Eric Banks 35fc2e13c3 Using the new PL cache, fix a bug: when only a subset of the genotyped alleles are used for assigning genotypes (because the exact model determined that they weren't all real) the PLs need to be adjusted to reflect this. While fixing this I discovered that the integration tests are busted because ref calls (ALT=.) were getting annotated with PLs, which makes no sense at all.		2011-12-14 15:31:09 -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	Using the new PL cache, fix a bug: when only a subset of the genotyped alleles are used for assigning genotypes (because the exact model determined that they weren't all real) the PLs need to be adjusted to reflect this. While fixing this I discovered that the integration tests are busted because ref calls (ALT=.) were getting annotated with PLs, which makes no sense at all.	2011-12-14 15:31:09 -05:00
test	Optimization: cache up front the PL index to the pair of alleles it represents for all possible numbers of alternate alleles.	2011-12-14 13:38:20 -05:00