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
..
net/sf	Removed annoying FastaSequenceIndexBuilderProgressListener infrastructure that was just a boolean switch on whether to print progress or not.	2011-07-27 22:06:23 -04:00
org/broadinstitute/sting	Modified VariantEval FunctionalClass stratification to remove hardcoded GenomicAnnotator keynames	2011-09-14 07:09:47 -04:00