def clean_inputs(data): """Clean BED input files to avoid overlapping segments that cause downstream issues. Per-merges inputs to avoid needing to call multiple times during later parallel steps. """ if not utils.get_in(data, ("config", "algorithm", "variant_regions_orig")): data["config"]["algorithm"][ "variant_regions_orig"] = dd.get_variant_regions(data) clean_vr = clean_file(dd.get_variant_regions(data), data) merged_vr = merge_overlaps(clean_vr, data) data["config"]["algorithm"]["variant_regions"] = clean_vr data["config"]["algorithm"]["variant_regions_merged"] = merged_vr if dd.get_coverage(data): if not utils.get_in(data, ("config", "algorithm", "coverage_orig")): data["config"]["algorithm"]["coverage_orig"] = dd.get_coverage( data) clean_cov_bed = clean_file(dd.get_coverage(data), data, prefix="cov-", simple=True) merged_cov_bed = merge_overlaps(clean_cov_bed, data) data["config"]["algorithm"]["coverage"] = clean_cov_bed data["config"]["algorithm"]["coverage_merged"] = merged_cov_bed if 'seq2c' in get_svcallers(data): seq2c_ready_bed = prep_seq2c_bed(data) if not seq2c_ready_bed: logger.warning( "Can't run Seq2C without a svregions or variant_regions BED file" ) else: data["config"]["algorithm"]["seq2c_bed_ready"] = seq2c_ready_bed return data
def clean_inputs(data): """Clean BED input files to avoid overlapping segments that cause downstream issues. Per-merges inputs to avoid needing to call multiple times during later parallel steps. """ if not utils.get_in(data, ("config", "algorithm", "variant_regions_orig")): data["config"]["algorithm"]["variant_regions_orig"] = dd.get_variant_regions(data) clean_vr = clean_file(dd.get_variant_regions(data), data) merged_vr = merge_overlaps(clean_vr, data) data["config"]["algorithm"]["variant_regions"] = clean_vr data["config"]["algorithm"]["variant_regions_merged"] = merged_vr if dd.get_coverage(data): if not utils.get_in(data, ("config", "algorithm", "coverage_orig")): data["config"]["algorithm"]["coverage_orig"] = dd.get_coverage(data) clean_cov_bed = clean_file(dd.get_coverage(data), data, prefix="cov-", simple=True) merged_cov_bed = merge_overlaps(clean_cov_bed, data) data["config"]["algorithm"]["coverage"] = clean_cov_bed data["config"]["algorithm"]["coverage_merged"] = merged_cov_bed if 'seq2c' in get_svcallers(data): seq2c_ready_bed = prep_seq2c_bed(data) if not seq2c_ready_bed: logger.warning("Can't run Seq2C without a svregions or variant_regions BED file") else: data["config"]["algorithm"]["seq2c_bed_ready"] = seq2c_ready_bed return data