aaron f64a4c66ac some tweaks for the GATK paper genotyper to better work with shared memory parallelization, added documentation changes for Matt's new help system. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2319 348d0f76-0448-11de-a6fe-93d51630548a		2009-12-10 22:33:51 +00:00
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alignment	Convenience changes. If no -BWT option is specified, pull the BWT location from the reference.	2009-11-23 22:46:05 +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	some tweaks for the GATK paper genotyper to better work with shared memory parallelization, added documentation changes for Matt's new help system.	2009-12-10 22:33:51 +00:00
oneoffprojects	Stage 1 of massive Variation/Genotype refactoring.	2009-12-06 03:12:41 +00:00
playground	some tweaks for the GATK paper genotyper to better work with shared memory parallelization, added documentation changes for Matt's new help system.	2009-12-10 22:33:51 +00:00
utils	Fixed deletion depth calculation plus mis-spelling in ReadBackedPileup method.	2009-12-10 21:11:42 +00:00