hanna 408f6f3dee Refactoring of prior commit: better handling of unnamed package within the help system. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2297 348d0f76-0448-11de-a6fe-93d51630548a		2009-12-09 20:12:35 +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	Refactoring of prior commit: better handling of unnamed package within the help system.	2009-12-09 20:12:35 +00:00
oneoffprojects	Stage 1 of massive Variation/Genotype refactoring.	2009-12-06 03:12:41 +00:00
playground	-Minor fix in UG for all-bases mode	2009-12-09 03:49:10 +00:00
utils	UG now outputs the FORMAT header fields when there's genotype data.	2009-12-09 16:31:07 +00:00