Detect somatic mutations with qSNP.

    This is used for paired tumor / normal samples.

def _run_qsnp_paired(align_bams, items, ref_file, assoc_files,
                     region=None, out_file=None):
    """Detect somatic mutations with qSNP.

    This is used for paired tumor / normal samples.
    """
    config = items[0]["config"]
    if out_file is None:
        out_file = "%s-paired-variants.vcf" % os.path.splitext(align_bams[0])[0]
    if not utils.file_exists(out_file):
        out_file = out_file.replace(".gz", "")
        with file_transaction(config, out_file) as tx_out_file:
            with tx_tmpdir(config) as tmpdir:
                with utils.chdir(tmpdir):
                    paired = get_paired_bams(align_bams, items)
                    qsnp = config_utils.get_program("qsnp", config)
                    resources = config_utils.get_resources("qsnp", config)
                    mem = " ".join(resources.get("jvm_opts", ["-Xms750m -Xmx4g"]))
                    qsnp_log = os.path.join(tmpdir, "qsnp.log")
                    qsnp_init = os.path.join(tmpdir, "qsnp.ini")
                    if region:
                        paired = _create_bam_region(paired, region, tmpdir)
                    _create_input(paired, tx_out_file, ref_file, assoc_files['dbsnp'], qsnp_init)
                    cl = ("{qsnp} {mem} -i {qsnp_init} -log {qsnp_log}")
                    do.run(cl.format(**locals()), "Genotyping paired variants with Qsnp", {})
        out_file = _filter_vcf(out_file)
        out_file = bgzip_and_index(out_file, config)
    return out_file