[med-svn] [htslib] branch debian/jessie-backports updated (0fcfccf -> c047803)
Charles Plessy
plessy at moszumanska.debian.org
Sun May 8 12:23:02 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 0fcfccf Update git-buildpackage configuration for Backports.
adds d4dbf8d Add README.source to explain the workflow of this Git repository
adds 04d85d9 In this repository the 'v' in front of the version number needs to be left out ...
adds 5fb0d2d Define PATH_MAX
adds 57b6def More verbose description vor -dev and -test package
adds c1eaca0 Fix lintian override
adds eb12aa0 Verified Mayhem bug report which is solved in this version
adds e6d7e9d Upload to unstable
adds d963c7d Add c++ name mangling protection where it's missing
adds 849ac47 Merge pull request #173 from mp15/cpp_mangling
adds 09d8617 Add macro for deprecating old APIs
adds 139317e Deprecate faidx_fetch_nseq in favour of faidx_nseq
adds 5d93cf1 Merge pull request #170 from mp15/deprecation
adds 94d13ce Merge hts_file_type() patch release from master
adds a233385 GCC added __deprecated__(message) in version 4.5
adds 90525e0 Add $(htslib_kfoo_h) make variables for htslib/k* headers
adds d1eef28 Fix dependencies
adds 0ec5202 Include unistd.h & exec bash instead of /bin/bash
adds e5a0124 Hard clips no longer add to the number of mismatches for the NM tag.
adds 83190e9 Added a function to compare @SQ headers against the .fai file.
adds 1f3ef0a Consist with calmd for undefined MD/NM tag behaviour.
adds b847349 Removal of now-defunct commented out code.
adds 38b5cfd Fixed faked up @SQ headers.
adds 11cee57 Fixed .crai loading of local irods:... caches.
adds 477e31e Moved hts_idx_getfn() into a newly created hts_internal.h.
adds 24e0337 Fixed additional prototype gaff.
adds 694ff3f Fixed Makefile dependencies for hts_internal.h.
adds 18ac533 Switched to using sam_* functions over bam_* functions so that index querying works on CRAM files too.
adds cc02b2e Merge fix to caching of remote .crai indices (PR #178)
adds b255985 Fixed cram header-ref parsing.
adds 47a2046 Added error checking for failed "-t file" option.
adds 889ee01 Configure fixes
adds c5521ee Tidy up header #ifdef __cplusplus / extern "C" wrappers
adds 2ff3610 Improvements to handling CRAM slices with multiple references.
adds 57a1015 Protection against various CIGAR/seq issues.
adds 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.
adds f83dfd2 Tests of mapped and unmapped data with "*" sequence.
adds a8f2afe Moved the cram/md5.[ch] code up a level to the public API and renamed it.
adds 73e0eb7 Changed the htslib MD5 interface.
adds 0555cd5 Changed hts_md5_hex args.
adds 3accd19 Merge addition of MD5 API (PR #180)
adds 67c074e Canonicalise md5.c whitespace
adds 6f64ca3 Const fixes; define hts_md5_context instead of adding hts_md5_ctx
adds 8cb307b Update md5.c from upstream sources
adds 8ca328a Merge minor MD5 API fixes
adds 9affea0 Check hts_verbose before printing various VCF warnings
adds 5ffc4a2 Prevent klib unused function warnings
adds 4b4349a Fixed the broken "special case" in index querying.
adds 772ba54 Allow scientific notation when specifying regions,
adds 3839b52 Add hts_parse_decimal() to parse scientific notation as int
adds 6b40323 Allow commas in hts_parse_decimal(), simplify hts_parse_reg()
adds 62e4541 Merge hts_parse_numeric() and hts_parse_reg() scientific notation (PR #171)
adds 767cea0 Rearrange hts_itr_querys() more comprehensibly [minor]
adds 5f5aa02 Set configure #defines via config.h
adds 3af49b4 Added mmap support for references.
adds 4cbbfe9 Merge mmap() support for CRAM reference sequences (PR #187)
adds 3524f63 Remove unneeded system #include
adds be6bd1e Adds handling of corrupted BAMs to bam_index()
adds 7a13faa fixes typo in perror
adds f79fc6a Merge bam_index() corruption detection (PR #189)
adds 45c14cc Use malloc(32K) rather than getpagesize()/valloc()
adds d620a73 Added support for CRAM_FLAG 0x8.
adds 40a401b Tests now use both CRAM v2.1 and v3.0.
adds 48e3b2f Check CRAM->CRAM conversion works
adds 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.
adds e86391f Avoid -Wundef warnings in compiler detection
adds 85bbb17 Use -include rather than sinclude [minor]
adds 1a2e234 Added C/Java cross-validation script for CRAM.
adds 6185ab7 Bug fix to the CRC32 checking for Java/C integration.
adds 35746af Fixed a Java/C integration failure.
adds 7725a74 Changed default quality value when unable to decode to 255. This then gets converted to "*" within BAM format.
adds ccd0a6b C/Java validation testing updates.
adds b8720d0 Fixed buffer overrun in MD tag calculation.
adds 7e59273 Don't create MD/NM tags on records with seq "*".
adds 2be9f9f Fixed compilation sign warning.
adds 3eb77b8 Added missing test file. Sorry!
adds b79f40a Added missing test file. Sorry!
adds 15c92bf vcf: New bcf_add_id() function
adds 30fb9ee allow underscore and dot in keys for structured header lines
adds 7a4f7e2 Added a -N INT option to stop decoding after INT reads.
adds 56f3d78 Added more decoding error detection.
adds 15a3be5 Fixed error handling in CRAM.
adds 7579577 Add and use safe_itf8_get() to avoid more buffer over-runs.
adds 2c20ba3 Add more codec sanity checks.
adds 62ad411 Prevent running on after decoding errors.
adds 3954ace rANS decoder error checking.
adds e33a6fe Make cram_get_seq loop round straight after calling cram_next_slice.
adds a30f906 Fix various reference related bugs in cram_decode_slice
adds 83a5001 Ensure last read group name is not NULL before trying to strcmp it.
adds 876e71d Catch slices with no data blocks.
adds c1c8909 Add more checks to cram_read_SAM_hdr
adds fb91924 Change assertion in cram_decode_slice_xref to if (...) return -1.
adds dee9260 Ensure header_len >= 0
adds f7be681 Make cram_byte_array_len_decode return errors from sub-codecs.
adds 81d6ea6 Fix buffer over-runs in cram_decode_seq for sequences starting beyond the ref
adds 3a2ddb8 Catch negative length in cram_byte_array_len_decode.
adds b43e9b7 Pull code to lookup external blocks into cram_get_block_by_id function.
adds f286349 Re-order test for end of input in cram_byte_array_stop_decode_block
adds 8013558 Better sanity checking when reading content_ids in cram_decode_slice_header
adds 05cd2fa Various fixes in cram_decode_seq.
adds ca1bcef Add more sanity checks to cram_decode_slice.
adds 93094c7 Better tests for bit-based codecs running out of input.
adds 6e3f665 Make cram_subexp_decode_init use safe_itf8_get.
adds 509b772 Set sub_size to -1 to catch cases where it doesn't get set.
adds e7c1102 Remove redundant code from cram_byte_array_stop_decode_init.
adds 4299ea1 Avoid possible integer wrap-around in cram_read_SAM_hdr
adds bbd1373 Merge pull request #207 from daviesrob/afl_1
adds 7b0edf5 [make] Add maintainer-clean as a synonym of distclean
adds 4854ee6 [faidx] Warn if duplicate sequence names are encountered
adds f957727 Use bam_endpos() to fix bins for unmapped reads
adds 949840b Bug fixed cram_load_reference().
adds ec7151a Added a -B (benchmarking) mode to test_view.
adds 2e7a222 Add more checks to beta codec.
adds a1d2bb5 Merge pull request #212 from daviesrob/afl_2
adds 7e3add3 Merge branch 'develop' of github.com:samtools/htslib into develop
adds e2743e6 Add missing entries
adds 7c1de4b Add rule to generate config.h
adds d8172f9 Made v3.0 the default version of CRAM (was 2.1).
adds d75ed7a CRAM ref of "*" bug-fix.
adds 1980e58 Improve faidx blank line handling
adds 826454f [make] Add distdir hook for Automake superprojects
adds 9de542c Fix various spelling errors
adds 10c4920 Fix in VCF header parsing
adds ea63c20 Fix handling of zero-bit beta codec case.
adds 9853332 Allow cram_not_enough_bits to return 0 if no bytes left but nbits is 0.
adds adec4d3 Ensure SAM query name length fits in a byte.
adds a03a15f Ensure names are present for @SQ/@RG/@PG lines in sam_hdr_update_hashes
adds e1a67ee Stop gzip header code from reading too far in bgzf_read_block.
adds e51893d Ensure sam_hdr_parse doesn't run off the end of the string it's reading.
adds 53a7528 Merge fuzz fixes (PR #218 and #223)
adds 633a4eb Specify signedness for bit-fields explicitly
adds 5c51f84 Always link with -pthread [minor]
adds 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.
adds a89f22f bcf_hdr_remove: NULL to remove all records of the given type
adds 1201e41 Merge pull request #220 from mcshane/feature/bcf_hdr_remove_all
adds acc2504 Increase size of max format string size from 2^16 to 2^32.
adds 56f0640 updated documentation for hts_open for uncompressed bcf.
adds a151ef0 Merge pull request #191 from atks/develop
adds 58358e1 warn if no BGZF EOF for VCF/BCF files
adds d8f5fa6 Detect index format in hts_idx_load_local()
adds e9b7db4 Add index build/load functions with explicit index filenames
adds 1f45b19 Merge pull request #236 from samtools/feature/idx-filenames
adds 3fcf7c9 vcf: Case-insensitive detection of the variant type
adds 897a34f Merge pull request #244 from samtools/feature/vcf_type_case
adds d72ce03 Add extra checks on input data and memory allocations to bam_hdr_read.
adds 5f5a7ae Add HTS_RESULT_USED for bam_hdr_read() and sam_hdr_read().
adds 14831e1 Make view_sam set status to EXIT_FAILURE if it fails.
adds 8380601 Add check for bam_hdr_read() returning NULL to bam_index.
adds 76f64da Fix check on return value of sam_write1.
adds ad122a7 Make view_vcf set status to EXIT_FAILURE if it fails.
adds 6eff525 Convert status to a global variable.
adds 0d94790 Make failure of bam_hdr_init in bam_hdr_read print an error if verbose.
adds ac4f829 Merge branch 'afl_2' of github.com:daviesrob/htslib into develop
adds 26d2504 Further improved Rob's PR (#215) with error checking on reads.
adds f187540 Remove HTS_RESULT_USED from bam_hdr_read() and sam_hdr_read()
adds 061c859 Check bam_hdr_read() mallocs without warnings
adds 90cf5c4 Remerge daviesrob/afl_2 (PR #215) with several fixes
adds 1af175e Add kgetline() to kstring.c/.h
adds 4d70794 Added ~ files and patch .rej/.orig.
adds eb357ef Moved cram option setting into htslib from test.
adds 41f1193 Added hts_open_opts() and an htsFileOpts struct.
adds 1f626c1 Fixed requests to output SAM when the default mode is "wb".
adds b689376 Added htsExactFormatString() to convert enum to string.
adds 431aafe Allow the nthreads=N option to control BAM encoding threads too.
adds 6011a93 Merge branch 'develop' into output-fmt-option
adds a419848 Use htsFormat instead of htsFileOpts struct for opening.
adds 06fc1d0 Protection against crashes when given broken data.
adds de59127 Improvements to inline documentation.
adds cd83252 Removed quality values from the CRAM_SEQ macro and added a CRAM_QUAL one.
adds 590a352 Improvements to htsFormat handling.
adds 0dbb3b8 Removed unused variable caused by hts_set_opt migration.
adds c313725 Fixed the ordering of enum so that the old CRAM_OPT enums stay constant.
adds eca68e8 Revert .gitignore additions
adds a4aa7b3 Merge hts_fmt_option, hts_open_format(), et al (PR #233)
adds 36bb0b6 Renamed int32_{get,put} to int32_{get,put}_blk.
adds 93ae5c6 Fixed bugs in CRAM header manipulation.
adds fe11d21 Added an external CRAM API to htslib/cram.h.
adds a902f29 Update dependencies and *.mk variables
adds 23c8f2e Change to MIT/Expat license for this public header
adds 3edc3a3 Merge initial CRAM public API (PR #235)
adds 2bb9370 deprecate bcf_hdr_combine in favour of new bcf_hdr_merge
adds 8872c10 Merge bcf_hdr_merge() addition (PR #238)
adds 4c82a74 tabix: fixes --only-header option so that it now works!
adds f790455 Constify hts_open_format() parameter and don't parse filename
adds 4494fa6 Change rANS O1 codecs to allocate large arrays on the heap.
adds e399970 Added support for samtools cat, along with some CRAM API improvements.
adds 778653c Merge CRAM public API additions for samtools cat (PR #237)
adds 23ba31e Remove debug printf [minor]
adds 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.
adds a17f23c Update Makefile dependencies [minor]
adds a72be23 Force safe_itf8_get to zero *val_p when failing, to simplify error handling elsewhere. (Eg in cram_transcode_rg)
adds 47da392 Fixes https://github.com/samtools/samtools/issues/455
adds 8eba63a Fixed bug with non-reference base CRAMs and indexing.
adds 42734f6 Improved the efficiency of reference loading again.
adds c50bfe0 Further improvement to index querying.
adds 6d2810c Reduced memory for CRAM decoding.
adds 5b0bb75 Added checks to return value of hts_opt_apply.
adds 82203a2 Fix whitespace [trivial]
adds 306664a Allow initial whitespace in FASTA ">" headers
adds e7e2b3d Add "all-htslib" target for third-party code
adds b82f5ef Add sam_parse1() "empty query name" warning
adds f859e8d Add hts_parse_decimal() flags parameter and HTS_PARSE_THOUSANDS_SEP
adds 81b173e hts_idx_destroy() now actively frees CRAM indices
adds 0004f1a Fixes bug that appeared with commit ca1bcefe.
adds eb4dcae Increment line number
adds 2c89e84 Check bam_header_to_cram() return value
adds d2c31ce Add NUL-padded BAM header CRAM conversion test cases
adds 04997f6 Allow NUL-termination in sam_hdr_add_lines()
adds 4c66fe0 Function bcf_hdr_parse_line now ignores trailing spaces. #248
adds d71004b Merge VCF header trailing whitespace fix (PR #267)
adds 2b486ed changed bcf_id2int to bcf_hdr_id2int.
adds 8197cfd Update to reflect bcf_hdr_id2int() renaming (PR #269)
adds a017f92 vcf: Symbolic allele <*> is not a variant
adds 852650c bcf_gt_type: Count "./1" genotypes as missing
adds 0697d01 Fix in vcf filtering:
adds 5c6b71b vcf: Prevent segfault when querying freshly removed tags
adds 6638308 Update bcf_translate() accordingly to reflect the bcf_hdr_merge commit 2bb9370f5a24938d8a2dc56f404e584661bf413f
adds 53ca19d vcf: update rlen when when adding/removing END tag
adds 57d8aba Allow a legitimate use case in bcf1_sync:
adds 297ac30 add bcf_sr_swap_line macro
adds 1e2ed48 Fixed typo in vcf.h documentation
adds d4482eb Define bcf_empty() to match its declaration in vcf.h
adds 8f3b53b Fix handling of BCF string dictionaries
adds d2ed7e6 Fix incorrect asserts
adds 66fbb28 Fixed a bug with CRAM compression level >= 6.
adds 9f6fa0f Add 'x' (O_EXCL) and 'e' (O_CLOEXEC) open mode letters
adds 1cdbbcd "make tags" should always remake the tag file
adds 91d4872 Add bit set data structure
adds 1a7fdc5 Fixed sam_hdr_add_PG to avoid va_copy requirement.
adds 4c35976 bcf_write: sync dirty header before writing
adds c700fb1 Merge pull request #287 from samtools/feature/fix.332
adds 34c3e59 Fixed sam_hdr_add_PG to avoid va_copy requirement.
adds 636d704 vcfutils: add bcf_remove_alleles_set
adds 1e5c377 Merge pull request #285 from samtools/feature/fix.319
adds f91da3c Remove obsolete -i/--file-info option from tabix man page
adds df3fcad Prevent segfault on empty data files
adds 0e2bc68 fix type in bcf_remove_allele_set doc (minor)
adds 9362101 Convert relative hseek(SEEK_CUR) offsets to absolute SEEK_SET positions
adds f0aaf9a Handle local "file://" URLs directly
adds 2c0ea51 Add libcurl hFILE backend
adds 0d0909a Implement libcurl hFILE backend writing/uploading
adds 6de7b82 Rewrite libcurl timeout calculation
adds aeb3c0a Add another error translation
adds b5a1536 Add support for S3 pseudo-URLs
adds b32afba Fall back to path-style S3 bucket access if necessary
adds 628eb5b Always link with -pthread [minor]
adds fa07527 Add generic plugin infrastructure
adds 823274d Make plugin handling API slightly less generic
adds 07d3be7 Add hFILE plugin interface and pluginise irods/libcurl backends
adds fe1f08a Merge libcurl backend and hFILE plugin infrastructure
adds ccc2cac Make hFILE_backend::flush() optional
adds 44d6cfc vcf.h macros should wrap args in brackets
adds c388175 [Makefile] Rename LDLIBS to LIBS
adds 2e4226f [libcurl] Set User-Agent header and optional verbosity
adds 7e4d2b1 Fix plugin installation rules
adds 360b67c Override iRODS 3.x/4.0.x's misguided SIGPIPE handler
adds 00080ba [iRODS] Set User-Agent and verbosity; basic iRODS 4.x support
adds fa6ed9a synced_bcf_reader: _regions_match_alleles exit with an error when payload is not available
adds 2072527 Add system includes and extern "C" to public cram.h header
adds a2656aa Add htsfile -v option to increase hts_verbose
adds d9e9e3a Fix error return value typos and clamp zfclose() return
adds 6462e34 Distinguish sam_index_build() file opening and can't-index failures
adds e9fcc57 Support S3 config files and temporary credentials
adds a356746 Register a plugin destroy() method rather than use atexit()
adds b8204c1 Eliminate bgzf_fdopen() from tabix and bgzip
adds 82bdc9f Make bgzf_compress() a public API function
adds bbd3334 Restore open(O_CREAT) mode arguments [minor]
adds cb6642a Allow for n_targets==0 in bam_hdr_read() malloc checking
adds d341aaf More fuzz-detected BAM file input checks
adds fe8b210 Set binary mode on stdin/stdout and improve Windows/MinGW compilation
adds 2b2239a Enable multithreaded BGZF compression in bgzip command
adds 449b20a Add "plugins-htslib" target for third-party code
adds b725667 Configure should fail when HMAC() cannot be found
adds 0f6c185 Explicitly define HAVE_HMAC
adds 87141ea Release 1.3: plugins, libcurl, CRAM v3.0, many bug fixes
adds 68e6f6c Merge tag '1.3' into debian/unstable
adds b333524 New upstream release; corrected path to a copyright statement.
adds d6a8f09 Upstream does not prefix tags with 'v'.
adds 1d38e31 use secure Vcs-Git
adds 6cd8493 update symbols file
adds 9eb5394 ignore metadata different between tarball and git repo
adds 3e3d9a2 update d/changelog
adds 6c3a0f5 set release distribution to unstable
adds e030698 Merge tag 'debian/1.3-1' into debian/jessie-backports
adds c047803 htslib (1.3-1~bpo8+1) jessie-backports; urgency=medium
No new revisions were added by this update.
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 +
debian/README.source | 34 ++
debian/changelog | 26 +
debian/control | 22 +-
debian/copyright | 4 +-
debian/libhts1.lintian-overrides | 2 +-
debian/libhts1.symbols | 97 +++-
debian/patches/define_PATH_MAX.patch | 23 +
debian/patches/series | 1 +
debian/source/options | 1 +
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 +-
122 files changed, 7497 insertions(+), 1625 deletions(-)
create mode 100644 config.h.in
create mode 100644 cram/cram_external.c
delete mode 100644 cram/md5.h
create mode 100644 debian/README.source
create mode 100644 debian/patches/define_PATH_MAX.patch
create mode 100644 debian/patches/series
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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