gatk-3.8

Author	SHA1	Message	Date
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