From 475398d0e831afa43abc53327abb14135df40aea Mon Sep 17 00:00:00 2001
From: Manuel Holtgrewe <manuel.holtgrewe@bih-charite.de>
Date: Fri, 24 Mar 2023 10:48:25 +0100
Subject: [PATCH] fix: issue with out of bounds deletion (#59)

---
 src/mapper/altseq.rs | 10 +++++++---
 1 file changed, 7 insertions(+), 3 deletions(-)

diff --git a/src/mapper/altseq.rs b/src/mapper/altseq.rs
index d4070ec..1080588 100644
--- a/src/mapper/altseq.rs
+++ b/src/mapper/altseq.rs
@@ -324,12 +324,16 @@ impl AltSeqBuilder {
             _ => panic!("invalid variant"),
         }
 
+        let seq = self.reference_data.transcript_sequence.to_owned();
+        let start = std::cmp::min(start_end[0], seq.len());
+        let end = std::cmp::min(start_end[1] + 1, seq.len());
+
         (
-            self.reference_data.transcript_sequence.to_owned(),
+            seq,
             self.reference_data.cds_start,
             self.reference_data.cds_stop,
-            start_end[0],
-            start_end[1] + 1,
+            start,
+            end,
         )
     }