{"push_id":841173357,"size":19,"distinct_size":19,"ref":"refs/heads/sra-support-release","head":"3e40db0c67b2782122051e9309e4bec54d501e03","before":"f877eaa1524ad7588a08fe7d3aba7cb93efb5d81","commits":[{"sha":"4c6be49ca5e922288e2975043a8b3ae3ca58001f","author":{"email":"73ddfdf0c2dacc65d8890847fb6f05cd6fbf0772@tfenne.com","name":"tfenne"},"message":"Added a pair of methods to manipulate the default options for VariantContextWriterBuilder\nso that it is possible to programmatically set the defaults for all future instances.","distinct":true,"url":"https://api.github.com/repos/a-nikitiuk/htsjdk/commits/4c6be49ca5e922288e2975043a8b3ae3ca58001f"},{"sha":"1297ab560ea684890fab127f825fa6bd18012717","author":{"email":"629c3e3d004b31c1ae42a6dc8c6729d15c6b15a2@broadinstitute.org","name":"Chris Norman"},"message":"Fix bugs in .crai 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tags","distinct":true,"url":"https://api.github.com/repos/a-nikitiuk/htsjdk/commits/b79855952177f500f0b42b25a8f43b0f2026856d"},{"sha":"26c28d22bdef2b42c78f417265ed0dd995046645","author":{"email":"1d0c6f32bb65b8defcf996a778a48a2d5cfb7c64@broadinstitute.org","name":"droazen"},"message":"Merge pull request #344 from samtools/yf_allow_only_compatible_dictionaries\n\nYf allow only compatible dictionaries...","distinct":true,"url":"https://api.github.com/repos/a-nikitiuk/htsjdk/commits/26c28d22bdef2b42c78f417265ed0dd995046645"},{"sha":"ae51415d0e21b2b7d34f866e76feab110b29e912","author":{"email":"73ddfdf0c2dacc65d8890847fb6f05cd6fbf0772@tfenne.com","name":"tfenne"},"message":"Removed the broken caching of getMean() and provided a slightly more efficient implementation of getMean() that didn't require traversing all the bins 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Fennell"},"message":"Merge pull request #348 from samtools/tf_histo_mean\n\nRemoved the broken caching of getMean() and provided a slightly more …","distinct":true,"url":"https://api.github.com/repos/a-nikitiuk/htsjdk/commits/5bac582769d32038c9e9c75b5eed571a8db8737e"},{"sha":"924753b2e20cff6369f87a11ecce8fb3349b050f","author":{"email":"1d0c6f32bb65b8defcf996a778a48a2d5cfb7c64@broadinstitute.org","name":"David Roazen"},"message":"Set TestNG verbosity back to 2, and reduce log file size by grepping out PASSED: lines.\n\nThis change allows submitters to once again see which tests are failing in\ntheir branches via travis.","distinct":true,"url":"https://api.github.com/repos/a-nikitiuk/htsjdk/commits/924753b2e20cff6369f87a11ecce8fb3349b050f"},{"sha":"0e4b4be3a5f6675b153e30c3cf3a29691c1985da","author":{"email":"1d0c6f32bb65b8defcf996a778a48a2d5cfb7c64@broadinstitute.org","name":"droazen"},"message":"Merge pull request #356 from samtools/dr_fix_test_verbosity\n\nSet TestNG verbosity back to 2, and reduce log file size by grepping out PASSED: lines.","distinct":true,"url":"https://api.github.com/repos/a-nikitiuk/htsjdk/commits/0e4b4be3a5f6675b153e30c3cf3a29691c1985da"},{"sha":"897bd96267b5419ea4388b686307b906ed9516d4","author":{"email":"1d0c6f32bb65b8defcf996a778a48a2d5cfb7c64@broadinstitute.org","name":"David Roazen"},"message":"Make the VCF/BCF Header tests less chatty\n\nThe VCFHeader tests were dumping extremely large String representations of VCFHeaders\nto the TestNG log due to the way they were using DataProviders -- this comprised\nthe vast majority of htsjdk test output. This refactors these tests to produce\nmuch less output.\n\nWith this change, grepping out the \"PASSED:\" lines should no longer be necessary\n(this approach didn't work well anyway, since it didn't correctly propagate the\nTestNG exit status to travis).","distinct":true,"url":"https://api.github.com/repos/a-nikitiuk/htsjdk/commits/897bd96267b5419ea4388b686307b906ed9516d4"},{"sha":"7ae894053fdeb52fac41cf73c94ab22d39090c63","author":{"email":"1d0c6f32bb65b8defcf996a778a48a2d5cfb7c64@broadinstitute.org","name":"droazen"},"message":"Merge pull request #357 from samtools/dr_suppress_vcfheader_test_output\n\nMake the VCF/BCF Header tests less chatty","distinct":true,"url":"https://api.github.com/repos/a-nikitiuk/htsjdk/commits/7ae894053fdeb52fac41cf73c94ab22d39090c63"},{"sha":"3e40db0c67b2782122051e9309e4bec54d501e03","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","distinct":true,"url":"https://api.github.com/repos/a-nikitiuk/htsjdk/commits/3e40db0c67b2782122051e9309e4bec54d501e03"}]}