depristo 9876645a5d Now drives the walker by reference, not by reads, so we see even loci with no reads. This allows us to accurately calculate the true total callable area ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2720 348d0f76-0448-11de-a6fe-93d51630548a		2010-01-28 11:12:46 +00:00
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alignment	Misc bug fixes.	2010-01-05 14:48:19 +00:00
analyzecovariates	Initial checkin of skeleton code for AnalyzeAnnotations	2010-01-15 21:52:34 +00:00
gatk	Now drives the walker by reference, not by reads, so we see even loci with no reads. This allows us to accurately calculate the true total callable area	2010-01-28 11:12:46 +00:00
oneoffprojects	V3 of VariantContext. Support for Genotypes and NO_CALL alleles. QUAL fields fully implemented. Can parse VCF records and dbSNP. More complete validation. Detailed testing routines for VariantContext and Allele.	2010-01-28 04:10:16 +00:00
playground	Added the ability to filter out variant (not truth) calls based on read depth. Using -NLD 5 will not update concordant counts for calls with 0, 1, 2, 3, or 4 reads supporting them. Not to be used with VCF files that do not have DP in the format field.	2010-01-27 23:28:04 +00:00
utils	New realigner now completely uses bytes, plus misc fixes. Still not ready for use.	2010-01-28 04:17:20 +00:00