fixup: handle ? end

browser/src/ClinvarVariantsTrack/ClinvarAllVariantsPlot.spec.tsx

@@ -290,5 +290,46 @@ describe('ClinvarAllVariantsPlot', () => {
       expect(() => plotLayoutMatches(expectedPlotLayout, plotBody)).not.toThrowError()
       expect(tree).toMatchSnapshot()
     })
+
+    test('clamps end to end of the downstream UTR when the end in the HGVSP is "?"', () => {
+      const variant = { ...baseVariant, hgvsp: 'p.Tyr30SerfsTer?' }
+      const tree = render(
+        <ClinvarAllVariantsPlot
+          scalePosition={scalePosition}
+          transcripts={[transcript]}
+          variants={[variant]}
+          width={width}
+          onClickVariant={onClickVariant}
+        />
+      ).asFragment()
+      const plotBody = extractPlotFragment(tree)
+
+      const plotLayouts: Record<Strand, PlotLayoutElement[]> = {
+        '+': [
+          ['overlay', 310, 822 - 310],
+          ['cds', 310, 322],
+          ['utr', 322, 423],
+          ['cds', 423, 522],
+          ['utr', 522, 623],
+          ['cds', 623, 722],
+          ['utr', 723, 822],
+          ['stop_marker', 822],
+        ],
+        '-': [
+          ['overlay', 123, 635 - 123],
+          ['utr', 123, 222],
+          ['cds', 223, 322],
+          ['utr', 322, 423],
+          ['cds', 423, 522],
+          ['utr', 522, 623],
+          ['cds', 623, 635],
+          ['stop_marker', 123],
+        ],
+      }
+      const expectedPlotLayout = plotLayouts[strand]
+
+      expect(() => plotLayoutMatches(expectedPlotLayout, plotBody)).not.toThrowError()
+      expect(tree).toMatchSnapshot()
+    })
   })
 })

browser/src/ClinvarVariantsTrack/ClinvarAllVariantsPlot.tsx

@@ -46,32 +46,29 @@ const getGlobalFrameshiftCoordinates = (
   const codingAndDownstreamExons = exons.slice(
     exons.findIndex((exon: Exon) => exon.feature_type === 'CDS')
   )
-  const codingRegionStart =
-    transcript.strand === '+' ? codingAndDownstreamExons[0].start : codingAndDownstreamExons[0].stop
-
   // Termination site position may be "?" if the new reading frame does not encounter a stop codon
   // In this case, place the termination site at the end of the transcript
   const lastExon = codingAndDownstreamExons[codingAndDownstreamExons.length - 1]
   const transcriptEnd = transcript.strand === '+' ? lastExon.stop : lastExon.start
 
+  // Codon numbers are 1 indexed
+  const startOffsetFromCDS = position * 3 - 2
+
+  const { remainingIntervals, globalCoordinate: startCoordinate } = advanceOverIntervals(
+    codingAndDownstreamExons,
+    startOffsetFromCDS,
+    transcript.strand
+  )
   if (terminationSitePosition === '?') {
-    return [codingRegionStart, transcriptEnd]
+    return [startCoordinate || transcriptEnd, transcriptEnd]
   }
 
   // Offset in bases from the start of the transcript's CDS region to the termination site
-  // Codon numbers are 1 indexed
-  const startOffsetFromCDS = position * 3 - 2
   // The extra "+2" at the end is because we start at the first nucleotide of
   // the first codon, and end with the last nucleotide (rather than the first)
   // of some downstream codon.
   const lengthInNucleotides = (Number(terminationSitePosition) - 1) * 3 + 2
 
-  // Both ends should always fall within an exon
-  const { remainingIntervals, globalCoordinate: startCoordinate } = advanceOverIntervals(
-    codingAndDownstreamExons,
-    startOffsetFromCDS,
-    transcript.strand
-  )
   const { globalCoordinate: endCoordinate } = advanceOverIntervals(
     remainingIntervals,
     lengthInNucleotides,