Ryan Poplin 35bb55f562 Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable		2012-04-22 13:23:36 -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	2012-04-22 13:23:36 -04:00
test	If we are subsetting alleles in the UG (either because there were too many or because some were not polymorphic), then we may need to trim the alleles (because the original VariantContext may have had to pad at the end). Thanks to Ryan for reporting this. Only one of the integration tests had even partially covered this case, so I added one that did.	2012-04-20 17:00:05 -04:00