ebanks 5a20bf0e64 3 changes to UG which break integration tests: ... 1. emit AA,AB,BB likelihoods in the FORMAT field for Mark 2. remove constraint that genotype alleles (in the GT field) need to be lexigraphically sorted. 3. Add bam file(s) used by genotyper to header for Kiran git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2963 348d0f76-0448-11de-a6fe-93d51630548a		2010-03-09 17:16:47 +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	3 changes to UG which break integration tests:	2010-03-09 17:16:47 +00:00