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9 Commits (5af3999a2d778231e0321b43203dcf85156fa2e8)

Author SHA1 Message Date
Ryan Poplin ace9333068 Active region walkers can now see the reads in a buffer around thier active reigons. This buffer size is specified as a walker annotation. Intervals are internally extended by this buffer size so that the extra reads make their way through the traversal engine but the walker author only needs to see the original interval. Also, several corner case bug fixes in active region traversal. 2012-01-19 22:05:08 -05:00
Ryan Poplin a6886a4cc0 Initial commit of the Active Region Traversal. Not ready to be used by anyone yet. 2012-01-04 17:03:21 -05:00
Mark DePristo 3060a4a15e Support for list of known CNVs in VariantEval 
-- VariantSummary now includes novelty of CNVs by reciprocal overlap detection using the standard variant eval -knownCNVs argument
-- Genericizes loading for intervals into interval tree by chromosome
-- GenomeLoc methods for reciprocal overlap detection, with unit tests
 2011-11-30 17:05:16 -05:00
Mark DePristo c2b97030a4 IntervalUtils for completely balanced locus-based scatter/gather 
-- scatterLocusIntervals master utility
-- Moved around some general functionality from GenomeLocSortedSet to GenomeLoc
-- Util function for reversing a list (List<T> -> List<T>, unlike Collections version)
-- DoC is PartitionType.INTERVAL
-- Significant unit tests on new functionality (all passing)
-- Ready for real-world testing, as soon as I can get LocusScatterFunction.scala to actually work
 2011-11-02 10:49:40 -04:00
Mark DePristo 3c8445b934 Performance bugfix for GenomeLoc.hashcode 
-- old version overflowed so most GenomeLocs had 0 hashcode.  Now uses or not plus to combine
 2011-09-09 14:25:37 -04:00
Mark DePristo c6436ee5f0 Whitespace cleanup 2011-09-09 14:24:29 -04:00
Mark DePristo 87dc5cfb24 Whitespace cleanup 2011-09-09 14:23:42 -04:00
Mark DePristo 9992c373be Optimize imports run on the whole project, public and private. I just got too tired of all of the unused imports floating around. Confirmed that the system builds after the changes. 2011-07-17 20:29:58 -04:00
David Roazen 3c9497788e Reorganized the codebase beneath top-level public and private directories, 
removing the playground and oneoffprojects directories in the process. Updated
build.xml accordingly.
 2011-06-28 06:55:19 -04:00