def mito(args):
    """
    %prog mito input.bam chrM chrM.fa

    Identify mitochondrial deletions.
    """
    from jcvi.formats.sam import get_minibam

    p = OptionParser(mito.__doc__)
    p.set_cpus()
    opts, args = p.parse_args(args)

    if len(args) not in 3:
        sys.exit(not p.print_help())

    inputbam, region, chrMfa = args
    minibam = get_minibam(inputbam, region)

    realign = minibam.rsplit(".", 1)[0] + ".realign"
    cmd = "speedseq realign -v -t {}".format(opts.cpus)
    cmd += " -o {} {} {}".format(realign, chrMfa, minibam)
    sh(cmd)
dataset/ETHPy150Open tanghaibao/jcvi/variation/delly.py/mito/operator `!=` -> `not in`