hanna d75d3a361a Clean up some of the walker help output based on additional experience and ... feedback received. Also, add a flag to build.xml to disable generation of docs on demand (use ant -Ddisable.doc=true to disable docs). git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2284 348d0f76-0448-11de-a6fe-93d51630548a		2009-12-07 21:33:11 +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	Clean up some of the walker help output based on additional experience and	2009-12-07 21:33:11 +00:00
test/org/broadinstitute/sting	Added --solid_recal_mode argument to experiment with different ways of dealing with solid reference bias. Currently the default option is DO_NOTHING which means use the same behavior as the old recalibrator. Eventually the new methods in RecalDataManager will be moved over to a SolidUtils class. Added transition and transversion methods to BaseUtils that work like simpleComplement, used with the color space in my solid methods. Also, initial check-in of HomopolymerCovariate.	2009-12-07 14:26:27 +00:00