Use shortened VCF feature description for some types of insertions an…

…d deletions (#3901)
GMOD · Sep 7, 2023 · 8e17ca6 · 8e17ca6
1 parent 7fcaa4e
commit 8e17ca6
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Showing 2 changed files with 23 additions and 13 deletions.
diff --git a/.../spreadsheet-view/src/SpreadsheetView/importAdapters/__snapshots__/VcfImport.test.ts.snap b/.../spreadsheet-view/src/SpreadsheetView/importAdapters/__snapshots__/VcfImport.test.ts.snap
@@ -15009,7 +15009,7 @@ exports[`vcf file import 1`] = `
             "QUAL": 1112.65,
             "REF": "AAAAAAAAAGAAAAG",
             "aliases": undefined,
-            "description": "deletion AAAAAAAAAGAAAAG -> A",
+            "description": "14bp DEL",
             "end": 41256103,
             "name": "rs373413425",
             "refName": "17",

diff --git a/plugins/variants/src/VcfFeature/util.ts b/plugins/variants/src/VcfFeature/util.ts
@@ -50,16 +50,16 @@ export function getSOTermAndDescription(
     )
 
     descriptions = new Set(
-      [...prefixes].map(prefix => {
-        const suffixes = descs
-          .map(desc => {
-            const pref = desc.split('-> ')
-            return pref[1] && pref[0] === prefix ? pref[1] : ''
-          })
-          .filter(f => !!f)
+      [...prefixes]
+        .map(r => r.trim())
+        .map(prefix => {
+          const suffixes = descs
+            .map(desc => desc.split('->').map(r => r.trim()))
+            .map(pref => (pref[1] && pref[0] === prefix ? pref[1] : ''))
+            .filter(f => !!f)
 
-        return suffixes.length ? prefix + '-> ' + suffixes.join(',') : prefix
-      }),
+          return suffixes.length ? `${prefix} -> ${suffixes.join(',')}` : prefix
+        }),
     )
   }
   if (soTerms.size) {
@@ -115,7 +115,7 @@ export function getSOAndDescByExamination(ref: string, alt: string) {
   } else if (alt === '<DEL>') {
     return ['deletion', alt]
   } else if (alt === '<INV>') {
-    return ['deletion', alt]
+    return ['inversion', alt]
   } else if (alt === '<TRA>') {
     return ['translocation', alt]
   } else if (alt.includes('<')) {
@@ -125,9 +125,19 @@ export function getSOAndDescByExamination(ref: string, alt: string) {
       ? ['inversion', makeDescriptionString('inversion', ref, alt)]
       : ['substitution', makeDescriptionString('substitution', ref, alt)]
   } else if (ref.length <= alt.length) {
-    return ['insertion', makeDescriptionString('insertion', ref, alt)]
+    const len = alt.length - ref.length
+    const lena = len.toLocaleString('en-US')
+    return [
+      'insertion',
+      len > 5 ? lena + 'bp INS' : makeDescriptionString('insertion', ref, alt),
+    ]
   } else if (ref.length > alt.length) {
-    return ['deletion', makeDescriptionString('deletion', ref, alt)]
+    const len = ref.length - alt.length
+    const lena = len.toLocaleString('en-US')
+    return [
+      'deletion',
+      len > 5 ? lena + 'bp DEL' : makeDescriptionString('deletion', ref, alt),
+    ]
   }
 
   return ['indel', makeDescriptionString('indel', ref, alt)]