Commit 6d7f1bb0 authored by Mathieu Giraud's avatar Mathieu Giraud

core/segment.{h,cpp}: use sequence_or_rc in codeFromBoxes()

We need to store sequence_or_rc in the Segmenter.
parent ddf3dc36
......@@ -806,7 +806,7 @@ FineSegmenter::FineSegmenter(Sequence seq, Germline *germline, Cost segment_c,
reversed = kseg->isReverse();
delete kseg ;
string sequence_or_rc = revcomp(sequence, reversed); // sequence, possibly reversed
sequence_or_rc = revcomp(sequence, reversed); // sequence, possibly reversed
/* Segmentation */
......@@ -863,7 +863,7 @@ FineSegmenter::FineSegmenter(Sequence seq, Germline *germline, Cost segment_c,
vector <AlignBox*> boxes ;
boxes.push_back(box_V);
boxes.push_back(box_J);
code = codeFromBoxes(boxes, sequence);
code = codeFromBoxes(boxes, sequence_or_rc);
info = string_of_int(box_V->end + FIRST_POS) + " " + string_of_int(box_J->start + FIRST_POS) ;
finishSegmentation();
......@@ -925,7 +925,7 @@ void FineSegmenter::FineSegmentD(Germline *germline, double evalue_threshold, in
boxes.push_back(box_V);
boxes.push_back(box_D);
boxes.push_back(box_J);
code = codeFromBoxes(boxes, sequence);
code = codeFromBoxes(boxes, sequence_or_rc);
finishSegmentationD();
}
......
......@@ -115,6 +115,7 @@ string check_and_resolve_overlap(string seq, int seq_begin, int seq_end,
class Segmenter {
protected:
string sequence;
string sequence_or_rc;
int Vend, Jstart;
int Dstart, Dend;
int CDR3start, CDR3end;
......
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