[med-svn] [htslib] branch debian/unstable updated (9750123 -> 0662716)
Charles Plessy
plessy at moszumanska.debian.org
Mon May 25 02:46:10 UTC 2015
This is an automated email from the git hooks/post-receive script.
plessy pushed a change to branch debian/unstable
in repository htslib.
from 9750123 Current changelog; not sure to upload or not.
adds 5ebf9b2 Fix regidx.o dependencies and htslib.mk; alphabetise
adds a0e35e0 Formatting fixes for man page
adds effc6fd Merge man page formatting fixes
adds 912a7d0 Support for Type=Character, in htslib same as Type=String
adds 34f8089 VCF header editing speedup for large number of ref sequences
adds 9d01cd6 New bcf_copy API
adds 061cd10 Minor speed increases to cram_byte_array_stop_decode_init and GET_BIT_MSB macros.
adds 6454bd4 Added a range coder (order 0 and 1) plus support for LZMA if compiled in (no option for this at present).
adds 94cf60a Tweaks for specifying version number. Now accepting version 3.0, and also correctly setting the globals.
adds 3d3f400 Updated the version checks to lop off major/minor components rather than using an exact == comparison.
adds 37f42cd Fixed BETA codec so that it honours beta offset value for zero length codes.
adds 1de851b Bug fix to the external decoders. If there is an attempt to decode 0 bytes then it no longer matters if the block does not exist. (This comes about when faced with silly CIGAR strings like "0S".)
adds 0d39459 Added support for more codecs, as part of refactoring how data is pushed. These were in the V2.1 spec, but not used.
adds 672f079 Major refactoring of the way CRAM handles external blocks. We now prefer to output as many things as possible to their own specific external block instead of utilising the CORE block more often. This has the impact that it is much easier to do a partial decode.
adds 100f2d0 Removal of a couple memory leaks added in the restructing of the last patch.
adds b73b527 Bug fix of use of TAG_ID macro and k vs key in hash for auxiliary headers.
adds 5a840da Modified the thread pool to use as few threads as possible. The intention is that when given, say, 16 threads but being I/O bound such that 12 cores is enough to keep up with the I/O then we have 12 threads kept busy and 4 totally idle.
adds 6929b9c Bug fixed scramble -x as it was not correctly setting the RI data series for some tests.
adds ef7eeed A mishmash of changes for CRAM v3.0 (not yet the default output format). Sorry it's munged together.
adds a254285 Minor gcc warnings fixups.
adds 2e29861 Added support for compressed SAM headers.
adds c7f8fee Final part of Staden io_lib's commit r3686.
adds 6d01daa Initialise refs_t ->ref_id in refs_load_fai(). This has no bearing on Samtools/htslib, but this function is used within Gap5 and calling it in this order gave arise to crashes unless this initialisation code is here, so it is a good belt and braces approach.
adds 22718e5 Added CRC32 to the blocks and containers.
adds 3ca319f Fixed the file format detection code so it handles CRAM v3.0 magic number as a valid CRAM file.
adds 10958ff Changed the hts_open code to support "C" as a format mode as well as "c". Both are CRAM, but "C" is version 3.0. This is a temporary hack while CRAM V3.0 is still undergoing work, but we will need a more formal way of indicating output version numbers in the future. Equally so the CRAM code itself for specifying versions also needs improvements, to avoid global variables. Test_view has a -3 option to use "C" instead of "c".
adds bf2d07c Fixed bam_construct_seq to cope with qual being NULL.
adds efa6537 Removed the previous "c" vs "C" hack and added a proper option parser to test_view. We still need to decide where this API belongs properly, but test_view is a good point to test it.
adds 1965be2 Fixed generation of MD and NM tags in cram_decode_seq() when using a non-reference encoding. These cannot be stored or regenerated in such cases.
adds b56f540 Added a special case for setting the reference. When converting from SAM to CRAM we tend to think of the reference as an input property; if it is not in the SAM headers (M5 & UR @SQ tags) then we want to specify it, as an input property.
adds ad3c4c5 Cope with cram_compress_slice failing. We were unwinding the stack returning -1 each time, but then called cram_close which attempting to flush any remaining data (dying in the process). We now free the current on-going container upon an error, to avoid this flush later.
adds 1ef04ee Removed the need for -DSAMTOOLS when compiling CRAM.
adds b5ecdf7 (Commented out): ugly auto-configuration of HAVE_LIBBZ2 and HAVE_LIBLZMA definitions.
adds a223cae Added multi-threading support for reading and writing CRAM.
adds 4835f53 CRAM_OPT_VERSION now works (and only works) on an open file descriptor, freshly opened before the call to sam_hdr_write.
adds ac13591 Added SAM_RGAUX as another column identifier to allow for tools that need to use RG tag without other tags to perform optimally.
adds 2f10ff9 Removed defunct comment.
adds 0cdb7b1 Minor tidyups to prevent some clang warnings.
adds eecc982 Fixes for handling range requests while also multi-threading.
adds d6cdff6 Fix for FSECONDARY reads; do not link into PNEXT/RNEXT.
adds 9eb4bed Removed various small memory leaks.
adds 432a224 Split off the rans_byte.h portion of rANS_static.c back into its own file, for reasons of copyright clarity.
adds b5d11c3 Added copyright notice.
adds 43f2d11 Remove -DSAMTOOLS vestiges
adds 24c8699 Fix cram/rANS_* dependencies
adds 233e159 Merge CRAM v3 updates (PR #132)
adds abd1efb Add htsFormat and format-detection API functions
adds 529ca88 Use htsFormat to replace htsFile's is_foo flags
adds 41ab01b Add htsfile utility
adds bf909d6 Removed old hts_file_type() API and replaced it with the new htsFormat;
adds 7c42dcc Clean up, is_compressed and is_cram no longer necessary
adds eda497b Do not use 0x80 & co for missing alleles
adds 3e24dfd Do not load remote index if already exists locally
adds 5dec96b Amended the compression level checking code in cram_dopen() to follow the same detection logic used in bgzf.c. Previously changing the compression level did not work for CRAM.
adds b0df3d1 Fix in bgzf's gzip reading plus added a test for this
adds 9c510fb bcf_translate: Be aware of gaps in BCF headers
adds b28efa4 In a bid to keep the DEBUG_printf line potentially printing up the value of 'i', while also avoiding the complaints about 'i' being set but unused, I changed the code to also handle potentially wide characters. (I haven't tested it works actually with wide characters, but it'll be better than before and the main goal was the silence the annoying warning!)
adds a98d88f Fix a bug where hts_set_fai_filename() didn't pass this through to CRAM. It appears this bug has been long standing, since https://github.com/samtools/htslib/commit/2402fc00fe1f2360cd9056173045f65bc0b683dc, but was not detected due to the tests finding the reference via a UR: @SQ tag instead.
adds 9e844e0 Fix bug spotted by valgrind when running "./test_view -D ce#unmap.tmp.cram".
adds 7a13d83 Fixed an error found via valgrind of test_view -D c1#pad1.tmp.cram.
adds dd08ee0 Reverting 9e844e0be26875d29b6e2c853c2b4d02c4f1faa4 and rewriting in a better manner.
adds 244dde8 tbx: Detect faulty tbi files
adds b7f74f4 Merge origin/develop, replacing htsFile.type by .format
adds 845c515 Parse SAM aux 'i' values > 2^31 correctly
adds 07c94ec Sped up cram_index_load some 200 fold by replacing sscanf with our own number decoding.
adds b96a302 Fixed an incorrect EOF-style case when seeking multiple times.
adds 4d13ff0 Fix of memmove bug in bcf_remove_filter()
adds 4aa494f Buffer overflow error in synced_bcf_reader.c
adds c4043c5 Merge pull request #142 from reinders/patch-1
adds bd6f52a Fix compilation when ALLOW_UAC is not defined
adds 7838da8 bcf_sr_add_reader(): do not increment nreaders or perform any reallocs upon file open errors
adds 54618dd Merge pull request #144 from broadinstitute/broad_bcf_sr_add_reader_segfault_fix
adds ee7343e bcf_sr_get_header() macro for accessing the synced readers' headers
adds 29305dd Add IDX to hdr tags of different type, fixes issue https://github.com/samtools/bcftools/issues/141
adds 83a4e30 Amended/removed comments about scram_* API.
adds 089c900 Merge short read() bug fix from upstream
adds 3c4f33a Fix ks_getuntil2() extra empty record at EOF bug
adds d8c03cf bcf_hdr_subset: Return NULL on duplicate sample names
adds 8916744 Sanity check to detect broken GT fields in bcf_calc_ac()
adds 9a88137 Add seq_nt16_int[], equivalent to the old API's bam_nt16_nt4_table[]
adds bf7e0ec bcf_*hrec* functions: check for existing/multiple IDX keys
adds 4770a41 Fixed the generation of read names to use record_counter properly, counting from 1, rather than slice:record-in-slice.
adds 876bfe4 Replaced sprintf with a home-brew append_uint64 function. This is a sizeable speed increase to the read name auto-generation code.
adds 89bfcc4 Fix comment in sam.h
adds 32a43b2 vcf: skip empty INFO tags ";;". (Error might be more appropriate?)
adds 8d921a5 Account for read buffering in hseek(SEEK_CUR)
adds 57462fb Minor improvement to binary searching in CRAM indices.
adds 9da961a bcf_hdr_combine: Complain when trying to merge different types
adds 7a0fdf4 Sanity-check tid in hts_itr_query()
adds 10ed34e bcf_calc_ac: Check for incorrect AC/AN counts
adds cef706f vcf_parse_format: Throw an error on extra FORMAT fields
adds dfd6773 vcf: Propagate hdr_add_sample() error
adds 5e76b1c Fix alleles trimming with format Number=R/A/G tags
adds 948a68c Removed spurious messages about missing EOF blocks in CRAM when dealing with older versions of the file format. It worries users to see messages about lack of an EOF block (although technically true) when reading v2.0 or earlier CRAM files.
adds ce1a547 Parse regions without begin/end as 1..MAX_INT rather than 1..2^29
adds e5a964e Update khash.h from upstream sources
adds 20238f3 Fix various simple memory leaks (cf #138)
adds fe88482 Added in the compressed length field to the rANS codec header.
adds ef59ef2 Deobfuscate memory allocations etc via sizeof()
adds 6ee481f vcf headers: Allow contig lines without length attribute. Resolves #155
adds 547a349 tabix: Remove bcf and bam from presets,
adds 21fbc8b vcf: Abort on duplicate sample names, resolves #184
adds ed3efe9 New -R/-T options to tabix.
adds f3e1602 Fix a typo, VCF contig length should be stored.
adds dcffda5 Two changes to cram_encode_container() related to efficient encoding of name-sorted data.
adds ca6f60e Fixed a memory leak when destroying a BYTE_ARRAY_LEN encoder.
adds f7caefc Fixed a small memory leak where we didn't deallocate a cram_block that we had created but later culled due to containing zero bytes.
adds cba1bf0 Fixed memory leak when trying to O1 compress a block <= 4 bytes long.
adds 8ad2912 Make the multi_seq parameter default to auto. This is the default in Scramble, but oddly not the default in the code (so scramble always reset it from 0 to -1).
adds 2b31b7d More ref and memory management fixes.
adds ab23898 Reverted the cram_encode_container change to call cram_ref_incr and added a ref incr in cram_get_ref instead. This better fixes the issue of sharing references between containers, fixing decoding as well as encoding.
adds 11a33a6 Merge pull request #160 from jkbonfield/fix_unsorted_cram
adds 5f7a4ea Fixed a bogus warning about using 'cp' before initialised. (Bogus as it's promptly reassigned again, so tidied up the code.)
adds 9b1cb94 Avoid aux.* filenames, which are invalid on Windows
adds 3768707 Update faidx.h
adds 3ac7d00 Add configure.ac script
adds 2ac7a82 Add notes for building from a Git repository
adds 0ccc935 Add iRODS hFILE backend
adds 8bc776d Add MIT/Expat license boilerplate
adds 83f1dbc Merge iRODS hFILE backend
adds 25e8fac Minor change to allow REQUIRED_FIELDS option to be specified in hex or octal.
adds dd70964 Overhauled the cram_dependent_data_series function and associated code.
adds 7bd8c08 Merge pull request #161 from jkbonfield/cram_dependent_data_series
adds ef3bd19 Document ./configure --with-irods
adds 91a471d Fixed unnecessary FAI building.
adds 97a7933 Bug fix to refs_from_header().
adds 0ad9965 Add hisremote(), and convert faidx.c from knet to hFILE
adds cf4811a Set resource when writing to iRODS
adds 519e0e7 Add htsfile(1) man page
adds b2cfe4e Remove tabix -i, which duplicates htsfile functionality
adds 61a79f1 Better index bugfix
adds 2244263 Detect file format versions in hts_detect_format()
adds 0ec1bb1 Temporarily avoid rcDataObjFsync() [workaround]
adds e13b690 Fixes imported from Staden io_lib revisions 3792/3795.
adds 8c80202 Additional comments.
adds 3ec78c1 Improved the CRAM stats array usage.
adds 92a0129 Merge CRAM TLEN updates (PR #165)
adds c360ce4 Enforce the use of a local cache (use home dir if not defined) whenever we automatically fall back to using the EBI reference sequence server.
adds 77cdbec Use TMPDIR and if not set TEMP (common on Windows) environment variables as the location of temporary files, in preference to a hard coded /tmp.
adds 0c74c75 Stylistic code change: !*ptr vs *ptr=='\0'.
adds 32b534f Added support for XDG_CACHE_HOME.
adds 1493ea0 Avoid hiding under .cache in temp directories
adds 6c6f02e Merge default local reference cache (PR #166)
adds af9768d Rationalise include guard macro name
adds 9ecdaae Move remainder of config.h to bgzf.c and remove it
adds 38d93e2 Reinstate faidx_fetch_nseq() alongside faidx_nseq()
adds 38b5374 Formatting fix for HTML man page
adds bff5efb Release 1.2: various bug fixes, htsfile utility, CRAM improvements, etc
adds b0742b0 Merge version number bump and NEWS file from master
adds 7ebc5ae Reinstate deprecated hts_file_type() and FT_*
adds 26229a3 Release 1.2.1: patch release over 1.2, reinstating hts_file_type()
new 0662716 Merge tag '1.2.1' into debian/unstable
The 1 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 | 10 +-
INSTALL | 88 +-
Makefile | 103 +-
NEWS | 50 +
README.md | 16 +
bgzf.c | 13 +-
bgzip.c | 2 +-
config.h | 3 -
config.mk.in | 72 ++
configure.ac | 93 ++
cram/cram.h | 9 +-
cram/cram_codecs.c | 230 ++--
cram/cram_codecs.h | 22 +-
cram/cram_decode.c | 1339 ++++++++++++++++------
cram/cram_encode.c | 1994 ++++++++++++++++++++-------------
cram/cram_index.c | 82 +-
cram/cram_io.c | 1382 ++++++++++++++++-------
cram/cram_io.h | 98 +-
cram/cram_samtools.c | 5 +-
cram/cram_stats.c | 123 +-
cram/cram_structs.h | 329 +++---
cram/os.h | 2 +
cram/rANS_byte.h | 336 ++++++
cram/rANS_static.c | 841 ++++++++++++++
cram/rANS_static.h | 44 +
cram/sam_header.c | 8 +-
cram/sam_header.h | 8 -
cram/thread_pool.c | 178 ++-
cram/thread_pool.h | 15 +-
cram/vlen.c | 2 +-
faidx.c | 36 +-
hfile.c | 23 +-
hfile_internal.h | 3 +-
hfile_irods.c | 243 ++++
hts.c | 531 +++++++--
htsfile.1 | 71 ++
htsfile.c | 168 +++
htslib.mk | 7 +-
htslib/faidx.h | 2 +-
htslib/hfile.h | 10 +-
htslib/hts.h | 146 ++-
htslib/khash.h | 8 +-
htslib/kseq.h | 10 +-
htslib/regidx.h | 13 +-
htslib/sam.h | 2 +-
htslib/synced_bcf_reader.h | 15 +-
htslib/vcf.h | 15 +-
htslib_vars.mk | 2 +-
knetfile.c | 11 +-
regidx.c | 18 +-
sam.c | 134 ++-
synced_bcf_reader.c | 82 +-
tabix.1 | 121 +-
tabix.c | 268 +++--
tbx.c | 5 +
test/{aux#aux.sam => auxf#values.sam} | 0
test/{aux.fa => auxf.fa} | 0
test/{aux.fa.fai => auxf.fa.fai} | 0
test/hfile.c | 4 +-
test/sam.c | 52 +-
test/test-vcf-api.c | 57 +-
test/test_view.c | 92 +-
vcf.c | 207 ++--
vcfutils.c | 63 +-
64 files changed, 7514 insertions(+), 2402 deletions(-)
create mode 100644 NEWS
delete mode 100644 config.h
create mode 100644 config.mk.in
create mode 100644 configure.ac
create mode 100644 cram/rANS_byte.h
create mode 100644 cram/rANS_static.c
create mode 100644 cram/rANS_static.h
create mode 100644 hfile_irods.c
create mode 100644 htsfile.1
create mode 100644 htsfile.c
rename test/{aux#aux.sam => auxf#values.sam} (100%)
rename test/{aux.fa => auxf.fa} (100%)
rename test/{aux.fa.fai => auxf.fa.fai} (100%)
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