chartl 77863d4940 @PowerBelowFrequency ... + Changes to doc @ BasicPoolVariantAnalysis + use char rather than ReferenceContext + calculate # alleles @ PooledFrequencyAnalysis + breakdown of call metrics by estimated number of alleles in pool @ VariantEvalWalker + add PooledFrequencyAnalysis to analysis set @ PooledGenotypeConcordance + correctly calculate maximal allele frequency for output git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1893 348d0f76-0448-11de-a6fe-93d51630548a		2009-10-21 15:17:11 +00:00
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config	Provide a default logger, some config settings, and some doc updates.	2009-04-29 02:06:05 +00:00
src/org/broadinstitute/sting	@PowerBelowFrequency	2009-10-21 15:17:11 +00:00
test/org/broadinstitute/sting	Enabling correct high-performance ROD walker and moved VariantEval over to it. Performance improvements in variantEval in general. See wiki for full description	2009-10-20 23:31:13 +00:00