Retrieve set of target regions for CNV analysis.

    Subsets to extended transcript regions for WGS experiments to avoid
    long runtimes.

def get_base_cnv_regions(data, work_dir, genome_default="transcripts1e4", include_gene_names=True):
    """Retrieve set of target regions for CNV analysis.

    Subsets to extended transcript regions for WGS experiments to avoid
    long runtimes.
    """
    cov_interval = dd.get_coverage_interval(data)
    base_regions = get_sv_bed(data, include_gene_names=include_gene_names)
    # if we don't have a configured BED or regions to use for SV caling
    if not base_regions:
        # For genome calls, subset to regions near genes as targets
        if cov_interval == "genome":
            base_regions = get_sv_bed(data, genome_default, work_dir, include_gene_names=include_gene_names)
            if base_regions:
                base_regions = remove_exclude_regions(base_regions, base_regions, [data])
        # Finally, default to the defined variant regions
        if not base_regions:
            base_regions = dd.get_variant_regions(data) or dd.get_sample_callable(data)
    return bedutils.clean_file(base_regions, data)