{"push_id":2073379087,"size":7,"distinct_size":3,"ref":"refs/heads/cw_annotate_with_cnv_calls","head":"70ed709e9ded26ad1f823fd789f4f93a5b3cde27","before":"aa5dbed980295c531601a758022c8d0e642ff4db","commits":[{"sha":"563c58b1bfb34bfed597f48606d2717f11f07f14","author":{"name":"Daniel Gómez-Sánchez","email":"6c7a63afcbe259bc4186a9d1e6e814ccf930cce5@users.noreply.github.com"},"message":"Fix skipped CigarConversionUtilsUnitTest.testHandleInvalidCigarElement (#3733)","distinct":false,"url":"https://api.github.com/repos/broadinstitute/gatk/commits/563c58b1bfb34bfed597f48606d2717f11f07f14"},{"sha":"ec3b595123a2902616fea7c1f6c091e2b18a145b","author":{"name":"Steve Huang","email":"6152e7429a8832e9ff6ec267720aaf07b5ae5f8c@broadinstitute.org"},"message":"Cpx SV PR series, part-5 (adding capability to discover inter-chr translocations breakpoints and dispersed duplication breakpoint suspects) (#3571)\n\n* add new subtype TransLocBND in BreakEndVariantType, also adds refactored method getOrderedMates()\r\n* expanded ChimericAlignment to include case for cross-chromosome splits\r\n* refactored and generalized overlap-on-read (suggesting ref homology) removal logic in SimpleStrandSwitchVariantDetector to new class ContigAlignmentsModifier\r\n* refactor breakpoint location fine tuning code\r\n* remove INV55BND and INV33BND by some refactoring\r\n* fix a confusing bug in alignment configuration scoring where two configurations should have the same score have scores differ by an Math.ulp","distinct":false,"url":"https://api.github.com/repos/broadinstitute/gatk/commits/ec3b595123a2902616fea7c1f6c091e2b18a145b"},{"sha":"2ddd082889e18b8d08c0090a190e7407d038b07f","author":{"name":"Chris Norman","email":"98da44b795f4b1efeae67001e263a0aa663d1807@broadinstitute.org"},"message":"Upgrade Picard to 2.14.0. (#3737)","distinct":false,"url":"https://api.github.com/repos/broadinstitute/gatk/commits/2ddd082889e18b8d08c0090a190e7407d038b07f"},{"sha":"62e339fb9150db19f80d4b48aed8d47608461690","author":{"name":"Chris Norman","email":"98da44b795f4b1efeae67001e263a0aa663d1807@broadinstitute.org"},"message":"Cache the FeatureCodec class used for a FeatureInput so we only have to discover it once. (#2740)","distinct":false,"url":"https://api.github.com/repos/broadinstitute/gatk/commits/62e339fb9150db19f80d4b48aed8d47608461690"},{"sha":"5b0261d35c07a0afadb9b051b905b86e3a9e5973","author":{"name":"Chris Whelan","email":"d43d63f551c8e8a136f7ad0e57e4e79c2ed544db@broadinstitute.org"},"message":"annotate calls with overlapping CNV calls","distinct":true,"url":"https://api.github.com/repos/broadinstitute/gatk/commits/5b0261d35c07a0afadb9b051b905b86e3a9e5973"},{"sha":"0e0c70dce656d86a9a9144e2b9224e6e5b8a0448","author":{"name":"Chris Whelan","email":"d43d63f551c8e8a136f7ad0e57e4e79c2ed544db@broadinstitute.org"},"message":"refactor integration tests so that input CNV files don't get validated with the same rules","distinct":true,"url":"https://api.github.com/repos/broadinstitute/gatk/commits/0e0c70dce656d86a9a9144e2b9224e6e5b8a0448"},{"sha":"70ed709e9ded26ad1f823fd789f4f93a5b3cde27","author":{"name":"Chris Whelan","email":"d43d63f551c8e8a136f7ad0e57e4e79c2ed544db@broadinstitute.org"},"message":"track sample ID through variant discovery","distinct":true,"url":"https://api.github.com/repos/broadinstitute/gatk/commits/70ed709e9ded26ad1f823fd789f4f93a5b3cde27"}]}
{"actor":{"display_login":"cwhelan"}}