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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alignment	Reinitialize random seed in the bwa bindings from the fixed seed stored in the	2011-07-22 13:41:53 -04:00
commandline	Bugfix for file that must not exist on disk	2011-08-29 17:00:10 -04:00
gatk	Revert "Modified VariantEval FunctionalClass stratification to remove hardcoded GenomicAnnotator keynames"	2011-09-14 10:47:28 -04:00
jna	Avoid segfaults due to out of date and possibly abandonded LSF DRMAA implementation when use'ing LSF instead of .combined_LSF_SGE	2011-08-23 23:49:36 -04:00
pipeline	Cleanup of the utils.broad package.	2011-07-01 20:47:03 -04:00
utils	SnpEff 2.0.2 support	2011-09-14 07:09:47 -04:00
BaseTest.java	Fixing syntax of BQSR and UG performance tests.	2011-08-11 17:04:09 -04:00
MD5DB.java	Go for global integrationtest path first, if possible.	2011-07-26 17:35:30 -04:00
StingTextReporter.java	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
WalkerTest.java	Walker test system refactoring. All MD5DB related functions are now in MD5DB.java.	2011-07-18 10:46:01 -04:00