Commit 221f79db authored by Mathieu Giraud's avatar Mathieu Giraud

core/segment.cpp: productivity check only inside V/J genes

Closes #2142
parent 89ba89a6
Pipeline #150816 passed with stages
in 36 minutes and 55 seconds
......@@ -1342,8 +1342,11 @@ void FineSegmenter::findCDR3(){
JUNCTIONaa = nuc_to_aa(subsequence(getSequence().sequence, JUNCTIONstart, CDR3start-1))
+ CDR3aa + nuc_to_aa(subsequence(getSequence().sequence, CDR3end+1, JUNCTIONend));
JUNCTIONproductive = (CDR3nuc.length() % 3 == 0) && (! hasInFrameStopCodon(getSequence().sequence, (JUNCTIONstart-1)%3));
string sequence_startV_stopJ = subsequence(getSequence().sequence, box_V->start+1, box_J->end+1);
int frame = (JUNCTIONstart-1 - box_V->start) % 3;
// Reminder: JUNCTIONstart is 1-based
JUNCTIONproductive = (CDR3nuc.length() % 3 == 0) && (!hasInFrameStopCodon(sequence_startV_stopJ, frame));
}
void FineSegmenter::checkWarnings(CloneOutput *clone, bool phony)
......
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