def chrom_sorted(in_chroms):
    """
    Sort a list of chromosomes in the order 1..22, X, Y, M, <others in alphabetical order>.

    :param list in_chroms: Input chromosomes
    :return: Sorted chromosomes
    :rtype: list[str]
    """
    in_chroms.sort()
    canonicals = [str(c) for c in range(1, 23)] + ['X', 'Y', 'M', 'MT']
    canonical_chr = ['chr' + c for c in canonicals]
    out_chroms_dict = {
        'can': [c for c in in_chroms if c in canonicals],
        'can_chr': [c for c in in_chroms if c in canonical_chr],
        'others': [c for c in in_chroms if c not in canonicals + canonical_chr]}

    assert not (out_chroms_dict['can'] and out_chroms_dict['can_chr'])
    assert not ('M' in out_chroms_dict['can']and 'MT' in out_chroms_dict['can'])
    assert not ('chrM' in out_chroms_dict['can_chr'] and 'chrMT' in out_chroms_dict['can_chr'])

    out_chroms_dict['can'] = canonical_chrom_sorted(out_chroms_dict['can'])
    out_chroms_dict['can_chr'] = canonical_chrom_sorted(out_chroms_dict['can_chr'])

    out_chroms = out_chroms_dict['can'] or out_chroms_dict['can_chr']
    out_chroms.extend(out_chroms_dict['others'])
    return out_chroms
Sort a list of chromosomes in the order 1..22, X, Y, M, <others in alphabetical order>.

    :param list in_chroms: Input chromosomes
    :return: Sorted chromosomes
    :rtype: list[str]