David Roazen 3db457ed01 Revert "Modified VariantEval FunctionalClass stratification to remove hardcoded GenomicAnnotator keynames" ... After discussing this with Mark, it seems clear that the old version of the VariantEval FunctionalClass stratification is preferable to this version. By reverting, we maintain backwards compatibility with legacy output files from the old GenomicAnnotator, and can add SnpEff support later without breaking that backwards compatibility. This reverts commit b44acd1abd9ab6eec37111a19fa797f9e2ca3326.		2011-09-14 10:47:28 -04:00
..
arguments	Removed -B support. Now explodes with error if -B provided.	2011-08-16 16:13:47 -04:00
datasources	Cleanup of codec locations. No more dbSNPHelper	2011-08-18 10:02:46 -04:00
executive	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
filters	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
iterators	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
refdata	Dynamic typing of vcf.gz files	2011-08-19 09:05:11 -04:00
report	GATKReport v0.2:	2011-08-03 00:24:47 -04:00
traversals	BugFix for unit test	2011-09-07 14:54:10 -04:00
walkers	Revert "Modified VariantEval FunctionalClass stratification to remove hardcoded GenomicAnnotator keynames"	2011-09-14 10:47:28 -04:00
EngineFeaturesIntegrationTest.java	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
GenomeAnalysisEngineUnitTest.java	Fixing broken paths to the testdata directory throughout the codebase.	2011-06-29 17:36:47 -04:00
WalkerManagerUnitTest.java	Moving more tools over to use the standard VC arg collection. Also, while I'm in there, I removed all of the empty references to @Requires given that it's no longer relevant.	2011-08-10 12:20:18 -04:00