depristo bbd7bec5db 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 ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1387 348d0f76-0448-11de-a6fe-93d51630548a		2009-08-05 22:25:30 +00:00
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genotyper	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
indels	Support for specifying SAMFileReaders and SAMFileWriters as @Arguments directly. *Very*	2009-07-29 16:11:45 +00:00
recalibration	Move the cleaned read injector test from playground to core. Remove CovariateCounterTest's dependency on the CleanedReadInjector. Start doing a bit of cleanup on the CLP's FieldParsers.	2009-07-24 19:44:04 +00:00
PrintReadsWalkerTest.java	Changed dataSources to datasources, to be consistant with the rest of our package names. Also, this makes me champion in the largest check-in contest.	2009-06-11 18:13:22 +00:00