From dbcc9d2fd587914947663c158bc57c70a14b1d38 Mon Sep 17 00:00:00 2001
From: Mathieu Giraud <mathieu@vidjil.org>
Date: Sun, 28 Feb 2016 13:06:29 +0100
Subject: [PATCH] core.segment.cpp: sequences may be too short to extract their
 CDR3

---
 algo/core/segment.cpp | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/algo/core/segment.cpp b/algo/core/segment.cpp
index ab19c75e0..b766f3b26 100644
--- a/algo/core/segment.cpp
+++ b/algo/core/segment.cpp
@@ -1058,6 +1058,10 @@ void FineSegmenter::findCDR3(){
   JUNCTIONstart = (box_V->end + 1 + 1) - V_104_offset;
   JUNCTIONend = (box_J->start + 1 - 1) + J_118_offset;
 
+  // Sequence may be too short
+  if (JUNCTIONstart < 1 || JUNCTIONend > getSequence().sequence.length())
+    return ;
+
   // IMGT-CDR3 is, on each side, 3 nucleotides shorter than IMGT-JUNCTION
   CDR3start = JUNCTIONstart + 3;
   CDR3end = JUNCTIONend - 3;
-- 
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