Mauricio Carneiro 6e6f0f10e1 BaseQualityScoreRecalibration walker (bqsr v2) first commit includes ... * Adding the context covariate standard in both modes (including old CountCovariates) with parameters * Updating all covariates and modules to use GATKSAMRecord throughout the code. * BQSR now processes indels in the pileup (but doesn't do anything with them yet)		2012-02-06 17:38:29 -05:00
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config	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
src	BaseQualityScoreRecalibration walker (bqsr v2) first commit includes	2012-02-06 17:38:29 -05:00
test	make the size of a GenomeLoc int instead of long	2012-02-03 17:12:42 -05:00