Merge pull request #322 from eweitz/fix-exon-utr-overlap

Fix CDS size when on same exon as 3'-UTR

src/js/kit/gene-structure.js

@@ -362,13 +362,25 @@ function spliceOut(subparts) {
     const subpart = subparts[i];
     const [subpartType, start, length] = subpart;
     const isSpliceOverlap = start === prevStart;
-    const isOtherOverlap = i > 0 && start === subparts[i - 1][1];
+    let prevRawStart, prevRawLength;
+    if (i > 0) {
+      [, prevRawStart, prevRawLength] = subparts[i - 1];
+    }
+
+    // e.g. 5'-UTRs of OXTR
+    const isOtherOverlap = i > 0 && start === prevRawStart;
+
+    // e.g. 3'-UTR of LDLR, or 3'-UTR of CD44
+    const isOther3UTROverlap = i > 0 && start <= prevRawStart + prevRawLength;
+
     let splicedStart;
     if (isSpliceOverlap) {
       splicedStart = start;
     } else if (isOtherOverlap) {
       // e.g. 5'-UTRs of OXTR
       splicedStart = prevStart;
+    } else if (isOther3UTROverlap) {
+      splicedStart = prevStart + prevRawLength - length;
     } else {
       splicedStart = prevEnd;
     }

test/offline/gene-structure.test.js

@@ -136,6 +136,25 @@ describe('Ideogram gene structure functionality', function() {
         const subparts = document.querySelectorAll('rect.subpart');
         assert.equal(subparts.length, 10); // includes introns
 
+        setTimeout(async function() {
+          // The last exon of gene LDLR includes both CDS and 3'-UTR
+          // There was a bug (see commit 7a43ba0) that caused drastically
+          // longer apparent CDS in these cases, whereas correct display
+          // has a relatively very small CDS compared to 3'-UTR.
+          const ldlrLabel = document.querySelector('#ideogramLabel__c18_a0');
+          ldlrLabel.dispatchEvent(new Event('mouseover'));
+
+          const lastExon = subparts[18];
+          const threePrimeUtr = subparts[19];
+
+          assert.equal(Math.round(lastExon.x.baseVal.value), 127);
+          assert.equal(Math.round(lastExon.width.baseVal.value), 123);
+
+          assert.equal(Math.round(threePrimeUtr.x.baseVal.value), 129);
+          assert.equal(Math.round(threePrimeUtr.width.baseVal.value), 121);
+
+        }, 500);
+
         done();
       }, 500);
     }