{"push_id":1000373077,"size":38,"distinct_size":1,"ref":"refs/heads/rhl_anyploid_likelihoods","head":"7ba2fc77689ae15fd83c92caf8b7e2cff301c32a","before":"2d2c4170f2346812668941ee12bfd1d9111d5f11","commits":[{"sha":"303c4a9de10eb356008cfd70bccb2c61df0a72e7","author":{"email":"935d41382d37a8df67056991c83f2f0aa31452c4@broadinstitute.org","name":"Louis Bergelson"},"message":"Genotype now treats empty filter strings as null\n\nThere was a potentially invalid case where a genotype could be constructed with an empty filter string\nthis was treated as being filtered, but without any filter specified, this is now impossible","distinct":false,"url":"https://api.github.com/repos/samtools/htsjdk/commits/303c4a9de10eb356008cfd70bccb2c61df0a72e7"},{"sha":"8a054ee4196d6d63a9b066ed840233e7ef1fe534","author":{"email":"935d41382d37a8df67056991c83f2f0aa31452c4@broadinstitute.org","name":"Louis Bergelson"},"message":"fixing tests that were being skipped\n\ntwo tests were being skipped because they had problems with their dataproviders\n\nIupacTest.basic() had a typo in the dataprovider name\nComparableTupleTest.testComparableTuple had a exception in the dataprovider\n  also renamed this to testComparableTupleNullData since it was misnamed\n  fixed a warning in the test class as well","distinct":false,"url":"https://api.github.com/repos/samtools/htsjdk/commits/8a054ee4196d6d63a9b066ed840233e7ef1fe534"},{"sha":"f9651c364278dd8d704d68271986a5df91d9e412","author":{"email":"935d41382d37a8df67056991c83f2f0aa31452c4@broadinstitute.org","name":"Louis Bergelson"},"message":"Merge pull request #468 from samtools/lb_fix_skipped_tests\n\nfixing tests that were being skipped","distinct":false,"url":"https://api.github.com/repos/samtools/htsjdk/commits/f9651c364278dd8d704d68271986a5df91d9e412"},{"sha":"d616ba29e401d4ebd6d558c9824dd0111aabbef0","author":{"email":"935d41382d37a8df67056991c83f2f0aa31452c4@broadinstitute.org","name":"Louis Bergelson"},"message":"moving SRA tests to their own test group\n\nremoving SRA tests from `ant test` and moving them to their own `ant sra-test` target\n  this should isolate SRA tests so that they can no longer fail during a picard release\n  once SRA tests have been shown to be more stable they can be moved back into the main test command\n\nadded a new ant target sra-test which exclusively runs the sra tests\nmade all SRA test classes descend from a new AbstractSRATest base class\n  this ensures they are all set in the appropriate test group\n  each SRA test method will run assertSRAIsSupported() and be skipped if it is not\n    removed the newly redundant checks in every SRA test\nupdated .travis.yml to run sra-test after the rest of the tests","distinct":false,"url":"https://api.github.com/repos/samtools/htsjdk/commits/d616ba29e401d4ebd6d558c9824dd0111aabbef0"},{"sha":"7203ecc6c54e97ea0c47078f94b70c3b5b31e497","author":{"email":"935d41382d37a8df67056991c83f2f0aa31452c4@broadinstitute.org","name":"Louis Bergelson"},"message":"Merge pull request #465 from samtools/lb_move_sra_tests_to_their_own_group\n\nmoving SRA tests to their own test group","distinct":false,"url":"https://api.github.com/repos/samtools/htsjdk/commits/7203ecc6c54e97ea0c47078f94b70c3b5b31e497"},{"sha":"a71f1373521b3d9153d4184a0cf99729b757feb0","author":{"email":"89257fe3fac3dd680aa98b4673848ace2d5cfa28@aurea.com","name":"Mohammed Ezzat"},"message":"squid:S1155 - Collection.isEmpty() should be used to test for emptiness","distinct":false,"url":"https://api.github.com/repos/samtools/htsjdk/commits/a71f1373521b3d9153d4184a0cf99729b757feb0"},{"sha":"f71d45c968ef5669e3bf4bcabdb91ac6c1ee5758","author":{"email":"ecd0cbdfcd6b30ea054daacf5620399c0b45c15b@gmail.com","name":"Adam Kiezun"},"message":"adding test code coverage collection and report","distinct":false,"url":"https://api.github.com/repos/samtools/htsjdk/commits/f71d45c968ef5669e3bf4bcabdb91ac6c1ee5758"},{"sha":"c340afec92d8e54fe014695a7499a08e1948a26d","author":{"email":"50a7ddf92921a0a4e876dc46c3597547d32d48f7@broadinstitute.org","name":"Yossi Farjoun"},"message":"Merge pull request #474 from DevFactory/release/Collection.isEmpty()-should-be-used-to-test-for-emptiness-fix-1\n\nsquid:S1155 - Collection.isEmpty() should be used to test for emptiness","distinct":false,"url":"https://api.github.com/repos/samtools/htsjdk/commits/c340afec92d8e54fe014695a7499a08e1948a26d"},{"sha":"1be7df89fea59bc675ab83227e03aaf824933435","author":{"email":"89257fe3fac3dd680aa98b4673848ace2d5cfa28@aurea.com","name":"Mohammed Ezzat"},"message":"pmd:ConsecutiveAppendsShouldReuse - Consecutive Appends Should Reuse","distinct":false,"url":"https://api.github.com/repos/samtools/htsjdk/commits/1be7df89fea59bc675ab83227e03aaf824933435"},{"sha":"58bb6d6e08b2551bfa2f199b015cb664da125dac","author":{"email":"50a7ddf92921a0a4e876dc46c3597547d32d48f7@broadinstitute.org","name":"Yossi Farjoun"},"message":"Merge pull request #476 from DevFactory/release/Consecutive-Appends-Should-Reuse-fix-1\n\npmd:ConsecutiveAppendsShouldReuse - Consecutive Appends Should Reuse","distinct":false,"url":"https://api.github.com/repos/samtools/htsjdk/commits/58bb6d6e08b2551bfa2f199b015cb664da125dac"},{"sha":"80fefcf7395a88fb01a259db21e5f6735d18d18e","author":{"email":"629c3e3d004b31c1ae42a6dc8c6729d15c6b15a2@broadinstitute.org","name":"Chris Norman"},"message":"Fix perf bug in IndexedFastaSequenceFile.","distinct":false,"url":"https://api.github.com/repos/samtools/htsjdk/commits/80fefcf7395a88fb01a259db21e5f6735d18d18e"},{"sha":"b244b62416fc5b897438ca1c44c8874804befcf6","author":{"email":"ecd0cbdfcd6b30ea054daacf5620399c0b45c15b@gmail.com","name":"Adam Kiezun"},"message":"add sra tests","distinct":false,"url":"https://api.github.com/repos/samtools/htsjdk/commits/b244b62416fc5b897438ca1c44c8874804befcf6"},{"sha":"547b21bc1ed04cbefdc40b282ba1c8415f7ec883","author":{"email":"935d41382d37a8df67056991c83f2f0aa31452c4@broadinstitute.org","name":"Louis Bergelson"},"message":"Merge pull request #412 from samtools/lb_improve_genotype_isFiltered\n\nGenotype now treats empty filter strings identically to null filter strings","distinct":false,"url":"https://api.github.com/repos/samtools/htsjdk/commits/547b21bc1ed04cbefdc40b282ba1c8415f7ec883"},{"sha":"389b8848215c12c8799ccc29b9f3338db5d87c95","author":{"email":"ecd0cbdfcd6b30ea054daacf5620399c0b45c15b@gmail.com","name":"Adam Kiezun"},"message":"Merge pull request #473 from samtools/ak_jacoco\n\nadding test code coverage collection and report using jacoco","distinct":false,"url":"https://api.github.com/repos/samtools/htsjdk/commits/389b8848215c12c8799ccc29b9f3338db5d87c95"},{"sha":"765b06107d388c932a70b1d1aba12e55c114fc91","author":{"email":"ecd0cbdfcd6b30ea054daacf5620399c0b45c15b@gmail.com","name":"Adam Kiezun"},"message":"Revert \"adding test code coverage collection and report using jacoco\"","distinct":false,"url":"https://api.github.com/repos/samtools/htsjdk/commits/765b06107d388c932a70b1d1aba12e55c114fc91"},{"sha":"20a7fddfcd7cc49d948352dceebb4ffe777278b8","author":{"email":"1d0c6f32bb65b8defcf996a778a48a2d5cfb7c64@broadinstitute.org","name":"droazen"},"message":"Merge pull request #484 from samtools/revert-473-ak_jacoco\n\nRevert \"adding test code coverage collection and report using jacoco\"","distinct":false,"url":"https://api.github.com/repos/samtools/htsjdk/commits/20a7fddfcd7cc49d948352dceebb4ffe777278b8"},{"sha":"68db182cb18f6c394f2120ebc9d77893ab6f9d14","author":{"email":"0b5823e9d45ad2c366d9b4e1e6a924fc70cafb8f@broadinstitute.org","name":"meganshand"},"message":"Adding ValidateSamFile test for duplicate reads\n\nAdding passing ValidateSamFile test with out of order reads","distinct":false,"url":"https://api.github.com/repos/samtools/htsjdk/commits/68db182cb18f6c394f2120ebc9d77893ab6f9d14"},{"sha":"d83e74bbbcd73975a979086764075a72da310d23","author":{"email":"89257fe3fac3dd680aa98b4673848ace2d5cfa28@aurea.com","name":"Mohammed Ezzat"},"message":"pmd:UseIndexOfChar - Use Index Of Char","distinct":false,"url":"https://api.github.com/repos/samtools/htsjdk/commits/d83e74bbbcd73975a979086764075a72da310d23"},{"sha":"17f8fd83336e7a8ea7fa0b1f94965c30269510c8","author":{"email":"50a7ddf92921a0a4e876dc46c3597547d32d48f7@broadinstitute.org","name":"Yossi Farjoun"},"message":"Merge pull request #490 from DevFactory/release/Use-Index-Of-Char-fix-1\n\npmd:UseIndexOfChar - Use Index Of Char","distinct":false,"url":"https://api.github.com/repos/samtools/htsjdk/commits/17f8fd83336e7a8ea7fa0b1f94965c30269510c8"},{"sha":"e64fa186ccc8d713c131f37271e5086aa17ca200","author":{"email":"50a7ddf92921a0a4e876dc46c3597547d32d48f7@broadinstitute.org","name":"Yossi Farjoun"},"message":"Merge pull request #488 from meganshand/master\n\nValidateSamFile doesn't catch duplicated unmapped reads depending on their order","distinct":false,"url":"https://api.github.com/repos/samtools/htsjdk/commits/e64fa186ccc8d713c131f37271e5086aa17ca200"}]}