@molgenis/vip-report-template 2.7.1 → 2.7.2

package/.scannerwork/report-task.txt

@@ -1,8 +1,8 @@
 organization=molgenis
 projectKey=molgenis_vip-report-template
 serverUrl=https://sonarcloud.io
-serverVersion=8.0.0.25123
-branch=v2.7.1
-dashboardUrl=https://sonarcloud.io/dashboard?id=molgenis_vip-report-template&branch=v2.7.1&resolved=false
-ceTaskId=AX1bK9rH9EclnW_8YXd3
-ceTaskUrl=https://sonarcloud.io/api/ce/task?id=AX1bK9rH9EclnW_8YXd3
+serverVersion=8.0.0.25242
+branch=v2.7.2
+dashboardUrl=https://sonarcloud.io/dashboard?id=molgenis_vip-report-template&branch=v2.7.2&resolved=false
+ceTaskId=AX1_0IyO7H9iSdhZGXlC
+ceTaskUrl=https://sonarcloud.io/api/ce/task?id=AX1_0IyO7H9iSdhZGXlC

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@molgenis/vip-report-template",
-  "version": "2.7.1",
+  "version": "2.7.2",
   "description": "Report Template for Variant Call Format (VCF) Report Generator",
   "scripts": {
     "serve": "vue-cli-service serve",

package/src/components/Gene.vue

@@ -4,14 +4,16 @@
       :href="'https://www.omim.org/search?search=' + encodeURIComponent(value.symbol) + '&field=approved_gene_symbol'"
       :text="value.symbol"
     />
-    <b-button pill
+    <b-button
+      pill
       v-if="value.incompletePenetrance"
       size="sm"
       variant="info"
-              class="ml-2 p-0"
+      class="ml-2 p-0"
       v-b-tooltip.click
       :title="$t('incompletePenetrance')"
-    >     <sup>IP</sup>
+    >
+      <sup>IP</sup>
     </b-button>
   </span>
 </template>

package/src/components/RecordTable.vue

@@ -49,24 +49,24 @@
         <Genotype
           :genotype="data.item.s[sample.index].GT"
           :alleles="[data.item.r].concat(data.item.a)"
-          :readDepth="data.item.s[sample.index].f ? data.item.s[sample.index].f.DP : undefined"
-          :allelicDepth="data.item.s[sample.index].f ? data.item.s[sample.index].f.AD : undefined"
+          :readDepth="data.item.s[sample.index].DP"
+          :allelicDepth="data.item.s[sample.index].AD"
         />
       </template>
       <template v-slot:cell(father)="data">
         <Genotype
           :genotype="data.item.s[samplePaternal.index].GT"
           :alleles="[data.item.r].concat(data.item.a)"
-          :readDepth="data.item.s[samplePaternal.index].f ? data.item.s[samplePaternal.index].f.DP : undefined"
-          :allelicDepth="data.item.s[samplePaternal.index].f ? data.item.s[samplePaternal.index].f.AD : undefined"
+          :readDepth="data.item.s[samplePaternal.index].DP"
+          :allelicDepth="data.item.s[samplePaternal.index].AD"
         />
       </template>
       <template v-slot:cell(mother)="data">
         <Genotype
           :genotype="data.item.s[sampleMaternal.index].GT"
           :alleles="[data.item.r].concat(data.item.a)"
-          :readDepth="data.item.s[sampleMaternal.index].f ? data.item.s[sampleMaternal.index].f.DP : undefined"
-          :allelicDepth="data.item.s[sampleMaternal.index].f ? data.item.s[sampleMaternal.index].f.AD : undefined"
+          :readDepth="data.item.s[sampleMaternal.index].DP"
+          :allelicDepth="data.item.s[sampleMaternal.index].AD"
         />
       </template>
       <template v-slot:cell(expand)="data">
@@ -511,7 +511,12 @@ export default Vue.extend({
           items: consequences.items.map((consequence) => consequence.effect)
         };
         row.gene = {
-          metadata: { id: 'GeneObject', type: 'Other', number: { type: 'NUMBER', count: 1 }, description: 'GeneObject' },
+          metadata: {
+            id: 'GeneObject',
+            type: 'Other',
+            number: { type: 'NUMBER', count: 1 },
+            description: 'GeneObject'
+          },
           items: consequences.items.map((consequence) =>
             consequence.symbol !== null
               ? {

package/src/globals/utils.ts

@@ -75,7 +75,8 @@ function createConsequence(
   return {
     effect: effectIndex !== undefined ? (info[effectIndex] as string[]) : [],
     symbol: symbolIndex !== undefined ? (info[symbolIndex] as string | null) : null,
-    incompletePenetrance: incompletePenetranceIndex !== undefined ? (info[incompletePenetranceIndex] as boolean) : false,
+    incompletePenetrance:
+      incompletePenetranceIndex !== undefined ? (info[incompletePenetranceIndex] as boolean) : false,
     inheritance: inheritanceIndex !== undefined ? (info[inheritanceIndex] as string[]) : [],
     hgvsC: hgvsCIndex !== undefined ? (info[hgvsCIndex] as string | null) : null,
     hgvsP: hgvsPIndex !== undefined ? (info[hgvsPIndex] as string | null) : null,

package/src/store/getters.ts

@@ -20,12 +20,14 @@ export default {
       return 0;
     });
   },
-  getSampleById: (state: State) => (id: string): Api.Sample | null => {
-    if (state.samples === null) {
-      return null;
-    }
-    return state.samples.items.find((sample) => sample.person.individualId === id) || null;
-  },
+  getSampleById:
+    (state: State) =>
+    (id: string): Api.Sample | null => {
+      if (state.samples === null) {
+        return null;
+      }
+      return state.samples.items.find((sample) => sample.person.individualId === id) || null;
+    },
   sampleMaternal: (state: State): Api.Sample | null => {
     if (state.selectedSample === null) {
       return null;
@@ -94,31 +96,33 @@ export default {
   isAnnotationEnabled: (state: State): boolean => {
     return state.annotations !== null;
   },
-  getAnnotation: (state: State) => (record: Vcf.Record): Annotation => {
-    if (state.annotations === null) {
-      throw 'Annotations disabled';
-    }
-    if (state.selectedSample == null) {
-      throw 'No sample selected';
-    }
+  getAnnotation:
+    (state: State) =>
+    (record: Vcf.Record): Annotation => {
+      if (state.annotations === null) {
+        throw 'Annotations disabled';
+      }
+      if (state.selectedSample == null) {
+        throw 'No sample selected';
+      }
 
-    const sampleId = state.selectedSample.person.individualId;
-    const key = `${sampleId}_${record.c}_${record.p}_${record.r}_${record.a.join(',')}`;
-    let annotation = state.annotations[key];
-    if (annotation === undefined) {
-      annotation = {
-        sampleId: sampleId,
-        chr: record.c,
-        pos: record.p,
-        ref: record.r,
-        alt: record.a,
-        geneMatch: null,
-        class: null,
-        txt: null
-      };
-    }
-    return annotation;
-  },
+      const sampleId = state.selectedSample.person.individualId;
+      const key = `${sampleId}_${record.c}_${record.p}_${record.r}_${record.a.join(',')}`;
+      let annotation = state.annotations[key];
+      if (annotation === undefined) {
+        annotation = {
+          sampleId: sampleId,
+          chr: record.c,
+          pos: record.p,
+          ref: record.r,
+          alt: record.a,
+          geneMatch: null,
+          class: null,
+          txt: null
+        };
+      }
+      return annotation;
+    },
   /**
    * Returns whether records contain mvl annotations.
    */
@@ -200,4 +204,4 @@ export default {
     }
     return hasReadDepth;
   }
-};
+};

package/tests/unit/store/getters.spec.ts

@@ -517,7 +517,7 @@ test('whether records contain MVL annotations - no meta', () => {
 
 test('whether records contain MVL annotations - no info meta', () => {
   const recordsMetadata = mock<Vcf.Metadata>();
-  recordsMetadata.info = { };
+  recordsMetadata.info = {};
 
   const metadata = mock<Api.Metadata>();
   metadata.records = recordsMetadata;

package/tests/unit/utils/treeDrawer.spec.ts

@@ -1,4 +1,4 @@
-import treeDrawer, { calculateScaleToFit, getGraphScale } from '@/utils/treeDrawer';
+import treeDrawer from '@/utils/treeDrawer';
 
 describe('retrieveTreeFromFile', () => {
   it('getLineThickness', () => {