{"commits":[{"author":{"name":"Mark DePristo","email":"2bdb44e58c8095f937b0a4757a168d16c90fe61e@broadinstitute.org"},"sha":"1b01e24e239c2ae39aed3e0b7453c87028a1040f","message":"Moving around comments","url":"https://api.github.com/repos/singerma/gatk/commits/1b01e24e239c2ae39aed3e0b7453c87028a1040f"},{"author":{"name":"Mark DePristo","email":"2bdb44e58c8095f937b0a4757a168d16c90fe61e@broadinstitute.org"},"sha":"b863390cb1a4c89d8a77cdc6a20c76aa5f810ac8","message":"Moving reduced read functionality into GATKSAMRecord\n\n-- More functions take / produce GATKSAMRecords instead of SAMRecord","url":"https://api.github.com/repos/singerma/gatk/commits/b863390cb1a4c89d8a77cdc6a20c76aa5f810ac8"},{"author":{"name":"Guillermo del Angel","email":"a094a099c5c8e68d37430e8201c1ea0f23e8348f@broadinstitute.org"},"sha":"f4b409fa0df0ffc601cbf9efc718ab58c19b9b5c","message":"CombineVariants bug fix: when merging records with disparate alleles we were leaving AC,AF fields intact. This had as a consequence that we could end up with a record with 3 alt alleles but only 2 values in AC,AF fields. Now, if alleles in combined vc are different from original, and if AC,AF fields can't be recomputed from genotypes, we remove attributes from vc map since they'll be invalid anyway. Integration test md5 changed since there were several badly merged records in result","url":"https://api.github.com/repos/singerma/gatk/commits/f4b409fa0df0ffc601cbf9efc718ab58c19b9b5c"},{"author":{"name":"Mauricio Carneiro","email":"9fbc60d54a4393092f0acd89a70ac3cbab00800e@broadinstitute.org"},"sha":"102dafdcbc84ccd1cddd671639ddddb79896186e","message":"Validation of GATKSamRecord in read filters\n\nMoved the validation of the GATKSamRecord to the MalformedReadFilter with the intent to make the read filter the ultimate validation location for sam records. This way we can opt to filter out malformed reads if we know what we are doing or blow up otherwise.","url":"https://api.github.com/repos/singerma/gatk/commits/102dafdcbc84ccd1cddd671639ddddb79896186e"},{"author":{"name":"Mauricio Carneiro","email":"9fbc60d54a4393092f0acd89a70ac3cbab00800e@broadinstitute.org"},"sha":"86305a5dcfc058a8a31bb27aaefe2576c993a3aa","message":"Adjusting the memory limits of the MDCP\n\nIndel caller needs more than 3G for large datasets.","url":"https://api.github.com/repos/singerma/gatk/commits/86305a5dcfc058a8a31bb27aaefe2576c993a3aa"},{"author":{"name":"Mauricio Carneiro","email":"9fbc60d54a4393092f0acd89a70ac3cbab00800e@broadinstitute.org"},"sha":"4913f8a60f69116d3bbe4416185a9e475daac7ec","message":"Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable","url":"https://api.github.com/repos/singerma/gatk/commits/4913f8a60f69116d3bbe4416185a9e475daac7ec"},{"author":{"name":"Mauricio Carneiro","email":"9fbc60d54a4393092f0acd89a70ac3cbab00800e@broadinstitute.org"},"sha":"c3cb07fc1d3d4e4109be8cce0aec1567d918365b","message":"Relocating the ReduceBAM script.","url":"https://api.github.com/repos/singerma/gatk/commits/c3cb07fc1d3d4e4109be8cce0aec1567d918365b"},{"author":{"name":"Mark DePristo","email":"2bdb44e58c8095f937b0a4757a168d16c90fe61e@broadinstitute.org"},"sha":"42bf9adede112282e8e8e45bf987ab01305b0a7e","message":"Initial version of \"fast\" FragmentPileup code\n\n-- Uses mayOverlapRoutine in ReadUtils\n-- Attempts to be smart when doing overlap calculation, to avoid unnecessary allocations\n-- PileupElement now comparable (sorts on offset than on start)\n-- Caliper microbenchmark to assess performance","url":"https://api.github.com/repos/singerma/gatk/commits/42bf9adede112282e8e8e45bf987ab01305b0a7e"},{"author":{"name":"Ryan Poplin","email":"0b614c665339680ffb865dc18139fec9db2eaea0@broadinstitute.org"},"sha":"f5d910b8a54b1dbceab506a7260ebaf1d9c4796b","message":"Haplotype caller now sends genotype likelihoods to the exact model to genotype the events found in the best haplotypes.","url":"https://api.github.com/repos/singerma/gatk/commits/f5d910b8a54b1dbceab506a7260ebaf1d9c4796b"},{"author":{"name":"Mark DePristo","email":"2bdb44e58c8095f937b0a4757a168d16c90fe61e@broadinstitute.org"},"sha":"585a45b7a3d145fbb1ed135c2a78d03bd6e8bf7c","message":"Bug fix for ClipReadsWalker when stats output isn't provided\n\n-- See http://getsatisfaction.com/gsa/topics/clipreadswalker?utm_content=topic_link&utm_medium=email&utm_source=reply_notification","url":"https://api.github.com/repos/singerma/gatk/commits/585a45b7a3d145fbb1ed135c2a78d03bd6e8bf7c"},{"author":{"name":"Mark DePristo","email":"2bdb44e58c8095f937b0a4757a168d16c90fe61e@broadinstitute.org"},"sha":"f6ccac889b4c91e5a7d36762228296cd82045060","message":"Merged bug fix from Stable into Unstable","url":"https://api.github.com/repos/singerma/gatk/commits/f6ccac889b4c91e5a7d36762228296cd82045060"},{"author":{"name":"Ryan Poplin","email":"0b614c665339680ffb865dc18139fec9db2eaea0@broadinstitute.org"},"sha":"090382ce03c5f792462f93d6ec59525dd6c49b50","message":"Now calculates proper multi-allelic likelihoods and sends them to the exact model if appropriate.","url":"https://api.github.com/repos/singerma/gatk/commits/090382ce03c5f792462f93d6ec59525dd6c49b50"},{"author":{"name":"Ryan Poplin","email":"0b614c665339680ffb865dc18139fec9db2eaea0@broadinstitute.org"},"sha":"13702939ac31c1e6123dbf1b27c87406c6d7d488","message":"HaplotypeCaller now calculates multi-sample likelihoods and passes them to the exact model to make multi-sample calls.","url":"https://api.github.com/repos/singerma/gatk/commits/13702939ac31c1e6123dbf1b27c87406c6d7d488"},{"author":{"name":"Mark DePristo","email":"2bdb44e58c8095f937b0a4757a168d16c90fe61e@broadinstitute.org"},"sha":"166174a551860fa18e8092f3dbe56e0ef28eb884","message":"Google caliper example execution script\n\n-- FragmentPileup with final performance testing","url":"https://api.github.com/repos/singerma/gatk/commits/166174a551860fa18e8092f3dbe56e0ef28eb884"},{"author":{"name":"Mark DePristo","email":"2bdb44e58c8095f937b0a4757a168d16c90fe61e@broadinstitute.org"},"sha":"502592671d7bfdbb9cff0575e94ca3c0946d000d","message":"Cleanup FragmentPileup before main repo commit\n\n-- removed intermiate functions.  Now only original version and best optimized new version remain\n-- Moved general artificial read backed pileup creation code into ArtificialSamUtils","url":"https://api.github.com/repos/singerma/gatk/commits/502592671d7bfdbb9cff0575e94ca3c0946d000d"},{"author":{"name":"Khalid Shakir","email":"308599bb85a62663c264fd1cba07698f9b7d0eb7@broadinstitute.org"},"sha":"89a581a66f2c6ae1437301ffa6ab7243ebc5ca32","message":"Added ability to specify arguments in files via -args/--arg_file\nPushing back downsample and read filter args so they show up in getApproximateCommandLineArgs()","url":"https://api.github.com/repos/singerma/gatk/commits/89a581a66f2c6ae1437301ffa6ab7243ebc5ca32"},{"author":{"name":"Khalid Shakir","email":"308599bb85a62663c264fd1cba07698f9b7d0eb7@broadinstitute.org"},"sha":"fac9932938f1275015aa0b93a82fb9bd52dd391d","message":"Embedding gsalib source and queueJobReport R scripts in the dist and package jars.\nMoved gsalib and queueJobReport.R to embeddable namespaced locations.\nUpdated packager dependencies/dir to add an @includes which filters the embedded fileset.\nRScriptExecutor can now JIT compiles the gsalib.\nRScriptExecutor uses ProcessController and sends the Rscript output to java's stdout when run under -l DEBUG.\nRefactored ProcessController and IOUtils from Queue to Sting Utils.\nAdded more unit tests to ProcessController along with a utility class to hard stop OutputStreams at a specified byte count.\nReplaced uses of some IOUtils with Apache Commons IO.\nShellJobRunner refactored to use direct ProcessController and now kills jobs on shutdown.\nBetter QGraph responsiveness on shutdown by using Object.wait() instead of Thread.sleep().","url":"https://api.github.com/repos/singerma/gatk/commits/fac9932938f1275015aa0b93a82fb9bd52dd391d"},{"author":{"name":"Matt Hanna","email":"846251899cbc801a4d307becd54393a88ad1536d@broadinstitute.org"},"sha":"9afe6fc7ac6ae0c1e4e3ccca779eb459ce72ba64","message":"Picard upgrade to 1.55.","url":"https://api.github.com/repos/singerma/gatk/commits/9afe6fc7ac6ae0c1e4e3ccca779eb459ce72ba64"},{"author":{"name":"Matt Hanna","email":"846251899cbc801a4d307becd54393a88ad1536d@broadinstitute.org"},"sha":"bf61393a7d53aefd1587aca5ac632036fd23825e","message":"Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable","url":"https://api.github.com/repos/singerma/gatk/commits/bf61393a7d53aefd1587aca5ac632036fd23825e"},{"author":{"name":"Guillermo del Angel","email":"a094a099c5c8e68d37430e8201c1ea0f23e8348f@broadinstitute.org"},"sha":"b559936b7abf9af0274f04f10d0a12a30ece0572","message":"a)New variant eval stratification module for indel size. b) Next iteration on indel caller runtime optimization: when computing likelihood of each haplotype for a given read, many computations will be redundant since pieces of haplotypes will be common to both REF and ALT haplotypes. So, we keep HMM matrices from one haplotype to the next one and recompute starting at the part where either haplotype is different or GOP/GCP are different.","url":"https://api.github.com/repos/singerma/gatk/commits/b559936b7abf9af0274f04f10d0a12a30ece0572"}],"ref":"refs/heads/master","head":"8bfd285cfa9eb1b43e16f4eb8c1af736c0222467","push_id":53686783,"size":150}