diff --git a/prp/models/phenotype.py b/prp/models/phenotype.py index 2e33f4d..2496d87 100644 --- a/prp/models/phenotype.py +++ b/prp/models/phenotype.py @@ -31,6 +31,7 @@ class VariantType(str, Enum): SNV = "SNV" MNV = "MNV" SV = "SV" + INDEL = "INDEL" STR = "STR" diff --git a/prp/models/sample.py b/prp/models/sample.py index 57328f4..ecdd8e2 100644 --- a/prp/models/sample.py +++ b/prp/models/sample.py @@ -90,6 +90,7 @@ class PipelineResult(SampleBase): # optional variant info snv_variants: Optional[list[VariantBase]] = None sv_variants: Optional[list[VariantBase]] = None + indel_variants: Optional[list[VariantBase]] = None # optional alignment info reference_genome: Optional[ReferenceGenome] = None read_mapping: Optional[str] = None diff --git a/prp/parse/variant.py b/prp/parse/variant.py index 7612880..d74f181 100644 --- a/prp/parse/variant.py +++ b/prp/parse/variant.py @@ -16,7 +16,7 @@ def _filter_variants(variant_list): # Initialize the results dictionary filetered_variants = { 'sv_variants': [], - 'mnv_variants': [], + 'indel_variants': [], 'snv_variants': [] } @@ -26,8 +26,8 @@ def _filter_variants(variant_list): # Append the variant to the appropriate key in the results dictionary if variant_type == "SV": filetered_variants['sv_variants'].append(variant) - elif variant_type == "MNV": - filetered_variants['mnv_variants'].append(variant) + elif variant_type == "INDEL": + filetered_variants['indel_variants'].append(variant) elif variant_type == "SNV": filetered_variants['snv_variants'].append(variant) return filetered_variants @@ -41,7 +41,7 @@ def _get_variant_type(variant) -> VariantType: case "mnp": var_type = VariantType.MNV case "indel": - var_type = VariantType.SV + var_type = VariantType.INDEL case _: var_type = VariantType(variant.var_type.upper()) return var_type