{"push_id":2520105628,"size":22,"distinct_size":7,"ref":"refs/heads/sh-sv-representation-change","head":"954cf6daf00a2fa0086f4293c1fa89129ff77b40","before":"5b8e571ecc90c8e8bc604f9dccdb0985bca2c39f","commits":[{"sha":"e53241be17e1a87c42c9ca533b01a159b0c9b55d","author":{"name":"Chris Norman","email":"629c3e3d004b31c1ae42a6dc8c6729d15c6b15a2@broadinstitute.org"},"message":"ReferenceConfidenceVariantContextMerger fixes for spanning deletions, use correct types for median calculation. (#4680)","distinct":false,"url":"https://api.github.com/repos/broadinstitute/gatk/commits/e53241be17e1a87c42c9ca533b01a159b0c9b55d"},{"sha":"b2ffd0eabd3c27b1220e2891de6397b7a00b96fd","author":{"name":"Jean-Philippe Martin","email":"5d411d68f6d6574d99db48432bd3560bdd4c2557@google.com"},"message":"NIO output support for multiple tools\n\nClipReads, LeftAlignIndels, RevertBaseQualityScores, UnmarkDuplicates,\nSplitNCigarReds","distinct":false,"url":"https://api.github.com/repos/broadinstitute/gatk/commits/b2ffd0eabd3c27b1220e2891de6397b7a00b96fd"},{"sha":"6fbad4f6cdcca67019cf78c36ffb7916510ac4df","author":{"name":"Jean-Philippe Martin","email":"5d411d68f6d6574d99db48432bd3560bdd4c2557@google.com"},"message":"Revert \"NIO output support for multiple tools\"\n\nIt was supposed to be in a branch, not master\n\nThis reverts commit b2ffd0eabd3c27b1220e2891de6397b7a00b96fd.","distinct":false,"url":"https://api.github.com/repos/broadinstitute/gatk/commits/6fbad4f6cdcca67019cf78c36ffb7916510ac4df"},{"sha":"e530c2e82c347c24f33be61e2172763db04273a2","author":{"name":"cwhelan","email":"7c60de5ea73afcafc91175249a550a338066d83e@gmail.com"},"message":"update sv scripts to only copy a single bam file and index, and respect project parameter (#4646)\n\n* update SV scripts to only copy a single bam file, respect project, include cluster name in results to avoid collisions, and fix an issue with preemptible workers","distinct":false,"url":"https://api.github.com/repos/broadinstitute/gatk/commits/e530c2e82c347c24f33be61e2172763db04273a2"},{"sha":"7d25ceb1f242fa3828cb005085cd24cea824fdc1","author":{"name":"Samuel Friedman","email":"7eb394279ae94188cf285cff20624a68af3843f3@gmail.com"},"message":"numerical consistency between python and java, transpose fix (#4652)","distinct":false,"url":"https://api.github.com/repos/broadinstitute/gatk/commits/7d25ceb1f242fa3828cb005085cd24cea824fdc1"},{"sha":"36eb37f72af95a366ba232676138adb607d07994","author":{"name":"David Benjamin","email":"348b1b6801801c3d890b2e1589a8e36441d09fdc@broadinstitute.org"},"message":"Better default AF for M2 tumor-normal mode; improved M2 STR filter (#4690)\n\n* different default AFs for Mutect2 tumor-only and tumor-normal\r\n\r\n* improved Mutect2 PCR slippage filter","distinct":false,"url":"https://api.github.com/repos/broadinstitute/gatk/commits/36eb37f72af95a366ba232676138adb607d07994"},{"sha":"420166a67ea4b4ffe1298ffa33101f33962f3f74","author":{"name":"Chris Norman","email":"629c3e3d004b31c1ae42a6dc8c6729d15c6b15a2@broadinstitute.org"},"message":"Replace StreamingProcessController println with a logger info message. (#4697)","distinct":false,"url":"https://api.github.com/repos/broadinstitute/gatk/commits/420166a67ea4b4ffe1298ffa33101f33962f3f74"},{"sha":"0975d9bbacbf6b9ffca717392fa3b6954a7f44ec","author":{"name":"JP Martin","email":"58f64d2fba3f24af877f626aad91e81a46dfdf39@users.noreply.github.com"},"message":"NIO output support for multiple tools (#4695)\n\nClipReads, LeftAlignIndels, RevertBaseQualityScores, UnmarkDuplicates,\r\nSplitNCigarReds","distinct":false,"url":"https://api.github.com/repos/broadinstitute/gatk/commits/0975d9bbacbf6b9ffca717392fa3b6954a7f44ec"},{"sha":"01fa44d66175182ddbdbc66475f018de8a7d6bb7","author":{"name":"Chris Norman","email":"629c3e3d004b31c1ae42a6dc8c6729d15c6b15a2@broadinstitute.org"},"message":"Fix and test for calculating CombineGVCFs intermediate band interval start locations. (#4681)","distinct":false,"url":"https://api.github.com/repos/broadinstitute/gatk/commits/01fa44d66175182ddbdbc66475f018de8a7d6bb7"},{"sha":"bc640b910d5ed5816c63b7ff02dcaa9da5d50bab","author":{"name":"droazen","email":"1d0c6f32bb65b8defcf996a778a48a2d5cfb7c64@broadinstitute.org"},"message":"Fix two instances of immutable collections being used to initialize List arguments (#4703)\n\nBarclay can't currently handle immutable collections in @Argument values due to\r\nhttps://github.com/broadinstitute/gatk/issues/4702\r\n\r\nTests for these arguments are coming in a separate, larger branch, but I\r\nwanted to get the fixes in first since it's such a simple fix.","distinct":false,"url":"https://api.github.com/repos/broadinstitute/gatk/commits/bc640b910d5ed5816c63b7ff02dcaa9da5d50bab"},{"sha":"949c69b4ba1ef943819d803221eccc99df6bd5a2","author":{"name":"David Benjamin","email":"348b1b6801801c3d890b2e1589a8e36441d09fdc@broadinstitute.org"},"message":"Cleaning Mutect2 code in various places (#4704)","distinct":false,"url":"https://api.github.com/repos/broadinstitute/gatk/commits/949c69b4ba1ef943819d803221eccc99df6bd5a2"},{"sha":"3e41aa5d9fe8ff3e624f77505f292b9e8b75cb45","author":{"name":"David Benjamin","email":"348b1b6801801c3d890b2e1589a8e36441d09fdc@broadinstitute.org"},"message":"New, supported M2 NIO wdl that works in Firecloud (#4710)","distinct":false,"url":"https://api.github.com/repos/broadinstitute/gatk/commits/3e41aa5d9fe8ff3e624f77505f292b9e8b75cb45"},{"sha":"7641f53458f9e7c8426ecf23cfb7d74f9f94f21b","author":{"name":"jamesemery","email":"5d2bc2ca0727559e1453d74e9f0ca7b14095fd8e@broadinstitute.org"},"message":"MarkDuplicatesSpark improvements checkpoint (#4656)\n\n\r\nCo-authored-by: Louis Bergelson <louisb@broadinstitute.org>\r\n\r\nFirst part of a major rewrite of MarkDuplicatesSpark to improve performance. Tool still has a number of known issues, but is much faster than the previous version.","distinct":false,"url":"https://api.github.com/repos/broadinstitute/gatk/commits/7641f53458f9e7c8426ecf23cfb7d74f9f94f21b"},{"sha":"845d74a781f89f5f5440429d031529295be57ccb","author":{"name":"tedsharpe","email":"a569053dedce2b4b589b850f95e05895f28158ac@users.noreply.github.com"},"message":"tweak bwa to allow gappier alignments in local assemblies (#4708)","distinct":false,"url":"https://api.github.com/repos/broadinstitute/gatk/commits/845d74a781f89f5f5440429d031529295be57ccb"},{"sha":"9f6838b445ae362e2138d4caa90786e6d7b4c8ab","author":{"name":"Steve Huang","email":"05c38da8517584609004cfd83c7dfb02125e87c9@broadinstitute.org"},"message":"(SV) bug-fixing commit: (#4677)\n\n* better exception message and fix bug in existing cpx variant test data\r\n\r\n(SV) new cpx variant scenario commit:\r\n  * optionally add reference segments when the would be segment is 2-bp long (before all such segments are skipped)","distinct":false,"url":"https://api.github.com/repos/broadinstitute/gatk/commits/9f6838b445ae362e2138d4caa90786e6d7b4c8ab"},{"sha":"a95a152f2ee0bb1b4e724948b779498f6f2d52ce","author":{"name":"Steve Huang","email":"05c38da8517584609004cfd83c7dfb02125e87c9@broadinstitute.org"},"message":"(SV) refactor commit 1:\nmove method parseOneContig() in ChimericAlignments to\n  DiscoverVariantsFromContigAlignmentsSAMSpark\n  considering it is only used there","distinct":true,"url":"https://api.github.com/repos/broadinstitute/gatk/commits/a95a152f2ee0bb1b4e724948b779498f6f2d52ce"},{"sha":"b7ce39c7a57785394acd702d35f97f944ec475a2","author":{"name":"Steve Huang","email":"05c38da8517584609004cfd83c7dfb02125e87c9@broadinstitute.org"},"message":"(SV) refactor commit 2:\nrefactor and update SvDiscoveryInputData","distinct":true,"url":"https://api.github.com/repos/broadinstitute/gatk/commits/b7ce39c7a57785394acd702d35f97f944ec475a2"},{"sha":"42505c9fa71766d8d839aa64c20c2d04977190bc","author":{"name":"Steve Huang","email":"05c38da8517584609004cfd83c7dfb02125e87c9@broadinstitute.org"},"message":"(SV) refactor commit 3:\n  * update SimpleNovelAdjacencyAndChimericAlignmentEvidence\n  * also add serialization and hashcode test for\n         NovelAdjacencyAndAltHaplotype\n         SimpleNovelAdjacencyAndChimericAlignmentEvidence","distinct":true,"url":"https://api.github.com/repos/broadinstitute/gatk/commits/42505c9fa71766d8d839aa64c20c2d04977190bc"},{"sha":"3d25a09db34d0d175cdbb9f0c6bfec419a07cf5c","author":{"name":"Steve Huang","email":"05c38da8517584609004cfd83c7dfb02125e87c9@broadinstitute.org"},"message":"(SV) refactor commit 4:\nrefactor to simplify contig alignment signature basic type (suspicious, simple, complex) classification","distinct":true,"url":"https://api.github.com/repos/broadinstitute/gatk/commits/3d25a09db34d0d175cdbb9f0c6bfec419a07cf5c"},{"sha":"83843ce3e71b8f518e42a5e2b84554c3e3bf9bb9","author":{"name":"Steve Huang","email":"05c38da8517584609004cfd83c7dfb02125e87c9@broadinstitute.org"},"message":"(SV) Representation change commit 1:\nchange SVLEN for CPX variants to the difference between [alt haplotype sequence length] and [affected reference region length]","distinct":true,"url":"https://api.github.com/repos/broadinstitute/gatk/commits/83843ce3e71b8f518e42a5e2b84554c3e3bf9bb9"}]}
{"actor":{"display_login":"SHuang-Broad"}}