From 54231b983b1cbc4480631bde05ab55e2a668ed72 Mon Sep 17 00:00:00 2001
From: Manuel Holtgrewe <manuel.holtgrewe@bih-charite.de>
Date: Fri, 24 Mar 2023 13:24:59 +0100
Subject: [PATCH] fix: truncate AA insertion at stop codon (#60)

---
 src/mapper/altseq.rs | 9 +++++++++
 1 file changed, 9 insertions(+)

diff --git a/src/mapper/altseq.rs b/src/mapper/altseq.rs
index 1080588..b05607f 100644
--- 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 {