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Additionally, I identified and fixed an error in the old\nFASTQ code that did a seek on the uncompressed input stream to backtrack if\nseeing a line of quality scores that began with @ when identifying the position\nof the first valid record in a split. Instead, we check for two successive lines\nthat start with an @, which indicates that the first line contains quality\nscores, while the second line contains read names.","distinct":false,"url":"https://api.github.com/repos/heuermh/adam/commits/fa078482f86fc8f44784ca0fd4b069a5b46eac0c"},{"sha":"c8a2202fcff5d096b0660a0453ace395fbe02f73","author":{"name":"Frank Austin Nothaft","email":"d9347962c16e697d97aca23107f7a15117076855@alumni.stanford.edu"},"message":"Addressing reviewer comments.","distinct":false,"url":"https://api.github.com/repos/heuermh/adam/commits/c8a2202fcff5d096b0660a0453ace395fbe02f73"},{"sha":"43dc42dd7b1ebeec2b1287af8d6f09e141bf3dc1","author":{"name":"Frank Austin Nothaft","email":"d9347962c16e697d97aca23107f7a15117076855@alumni.stanford.edu"},"message":"[ADAM-1647] Fix bad JAR discovery grep in bin/pyadam.\n\nResolves #1647.","distinct":false,"url":"https://api.github.com/repos/heuermh/adam/commits/43dc42dd7b1ebeec2b1287af8d6f09e141bf3dc1"},{"sha":"657399776914ec2075cf5e1ebf3dcdeac176a1ce","author":{"name":"Gunjan Baid","email":"7d1dc3d964666bab168d0ac54da8d07dc8399dd9@berkeley.edu"},"message":"[ADAM-1631] Added a section for homebrew.\n\nResolves #1631.","distinct":false,"url":"https://api.github.com/repos/heuermh/adam/commits/657399776914ec2075cf5e1ebf3dcdeac176a1ce"},{"sha":"90326981999690f3224ba930b61453ec1602299d","author":{"name":"Gunjan Baid","email":"b2876e5c1b9379e128013432f65c218c19f41b11@users.noreply.github.com"},"message":"General cleanup of documentation.\n\n* Removed URL text from view.\n* Removed broken links.\n* Moved intro paragraph to top, consistent w/ README\n* Updating links to be consistent w/ intro in docs\n* Removed contractions.\n* Minor edits to:\n  * 01_intro.md\n  * 02_installation.md\n  * 30_running_example.md\n  * 40_deploying_ADAM.md","distinct":false,"url":"https://api.github.com/repos/heuermh/adam/commits/90326981999690f3224ba930b61453ec1602299d"},{"sha":"544f78ee1c11e91ed98c25a6ef310a405911fcd9","author":{"name":"Frank Austin Nothaft","email":"d9347962c16e697d97aca23107f7a15117076855@alumni.stanford.edu"},"message":"[ADAM-1615] Add transform and transmute APIs to Java, R, and Python\n\nResolves #1615. Adds `GenomicDatasetConversion` class to adam-core API, along\nwith accompanying implementations in `org.bdgenomics.adam.api.java` package.\nAdds `transformDataFrame` and `transmuteDataFrame` to `GenomicRDD` API. To\nenable use from Python and R, we provide a `DataFrameConversionWrapper` that\nwraps the product of an R/Python function in a Spark Java API `Function`.","distinct":false,"url":"https://api.github.com/repos/heuermh/adam/commits/544f78ee1c11e91ed98c25a6ef310a405911fcd9"},{"sha":"ca3c5872b51660e1789fa0e9d9facc26337b8862","author":{"name":"Frank Austin Nothaft","email":"d9347962c16e697d97aca23107f7a15117076855@alumni.stanford.edu"},"message":"R CoverageRDD collapse method was misnamed.","distinct":false,"url":"https://api.github.com/repos/heuermh/adam/commits/ca3c5872b51660e1789fa0e9d9facc26337b8862"},{"sha":"96fc37f17245e0f16c2dd52bec6996c576dc93a9","author":{"name":"Devin Petersohn","email":"6b6c15ffcc2d04cfb5659accdcf6b0868959b8ee@users.noreply.github.com"},"message":"Cleaning up formatting and spacing of docs. (#1640)\n\nResolves #1638.\r\n\r\nWrapped lines at 80 if possible, also addressed formatting and spacing issues\r\nfrom rendering of the doc.","distinct":false,"url":"https://api.github.com/repos/heuermh/adam/commits/96fc37f17245e0f16c2dd52bec6996c576dc93a9"},{"sha":"50d29af4a65d51f6db75361e1ddf32c12a9e149a","author":{"name":"antonkulaga","email":"b4ddf617cbf27fbd125f64cbe68c0a120d2192aa@gmail.com"},"message":"added ExtractRegions function to NucleotideContigFragmentRDD","distinct":false,"url":"https://api.github.com/repos/heuermh/adam/commits/50d29af4a65d51f6db75361e1ddf32c12a9e149a"},{"sha":"6c8f8d7c752583261ab8aeb65edacc8cfe8938f8","author":{"name":"Frank Austin Nothaft","email":"d9347962c16e697d97aca23107f7a15117076855@alumni.stanford.edu"},"message":"[ADAM-1663] Enable read groups with repeated names when unioning.\n\nResolves #1663. When unioning two read groups together, calls distinct after\nappending the two RecordGroupDictionaries.","distinct":false,"url":"https://api.github.com/repos/heuermh/adam/commits/6c8f8d7c752583261ab8aeb65edacc8cfe8938f8"},{"sha":"b46b58342190de2c5d5a36e5c1c63b8f57778357","author":{"name":"Frank Austin Nothaft","email":"d9347962c16e697d97aca23107f7a15117076855@alumni.stanford.edu"},"message":"[ADAM-1673] Don't set PL to empty when no PL is attached to a gVCF record.\n\nResolves #1763.","distinct":false,"url":"https://api.github.com/repos/heuermh/adam/commits/b46b58342190de2c5d5a36e5c1c63b8f57778357"},{"sha":"209f997aa80b44f66b26525f82f6a2f9bda722c7","author":{"name":"Alyssa Morrow","email":"7e6ad2f046ed4c97b37f78bb70db749a813a60ce@berkeley.edu"},"message":"updated payday script for correct adam jars","distinct":false,"url":"https://api.github.com/repos/heuermh/adam/commits/209f997aa80b44f66b26525f82f6a2f9bda722c7"},{"sha":"9b51df59891abfe0e544ff038c216636be835dd2","author":{"name":"Alyssa Morrow","email":"7e6ad2f046ed4c97b37f78bb70db749a813a60ce@berkeley.edu"},"message":"Minor fixes to adam-python API","distinct":false,"url":"https://api.github.com/repos/heuermh/adam/commits/9b51df59891abfe0e544ff038c216636be835dd2"},{"sha":"12c56fdede7063bd87ffd904da6ed33f72961e32","author":{"name":"Frank Austin Nothaft","email":"d9347962c16e697d97aca23107f7a15117076855@alumni.stanford.edu"},"message":"[ADAM-1679] Unmapped items should not get caught in requirement when sorting.\n\nResolves #1679.","distinct":false,"url":"https://api.github.com/repos/heuermh/adam/commits/12c56fdede7063bd87ffd904da6ed33f72961e32"},{"sha":"5b6cf04a27f0e6752db40634a2cccf3d3a1cb71a","author":{"name":"Michael L Heuer","email":"23d74b3b68b7a159a31171bf7ce7f8f2768d7898@acm.org"},"message":"Add adam-shell friendly VariantContextRDD.saveAsVcf method.","distinct":false,"url":"https://api.github.com/repos/heuermh/adam/commits/5b6cf04a27f0e6752db40634a2cccf3d3a1cb71a"},{"sha":"c6b448d54d4cceee8c880fd8bc01d2622e1cc089","author":{"name":"Michael Heuer","email":"23d74b3b68b7a159a31171bf7ce7f8f2768d7898@acm.org"},"message":"Add bdg-formats exclusion to org.hammerlab:genomic-loci dependency.","distinct":false,"url":"https://api.github.com/repos/heuermh/adam/commits/c6b448d54d4cceee8c880fd8bc01d2622e1cc089"},{"sha":"511f9253f9e52f8142911c807df2e538d0413cc9","author":{"name":"Michael Heuer","email":"23d74b3b68b7a159a31171bf7ce7f8f2768d7898@acm.org"},"message":"Merge VCF header lines with VCFHeaderLineCount.INTEGER correctly.","distinct":false,"url":"https://api.github.com/repos/heuermh/adam/commits/511f9253f9e52f8142911c807df2e538d0413cc9"},{"sha":"51efbafef44062dc0616735923ebd3fbf6051db2","author":{"name":"Michael L Heuer","email":"23d74b3b68b7a159a31171bf7ce7f8f2768d7898@acm.org"},"message":"Add short readable descriptions for toString in subclasses of GenomicRDD.","distinct":false,"url":"https://api.github.com/repos/heuermh/adam/commits/51efbafef44062dc0616735923ebd3fbf6051db2"},{"sha":"28bbb487fc69e68febf900655954e81d4393715b","author":{"name":"Frank Austin Nothaft","email":"d9347962c16e697d97aca23107f7a15117076855@alumni.stanford.edu"},"message":"[ADAM-1709] Add ability to left normalize reads containing INDELs.\n\nResolves #1709. Opens protection on main method in NormalizationUtils to be\npackage-private to org.bdgenomics.adam. Adds code to AlignmentRecordRDD\nexposing INDEL normalization as a transformation.","distinct":false,"url":"https://api.github.com/repos/heuermh/adam/commits/28bbb487fc69e68febf900655954e81d4393715b"},{"sha":"3dad5fce17ae9f924adb6b9b8e08121b546d69d8","author":{"name":"Frank Austin Nothaft","email":"d9347962c16e697d97aca23107f7a15117076855@alumni.stanford.edu"},"message":"[ADAM-1691] Move bdgenomics.adam to use a namespace package.\n\nResolves #1691.","distinct":false,"url":"https://api.github.com/repos/heuermh/adam/commits/3dad5fce17ae9f924adb6b9b8e08121b546d69d8"}]}
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