diff --git a/src/rdds/variant_rank_score/model/default_model/v1.12.0-rc1-10-g0a7de5f/README.md b/src/rdds/variant_rank_score/model/default_model/v1.12.0-rc1-10-g0a7de5f/README.md index 44c97bd0..6cc2add9 100644 --- a/src/rdds/variant_rank_score/model/default_model/v1.12.0-rc1-10-g0a7de5f/README.md +++ b/src/rdds/variant_rank_score/model/default_model/v1.12.0-rc1-10-g0a7de5f/README.md @@ -53,9 +53,9 @@ Expect no change in ranking performance. ## Thresholds The following thresholds are equivalent GICAM thresholds to GENMOD (-30,+51 range): -Genmod threshold 20 -> 0.618 normaliserat -> 0.85 recall -> 0.932 gicam threshold +Genmod threshold 20 -> 0.618 normalized -> 0.85 recall -> 0.946 gicam threshold -genmod threshold 15 -> 0.556 normaliserat -> 0.911 recall -> 0.757 gicam threshold +genmod threshold 15 -> 0.556 normalized -> 0.911 recall -> 0.743 gicam threshold -genmod threshold 10 -> 0.494 normaliserat -> 0.927 recall -> 0.730 gicam threshold +genmod threshold 10 -> 0.494 normalized -> 0.927 recall -> 0.703 gicam threshold diff --git a/src/rdds/variant_rank_score/model/default_model/v1.12.0-rc1-10-g0a7de5f/mivmirnf-v1.12.0-rc1-18-ge950d18-only-patient-in-trios.tar b/src/rdds/variant_rank_score/model/default_model/v1.12.0-rc1-10-g0a7de5f/mivmirnf-v1.12.0-rc1-18-ge950d18-only-patient-in-trios.tar deleted file mode 100644 index eb5df9d6..00000000 Binary files a/src/rdds/variant_rank_score/model/default_model/v1.12.0-rc1-10-g0a7de5f/mivmirnf-v1.12.0-rc1-18-ge950d18-only-patient-in-trios.tar and /dev/null differ diff --git a/src/rdds/variant_rank_score/model/default_model/v1.12.0-rc1-10-g0a7de5f/mivmirnf-v1.12.0-rc1-18-ge950d18-plots.tar b/src/rdds/variant_rank_score/model/default_model/v1.12.0-rc1-10-g0a7de5f/mivmirnf-v1.12.0-rc1-18-ge950d18-plots.tar deleted file mode 100644 index af895ff4..00000000 Binary files a/src/rdds/variant_rank_score/model/default_model/v1.12.0-rc1-10-g0a7de5f/mivmirnf-v1.12.0-rc1-18-ge950d18-plots.tar and /dev/null differ diff --git a/src/rdds/variant_rank_score/model/default_model/v1.12.0-rc1-10-g0a7de5f/mivmirnf-v1.13.0-issue-399-no-assoc-other.tar b/src/rdds/variant_rank_score/model/default_model/v1.12.0-rc1-10-g0a7de5f/mivmirnf-v1.13.0-issue-399-no-assoc-other.tar new file mode 100644 index 00000000..3aa71c56 Binary files /dev/null and b/src/rdds/variant_rank_score/model/default_model/v1.12.0-rc1-10-g0a7de5f/mivmirnf-v1.13.0-issue-399-no-assoc-other.tar differ diff --git a/src/rdds/variant_rank_score/model/model.py b/src/rdds/variant_rank_score/model/model.py index 0cf04294..1b046e31 100644 --- a/src/rdds/variant_rank_score/model/model.py +++ b/src/rdds/variant_rank_score/model/model.py @@ -1040,6 +1040,8 @@ def get_num_feature(variant: ParsableVariant, clinvar_clnsig = str(variant.__getattribute__('CSQ_CLINVAR_CLNSIG')).lower() if 'uncertain' in clinvar_clnsig or 'conflicting' in clinvar_clnsig: str_data = b'' + if clinvar_clnsig == 'other' or clinvar_clnsig == 'association': + str_data = b'' except AttributeError: pass input_dict[tensor_spec.name].append(str_data)