Commit 581dd39d authored by Mathieu Giraud's avatar Mathieu Giraud
Browse files

core/segment.{h,cpp}: computeSegmentation takes germline as an argument

Moreover, the argument 's' was not used
parent a3dba9fe
......@@ -215,7 +215,7 @@ KmerSegmenter::KmerSegmenter(Sequence seq, MultiGermline *multigermline)
strand = 2;
}
computeSegmentation(strand, germline->delta_min, germline->delta_max, s);
computeSegmentation(strand, germline);
if (segmented)
{
......@@ -241,7 +241,7 @@ KmerSegmenter::~KmerSegmenter() {
delete kaa;
}
void KmerSegmenter::computeSegmentation(int strand, int delta_min, int delta_max, int s) {
void KmerSegmenter::computeSegmentation(int strand, Germline* germline) {
// Try to segment, computing 'Vend' and 'Jstart', and 'segmented'
// If not segmented, put the cause of unsegmentation in 'because'
......@@ -291,12 +291,12 @@ void KmerSegmenter::computeSegmentation(int strand, int delta_min, int delta_max
{
// Now we check the delta between Vend and right
if (Jstart - Vend < delta_min)
if (Jstart - Vend < germline->delta_min)
{
because = UNSEG_BAD_DELTA_MIN ;
}
if (Jstart - Vend > delta_max)
if (Jstart - Vend > germline->delta_max)
{
because = UNSEG_BAD_DELTA_MAX ;
}
......
......@@ -158,7 +158,7 @@ class KmerSegmenter : public Segmenter
int getSegmentationStatus() const;
private:
void computeSegmentation(int strand, int delta_min, int delta_max, int s);
void computeSegmentation(int strand, Germline* germline);
};
class FineSegmenter : public Segmenter
......
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