Ensure a pre-aligned BAM file matches the expected reference genome.

def _check_bam_contigs(in_bam, ref_file, config):
    """Ensure a pre-aligned BAM file matches the expected reference genome.
    """
    # GATK allows chromosome M to be in multiple locations, skip checking it
    allowed_outoforder = ["chrM", "MT"]
    ref_contigs = [c.name for c in ref.file_contigs(ref_file, config)]
    with pysam.Samfile(in_bam, "rb") as bamfile:
        bam_contigs = [c["SN"] for c in bamfile.header["SQ"]]
    extra_bcs = [x for x in bam_contigs if x not in ref_contigs]
    extra_rcs = [x for x in ref_contigs if x not in bam_contigs]
    problems = []
    warnings = []
    for bc, rc in zip_longest([x for x in bam_contigs if (x not in extra_bcs and
                                                                     x not in allowed_outoforder)],
                                         [x for x in ref_contigs if (x not in extra_rcs and
                                                                     x not in allowed_outoforder)]):
        if bc != rc:
            if bc and rc:
                problems.append("Reference mismatch. BAM: %s Reference: %s" % (bc, rc))
            elif bc:
                warnings.append("Extra BAM chromosomes: %s" % bc)
            elif rc:
                warnings.append("Extra reference chromosomes: %s" % rc)
    for bc in extra_bcs:
        warnings.append("Extra BAM chromosomes: %s" % bc)
    for rc in extra_rcs:
        warnings.append("Extra reference chromosomes: %s" % rc)
    if problems:
        raise ValueError("Unexpected order, name or contig mismatches between input BAM and reference file:\n%s\n"
                         "Setting `bam_clean: remove_extracontigs` in the configuration can often fix this issue."
                         % "\n".join(problems))
    if warnings:
        print("*** Potential problems in input BAM compared to reference:\n%s\n" %
              "\n".join(warnings))