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
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R	Fixing units in queue job report Gantt plots	2011-09-12 09:01:34 -04:00
c	Reinitialize random seed in the bwa bindings from the fixed seed stored in the	2011-07-22 13:41:53 -04:00
chainFiles	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
doc	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
java	Revert "Modified VariantEval FunctionalClass stratification to remove hardcoded GenomicAnnotator keynames"	2011-09-14 10:47:28 -04:00
packages	Removing some old cruft from the packages dir. Updating AnalyzeCovariates to include all Covariates.	2011-09-12 15:09:25 -04:00
perl	Moving these supported perl scripts to public	2011-07-01 17:26:25 -04:00
scala	Changing the VQSR command line syntax back to the parsed tags approach. This cleans up the code and makes sure we won't be parsing the same rod file multiple times. I've tried to update the appropriate qscripts.	2011-09-12 12:17:43 -04:00
testdata	GZIP VCF for testing	2011-08-19 09:05:39 -04:00