hanna d1815f3559 More documentation for walkers that I'm familiar with in the collection of core walkers. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2328 348d0f76-0448-11de-a6fe-93d51630548a		2009-12-11 18:02:33 +00:00
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alignment	Help system content for the alignment module.	2009-12-11 16:01:25 +00:00
analyzecovariates	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
gatk	More documentation for walkers that I'm familiar with in the collection of core walkers.	2009-12-11 18:02:33 +00:00
oneoffprojects	Stage 1 of massive Variation/Genotype refactoring.	2009-12-06 03:12:41 +00:00
playground	Punch up the help documentation for CombineDuplicates.	2009-12-11 17:09:35 +00:00
utils	A few improvements to pooled concordance calcluations. Now will show you FN with the -V option. BasicGenotype now prints out a reasonable representaiton wiwth toString	2009-12-10 23:09:10 +00:00