ebanks 5fab934f4e - moved the reference maker to its own directory ... - added first version of a more complicated reference maker which takes in RODs and creates an alternative reference based on the variants (indels and/or SNPs) git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1409 348d0f76-0448-11de-a6fe-93d51630548a		2009-08-11 18:01:06 +00:00
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gatk	fixing a bug where reads in overlapping interval based locus traversals could get assigned to only one of two the regions	2009-08-11 17:50:16 +00:00
playground	- moved the reference maker to its own directory	2009-08-11 18:01:06 +00:00
secondarybase	Cleanup...deprecate FastaSequenceFile2 in favor of IndexedFastaSequenceFile or ReferenceSequenceFile from Picard, depending on the application.	2009-07-08 18:49:08 +00:00
utils	Continuing cleanup of SSG. GenotypeLikelihoods now have extensive testing routines. DiploidGenotype supports het, homref, etc calculations. SSG has been cleaned up to remove old garbage functionality. Also now supports output to standard output by simply omitting varout	2009-08-05 22:25:30 +00:00