Commit dbcc9d2f authored by Mathieu Giraud's avatar Mathieu Giraud

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

parent 5beb3cbf
......@@ -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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