Merge pull request #5015 from leexgh/fix-ma-v4

API client update about Mutation Assessor v4 data and UI changes

Author: onursumer

packages/genome-nexus-ts-api-client/src/generated/GenomeNexusAPI-docs.json

@@ -2506,6 +2506,26 @@
         }
       }
     },
+    "IntergenicConsequenceSummary": {
+      "type": "object",
+      "properties": {
+        "consequenceTerms": {
+          "type": "array",
+          "items": {
+            "type": "string"
+          }
+        },
+        "impact": {
+          "type": "string"
+        },
+        "variantAllele": {
+          "type": "string"
+        },
+        "variantClassification": {
+          "type": "string"
+        }
+      }
+    },
     "IntergenicConsequences": {
       "type": "object",
       "required": [
@@ -2554,124 +2574,32 @@
     },
     "MutationAssessor": {
       "type": "object",
-      "required": [
-        "input"
-      ],
       "properties": {
-        "codonStartPosition": {
-          "type": "string",
-          "description": "Codon start position"
-        },
-        "cosmicCount": {
-          "type": "integer",
-          "format": "int32",
-          "description": "Number of mutations in COSMIC for this protein"
-        },
-        "functionalImpact": {
-          "type": "string",
-          "description": "Functional impact"
+        "functionalImpactPrediction": {
+          "type": "string"
         },
         "functionalImpactScore": {
           "type": "number",
           "format": "double",
           "description": "Functional impact score"
         },
-        "hgvs": {
+        "hgvspShort": {
           "type": "string"
         },
-        "hugoSymbol": {
-          "type": "string",
-          "description": "Hugo gene symbol"
-        },
-        "input": {
-          "type": "string",
-          "description": "User-input variants"
-        },
-        "mappingIssue": {
-          "type": "string",
-          "description": "Mapping issue info"
-        },
-        "msaGaps": {
-          "type": "number",
-          "format": "double",
-          "description": "Portion of gaps in variant position in multiple sequence alignment"
-        },
-        "msaHeight": {
+        "mav": {
           "type": "integer",
-          "format": "int32",
-          "description": "Number of diverse sequences in multiple sequence alignment (identical or highly similar sequences filtered out)"
-        },
-        "msaLink": {
-          "type": "string",
-          "description": "Link to multiple sequence alignment"
-        },
-        "pdbLink": {
-          "type": "string",
-          "description": "Link to 3d structure browser"
-        },
-        "referenceGenomeVariant": {
-          "type": "string",
-          "description": "Reference genome variant"
-        },
-        "referenceGenomeVariantType": {
-          "type": "string",
-          "description": "Reference genome variant type"
-        },
-        "refseqId": {
-          "type": "string",
-          "description": "Refseq protein ID"
-        },
-        "refseqPosition": {
-          "type": "integer",
-          "format": "int32",
-          "description": "Variant position in Refseq protein, can be different from the one in Uniprot"
+          "format": "int32"
         },
-        "refseqResidue": {
-          "type": "string",
-          "description": "Reference residue in Refseq protein, can be different from the one in Uniprot"
+        "msa": {
+          "type": "string"
         },
-        "snpCount": {
+        "sv": {
           "type": "integer",
-          "format": "int32",
-          "description": "Number of SNPs in dbSNP for this protein"
+          "format": "int32"
         },
         "uniprotId": {
           "type": "string",
           "description": "Uniprot protein accession ID"
-        },
-        "uniprotPosition": {
-          "type": "integer",
-          "format": "int32",
-          "description": "Variant position in Uniprot protein, can be different from the one in Refseq"
-        },
-        "uniprotResidue": {
-          "type": "string",
-          "description": "Reference residue in Uniprot protein, can be different from the one in Refseq"
-        },
-        "variant": {
-          "type": "string",
-          "description": "Amino acid substitution"
-        },
-        "variantConservationScore": {
-          "type": "number",
-          "format": "double",
-          "description": "Variant conservation score"
-        },
-        "variantSpecificityScore": {
-          "type": "number",
-          "format": "double",
-          "description": "Variant specificity score"
-        }
-      }
-    },
-    "MutationAssessorAnnotation": {
-      "type": "object",
-      "properties": {
-        "annotation": {
-          "$ref": "#/definitions/MutationAssessor"
-        },
-        "license": {
-          "type": "string"
         }
       }
     },
@@ -3676,8 +3604,8 @@
           "description": "Most severe consequence"
         },
         "mutation_assessor": {
-          "description": "Mutation Assessor Annotation",
-          "$ref": "#/definitions/MutationAssessorAnnotation"
+          "description": "Mutation Assessor",
+          "$ref": "#/definitions/MutationAssessor"
         },
         "my_variant_info": {
           "description": "My Variant Info Annotation",
@@ -3758,6 +3686,12 @@
           "description": "Genomic location",
           "$ref": "#/definitions/GenomicLocation"
         },
+        "intergenicConsequenceSummaries": {
+          "type": "array",
+          "items": {
+            "$ref": "#/definitions/IntergenicConsequenceSummary"
+          }
+        },
         "strandSign": {
           "type": "string",
           "description": "Strand (- or +)"

packages/genome-nexus-ts-api-client/src/generated/GenomeNexusAPI.ts

@@ -483,6 +483,16 @@ export type IntegerRange = {
 
         'start': number
 
+};
+export type IntergenicConsequenceSummary = {
+    'consequenceTerms': Array < string >
+
+        'impact': string
+
+        'variantAllele': string
+
+        'variantClassification': string
+
 };
 export type IntergenicConsequences = {
     'impact': string
@@ -501,60 +511,20 @@ export type MainType = {
 
 };
 export type MutationAssessor = {
-    'codonStartPosition': string
-
-        'cosmicCount': number
-
-        'functionalImpact': string
+    'functionalImpactPrediction': string
 
         'functionalImpactScore': number
 
-        'hgvs': string
-
-        'hugoSymbol': string
-
-        'input': string
-
-        'mappingIssue': string
-
-        'msaGaps': number
-
-        'msaHeight': number
-
-        'msaLink': string
-
-        'pdbLink': string
-
-        'referenceGenomeVariant': string
-
-        'referenceGenomeVariantType': string
-
-        'refseqId': string
+        'hgvspShort': string
 
-        'refseqPosition': number
+        'mav': number
 
-        'refseqResidue': string
+        'msa': string
 
-        'snpCount': number
+        'sv': number
 
         'uniprotId': string
 
-        'uniprotPosition': number
-
-        'uniprotResidue': string
-
-        'variant': string
-
-        'variantConservationScore': number
-
-        'variantSpecificityScore': number
-
-};
-export type MutationAssessorAnnotation = {
-    'annotation': MutationAssessor
-
-        'license': string
-
 };
 export type MutationEffectResp = {
     'citations': Citations
@@ -1008,7 +978,7 @@ export type VariantAnnotation = {
 
         'most_severe_consequence': string
 
-        'mutation_assessor': MutationAssessorAnnotation
+        'mutation_assessor': MutationAssessor
 
         'my_variant_info': MyVariantInfoAnnotation
 
@@ -1044,6 +1014,8 @@ export type VariantAnnotationSummary = {
 
         'genomicLocation': GenomicLocation
 
+        'intergenicConsequenceSummaries': Array < IntergenicConsequenceSummary >
+
         'strandSign': string
 
         'transcriptConsequenceSummaries': Array < TranscriptConsequenceSummary >