hanna 11cbfcec9c Get rid of backlink from ArgumentDefinitions to ArgumentSources. This will help in the future with multiple ... source -> single definition mapping sets. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2417 348d0f76-0448-11de-a6fe-93d51630548a		2009-12-21 00:39:36 +00:00
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alignment	Help system content for the alignment module.	2009-12-11 16:01:25 +00:00
analyzecovariates	Updated AnalyzeCovariates to extend org.broadinstitute.sting.utils.cmdLine.CommandLineProgram and use the standard argument parsing.	2009-12-11 21:57:18 +00:00
gatk	Get rid of backlink from ArgumentDefinitions to ArgumentSources. This will help in the future with multiple	2009-12-21 00:39:36 +00:00
oneoffprojects	The previous commit broke the build, so this is a temporary patch to get it to compile. ConcordanceTruthTable should use enums (esp. now that all of the concordance variables need to be public), but VariantEval will need to be rewritten soon anyways so I'll just push it off until then.	2009-12-20 02:34:41 +00:00
playground	The previous commit broke the build, so this is a temporary patch to get it to compile. ConcordanceTruthTable should use enums (esp. now that all of the concordance variables need to be public), but VariantEval will need to be rewritten soon anyways so I'll just push it off until then.	2009-12-20 02:34:41 +00:00
utils	Get rid of backlink from ArgumentDefinitions to ArgumentSources. This will help in the future with multiple	2009-12-21 00:39:36 +00:00