() returns the character pushed, or -1 on failure. gzungetc() will
- fail if c is -1, and may fail if a character has been pushed but not read
- yet. If gzungetc is used immediately after gzopen or gzdopen, at least the
- output buffer size of pushed characters is allowed. (See gzbuffer above.)
- The pushed character will be discarded if the stream is repositioned with
- gzseek() or gzrewind().
-*/
-
-ZEXTERN int ZEXPORT gzflush OF((gzFile file, int flush));
-/*
- Flushes all pending output into the compressed file. The parameter flush
- is as in the deflate() function. The return value is the zlib error number
- (see function gzerror below). gzflush is only permitted when writing.
-
- If the flush parameter is Z_FINISH, the remaining data is written and the
- gzip stream is completed in the output. If gzwrite() is called again, a new
- gzip stream will be started in the output. gzread() is able to read such
- concatented gzip streams.
-
- gzflush should be called only when strictly necessary because it will
- degrade compression if called too often.
-*/
-
-/*
-ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile file,
- z_off_t offset, int whence));
-
- Sets the starting position for the next gzread or gzwrite on the given
- compressed file. The offset represents a number of bytes in the
- uncompressed data stream. The whence parameter is defined as in lseek(2);
- the value SEEK_END is not supported.
-
- If the file is opened for reading, this function is emulated but can be
- extremely slow. If the file is opened for writing, only forward seeks are
- supported; gzseek then compresses a sequence of zeroes up to the new
- starting position.
-
- gzseek returns the resulting offset location as measured in bytes from
- the beginning of the uncompressed stream, or -1 in case of error, in
- particular if the file is opened for writing and the new starting position
- would be before the current position.
-*/
-
-ZEXTERN int ZEXPORT gzrewind OF((gzFile file));
-/*
- Rewinds the given file. This function is supported only for reading.
-
- gzrewind(file) is equivalent to (int)gzseek(file, 0L, SEEK_SET)
-*/
-
-/*
-ZEXTERN z_off_t ZEXPORT gztell OF((gzFile file));
-
- Returns the starting position for the next gzread or gzwrite on the given
- compressed file. This position represents a number of bytes in the
- uncompressed data stream, and is zero when starting, even if appending or
- reading a gzip stream from the middle of a file using gzdopen().
-
- gztell(file) is equivalent to gzseek(file, 0L, SEEK_CUR)
-*/
-
-/*
-ZEXTERN z_off_t ZEXPORT gzoffset OF((gzFile file));
-
- Returns the current offset in the file being read or written. This offset
- includes the count of bytes that precede the gzip stream, for example when
- appending or when using gzdopen() for reading. When reading, the offset
- does not include as yet unused buffered input. This information can be used
- for a progress indicator. On error, gzoffset() returns -1.
-*/
-
-ZEXTERN int ZEXPORT gzeof OF((gzFile file));
-/*
- Returns true (1) if the end-of-file indicator has been set while reading,
- false (0) otherwise. Note that the end-of-file indicator is set only if the
- read tried to go past the end of the input, but came up short. Therefore,
- just like feof(), gzeof() may return false even if there is no more data to
- read, in the event that the last read request was for the exact number of
- bytes remaining in the input file. This will happen if the input file size
- is an exact multiple of the buffer size.
-
- If gzeof() returns true, then the read functions will return no more data,
- unless the end-of-file indicator is reset by gzclearerr() and the input file
- has grown since the previous end of file was detected.
-*/
-
-ZEXTERN int ZEXPORT gzdirect OF((gzFile file));
-/*
- Returns true (1) if file is being copied directly while reading, or false
- (0) if file is a gzip stream being decompressed.
-
- If the input file is empty, gzdirect() will return true, since the input
- does not contain a gzip stream.
-
- If gzdirect() is used immediately after gzopen() or gzdopen() it will
- cause buffers to be allocated to allow reading the file to determine if it
- is a gzip file. Therefore if gzbuffer() is used, it should be called before
- gzdirect().
-
- When writing, gzdirect() returns true (1) if transparent writing was
- requested ("wT" for the gzopen() mode), or false (0) otherwise. (Note:
- gzdirect() is not needed when writing. Transparent writing must be
- explicitly requested, so the application already knows the answer. When
- linking statically, using gzdirect() will include all of the zlib code for
- gzip file reading and decompression, which may not be desired.)
-*/
-
-ZEXTERN int ZEXPORT gzclose OF((gzFile file));
-/*
- Flushes all pending output if necessary, closes the compressed file and
- deallocates the (de)compression state. Note that once file is closed, you
- cannot call gzerror with file, since its structures have been deallocated.
- gzclose must not be called more than once on the same file, just as free
- must not be called more than once on the same allocation.
-
- gzclose will return Z_STREAM_ERROR if file is not valid, Z_ERRNO on a
- file operation error, Z_MEM_ERROR if out of memory, Z_BUF_ERROR if the
- last read ended in the middle of a gzip stream, or Z_OK on success.
-*/
-
-ZEXTERN int ZEXPORT gzclose_r OF((gzFile file));
-ZEXTERN int ZEXPORT gzclose_w OF((gzFile file));
-/*
- Same as gzclose(), but gzclose_r() is only for use when reading, and
- gzclose_w() is only for use when writing or appending. The advantage to
- using these instead of gzclose() is that they avoid linking in zlib
- compression or decompression code that is not used when only reading or only
- writing respectively. If gzclose() is used, then both compression and
- decompression code will be included the application when linking to a static
- zlib library.
-*/
-
-ZEXTERN const char * ZEXPORT gzerror OF((gzFile file, int *errnum));
-/*
- Returns the error message for the last error which occurred on the given
- compressed file. errnum is set to zlib error number. If an error occurred
- in the file system and not in the compression library, errnum is set to
- Z_ERRNO and the application may consult errno to get the exact error code.
-
- The application must not modify the returned string. Future calls to
- this function may invalidate the previously returned string. If file is
- closed, then the string previously returned by gzerror will no longer be
- available.
-
- gzerror() should be used to distinguish errors from end-of-file for those
- functions above that do not distinguish those cases in their return values.
-*/
-
-ZEXTERN void ZEXPORT gzclearerr OF((gzFile file));
-/*
- Clears the error and end-of-file flags for file. This is analogous to the
- clearerr() function in stdio. This is useful for continuing to read a gzip
- file that is being written concurrently.
-*/
-
-#endif /* !Z_SOLO */
-
- /* checksum functions */
-
-/*
- These functions are not related to compression but are exported
- anyway because they might be useful in applications using the compression
- library.
-*/
-
-ZEXTERN uLong ZEXPORT adler32 OF((uLong adler, const Bytef *buf, uInt len));
-/*
- Update a running Adler-32 checksum with the bytes buf[0..len-1] and
- return the updated checksum. If buf is Z_NULL, this function returns the
- required initial value for the checksum.
-
- An Adler-32 checksum is almost as reliable as a CRC32 but can be computed
- much faster.
-
- Usage example:
-
- uLong adler = adler32(0L, Z_NULL, 0);
-
- while (read_buffer(buffer, length) != EOF) {
- adler = adler32(adler, buffer, length);
- }
- if (adler != original_adler) error();
-*/
-
-/*
-ZEXTERN uLong ZEXPORT adler32_combine OF((uLong adler1, uLong adler2,
- z_off_t len2));
-
- Combine two Adler-32 checksums into one. For two sequences of bytes, seq1
- and seq2 with lengths len1 and len2, Adler-32 checksums were calculated for
- each, adler1 and adler2. adler32_combine() returns the Adler-32 checksum of
- seq1 and seq2 concatenated, requiring only adler1, adler2, and len2. Note
- that the z_off_t type (like off_t) is a signed integer. If len2 is
- negative, the result has no meaning or utility.
-*/
-
-ZEXTERN uLong ZEXPORT crc32 OF((uLong crc, const Bytef *buf, uInt len));
-/*
- Update a running CRC-32 with the bytes buf[0..len-1] and return the
- updated CRC-32. If buf is Z_NULL, this function returns the required
- initial value for the crc. Pre- and post-conditioning (one's complement) is
- performed within this function so it shouldn't be done by the application.
-
- Usage example:
-
- uLong crc = crc32(0L, Z_NULL, 0);
-
- while (read_buffer(buffer, length) != EOF) {
- crc = crc32(crc, buffer, length);
- }
- if (crc != original_crc) error();
-*/
-
-/*
-ZEXTERN uLong ZEXPORT crc32_combine OF((uLong crc1, uLong crc2, z_off_t len2));
-
- Combine two CRC-32 check values into one. For two sequences of bytes,
- seq1 and seq2 with lengths len1 and len2, CRC-32 check values were
- calculated for each, crc1 and crc2. crc32_combine() returns the CRC-32
- check value of seq1 and seq2 concatenated, requiring only crc1, crc2, and
- len2.
-*/
-
-
- /* various hacks, don't look :) */
-
-/* deflateInit and inflateInit are macros to allow checking the zlib version
- * and the compiler's view of z_stream:
- */
-ZEXTERN int ZEXPORT deflateInit_ OF((z_streamp strm, int level,
- const char *version, int stream_size));
-ZEXTERN int ZEXPORT inflateInit_ OF((z_streamp strm,
- const char *version, int stream_size));
-ZEXTERN int ZEXPORT deflateInit2_ OF((z_streamp strm, int level, int method,
- int windowBits, int memLevel,
- int strategy, const char *version,
- int stream_size));
-ZEXTERN int ZEXPORT inflateInit2_ OF((z_streamp strm, int windowBits,
- const char *version, int stream_size));
-ZEXTERN int ZEXPORT inflateBackInit_ OF((z_streamp strm, int windowBits,
- unsigned char FAR *window,
- const char *version,
- int stream_size));
-#define deflateInit(strm, level) \
- deflateInit_((strm), (level), ZLIB_VERSION, (int)sizeof(z_stream))
-#define inflateInit(strm) \
- inflateInit_((strm), ZLIB_VERSION, (int)sizeof(z_stream))
-#define deflateInit2(strm, level, method, windowBits, memLevel, strategy) \
- deflateInit2_((strm),(level),(method),(windowBits),(memLevel),\
- (strategy), ZLIB_VERSION, (int)sizeof(z_stream))
-#define inflateInit2(strm, windowBits) \
- inflateInit2_((strm), (windowBits), ZLIB_VERSION, \
- (int)sizeof(z_stream))
-#define inflateBackInit(strm, windowBits, window) \
- inflateBackInit_((strm), (windowBits), (window), \
- ZLIB_VERSION, (int)sizeof(z_stream))
-
-#ifndef Z_SOLO
-
-/* gzgetc() macro and its supporting function and exposed data structure. Note
- * that the real internal state is much larger than the exposed structure.
- * This abbreviated structure exposes just enough for the gzgetc() macro. The
- * user should not mess with these exposed elements, since their names or
- * behavior could change in the future, perhaps even capriciously. They can
- * only be used by the gzgetc() macro. You have been warned.
- */
-struct gzFile_s {
- unsigned have;
- unsigned char *next;
- z_off64_t pos;
-};
-ZEXTERN int ZEXPORT gzgetc_ OF((gzFile file)); /* backward compatibility */
-#ifdef Z_PREFIX_SET
-# undef z_gzgetc
-# define z_gzgetc(g) \
- ((g)->have ? ((g)->have--, (g)->pos++, *((g)->next)++) : gzgetc(g))
-#else
-# define gzgetc(g) \
- ((g)->have ? ((g)->have--, (g)->pos++, *((g)->next)++) : gzgetc(g))
-#endif
-
-/* provide 64-bit offset functions if _LARGEFILE64_SOURCE defined, and/or
- * change the regular functions to 64 bits if _FILE_OFFSET_BITS is 64 (if
- * both are true, the application gets the *64 functions, and the regular
- * functions are changed to 64 bits) -- in case these are set on systems
- * without large file support, _LFS64_LARGEFILE must also be true
- */
-#ifdef Z_LARGE64
- ZEXTERN gzFile ZEXPORT gzopen64 OF((const char *, const char *));
- ZEXTERN z_off64_t ZEXPORT gzseek64 OF((gzFile, z_off64_t, int));
- ZEXTERN z_off64_t ZEXPORT gztell64 OF((gzFile));
- ZEXTERN z_off64_t ZEXPORT gzoffset64 OF((gzFile));
- ZEXTERN uLong ZEXPORT adler32_combine64 OF((uLong, uLong, z_off64_t));
- ZEXTERN uLong ZEXPORT crc32_combine64 OF((uLong, uLong, z_off64_t));
-#endif
-
-#if !defined(ZLIB_INTERNAL) && defined(Z_WANT64)
-# ifdef Z_PREFIX_SET
-# define z_gzopen z_gzopen64
-# define z_gzseek z_gzseek64
-# define z_gztell z_gztell64
-# define z_gzoffset z_gzoffset64
-# define z_adler32_combine z_adler32_combine64
-# define z_crc32_combine z_crc32_combine64
-# else
-# define gzopen gzopen64
-# define gzseek gzseek64
-# define gztell gztell64
-# define gzoffset gzoffset64
-# define adler32_combine adler32_combine64
-# define crc32_combine crc32_combine64
-# endif
-# ifndef Z_LARGE64
- ZEXTERN gzFile ZEXPORT gzopen64 OF((const char *, const char *));
- ZEXTERN z_off_t ZEXPORT gzseek64 OF((gzFile, z_off_t, int));
- ZEXTERN z_off_t ZEXPORT gztell64 OF((gzFile));
- ZEXTERN z_off_t ZEXPORT gzoffset64 OF((gzFile));
- ZEXTERN uLong ZEXPORT adler32_combine64 OF((uLong, uLong, z_off_t));
- ZEXTERN uLong ZEXPORT crc32_combine64 OF((uLong, uLong, z_off_t));
-# endif
-#else
- ZEXTERN gzFile ZEXPORT gzopen OF((const char *, const char *));
- ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int));
- ZEXTERN z_off_t ZEXPORT gztell OF((gzFile));
- ZEXTERN z_off_t ZEXPORT gzoffset OF((gzFile));
- ZEXTERN uLong ZEXPORT adler32_combine OF((uLong, uLong, z_off_t));
- ZEXTERN uLong ZEXPORT crc32_combine OF((uLong, uLong, z_off_t));
-#endif
-
-#else /* Z_SOLO */
-
- ZEXTERN uLong ZEXPORT adler32_combine OF((uLong, uLong, z_off_t));
- ZEXTERN uLong ZEXPORT crc32_combine OF((uLong, uLong, z_off_t));
-
-#endif /* !Z_SOLO */
-
-/* hack for buggy compilers */
-#if !defined(ZUTIL_H) && !defined(NO_DUMMY_DECL)
- struct internal_state {int dummy;};
-#endif
-
-/* undocumented functions */
-ZEXTERN const char * ZEXPORT zError OF((int));
-ZEXTERN int ZEXPORT inflateSyncPoint OF((z_streamp));
-ZEXTERN const z_crc_t FAR * ZEXPORT get_crc_table OF((void));
-ZEXTERN int ZEXPORT inflateUndermine OF((z_streamp, int));
-ZEXTERN int ZEXPORT inflateResetKeep OF((z_streamp));
-ZEXTERN int ZEXPORT deflateResetKeep OF((z_streamp));
-#if defined(_WIN32) && !defined(Z_SOLO)
-ZEXTERN gzFile ZEXPORT gzopen_w OF((const wchar_t *path,
- const char *mode));
-#endif
-#if defined(STDC) || defined(Z_HAVE_STDARG_H)
-# ifndef Z_SOLO
-ZEXTERN int ZEXPORTVA gzvprintf Z_ARG((gzFile file,
- const char *format,
- va_list va));
-# endif
-#endif
-
-#ifdef __cplusplus
-}
-#endif
-
-#endif /* ZLIB_H */
diff --git a/third-party/zlib/zlib.map b/third-party/zlib/zlib.map
deleted file mode 100644
index 55c6647..0000000
--- a/third-party/zlib/zlib.map
+++ /dev/null
@@ -1,83 +0,0 @@
-ZLIB_1.2.0 {
- global:
- compressBound;
- deflateBound;
- inflateBack;
- inflateBackEnd;
- inflateBackInit_;
- inflateCopy;
- local:
- deflate_copyright;
- inflate_copyright;
- inflate_fast;
- inflate_table;
- zcalloc;
- zcfree;
- z_errmsg;
- gz_error;
- gz_intmax;
- _*;
-};
-
-ZLIB_1.2.0.2 {
- gzclearerr;
- gzungetc;
- zlibCompileFlags;
-} ZLIB_1.2.0;
-
-ZLIB_1.2.0.8 {
- deflatePrime;
-} ZLIB_1.2.0.2;
-
-ZLIB_1.2.2 {
- adler32_combine;
- crc32_combine;
- deflateSetHeader;
- inflateGetHeader;
-} ZLIB_1.2.0.8;
-
-ZLIB_1.2.2.3 {
- deflateTune;
- gzdirect;
-} ZLIB_1.2.2;
-
-ZLIB_1.2.2.4 {
- inflatePrime;
-} ZLIB_1.2.2.3;
-
-ZLIB_1.2.3.3 {
- adler32_combine64;
- crc32_combine64;
- gzopen64;
- gzseek64;
- gztell64;
- inflateUndermine;
-} ZLIB_1.2.2.4;
-
-ZLIB_1.2.3.4 {
- inflateReset2;
- inflateMark;
-} ZLIB_1.2.3.3;
-
-ZLIB_1.2.3.5 {
- gzbuffer;
- gzoffset;
- gzoffset64;
- gzclose_r;
- gzclose_w;
-} ZLIB_1.2.3.4;
-
-ZLIB_1.2.5.1 {
- deflatePending;
-} ZLIB_1.2.3.5;
-
-ZLIB_1.2.5.2 {
- deflateResetKeep;
- gzgetc_;
- inflateResetKeep;
-} ZLIB_1.2.5.1;
-
-ZLIB_1.2.7.1 {
- inflateGetDictionary;
- gzvprintf;
-} ZLIB_1.2.5.2;
diff --git a/third-party/zlib/zlib.pc.cmakein b/third-party/zlib/zlib.pc.cmakein
deleted file mode 100644
index a5e6429..0000000
--- a/third-party/zlib/zlib.pc.cmakein
+++ /dev/null
@@ -1,13 +0,0 @@
-prefix=@CMAKE_INSTALL_PREFIX@
-exec_prefix=@CMAKE_INSTALL_PREFIX@
-libdir=@INSTALL_LIB_DIR@
-sharedlibdir=@INSTALL_LIB_DIR@
-includedir=@INSTALL_INC_DIR@
-
-Name: zlib
-Description: zlib compression library
-Version: @VERSION@
-
-Requires:
-Libs: -L${libdir} -L${sharedlibdir} -lz
-Cflags: -I${includedir}
diff --git a/third-party/zlib/zlib.pc.in b/third-party/zlib/zlib.pc.in
deleted file mode 100644
index 7e5acf9..0000000
--- a/third-party/zlib/zlib.pc.in
+++ /dev/null
@@ -1,13 +0,0 @@
-prefix=@prefix@
-exec_prefix=@exec_prefix@
-libdir=@libdir@
-sharedlibdir=@sharedlibdir@
-includedir=@includedir@
-
-Name: zlib
-Description: zlib compression library
-Version: @VERSION@
-
-Requires:
-Libs: -L${libdir} -L${sharedlibdir} -lz
-Cflags: -I${includedir}
diff --git a/third-party/zlib/zlib2ansi b/third-party/zlib/zlib2ansi
deleted file mode 100755
index 15e3e16..0000000
--- a/third-party/zlib/zlib2ansi
+++ /dev/null
@@ -1,152 +0,0 @@
-#!/usr/bin/perl
-
-# Transform K&R C function definitions into ANSI equivalent.
-#
-# Author: Paul Marquess
-# Version: 1.0
-# Date: 3 October 2006
-
-# TODO
-#
-# Asumes no function pointer parameters. unless they are typedefed.
-# Assumes no literal strings that look like function definitions
-# Assumes functions start at the beginning of a line
-
-use strict;
-use warnings;
-
-local $/;
-$_ = <>;
-
-my $sp = qr{ \s* (?: /\* .*? \*/ )? \s* }x; # assume no nested comments
-
-my $d1 = qr{ $sp (?: [\w\*\s]+ $sp)* $sp \w+ $sp [\[\]\s]* $sp }x ;
-my $decl = qr{ $sp (?: \w+ $sp )+ $d1 }xo ;
-my $dList = qr{ $sp $decl (?: $sp , $d1 )* $sp ; $sp }xo ;
-
-
-while (s/^
- ( # Start $1
- ( # Start $2
- .*? # Minimal eat content
- ( ^ \w [\w\s\*]+ ) # $3 -- function name
- \s* # optional whitespace
- ) # $2 - Matched up to before parameter list
-
- \( \s* # Literal "(" + optional whitespace
- ( [^\)]+ ) # $4 - one or more anythings except ")"
- \s* \) # optional whitespace surrounding a Literal ")"
-
- ( (?: $dList )+ ) # $5
-
- $sp ^ { # literal "{" at start of line
- ) # Remember to $1
- //xsom
- )
-{
- my $all = $1 ;
- my $prefix = $2;
- my $param_list = $4 ;
- my $params = $5;
-
- StripComments($params);
- StripComments($param_list);
- $param_list =~ s/^\s+//;
- $param_list =~ s/\s+$//;
-
- my $i = 0 ;
- my %pList = map { $_ => $i++ }
- split /\s*,\s*/, $param_list;
- my $pMatch = '(\b' . join('|', keys %pList) . '\b)\W*$' ;
-
- my @params = split /\s*;\s*/, $params;
- my @outParams = ();
- foreach my $p (@params)
- {
- if ($p =~ /,/)
- {
- my @bits = split /\s*,\s*/, $p;
- my $first = shift @bits;
- $first =~ s/^\s*//;
- push @outParams, $first;
- $first =~ /^(\w+\s*)/;
- my $type = $1 ;
- push @outParams, map { $type . $_ } @bits;
- }
- else
- {
- $p =~ s/^\s+//;
- push @outParams, $p;
- }
- }
-
-
- my %tmp = map { /$pMatch/; $_ => $pList{$1} }
- @outParams ;
-
- @outParams = map { " $_" }
- sort { $tmp{$a} <=> $tmp{$b} }
- @outParams ;
-
- print $prefix ;
- print "(\n" . join(",\n", @outParams) . ")\n";
- print "{" ;
-
-}
-
-# Output any trailing code.
-print ;
-exit 0;
-
-
-sub StripComments
-{
-
- no warnings;
-
- # Strip C & C++ coments
- # From the perlfaq
- $_[0] =~
-
- s{
- /\* ## Start of /* ... */ comment
- [^*]*\*+ ## Non-* followed by 1-or-more *'s
- (
- [^/*][^*]*\*+
- )* ## 0-or-more things which don't start with /
- ## but do end with '*'
- / ## End of /* ... */ comment
-
- | ## OR C++ Comment
- // ## Start of C++ comment //
- [^\n]* ## followed by 0-or-more non end of line characters
-
- | ## OR various things which aren't comments:
-
- (
- " ## Start of " ... " string
- (
- \\. ## Escaped char
- | ## OR
- [^"\\] ## Non "\
- )*
- " ## End of " ... " string
-
- | ## OR
-
- ' ## Start of ' ... ' string
- (
- \\. ## Escaped char
- | ## OR
- [^'\\] ## Non '\
- )*
- ' ## End of ' ... ' string
-
- | ## OR
-
- . ## Anything other char
- [^/"'\\]* ## Chars which doesn't start a comment, string or escape
- )
- }{$2}gxs;
-
-}
diff --git a/third-party/zlib/zutil.c b/third-party/zlib/zutil.c
deleted file mode 100644
index 23d2ebe..0000000
--- a/third-party/zlib/zutil.c
+++ /dev/null
@@ -1,324 +0,0 @@
-/* zutil.c -- target dependent utility functions for the compression library
- * Copyright (C) 1995-2005, 2010, 2011, 2012 Jean-loup Gailly.
- * For conditions of distribution and use, see copyright notice in zlib.h
- */
-
-/* @(#) $Id$ */
-
-#include "zutil.h"
-#ifndef Z_SOLO
-# include "gzguts.h"
-#endif
-
-#ifndef NO_DUMMY_DECL
-struct internal_state {int dummy;}; /* for buggy compilers */
-#endif
-
-z_const char * const z_errmsg[10] = {
-"need dictionary", /* Z_NEED_DICT 2 */
-"stream end", /* Z_STREAM_END 1 */
-"", /* Z_OK 0 */
-"file error", /* Z_ERRNO (-1) */
-"stream error", /* Z_STREAM_ERROR (-2) */
-"data error", /* Z_DATA_ERROR (-3) */
-"insufficient memory", /* Z_MEM_ERROR (-4) */
-"buffer error", /* Z_BUF_ERROR (-5) */
-"incompatible version",/* Z_VERSION_ERROR (-6) */
-""};
-
-
-const char * ZEXPORT zlibVersion()
-{
- return ZLIB_VERSION;
-}
-
-uLong ZEXPORT zlibCompileFlags()
-{
- uLong flags;
-
- flags = 0;
- switch ((int)(sizeof(uInt))) {
- case 2: break;
- case 4: flags += 1; break;
- case 8: flags += 2; break;
- default: flags += 3;
- }
- switch ((int)(sizeof(uLong))) {
- case 2: break;
- case 4: flags += 1 << 2; break;
- case 8: flags += 2 << 2; break;
- default: flags += 3 << 2;
- }
- switch ((int)(sizeof(voidpf))) {
- case 2: break;
- case 4: flags += 1 << 4; break;
- case 8: flags += 2 << 4; break;
- default: flags += 3 << 4;
- }
- switch ((int)(sizeof(z_off_t))) {
- case 2: break;
- case 4: flags += 1 << 6; break;
- case 8: flags += 2 << 6; break;
- default: flags += 3 << 6;
- }
-#ifdef DEBUG
- flags += 1 << 8;
-#endif
-#if defined(ASMV) || defined(ASMINF)
- flags += 1 << 9;
-#endif
-#ifdef ZLIB_WINAPI
- flags += 1 << 10;
-#endif
-#ifdef BUILDFIXED
- flags += 1 << 12;
-#endif
-#ifdef DYNAMIC_CRC_TABLE
- flags += 1 << 13;
-#endif
-#ifdef NO_GZCOMPRESS
- flags += 1L << 16;
-#endif
-#ifdef NO_GZIP
- flags += 1L << 17;
-#endif
-#ifdef PKZIP_BUG_WORKAROUND
- flags += 1L << 20;
-#endif
-#ifdef FASTEST
- flags += 1L << 21;
-#endif
-#if defined(STDC) || defined(Z_HAVE_STDARG_H)
-# ifdef NO_vsnprintf
- flags += 1L << 25;
-# ifdef HAS_vsprintf_void
- flags += 1L << 26;
-# endif
-# else
-# ifdef HAS_vsnprintf_void
- flags += 1L << 26;
-# endif
-# endif
-#else
- flags += 1L << 24;
-# ifdef NO_snprintf
- flags += 1L << 25;
-# ifdef HAS_sprintf_void
- flags += 1L << 26;
-# endif
-# else
-# ifdef HAS_snprintf_void
- flags += 1L << 26;
-# endif
-# endif
-#endif
- return flags;
-}
-
-#ifdef DEBUG
-
-# ifndef verbose
-# define verbose 0
-# endif
-int ZLIB_INTERNAL z_verbose = verbose;
-
-void ZLIB_INTERNAL z_error (m)
- char *m;
-{
- fprintf(stderr, "%s\n", m);
- exit(1);
-}
-#endif
-
-/* exported to allow conversion of error code to string for compress() and
- * uncompress()
- */
-const char * ZEXPORT zError(err)
- int err;
-{
- return ERR_MSG(err);
-}
-
-#if defined(_WIN32_WCE)
- /* The Microsoft C Run-Time Library for Windows CE doesn't have
- * errno. We define it as a global variable to simplify porting.
- * Its value is always 0 and should not be used.
- */
- int errno = 0;
-#endif
-
-#ifndef HAVE_MEMCPY
-
-void ZLIB_INTERNAL zmemcpy(dest, source, len)
- Bytef* dest;
- const Bytef* source;
- uInt len;
-{
- if (len == 0) return;
- do {
- *dest++ = *source++; /* ??? to be unrolled */
- } while (--len != 0);
-}
-
-int ZLIB_INTERNAL zmemcmp(s1, s2, len)
- const Bytef* s1;
- const Bytef* s2;
- uInt len;
-{
- uInt j;
-
- for (j = 0; j < len; j++) {
- if (s1[j] != s2[j]) return 2*(s1[j] > s2[j])-1;
- }
- return 0;
-}
-
-void ZLIB_INTERNAL zmemzero(dest, len)
- Bytef* dest;
- uInt len;
-{
- if (len == 0) return;
- do {
- *dest++ = 0; /* ??? to be unrolled */
- } while (--len != 0);
-}
-#endif
-
-#ifndef Z_SOLO
-
-#ifdef SYS16BIT
-
-#ifdef __TURBOC__
-/* Turbo C in 16-bit mode */
-
-# define MY_ZCALLOC
-
-/* Turbo C malloc() does not allow dynamic allocation of 64K bytes
- * and farmalloc(64K) returns a pointer with an offset of 8, so we
- * must fix the pointer. Warning: the pointer must be put back to its
- * original form in order to free it, use zcfree().
- */
-
-#define MAX_PTR 10
-/* 10*64K = 640K */
-
-local int next_ptr = 0;
-
-typedef struct ptr_table_s {
- voidpf org_ptr;
- voidpf new_ptr;
-} ptr_table;
-
-local ptr_table table[MAX_PTR];
-/* This table is used to remember the original form of pointers
- * to large buffers (64K). Such pointers are normalized with a zero offset.
- * Since MSDOS is not a preemptive multitasking OS, this table is not
- * protected from concurrent access. This hack doesn't work anyway on
- * a protected system like OS/2. Use Microsoft C instead.
- */
-
-voidpf ZLIB_INTERNAL zcalloc (voidpf opaque, unsigned items, unsigned size)
-{
- voidpf buf = opaque; /* just to make some compilers happy */
- ulg bsize = (ulg)items*size;
-
- /* If we allocate less than 65520 bytes, we assume that farmalloc
- * will return a usable pointer which doesn't have to be normalized.
- */
- if (bsize < 65520L) {
- buf = farmalloc(bsize);
- if (*(ush*)&buf != 0) return buf;
- } else {
- buf = farmalloc(bsize + 16L);
- }
- if (buf == NULL || next_ptr >= MAX_PTR) return NULL;
- table[next_ptr].org_ptr = buf;
-
- /* Normalize the pointer to seg:0 */
- *((ush*)&buf+1) += ((ush)((uch*)buf-0) + 15) >> 4;
- *(ush*)&buf = 0;
- table[next_ptr++].new_ptr = buf;
- return buf;
-}
-
-void ZLIB_INTERNAL zcfree (voidpf opaque, voidpf ptr)
-{
- int n;
- if (*(ush*)&ptr != 0) { /* object < 64K */
- farfree(ptr);
- return;
- }
- /* Find the original pointer */
- for (n = 0; n < next_ptr; n++) {
- if (ptr != table[n].new_ptr) continue;
-
- farfree(table[n].org_ptr);
- while (++n < next_ptr) {
- table[n-1] = table[n];
- }
- next_ptr--;
- return;
- }
- ptr = opaque; /* just to make some compilers happy */
- Assert(0, "zcfree: ptr not found");
-}
-
-#endif /* __TURBOC__ */
-
-
-#ifdef M_I86
-/* Microsoft C in 16-bit mode */
-
-# define MY_ZCALLOC
-
-#if (!defined(_MSC_VER) || (_MSC_VER <= 600))
-# define _halloc halloc
-# define _hfree hfree
-#endif
-
-voidpf ZLIB_INTERNAL zcalloc (voidpf opaque, uInt items, uInt size)
-{
- if (opaque) opaque = 0; /* to make compiler happy */
- return _halloc((long)items, size);
-}
-
-void ZLIB_INTERNAL zcfree (voidpf opaque, voidpf ptr)
-{
- if (opaque) opaque = 0; /* to make compiler happy */
- _hfree(ptr);
-}
-
-#endif /* M_I86 */
-
-#endif /* SYS16BIT */
-
-
-#ifndef MY_ZCALLOC /* Any system without a special alloc function */
-
-#ifndef STDC
-extern voidp malloc OF((uInt size));
-extern voidp calloc OF((uInt items, uInt size));
-extern void free OF((voidpf ptr));
-#endif
-
-voidpf ZLIB_INTERNAL zcalloc (opaque, items, size)
- voidpf opaque;
- unsigned items;
- unsigned size;
-{
- if (opaque) items += size - size; /* make compiler happy */
- return sizeof(uInt) > 2 ? (voidpf)malloc(items * size) :
- (voidpf)calloc(items, size);
-}
-
-void ZLIB_INTERNAL zcfree (opaque, ptr)
- voidpf opaque;
- voidpf ptr;
-{
- free(ptr);
- if (opaque) return; /* make compiler happy */
-}
-
-#endif /* MY_ZCALLOC */
-
-#endif /* !Z_SOLO */
diff --git a/third-party/zlib/zutil.h b/third-party/zlib/zutil.h
deleted file mode 100644
index 24ab06b..0000000
--- a/third-party/zlib/zutil.h
+++ /dev/null
@@ -1,253 +0,0 @@
-/* zutil.h -- internal interface and configuration of the compression library
- * Copyright (C) 1995-2013 Jean-loup Gailly.
- * For conditions of distribution and use, see copyright notice in zlib.h
- */
-
-/* WARNING: this file should *not* be used by applications. It is
- part of the implementation of the compression library and is
- subject to change. Applications should only use zlib.h.
- */
-
-/* @(#) $Id$ */
-
-#ifndef ZUTIL_H
-#define ZUTIL_H
-
-#ifdef HAVE_HIDDEN
-# define ZLIB_INTERNAL __attribute__((visibility ("hidden")))
-#else
-# define ZLIB_INTERNAL
-#endif
-
-#include "zlib.h"
-
-#if defined(STDC) && !defined(Z_SOLO)
-# if !(defined(_WIN32_WCE) && defined(_MSC_VER))
-# include <stddef.h>
-# endif
-# include <string.h>
-# include <stdlib.h>
-#endif
-
-#ifdef Z_SOLO
- typedef long ptrdiff_t; /* guess -- will be caught if guess is wrong */
-#endif
-
-#ifndef local
-# define local static
-#endif
-/* compile with -Dlocal if your debugger can't find static symbols */
-
-typedef unsigned char uch;
-typedef uch FAR uchf;
-typedef unsigned short ush;
-typedef ush FAR ushf;
-typedef unsigned long ulg;
-
-extern z_const char * const z_errmsg[10]; /* indexed by 2-zlib_error */
-/* (size given to avoid silly warnings with Visual C++) */
-
-#define ERR_MSG(err) z_errmsg[Z_NEED_DICT-(err)]
-
-#define ERR_RETURN(strm,err) \
- return (strm->msg = ERR_MSG(err), (err))
-/* To be used only when the state is known to be valid */
-
- /* common constants */
-
-#ifndef DEF_WBITS
-# define DEF_WBITS MAX_WBITS
-#endif
-/* default windowBits for decompression. MAX_WBITS is for compression only */
-
-#if MAX_MEM_LEVEL >= 8
-# define DEF_MEM_LEVEL 8
-#else
-# define DEF_MEM_LEVEL MAX_MEM_LEVEL
-#endif
-/* default memLevel */
-
-#define STORED_BLOCK 0
-#define STATIC_TREES 1
-#define DYN_TREES 2
-/* The three kinds of block type */
-
-#define MIN_MATCH 3
-#define MAX_MATCH 258
-/* The minimum and maximum match lengths */
-
-#define PRESET_DICT 0x20 /* preset dictionary flag in zlib header */
-
- /* target dependencies */
-
-#if defined(MSDOS) || (defined(WINDOWS) && !defined(WIN32))
-# define OS_CODE 0x00
-# ifndef Z_SOLO
-# if defined(__TURBOC__) || defined(__BORLANDC__)
-# if (__STDC__ == 1) && (defined(__LARGE__) || defined(__COMPACT__))
- /* Allow compilation with ANSI keywords only enabled */
- void _Cdecl farfree( void *block );
- void *_Cdecl farmalloc( unsigned long nbytes );
-# else
-# include <alloc.h>
-# endif
-# else /* MSC or DJGPP */
-# include <malloc.h>
-# endif
-# endif
-#endif
-
-#ifdef AMIGA
-# define OS_CODE 0x01
-#endif
-
-#if defined(VAXC) || defined(VMS)
-# define OS_CODE 0x02
-# define F_OPEN(name, mode) \
- fopen((name), (mode), "mbc=60", "ctx=stm", "rfm=fix", "mrs=512")
-#endif
-
-#if defined(ATARI) || defined(atarist)
-# define OS_CODE 0x05
-#endif
-
-#ifdef OS2
-# define OS_CODE 0x06
-# if defined(M_I86) && !defined(Z_SOLO)
-# include <malloc.h>
-# endif
-#endif
-
-#if defined(MACOS) || defined(TARGET_OS_MAC)
-# define OS_CODE 0x07
-# ifndef Z_SOLO
-# if defined(__MWERKS__) && __dest_os != __be_os && __dest_os != __win32_os
-# include <unix.h> /* for fdopen */
-# else
-# ifndef fdopen
-# define fdopen(fd,mode) NULL /* No fdopen() */
-# endif
-# endif
-# endif
-#endif
-
-#ifdef TOPS20
-# define OS_CODE 0x0a
-#endif
-
-#ifdef WIN32
-# ifndef __CYGWIN__ /* Cygwin is Unix, not Win32 */
-# define OS_CODE 0x0b
-# endif
-#endif
-
-#ifdef __50SERIES /* Prime/PRIMOS */
-# define OS_CODE 0x0f
-#endif
-
-#if defined(_BEOS_) || defined(RISCOS)
-# define fdopen(fd,mode) NULL /* No fdopen() */
-#endif
-
-#if (defined(_MSC_VER) && (_MSC_VER > 600)) && !defined __INTERIX
-# if defined(_WIN32_WCE)
-# define fdopen(fd,mode) NULL /* No fdopen() */
-# ifndef _PTRDIFF_T_DEFINED
- typedef int ptrdiff_t;
-# define _PTRDIFF_T_DEFINED
-# endif
-# else
-# define fdopen(fd,type) _fdopen(fd,type)
-# endif
-#endif
-
-#if defined(__BORLANDC__) && !defined(MSDOS)
- #pragma warn -8004
- #pragma warn -8008
- #pragma warn -8066
-#endif
-
-/* provide prototypes for these when building zlib without LFS */
-#if !defined(_WIN32) && \
- (!defined(_LARGEFILE64_SOURCE) || _LFS64_LARGEFILE-0 == 0)
- ZEXTERN uLong ZEXPORT adler32_combine64 OF((uLong, uLong, z_off_t));
- ZEXTERN uLong ZEXPORT crc32_combine64 OF((uLong, uLong, z_off_t));
-#endif
-
- /* common defaults */
-
-#ifndef OS_CODE
-# define OS_CODE 0x03 /* assume Unix */
-#endif
-
-#ifndef F_OPEN
-# define F_OPEN(name, mode) fopen((name), (mode))
-#endif
-
- /* functions */
-
-#if defined(pyr) || defined(Z_SOLO)
-# define NO_MEMCPY
-#endif
-#if defined(SMALL_MEDIUM) && !defined(_MSC_VER) && !defined(__SC__)
- /* Use our own functions for small and medium model with MSC <= 5.0.
- * You may have to use the same strategy for Borland C (untested).
- * The __SC__ check is for Symantec.
- */
-# define NO_MEMCPY
-#endif
-#if defined(STDC) && !defined(HAVE_MEMCPY) && !defined(NO_MEMCPY)
-# define HAVE_MEMCPY
-#endif
-#ifdef HAVE_MEMCPY
-# ifdef SMALL_MEDIUM /* MSDOS small or medium model */
-# define zmemcpy _fmemcpy
-# define zmemcmp _fmemcmp
-# define zmemzero(dest, len) _fmemset(dest, 0, len)
-# else
-# define zmemcpy memcpy
-# define zmemcmp memcmp
-# define zmemzero(dest, len) memset(dest, 0, len)
-# endif
-#else
- void ZLIB_INTERNAL zmemcpy OF((Bytef* dest, const Bytef* source, uInt len));
- int ZLIB_INTERNAL zmemcmp OF((const Bytef* s1, const Bytef* s2, uInt len));
- void ZLIB_INTERNAL zmemzero OF((Bytef* dest, uInt len));
-#endif
-
-/* Diagnostic functions */
-#ifdef DEBUG
-# include <stdio.h>
- extern int ZLIB_INTERNAL z_verbose;
- extern void ZLIB_INTERNAL z_error OF((char *m));
-# define Assert(cond,msg) {if(!(cond)) z_error(msg);}
-# define Trace(x) {if (z_verbose>=0) fprintf x ;}
-# define Tracev(x) {if (z_verbose>0) fprintf x ;}
-# define Tracevv(x) {if (z_verbose>1) fprintf x ;}
-# define Tracec(c,x) {if (z_verbose>0 && (c)) fprintf x ;}
-# define Tracecv(c,x) {if (z_verbose>1 && (c)) fprintf x ;}
-#else
-# define Assert(cond,msg)
-# define Trace(x)
-# define Tracev(x)
-# define Tracevv(x)
-# define Tracec(c,x)
-# define Tracecv(c,x)
-#endif
-
-#ifndef Z_SOLO
- voidpf ZLIB_INTERNAL zcalloc OF((voidpf opaque, unsigned items,
- unsigned size));
- void ZLIB_INTERNAL zcfree OF((voidpf opaque, voidpf ptr));
-#endif
-
-#define ZALLOC(strm, items, size) \
- (*((strm)->zalloc))((strm)->opaque, (items), (size))
-#define ZFREE(strm, addr) (*((strm)->zfree))((strm)->opaque, (voidpf)(addr))
-#define TRY_FREE(s, p) {if (p) ZFREE(s, p);}
-
-/* Reverse the bytes in a 32-bit value */
-#define ZSWAP32(q) ((((q) >> 24) & 0xff) + (((q) >> 8) & 0xff00) + \
- (((q) & 0xff00) << 8) + (((q) & 0xff) << 24))
-
-#endif /* ZUTIL_H */
diff --git a/versioneer.py b/versioneer.py
index f624309..c00770f 100644
--- a/versioneer.py
+++ b/versioneer.py
@@ -280,7 +280,6 @@ public domain. The `_version.py` that it creates is also in the public
domain.
"""
-from __future__ import print_function
import errno
import os
--
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