def fastq(args):
    """
    %prog fastq bamfile prefix

    Convert BAM files to paired FASTQ files.
    """
    p = OptionParser(fastq.__doc__)
    opts, args = p.parse_args(args)

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

    bamfile, pf = args
    singletons = pf + ".se.fastq"
    a = pf + ".read1.fastq"
    b = pf + ".read2.fastq"

    cmd  = "samtools collate -uOn 128 {} tmp-prefix".format(bamfile)
    cmd += " | samtools fastq -s {} -1 {} -2 {} -"\
                .format(singletons, a, b)
    sh(cmd)

    if os.stat(singletons).st_size == 0:  # singleton file is empty
        os.remove(singletons)
    return a, b
%prog fastq bamfile prefix

    Convert BAM files to paired FASTQ files.