Convert GATK CNV calls seg output to a VCF line.

def _seg_to_vcf(vals):
    """Convert GATK CNV calls seg output to a VCF line.
    """
    call_to_cn = {"+": 3, "-": 1}
    call_to_type = {"+": "DUP", "-": "DEL"}
    if vals["CALL"] not in ["0"]:
        info = ["FOLD_CHANGE_LOG=%s" % vals["MEAN_LOG2_COPY_RATIO"],
                "PROBES=%s" % vals["NUM_POINTS_COPY_RATIO"],
                "SVTYPE=%s" % call_to_type[vals["CALL"]],
                "SVLEN=%s" % (int(vals["END"]) - int(vals["START"])),
                "END=%s" % vals["END"],
                "CN=%s" % call_to_cn[vals["CALL"]]]
        return [vals["CONTIG"], vals["START"], ".", "N", "<%s>" % call_to_type[vals["CALL"]], ".",
                ".", ";".join(info), "GT", "0/1"]