aaron 88a48821ea removed the dependence on removeRegion() in GenomeLocSortedSet ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2993 348d0f76-0448-11de-a6fe-93d51630548a		2010-03-12 22:35:49 +00:00
..
arguments	Bug fix in variant eval 2. Preliminary (slow and buggy) support for -XL exclude lists.	2010-03-12 19:23:12 +00:00
contexts/variantcontext	Update to VCF code to get it up to spec.	2010-03-03 06:12:42 +00:00
datasources	removed the dependence on removeRegion() in GenomeLocSortedSet	2010-03-12 22:35:49 +00:00
executive	Added IterableLocusContextQueue and test. Cleaned up tests, adding BaseTest where it didn't exist. Enhanced test runner to run only classes ending in ...Test.java, so that utility classes can sit alongside the tests but won't be run by JUnit.	2009-05-13 21:32:05 +00:00
io	Fix for problem where err stream remapped to output stream in certain cases, (hopefully) completing Matt's hat trick of fail. Thanks, unit tests.	2009-09-16 08:33:56 +00:00
iterators	Fix off-by-one error in original implementation of read sharding. Tested by	2010-03-06 18:52:53 +00:00
refdata	adding methods to get RODs by name or type in read traversals, performance improvements to RODs for Reads in general, and some more Tribble infrastructure.	2010-03-11 21:13:39 +00:00
traversals	Rework the way the MicroScheduler handles locus shards to handle intervals that span shards	2010-03-11 18:40:31 +00:00
walkers	Added test of Nway cleaning for Matt; thanks to Aaron for the help.	2010-03-10 21:00:41 +00:00