aaron 33dcfc858d updates to the paper genotyper based on Mark's comments. There's still more work to do, including more testing. ... Also a 250% improvement in the getBases() and getQuals() of BasicPileup, which was nearly all of the runtime for the genotyper (using primitives instead of objects when possible). git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2097 348d0f76-0448-11de-a6fe-93d51630548a		2009-11-19 23:06:49 +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/org/broadinstitute/sting	updates to the paper genotyper based on Mark's comments. There's still more work to do, including more testing.	2009-11-19 23:06:49 +00:00
test/org/broadinstitute/sting	Added the old recalibrator integration tests to the refactored recalibrator sitting in playground.	2009-11-19 22:43:28 +00:00