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
..
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	Moving UnifiedGenotyper and VariantAnnotator over to VariantContext system.	2010-03-09 03:41:07 +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