Top level entry to regional de-novo based variant calling with cortex_var.

def run_cortex(align_bams, items, ref_file, assoc_files, region=None,
               out_file=None):
    """Top level entry to regional de-novo based variant calling with cortex_var.
    """
    raise NotImplementedError("Cortex currently out of date and needs reworking.")
    if len(align_bams) == 1:
        align_bam = align_bams[0]
        config = items[0]["config"]
    else:
        raise NotImplementedError("Need to add multisample calling for cortex_var")
    if out_file is None:
        out_file = "%s-cortex.vcf" % os.path.splitext(align_bam)[0]
    if region is not None:
        work_dir = safe_makedir(os.path.join(os.path.dirname(out_file),
                                             region.replace(".", "_")))
    else:
        work_dir = os.path.dirname(out_file)
    if not file_exists(out_file):
        bam.index(align_bam, config)
        variant_regions = config["algorithm"].get("variant_regions", None)
        if not variant_regions:
            raise ValueError("Only support regional variant calling with cortex_var: set variant_regions")
        target_regions = subset_variant_regions(variant_regions, region, out_file)
        if os.path.isfile(target_regions):
            with open(target_regions) as in_handle:
                regional_vcfs = [_run_cortex_on_region(x.strip().split("\t")[:3], align_bam,
                                                       ref_file, work_dir, out_file, config)
                                 for x in in_handle]

            combine_file = "{0}-raw{1}".format(*os.path.splitext(out_file))
            _combine_variants(regional_vcfs, combine_file, ref_file, config)
            _select_final_variants(combine_file, out_file, config)
        else:
            vcfutils.write_empty_vcf(out_file)
    return out_file