Presently, make_compatible_genotypes has the option acgt_alleles. When acgt_alleles is set to False (default), it remaps all the genotypes in ds2 so that its remapped genotypes have the same allele lists as ds1. When that option is set to True, it remaps all the genotypes in both ds2 and ds1 to ACGT (so remap_genotypes is run twice, which can be wasteful if different ds2 is remapped to the same ds1, e.g., lshmm-imputed and BEAGLE-imputed genotypes to reference panel genotypes). This function should be refactored into two separate functions, so that remap_genotypes is run once.
Presently,
make_compatible_genotypeshas the optionacgt_alleles. Whenacgt_allelesis set toFalse(default), it remaps all the genotypes inds2so that its remapped genotypes have the same allele lists asds1. When that option is set toTrue, it remaps all the genotypes in bothds2andds1to ACGT (soremap_genotypesis run twice, which can be wasteful if differentds2is remapped to the sameds1, e.g., lshmm-imputed and BEAGLE-imputed genotypes to reference panel genotypes). This function should be refactored into two separate functions, so thatremap_genotypesis run once.