Eric Banks 41f3da75d7 Implementation in VE was confusing 'variant' status vs. 'polymorphic' status. This led to issues because we now match types of eval and comp; specifically, subsetting a VC to a monomorphic sample can't change the 'variant' status of the VC (it's still a variant site or otherwise we'll never match the comps, which breaks GenotypeConcordance). CountVariants really got this wrong. Fixed. VE now passes all integration tests.		2011-08-12 02:22:44 -04:00
..
annotator	Better interface for getting RodBindings to the VariantAnnotatorEngine and its annotations: pass around an AnnotatorCompatibleWalker (interface) object. Updating VA to use the new rod system.	2011-08-10 22:43:08 -04:00
beagle	Thanks to Mark for agreeing to transition from 'variants' back to 'variant'. I think I got them all but I've been jumping all around the code, so there might be a straggler or two.	2011-08-09 12:04:55 -04:00
coverage	Moving more tools over to the new rod system	2011-08-10 13:42:35 -04:00
diffengine	GATKReport v0.2:	2011-08-03 00:24:47 -04:00
fasta	More updates to be consistent with the new rod syntax.	2011-08-09 10:11:37 -04:00
filters	Thanks to Mark for agreeing to transition from 'variants' back to 'variant'. I think I got them all but I've been jumping all around the code, so there might be a straggler or two.	2011-08-09 12:04:55 -04:00
genotyper	Fixing syntax of BQSR and UG performance tests.	2011-08-11 17:04:09 -04:00
indels	Moving more tools over to the new rod system	2011-08-10 13:42:35 -04:00
phasing	Moving more tools over to the new rod system	2011-08-10 13:42:35 -04:00
qc	Thanks to Mark for agreeing to transition from 'variants' back to 'variant'. I think I got them all but I've been jumping all around the code, so there might be a straggler or two.	2011-08-09 12:04:55 -04:00
recalibration	Fixing syntax of BQSR and UG performance tests.	2011-08-11 17:04:09 -04:00
validation	Continuing progress towards RodBinding 1.0	2011-08-03 17:19:28 -04:00
varianteval	Implementation in VE was confusing 'variant' status vs. 'polymorphic' status. This led to issues because we now match types of eval and comp; specifically, subsetting a VC to a monomorphic sample can't change the 'variant' status of the VC (it's still a variant site or otherwise we'll never match the comps, which breaks GenotypeConcordance). CountVariants really got this wrong. Fixed. VE now passes all integration tests.	2011-08-12 02:22:44 -04:00
variantrecalibration	Updating VQSR for new RodBinding syntax. Cleaning up indel specific parts of VQSR.	2011-08-10 10:20:37 -04:00
variantutils	More tools moved over. Fixed the VariantContextIntegrationTest which was not useful because the md5s were all removed. In the future, instead of removing md5s (putting it in 'parameterization' mode), you should instead use @Test{enabled=false} since it's easier to track.	2011-08-10 14:24:40 -04:00
BAQIntegrationTest.java	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
ClipReadsWalkersIntegrationTest.java	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
PileupWalkerIntegrationTest.java	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
PrintReadsIntegrationTest.java	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
PrintReadsWalkerUnitTest.java	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00