[med-svn] [khmer] branch master updated (cdd3ca1 -> 9eae920)
Michael Crusoe
misterc-guest at moszumanska.debian.org
Thu May 28 00:34:05 UTC 2015
This is an automated email from the git hooks/post-receive script.
misterc-guest pushed a change to branch master
in repository khmer.
from cdd3ca1 Remove the 'module' infix from the CPython extension
new f031ff0 Imported Upstream version 1.4+dfsg
new ce38967 Merge tag 'upstream/1.4+dfsg'
new da9bf35 update d/changelog for new release
new bcf5243 freshen patches
new b3ade39 retrieve the version from the Debian ChangeLog
new 9eae920 document MurmurHash copyright
The 6 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails. The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.
Summary of changes:
.gitignore | 3 +
CONTRIBUTING.md | 2 +
ChangeLog | 712 ++++-
Doxyfile.in | 2 +-
Makefile | 90 +-
README.rst | 23 +-
debian/changelog | 4 +-
debian/copyright | 7 +
debian/patches/disable_google_analytics | 12 +-
debian/patches/get_version | 30 +
debian/patches/local-libs | 6 +-
debian/patches/older-setuptools | 24 +-
debian/patches/series | 1 +
doc/{LICENSE.txt => LICENSE.rst} | 0
doc/README.html | 403 ---
doc/{citations.txt => citations.rst} | 0
doc/conf.py | 25 +-
doc/{contributors.txt => contributors.rst} | 0
.../{CODE_OF_CONDUCT.txt => CODE_OF_CONDUCT.rst} | 0
...to-testing.txt => a-quick-guide-to-testing.rst} | 5 +
doc/dev/{codebase-guide.txt => codebase-guide.rst} | 0
...review.txt => coding-guidelines-and-review.rst} | 39 +-
doc/dev/{crazy-ideas.txt => crazy-ideas.rst} | 0
doc/dev/{details.txt => details.rst} | 0
doc/dev/{development.txt => development.rst} | 0
...mer-developers.txt => for-khmer-developers.rst} | 0
.../{getting-started.txt => getting-started.rst} | 68 +-
doc/dev/{hackathon.txt => hackathon.rst} | 0
doc/dev/{index.txt => index.rst} | 3 +-
doc/dev/{release.txt => release.rst} | 17 +-
doc/dev/scripts-and-sandbox.rst | 120 +
doc/{index.txt => index.rst} | 8 +-
doc/introduction.rst | 99 +
doc/introduction.txt | 93 -
doc/release-notes/index.rst | 12 +
doc/release-notes/release-1.0.1.md | 2 +
doc/release-notes/release-1.0.1.rst | 71 +
doc/release-notes/release-1.0.md | 2 +
doc/release-notes/release-1.0.rst | 110 +
doc/release-notes/release-1.1.md | 2 +
doc/release-notes/release-1.1.rst | 77 +
doc/release-notes/release-1.2.md | 12 +-
doc/release-notes/release-1.2.rst | 106 +
doc/release-notes/release-1.3.md | 2 +
doc/release-notes/release-1.3.rst | 62 +
doc/release-notes/release-1.4.md | 237 ++
doc/release-notes/release-1.4.rst | 257 ++
doc/requirements.txt | 1 +
doc/{roadmap.txt => roadmap.rst} | 0
doc/user/{biblio.txt => biblio.rst} | 0
doc/user/{blog-posts.txt => blog-posts.rst} | 10 +-
...ng-table-sizes.txt => choosing-table-sizes.rst} | 8 +-
doc/user/{examples.txt => examples.rst} | 0
doc/user/{galaxy.txt => galaxy.rst} | 0
doc/user/getting-help.rst | 54 +
doc/user/{guide.txt => guide.rst} | 6 +-
doc/user/{index.txt => index.rst} | 1 +
doc/user/{install.txt => install.rst} | 4 +-
doc/user/{known-issues.txt => known-issues.rst} | 0
...ning-big-data.txt => partitioning-big-data.rst} | 0
doc/user/{scripts.txt => scripts.rst} | 6 +
examples/stamps/do.sh | 44 +-
jenkins-build.sh | 14 +-
khmer/__init__.py | 131 +-
khmer/_khmermodule.cc | 2758 ++++++++++++--------
khmer/_version.py | 110 +-
khmer/{file.py => kfile.py} | 66 +-
khmer/khmer_args.py | 31 +-
khmer/load_pe.py | 53 -
khmer/thread_utils.py | 28 +-
khmer/utils.py | 155 +-
lib/.check_openmp.cc | 17 +
lib/.gitignore | 11 +-
lib/Makefile | 342 ++-
lib/counting.cc | 118 +-
lib/counting.hh | 16 +-
lib/get_version.py | 22 +-
lib/graphtest.cc | 2 +-
lib/hashbits.cc | 55 +-
lib/hashbits.hh | 14 +-
lib/hashtable.cc | 138 +-
lib/hashtable.hh | 33 +-
lib/hllcounter.cc | 461 ++++
lib/hllcounter.hh | 221 ++
lib/ht-diff.cc | 2 +-
lib/khmer.hh | 7 +-
lib/khmer.pc.in | 14 +
lib/khmer_exception.hh | 37 +-
lib/kmer_hash.cc | 66 +-
lib/kmer_hash.hh | 10 +-
lib/labelhash.cc | 2 +-
lib/labelhash.hh | 2 +-
lib/perf_metrics.cc | 2 +-
lib/perf_metrics.hh | 2 +-
lib/primes.hh | 2 +-
lib/read_aligner.cc | 4 +-
lib/read_aligner.hh | 2 +-
lib/read_parsers.cc | 60 +-
lib/read_parsers.hh | 44 +-
lib/subset.cc | 23 +-
lib/subset.hh | 2 +-
lib/test-CacheManager.cc | 189 --
lib/test-Colors.cc | 2 +-
lib/test-HashTables.cc | 2 +-
lib/test-Parser.cc | 2 +-
lib/test-StreamReader.cc | 173 --
lib/test-compile.cc | 17 +
lib/{test_read_aligner.cc => test-read-aligner.cc} | 4 +-
lib/trace_logger.cc | 2 +-
lib/trace_logger.hh | 2 +-
sandbox/README.rst | 56 +-
sandbox/abundance-hist-by-position.py | 2 +-
sandbox/assembly-diff-2.py | 2 +-
sandbox/assembly-diff.py | 2 +-
sandbox/assemstats3.py | 2 +-
...intersection.py => bloom-count-intersection.py} | 2 +-
sandbox/{bloom_count.py => bloom-count.py} | 2 +-
sandbox/build-sparse-graph.py | 2 +-
sandbox/calc-best-assembly.py | 6 +-
sandbox/calc-error-profile.py | 6 +-
sandbox/calc-median-distribution.py | 2 +-
sandbox/collect-reads.py | 29 +-
sandbox/collect-variants.py | 13 +-
sandbox/combine-pe.py | 66 -
sandbox/compare-partitions.py | 68 -
sandbox/correct-errors.py | 21 +-
sandbox/count-within-radius.py | 60 -
sandbox/degree-by-position.py | 47 -
sandbox/dn-identify-errors.py | 147 --
sandbox/ec.py | 60 -
sandbox/error-correct-pass2.py | 85 -
sandbox/extract-single-partition.py | 2 +-
sandbox/fasta-to-abundance-hist.py | 2 +-
sandbox/filter-below-abund.py | 2 +-
sandbox/filter-median-and-pct.py | 4 +-
sandbox/filter-median.py | 4 +-
sandbox/find-high-abund-kmers.py | 2 +-
sandbox/find-unpart.py | 53 -
sandbox/graph-size.py | 2 +-
sandbox/hi-lo-abundance-by-position.py | 2 +-
sandbox/make-coverage.py | 47 +
sandbox/multi-rename.py | 2 +-
sandbox/normalize-by-align.py | 150 --
sandbox/normalize-by-median-pct.py | 6 +-
sandbox/print-stoptags.py | 2 +-
sandbox/print-tagset.py | 2 +-
sandbox/read_aligner.py | 64 -
sandbox/readstats.py | 51 -
sandbox/renumber-partitions.py | 2 +-
sandbox/saturate-by-median.py | 27 +-
sandbox/shuffle-fasta.py | 27 -
sandbox/shuffle-reverse-rotary.py | 2 +-
sandbox/slice-reads-by-coverage.py | 11 +-
sandbox/split-fasta.py | 2 +-
sandbox/split-sequences-by-length.py | 4 +-
sandbox/stoptag-abundance-hist.py | 2 +-
sandbox/stoptags-by-position.py | 2 +-
sandbox/strip-partition.py | 2 +-
sandbox/subset-report.py | 2 +-
sandbox/sweep-files.py | 10 +-
sandbox/sweep-out-reads-with-contigs.py | 2 +-
sandbox/sweep-reads.py | 38 +-
sandbox/sweep-reads2.py | 2 +-
sandbox/sweep-reads3.py | 6 +-
sandbox/to-casava-1.8-fastq.py | 61 -
sandbox/trim-low-abund.py | 236 --
sandbox/uniqify-sequences.py | 67 -
sandbox/unique-kmers.py | 96 +
sandbox/write-interleave.py | 29 -
sandbox/write-trimmomatic.py | 2 +-
scripts/abundance-dist-single.py | 29 +-
scripts/abundance-dist.py | 35 +-
scripts/annotate-partitions.py | 14 +-
scripts/count-median.py | 58 +-
scripts/count-overlap.py | 29 +-
scripts/do-partition.py | 24 +-
scripts/extract-long-sequences.py | 24 +-
scripts/extract-paired-reads.py | 83 +-
scripts/extract-partitions.py | 30 +-
scripts/fastq-to-fasta.py | 5 +-
scripts/filter-abund-single.py | 14 +-
scripts/filter-abund.py | 21 +-
scripts/filter-stoptags.py | 14 +-
scripts/find-knots.py | 17 +-
scripts/galaxy/gedlab.py | 4 +-
scripts/interleave-reads.py | 65 +-
scripts/load-graph.py | 23 +-
scripts/load-into-counting.py | 54 +-
scripts/make-initial-stoptags.py | 8 +-
scripts/merge-partitions.py | 12 +-
scripts/normalize-by-median.py | 215 +-
scripts/partition-graph.py | 14 +-
scripts/readstats.py | 184 ++
scripts/sample-reads-randomly.py | 73 +-
scripts/split-paired-reads.py | 125 +-
scripts/trim-low-abund.py | 331 +++
setup.cfg | 4 +-
setup.py | 92 +-
tests/khmer_tst_utils.py | 14 +-
.../{badversion-k12.kh => badversion-k12.ct} | Bin
tests/test-data/casava_18-pe.fq | 16 +
tests/test-data/{normC20k20.kh => normC20k20.ct} | Bin
...-mixed.fq.pe => old-style-format-w-comments.fq} | 12 +-
tests/test-data/overlap.curve | 200 --
.../test-data/{paired.fq.1 => paired-broken.fq.1} | 4 +-
.../test-data/{paired.fq.2 => paired-broken.fq.2} | 6 +-
.../test-data/{paired.fq.1 => paired-broken2.fq.1} | 6 +-
.../test-data/{paired.fq.2 => paired-broken2.fq.2} | 4 +-
.../test-data/{paired.fq.1 => paired-broken3.fq.1} | 4 +-
.../test-data/{paired.fq.2 => paired-broken3.fq.2} | 8 +-
.../{paired-mixed.fq => paired-mixed-2.fq} | 6 +-
tests/test-data/paired-mixed-broken.fq | 4 +
tests/test-data/paired-mixed.fq | 4 +-
tests/test-data/paired-mixed.fq.pe | 4 +-
tests/test-data/random-20-a.fq | 4 +-
tests/test-data/simple_1.fa | 6 -
tests/test-data/simple_2.fa | 8 -
tests/test-data/simple_3.fa | 4 -
tests/test-data/test-abund-read-2.fq | 4 +-
...red-mixed.fq.pe => test-abund-read-2.paired.fq} | 52 +-
.../{paired.fq => test-abund-read-2.paired2.fq} | 52 +-
tests/test-data/test-abund-read-paired.fa | 4 +-
...aired-mixed.fq.pe => test-abund-read-paired.fq} | 4 +-
tests/test-data/test-colors.fa | 8 -
tests/test-data/test-est.fa | 2 -
tests/test-data/test-graph3.fa | 8 -
tests/test-data/test-graph4.fa | 12 -
tests/test-data/test-graph6.fa | 464 ----
tests/test-data/test-reads.fq.gz | Bin 0 -> 763372 bytes
tests/test-data/truncated.fq | 5 +
tests/test_c_wrapper.py | 48 -
tests/test_counting_hash.py | 144 +-
tests/test_counting_single.py | 13 +-
tests/test_filter.py | 2 +-
tests/test_functions.py | 233 +-
tests/test_graph.py | 24 +-
tests/test_hashbits.py | 11 +-
tests/test_hashbits_obj.py | 13 +-
tests/test_hll.py | 250 ++
tests/test_labelhash.py | 11 +-
tests/test_lump.py | 2 +-
tests/test_read_aligner.py | 10 +-
tests/test_read_parsers.py | 78 +-
tests/test_sandbox_scripts.py | 169 +-
tests/test_script_arguments.py | 26 +-
tests/test_scripts.py | 1524 +++++++++--
tests/test_subset_graph.py | 30 +-
tests/test_threaded_sequence_processor.py | 6 +-
tests/test_version.py | 2 +-
third-party/.gitignore | 6 +
third-party/smhasher/MurmurHash3.cc | 147 ++
third-party/smhasher/MurmurHash3.h | 34 +
versioneer.py | 331 ++-
253 files changed, 9772 insertions(+), 5933 deletions(-)
create mode 100644 debian/patches/get_version
rename doc/{LICENSE.txt => LICENSE.rst} (100%)
delete mode 100644 doc/README.html
rename doc/{citations.txt => citations.rst} (100%)
rename doc/{contributors.txt => contributors.rst} (100%)
rename doc/dev/{CODE_OF_CONDUCT.txt => CODE_OF_CONDUCT.rst} (100%)
rename doc/dev/{a-quick-guide-to-testing.txt => a-quick-guide-to-testing.rst} (94%)
rename doc/dev/{codebase-guide.txt => codebase-guide.rst} (100%)
rename doc/dev/{coding-guidelines-and-review.txt => coding-guidelines-and-review.rst} (58%)
rename doc/dev/{crazy-ideas.txt => crazy-ideas.rst} (100%)
rename doc/dev/{details.txt => details.rst} (100%)
rename doc/dev/{development.txt => development.rst} (100%)
rename doc/dev/{for-khmer-developers.txt => for-khmer-developers.rst} (100%)
rename doc/dev/{getting-started.txt => getting-started.rst} (83%)
rename doc/dev/{hackathon.txt => hackathon.rst} (100%)
rename doc/dev/{index.txt => index.rst} (96%)
rename doc/dev/{release.txt => release.rst} (93%)
create mode 100644 doc/dev/scripts-and-sandbox.rst
rename doc/{index.txt => index.rst} (93%)
create mode 100644 doc/introduction.rst
delete mode 100644 doc/introduction.txt
create mode 100644 doc/release-notes/index.rst
create mode 100644 doc/release-notes/release-1.0.1.rst
create mode 100644 doc/release-notes/release-1.0.rst
create mode 100644 doc/release-notes/release-1.1.rst
create mode 100644 doc/release-notes/release-1.2.rst
create mode 100644 doc/release-notes/release-1.3.rst
create mode 100644 doc/release-notes/release-1.4.md
create mode 100644 doc/release-notes/release-1.4.rst
rename doc/{roadmap.txt => roadmap.rst} (100%)
rename doc/user/{biblio.txt => biblio.rst} (100%)
rename doc/user/{blog-posts.txt => blog-posts.rst} (85%)
rename doc/user/{choosing-table-sizes.txt => choosing-table-sizes.rst} (97%)
rename doc/user/{examples.txt => examples.rst} (100%)
rename doc/user/{galaxy.txt => galaxy.rst} (100%)
create mode 100644 doc/user/getting-help.rst
rename doc/user/{guide.txt => guide.rst} (97%)
rename doc/user/{index.txt => index.rst} (93%)
rename doc/user/{install.txt => install.rst} (95%)
rename doc/user/{known-issues.txt => known-issues.rst} (100%)
rename doc/user/{partitioning-big-data.txt => partitioning-big-data.rst} (100%)
rename doc/user/{scripts.txt => scripts.rst} (96%)
mode change 100644 => 100755 examples/stamps/do.sh
rename khmer/{file.py => kfile.py} (70%)
delete mode 100644 khmer/load_pe.py
create mode 100644 lib/.check_openmp.cc
mode change 100755 => 100644 lib/get_version.py
create mode 100644 lib/hllcounter.cc
create mode 100644 lib/hllcounter.hh
create mode 100644 lib/khmer.pc.in
delete mode 100644 lib/test-CacheManager.cc
delete mode 100644 lib/test-StreamReader.cc
create mode 100644 lib/test-compile.cc
rename lib/{test_read_aligner.cc => test-read-aligner.cc} (92%)
rename sandbox/{bloom_count_intersection.py => bloom-count-intersection.py} (97%)
rename sandbox/{bloom_count.py => bloom-count.py} (94%)
mode change 100644 => 100755 sandbox/calc-best-assembly.py
mode change 100644 => 100755 sandbox/collect-variants.py
delete mode 100755 sandbox/combine-pe.py
delete mode 100755 sandbox/compare-partitions.py
delete mode 100755 sandbox/count-within-radius.py
delete mode 100755 sandbox/degree-by-position.py
delete mode 100755 sandbox/dn-identify-errors.py
delete mode 100755 sandbox/ec.py
delete mode 100755 sandbox/error-correct-pass2.py
delete mode 100755 sandbox/find-unpart.py
mode change 100644 => 100755 sandbox/graph-size.py
create mode 100755 sandbox/make-coverage.py
delete mode 100755 sandbox/normalize-by-align.py
delete mode 100755 sandbox/read_aligner.py
delete mode 100755 sandbox/readstats.py
delete mode 100755 sandbox/shuffle-fasta.py
delete mode 100755 sandbox/to-casava-1.8-fastq.py
delete mode 100755 sandbox/trim-low-abund.py
delete mode 100755 sandbox/uniqify-sequences.py
create mode 100755 sandbox/unique-kmers.py
delete mode 100755 sandbox/write-interleave.py
create mode 100755 scripts/readstats.py
create mode 100755 scripts/trim-low-abund.py
rename tests/test-data/{badversion-k12.kh => badversion-k12.ct} (100%)
create mode 100644 tests/test-data/casava_18-pe.fq
rename tests/test-data/{normC20k20.kh => normC20k20.ct} (100%)
copy tests/test-data/{paired-mixed.fq.pe => old-style-format-w-comments.fq} (84%)
delete mode 100644 tests/test-data/overlap.curve
copy tests/test-data/{paired.fq.1 => paired-broken.fq.1} (93%)
copy tests/test-data/{paired.fq.2 => paired-broken.fq.2} (63%)
copy tests/test-data/{paired.fq.1 => paired-broken2.fq.1} (63%)
copy tests/test-data/{paired.fq.2 => paired-broken2.fq.2} (93%)
copy tests/test-data/{paired.fq.1 => paired-broken3.fq.1} (93%)
copy tests/test-data/{paired.fq.2 => paired-broken3.fq.2} (60%)
copy tests/test-data/{paired-mixed.fq => paired-mixed-2.fq} (96%)
create mode 100644 tests/test-data/paired-mixed-broken.fq
delete mode 100644 tests/test-data/simple_1.fa
delete mode 100644 tests/test-data/simple_2.fa
delete mode 100644 tests/test-data/simple_3.fa
copy tests/test-data/{paired-mixed.fq.pe => test-abund-read-2.paired.fq} (62%)
copy tests/test-data/{paired.fq => test-abund-read-2.paired2.fq} (60%)
copy tests/test-data/{paired-mixed.fq.pe => test-abund-read-paired.fq} (96%)
delete mode 100644 tests/test-data/test-colors.fa
delete mode 100644 tests/test-data/test-est.fa
delete mode 100644 tests/test-data/test-graph3.fa
delete mode 100644 tests/test-data/test-graph4.fa
delete mode 100644 tests/test-data/test-graph6.fa
create mode 100644 tests/test-data/test-reads.fq.gz
create mode 100644 tests/test-data/truncated.fq
delete mode 100644 tests/test_c_wrapper.py
create mode 100644 tests/test_hll.py
create mode 100644 third-party/.gitignore
create mode 100644 third-party/smhasher/MurmurHash3.cc
create mode 100644 third-party/smhasher/MurmurHash3.h
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