[med-svn] [htslib] branch master updated (26229a3 -> 87141ea)
Charles Plessy
plessy at moszumanska.debian.org
Thu Dec 24 04:21:42 UTC 2015
This is an automated email from the git hooks/post-receive script.
plessy pushed a change to branch master
in repository htslib.
from 26229a3 Release 1.2.1: patch release over 1.2, reinstating hts_file_type()
new d963c7d Add c++ name mangling protection where it's missing
new 849ac47 Merge pull request #173 from mp15/cpp_mangling
new 09d8617 Add macro for deprecating old APIs
new 139317e Deprecate faidx_fetch_nseq in favour of faidx_nseq
new 5d93cf1 Merge pull request #170 from mp15/deprecation
new 94d13ce Merge hts_file_type() patch release from master
new a233385 GCC added __deprecated__(message) in version 4.5
new 90525e0 Add $(htslib_kfoo_h) make variables for htslib/k* headers
new d1eef28 Fix dependencies
new 0ec5202 Include unistd.h & exec bash instead of /bin/bash
new e5a0124 Hard clips no longer add to the number of mismatches for the NM tag.
new 83190e9 Added a function to compare @SQ headers against the .fai file.
new 1f3ef0a Consist with calmd for undefined MD/NM tag behaviour.
new b847349 Removal of now-defunct commented out code.
new 38b5cfd Fixed faked up @SQ headers.
new 11cee57 Fixed .crai loading of local irods:... caches.
new 477e31e Moved hts_idx_getfn() into a newly created hts_internal.h.
new 24e0337 Fixed additional prototype gaff.
new 694ff3f Fixed Makefile dependencies for hts_internal.h.
new 18ac533 Switched to using sam_* functions over bam_* functions so that index querying works on CRAM files too.
new cc02b2e Merge fix to caching of remote .crai indices (PR #178)
new b255985 Fixed cram header-ref parsing.
new 47a2046 Added error checking for failed "-t file" option.
new 889ee01 Configure fixes
new c5521ee Tidy up header #ifdef __cplusplus / extern "C" wrappers
new 2ff3610 Improvements to handling CRAM slices with multiple references.
new 57a1015 Protection against various CIGAR/seq issues.
new fbb9e25 Fix for unmapped reads with "*" sequence. These were defaulting to a sequence length of -1 instead of 0 (it's unknown really), causing an attempt to extract -1 bytes.
new f83dfd2 Tests of mapped and unmapped data with "*" sequence.
new a8f2afe Moved the cram/md5.[ch] code up a level to the public API and renamed it.
new 73e0eb7 Changed the htslib MD5 interface.
new 0555cd5 Changed hts_md5_hex args.
new 3accd19 Merge addition of MD5 API (PR #180)
new 67c074e Canonicalise md5.c whitespace
new 6f64ca3 Const fixes; define hts_md5_context instead of adding hts_md5_ctx
new 8cb307b Update md5.c from upstream sources
new 8ca328a Merge minor MD5 API fixes
new 9affea0 Check hts_verbose before printing various VCF warnings
new 5ffc4a2 Prevent klib unused function warnings
new 4b4349a Fixed the broken "special case" in index querying.
new 772ba54 Allow scientific notation when specifying regions,
new 3839b52 Add hts_parse_decimal() to parse scientific notation as int
new 6b40323 Allow commas in hts_parse_decimal(), simplify hts_parse_reg()
new 62e4541 Merge hts_parse_numeric() and hts_parse_reg() scientific notation (PR #171)
new 767cea0 Rearrange hts_itr_querys() more comprehensibly [minor]
new 5f5aa02 Set configure #defines via config.h
new 3af49b4 Added mmap support for references.
new 4cbbfe9 Merge mmap() support for CRAM reference sequences (PR #187)
new 3524f63 Remove unneeded system #include
new be6bd1e Adds handling of corrupted BAMs to bam_index()
new 7a13faa fixes typo in perror
new f79fc6a Merge bam_index() corruption detection (PR #189)
new 45c14cc Use malloc(32K) rather than getpagesize()/valloc()
new d620a73 Added support for CRAM_FLAG 0x8.
new 40a401b Tests now use both CRAM v2.1 and v3.0.
new 48e3b2f Check CRAM->CRAM conversion works
new 4c8fb66 Improved error handling for when we have no bases at all due to cr->len being zero. This is a specific case triggered by the torturous xx#minimal.sam.
new e86391f Avoid -Wundef warnings in compiler detection
new 85bbb17 Use -include rather than sinclude [minor]
new 1a2e234 Added C/Java cross-validation script for CRAM.
new 6185ab7 Bug fix to the CRC32 checking for Java/C integration.
new 35746af Fixed a Java/C integration failure.
new 7725a74 Changed default quality value when unable to decode to 255. This then gets converted to "*" within BAM format.
new ccd0a6b C/Java validation testing updates.
new b8720d0 Fixed buffer overrun in MD tag calculation.
new 7e59273 Don't create MD/NM tags on records with seq "*".
new 2be9f9f Fixed compilation sign warning.
new 3eb77b8 Added missing test file. Sorry!
new b79f40a Added missing test file. Sorry!
new 15c92bf vcf: New bcf_add_id() function
new 30fb9ee allow underscore and dot in keys for structured header lines
new 7a4f7e2 Added a -N INT option to stop decoding after INT reads.
new 56f3d78 Added more decoding error detection.
new 15a3be5 Fixed error handling in CRAM.
new 7579577 Add and use safe_itf8_get() to avoid more buffer over-runs.
new 2c20ba3 Add more codec sanity checks.
new 62ad411 Prevent running on after decoding errors.
new 3954ace rANS decoder error checking.
new e33a6fe Make cram_get_seq loop round straight after calling cram_next_slice.
new a30f906 Fix various reference related bugs in cram_decode_slice
new 83a5001 Ensure last read group name is not NULL before trying to strcmp it.
new 876e71d Catch slices with no data blocks.
new c1c8909 Add more checks to cram_read_SAM_hdr
new fb91924 Change assertion in cram_decode_slice_xref to if (...) return -1.
new dee9260 Ensure header_len >= 0
new f7be681 Make cram_byte_array_len_decode return errors from sub-codecs.
new 81d6ea6 Fix buffer over-runs in cram_decode_seq for sequences starting beyond the ref
new 3a2ddb8 Catch negative length in cram_byte_array_len_decode.
new b43e9b7 Pull code to lookup external blocks into cram_get_block_by_id function.
new f286349 Re-order test for end of input in cram_byte_array_stop_decode_block
new 8013558 Better sanity checking when reading content_ids in cram_decode_slice_header
new 05cd2fa Various fixes in cram_decode_seq.
new ca1bcef Add more sanity checks to cram_decode_slice.
new 93094c7 Better tests for bit-based codecs running out of input.
new 6e3f665 Make cram_subexp_decode_init use safe_itf8_get.
new 509b772 Set sub_size to -1 to catch cases where it doesn't get set.
new e7c1102 Remove redundant code from cram_byte_array_stop_decode_init.
new 4299ea1 Avoid possible integer wrap-around in cram_read_SAM_hdr
new bbd1373 Merge pull request #207 from daviesrob/afl_1
new 7b0edf5 [make] Add maintainer-clean as a synonym of distclean
new 4854ee6 [faidx] Warn if duplicate sequence names are encountered
new f957727 Use bam_endpos() to fix bins for unmapped reads
new 949840b Bug fixed cram_load_reference().
new ec7151a Added a -B (benchmarking) mode to test_view.
new 2e7a222 Add more checks to beta codec.
new a1d2bb5 Merge pull request #212 from daviesrob/afl_2
new 7e3add3 Merge branch 'develop' of github.com:samtools/htslib into develop
new e2743e6 Add missing entries
new 7c1de4b Add rule to generate config.h
new d8172f9 Made v3.0 the default version of CRAM (was 2.1).
new d75ed7a CRAM ref of "*" bug-fix.
new 1980e58 Improve faidx blank line handling
new 826454f [make] Add distdir hook for Automake superprojects
new 9de542c Fix various spelling errors
new 10c4920 Fix in VCF header parsing
new ea63c20 Fix handling of zero-bit beta codec case.
new 9853332 Allow cram_not_enough_bits to return 0 if no bytes left but nbits is 0.
new adec4d3 Ensure SAM query name length fits in a byte.
new a03a15f Ensure names are present for @SQ/@RG/@PG lines in sam_hdr_update_hashes
new e1a67ee Stop gzip header code from reading too far in bgzf_read_block.
new e51893d Ensure sam_hdr_parse doesn't run off the end of the string it's reading.
new 53a7528 Merge fuzz fixes (PR #218 and #223)
new 633a4eb Specify signedness for bit-fields explicitly
new 5c51f84 Always link with -pthread [minor]
new 3a95a67 Fixed a bug in CRAM container num_blocks field when dealing with multiple slices per container. It was counting the compression header per slice rather than only once.
new a89f22f bcf_hdr_remove: NULL to remove all records of the given type
new 1201e41 Merge pull request #220 from mcshane/feature/bcf_hdr_remove_all
new acc2504 Increase size of max format string size from 2^16 to 2^32.
new 56f0640 updated documentation for hts_open for uncompressed bcf.
new a151ef0 Merge pull request #191 from atks/develop
new 58358e1 warn if no BGZF EOF for VCF/BCF files
new d8f5fa6 Detect index format in hts_idx_load_local()
new e9b7db4 Add index build/load functions with explicit index filenames
new 1f45b19 Merge pull request #236 from samtools/feature/idx-filenames
new 3fcf7c9 vcf: Case-insensitive detection of the variant type
new 897a34f Merge pull request #244 from samtools/feature/vcf_type_case
new d72ce03 Add extra checks on input data and memory allocations to bam_hdr_read.
new 5f5a7ae Add HTS_RESULT_USED for bam_hdr_read() and sam_hdr_read().
new 14831e1 Make view_sam set status to EXIT_FAILURE if it fails.
new 8380601 Add check for bam_hdr_read() returning NULL to bam_index.
new 76f64da Fix check on return value of sam_write1.
new ad122a7 Make view_vcf set status to EXIT_FAILURE if it fails.
new 6eff525 Convert status to a global variable.
new 0d94790 Make failure of bam_hdr_init in bam_hdr_read print an error if verbose.
new ac4f829 Merge branch 'afl_2' of github.com:daviesrob/htslib into develop
new 26d2504 Further improved Rob's PR (#215) with error checking on reads.
new f187540 Remove HTS_RESULT_USED from bam_hdr_read() and sam_hdr_read()
new 061c859 Check bam_hdr_read() mallocs without warnings
new 90cf5c4 Remerge daviesrob/afl_2 (PR #215) with several fixes
new 1af175e Add kgetline() to kstring.c/.h
new 4d70794 Added ~ files and patch .rej/.orig.
new eb357ef Moved cram option setting into htslib from test.
new 41f1193 Added hts_open_opts() and an htsFileOpts struct.
new 1f626c1 Fixed requests to output SAM when the default mode is "wb".
new b689376 Added htsExactFormatString() to convert enum to string.
new 431aafe Allow the nthreads=N option to control BAM encoding threads too.
new 6011a93 Merge branch 'develop' into output-fmt-option
new a419848 Use htsFormat instead of htsFileOpts struct for opening.
new 06fc1d0 Protection against crashes when given broken data.
new de59127 Improvements to inline documentation.
new cd83252 Removed quality values from the CRAM_SEQ macro and added a CRAM_QUAL one.
new 590a352 Improvements to htsFormat handling.
new 0dbb3b8 Removed unused variable caused by hts_set_opt migration.
new c313725 Fixed the ordering of enum so that the old CRAM_OPT enums stay constant.
new eca68e8 Revert .gitignore additions
new a4aa7b3 Merge hts_fmt_option, hts_open_format(), et al (PR #233)
new 36bb0b6 Renamed int32_{get,put} to int32_{get,put}_blk.
new 93ae5c6 Fixed bugs in CRAM header manipulation.
new fe11d21 Added an external CRAM API to htslib/cram.h.
new a902f29 Update dependencies and *.mk variables
new 23c8f2e Change to MIT/Expat license for this public header
new 3edc3a3 Merge initial CRAM public API (PR #235)
new 2bb9370 deprecate bcf_hdr_combine in favour of new bcf_hdr_merge
new 8872c10 Merge bcf_hdr_merge() addition (PR #238)
new 4c82a74 tabix: fixes --only-header option so that it now works!
new f790455 Constify hts_open_format() parameter and don't parse filename
new 4494fa6 Change rANS O1 codecs to allocate large arrays on the heap.
new e399970 Added support for samtools cat, along with some CRAM API improvements.
new 778653c Merge CRAM public API additions for samtools cat (PR #237)
new 23ba31e Remove debug printf [minor]
new d754151 Bug fix for CRAM index querying when the query sequence has zero entries in the index. It was accessing element -1 in a NULL array.
new a17f23c Update Makefile dependencies [minor]
new a72be23 Force safe_itf8_get to zero *val_p when failing, to simplify error handling elsewhere. (Eg in cram_transcode_rg)
new 47da392 Fixes https://github.com/samtools/samtools/issues/455
new 8eba63a Fixed bug with non-reference base CRAMs and indexing.
new 42734f6 Improved the efficiency of reference loading again.
new c50bfe0 Further improvement to index querying.
new 6d2810c Reduced memory for CRAM decoding.
new 5b0bb75 Added checks to return value of hts_opt_apply.
new 82203a2 Fix whitespace [trivial]
new 306664a Allow initial whitespace in FASTA ">" headers
new e7e2b3d Add "all-htslib" target for third-party code
new b82f5ef Add sam_parse1() "empty query name" warning
new f859e8d Add hts_parse_decimal() flags parameter and HTS_PARSE_THOUSANDS_SEP
new 81b173e hts_idx_destroy() now actively frees CRAM indices
new 0004f1a Fixes bug that appeared with commit ca1bcefe.
new eb4dcae Increment line number
new 2c89e84 Check bam_header_to_cram() return value
new d2c31ce Add NUL-padded BAM header CRAM conversion test cases
new 04997f6 Allow NUL-termination in sam_hdr_add_lines()
new 4c66fe0 Function bcf_hdr_parse_line now ignores trailing spaces. #248
new d71004b Merge VCF header trailing whitespace fix (PR #267)
new 2b486ed changed bcf_id2int to bcf_hdr_id2int.
new 8197cfd Update to reflect bcf_hdr_id2int() renaming (PR #269)
new a017f92 vcf: Symbolic allele <*> is not a variant
new 852650c bcf_gt_type: Count "./1" genotypes as missing
new 0697d01 Fix in vcf filtering:
new 5c6b71b vcf: Prevent segfault when querying freshly removed tags
new 6638308 Update bcf_translate() accordingly to reflect the bcf_hdr_merge commit 2bb9370f5a24938d8a2dc56f404e584661bf413f
new 53ca19d vcf: update rlen when when adding/removing END tag
new 57d8aba Allow a legitimate use case in bcf1_sync:
new 297ac30 add bcf_sr_swap_line macro
new 1e2ed48 Fixed typo in vcf.h documentation
new d4482eb Define bcf_empty() to match its declaration in vcf.h
new 8f3b53b Fix handling of BCF string dictionaries
new d2ed7e6 Fix incorrect asserts
new 66fbb28 Fixed a bug with CRAM compression level >= 6.
new 9f6fa0f Add 'x' (O_EXCL) and 'e' (O_CLOEXEC) open mode letters
new 1cdbbcd "make tags" should always remake the tag file
new 91d4872 Add bit set data structure
new 1a7fdc5 Fixed sam_hdr_add_PG to avoid va_copy requirement.
new 4c35976 bcf_write: sync dirty header before writing
new c700fb1 Merge pull request #287 from samtools/feature/fix.332
new 34c3e59 Fixed sam_hdr_add_PG to avoid va_copy requirement.
new 636d704 vcfutils: add bcf_remove_alleles_set
new 1e5c377 Merge pull request #285 from samtools/feature/fix.319
new f91da3c Remove obsolete -i/--file-info option from tabix man page
new df3fcad Prevent segfault on empty data files
new 0e2bc68 fix type in bcf_remove_allele_set doc (minor)
new 9362101 Convert relative hseek(SEEK_CUR) offsets to absolute SEEK_SET positions
new f0aaf9a Handle local "file://" URLs directly
new 2c0ea51 Add libcurl hFILE backend
new 0d0909a Implement libcurl hFILE backend writing/uploading
new 6de7b82 Rewrite libcurl timeout calculation
new aeb3c0a Add another error translation
new b5a1536 Add support for S3 pseudo-URLs
new b32afba Fall back to path-style S3 bucket access if necessary
new 628eb5b Always link with -pthread [minor]
new fa07527 Add generic plugin infrastructure
new 823274d Make plugin handling API slightly less generic
new 07d3be7 Add hFILE plugin interface and pluginise irods/libcurl backends
new fe1f08a Merge libcurl backend and hFILE plugin infrastructure
new ccc2cac Make hFILE_backend::flush() optional
new 44d6cfc vcf.h macros should wrap args in brackets
new c388175 [Makefile] Rename LDLIBS to LIBS
new 2e4226f [libcurl] Set User-Agent header and optional verbosity
new 7e4d2b1 Fix plugin installation rules
new 360b67c Override iRODS 3.x/4.0.x's misguided SIGPIPE handler
new 00080ba [iRODS] Set User-Agent and verbosity; basic iRODS 4.x support
new fa6ed9a synced_bcf_reader: _regions_match_alleles exit with an error when payload is not available
new 2072527 Add system includes and extern "C" to public cram.h header
new a2656aa Add htsfile -v option to increase hts_verbose
new d9e9e3a Fix error return value typos and clamp zfclose() return
new 6462e34 Distinguish sam_index_build() file opening and can't-index failures
new e9fcc57 Support S3 config files and temporary credentials
new a356746 Register a plugin destroy() method rather than use atexit()
new b8204c1 Eliminate bgzf_fdopen() from tabix and bgzip
new 82bdc9f Make bgzf_compress() a public API function
new bbd3334 Restore open(O_CREAT) mode arguments [minor]
new cb6642a Allow for n_targets==0 in bam_hdr_read() malloc checking
new d341aaf More fuzz-detected BAM file input checks
new fe8b210 Set binary mode on stdin/stdout and improve Windows/MinGW compilation
new 2b2239a Enable multithreaded BGZF compression in bgzip command
new 449b20a Add "plugins-htslib" target for third-party code
new b725667 Configure should fail when HMAC() cannot be found
new 0f6c185 Explicitly define HAVE_HMAC
new 87141ea Release 1.3: plugins, libcurl, CRAM v3.0, many bug fixes
The 267 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 | 4 +
INSTALL | 23 ++
Makefile | 224 ++++++-----
NEWS | 24 ++
bgzf.c | 33 +-
bgzip.c | 75 ++--
config.h.in | 27 ++
config.mk.in | 53 ++-
configure.ac | 99 +++++
cram/cram.h | 12 +-
cram/cram_codecs.c | 385 ++++++++++++-------
cram/cram_codecs.h | 35 +-
cram/cram_decode.c | 608 ++++++++++++++++++++++++------
cram/cram_encode.c | 92 +++--
cram/cram_external.c | 377 +++++++++++++++++++
cram/cram_index.c | 103 +++--
cram/cram_index.h | 9 +-
cram/cram_io.c | 599 +++++++++++++++++++++++------
cram/cram_io.h | 85 ++++-
cram/cram_samtools.c | 2 +
cram/cram_samtools.h | 8 +
cram/cram_stats.c | 4 +-
cram/cram_structs.h | 37 +-
cram/files.c | 4 +-
cram/mFILE.c | 78 +++-
cram/mFILE.h | 1 +
cram/md5.h | 54 ---
cram/open_trace_file.c | 93 ++++-
cram/open_trace_file.h | 10 +
cram/pooled_alloc.c | 28 +-
cram/pooled_alloc.h | 8 +
cram/rANS_static.c | 67 +++-
cram/rANS_static.h | 7 +
cram/sam_header.c | 124 ++++--
cram/sam_header.h | 35 +-
cram/string_alloc.c | 2 +
cram/string_alloc.h | 7 +-
cram/thread_pool.c | 2 +
cram/thread_pool.h | 8 +
cram/vlen.c | 4 +-
cram/zfio.c | 4 +-
cram/zfio.h | 8 +
faidx.5 | 9 +-
faidx.c | 85 +++--
hfile.c | 257 +++++++++++--
hfile_internal.h | 75 +++-
hfile_irods.c | 72 ++--
hfile_libcurl.c | 919 +++++++++++++++++++++++++++++++++++++++++++++
hfile_net.c | 15 +-
hts.c | 672 ++++++++++++++++++++++++++-------
hts_internal.h | 69 ++++
htsfile.1 | 8 +-
htsfile.c | 114 ++++--
htslib.mk | 27 +-
htslib/bgzf.h | 26 +-
htslib/cram.h | 492 ++++++++++++++++++++++++
htslib/faidx.h | 12 +-
htslib/hfile.h | 5 +-
htslib/hts.h | 245 ++++++++++--
htslib/hts_defs.h | 35 +-
htslib/kbitset.h | 160 ++++++++
htslib/kfunc.h | 8 +
htslib/khash.h | 10 +-
htslib/klist.h | 36 +-
htslib/kstring.h | 9 +-
htslib/regidx.h | 7 +
htslib/sam.h | 70 ++--
htslib/synced_bcf_reader.h | 15 +-
htslib/tbx.h | 12 +-
htslib/vcf.h | 74 ++--
htslib/vcf_sweep.h | 8 +
htslib/vcfutils.h | 26 +-
htslib_vars.mk | 16 +-
kstring.c | 20 +
cram/md5.c => md5.c | 241 ++++++++----
plugin.c | 171 +++++++++
regidx.c | 10 +-
sam.c | 303 +++++++++++----
synced_bcf_reader.c | 49 ++-
tabix.1 | 5 +-
tabix.c | 39 +-
tbx.c | 25 +-
test/c1#noseq.sam | 10 +
test/c1#pad2.sam | 2 +-
test/c1#pad3.sam | 2 +-
test/c1#unknown.sam | 9 +
test/c2#pad.sam | 26 ++
test/c2.fa | 2 +
test/c2.fa.fai | 1 +
test/ce#1.sam | 2 +-
test/ce#2.sam | 2 +-
test/ce#5.sam | 10 +-
test/ce#5b.sam | 10 +-
test/ce#large_seq.sam | 2 +-
test/ce#supp.sam | 6 +
test/ce#tag_depadded.sam | 2 +-
test/ce#tag_padded.sam | 2 +-
test/ce#unmap1.sam | 14 +-
test/ce#unmap2.sam | 14 +-
test/compare_sam.pl | 24 +-
test/cross_validate.sh | 126 +++++++
test/faidx.fa | 17 +
test/sam.c | 33 +-
test/test-vcf-hdr-in.vcf | 25 ++
test/test-vcf-hdr.out | 16 +
test/test.pl | 27 +-
test/test_view.c | 149 +++-----
test/test_view.pl | 22 ++
test/xx#tlen.sam | 34 ++
test/xx#tlen2.sam | 36 ++
vcf.c | 321 ++++++++++++----
vcf_sweep.c | 3 +-
vcfutils.c | 50 ++-
113 files changed, 7303 insertions(+), 1609 deletions(-)
create mode 100644 config.h.in
create mode 100644 cram/cram_external.c
delete mode 100644 cram/md5.h
create mode 100644 hfile_libcurl.c
create mode 100644 hts_internal.h
create mode 100644 htslib/cram.h
create mode 100644 htslib/kbitset.h
rename cram/md5.c => md5.c (67%)
create mode 100644 plugin.c
create mode 100644 test/c1#noseq.sam
create mode 100644 test/c1#unknown.sam
create mode 100644 test/c2#pad.sam
create mode 100644 test/c2.fa
create mode 100644 test/c2.fa.fai
create mode 100644 test/ce#supp.sam
create mode 100755 test/cross_validate.sh
create mode 100644 test/faidx.fa
create mode 100644 test/test-vcf-hdr-in.vcf
create mode 100644 test/test-vcf-hdr.out
create mode 100644 test/xx#tlen.sam
create mode 100644 test/xx#tlen2.sam
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