def _add_region_params(region, out_file, items, gatk_type):
    """Add parameters for selecting by region to command line.
    """
    params = []
    variant_regions = bedutils.population_variant_regions(items)
    region = subset_variant_regions(variant_regions, region, out_file, items)
    if region:
        if gatk_type == "gatk4":
            params += ["-L", bamprep.region_to_gatk(region), "--interval-set-rule", "INTERSECTION"]
        else:
            params += ["-L", bamprep.region_to_gatk(region), "--interval_set_rule", "INTERSECTION"]
    params += gatk.standard_cl_params(items)
    return params
def _add_region_params ( region , out_file , items , gatk_type ) : params = [ ] variant_regions = bedutils . population_variant_regions ( items ) region = subset_variant_regions ( variant_regions , region , out_file , items ) if region : if gatk_type == "gatk4" : params += [ "-L" , bamprep . region_to_gatk ( region ) , "--interval-set-rule" , "INTERSECTION" ] else : params += [ "-L" , bamprep . region_to_gatk ( region ) , "--interval_set_rule" , "INTERSECTION" ] params += gatk . standard_cl_params ( items ) return params
Add parameters for selecting by region to command line.