ebanks 8b087305f3 Added back the MQ0 annotation - however, it's not yet standard (since mq0 reads are filtered out by default in the genotyper). But it'll work when using the Annotator as a standalone. ... While I'm at it, change getPileup to getBasePileup to remove all of the deprecation warnings. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2502 348d0f76-0448-11de-a6fe-93d51630548a		2010-01-05 17:07:19 +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	Added back the MQ0 annotation - however, it's not yet standard (since mq0 reads are filtered out by default in the genotyper). But it'll work when using the Annotator as a standalone.	2010-01-05 17:07:19 +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