depristo df4fd498c5 Improvements and bug fixes galore. (1) Now properly handles Q0 bases, filtering them out, you can disable this if you need to (2) support for three-state base probabilities (see email), which is disabled by default (still experimental) but appears to be more emppowered to detect variants (see email too) ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1327 348d0f76-0448-11de-a6fe-93d51630548a		2009-07-28 13:21:38 +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	Improvements and bug fixes galore. (1) Now properly handles Q0 bases, filtering them out, you can disable this if you need to (2) support for three-state base probabilities (see email), which is disabled by default (still experimental) but appears to be more emppowered to detect variants (see email too)	2009-07-28 13:21:38 +00:00
test/org/broadinstitute/sting	Move the cleaned read injector test from playground to core. Remove CovariateCounterTest's dependency on the CleanedReadInjector. Start doing a bit of cleanup on the CLP's FieldParsers.	2009-07-24 19:44:04 +00:00