ebanks a5f75cbfd4 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. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2413 348d0f76-0448-11de-a6fe-93d51630548a		2009-12-20 02:34:41 +00:00
..
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	PooledConcordance calculations have been reformatted and bugs fixed. Now properly handles monomorphic sites. Also works with -G option now, correctly	2009-12-19 23:22:36 +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	Changed the GLF record to store it's contig name and position in each record instead of in the Reader. Integration tests all stay the same.	2009-12-18 22:54:56 +00:00