def code_minor(genotypes):
    """Encode the genotypes with respect to the minor allele.

    This confirms that "reference" is the major allele and that "coded" is
    the minor allele.

    In other words, this function can be used to make sure that the genotype
    value is the number of minor alleles for an individual.

    """
    warnings.warn("deprecated: use 'Genotypes.code_minor'", DeprecationWarning)
    _, minor_coded = maf(genotypes)
    if not minor_coded:
        return flip_alleles(genotypes)

    return genotypes