{"push_id":991129910,"size":9,"distinct_size":0,"ref":"refs/heads/medium-tests","head":"d7d13b140a54e428ff327a91f3a1c7d36e0a9697","before":"12469451475e450912339eca5887f79e9cfab547","commits":[{"sha":"38163eec0548d92f0555d4d4423687f25b7baa0d","author":{"email":"e9c1a834de95a4de7351a399a0c647228b0b0de5@mlin.net","name":"Mike Lin"},"message":"genotyper: refactor AlleleDepthHelper to simplify and reduce heap allocation","distinct":false,"url":"https://api.github.com/repos/dnanexus-rnd/GLnexus/commits/38163eec0548d92f0555d4d4423687f25b7baa0d"},{"sha":"976123d26b425ce0ac0c2eda5621722db07aa9d8","author":{"email":"e9c1a834de95a4de7351a399a0c647228b0b0de5@mlin.net","name":"Mike Lin"},"message":"Merge pull request #59 from dnanexus-rnd/mlin-AlleleDepthHelper-refactor\n\ngenotyper: refactor AlleleDepthHelper to simplify and reduce heap allocation","distinct":false,"url":"https://api.github.com/repos/dnanexus-rnd/GLnexus/commits/976123d26b425ce0ac0c2eda5621722db07aa9d8"},{"sha":"6e9b34ea5843386ac37801e0d3faa0861968d86c","author":{"email":"e9c1a834de95a4de7351a399a0c647228b0b0de5@mlin.net","name":"Mike Lin"},"message":"Handling \"pseudo\" reference confidence records (0/0 and QUAL=0)\n\nSignificant genotyper refactoring for more flexibility in handling\noverlapping variant records.","distinct":false,"url":"https://api.github.com/repos/dnanexus-rnd/GLnexus/commits/6e9b34ea5843386ac37801e0d3faa0861968d86c"},{"sha":"aa9d6bdc4a54161527748dbd418f8e4877d3d1b5","author":{"email":"e9c1a834de95a4de7351a399a0c647228b0b0de5@mlin.net","name":"Mike Lin"},"message":"Merge pull request #60 from dnanexus-rnd/mlin-pseudo-ref-records\n\nHandling \"pseudo\" reference confidence records","distinct":false,"url":"https://api.github.com/repos/dnanexus-rnd/GLnexus/commits/aa9d6bdc4a54161527748dbd418f8e4877d3d1b5"},{"sha":"9b813c3c6761d9ff877f37b859c16fa9dc90ce21","author":{"email":"e9c1a834de95a4de7351a399a0c647228b0b0de5@mlin.net","name":"Mike Lin"},"message":"unifier: add a configuration setting to prefer small alleles as opposed to common alleles\n\n\"small\" alleles, by which we mean editing the smallest stretch of the reference genome,\nare (heuristically) the least likely to conflict with other overlapping alleles and\ncause UnphasedVariants losses. Common remains the default preference for now because\nit seems the right heuristic to minimize total loss, however.","distinct":false,"url":"https://api.github.com/repos/dnanexus-rnd/GLnexus/commits/9b813c3c6761d9ff877f37b859c16fa9dc90ce21"},{"sha":"708156a27a606792aea7dab6b673b36790ffa734","author":{"email":"e9c1a834de95a4de7351a399a0c647228b0b0de5@mlin.net","name":"Mike Lin"},"message":"Merge pull request #61 from dnanexus-rnd/mlin-unifier-prefer-small-alleles\n\nunifier: add a configuration setting to prefer small alleles","distinct":false,"url":"https://api.github.com/repos/dnanexus-rnd/GLnexus/commits/708156a27a606792aea7dab6b673b36790ffa734"},{"sha":"65d4980a06aabcf57c5e1c5bde5c010870e98b7f","author":{"email":"e9c1a834de95a4de7351a399a0c647228b0b0de5@mlin.net","name":"Mike Lin"},"message":"Add min_alleles predicate to BCFData query methods\n\nThis will support a discover_alleles optimization to skip scanning through\nreference confidence records (which it effectively ignores anyway)","distinct":false,"url":"https://api.github.com/repos/dnanexus-rnd/GLnexus/commits/65d4980a06aabcf57c5e1c5bde5c010870e98b7f"},{"sha":"9c697b817e86b01574ab2fe4cd4b0db04f804e43","author":{"email":"e9c1a834de95a4de7351a399a0c647228b0b0de5@mlin.net","name":"Mike Lin"},"message":"discover_alleles: use min_alleles predicate in BCFData queries\n\nAllows BCFKeyValueData to avoid unpacking reference confidence records which\ndiscover_alleles ignores anyway.","distinct":false,"url":"https://api.github.com/repos/dnanexus-rnd/GLnexus/commits/9c697b817e86b01574ab2fe4cd4b0db04f804e43"},{"sha":"d7d13b140a54e428ff327a91f3a1c7d36e0a9697","author":{"email":"e9c1a834de95a4de7351a399a0c647228b0b0de5@mlin.net","name":"Mike Lin"},"message":"BCFKeyValueData::scan_bucket: optimize min_alleles predicate by having BCFScanner extract bcf1_t::n_allele without copying","distinct":false,"url":"https://api.github.com/repos/dnanexus-rnd/GLnexus/commits/d7d13b140a54e428ff327a91f3a1c7d36e0a9697"}]}