Commit 1967b490 authored by Mathieu Giraud's avatar Mathieu Giraud

core/segment.{h,cpp}: FineSegmenter takes a 'several_D' argument

parent 78bdbe5f
......@@ -921,7 +921,8 @@ bool FineSegmenter::FineSegmentD(Germline *germline,
return true;
}
void FineSegmenter::FineSegmentD(Germline *germline, double evalue_threshold, int multiplier){
void FineSegmenter::FineSegmentD(Germline *germline, bool several_D,
double evalue_threshold, int multiplier){
if (segmented){
......@@ -942,7 +943,7 @@ void FineSegmenter::FineSegmentD(Germline *germline, double evalue_threshold, in
vector <AlignBox*> boxes ;
boxes.push_back(box_V);
if (box_D->start - box_V->end >= DD_MIN_SEARCH)
if (several_D && (box_D->start - box_V->end >= DD_MIN_SEARCH))
{
bool d1 = FineSegmentD(germline,
box_V, box_D1, box_D,
......@@ -956,7 +957,7 @@ void FineSegmenter::FineSegmentD(Germline *germline, double evalue_threshold, in
boxes.push_back(box_D);
if (box_J->start - box_D->end >= DD_MIN_SEARCH)
if (several_D && (box_J->start - box_D->end >= DD_MIN_SEARCH))
{
bool d2 = FineSegmentD(germline,
box_D, box_D2, box_J,
......
......@@ -306,7 +306,7 @@ class FineSegmenter : public Segmenter
* extend segmentation from VJ to VDJ
* @param germline: germline used
*/
void FineSegmentD(Germline *germline,
void FineSegmentD(Germline *germline, bool several_D,
double threshold = THRESHOLD_NB_EXPECTED_D, int multiplier=1);
bool FineSegmentD(Germline *germline,
......
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