hanna a4b69d0adf Misc bug fixes. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2501 348d0f76-0448-11de-a6fe-93d51630548a		2010-01-05 14:48:19 +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	Misc bug fixes.	2010-01-05 14:48:19 +00:00
test/org/broadinstitute/sting	CycleCovariate is now one-based so that 0 and -0 don't collide with each other. Solid recal modes now only change the inconsistent base and the previous base (along the direction of the read) instead of both the bases before and after. Removed estimatedNumberOfBins from the Covariate interface because it wasn't being used.	2010-01-04 20:52:15 +00:00