def bam(args):
    """
    %prog snp input.gsnap ref.fasta

    Convert GSNAP output to BAM.
    """
    from jcvi.formats.sizes import Sizes
    from jcvi.formats.sam import index

    p = OptionParser(bam.__doc__)
    p.set_home("eddyyeh")
    p.set_cpus()
    opts, args = p.parse_args(args)

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

    gsnapfile, fastafile = args
    EYHOME = opts.eddyyeh_home
    pf = gsnapfile.rsplit(".", 1)[0]
    uniqsam = pf + ".unique.sam"
    samstats = uniqsam + ".stats"
    sizesfile = Sizes(fastafile).filename
    if need_update((gsnapfile, sizesfile), samstats):
        cmd = op.join(EYHOME, "gsnap2gff3.pl")
        cmd += " --format sam -i {0} -o {1}".format(gsnapfile, uniqsam)
        cmd += " -u -l {0} -p {1}".format(sizesfile, opts.cpus)
        sh(cmd)

    index([uniqsam])

    return uniqsam
%prog snp input.gsnap ref.fasta

    Convert GSNAP output to BAM.