viterbi_allele function

Viterbi algorithm for allele HMM

viterbi_allele(hmm)

Arguments

• hmm: HMM object; expect variables x (allele depth), d (total depth), logPi (log transition prob matrix), delta (prior for each state), alpha (alpha for each state), beta (beta for each state), states (states), p_s (phase switch probs)

Returns

character vector Decoded states