{"push_id":908822654,"size":75,"distinct_size":1,"ref":"refs/heads/vrr_rename_exome_read_counts","head":"feb60b7281a4815e7efd27861c0b4e9d0ff50642","before":"04340600c36422e0518c6a0bedb59c0a7535663d","commits":[{"sha":"1cdfbda34da873bccb997fe4051f40c0a83e4ae1","author":{"email":"eb2ff7e9da6be553269aef996dd6d1d520e0c477@google.com","name":"David Adams"},"message":"Making tools to compare MarkDuplicates and BQSR relative to legacy versions of tools.","distinct":false,"url":"https://api.github.com/repos/broadinstitute/gatk/commits/1cdfbda34da873bccb997fe4051f40c0a83e4ae1"},{"sha":"b7be0f5e603306e230b048e10b5c10f50eafcb06","author":{"email":"eb2ff7e9da6be553269aef996dd6d1d520e0c477@google.com","name":"davidadamsphd"},"message":"Merge pull request #1240 from broadinstitute/da_compare_tools\n\nCreating tools and simple command-line for validation","distinct":false,"url":"https://api.github.com/repos/broadinstitute/gatk/commits/b7be0f5e603306e230b048e10b5c10f50eafcb06"},{"sha":"0c29dfdd6bdcd8d64a484260a0f877c3a8e4342d","author":{"email":"935d41382d37a8df67056991c83f2f0aa31452c4@broadinstitute.org","name":"Louis Bergelson"},"message":"adding scripts/gatk-submit.sh\n\nthis is a script which can be used after running gradle installDist to run spark jobs\nit can be used identically to ths build/install/bin/gatk script, but has extra features for dealing with spark\n\nrunning a spark tool and supplying the option --sparkRunner with DIRECT, SUBMIT, or GCS has special behavior\nDIRECT will run the tool in the in memory spark runner\nSUBMIT along with an appropriate --sparkMaster will run on an accessible spark cluster using spark-submit\narguments to spark-submit may be specified before the arguments to GATK by separating them with a --\nGCS will submit jobs to google dataproc using gcloud\ncommon arguments for spark submit will be adapted to match the gcloud formating\nthis will fail if gcloud isn't installed\n\nif GATK_GCS_STAGING is specified, the jar will be uploaded and cached in the specified bucket for rapid re-use\n\ninput files will not be autouploaded to the cloud\n\n--dry-run may be specified before the --, this will only print the commands that will be run instead of actually running them\n\nAdding DataProcArgumentReplace simple tool to convert spark-submit args into gcloud args.\nThis conversion is not guaranteed to translate all spark command line options to matching gcloud ones.\nIf you find options that are not translated or are miss-translated please file an issue.\n\nadded settings.gradle so the project name doesn't depend on the folder it's placed in","distinct":false,"url":"https://api.github.com/repos/broadinstitute/gatk/commits/0c29dfdd6bdcd8d64a484260a0f877c3a8e4342d"},{"sha":"af880c3c1eecadb8378a42cf00056f1a21a74cd0","author":{"email":"629c3e3d004b31c1ae42a6dc8c6729d15c6b15a2@broadinstitute.org","name":"Chris Norman"},"message":"Revert htsjdk clearOptions workaround in createVCFWriter.","distinct":false,"url":"https://api.github.com/repos/broadinstitute/gatk/commits/af880c3c1eecadb8378a42cf00056f1a21a74cd0"},{"sha":"477e9d89651df8f7cfe1b70cbba8a3f846559b2e","author":{"email":"ecd0cbdfcd6b30ea054daacf5620399c0b45c15b@gmail.com","name":"Adam Kiezun"},"message":"Merge pull request #1211 from broadinstitute/lb_gatk_submit_script\n\nadding gatk-launch script to make it easier to run spark","distinct":false,"url":"https://api.github.com/repos/broadinstitute/gatk/commits/477e9d89651df8f7cfe1b70cbba8a3f846559b2e"},{"sha":"bfc526c9cca8d303e55f4fbba40026c84a38070f","author":{"email":"ecd0cbdfcd6b30ea054daacf5620399c0b45c15b@gmail.com","name":"Adam Kiezun"},"message":"cram tests on spark","distinct":false,"url":"https://api.github.com/repos/broadinstitute/gatk/commits/bfc526c9cca8d303e55f4fbba40026c84a38070f"},{"sha":"1986253b4d82bada7b24a21f9c7e82f99ea54ff2","author":{"email":"1d0c6f32bb65b8defcf996a778a48a2d5cfb7c64@broadinstitute.org","name":"droazen"},"message":"Merge pull request #1274 from broadinstitute/cn_vcfwriter_fix\n\nRevert htsjdk clearOptions workaround in createVCFWriter.","distinct":false,"url":"https://api.github.com/repos/broadinstitute/gatk/commits/1986253b4d82bada7b24a21f9c7e82f99ea54ff2"},{"sha":"9e7b0abb0344c732f6f142d5c3c8a606a8dd1c26","author":{"email":"ecd0cbdfcd6b30ea054daacf5620399c0b45c15b@gmail.com","name":"Adam Kiezun"},"message":"Merge pull request #1268 from broadinstitute/ak_spark_cram\n\nAk spark cram","distinct":false,"url":"https://api.github.com/repos/broadinstitute/gatk/commits/9e7b0abb0344c732f6f142d5c3c8a606a8dd1c26"},{"sha":"de0a9259e6e173f3eb361f13b9682389582217f2","author":{"email":"ecd0cbdfcd6b30ea054daacf5620399c0b45c15b@gmail.com","name":"Adam Kiezun"},"message":"fix for sequence dict validation on cram","distinct":false,"url":"https://api.github.com/repos/broadinstitute/gatk/commits/de0a9259e6e173f3eb361f13b9682389582217f2"},{"sha":"d463f5369f6558fb905f0924def93a8dbcbd576c","author":{"email":"935d41382d37a8df67056991c83f2f0aa31452c4@broadinstitute.org","name":"Louis Bergelson"},"message":"try setting parallelism to 1","distinct":false,"url":"https://api.github.com/repos/broadinstitute/gatk/commits/d463f5369f6558fb905f0924def93a8dbcbd576c"},{"sha":"eae24d0269a1457a7a3f9089d253c04030e5696c","author":{"email":"935d41382d37a8df67056991c83f2f0aa31452c4@broadinstitute.org","name":"Louis Bergelson"},"message":"Revert \"try setting parallelism to 1\"\n\nThis reverts commit d463f5369f6558fb905f0924def93a8dbcbd576c.","distinct":false,"url":"https://api.github.com/repos/broadinstitute/gatk/commits/eae24d0269a1457a7a3f9089d253c04030e5696c"},{"sha":"e8dddd9eceb4dba7335176ff5d150de395402460","author":{"email":"935d41382d37a8df67056991c83f2f0aa31452c4@broadinstitute.org","name":"Louis Bergelson"},"message":"Merge pull request #1275 from broadinstitute/ak_cram_dict_validation\n\nfix for sequence dict validation on cram","distinct":false,"url":"https://api.github.com/repos/broadinstitute/gatk/commits/e8dddd9eceb4dba7335176ff5d150de395402460"},{"sha":"c2b022f8535f1e3f49eeb69e8e0801cbd27dbdbe","author":{"email":"1d0c6f32bb65b8defcf996a778a48a2d5cfb7c64@broadinstitute.org","name":"David Roazen"},"message":"Make HeaderlessSAMRecordCoordinateComparator safer\n\nInstead of calling setHeader() to temporarily give headerless reads\na header and then calling into htsjdk's SAMRecordCoordinateComparator,\nadapt the htsjdk code directly to work with headerless reads. This should\nbe safer (especially in a multithreaded context), as mutating the objects\nbeing compared within a comparator is a violation of contract.","distinct":false,"url":"https://api.github.com/repos/broadinstitute/gatk/commits/c2b022f8535f1e3f49eeb69e8e0801cbd27dbdbe"},{"sha":"0cbbea5aa103ef89fc9f6c4de3842db504809eb6","author":{"email":"1d0c6f32bb65b8defcf996a778a48a2d5cfb7c64@broadinstitute.org","name":"droazen"},"message":"Merge pull request #1276 from broadinstitute/dr_make_headersamcomparator_safer\n\nMake HeaderlessSAMRecordCoordinateComparator safer","distinct":false,"url":"https://api.github.com/repos/broadinstitute/gatk/commits/0cbbea5aa103ef89fc9f6c4de3842db504809eb6"},{"sha":"2ccd892dee3a2187666630f274533904a01f19c3","author":{"email":"1d0c6f32bb65b8defcf996a778a48a2d5cfb7c64@broadinstitute.org","name":"David Roazen"},"message":"Explicitly sort the list of bam fragments before merging in ReadsSparkSink\n\nWe were victims of a known bug in Hadoop (https://issues.apache.org/jira/browse/HADOOP-10798)\nthat caused us to sometimes assemble our bam fragments in ReadsSparkSink out-of-order.\nAdding an explicit sort fixes this.\n\nResolves #1258","distinct":false,"url":"https://api.github.com/repos/broadinstitute/gatk/commits/2ccd892dee3a2187666630f274533904a01f19c3"},{"sha":"9702411391cae2e57255b84a8d174216a353d399","author":{"email":"1d0c6f32bb65b8defcf996a778a48a2d5cfb7c64@broadinstitute.org","name":"droazen"},"message":"Merge pull request #1279 from broadinstitute/dr_fix_readsparksink_ordering_bug\n\nExplicitly sort the list of bam fragments before merging in ReadsSparkSink","distinct":false,"url":"https://api.github.com/repos/broadinstitute/gatk/commits/9702411391cae2e57255b84a8d174216a353d399"},{"sha":"8ff06d12a962715cd2e79bd1a0de1b831b7cee5e","author":{"email":"1d0c6f32bb65b8defcf996a778a48a2d5cfb7c64@broadinstitute.org","name":"David Roazen"},"message":"Fix NPE in FlagStatSpark when -O is not specified\n\nResolves #1202","distinct":false,"url":"https://api.github.com/repos/broadinstitute/gatk/commits/8ff06d12a962715cd2e79bd1a0de1b831b7cee5e"},{"sha":"29dfbf581b8247aeb91579d08a2cd9aad777279a","author":{"email":"1d0c6f32bb65b8defcf996a778a48a2d5cfb7c64@broadinstitute.org","name":"droazen"},"message":"Merge pull request #1298 from broadinstitute/dr_fix_npe_in_flagstatspark\n\nFix NPE in FlagStatSpark when -O is not specified","distinct":false,"url":"https://api.github.com/repos/broadinstitute/gatk/commits/29dfbf581b8247aeb91579d08a2cd9aad777279a"},{"sha":"90ffe3215959341c4babc30ca38bebdb9da39abe","author":{"email":"ecd0cbdfcd6b30ea054daacf5620399c0b45c15b@gmail.com","name":"Adam Kiezun"},"message":"consistent exception for compare SAMs","distinct":false,"url":"https://api.github.com/repos/broadinstitute/gatk/commits/90ffe3215959341c4babc30ca38bebdb9da39abe"},{"sha":"7dc887cf410fb7274f05b4023b4b0513a24fafbe","author":{"email":"ecd0cbdfcd6b30ea054daacf5620399c0b45c15b@gmail.com","name":"Adam Kiezun"},"message":"resolve parameter collision","distinct":false,"url":"https://api.github.com/repos/broadinstitute/gatk/commits/7dc887cf410fb7274f05b4023b4b0513a24fafbe"}]}