diff --git a/src/sv_utils/src/sv_utils/get_confident_variant_lists_from_vapor_and_irs_test.py b/src/sv_utils/src/sv_utils/get_confident_variant_lists_from_vapor_and_irs_test.py index 48f0b67cc..ac59c8c95 100755 --- a/src/sv_utils/src/sv_utils/get_confident_variant_lists_from_vapor_and_irs_test.py +++ b/src/sv_utils/src/sv_utils/get_confident_variant_lists_from_vapor_and_irs_test.py @@ -56,11 +56,13 @@ def get_irs_sample_confident_variants(vcf: str, matched_record_ids_bad = 0 matched_samples_good = 0 matched_samples_bad = 0 + total_calls = 0 with VariantFile(vcf) as vcf: for record in vcf: if record.id in valid_irs_variant_ids: matched_record_ids += 1 called_samples = get_called_samples(record) + total_calls += len(called_samples) for sample_list in samples_list_to_report_mapping: if record.id in samples_list_to_report_mapping[sample_list][0]: matched_record_ids_good += 1 @@ -94,11 +96,12 @@ def get_irs_sample_confident_variants(vcf: str, get_truth_overlap.SampleConfidentVariants( good_variant_ids=set(irs_confident_variants[sample].__dict__['good_variant_ids']), bad_variant_ids=new_bad_ids) - logging.info(f"Valid vcf record ids: {matched_record_ids}") + logging.info(f"Valid vcf IRS record ids: {matched_record_ids}") + logging.info(f"Total calls in valid IRS variants: {total_calls}") logging.info(f"Number times a good variant was matched in an IRS batch: {matched_record_ids_good}") logging.info(f"Number times a bad variant was matched in an IRS batch: {matched_record_ids_bad}") - logging.info(f"Matched good variant sample calls: {matched_samples_good}") - logging.info(f"Matched bad variant sample calls: {matched_samples_bad}") + logging.info(f"Matched good IRS variant sample calls: {matched_samples_good}") + logging.info(f"Matched bad IRS variant sample calls: {matched_samples_bad}") return irs_confident_variants