fix: adjust mt chromosome in igv calls (#1562) (#1563)

varfish-org · Apr 19, 2024 · a28a279 · a28a279
1 parent c4bc4ef
commit a28a279
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Showing 5 changed files with 8 additions and 20 deletions.
diff --git a/svs/vueapp/src/components/StrucvarDetailsNavi/lib.ts b/svs/vueapp/src/components/StrucvarDetailsNavi/lib.ts
@@ -8,10 +8,7 @@ export const jumpToLocus = async (strucvar?: Strucvar) => {
     return
   }
   let url: string
-  let chrom = strucvar.chrom
-  if (chrom?.startsWith('chr')) {
-    chrom = chrom.slice(3)
-  }
+  const chrom = strucvar.chrom == 'chrMT' ? 'chrM' : strucvar.chrom
   if (strucvar.svType === 'BND' || strucvar.svType === 'INS') {
     url = `http://127.0.0.1:60151/goto?locus=${chrom}:${strucvar.start ?? 1}-${(strucvar.start ?? 1) + 1}`
   } else {

diff --git a/svs/vueapp/src/components/SvFilterResultsTable.vue b/svs/vueapp/src/components/SvFilterResultsTable.vue
@@ -204,10 +204,7 @@ const loadFromServer = async () => {
 }
 
 const goToLocus = async ({ chromosome, start, end }) => {
-  let chrom = chromosome
-  if (chrom?.startsWith('chr')) {
-    chrom = chrom.slice(3)
-  }
+  const chrom = chromosome == 'chrMT' ? 'chrM' : chromosome
   await fetch(`http://127.0.0.1:60151/goto?locus=${chrom}:${start}-${end}`)
 }
 

diff --git a/variants/vueapp/src/components/FilterResultsTable.vue b/variants/vueapp/src/components/FilterResultsTable.vue
@@ -388,10 +388,7 @@ const effectSummary = (item) => {
   return [null, 'p.?', 'p.='].includes(item.hgvs_p) ? item.hgvs_c : item.hgvs_p
 }
 const goToLocus = async (item) => {
-  let chrom = item.chromosome
-  if (chrom.startsWith('chr')) {
-    chrom = chrom.slice(3)
-  }
+  const chrom = item.chromosome == 'chrMT' ? 'chrM' : item.chromosome
   await fetch(
     `http://127.0.0.1:60151/goto?locus=${chrom}:${item.start}-${item.end}`,
   ).catch(() => {

diff --git a/variants/vueapp/src/components/FilterResultsTable/CellRendererIgv.vue b/variants/vueapp/src/components/FilterResultsTable/CellRendererIgv.vue
@@ -4,10 +4,10 @@ const props = defineProps({
 })
 
 const goToLocus = async () => {
-  let chrom = props.params.data.chromosome
-  if (chrom?.startsWith('chr')) {
-    chrom = chrom.slice(3)
-  }
+  const chrom =
+    props.params.data.chromosome == 'chrMT'
+      ? 'chrM'
+      : props.params.data.chromosome
   await fetch(
     `http://127.0.0.1:60151/goto?locus=${chrom}:${props.params.data.start}-${props.params.data.end}`,
   ).catch(() => {

diff --git a/variants/vueapp/src/components/SeqvarDetailsNavi/lib.ts b/variants/vueapp/src/components/SeqvarDetailsNavi/lib.ts
@@ -5,10 +5,7 @@ import { Seqvar } from '@bihealth/reev-frontend-lib/lib/genomicVars'
  */
 export const jumpToLocus = async (seqvar?: Seqvar) => {
   // NB: we allow the call to fetch here as it goes to local IGV.
-  let chrom = seqvar?.chrom
-  if (chrom?.startsWith('chr')) {
-    chrom = chrom.slice(3)
-  }
+  const chrom = seqvar?.chrom == 'chrMT' ? 'chrM' : seqvar?.chrom
   await fetch(
     `http://127.0.0.1:60151/goto?locus=${chrom}:${seqvar?.pos}-${
       (seqvar?.pos ?? 0) + (seqvar?.del?.length ?? 0)