From 4fccdb826fea15539b59630b2f9d742271aac3c4 Mon Sep 17 00:00:00 2001
From: Manuel Holtgrewe <manuel.holtgrewe@bih-charite.de>
Date: Thu, 6 Apr 2023 12:48:45 +0200
Subject: [PATCH] fix: out of bounds issue on 5'-to-3' shifting beyond CDS
 (#94)

---
 src/mapper/altseq.rs | 11 +++++++++++
 src/normalizer.rs    |  2 +-
 2 files changed, 12 insertions(+), 1 deletion(-)

diff --git a/src/mapper/altseq.rs b/src/mapper/altseq.rs
index e2f8670..b8f5135 100644
--- a/src/mapper/altseq.rs
+++ b/src/mapper/altseq.rs
@@ -777,6 +777,17 @@ impl AltSeqToHgvsp {
             is_frameshift,
         } = &record;
 
+        // Handle the case of the variant being after the end of the protein sequence.  This can
+        // happen when the variant is 5'-to-3' shifted beyond the stop codon.  In this case, we
+        // can simply return `ProtLocEdit::NoChange` which will display as `p.=`.
+        if *start as usize > self.ref_seq().len() {
+            return Ok(HgvsVariant::ProtVariant {
+                accession: Accession::new(protein_accession),
+                gene_symbol: None,
+                loc_edit: ProtLocEdit::NoChange,
+            });
+        }
+
         // defaults
         let mut is_dup = false; // assume no dup
         let mut fsext_len = UncertainLengthChange::default(); // fs or ext length
diff --git a/src/normalizer.rs b/src/normalizer.rs
index 5a23a07..4825dcb 100644
--- a/src/normalizer.rs
+++ b/src/normalizer.rs
@@ -413,7 +413,7 @@ impl<'a> Normalizer<'a> {
             if stop < ref_seq.len().try_into()? || start == orig_start {
                 break;
             }
-            // If stop at the end of the window, try to extend teh shuffling to the right.
+            // If stop at the end of the window, try to extend the shuffling to the right.
             base += start - orig_start;
             stop -= start - orig_start;
             start = orig_start;