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These changes depend on pull request #233 - the changes to htsjdk for the same purpose.","distinct":false,"url":"https://api.github.com/repos/broadinstitute/picard/commits/e15ebce93076fa4314ce39c005c0e91bf4cdd175"},{"sha":"a4369ef0b70dec53ed13483024b4c602f1f7e971","author":{"email":"1348f174e6aba549c3457e87ad1ee4ecf75c6292@broadinstitute.org","name":"Nils Homer"},"message":"Adding a tool SimpleMarkDuplicatesWithMateCigar that uses the new HTSJDK\nDuplicateSetIterator.","distinct":false,"url":"https://api.github.com/repos/broadinstitute/picard/commits/a4369ef0b70dec53ed13483024b4c602f1f7e971"},{"sha":"629915c882e6597b377143670c47da1cbb209c8c","author":{"email":"cfc2b2d6091a79861a70745f59aae46c3bd57858@broadinstitute.org","name":"kbergin"},"message":"Fixing previous mistake with scheme logic\n\nForgot to update one test","distinct":false,"url":"https://api.github.com/repos/broadinstitute/picard/commits/629915c882e6597b377143670c47da1cbb209c8c"},{"sha":"f59f82ac8f5eb420758069998894ddf1745d79d2","author":{"email":"cfc2b2d6091a79861a70745f59aae46c3bd57858@broadinstitute.org","name":"Kylee Bergin"},"message":"Merge pull request #238 from broadinstitute/kb_genotypeConcordanceOption\n\nFixing previous mistake with scheme logic","distinct":false,"url":"https://api.github.com/repos/broadinstitute/picard/commits/f59f82ac8f5eb420758069998894ddf1745d79d2"},{"sha":"a0ba111d9e9bc89e8138dd1da3d57f7510bf9577","author":{"email":"7dc00c7c1f03d437a30680983a68995c40d3ec02@broadinstitute.org","name":"Alex Baumann"},"message":"Added ability to pass argument to ViewSam for an interval file\nthat the output will be restricted to.  This does not support\nboth the in-line intervals as well as interval file that the\nGATK -L command supports.  Unit test added to verify records\nfrom a given SAM are matched with overlapping intervals file,\nand no others are output.  Updated existing TODOs to make use\nof PicardCommandLine rather than direct calls into ViewSam class\nwithin unit tests.\n\nResolves: #173","distinct":false,"url":"https://api.github.com/repos/broadinstitute/picard/commits/a0ba111d9e9bc89e8138dd1da3d57f7510bf9577"},{"sha":"b27f1bbc6dd6dbb513f027111414c0cf04fbb428","author":{"email":"7dc00c7c1f03d437a30680983a68995c40d3ec02@broadinstitute.org","name":"Alex Baumann"},"message":"Modify BedToIntervalList to accept other dictionary files\n\nAdded ability to use any of the file formats specified within\nSAMSequenceDictionaryExtractor as dictionary files for\nBedToIntervalList.  Updated test at BedToIntervalListTest to test\neach file format that is appropriate.  Each test has associated\ndictionary that matches the requirement for producting the expected\nseq_dict_test.bed.interval_list output from the input file\nseq_dict_test.bed.  We also test for bad dictionary input to make\nsure that fails properly - both the case of a non-dictionary passed\nand a dictionary that is not sufficient passed.\n\nResolves: #143","distinct":false,"url":"https://api.github.com/repos/broadinstitute/picard/commits/b27f1bbc6dd6dbb513f027111414c0cf04fbb428"},{"sha":"f30d2b839f23ee61cea598a05f686015d3610712","author":{"email":"319fe1792583fc8870d40099159c8895f7a769c9@gmail.com","name":"Nils Homer"},"message":"Merge pull request #192 from broadinstitute/ab_bed_to_interval_seq_dict_extractor\n\nModify BedToIntervalList to accept other dictionary files","distinct":false,"url":"https://api.github.com/repos/broadinstitute/picard/commits/f30d2b839f23ee61cea598a05f686015d3610712"},{"sha":"6049fcf4fe5d86653d9b77c26e289a8d4be02640","author":{"email":"319fe1792583fc8870d40099159c8895f7a769c9@gmail.com","name":"Nils Homer"},"message":"Merge pull request #191 from broadinstitute/ab_restrict_viewsam_to_intervals\n\nAdd intervals handling to ViewSam and associated unit test","distinct":false,"url":"https://api.github.com/repos/broadinstitute/picard/commits/6049fcf4fe5d86653d9b77c26e289a8d4be02640"},{"sha":"da5e94e845935344113333a297a8f8ee310609d9","author":{"email":"319fe1792583fc8870d40099159c8895f7a769c9@gmail.com","name":"Nils Homer"},"message":"Merge pull request #200 from broadinstitute/nh_dup_set\n\nAdding a tool SimpleMarkDuplicatesWithMateCigar that uses the new HTSJDK","distinct":false,"url":"https://api.github.com/repos/broadinstitute/picard/commits/da5e94e845935344113333a297a8f8ee310609d9"},{"sha":"454236194a6f830910ec3e520c21aa12f365234d","author":{"email":"1348f174e6aba549c3457e87ad1ee4ecf75c6292@broadinstitute.org","name":"Nils Homer"},"message":"fixing bed to interval test by not catching an Exception","distinct":false,"url":"https://api.github.com/repos/broadinstitute/picard/commits/454236194a6f830910ec3e520c21aa12f365234d"},{"sha":"781f25362400210299d7f2d7efe4ded3a92adfa4","author":{"email":"319fe1792583fc8870d40099159c8895f7a769c9@gmail.com","name":"Nils Homer"},"message":"Merge pull request #240 from broadinstitute/nh_nenewell_master\n\nChanges to accommodate v1.5 of the SAM file specification","distinct":false,"url":"https://api.github.com/repos/broadinstitute/picard/commits/781f25362400210299d7f2d7efe4ded3a92adfa4"},{"sha":"0c17939e96ad72f7cf3fccc17afd8d05f32612be","author":{"email":"319fe1792583fc8870d40099159c8895f7a769c9@gmail.com","name":"Nils Homer"},"message":"fixing up more BED tests for moving SAM version to 1.5","distinct":false,"url":"https://api.github.com/repos/broadinstitute/picard/commits/0c17939e96ad72f7cf3fccc17afd8d05f32612be"},{"sha":"e1d38e95fc65043bce1aedb770392e8371cba598","author":{"email":"319fe1792583fc8870d40099159c8895f7a769c9@gmail.com","name":"Nils Homer"},"message":"Merge pull request #241 from broadinstitute/nh_fixup_bed_tests\n\nfixing up more BED tests for moving SAM version to 1.5","distinct":false,"url":"https://api.github.com/repos/broadinstitute/picard/commits/e1d38e95fc65043bce1aedb770392e8371cba598"},{"sha":"439091b67c5149bd06486f7b6a141d13e79bcf94","author":{"email":"a52f96ca7ed413cdb0b3f7b732a692cfb901aebf@gmail.com","name":"Ryan"},"message":"Update RExecutor.java\n\nProvide file location as part of error.  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