ebanks 54c61c663c -Cleanup of the Joint Estimation code ... -Don't print verbose/debugging output to logger, but instead specify a file in the argument collection (and then we only need to print conditionally) git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1899 348d0f76-0448-11de-a6fe-93d51630548a		2009-10-22 15:25:29 +00:00
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alignment	Read uints directly into longs.	2009-10-15 16:15:11 +00:00
gatk	-Cleanup of the Joint Estimation code	2009-10-22 15:25:29 +00:00
playground	Base transition table now forces epsilon/3 (three-state) model for the unified genotyper. Verified to be identical with changing the default model to being epsilon/3. This of course changes the observed counts, so the integration test has been updated.	2009-10-21 21:18:26 +00:00
secondarybase	Rev'ing Picard, which includes the update to get all the reads in the query region (GSA-173). With it come a bunch of fixes, including retiring the FourBaseRecaller code, and updated md5 for some walker tests.	2009-09-30 20:37:59 +00:00
utils	Major code refactoring:	2009-10-20 14:58:04 +00:00