rpoplin b677080858 Initial checkin of the ValidationGenotyper. Not intended to be used by anybody yet. Only here for archival purposes at this point. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4685 348d0f76-0448-11de-a6fe-93d51630548a		2010-11-15 22:33:49 +00:00
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config	Provide a default logger, some config settings, and some doc updates.	2009-04-29 02:06:05 +00:00
src	Initial checkin of the ValidationGenotyper. Not intended to be used by anybody yet. Only here for archival purposes at this point.	2010-11-15 22:33:49 +00:00
test	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	2010-11-15 22:19:22 +00:00