Provide base functionality for prepping and indexing for variant calling.

def shared_variantcall(call_fn, name, align_bams, ref_file, items,
                       assoc_files, region=None, out_file=None):
    """Provide base functionality for prepping and indexing for variant calling.
    """
    config = items[0]["config"]
    if out_file is None:
        if vcfutils.is_paired_analysis(align_bams, items):
            out_file = "%s-paired-variants.vcf.gz" % config["metdata"]["batch"]
        else:
            out_file = "%s-variants.vcf.gz" % os.path.splitext(align_bams[0])[0]
    if not file_exists(out_file):
        logger.debug("Genotyping with {name}: {region} {fname}".format(
              name=name, region=region, fname=os.path.basename(align_bams[0])))
        variant_regions = bedutils.population_variant_regions(items, merged=True)
        target_regions = subset_variant_regions(variant_regions, region, out_file, items=items)
        if (variant_regions is not None and isinstance(target_regions, six.string_types)
              and not os.path.isfile(target_regions)):
            vcfutils.write_empty_vcf(out_file, config)
        else:
            with file_transaction(config, out_file) as tx_out_file:
                call_fn(align_bams, ref_file, items, target_regions,
                        tx_out_file)
    if out_file.endswith(".gz"):
        out_file = vcfutils.bgzip_and_index(out_file, config)
    return out_file