Fix realStart

GMOD · Feb 13, 2021 · ebcbfa6 · ebcbfa6
1 parent 2edd30d
commit ebcbfa6
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Showing 2 changed files with 6 additions and 5 deletions.
diff --git a/plugins/dotplot-view/src/index.ts b/plugins/dotplot-view/src/index.ts
@@ -191,7 +191,7 @@ export default class DotplotPlugin extends Plugin {
                     const saLengthSansClipping = getLengthSansClipping(saCigar)
                     const saStrandNormalized = saStrand === '-' ? -1 : 1
                     const saClipPos = getClip(saCigar, saStrandNormalized)
-                    const saRealStart = +saStart - 1 + saClipPos
+                    const saRealStart = +saStart - 1
                     return {
                       refName: saRef,
                       start: saRealStart,
@@ -217,9 +217,10 @@ export default class DotplotPlugin extends Plugin {
                   end: clipPos + getLengthSansClipping(cigar),
                 }
 
-                // if secondary alignment or supplementary, calculate length from SA[0]'s CIGAR
-                // which is the primary alignments. otherwise it is the primary alignment just use
-                // seq.length if primary alignment
+                // if secondary alignment or supplementary, calculate length
+                // from SA[0]'s CIGAR which is the primary alignments.
+                // otherwise it is the primary alignment just use seq.length if
+                // primary alignment
                 const totalLength =
                   // eslint-disable-next-line no-bitwise
                   flags & 2048

diff --git a/plugins/linear-comparative-view/src/index.tsx b/plugins/linear-comparative-view/src/index.tsx
@@ -191,7 +191,7 @@ function WindowSizeDlg(props: {
           const saLengthSansClipping = getLengthSansClipping(saCigar)
           const saStrandNormalized = saStrand === '-' ? -1 : 1
           const saClipPos = getClip(saCigar, saStrandNormalized)
-          const saRealStart = +saStart - 1 + saClipPos
+          const saRealStart = +saStart - 1
           return {
             refName: saRef,
             start: saRealStart,