Mauricio Carneiro d7367c152a Fixing 'revert' when not realigning ... RevertSam was reverting the alignment information and that was screwing up the pipeline if you didn't want to run it with BWA. Fixed.		2011-10-20 17:01:54 -04:00
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examples	Fixed issue reported by chartl where cloned functions lost tags on @Inputs.	2011-09-16 12:46:07 -04:00
lib	…
DataProcessingPipeline.scala	Fixing 'revert' when not realigning	2011-10-20 17:01:54 -04:00
GATKResourcesBundle.scala	…
MethodsDevelopmentCallingPipeline.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
PacbioProcessingPipeline.scala	BLASR BAMs and new BWA parameters	2011-08-24 17:04:07 -04:00
StandardVariantEvaluation.scala	…