Fix for regex sequence search on reverse strand features (#4366)

GMOD · May 1, 2024 · 0c3707e · 0c3707e
1 parent 4ad28ed
commit 0c3707e
Showing 1 changed file with 14 additions and 14 deletions.
diff --git a/plugins/sequence/src/SequenceSearchAdapter/SequenceSearchAdapter.ts b/plugins/sequence/src/SequenceSearchAdapter/SequenceSearchAdapter.ts
@@ -30,10 +30,9 @@ export default class SequenceSearchAdapter extends BaseFeatureDataAdapter {
   public getFeatures(query: Region, opts: BaseOptions) {
     return ObservableCreate<Feature>(async observer => {
       const sequenceAdapter = await this.configure()
-      const hw = 1000
-      let { start: queryStart, end: queryEnd } = query
-      queryStart = Math.max(0, queryStart - hw)
-      queryEnd += hw
+      const hw = 10000
+      const queryEnd = query.end + hw
+      const queryStart = Math.max(0, query.start - hw)
 
       if (queryEnd < 0 || queryStart > queryEnd) {
         observer.complete()
@@ -60,15 +59,15 @@ export default class SequenceSearchAdapter extends BaseFeatureDataAdapter {
         if (searchForward) {
           const matches = residues.matchAll(re)
           for (const match of matches) {
-            const s = queryStart + (match.index || 0)
-
-            if (doesIntersect2(s, s + search.length, query.start, query.end)) {
+            const s = queryStart + match.index
+            const e = queryStart + match.index + match[0].length
+            if (doesIntersect2(s, e, query.start, query.end)) {
               observer.next(
                 new SimpleFeature({
-                  uniqueId: `${this.id}-match-${s}-p`,
+                  uniqueId: `${this.id}-${s}-${match[0]}-pos`,
                   refName: query.refName,
                   start: s,
-                  end: s + match[0].length,
+                  end: e,
                   name: match[0],
                   strand: 1,
                 }),
@@ -79,15 +78,16 @@ export default class SequenceSearchAdapter extends BaseFeatureDataAdapter {
         if (searchReverse) {
           const matches = revcom(residues).matchAll(re)
           for (const match of matches) {
-            const s = queryEnd - (match.index || 0)
-            if (doesIntersect2(s, s + search.length, query.start, query.end)) {
+            const e = queryEnd - match.index
+            const s = queryEnd - match.index - match[0].length
+            if (doesIntersect2(s, e, query.start, query.end)) {
               observer.next(
                 new SimpleFeature({
-                  uniqueId: `${this.id}-match-${s}-n`,
+                  uniqueId: `${this.id}-${s}-${match[0]}-neg`,
                   refName: query.refName,
-                  start: s - match[0].length,
+                  start: s,
+                  end: e,
                   name: match[0],
-                  end: s,
                   strand: -1,
                 }),
               )