{"push_id":1137363149,"size":5,"distinct_size":1,"ref":"refs/heads/issue-225-cnloh_caller","head":"ba6fa2ac427faa3b4821ab1c969cb4864cecbae3","before":"d5c3716285ece7022332f145abddca1555cc7dc6","commits":[{"sha":"bab58e5a8051b0866259c5db814b8e3190df6231","author":{"name":"Valentin Ruano Rubio","email":"c13705d36a65634fb2e85000d9c75d60ac422265@broadinstitute.org"},"message":"Adds an evaluation tool for CNV germline calls.\n\nCloses issue #406","distinct":false,"url":"https://api.github.com/repos/broadinstitute/gatk-protected/commits/bab58e5a8051b0866259c5db814b8e3190df6231"},{"sha":"1b391876a6fe841de1b61487c8bd1a3d3e3c0591","author":{"name":"Valentin Ruano Rubio","email":"c13705d36a65634fb2e85000d9c75d60ac422265@broadinstitute.org"},"message":"Merge pull request #502 from broadinstitute/vrr_germline_evaluation\n\nGermline CNV evaluation tool.","distinct":false,"url":"https://api.github.com/repos/broadinstitute/gatk-protected/commits/1b391876a6fe841de1b61487c8bd1a3d3e3c0591"},{"sha":"0c4cd13ee5dfb6c169d1c6094588e8c7a9629abe","author":{"name":"Mehrtash Babadi","email":"247c8a7fc846fd29a5cef89603fba2755b39c96c@broadinstitute.org"},"message":"Updates to the CNV notes.","distinct":false,"url":"https://api.github.com/repos/broadinstitute/gatk-protected/commits/0c4cd13ee5dfb6c169d1c6094588e8c7a9629abe"},{"sha":"0848fbc90e02839a07043f06c867025e56a55277","author":{"name":"Mehrtash Babadi","email":"247c8a7fc846fd29a5cef89603fba2755b39c96c@broadinstitute.org"},"message":"Revert \"Updates to the CNV notes.\"\n\nThis reverts commit 0c4cd13ee5dfb6c169d1c6094588e8c7a9629abe.","distinct":false,"url":"https://api.github.com/repos/broadinstitute/gatk-protected/commits/0848fbc90e02839a07043f06c867025e56a55277"},{"sha":"ba6fa2ac427faa3b4821ab1c969cb4864cecbae3","author":{"name":"lichtens","email":"a1d34b14fe2f41c01e789aaba82f390136609945@broadinstitute.org"},"message":"Beginning the implementation of the CNLOH/Balanced caller.\n\nIncomplete first cut.  Basic outline, but many holes left and needs automated tests\n\nStill not complete.  Adding more utilities and the last objective function.\n\nImplementing objective function.  Still unfinished.\n\nAll necessary classes are serializable.  Need to find NaN generation and correct it, since it causes digamma to fail.\n\nSuccessful first run of iterations.  Need to make calls and address many TODOs\n\nAdded CLI for CNLoH caller.  About to rebase from master to get refactorings.\n\nMinor changes\n\nFixes so that the automated test failure may just be an issue in the test.\n\nFixes so that the automated tests of CNLOH caller pass.\n\nAddressing docs.\n\nFixing the cases where credible mode is outside the interval.\n\nFixing the case where credible mode is lying on one of the boundaries..\n\nFixing serialization issues.  Made the CNLoHCall singular.  Updated docs.  Corrected an issue with reading ACNV seg files.\n\nBias and variance correction added.\n\nAdding documentation and unit tests.\n\nTitan conversion added.\n\nTitan conversion automated tests added.\n\nEliminated 2 warnings\n\nCorrected file output\n\nAdded more columns to the calls, to better debug/evaluate the results.\n\nFixed max2dIndices\n\nA bunch of bug fixes to get it inline with the prototype.  Now, the results look a little better (qualitative; small sample size) in this version.\n\nLast minute changes to unit test to cover double gaussian\n\nLast minute update to docs","distinct":true,"url":"https://api.github.com/repos/broadinstitute/gatk-protected/commits/ba6fa2ac427faa3b4821ab1c969cb4864cecbae3"}]}
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