Eric Banks 364f1a030b Plumbing added so that the UG engine can handle multiple alleles and they can successfully be genotyped. Alleles that aren't likely are not allowed to be used when assigning genotypes, but otherwise the greedy PL-based approach is what is used. Moved assign genotypes code to UG engine since it has nothing to do with the Exact model. Still have some TODOs in here before I can push this out to everyone.		2011-12-09 14:25:28 -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	Plumbing added so that the UG engine can handle multiple alleles and they can successfully be genotyped. Alleles that aren't likely are not allowed to be used when assigning genotypes, but otherwise the greedy PL-based approach is what is used. Moved assign genotypes code to UG engine since it has nothing to do with the Exact model. Still have some TODOs in here before I can push this out to everyone.	2011-12-09 14:25:28 -05:00
test	The Exact model now computes both the likelihoods and posteriors (in separate arrays); likelihoods are used for assigning genotypes, not the posteriors.	2011-12-09 10:16:44 -05:00