[med-svn] [htslib] branch debian/jessie-backports updated (c047803 -> 83fbdd9)
Charles Plessy
plessy at moszumanska.debian.org
Sun May 8 12:42:33 UTC 2016
This is an automated email from the git hooks/post-receive script.
plessy pushed a change to branch debian/jessie-backports
in repository htslib.
from c047803 htslib (1.3-1~bpo8+1) jessie-backports; urgency=medium
adds 59917d4 add upstream's patch for largefile issue
adds 87e9cf5 add patch to run configure
adds a0b3241 run configure step before build
adds 00bd24c update changelog
adds 67634ef Introduced EDAM annotation for TABIX
adds e25e971 Newly introduced Tabix index file format
adds 5632d5d Tabix index file format, longer form
adds 231557d Merge branch 'debian/unstable' of ssh://git.debian.org/git/debian-med/htslib into debian/unstable
adds 388bb16 dch -r
adds 48353e1 move around team upload notice
adds c72ae90 Merge version number bump and NEWS file from master
adds ae4c86a Avoid POSIX Issue 7-specific errno value [minor]
adds 0382edf Use getopt.h's descriptive constants in long options array
adds 70bfd53 Happy New Year
adds df4a80e Free all in-flight pileups in bam_plp_destroy()
adds a6e4883 Ignore .exe and .dSYM extensions
adds 4c0c448 Clarify misleading code formatting [minor]
adds 92654ef Fixed crash in CRAM generation with cigar ops > 2^27 in size.
adds c789bed Force detached read-pairs if they span references.
adds f1327a7 Add AC_SYS_LARGEFILE test so 32-bit systems can access 2GiB+ files
adds 72cb247 allow spaces in vcf header lines
adds 3fac82b remove code duplication from thread_pool.c
adds 406c7d0 Squash a duplicated conditional into a single one.
adds cc07c66 Silence faidx_fetch_nseq() deprecation warning in test suite
adds 2805ae8 Fix compilation with ancient libcurl (7.18 to 7.21.x)
adds 4f98dcd Improved robustness of fai_build_core.
adds ab9e80d Fixed a CRAM encoding assertion failure on repeated templates.
adds f8441c3 Merge pull request #312 from samtools/cram_stats_fix
adds 1e94726 Make local vcf_parse_format() function static [minor]
adds cad00ea Fix format string length computation
adds ed35e41 Detect non-numeric characters in numeric format fields
adds acc0763 Adds a warning about RNEXT fields with no matching @SQ record.
adds d7ecf68 Extra validity checking when caching a local copy of the reference.
adds 7c84a4a File format strings can now be specified uppercase or lowercase.
adds 62ed90a Merge file format string case insensitivity (PR #337)
adds eb3481f Bug fix to CRAM required_fields option.
adds fc9aeb6 Add internal isdigit_c()/etc functions for plain chars
adds a918794 Interpret digits directly in parse_version()
adds 091c89c Avoid tautology warning [minor]
adds f471829 Wrap load_hfile_plugins() in a critical section
adds 64b788f Avoid unnecessary warning on unknown sort order
adds ecdc348 Fixed build with -DTEST_MAIN.
adds 3b2de7b Incorporate test_view.pl into the test.pl harness
adds 820689c Write failure messages to stderr
adds 26b3085 Constify cram_encoding2str() and remove duplicate function [minor]
adds 5523a23 Fix tabix man page CSI option
adds fc93dfc More efficient index loading.
adds c618771 vcf.h:vcf_parse() add documentation
adds 1a050b4 Fixed memory allocation issue when decoding CRAM.
adds 5ff6cf0 Added a few prebuilt CRAM files.
adds ad6fa24 Set Git attributes for BAM and CRAM files in the repository
adds 5af1b93 Change test output filenames
adds 1dee8d5 Merge CRAM decoding memory allocation fixes (PR #357)
adds 103f55a Change test output filenames [minor]
adds 3857875 Add BCF_ERR_CHAR bcf1_t::errcode and improve diagnostic
adds 53c064c Check dummy header IDs can be retrieved
adds 68867ea Miscellaneous VCF parsing fixes
adds 1afaf0c Also escape quotes and backslash in dump_char() [minor]
adds 8f782d1 VCF GT parsing fix
adds 653f45e Catch negative IDX tags; treat like other IDX parse failures.
adds 55ff37c Correct constant passed to bcf_hdr_id2int in bcf_hdr_check_sanity.
adds 33de0e9 Limit number of FORMAT items to maximum allowed by bcf1_t n_fmt field
adds 601f7e5 Add read error check to fai_load
adds 30fb013 Simplify hts_idx_save_core() endianness handling
adds c5187a8 Tidy up hts_idx_save_core() / hts_idx_save_as() code
adds dd69d7a Report zlib error codes in bgzf.c
adds c32590a Remove abort() and improve multi-threaded worker error handling
adds 6d5124b Add HTS_RESULT_USED to some function prototypes and fix resulting warnings.
adds fc9c7bd Fix warnings; don't mark bgzf_mt() as HTS_RESULT_USED
adds 5220488 Tidy up error reporting and fix possible memory leaks.
adds aef535c Makes bgzf_zerr return the z_stream msg parameter where useful.
adds 27d1c80 Simplify bgzf_index_dump() / bgzf_index_load() endianness handling
adds d557cb0 Various minor tidy ups
adds 5285dc0 Merge error checking improvements (PR #271)
adds a9529a4 Print message when first creating default cache directory
adds 314cd1e Populating CRAM cache is now much less likely to have a race condition.
adds e778269 Removed the MD5 checking code.
adds cf3e55c Avoid random number generator library functions
adds 1bc6398 Merge uniquified ref cache temporary filename (PR #320)
adds 50c4f39 Avoid pointer/integer cast warning
adds 0e5af18 Ensure vcf_parse_format always fills out end of vector values.
adds eeec649 Merge vcf_parse_format() end-of-vector bug fix (PR #370)
adds 0f298ce Release 1.3.1: bug fix release, notably error checking
adds 36bf59a Merge tag '1.3.1' into debian/unstable
adds c2ca1bf First go back on debian/unstable, otherwise debian/watch is not there.
adds b9ed6fc A To Do list.
adds 559f8b4 Remove add_largefile.patch, applied upstream.
adds 7163afb Update symbols file. Missing _vcf_parse_format at Base and fai_read at Base.
adds 973e9ac Updated changelog.
adds 3b219b8 Enable libcurl.
adds ac22c29 Enabled libcurl, Do not enable plugins (no plugins available...).
adds c2c1df3 Build-depend on libcurl4-gnutls-dev and libssl-dev.
adds 8b10347 New upstream release; no new copyright nor license notice.
adds 9101580 Conforms to the Policy version 3.9.8.
adds 6e23269 htslib (1.3.1-1) unstable; urgency=medium
adds 68a17aa htslib (1.3.1-1) unstable; urgency=medium
adds df9bd0e Breaks: samtools (<< 1.3.1)
adds 80a1c1c Current changelog.
adds 5f4f573 Revert "Breaks: samtools (<< 1.3.1)"
adds c8c5494 Step back to 1.3.1-1, ready for backport.
new b8ab89e Merge branch 'debian/unstable' into debian/jessie-backports
new 83fbdd9 htslib (1.3.1-1~bpo8+1) jessie-backports; urgency=medium
The 2 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:
.gitattributes | 8 +
.gitignore | 2 +
Makefile | 25 ++-
NEWS | 35 ++++
bgzf.c | 337 ++++++++++++++++++++++++++++-------
bgzip.c | 52 ++++--
config.h.in | 11 ++
configure.ac | 2 +
cram/cram_codecs.c | 61 +++----
cram/cram_codecs.h | 2 +-
cram/cram_decode.c | 50 ++++--
cram/cram_encode.c | 39 ++--
cram/cram_external.c | 4 +-
cram/cram_index.c | 2 +-
cram/cram_io.c | 61 ++++++-
cram/cram_structs.h | 5 +
cram/open_trace_file.c | 2 +-
cram/rANS_static.c | 8 +-
cram/sam_header.c | 2 +-
cram/thread_pool.c | 62 +------
debian/README.source | 14 +-
debian/changelog | 30 ++++
debian/control | 7 +-
debian/copyright | 4 +-
debian/libhts1.symbols | 9 +-
debian/patches/literal_version.patch | 16 ++
debian/patches/series | 1 +
debian/rules | 4 +
debian/upstream/tabix.edam | 16 ++
faidx.c | 77 ++++++--
hfile.c | 17 +-
hfile_libcurl.c | 6 +-
hts.c | 211 +++++++++++-----------
hts_internal.h | 23 ++-
htsfile.1 | 2 +-
htsfile.c | 4 +-
htslib/bgzf.h | 26 +--
htslib/faidx.h | 2 +-
htslib/hts.h | 8 +-
htslib/sam.h | 20 +--
htslib/vcf.h | 9 +-
htslib_vars.mk | 6 +-
kfunc.c | 2 +
knetfile.c | 2 +
kstring.c | 2 +
sam.c | 102 ++++++-----
tabix.1 | 4 +-
tabix.c | 44 +++--
test/aux#aux_java.cram | Bin 0 -> 3774 bytes
test/ce#5b_java.cram | Bin 0 -> 6784 bytes
test/fieldarith.c | 2 +
test/formatcols.vcf | 6 +
test/hfile.c | 2 +
test/noroundtrip-out.vcf | 9 +
test/noroundtrip.vcf | 8 +
test/sam.c | 7 +
test/test-regidx.c | 2 +
test/test-vcf-api.c | 2 +
test/test-vcf-hdr-in.vcf | 4 +-
test/test-vcf-hdr.out | 2 +-
test/test-vcf-sweep.c | 2 +
test/test.pl | 104 ++++++++++-
test/test_view.c | 8 +-
test/test_view.pl | 93 ----------
test/xx#large_aux_java.cram | Bin 0 -> 22668 bytes
test/xx#repeated.sam | 7 +
vcf.c | 216 +++++++++++++++-------
67 files changed, 1277 insertions(+), 635 deletions(-)
create mode 100644 debian/patches/literal_version.patch
create mode 100644 debian/upstream/tabix.edam
create mode 100644 test/aux#aux_java.cram
create mode 100644 test/ce#5b_java.cram
create mode 100644 test/formatcols.vcf
create mode 100644 test/noroundtrip-out.vcf
create mode 100644 test/noroundtrip.vcf
delete mode 100755 test/test_view.pl
create mode 100644 test/xx#large_aux_java.cram
create mode 100644 test/xx#repeated.sam
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