{"push_id":891250566,"size":2,"distinct_size":1,"ref":"refs/heads/master","head":"a6391f033ec109637d510723043ed7a1bc0e5dbf","before":"9fee722ce7e26f54f67cc88c620c431b604e29ce","commits":[{"sha":"60ef532bb23318040f8eddbf1e03ec5df1070bc1","author":{"email":"1d0c6f32bb65b8defcf996a778a48a2d5cfb7c64@broadinstitute.org","name":"David Roazen"},"message":"Make ReadsSparkSink write reads in an order 100% consistent with htsjdk's SAMRecordCoordinateComparator\n\nWe were not totally consistent with htsjdk BAM ordering in our Spark bam output\npreviously (particularly with unmapped reads that have the position of their mates).\nWith this change, we are.\n\n-Modified ReadsSparkSink to operate directly on raw, headerless SAMRecords, and use a new\n comparator for headerless SAMRecords that calls directly into htsjdk's SAMRecordCoordinateComparator\n\n-To make this performant, added a new serializer for raw SAMRecords that uses the same\n approach as the existing SAMRecordToGATKReadAdapterSerializer in using a modified BAM\n codec as the encoder.\n\n-Added test cases that failed in the previous implementation due to ordering issues, and\n pass now.\n\nResolves #1249","distinct":false,"url":"https://api.github.com/repos/broadinstitute/gatk/commits/60ef532bb23318040f8eddbf1e03ec5df1070bc1"},{"sha":"a6391f033ec109637d510723043ed7a1bc0e5dbf","author":{"email":"1d0c6f32bb65b8defcf996a778a48a2d5cfb7c64@broadinstitute.org","name":"droazen"},"message":"Merge pull request #1251 from broadinstitute/dr_fix_readssparksink_ordering\n\nMake ReadsSparkSink write reads in an order 100% consistent with htsjdk's SAMRecordCoordinateComparator","distinct":true,"url":"https://api.github.com/repos/broadinstitute/gatk/commits/a6391f033ec109637d510723043ed7a1bc0e5dbf"}]}