{"push_id":593913489,"size":40,"distinct_size":20,"ref":"refs/heads/CRAMv3","head":"437bfe7e7babdf2c6b484b2bc3bb29748730fb7b","before":"4a23b187f6115fba228772e934f4385708fa9149","commits":[{"sha":"cca94d5f092e7bd48f9ebd87d1828de214f090c1","author":{"email":"4081f471c57da10c91f8e26ca2a349938ce26dd5@sanger.ac.uk","name":"John Marshall"},"message":"Make READ1/READ2 flags correspond to the example\n\nHat tip @arlin, fixes #26.","distinct":false,"url":"https://api.github.com/repos/samtools/hts-specs/commits/cca94d5f092e7bd48f9ebd87d1828de214f090c1"},{"sha":"866a46a6e20ad6daa2891ac1769ce5b5d13628ea","author":{"email":"4081f471c57da10c91f8e26ca2a349938ce26dd5@sanger.ac.uk","name":"John Marshall"},"message":"Reinstate line breaks (trailing whitespace)","distinct":false,"url":"https://api.github.com/repos/samtools/hts-specs/commits/866a46a6e20ad6daa2891ac1769ce5b5d13628ea"},{"sha":"176ffdce88d8c0bc7ac621e69f713f63f6848200","author":{"email":"4081f471c57da10c91f8e26ca2a349938ce26dd5@sanger.ac.uk","name":"John Marshall"},"message":"Update Padded SAM example to match Introduction's example\n\nFix r001's flags (hat tip @arlin, further fixes #26), r003's flags,\nand the header VN.  Add r001/2's sequence mismatch as introduced\nin 80bc68f7619da60eaa4f43a16878c4675e930570 and c8c0a443c0ebfea4deb8484fb77f9cb428e65476.","distinct":false,"url":"https://api.github.com/repos/samtools/hts-specs/commits/176ffdce88d8c0bc7ac621e69f713f63f6848200"},{"sha":"b882850659f9356a95eea78b7fc26258b6445b37","author":{"email":"4081f471c57da10c91f8e26ca2a349938ce26dd5@sanger.ac.uk","name":"John Marshall"},"message":"Tidy up footnotes\n\nSwap MD and CT footnote texts so they are notes for the right items\n(hat tip @lajoiem, fixes #25), use autoincrementing counter, place the\nfootnote marker *after* punctuation, disable hyperfootnotes as they\ndon't work from within tables.","distinct":false,"url":"https://api.github.com/repos/samtools/hts-specs/commits/b882850659f9356a95eea78b7fc26258b6445b37"},{"sha":"f76513779139bc99d21c43885c9c9838e5ebf6fb","author":{"email":"c01a39a76d96e917f87dcda7aac0ff07d778d5c1@googlemail.com","name":"peterjc"},"message":"Describe BAI changes for 'samtools idxstats' and details of BIN value\n\n(Original commit 16 Mar 2012, rebased 8 April 2014)","distinct":false,"url":"https://api.github.com/repos/samtools/hts-specs/commits/f76513779139bc99d21c43885c9c9838e5ebf6fb"},{"sha":"b94e532935464a924a03681255c81b2b6e12146a","author":{"email":"90319b329246a0610c363736effd3f5d0cdffd33@sanger.ac.uk","name":"Martin Pollard"},"message":"Add n_no_coor to index formats given that it has been being written by samtools for a few years.","distinct":false,"url":"https://api.github.com/repos/samtools/hts-specs/commits/b94e532935464a924a03681255c81b2b6e12146a"},{"sha":"089f34f7d0e6d7ea9cfa9d61f7b5b462940ff4b3","author":{"email":"4081f471c57da10c91f8e26ca2a349938ce26dd5@sanger.ac.uk","name":"John Marshall"},"message":"Add links to mailing lists\n\n(As suggested in passing in #28)","distinct":false,"url":"https://api.github.com/repos/samtools/hts-specs/commits/089f34f7d0e6d7ea9cfa9d61f7b5b462940ff4b3"},{"sha":"16ede77ad5288e777fa0d7aec143fb4c9f88ab16","author":{"email":"4081f471c57da10c91f8e26ca2a349938ce26dd5@sanger.ac.uk","name":"John Marshall"},"message":"Add links to CSI specification and UCSC binning paper\n\nNote that the 2^29-1 limitation is specific to the BAI format,\nand add links to the generalised binning scheme in CSI.  Fixes #35.\n\nAdd footnote referencing Kent et al.  Fixes #29.","distinct":false,"url":"https://api.github.com/repos/samtools/hts-specs/commits/16ede77ad5288e777fa0d7aec143fb4c9f88ab16"},{"sha":"b2416a9cfd42c96ee771f9ae2a50374e91efda62","author":{"email":"811ae55e6abfa3741476eb344dc5456f58f11846@adelaide.edu.au","name":"Dan Kortschak"},"message":"Fix typo in bin number for last 48kb bin","distinct":false,"url":"https://api.github.com/repos/samtools/hts-specs/commits/b2416a9cfd42c96ee771f9ae2a50374e91efda62"},{"sha":"f35504b9b5fc86d6a4f2163b51396ff159ab1ebb","author":{"email":"4081f471c57da10c91f8e26ca2a349938ce26dd5@sanger.ac.uk","name":"John Marshall"},"message":"Correct final BAI bin number\n\nThere is an even number of bins on the last row too -- previously this\nwas typoed or off-by-one.  Hat tip Pavel Sinitcyn.","distinct":false,"url":"https://api.github.com/repos/samtools/hts-specs/commits/f35504b9b5fc86d6a4f2163b51396ff159ab1ebb"},{"sha":"1d490da929aec571cde09d5c71c6c1de55fd2db0","author":{"email":"4081f471c57da10c91f8e26ca2a349938ce26dd5@sanger.ac.uk","name":"John Marshall"},"message":"Move \"optional\" to the first column\n\nAlso regularise \\cline and fix tabix header typo.","distinct":false,"url":"https://api.github.com/repos/samtools/hts-specs/commits/1d490da929aec571cde09d5c71c6c1de55fd2db0"},{"sha":"17a0201f8ca8eed140888e35c020a605fe07902f","author":{"email":"4081f471c57da10c91f8e26ca2a349938ce26dd5@sanger.ac.uk","name":"John Marshall"},"message":"Describe pseudo-bins in a separate table\n\nHopefully makes clearer that the pseudo-bin is just another bin -- in\nfact it doesn't even need to be the final bin in the list!  Add footnote\nexplaining placed/unplaced.","distinct":false,"url":"https://api.github.com/repos/samtools/hts-specs/commits/17a0201f8ca8eed140888e35c020a605fe07902f"},{"sha":"2bc78e17e7368511c5715d22250e67947dd3454c","author":{"email":"4081f471c57da10c91f8e26ca2a349938ce26dd5@sanger.ac.uk","name":"John Marshall"},"message":"Merge BAI/CSI/tabix idxstats details (PR #2)","distinct":false,"url":"https://api.github.com/repos/samtools/hts-specs/commits/2bc78e17e7368511c5715d22250e67947dd3454c"},{"sha":"b3639d649d9740689315af40deea9404602489b0","author":{"email":"4081f471c57da10c91f8e26ca2a349938ce26dd5@sanger.ac.uk","name":"John Marshall"},"message":"Remove SAM's artificial 'i' optional field range limit\n\nSAM is a textual format, so there is no intrinsic limit on the number\nof digits in an 'i' value.  In particular, SAM should be able to express\nat least the same range as BAM, namely -2^31 (as 'i') to 2^32-1 (as 'I').\n\nFixes #36.","distinct":false,"url":"https://api.github.com/repos/samtools/hts-specs/commits/b3639d649d9740689315af40deea9404602489b0"},{"sha":"90b9d9edad9cd9c7c07318dbb37cacc543d0e62e","author":{"email":"4081f471c57da10c91f8e26ca2a349938ce26dd5@sanger.ac.uk","name":"John Marshall"},"message":"Clarify that BGZF blocks are limited to 64K before compression\n\nFixes #9.  Also add footnote referencing the GZIP RFC.","distinct":false,"url":"https://api.github.com/repos/samtools/hts-specs/commits/90b9d9edad9cd9c7c07318dbb37cacc543d0e62e"},{"sha":"b6abaee0bab868437df7e4b78900d9aa18a90e3d","author":{"email":"edd51ceff19ae47ac43f5213eadc13a2adf78343@nau.edu","name":"Jason Travis"},"message":"Fix typo in Genotype encoding example","distinct":false,"url":"https://api.github.com/repos/samtools/hts-specs/commits/b6abaee0bab868437df7e4b78900d9aa18a90e3d"},{"sha":"13c3d171a6cd2c16068af57b912210bd714bdf76","author":{"email":"b48e0e91d6a7b0f03328f39c48db102a17c97190@sanger.ac.uk","name":"pd3"},"message":"Merge pull request #62 from corburn/patch-1\n\nFix typo in Genotype encoding example","distinct":false,"url":"https://api.github.com/repos/samtools/hts-specs/commits/13c3d171a6cd2c16068af57b912210bd714bdf76"},{"sha":"68bab2f9d17fb47fbc0023917681e22bf5670ed8","author":{"email":"4081f471c57da10c91f8e26ca2a349938ce26dd5@sanger.ac.uk","name":"John Marshall"},"message":"Reverse flag *is* meaningful for unmapped reads\n\nReinstate language similar to before e6ca319516752ecdbc25b5880c41b1a4970dd0ec\nas to the reverse flag being significant when the unmapped flag is set.\nRecommend that unmapped reads be stored as they came off the machine.\n\nFixes #52.","distinct":false,"url":"https://api.github.com/repos/samtools/hts-specs/commits/68bab2f9d17fb47fbc0023917681e22bf5670ed8"},{"sha":"0e9ca57ce58770773747d9b7681aa99a5805194b","author":{"email":"4081f471c57da10c91f8e26ca2a349938ce26dd5@sanger.ac.uk","name":"John Marshall"},"message":"Merge SAM 'i' range limit removal (PR #50)","distinct":false,"url":"https://api.github.com/repos/samtools/hts-specs/commits/0e9ca57ce58770773747d9b7681aa99a5805194b"},{"sha":"ec1fec2dc1d6369fcdfb304614601eb4f2669921","author":{"email":"4081f471c57da10c91f8e26ca2a349938ce26dd5@sanger.ac.uk","name":"John Marshall"},"message":"Add HD-GO, RG-PL:ONT, and RG-PM header tags\n\nReinstate the previously-specified @HD-GO tag.  Fixes #15.\nAdd ONT (Oxford Nanopore) as a valid value for @RG-PL.  Fixes #39.\nAdd new free-form @RG-PM tag to allow more details about the platform\nto be given, e.g., machine models such as 'HiSeq 2500'.  Fixes #16.\n\n(The header table now spans a page break and needs reformatting,\nwhich will happen presently.)","distinct":false,"url":"https://api.github.com/repos/samtools/hts-specs/commits/ec1fec2dc1d6369fcdfb304614601eb4f2669921"}]}