{"push_id":715083214,"size":25,"distinct_size":25,"ref":"refs/heads/develop","head":"86beeeaf6e3af29a0623b520a70ec65475bb56d3","before":"3e924619772ba991b3a636d5ac86d42a2a49eb02","commits":[{"sha":"7b0edf5586a3556b36998dd55d4be7cc74e5e7c6","author":{"email":"4081f471c57da10c91f8e26ca2a349938ce26dd5@sanger.ac.uk","name":"John Marshall"},"message":"[make] Add maintainer-clean as a synonym of distclean","distinct":true,"url":"https://api.github.com/repos/pd3/htslib/commits/7b0edf5586a3556b36998dd55d4be7cc74e5e7c6"},{"sha":"4854ee6688593c6d66f2886af1f878c1c855fc92","author":{"email":"4081f471c57da10c91f8e26ca2a349938ce26dd5@sanger.ac.uk","name":"John Marshall"},"message":"[faidx] Warn if duplicate sequence names are encountered\n\nAdd only the first sequence of each name to the faidx_t and .fai file.\nAn alternative would be to uniquify subsequent duplicates by changing\ntheir names to \"<NAME>_<N>\" or something, but there's a risk of introducing\nfurther clashes -- better to leave the user to sort it out.\n\nFixes samtools/samtools#380.  An upcoming samtools documentation change\nwill note that subsequences retrieved are from the *first* instance of\nduplicate-named reference sequences.","distinct":true,"url":"https://api.github.com/repos/pd3/htslib/commits/4854ee6688593c6d66f2886af1f878c1c855fc92"},{"sha":"f9577275015eee20fa6c6d834b56d8a9950855f3","author":{"email":"4081f471c57da10c91f8e26ca2a349938ce26dd5@sanger.ac.uk","name":"John Marshall"},"message":"Use bam_endpos() to fix bins for unmapped reads\n\nIn sam_parse1() we can't use bam_endpos() but we now do the same\nBAM_FUNMAP test as bam_endpos() would do.  (Add \"no CIGAR operations\"\nparse error so that we can assume that n_cigar>0 here.)\n\nHat tip @dpryan79.  Fixes #206.\n\nAlso deobfuscate one more memory allocation via sizeof() (cf ef59ef2d6425985732d41bf7389df569a2a14c0a).","distinct":true,"url":"https://api.github.com/repos/pd3/htslib/commits/f9577275015eee20fa6c6d834b56d8a9950855f3"},{"sha":"949840b04f920e56a771453bf2f32ac5722bb69c","author":{"email":"d45da8a7f1a5093131462c125914e67903e93ebb@sanger.ac.uk","name":"James Bonfield"},"message":"Bug fixed cram_load_reference().\n\nWhen given NULL as the filename it is meant to, and indeed does, just\nload the reference by extracting the @SQ headers.  Unfortunately it\nreturned -1 as it also reuses fn to go from .fai to .fa and detects\nNULL as a failure to process the .fai.","distinct":true,"url":"https://api.github.com/repos/pd3/htslib/commits/949840b04f920e56a771453bf2f32ac5722bb69c"},{"sha":"2e7a222353f8e226c8c26fa88bcd029925d550ff","author":{"email":"3243a2766bb737188235920577f6adab5919ad82@sanger.ac.uk","name":"Rob Davies"},"message":"Add more checks to beta codec.\n\nAdd missing check for enough bits to cram_beta_decode_char().\n\nEnsure that beta.nbits is within the valid range in cram_beta_decode_init().","distinct":true,"url":"https://api.github.com/repos/pd3/htslib/commits/2e7a222353f8e226c8c26fa88bcd029925d550ff"},{"sha":"a1d2bb5cf9071af5a51cfb0ca87cf7128979b446","author":{"email":"d45da8a7f1a5093131462c125914e67903e93ebb@sanger.ac.uk","name":"James Bonfield"},"message":"Merge pull request #212 from daviesrob/afl_2\n\nAdd more checks to beta codec.","distinct":true,"url":"https://api.github.com/repos/pd3/htslib/commits/a1d2bb5cf9071af5a51cfb0ca87cf7128979b446"},{"sha":"ec7151a2d18229ae7cee6d6fb383465fb8d2b33a","author":{"email":"d45da8a7f1a5093131462c125914e67903e93ebb@sanger.ac.uk","name":"James Bonfield"},"message":"Added a -B (benchmarking) mode to test_view.\n\nThe purpose of this is simply to be able to run benchmarks of format\ndecoding only, without requiring other analysis to be run (eg samtools\nflagstat, etc).","distinct":true,"url":"https://api.github.com/repos/pd3/htslib/commits/ec7151a2d18229ae7cee6d6fb383465fb8d2b33a"},{"sha":"7e3add3f004202a4c49449e7c88b256aeb09a012","author":{"email":"d45da8a7f1a5093131462c125914e67903e93ebb@sanger.ac.uk","name":"James Bonfield"},"message":"Merge branch 'develop' of github.com:samtools/htslib into develop","distinct":true,"url":"https://api.github.com/repos/pd3/htslib/commits/7e3add3f004202a4c49449e7c88b256aeb09a012"},{"sha":"e2743e6a6316c57928fc327e262f38ee92a8a732","author":{"email":"4081f471c57da10c91f8e26ca2a349938ce26dd5@sanger.ac.uk","name":"John Marshall"},"message":"Add missing entries","distinct":true,"url":"https://api.github.com/repos/pd3/htslib/commits/e2743e6a6316c57928fc327e262f38ee92a8a732"},{"sha":"7c1de4ba73fc63122173c6c787e3772f1392cbf5","author":{"email":"4081f471c57da10c91f8e26ca2a349938ce26dd5@sanger.ac.uk","name":"John Marshall"},"message":"Add rule to generate config.h\n\nUsually config.h will be made by running configure, but while we have\nthe Makefile-makes-fallback-config.h approach (and until samtools et al\nget their own configure scripts that call htslib's configure) we need a\nrule here to invoke it.","distinct":true,"url":"https://api.github.com/repos/pd3/htslib/commits/7c1de4ba73fc63122173c6c787e3772f1392cbf5"},{"sha":"d8172f91d7783274f7d4a3d7d4e9a54021452111","author":{"email":"d45da8a7f1a5093131462c125914e67903e93ebb@sanger.ac.uk","name":"James Bonfield"},"message":"Made v3.0 the default version of CRAM (was 2.1).","distinct":true,"url":"https://api.github.com/repos/pd3/htslib/commits/d8172f91d7783274f7d4a3d7d4e9a54021452111"},{"sha":"d75ed7a5f40e9adc3c823cc753830c7f1678234e","author":{"email":"d45da8a7f1a5093131462c125914e67903e93ebb@sanger.ac.uk","name":"James Bonfield"},"message":"CRAM ref of \"*\" bug-fix.\n\nThe bug was that ref seq '*' was being converted to '\\n' due to\n'*' & ~0x20.   A quick test shows it's ~1% time saving on a low depth\n(~10%) chr20 cram.  Hence this is just a case of over-optimisation.","distinct":true,"url":"https://api.github.com/repos/pd3/htslib/commits/d75ed7a5f40e9adc3c823cc753830c7f1678234e"},{"sha":"1980e5859251741f7905e754c07112a0fe3ec3e5","author":{"email":"4081f471c57da10c91f8e26ca2a349938ce26dd5@sanger.ac.uk","name":"John Marshall"},"message":"Improve faidx blank line handling\n\nMultiple sequence FASTA files shouldn't have blank lines before subsequent\n\">\" headers, but we mostly support that so we need to support it in the\ncase where all sequence lines are the same length too.\n\nFixes http://seqanswers.com/forums/showpost.php?p=172494&postcount=6\n\nProbably other bugs are lurking here; this incomprehensible state\nmachine could benefit from some rewriting...","distinct":true,"url":"https://api.github.com/repos/pd3/htslib/commits/1980e5859251741f7905e754c07112a0fe3ec3e5"},{"sha":"826454f815672f29635630fb4c9c8663a59ea98c","author":{"email":"4081f471c57da10c91f8e26ca2a349938ce26dd5@sanger.ac.uk","name":"John Marshall"},"message":"[make] Add distdir hook for Automake superprojects\n\nWe would prefer clients to build against an already-installed separate\nhtslib; but we'll also grudgingly enable \"make dist\" when we are bundled\nas a subdirectory of an Automade project.\n\n(See info automake \"Third-Party Makefiles\".)\n\nAlso build tags with either \"TAGS\" or \"tags\" targets.","distinct":true,"url":"https://api.github.com/repos/pd3/htslib/commits/826454f815672f29635630fb4c9c8663a59ea98c"},{"sha":"9de542c6c919b96ba3fe0f44fc8aa06cb1c3307c","author":{"email":"5399fd5b15fc3c0608ee5ee2d345476e1dc26f92@ghraoui.name","name":"Afif Elghraoui"},"message":"Fix various spelling errors\n\nDebian QC tools complained about spelling errors in the source\ncode. This patch corrects them.\n\n[Applied pysam-developers/pysam#122.]","distinct":true,"url":"https://api.github.com/repos/pd3/htslib/commits/9de542c6c919b96ba3fe0f44fc8aa06cb1c3307c"},{"sha":"10c4920894eeba6911413e13e59a3cc574f48346","author":{"email":"b48e0e91d6a7b0f03328f39c48db102a17c97190@sanger.ac.uk","name":"Petr Danecek"},"message":"Fix in VCF header parsing\n\nbcf_hdr_append() followed by bcf_hdr_write() should not make a\nsubsequent bcf_read() call fail if tag IDs remain unchanged, as\nin the issue #213","distinct":true,"url":"https://api.github.com/repos/pd3/htslib/commits/10c4920894eeba6911413e13e59a3cc574f48346"},{"sha":"adec4d334d7960fb90e28b7f62bbe4138a8a477a","author":{"email":"3243a2766bb737188235920577f6adab5919ad82@sanger.ac.uk","name":"Rob Davies"},"message":"Ensure SAM query name length fits in a byte.","distinct":true,"url":"https://api.github.com/repos/pd3/htslib/commits/adec4d334d7960fb90e28b7f62bbe4138a8a477a"},{"sha":"a03a15fdc8e7ecb42f45596e8b7568687e5617c8","author":{"email":"3243a2766bb737188235920577f6adab5919ad82@sanger.ac.uk","name":"Rob Davies"},"message":"Ensure names are present for @SQ/@RG/@PG lines in sam_hdr_update_hashes\n\nsam_hdr_update_hashes goes through the tags on a header line that it's\ninterested in, filling in values in a SAM_hdr_tag struct as it goes.\nOne of these is name, which is set to a copy of the SN tag for @SQ lines\nand ID for @RG and @PG lines.  These must be present according to the SAM\nspecification, so ensure that name has been set after going through all\nthe tags for the line.  This means anything using the name field (notably\nrefs_from_header) can assume that it isn't NULL.\n\nFixes a crash found by the Americal Fuzzy Lop fuzz tester.\n\nAlso fix some potential memory leaks that could happen if realloc\nfails in this function.","distinct":true,"url":"https://api.github.com/repos/pd3/htslib/commits/a03a15fdc8e7ecb42f45596e8b7568687e5617c8"},{"sha":"e1a67ee3fe2479e9b29f806cba4c6e06d4e74193","author":{"email":"3243a2766bb737188235920577f6adab5919ad82@sanger.ac.uk","name":"Rob Davies"},"message":"Stop gzip header code from reading too far in bgzf_read_block.\n\nWhen working out how many bytes to skip, make it compare to count (the\nnumber of bytes read) instead of BGZF_BLOCK_SIZE.  This prevents it from\nreading uninitialised memory if the file finishes part way through the\nheader.","distinct":true,"url":"https://api.github.com/repos/pd3/htslib/commits/e1a67ee3fe2479e9b29f806cba4c6e06d4e74193"},{"sha":"ea63c205742c31317563d90143a466106a844eb9","author":{"email":"3243a2766bb737188235920577f6adab5919ad82@sanger.ac.uk","name":"Rob Davies"},"message":"Fix handling of zero-bit beta codec case.\n\nUsing the beta codec with nbits=0 is valid, but confuses\ncram_not_enough_bits() as it's possible to have no input data in\nthis case so cram_not_enough_bits thinks it has run out.\n\nMove the calls to cram_not_enough_bits inside checks that c->beta.nbits\nis non-zero to avoid the problem.","distinct":true,"url":"https://api.github.com/repos/pd3/htslib/commits/ea63c205742c31317563d90143a466106a844eb9"}]}