fix: do not prefix chromosomes with chr in igv link (#189)

bihealth · Apr 22, 2024 · a07e360 · a07e360
1 parent 73436d9
commit a07e360
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Showing 2 changed files with 4 additions and 10 deletions.
diff --git a/src/components/SeqvarToolsCard/SeqvarToolsCard.vue b/src/components/SeqvarToolsCard/SeqvarToolsCard.vue
@@ -123,12 +123,10 @@ const franklinLinkout = computed<string>(() => {
 })
 
 const jumpToLocus = async () => {
-  const chrPrefixed = props.seqvar?.chrom.startsWith('chr')
-    ? props.seqvar?.chrom
-    : `chr${props.seqvar?.chrom}`
+  const chrom = props.seqvar?.chrom == 'chrMT' ? 'chrM' : props.seqvar?.chrom
   // NB: we allow the call to fetch here as it goes to local IGV.
   await fetch(
-    `http://127.0.0.1:60151/goto?locus=${chrPrefixed}:${props.seqvar?.pos}-${
+    `http://127.0.0.1:60151/goto?locus=${chrom}:${props.seqvar?.pos}-${
       (props.seqvar?.pos ?? 0) + (props.seqvar?.del?.length ?? 0)
     }`
   ).catch((e) => {

diff --git a/src/components/StrucvarToolsCard/StrucvarToolsCard.vue b/src/components/StrucvarToolsCard/StrucvarToolsCard.vue
@@ -98,14 +98,10 @@ const franklinLinkout = computed((): string => {
 })
 
 const jumpToLocus = async () => {
-  const chrPrefixed = props.strucvar?.chrom.startsWith('chr')
-    ? props.strucvar?.chrom
-    : `chr${props.strucvar?.chrom}`
+  const chrom = props.strucvar?.chrom == 'chrMT' ? 'chrM' : props.strucvar?.chrom
   // NB: we allow the call to fetch here as it goes to local IGV.
   await fetch(
-    `http://127.0.0.1:60151/goto?locus=${chrPrefixed}:${props.strucvar?.start}-${svStop(
-      props.strucvar!
-    )}`
+    `http://127.0.0.1:60151/goto?locus=${chrom}:${props.strucvar?.start}-${svStop(props.strucvar!)}`
   ).catch((e) => {
     const msg = "Couldn't connect to IGV. Please make sure IGV is running and try again."
     emit('error', msg)