{"push_id":876645370,"size":1,"distinct_size":1,"ref":"refs/heads/sra-support-release","head":"9d0614e81d926c3e0a5c57febad761f12230671a","before":"9aec792d5594e9012b360a2c99093a5e29d46b74","commits":[{"sha":"9d0614e81d926c3e0a5c57febad761f12230671a","author":{"email":"3c49018cd47c46d816b353008a8ef00ae8d35024@nih.gov","name":"Andrii Nikitiuk"},"message":"Added a support of reading from SRA directly\n\nPartially implemented reading from SRA archives\nSRA reader: implemented getting of unaligned reads, fixed tests, created SRA tests, general improvements\nImplemented basic lazy loading. Need to implement couple of other methods\nOverrode couple of more lazy method for SAMRecord.\nPartially implemented reading from SRA archives\nSRA reader: implemented getting of unaligned reads, fixed tests, created SRA tests, general improvements\nImplemented basic lazy loading. Need to implement couple of other methods\nOverrode couple of more lazy method for SAMRecord.\nCode cleanup. Refactored code for lazy retrieval of flags and attributes\nAdded lazy record detach tests, validation of records in tests. Moved SRA classes into separate package.\nFixed ordering issue with circular references. Now HTSJDK reports it to SRA engine about who runs it\nImplemented iterators which read by chunks. Covered that with tests. Refactoring\nFixed several flags implementation. Mate references to be alligned at 5000 bases so they are optimized for chunks.\nImplemented BAM index emulation from SRA. Made class BAMFileSpan public\nUpdated SRATest to only use public APIs\nCovered SRA index emulation with test. Fixed small issue\nAdded references caching\nAdded NCBI copyright notices to SRA files\nOptimized synchronized block that caches an ngs.Reference object\nNow all read groups in SRA files use the same sample - accession name\nFixed test after changing sample name to SRA run name\nImplemented reference sequence reading from SRA and covered with tests\nImplemented query* methods in SRAFileReader. Added more SRA SAMRecord tests","distinct":true,"url":"https://api.github.com/repos/a-nikitiuk/htsjdk/commits/9d0614e81d926c3e0a5c57febad761f12230671a"}]}