David Roazen d9ea764611 SnpEff annotator now adds OriginalSnpEffVersion and OriginalSnpEffCmd lines to the header of the VCF output file. ... This change is urgently required for production, which is why it's going into Stable+Unstable instead of just Unstable. The keys for the SnpEff version and command header lines in the VCF file output by VariantAnnotator (OriginalSnpEffVersion and OriginalSnpEffCmd) are intentionally different from the keys for those same lines in the SnpEff output file (SnpEffVersion and SnpEffCmd), so that output files from VariantAnnotator won't be confused with output files from SnpEff itself.		2011-09-20 16:30:55 -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	SnpEff annotator now adds OriginalSnpEffVersion and OriginalSnpEffCmd lines to the header of the VCF output file.	2011-09-20 16:30:55 -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	Update to the bindings for liftOverVCF.pl (to -V from -B)	2011-09-15 15:33:09 -04:00
scala	Fixed issue reported by chartl where cloned functions lost tags on @Inputs.	2011-09-16 12:46:07 -04:00
testdata	GZIP VCF for testing	2011-08-19 09:05:39 -04:00