David Roazen e0c8c0ddcb Modified VariantEval FunctionalClass stratification to remove hardcoded GenomicAnnotator keynames ... This is a temporary and hopefully short-lived solution. I've modified the FunctionalClass stratification to stratify by effect impact as defined by SnpEff annotations (high, moderate, and low impact) rather than by the silent/missense/nonsense categories. If we want to bring back the silent/missense/nonsense stratification, we should probably take the approach of asking the SnpEff author to add it as a feature to SnpEff rather than coding it ourselves, since the whole point of moving to SnpEff was to outsource genomic annotation.		2011-09-14 07:09:47 -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	Modified VariantEval FunctionalClass stratification to remove hardcoded GenomicAnnotator keynames	2011-09-14 07:09:47 -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jna	Avoid segfaults due to out of date and possibly abandonded LSF DRMAA implementation when use'ing LSF instead of .combined_LSF_SGE	2011-08-23 23:49:36 -04:00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