core.segment.cpp: sequences may be too short to extract their CDR3

dbcc9d2f · Mathieu Giraud · 5beb3cbf · dbcc9d2f
Commit dbcc9d2f authored Feb 28, 2016 by Mathieu Giraud
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algo/core/segment.cpp algo/core/segment.cpp +4 -0

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--- 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;