{"push_id":857350962,"size":6,"distinct_size":1,"ref":"refs/heads/tf_downsampling_accuracy","head":"6602a5caebbc70babf9df49e03813d1b97204302","before":"d6f40b15dc6109a6246afbe27abc1eed2b3a793d","commits":[{"sha":"6dc4c006b92db69c739a5e26eb8779769f37980f","author":{"email":"319fe1792583fc8870d40099159c8895f7a769c9@gmail.com","name":"Nils Homer"},"message":"only sort the duplicate set records when we someone wans all the\nrecords, rather than just the representative record.","distinct":false,"url":"https://api.github.com/repos/samtools/htsjdk/commits/6dc4c006b92db69c739a5e26eb8779769f37980f"},{"sha":"8f4db17b3b3712c714986860b50c9f0732dfaded","author":{"email":"73ddfdf0c2dacc65d8890847fb6f05cd6fbf0772@tfenne.com","name":"tfenne"},"message":"Modified SAMRecord to have a transient Map of temporary attributes that other classes can use to store expensive derived values, and then used that to make DuplicateSetIterator and friends significantly faster.","distinct":false,"url":"https://api.github.com/repos/samtools/htsjdk/commits/8f4db17b3b3712c714986860b50c9f0732dfaded"},{"sha":"551bc252bf8ddcb4dcf3b86610f016e8103ccbf8","author":{"email":"73ddfdf0c2dacc65d8890847fb6f05cd6fbf0772@tfenne.com","name":"Tim Fennell"},"message":"Merge pull request #370 from samtools/tf_speedup_duplicate_set_iterator\n\nSignificant performance improvements in the DuplicateSetIterator and friends...","distinct":false,"url":"https://api.github.com/repos/samtools/htsjdk/commits/551bc252bf8ddcb4dcf3b86610f016e8103ccbf8"},{"sha":"6c326c08fa37a0beb44666bed77b4e88cb828579","author":{"email":"319fe1792583fc8870d40099159c8895f7a769c9@gmail.com","name":"Nils Homer"},"message":"fixing a compile warning in ProgressLogger","distinct":false,"url":"https://api.github.com/repos/samtools/htsjdk/commits/6c326c08fa37a0beb44666bed77b4e88cb828579"},{"sha":"e64903b5e977a6ee88748ee71581db341758d457","author":{"email":"0986eae1dcbfa3218f50e2513cdc35efa92fa381@users.noreply.github.com","name":"Nils Homer"},"message":"Merge pull request #375 from samtools/nh_fix_progress_logger_warning\n\nfixing a compile warning in ProgressLogger","distinct":false,"url":"https://api.github.com/repos/samtools/htsjdk/commits/e64903b5e977a6ee88748ee71581db341758d457"},{"sha":"6602a5caebbc70babf9df49e03813d1b97204302","author":{"email":"73ddfdf0c2dacc65d8890847fb6f05cd6fbf0772@tfenne.com","name":"tfenne"},"message":"Introduces multiple DownsamplingIteartors that implement different strategies for downsampling a stream of SAMRecords, including one that works in constant memory while correctly handling secondary and supplemental records, one that attempts to minimize the difference between the actual emitted proportion and the requested proportion, and one that is a hybrid of the two - trying for lower but not fixed memory usage while increasing accuracy.\n\nIncluded is a Strategy enum to describe the strategies used, and a factory for creating downsampling iterators.\n\nLastly some tests are included.  The attempt to test the approximate accuracy of the downsamplers, but they are a compromise between runtime and accuracy (accuracy is increased by using more reads, but so is test runtime).","distinct":true,"url":"https://api.github.com/repos/samtools/htsjdk/commits/6602a5caebbc70babf9df49e03813d1b97204302"}]}