{"push_id":1220730023,"size":35,"distinct_size":1,"ref":"refs/heads/variant-filter","head":"37e1673858788d532733578952403eb6a18a556e","before":"006ab046e522daf63bed53e4fc1107c0526284a5","commits":[{"sha":"3dac3a496386a69323f1b788b2a3c0edf8b4693f","author":{"name":"Michael L Heuer","email":"23d74b3b68b7a159a31171bf7ce7f8f2768d7898@acm.org"},"message":"Whitespace code style fixes","distinct":false,"url":"https://api.github.com/repos/heuermh/adam/commits/3dac3a496386a69323f1b788b2a3c0edf8b4693f"},{"sha":"ae3160f1413658098e5918ada94a6502dce62994","author":{"name":"Frank Austin Nothaft","email":"d9347962c16e697d97aca23107f7a15117076855@alumni.stanford.edu"},"message":"[ADAM-1008] Modify jenkins-test script to support Java 8 build.\n\nResolves #1008. As per discussion with @shaneknapp, it is preferable to support\nbuilds across Java versions by manually setting JAVA_HOME in a shell script run\ninside of Jenkins. This is due to certain configuration limitations inside of\nJenkins. Currently, we are doing this via a script tracked inside of Jenkins.\nI would rather roll all of that config into the ./scripts/jenkins-test script\nso that we have revision control, etc.","distinct":false,"url":"https://api.github.com/repos/heuermh/adam/commits/ae3160f1413658098e5918ada94a6502dce62994"},{"sha":"4ba0b62bb6370c1c59108381b9dbafd83d7db007","author":{"name":"Frank Austin Nothaft","email":"d9347962c16e697d97aca23107f7a15117076855@alumni.stanford.edu"},"message":"[ADAM-827] Check for Hadoop/Spark version when running jenkins-test script.\n\nResolves #827.","distinct":false,"url":"https://api.github.com/repos/heuermh/adam/commits/4ba0b62bb6370c1c59108381b9dbafd83d7db007"},{"sha":"72dee78b97f329b8f354887c79151ae374ff2974","author":{"name":"Frank Austin Nothaft","email":"d9347962c16e697d97aca23107f7a15117076855@alumni.stanford.edu"},"message":"[ADAM-602] Remove plugin code.\n\nResolves #602:\n\n* Removed the `org.bdgenomics.adam.plugins` package.\n* Removed the `PluginExecutor` command.\n* Removed the `JavaADAMPlugin` from the Java API.","distinct":false,"url":"https://api.github.com/repos/heuermh/adam/commits/72dee78b97f329b8f354887c79151ae374ff2974"},{"sha":"9764b2cb0b723919f3647616b633f8ed5b5e64a4","author":{"name":"Frank Austin Nothaft","email":"d9347962c16e697d97aca23107f7a15117076855@alumni.stanford.edu"},"message":"Cleanup in org.bdgenomics.adam.converters package.\n\n* Remove unused GenotypesToVariantsConverter.\n* Made all classes package private to [converters] if they had no external\n  references, or package private to [adam] if they were referenced elsewhere\n  in ADAM.\n* Added documentation where necessary.\n* Added SupportedHeaderLines object. This contains code previously in\n  VariantAnnotationConverter that was called in the ADAMVCFOutputFormat. This\n  allows us to make VariantAnnotationConverter package private to converters\n  and allows us to make the AttrKeys class and object private.\n* Additionally, pulled `mergeAnnotations` out to\n  org.bdgenomics.adam.models.VariantContext, which is also needed to make\n  VariantAnnotationConverter package private to converters. This also cleaned up\n  some code in org.bdgenomics.adam.rdd.variation.VariationRDDFunctions.\n* Rename `BroadVariantContext` to `HtsjdkVariantContext`.","distinct":false,"url":"https://api.github.com/repos/heuermh/adam/commits/9764b2cb0b723919f3647616b633f8ed5b5e64a4"},{"sha":"627c4d42405a00b44b187f09b47053fcb624b9ff","author":{"name":"Frank Austin Nothaft","email":"d9347962c16e697d97aca23107f7a15117076855@alumni.stanford.edu"},"message":"Refactoring `org.bdgenomics.adam.io` package.\n\n* Added documentation to all classes, methods, and fields that were missing\n  descriptions.\n* Factored duplicated code from `SingleFastqRecordReader` and\n  `InterleavedFastqRecordReader` out into a new abstract base class\n  `FastqRecordReader`.\n* Tightened up access modifiers where possible. Sadly, the two input formats\n  cannot be made more private, since Java has a more restricted form of\n  package-private than scala, and the input formats are used from inside of\n  `org.bdgenomics.adam.rdd`.\n* Removed `@author` tags.","distinct":false,"url":"https://api.github.com/repos/heuermh/adam/commits/627c4d42405a00b44b187f09b47053fcb624b9ff"},{"sha":"072f97df75f075d4c298624b84842f8abdb0eeed","author":{"name":"Michael L Heuer","email":"23d74b3b68b7a159a31171bf7ce7f8f2768d7898@acm.org"},"message":"Remove code workarounds necessary for Spark 1.2.1/Hadoop 1.0.x support","distinct":false,"url":"https://api.github.com/repos/heuermh/adam/commits/072f97df75f075d4c298624b84842f8abdb0eeed"},{"sha":"51b755b9d9eb105dbc9a960eb68ce2ca01ab486c","author":{"name":"Frank Austin Nothaft","email":"d9347962c16e697d97aca23107f7a15117076855@alumni.stanford.edu"},"message":"[ADAM-1006] Split uberjar out to adam-assembly submodule.","distinct":false,"url":"https://api.github.com/repos/heuermh/adam/commits/51b755b9d9eb105dbc9a960eb68ce2ca01ab486c"},{"sha":"2211d5d76ad7658589f075913c6955cf3db3dfa5","author":{"name":"Frank Austin Nothaft","email":"d9347962c16e697d97aca23107f7a15117076855@alumni.stanford.edu"},"message":"Refactor GenomicRDD to use F-bounded polymorphism.","distinct":false,"url":"https://api.github.com/repos/heuermh/adam/commits/2211d5d76ad7658589f075913c6955cf3db3dfa5"},{"sha":"021f59a129cdaae8d3c6562a54294a8db65fd33c","author":{"name":"Frank Austin Nothaft","email":"d9347962c16e697d97aca23107f7a15117076855@alumni.stanford.edu"},"message":"Add NucleotideContigFragmentRDD.\n\n* Add NucleotideContigFragmentRDD to replace RDD[NucleotideContigFragment] and\n  updated various ADAMContext functions.\n* Added test suite for Fasta2ADAM to validate round trip loading.","distinct":false,"url":"https://api.github.com/repos/heuermh/adam/commits/021f59a129cdaae8d3c6562a54294a8db65fd33c"},{"sha":"14c5683b45c356e995dc9ce850988e597ef9a0b3","author":{"name":"Frank Austin Nothaft","email":"d9347962c16e697d97aca23107f7a15117076855@alumni.stanford.edu"},"message":"Added FeatureRDD and GeneRDD.\n\n* Added Feature and Gene RDDs and updated loading functions.\n* Modified Features2ADAMSuite to use sc.loadFeatures to test end-to-end\n  conversion.","distinct":false,"url":"https://api.github.com/repos/heuermh/adam/commits/14c5683b45c356e995dc9ce850988e597ef9a0b3"},{"sha":"1af0a0ccc186c7ed26c7a0a7fb9f581664dcdbcf","author":{"name":"Frank Austin Nothaft","email":"d9347962c16e697d97aca23107f7a15117076855@alumni.stanford.edu"},"message":"Add DatabaseVariantAnnotationRDD.","distinct":false,"url":"https://api.github.com/repos/heuermh/adam/commits/1af0a0ccc186c7ed26c7a0a7fb9f581664dcdbcf"},{"sha":"a4a94ff53a37601f55af0a952f3170585cf5234b","author":{"name":"Frank Austin Nothaft","email":"d9347962c16e697d97aca23107f7a15117076855@alumni.stanford.edu"},"message":"Added FragmentRDD.\n\n* Added FragmentRDD to replace RDD[Fragment]; refactored load/save methods\n* Moved toFragments method from implicit on RDD[AlignmentRecord] to AlignmentRecordRDD\n* Added `-single` option to Fragments2Reads.\n* Added test suites for Fragments2Reads and Reads2Fragments.","distinct":false,"url":"https://api.github.com/repos/heuermh/adam/commits/a4a94ff53a37601f55af0a952f3170585cf5234b"},{"sha":"bd56167290cd03e67a3494bcc45bd1dfc9802e88","author":{"name":"Frank Austin Nothaft","email":"d9347962c16e697d97aca23107f7a15117076855@alumni.stanford.edu"},"message":"Refactored GenomicRDD support for overlaps.\n\n* Made region join implementations package private to `org.bdgenomics.adam.rdd`.\n* Added support for `broadcastRegionJoin`, `shuffleRegionJoin`, and\n  `filterByOverlappingRegion` to `GenomicRDD`.\n* Added private `GenericGenomicRDD` class.\n* Cleaned up `CalculateDepth`, which used the old `broadcastRegionJoin`\n  implementation.","distinct":false,"url":"https://api.github.com/repos/heuermh/adam/commits/bd56167290cd03e67a3494bcc45bd1dfc9802e88"},{"sha":"aa48c20f1de7167099e74bb6b53e4adaa031d4a9","author":{"name":"Frank Austin Nothaft","email":"d9347962c16e697d97aca23107f7a15117076855@alumni.stanford.edu"},"message":"Removed AlignmentRecordRDDFunctions.\n\n* Removed `AlignmentRecordRDDFunctions` and moved all functions into\n  `AlignmentRecordRDD`. Moved test suite along with the main class move.\n* Removed `countTag` functions and `PrintTags` CLI.\n* Removed `JavaAlignmentRecordRDD`. The Java API just uses the\n  `AlignmentRecordRDD` now. To do this, I moved the Java friendly save methods\n  and JavaRDD to `GenomicRDD`.","distinct":false,"url":"https://api.github.com/repos/heuermh/adam/commits/aa48c20f1de7167099e74bb6b53e4adaa031d4a9"},{"sha":"f52554a2cf946e81763d30b028a5de177b803a8e","author":{"name":"Frank Austin Nothaft","email":"d9347962c16e697d97aca23107f7a15117076855@alumni.stanford.edu"},"message":"Removed NucleotideContigFragmentRDDFunctions.\n\n* Removed `NucleotideContigFragmentRDDFunctions` and moved all functions to\n  `NucleotideContigFragmentRDD`. Moved test suite to accompany refactor.\n* Added Java helper functions, and added functions for loading sequence data\n  from the `JavaADAMContext`.\n* Refactored JavaADAMContext test code to make it easier to test Java API.\n* Fixed `ADAMContext.loadSequences` so that it correctly identifies `.fa.gz`\n  and `.fasta.gz` file extensions.\n* Fixed `ADAMFunSuite.copyResource` so that it correctly copies resource files\n  with compound file extensions.","distinct":false,"url":"https://api.github.com/repos/heuermh/adam/commits/f52554a2cf946e81763d30b028a5de177b803a8e"},{"sha":"b7fbf2d6c70a44a8cbf14c4ec5f2c6722d71f3bc","author":{"name":"Frank Austin Nothaft","email":"d9347962c16e697d97aca23107f7a15117076855@alumni.stanford.edu"},"message":"Moderate additional refactor to FragmentRDD.\n\n* Adding documentation to FragmentRDD.\n* Added Java-friendly save method to FragmentRDD.\n* Added method for loading Fragments from the `JavaADAMContext`.","distinct":false,"url":"https://api.github.com/repos/heuermh/adam/commits/b7fbf2d6c70a44a8cbf14c4ec5f2c6722d71f3bc"},{"sha":"4ed787ce61826fa2b7cd0f8800abcc10b7bd4b9d","author":{"name":"Frank Austin Nothaft","email":"d9347962c16e697d97aca23107f7a15117076855@alumni.stanford.edu"},"message":"Removed FeatureRDDFunctions class.\n\n* Removed `FeatureRDDFunctions` class and moved all methods into `FeatureRDD`.\n  Renamed test suite to match, and added Java helper functions.\n* Moved all `adam-*/src/test/resources/features/*` files into their respective\n  `resources` directory. This is necessary due to an issue when using\n  `copyResources` with subdirectories.\n* Removed `ignore` on test in `org.bdgenomics.adam.cli.Features2ADAMSuite`.","distinct":false,"url":"https://api.github.com/repos/heuermh/adam/commits/4ed787ce61826fa2b7cd0f8800abcc10b7bd4b9d"},{"sha":"da2a142e998006d909e97a95a10745f11f3d4ef4","author":{"name":"Frank Austin Nothaft","email":"d9347962c16e697d97aca23107f7a15117076855@alumni.stanford.edu"},"message":"Removed VariationRDDFunctions.\n\n* Removed `VariationRDDFunctions` and moved remaining methods to\n  `VariantContextRDD`. Moved test suite code as well.\n* Removed abstract class `ADAMSequenceDictionaryRDDAggregator`.\n* Added Java helper methods to various variation RDDs and accompanying loader\n  methods in `JavaADAMContext`.\n* Miscellaneous documentation cleanup in `org.bdgenomics.adam.rdd.variation`.\n\nResolves #1011.","distinct":false,"url":"https://api.github.com/repos/heuermh/adam/commits/da2a142e998006d909e97a95a10745f11f3d4ef4"},{"sha":"9c1437e323b4dacb354183f1f22f86b05f3f7bf1","author":{"name":"Frank Austin Nothaft","email":"d9347962c16e697d97aca23107f7a15117076855@alumni.stanford.edu"},"message":"[ADAM-1040] Remove implicit GenomicRDD to RDD conversion.\n\nResolves #1040.","distinct":false,"url":"https://api.github.com/repos/heuermh/adam/commits/9c1437e323b4dacb354183f1f22f86b05f3f7bf1"}]}
{"actor":{"display_login":"heuermh"}}