ebanks 9f3b99c11b Moving UnifiedGenotyper and VariantAnnotator over to VariantContext system. ... Removing obsolete genotyping classes. First stage of removing dependence on old Genotype class. More changes to come. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2960 348d0f76-0448-11de-a6fe-93d51630548a		2010-03-09 03:41:07 +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	Moving UnifiedGenotyper and VariantAnnotator over to VariantContext system.	2010-03-09 03:41:07 +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	Moving UnifiedGenotyper and VariantAnnotator over to VariantContext system.	2010-03-09 03:41:07 +00:00