Joel Thibault c255dd5917 Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable		2012-05-01 16:10:38 -04:00
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config	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
src	Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable	2012-05-01 16:10:38 -04:00
test	Adding an option to SelectVariants which allows the user to re-genotype through the exact model (if PLs are present) the samples in order to recalculate the QUAL and genotypes. This is really the correct way to select a subset of samples, especially when originally called from low coverage data. Also added integration test to cover this case.	2012-05-01 14:58:06 -04:00