gatk-3.8

Author	SHA1	Message	Date
aaron	b401929e41	incremental clean-up and changes for VariantEval, moved DiploidGenotype to a better home, and fixed a spelling error. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1624 348d0f76-0448-11de-a6fe-93d51630548a	2009-09-15 04:48:42 +00:00
aaron	e03fccb223	Changes to switch Variant Eval over to the new Variation system. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1611 348d0f76-0448-11de-a6fe-93d51630548a	2009-09-14 05:34:33 +00:00
aaron	bca894ebce	Adding the intial changes for the new Genotyping interface. The bullet points are: - SSG is much simpler now - GeliText has been added as a GenotypeWriter - AlleleFrequencyWalker will be deleted when I untangle the AlleleMetric's dependance on it - GenotypeLikelihoods now implements GenotypeGenerator, but could still use cleanup There is still a lot more work to do, but this is a good initial check-in. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1335 348d0f76-0448-11de-a6fe-93d51630548a	2009-07-29 19:43:59 +00:00
aaron	b4adb5133a	GLF rod as a AllelicVariant object. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1282 348d0f76-0448-11de-a6fe-93d51630548a	2009-07-21 00:55:52 +00:00
aaron	9ecb3e0015	adding GLFRods with tests and some other code changes git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1251 348d0f76-0448-11de-a6fe-93d51630548a	2009-07-15 15:30:19 +00:00