Sometimes, get_ancestral_haplotypes returns ancestral haplotypes that are non-ancestral at variable sites (e.g. in simulations where the recombination rate is high enough and the mutation rate is low enough), so that the haplotypes contain only NONCOPY values. They should be removed before returning the genotype matrix.
Sometimes,
get_ancestral_haplotypesreturns ancestral haplotypes that are non-ancestral at variable sites (e.g. in simulations where the recombination rate is high enough and the mutation rate is low enough), so that the haplotypes contain onlyNONCOPYvalues. They should be removed before returning the genotype matrix.