def mpileup(args):
    p = OptionParser(mpileup.__doc__)
    opts, args = p.parse_args(args)

    if len(args) < 2:
        sys.exit(not p.print_help())

    prefix, ref = args[0:2]
    bams = args[2:]
    cmd = "samtools mpileup -P ILLUMINA -E -ugD -r {0}"
    cmd += " -f {0} {1}".format(ref, " ".join(bams))
    fmd = "bcftools view -cvg -"
    seqids = list(Fasta(ref).iterkeys_ordered())
    for s in seqids:
        outfile = prefix + ".{0}.vcf".format(s)
        print cmd.format(s), "|", fmd, ">", outfile
Remove tiles that were in coverage but have no data. Also remove
dataset/ETHPy150Open tanghaibao/jcvi/variation/snp.py/mpileup--crossover with--dataset/ETHPy150Open GeoscienceAustralia/agdc/src/abstract_ingester/tile_contents.py/TileContents.remove