rpoplin 1e7ddd2d9f Added a validateOldRecalibrator option to CovariateCounterWalker which reorders the output to match the old recalibrator exactly. This facilitates direct comparison of output. Changed the -cov argument slightly to require the user to specify both ReadGroupCovariate and QualityScoreCovariate to make it more clear to the user which covariates are being used. Some speed up improvements throughout. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2010 348d0f76-0448-11de-a6fe-93d51630548a		2009-11-10 15:55:56 +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	Added a validateOldRecalibrator option to CovariateCounterWalker which reorders the output to match the old recalibrator exactly. This facilitates direct comparison of output. Changed the -cov argument slightly to require the user to specify both ReadGroupCovariate and QualityScoreCovariate to make it more clear to the user which covariates are being used. Some speed up improvements throughout.	2009-11-10 15:55:56 +00:00
test/org/broadinstitute/sting	VariantFilteration now accepts a VCF rod in addition to an input geli. It will then annotate this VCF file with filtering information in the INFO field too. --OnlyAnnotate will not write in filtering output	2009-11-10 13:24:58 +00:00