improve internal deletion detection

cfe-lab · Jul 4, 2023 · fda4d64 · fda4d64
1 parent ff368bd
commit fda4d64
Showing 1 changed file with 1 addition and 1 deletion.
diff --git a/intact/intact.py b/intact/intact.py
@@ -618,7 +618,7 @@ def get_indel_impact(alignment):
         # Max deletion allowed in ORF exceeded
         if deletions > e.deletion_tolerence:
 
-            if "*" in best_match.aminoseq[1:-1]:
+            if "*" in best_match.aminoseq[:(-e.deletion_tolerence // 3)]:
                 errors.append(IntactnessError(
                     sequence.id, INTERNALSTOP_ERROR,
                     ("Smaller " if is_small else "")