Modify set_emission_probabilities to take num_alleles as a required parameter rather than a variable calculated from reference_panel and query. The functions forwards, backwards, viterbi, and path_loglik have to be modified accordingly. The tests have to be modified as well. The result of this is that either form of reference panel and query (as haplotypes or genotypes encoded as allele dosages) can be passed to the API functions without needing to pass in both forms when running the diploid implementations.
Modify
set_emission_probabilitiesto takenum_allelesas a required parameter rather than a variable calculated fromreference_panelandquery. The functionsforwards,backwards,viterbi, andpath_loglikhave to be modified accordingly. The tests have to be modified as well. The result of this is that either form of reference panel and query (as haplotypes or genotypes encoded as allele dosages) can be passed to the API functions without needing to pass in both forms when running the diploid implementations.