fix: truncate AA insertion at stop codon (#60)

varfish-org · Mar 24, 2023 · 54231b9 · 54231b9
1 parent 475398d
commit 54231b9
Showing 1 changed file with 9 additions and 0 deletions.
diff --git a/src/mapper/altseq.rs b/src/mapper/altseq.rs
@@ -947,6 +947,15 @@ impl AltSeqToHgvsp {
     ) -> Result<HgvsVariant, anyhow::Error> {
         assert!(start.is_some() == end.is_some());
 
+        // If the `alternative` contains a stop codon (`*`/`X`) then we have to truncate
+        // after it.
+        let alternative = if let Some(pos) = alternative.find('*').or_else(|| alternative.find('X'))
+        {
+            &alternative[..=pos]
+        } else {
+            alternative
+        };
+
         let loc_edit = if is_init_met {
             ProtLocEdit::InitiationUncertain
         } else if is_ambiguous {