delangel ece694d0af Next iteration on new UG framework: ... - Brought over exact AF estimation from branch (which is now dead). Exact model is default in UnifiedGenotyperV2. - Implemented completely new genotyping algorithm given best AF estimate using dynamic programming, which in theory should be better than both greedy search and any HWE-based genotyper. - Integrated and added new Dindel likelihood estimation model. - Corrected annotators that would call readBasePileup: since we can be annotating extended events, best way is to interrogate context for kind of pileup and either readBasePileup or readExtendedEventPileup. All changes above except last one are still in playground since they require more testing. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4396 348d0f76-0448-11de-a6fe-93d51630548a		2010-09-30 21:33:59 +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	Next iteration on new UG framework:	2010-09-30 21:33:59 +00:00
test	Basic unit tests for WalkerManager.	2010-09-30 19:27:41 +00:00