From 557598beacdf4169a7405df3d3eb729d73b1b315 Mon Sep 17 00:00:00 2001
From: Dennis Hendriksen <d.hendriksen@umcg.nl>
Date: Mon, 18 Jan 2021 10:39:40 +0100
Subject: [PATCH] Fix #106 Show warning in case of low read depth

---
 src/components/Genotype.vue    | 15 +++++++++++++--
 src/components/RecordTable.vue |  3 +++
 src/locales/en.json            |  3 ++-
 3 files changed, 18 insertions(+), 3 deletions(-)

diff --git a/src/components/Genotype.vue b/src/components/Genotype.vue
index a2d679c9..83114bed 100644
--- a/src/components/Genotype.vue
+++ b/src/components/Genotype.vue
@@ -7,12 +7,15 @@
       </span>
     </span>
     <b-button
-      v-if="allelicImbalance"
+      v-if="allelicImbalance || lowReadDepth"
       size="sm"
       variant="link"
       class="ml-2 p-0"
       v-b-tooltip.click
-      :title="$t('allelicImbalance')"
+      :title="
+        (lowReadDepth ? $t('lowReadDepth') : '') +
+          (allelicImbalance ? (lowReadDepth ? ' & ' : '') + $t('allelicImbalance') : '')
+      "
     >
       <b-icon-exclamation-circle variant="danger" />
     </b-button>
@@ -28,9 +31,17 @@ export default Vue.extend({
   components: { Allele },
   props: {
     genotype: Object as PropType<Genotype>,
+    readDepth: { type: Number as PropType<number>, required: false },
     allelicDepth: { type: Array as PropType<number[]>, required: false }
   },
   computed: {
+    lowReadDepth(): boolean {
+      let lowReadDepth = false;
+      if (this.readDepth && this.readDepth < 20) {
+        lowReadDepth = true;
+      }
+      return lowReadDepth;
+    },
     allelicImbalance(): boolean {
       let allelicImbalance = false;
       if (this.allelicDepth && this.genotype.t === 'het') {
diff --git a/src/components/RecordTable.vue b/src/components/RecordTable.vue
index df89d110..45957232 100644
--- a/src/components/RecordTable.vue
+++ b/src/components/RecordTable.vue
@@ -56,18 +56,21 @@
       <template v-slot:cell(s)="data">
         <Genotype
           :genotype="data.item.s[sample.index].gt"
+          :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"
         />
       </template>
       <template v-slot:cell(father)="data">
         <Genotype
           :genotype="data.item.s[samplePaternal.index].gt"
+          :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"
         />
       </template>
       <template v-slot:cell(mother)="data">
         <Genotype
           :genotype="data.item.s[sampleMaternal.index].gt"
+          :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"
         />
       </template>
diff --git a/src/locales/en.json b/src/locales/en.json
index a92a8626..a0a21adc 100644
--- a/src/locales/en.json
+++ b/src/locales/en.json
@@ -64,5 +64,6 @@
   "femaleAffected": "Female, Affected.",
   "femaleUnaffected": "Female, Unaffected.",
   "femaleUnknown": "Female, Unknown affected status.",
-  "allelicImbalance": "Allelic imbalance"
+  "allelicImbalance": "Allelic imbalance",
+  "lowReadDepth": "Read depth < 20"
 }
\ No newline at end of file