Add update ##contig lines to VCF header, required for bcftools/GATK compatibility.

def add_contig_to_header_cl(ref_file, out_file):
    """Add update ##contig lines to VCF header, required for bcftools/GATK compatibility.
    """
    header_file = "%s-contig_header.txt" % utils.splitext_plus(out_file)[0]
    with open(header_file, "w") as out_handle:
        for region in ref.file_contigs(ref_file, {}):
            out_handle.write("##contig=<ID=%s,length=%s>\n" % (region.name, region.size))
    return ("grep -v ^##contig | bcftools annotate -h %s" % header_file)