This PR adds a second likelihood calculation that incorporates how all of the reads "cover" a pair of alleles. The distribution is two independent multinomials and odd stretches where no reads align are unlikely. This "regularizes" the previous maximum-emission PHMM likelihood.
This PR adds a second likelihood calculation that incorporates how all of the reads "cover" a pair of alleles. The distribution is two independent multinomials and odd stretches where no reads align are unlikely. This "regularizes" the previous maximum-emission PHMM likelihood.