hanna a7fe07c404 A few stopgap fixes to get the GATK to the point where the old sharding ... infrastructure can be torn down: 1) New sharding system emulates old MonolithicSharding mechanism. 2) Better awareness of differences between fasta and BAM files when creating shards. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2948 348d0f76-0448-11de-a6fe-93d51630548a		2010-03-07 21:01:25 +00:00
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arguments	Looks bigger than it is:	2010-01-15 00:14:35 +00:00
contexts/variantcontext	Update to VCF code to get it up to spec.	2010-03-03 06:12:42 +00:00
datasources	A few stopgap fixes to get the GATK to the point where the old sharding	2010-03-07 21:01:25 +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	a little clean-up: move setting the bases of generated reads into Artificial SAM Utils now that the clean read injector test is gone.	2010-03-03 16:31:45 +00:00
traversals	A few stopgap fixes to get the GATK to the point where the old sharding	2010-03-07 21:01:25 +00:00
walkers	Fixed another bug in the original sharding system. Updated integration tests	2010-03-07 15:32:18 +00:00