Christopher Hartl 365f1d2429 hmk123's error on the forum came from the reference context occasionally lacking bases needed for validating the reference bases in the variant context. (no @Window for VariantsToBinaryPed). This bugfix adresses this and other minor items: ... 1) ValidateVariants removed in favor of direct validation VariantContexts. Integration test added to test broken contexts. 2) Enabling indel and SV output. Still bi-allelic sites only. Integration tests added for these cases. 3) Found a bug where GQ recalculation (if a genotype has PLs but no GQ) would only happen for flipped encoding. Fixed. Integration test added.		2012-09-29 00:55:31 -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	hmk123's error on the forum came from the reference context occasionally lacking bases needed for validating the reference bases in the variant context. (no @Window for VariantsToBinaryPed). This bugfix adresses this and other minor items:	2012-09-29 00:55:31 -04:00
test	hmk123's error on the forum came from the reference context occasionally lacking bases needed for validating the reference bases in the variant context. (no @Window for VariantsToBinaryPed). This bugfix adresses this and other minor items:	2012-09-29 00:55:31 -04:00