3 Commits (586d3f05d9a65894d7fd1ae0a7df91619a793ed9)

Author	SHA1	Message	Date
depristo	ef2f6d90d2	VQSR now operates on LOD scores in the INFO field directly, and doesn't adjust the QUAL field. New format for tranches file uses LOD score. Old file format no longer supported. log10sumlog10() function, a very useful utility in MathUtils. No more ExtendedPileupElement! Robust math calculations in GMM so that no infinities are generated! HaplotypeScore refactored to enable use of filtered context. Not yet enabled... InferredContext getDouble and getInteger arguments now parse values from Strings if necessary ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4684 348d0f76-0448-11de-a6fe-93d51630548a	2010-11-15 22:19:22 +00:00
depristo	ac52b64b77	correct test data ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4665 348d0f76-0448-11de-a6fe-93d51630548a	2010-11-13 22:17:38 +00:00
depristo	c5f8c4dd0d	VariantEval test for tranches file, plus cutting over VE to use the generic Tranches framework ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4656 348d0f76-0448-11de-a6fe-93d51630548a	2010-11-12 13:52:40 +00:00