GitHub PushEvent at 2014-12-02 19:46:48
Repository: adam
Actor: tdanford
Payload: {"shas":[["bcacc574f9c518889470f49a16c348d11aabddaf","9dcf5e33cfb31a2872893d1fd44fa7914cac0864@gmail.com","[ADAM-462] Coverage region calculation\n\nThis commit includes an new class, Coverage, which contains methods for\ncalculating coverage RDDs from RDDs of Region values.\n\nAlso included is a helper class, the PairingRDD class, which calculates\nsimple 'sliding' and 'pair' methods on sorted RDDs using the\n\"zipWithIndex trick.\"\n\n(Joint work with Carl Yeksigian.)","Timothy Danford",true],["4a28c964e52001e9574a5a545406fc82afabbac2","9dcf5e33cfb31a2872893d1fd44fa7914cac0864@gmail.com","[ADAM-511] Provide Ordering for ReferenceRegion\n\nAs covered in issue #511, ReferenceRegion shouldn't extend Ordered, but\nrather should be ordered by an Ordering value which can be imported\nimplicitly.  This will fix some \"diverging implicit expansion\" errors,\nand bring us more in line with the Scala documentation on Ordered (which\nis intended to be used in classes that have \"a single, natural ordering\"\n-- a description that doesn't apply to ReferenceRegion).\n\nThis commit makes these changes, with the new Ordering provided\nimplicitly in ReferenceRegionContext.  It also includes corresponding\nchanges to the ReferenceRegionWithOrientation handling, and (finally)\nincludes changes to downstream classes that use(d) the Region.compareTo\nmethod.\n\nAlso bundled in to this commit are two additional changes to\nReferenceRegion:\n* Adding explanations to ReferenceRegion asserts.\n* Adding 'extend' to ReferenceRegionWithOrientation, allowing a\n  strand-specific extension of the region in a single direction.","Timothy Danford",true],["c94e2b4e2ef96bd75ea9ecb0f7e3bbe8d1ae876b","9dcf5e33cfb31a2872893d1fd44fa7914cac0864@gmail.com","[ADAM-512] Creating RegionRDDFunctions\n\nCreated RegionRDDFunctions, a class that wraps an RDD[ReferenceRegion]\nand provides common join, filter, grouping, and counting methods on top\nof that RDD.\n\nAlso included is a similar implementation for region-keyed RDDs (i.e.\nRDD[(ReferenceRegion, T)] for some type T, and another class that wraps\noriented regions.","Timothy Danford",true],["726a2f6fd13df2149e7cd2a652b878e396f1a89f","9dcf5e33cfb31a2872893d1fd44fa7914cac0864@gmail.com","formatting","Timothy Danford",true],["c3055263a620f6992ad954e0392d5d014837ab2e","9dcf5e33cfb31a2872893d1fd44fa7914cac0864@gmail.com","Adding a ReferenceMapping for VariantContext","Timothy Danford",true],["2450510801492d58ac0de06d6685287ea25b9120","9dcf5e33cfb31a2872893d1fd44fa7914cac0864@gmail.com","Adding an RDD->RDD[ReferenceRegion] implicit, using the ReferenceMapping","Timothy Danford",true],["dc99f08a913f894a0bdfe6452da9b0220ec8d828","9dcf5e33cfb31a2872893d1fd44fa7914cac0864@gmail.com","Removing the 'sc' parameter from RegionJoin.partitionAndJoin","Timothy Danford",true],["7a155cf67d8e7a319e381e9fa35986829b4c0fa8","9dcf5e33cfb31a2872893d1fd44fa7914cac0864@gmail.com","Starting to fill out the methods in RegionKeyedRDDFunctions","Timothy Danford",true],["b5842549b1bc583ef553b47062128df5f4a21dbe","9dcf5e33cfb31a2872893d1fd44fa7914cac0864@gmail.com","Adding in the groupBy operations on the keyed rdd","Timothy Danford",true],["ecf97b9a3324c1271e386a2b1e822e31126a3931","9dcf5e33cfb31a2872893d1fd44fa7914cac0864@gmail.com","Starting to fillin the Regionmappable RDD","Timothy Danford",true]],"size":10,"ref":"refs/heads/vc-ref-mapping","head":"ecf97b9a3324c1271e386a2b1e822e31126a3931"}