def filtervcf(args):
    """
    %prog filtervcf NA12878.hg38.vcf.gz

    Filter lobSTR VCF using script shipped in lobSTR. Input file can be a list
    of vcf files.
    """
    p = OptionParser(filtervcf.__doc__)
    p.set_home("lobstr", default="/mnt/software/lobSTR")
    p.set_aws_opts(store="hli-mv-data-science/htang/str")
    p.set_cpus()
    opts, args = p.parse_args(args)

    if len(args) != 1:
        sys.exit(not p.print_help())

    samples, = args
    lhome = opts.lobstr_home
    store = opts.output_path

    if samples.endswith(".vcf") or samples.endswith(".vcf.gz"):
        vcffiles = [samples]
    else:
        vcffiles = [x.strip() for x in must_open(samples)]

    vcffiles = [x for x in vcffiles if ".filtered." not in x]

    run_args = [(x, lhome, x.startswith("s3://") and store) for x in vcffiles]
    cpus = min(opts.cpus, len(run_args))
    p = Pool(processes=cpus)
    for res in p.map_async(run_filter, run_args).get():
        continue
dataset/ETHPy150Open tanghaibao/jcvi/variation/str.py/filtervcf/original