Fix chr name aliasing for genome.getSequence(). See issue #1475

igvteam · Mar 18, 2022 · 3ff7cfc · 3ff7cfc
1 parent 526df2d
commit 3ff7cfc
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Showing 2 changed files with 2 additions and 1 deletion.
diff --git a/js/feature/featureTrack.js b/js/feature/featureTrack.js
@@ -370,14 +370,14 @@ class FeatureTrack extends TrackBase {
         const f = features[0]   // The shortest clicked feature
 
         if ((f.end - f.start) <= 1000000) {
-
             const list = [{
                 label: 'View feature sequence',
                 click: async () => {
                     let seq = await this.browser.genome.getSequence(f.chr, f.start, f.end)
                     if (f.strand === '-') {
                         seq = reverseComplementSequence(seq)
                     }
+                    if (!seq) seq = "Unknown sequence"
                     Alert.presentAlert(seq)
 
                 }

diff --git a/js/genome/genome.js b/js/genome/genome.js
@@ -354,6 +354,7 @@ class Genome {
     }
 
     async getSequence(chr, start, end) {
+        chr = this.getChromosomeName(chr)
         return this.sequence.getSequence(chr, start, end)
     }
 }
-Original file line number
+Diff line change
@@ Expand Up / @@ -354,6 +354,7 @@ class Genome { @@
         }
         async getSequence(chr, start, end) {
+            chr = this.getChromosomeName(chr)
             return this.sequence.getSequence(chr, start, end)
         }
     }
@@ Expand Down @@