Fixing problem with left-trimming variants (#99)

Closes: #99 Related-Issue: #99 Projected-Results-Impact: require-revalidation
varfish-org · Oct 11, 2023 · 5a46f9f · 5a46f9f
1 parent 3da0bc3
commit 5a46f9f
Showing 1 changed file with 2 additions and 1 deletion.
diff --git a/...tor-core/src/main/java/com/github/bihealth/varfish_annotator/utils/VariantNormalizer.java b/...tor-core/src/main/java/com/github/bihealth/varfish_annotator/utils/VariantNormalizer.java
@@ -72,7 +72,7 @@ private VariantDescription shiftLeft(VariantDescription desc) {
     while (anyChange) {
       anyChange = false;
 
-      // Trim left-most nucletoide
+      // Trim right-most nucletoide
       if (ref.length() > 0
           && alt.length() > 0
           && ref.charAt(ref.length() - 1) == alt.charAt(alt.length() - 1)) {
@@ -103,6 +103,7 @@ private VariantDescription trimBasesLeft(VariantDescription desc, int minSize) {
       if (ref.length() > minSize && alt.length() > minSize && ref.charAt(0) == alt.charAt(0)) {
         ref = ref.substring(1);
         alt = alt.substring(1);
+        start += 1;
       } else {
         break;
       }