From 15c3654e19c69d63c21f1d5bd90e1e79e6b462c2 Mon Sep 17 00:00:00 2001
From: Manuel Holtgrewe <manuel.holtgrewe@bih-charite.de>
Date: Wed, 11 Oct 2023 09:08:05 +0200
Subject: [PATCH] Fixing problem with left-trimming variants (#99)

---
 .../bihealth/varfish_annotator/utils/VariantNormalizer.java    | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/varfish-annotator-core/src/main/java/com/github/bihealth/varfish_annotator/utils/VariantNormalizer.java b/varfish-annotator-core/src/main/java/com/github/bihealth/varfish_annotator/utils/VariantNormalizer.java
index 71f264c..8048861 100644
--- a/varfish-annotator-core/src/main/java/com/github/bihealth/varfish_annotator/utils/VariantNormalizer.java
+++ b/varfish-annotator-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;
       }