GitHub PushEvent at 2014-04-25 15:49:03
Repository: adam
Actor: tdanford
Payload: {"shas":[["c7a17a909565d8cd5e5b86fa796d6d201284635d","3118c73689a9e5bf0f80c85b743e227a5a138c5e@cs.berkeley.edu","BQSR cleanups and fixes","Jey Kottalam",true],["dafb8da2c73b01e8d17ce7ecfc6e34055402dd76","3118c73689a9e5bf0f80c85b743e227a5a138c5e@cs.berkeley.edu","Add BQSR debug flags","Jey Kottalam",true],["d3ee590526de9732c86fd696b655104bd1fe71a5","3118c73689a9e5bf0f80c85b743e227a5a138c5e@cs.berkeley.edu","Remove attempted emulation of GATK 1.6","Jey Kottalam",true],["0e109e9ca5cf99e12d19fc2742afb10923e4dbb4","3118c73689a9e5bf0f80c85b743e227a5a138c5e@cs.berkeley.edu","style and naming fixes","Jey Kottalam",true],["3db1484335f41ff9efe2648a843c0b11f9119c04","3118c73689a9e5bf0f80c85b743e227a5a138c5e@cs.berkeley.edu","Add CycleCovariate","Jey Kottalam",true],["1489c4a5dbdcef3dada530dcb87b8a54cef25642","3118c73689a9e5bf0f80c85b743e227a5a138c5e@cs.berkeley.edu","remove tabs in pom.xml","Jey Kottalam",true],["e70bcef01f749c3296eac3527e12d12c99bb321f","3b18a4d825c09194f43025a5968ea840df7dd872@mac.com","Update SAM to ADAM conversion\n\nParse out the OQ (original quality) common attribute and populate the ADAMRecord with it\n(if it exists).","Isaac Hodes",true],["6bd83d93de35ed912ceb8fa177af4816ca87f785","3118c73689a9e5bf0f80c85b743e227a5a138c5e@cs.berkeley.edu","Clarify BQSR debug flags","Jey Kottalam",true],["a13c75843bb74e80e9e736e233f418113320bfb8","7841830342f748a54814a395669113bed0a8f742@berkeley.edu","Merge pull request #213 from jey/bqsr-updates\n\nBQSR updates","Matt Massie",true],["8252f3585c86e1dfe328996d6244b19674c6c525","7841830342f748a54814a395669113bed0a8f742@berkeley.edu","Merge pull request #220 from hammerlab/parse-origQual-from-sam\n\nUpdate SAM to ADAM conversion","Matt Massie",true],["d92f32b5926778439ba8aa31dbcf9a4fcccbda45","272127e96291ad54599290eb3e66fd99a8732d13@gmail.com","Cleanup and optimize basic variant conversion","Michael Linderman",true],["70d0c325326fbb128f94ebf4f5500c9638afe10e","272127e96291ad54599290eb3e66fd99a8732d13@gmail.com","Sites-only multi-allelic variant conversion","Michael Linderman",true],["9bd284954616c9a919dedb1a14c3d2b51147503d","272127e96291ad54599290eb3e66fd99a8732d13@gmail.com","Basic multi-allelic conversion of genotypes","Michael Linderman",true],["964ce7c0ffaa517f1fda4df40099f8efdbaedac4","272127e96291ad54599290eb3e66fd99a8732d13@gmail.com","Now with scalariform...","Michael Linderman",true],["1da1c6e1b94555f7ac7ea27264db9fa9fa072fe5","ae837235f8a7be8c036b474a20347e1ce359332c@gmail.com","Migrate from reference ids to reference names\n\nWe decided that using RefSeq names for our contigs was better practice\nthan minting our own IDs and handling complicated sequence dictionary\nmerges.","Neal Sidhwaney",true],["b7779450d91c42f287154e4e7d8ce671bdeba604","1b7fbefd792d7a9793d7aac527d8c759c32763c6@berkeley.edu","Merge pull request #217 from hammerlab/ref-id-to-name\n\nStop using reference IDs and use reference names instead","Frank Austin Nothaft",true],["12b5355df69a74e0a6c82ff33d7e27065bd52267","7841830342f748a54814a395669113bed0a8f742@cs.berkeley.edu","Use SparkConf object to configure SparkContext\n\nThe new Spark SparkConf object replaces the old configuration system that uses\nJava system properties and environment variables. SparkConf is thread-safe and\nself-contained. For now, SparkConf is constructed to honor the old system and\nenvironment properties. With time, we should change this behavior.\n\nOne effect of this move to SparkConf is to prevent errors around binding a port\nfor the SparkContext in each test case.\n\nThis commit also fixes a race condition in GenotypePredicatesSuites.","Matt Massie",true],["cf422390b062a54ae297ff9c091a9b57f041f2e8","1b7fbefd792d7a9793d7aac527d8c759c32763c6@berkeley.edu","Merge pull request #223 from massie/sparkconf\n\nUse SparkConf object to configure SparkContext","Frank Austin Nothaft",true],["61139b3dab7c020ee0bb9c7f36cb02d09d7b27bf","c08192e8fe669f6ecbd6dba0a906fecf8baad8f9@gmail.com","change some to option to avoid null pointer exceptions when accessing adamrecord fields","arahuja",true],["513ca32fd7e04316a117a094d4884b153ea825d1","1b7fbefd792d7a9793d7aac527d8c759c32763c6@berkeley.edu","Merge pull request #225 from hammerlab/refpos-null\n\nChange Some to Option to check for unmapped reads","Frank Austin Nothaft",true]],"size":20,"ref":"refs/heads/master","head":"513ca32fd7e04316a117a094d4884b153ea825d1"}