@molgenis/vip-report-template 2.6.4 → 2.7.3

package/.travis.yml

@@ -1,6 +1,10 @@
 language: node_js
 node_js:
 - lts/*
+branches:
+  only:
+    - master
+    - /^v\d+\.\d+(\.\d+)?(-\S*)?$/    
 addons:
   sonarcloud:
     organization: molgenis
@@ -26,4 +30,4 @@ deploy:
     file: dist/vip-report-template.html
     on:
       tags: true
-    edge: true # opt in to dpl v2
+    edge: true # opt in to dpl v2

package/README.md

@@ -1,4 +1,4 @@
-[![Build Status](https://travis-ci.com/molgenis/vip-report-template.svg?branch=master)](https://travis-ci.com/molgenis/vip-report-template)
+[![Build Status](https://app.travis-ci.com/molgenis/vip-report-template.svg?branch=master)](https://app.travis-ci.com/molgenis/vip-report-template)
 [![Quality Status](https://sonarcloud.io/api/project_badges/measure?project=molgenis_vip-report-template&metric=alert_status)](https://sonarcloud.io/dashboard?id=molgenis_vip-report-template)
 # Variant Interpretation Pipeline - VCF Report Generator
 See https://github.com/molgenis/vip-report#readme

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@molgenis/vip-report-template",
-  "version": "2.6.4",
+  "version": "2.7.3",
   "description": "Report Template for Variant Call Format (VCF) Report Generator",
   "scripts": {
     "serve": "vue-cli-service serve",
@@ -17,7 +17,7 @@
     "dagre": "^0.8.5",
     "fflate": "^0.6.10",
     "file-saver": "^2.0.5",
-    "igv": "^2.10.0",
+    "igv": "^2.10.4",
     "vue": "^2.6.12",
     "vue-class-component": "^7.2.6",
     "vue-i18n": "^8.24.0",

package/src/components/Gene.vue

@@ -0,0 +1,32 @@
+<template>
+  <span>
+    <Anchor
+      :href="'https://www.omim.org/search?search=' + encodeURIComponent(value.symbol) + '&field=approved_gene_symbol'"
+      :text="value.symbol"
+    />
+    <b-button
+      pill
+      v-if="value.incompletePenetrance"
+      size="sm"
+      variant="info"
+      class="ml-2 p-0"
+      v-b-tooltip.click
+      :title="$t('incompletePenetrance')"
+    >
+      <sup>IP</sup>
+    </b-button>
+  </span>
+</template>
+
+<script lang="ts">
+import Vue, { PropType } from 'vue';
+import Anchor from '@/components/Anchor.vue';
+import { Gene } from '@/types/Gene';
+
+export default Vue.extend({
+  components: { Anchor },
+  props: {
+    value: { type: Object as PropType<Gene> }
+  }
+});
+</script>

package/src/components/RecordInfoDetailsItem.vue

@@ -1,11 +1,17 @@
 <template>
   <span v-if="metadata.number.type === 'NUMBER' && metadata.number.count === 1">
+    <span v-if="metadata.id === 'GeneObject'">
+      <Gene v-if="value.length > 0" :value="value" />
+    </span>
     <RecordInfoDetailsItemValue v-if="value !== null" :metadataId="metadata.id" :value="value" :details="details" />
   </span>
   <span v-else>
     <span v-if="metadata.id === 'PUBMED'">
       <PubMedAnchor v-if="value.length > 0" :pubMedIds="value" />
     </span>
+    <span v-else-if="metadata.id === 'GeneObject'">
+      <Gene v-if="value.length > 0" :value="value" />
+    </span>
     <span v-else>
       <span v-for="(item, index) in value" :key="index">
         <RecordInfoDetailsItemValue v-if="value !== null" :metadataId="metadata.id" :value="item" :details="details" />
@@ -20,9 +26,10 @@ import Vue, { PropType } from 'vue';
 import { Vcf } from '@molgenis/vip-report-api';
 import RecordInfoDetailsItemValue from '@/components/RecordInfoDetailsItemValue.vue';
 import PubMedAnchor from '@/components/PubMedAnchor.vue';
+import Gene from '@/components/Gene.vue';
 
 export default Vue.extend({
-  components: { PubMedAnchor, RecordInfoDetailsItemValue },
+  components: { Gene, PubMedAnchor, RecordInfoDetailsItemValue },
   props: {
     metadata: Object as PropType<Vcf.InfoMetadata>,
     value: [String, Number, Boolean, Array, Object] as PropType<

package/src/components/RecordInfoDetailsItemValue.vue

@@ -9,7 +9,10 @@
       :text="details ? value : value.replace(/_variant$/, '')"
     />
   </span>
-  <span v-else-if="metadataId === 'SYMBOL' || metadataId === 'Gene_Name'">
+  <span v-else-if="metadataId === 'GeneObject'">
+    <Gene :value="value" />
+  </span>
+  <span v-else-if="metadataId === 'Gene_Name'">
     <Anchor
       :href="'https://www.omim.org/search?search=' + encodeURIComponent(value) + '&field=approved_gene_symbol'"
       :text="value"
@@ -73,10 +76,11 @@
 <script lang="ts">
 import Vue, { PropType } from 'vue';
 import Anchor from '@/components/Anchor.vue';
+import Gene from '@/components/Gene.vue';
 import { mapState } from 'vuex';
 
 export default Vue.extend({
-  components: { Anchor },
+  components: { Anchor, Gene },
   props: {
     metadataId: String as PropType<string>,
     value: [String, Number, Boolean, Object] as PropType<string | number | boolean | unknown>,

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">
@@ -86,10 +86,10 @@
           :values="data.item.expand ? data.item.effect.items : data.item.effect.items.slice(0, 1)"
         />
       </template>
-      <template v-slot:cell(symbol)="data">
+      <template v-slot:cell(gene)="data">
         <RecordInfoDetailsItemMultiline
-          :metadata="data.item.symbol.metadata"
-          :values="data.item.expand ? data.item.symbol.items : data.item.symbol.items.slice(0, 1)"
+          :metadata="data.item.gene.metadata"
+          :values="data.item.expand ? data.item.gene.items : data.item.gene.items.slice(0, 1)"
         />
       </template>
       <template v-slot:cell(inheritance)="data">
@@ -229,7 +229,7 @@ interface Row {
   f: string[];
   s: Vcf.RecordSample[];
   effect?: unknown;
-  symbol?: unknown;
+  gene?: unknown;
   inheritance?: unknown;
   hgvsC?: unknown;
   hgvsP?: unknown;
@@ -281,6 +281,7 @@ export default Vue.extend({
       'isSamplesContainInheritance',
       'isSamplesContainDenovo',
       'isSamplesContainDepth',
+      'isRecordsContainIncompletePenetrance',
       'sampleMaternal',
       'samplePaternal'
     ]),
@@ -316,7 +317,7 @@ export default Vue.extend({
       if (this.hasConsequences) {
         fields.push({ key: 'expand', label: '', class: ['compact', 'align-top'] });
         fields.push({ key: 'effect', label: 'effect' });
-        fields.push({ key: 'symbol', label: 'symbol' });
+        fields.push({ key: 'gene', label: 'symbol' });
         if (this.isSamplesContainInheritance) {
           fields.push({ key: 'inheritance', label: 'inheritance' });
         }
@@ -509,9 +510,21 @@ export default Vue.extend({
           metadata: consequences.metadata.effect,
           items: consequences.items.map((consequence) => consequence.effect)
         };
-        row.symbol = {
-          metadata: consequences.metadata.symbol,
-          items: consequences.items.map((consequence) => consequence.symbol)
+        row.gene = {
+          metadata: {
+            id: 'GeneObject',
+            type: 'Other',
+            number: { type: 'NUMBER', count: 1 },
+            description: 'GeneObject'
+          },
+          items: consequences.items.map((consequence) =>
+            consequence.symbol !== null
+              ? {
+                  symbol: consequence.symbol,
+                  incompletePenetrance: consequence.incompletePenetrance
+                }
+              : null
+          )
         };
         if (this.isSamplesContainInheritance) {
           row.inheritance = {

package/src/globals/utils.ts

@@ -10,6 +10,12 @@ const consequenceMetadata: ConsequenceMetadata = {
     description: 'Consequence'
   },
   symbol: { id: 'SYMBOL', type: 'STRING', number: { type: 'NUMBER', count: 1 }, description: 'SYMBOL' },
+  incompletePenetrance: {
+    id: 'IncompletePenetrance',
+    type: 'FLAG',
+    number: { type: 'NUMBER', count: 1 },
+    description: 'IncompletePenetrance'
+  },
   inheritance: {
     id: 'InheritanceModesGene',
     type: 'STRING',
@@ -54,6 +60,7 @@ function createConsequence(
   info: Vcf.Value[],
   effectIndex: number | undefined,
   symbolIndex: number | undefined,
+  incompletePenetranceIndex: number | undefined,
   inheritanceIndex: number | undefined,
   hgvsCIndex: number | undefined,
   hgvsPIndex: number | undefined,
@@ -68,6 +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,
     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,
@@ -85,6 +94,7 @@ function createConsequences(
   info: Vcf.Value[][],
   effectIndex: number | undefined,
   symbolIndex: number | undefined,
+  incompletePenetranceIndex: number | undefined,
   inheritanceIndex: number | undefined,
   hgvsCIndex: number | undefined,
   hgvsPIndex: number | undefined,
@@ -102,6 +112,7 @@ function createConsequences(
       item,
       effectIndex,
       symbolIndex,
+      incompletePenetranceIndex,
       inheritanceIndex,
       hgvsCIndex,
       hgvsPIndex,
@@ -124,6 +135,7 @@ function getInfoConsequences(
   info: Vcf.Value[][],
   effectId: string,
   symbolId: string,
+  incompletePenetranceId: string | null,
   inheritanceId: string | null,
   hgvsCId: string,
   hgvsPId: string,
@@ -141,6 +153,7 @@ function getInfoConsequences(
 
   let effectIndex,
     symbolIndex,
+    incompletePenetranceIndex,
     inheritanceIndex,
     hgvsCIndex,
     hgvsPIndex,
@@ -160,6 +173,9 @@ function getInfoConsequences(
       case symbolId:
         symbolIndex = index;
         break;
+      case incompletePenetranceId:
+        incompletePenetranceIndex = index;
+        break;
       case inheritanceId:
         inheritanceIndex = index;
         break;
@@ -200,6 +216,7 @@ function getInfoConsequences(
     info,
     effectIndex,
     symbolIndex,
+    incompletePenetranceIndex,
     inheritanceIndex,
     hgvsCIndex,
     hgvsPIndex,
@@ -233,6 +250,7 @@ function getVepConsequences(record: Vcf.Record, metadata: Vcf.Metadata): Consequ
     csqInfo,
     'Consequence',
     'SYMBOL',
+    'IncompletePenetrance',
     'InheritanceModesGene',
     'HGVSc',
     'HGVSp',
@@ -267,6 +285,7 @@ function getSnpEffConsequences(record: Vcf.Record, metadata: Vcf.Metadata): Cons
     'Annotation',
     'Gene_Name',
     null,
+    null,
     'HGVS.c',
     'HGVS.p',
     null,

package/src/locales/en.json

@@ -77,5 +77,6 @@
   "genomeBrowserUnavailable": "Genome browser unavailable for selected record.",
   "treeViewer": "Decision tree",
   "missingDecisionTree": "Decision tree unavailable",
-  "treeInfo": "Click and drag in the tree to navigate, scroll to zoom."
+  "treeInfo": "Click and drag in the tree to navigate, scroll to zoom.",
+  "incompletePenetrance": "Gene associated with incomplete penetrance."
 }