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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annotator	Moving UnifiedGenotyper and VariantAnnotator over to VariantContext system.	2010-03-09 03:41:07 +00:00
concordance	Update to VCF code to get it up to spec.	2010-03-03 06:12:42 +00:00
fasta	Fix off-by-one error in original implementation of read sharding. Tested by	2010-03-06 18:52:53 +00:00
filters	Update to VCF code to get it up to spec.	2010-03-03 06:12:42 +00:00
genotyper	3 changes to UG which break integration tests:	2010-03-09 17:16:47 +00:00
indels	Various improvements to plink, variant context, and VCF code.	2010-03-04 17:58:01 +00:00
recalibration	Fixed another bug in the original sharding system. Updated integration tests	2010-03-07 15:32:18 +00:00
varianteval	Moving UnifiedGenotyper and VariantAnnotator over to VariantContext system.	2010-03-09 03:41:07 +00:00
DepthOfCoverageIntegrationTest.java	Fix for accumulator exception when running reduce by interval walkers without	2010-03-05 01:04:08 +00:00
PileupWalkerIntegrationTest.java	Now that we changed how deletions are represented, got to update MD5...	2009-12-30 22:00:58 +00:00
PrintReadsWalkerTest.java	adding the initial ROD for Reads support; more convenience methods in ReadMetaDataTracker to come.	2010-03-03 15:56:44 +00:00