depristo 5af4bb628b Intermediate checking before code reorganization. Full blown support for empirical transition probs in SSG for all platforms. Support for defaultPlatform arg in SSG. Renaming classes for final cleanup ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1479 348d0f76-0448-11de-a6fe-93d51630548a		2009-08-30 17:34:43 +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	Intermediate checking before code reorganization. Full blown support for empirical transition probs in SSG for all platforms. Support for defaultPlatform arg in SSG. Renaming classes for final cleanup	2009-08-30 17:34:43 +00:00
test/org/broadinstitute/sting	Support for original quality scores OQ flag. pQ flag in TableRecalibation to preserve quality scores below a threshold (defaulting to 5)	2009-08-28 14:14:21 +00:00