[med-svn] [htslib] branch debian/unstable updated (48353e1 -> c2ca1bf)
Charles Plessy
plessy at moszumanska.debian.org
Mon Apr 25 11:57:55 UTC 2016
This is an automated email from the git hooks/post-receive script.
plessy pushed a change to branch debian/unstable
in repository htslib.
from 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.
new cc07c66 Silence faidx_fetch_nseq() deprecation warning in test suite
new 2805ae8 Fix compilation with ancient libcurl (7.18 to 7.21.x)
new 4f98dcd Improved robustness of fai_build_core.
new ab9e80d Fixed a CRAM encoding assertion failure on repeated templates.
new f8441c3 Merge pull request #312 from samtools/cram_stats_fix
new 1e94726 Make local vcf_parse_format() function static [minor]
new cad00ea Fix format string length computation
new ed35e41 Detect non-numeric characters in numeric format fields
new acc0763 Adds a warning about RNEXT fields with no matching @SQ record.
new d7ecf68 Extra validity checking when caching a local copy of the reference.
new 7c84a4a File format strings can now be specified uppercase or lowercase.
new 62ed90a Merge file format string case insensitivity (PR #337)
new eb3481f Bug fix to CRAM required_fields option.
new fc9aeb6 Add internal isdigit_c()/etc functions for plain chars
new a918794 Interpret digits directly in parse_version()
new 091c89c Avoid tautology warning [minor]
new f471829 Wrap load_hfile_plugins() in a critical section
new 64b788f Avoid unnecessary warning on unknown sort order
new ecdc348 Fixed build with -DTEST_MAIN.
new 3b2de7b Incorporate test_view.pl into the test.pl harness
new 820689c Write failure messages to stderr
new 26b3085 Constify cram_encoding2str() and remove duplicate function [minor]
new 5523a23 Fix tabix man page CSI option
new fc93dfc More efficient index loading.
new c618771 vcf.h:vcf_parse() add documentation
new 1a050b4 Fixed memory allocation issue when decoding CRAM.
new 5ff6cf0 Added a few prebuilt CRAM files.
new ad6fa24 Set Git attributes for BAM and CRAM files in the repository
new 5af1b93 Change test output filenames
new 1dee8d5 Merge CRAM decoding memory allocation fixes (PR #357)
new 103f55a Change test output filenames [minor]
new 3857875 Add BCF_ERR_CHAR bcf1_t::errcode and improve diagnostic
new 53c064c Check dummy header IDs can be retrieved
new 68867ea Miscellaneous VCF parsing fixes
new 1afaf0c Also escape quotes and backslash in dump_char() [minor]
new 8f782d1 VCF GT parsing fix
new 653f45e Catch negative IDX tags; treat like other IDX parse failures.
new 55ff37c Correct constant passed to bcf_hdr_id2int in bcf_hdr_check_sanity.
new 33de0e9 Limit number of FORMAT items to maximum allowed by bcf1_t n_fmt field
new 601f7e5 Add read error check to fai_load
new 30fb013 Simplify hts_idx_save_core() endianness handling
new c5187a8 Tidy up hts_idx_save_core() / hts_idx_save_as() code
new dd69d7a Report zlib error codes in bgzf.c
new c32590a Remove abort() and improve multi-threaded worker error handling
new 6d5124b Add HTS_RESULT_USED to some function prototypes and fix resulting warnings.
new fc9c7bd Fix warnings; don't mark bgzf_mt() as HTS_RESULT_USED
new 5220488 Tidy up error reporting and fix possible memory leaks.
new aef535c Makes bgzf_zerr return the z_stream msg parameter where useful.
new 27d1c80 Simplify bgzf_index_dump() / bgzf_index_load() endianness handling
new d557cb0 Various minor tidy ups
new 5285dc0 Merge error checking improvements (PR #271)
new a9529a4 Print message when first creating default cache directory
new 314cd1e Populating CRAM cache is now much less likely to have a race condition.
new e778269 Removed the MD5 checking code.
new cf3e55c Avoid random number generator library functions
new 1bc6398 Merge uniquified ref cache temporary filename (PR #320)
new 50c4f39 Avoid pointer/integer cast warning
new 0e5af18 Ensure vcf_parse_format always fills out end of vector values.
new eeec649 Merge vcf_parse_format() end-of-vector bug fix (PR #370)
new 0f298ce Release 1.3.1: bug fix release, notably error checking
new 36bf59a Merge tag '1.3.1' into debian/unstable
new c2ca1bf First go back on debian/unstable, otherwise debian/watch is not there.
The 62 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 +-
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 ++++++++++++++++++++--------
59 files changed, 1197 insertions(+), 628 deletions(-)
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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