ebanks d549347f25 Refactored GenotypeLikelihoods to use an underlying 4-base model. ... It needs to be modified a bit and then hooked up to a pooled model, but that is now possible. At this point, there is no difference to the Unified Genotyper. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1978 348d0f76-0448-11de-a6fe-93d51630548a		2009-11-05 21:59:25 +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/org/broadinstitute/sting	Refactored GenotypeLikelihoods to use an underlying 4-base model.	2009-11-05 21:59:25 +00:00
test/org/broadinstitute/sting	a fix for a bug Andrey discovered: in read-based interval traversals we're dupplicating reads in rare cases. The problem was that to accomidate a bug in SAM JDK indexing, we were forced to add one to the stop of our QueryOverlapping() calls to ensure we always got all of the overlapping reads.	2009-11-05 05:26:33 +00:00