Commit 7187fbcc authored by Mathieu Giraud's avatar Mathieu Giraud

core/segment.cpp: clean

parent 6dd212ad
......@@ -729,38 +729,19 @@ FineSegmenter::FineSegmenter(Sequence seq, Germline *germline, Cost segment_c,
string sequence_or_rc = revcomp(sequence, reversed); // sequence, possibly reversed
// Strand +
int plus_score = 0 ;
int tag_plus_V, tag_plus_J;
/* Segmentation */
int plus_length = 0 ;
int del_plus_V, del_plus_J ;
int del2=0;
int beg=0;
vector<pair<int, int> > score_plus_V;
vector<pair<int, int> > score_plus_J;
int plus_left = align_against_collection(sequence_or_rc, germline->rep_5, false, false, &tag_plus_V, &del_plus_V, &del2, &beg,
&plus_length, &score_plus_V
Vend = align_against_collection(sequence_or_rc, germline->rep_5, false, false, &best_V, &del_V, &del2, &beg,
&plus_length, &score_V
, segment_cost);
int plus_right = align_against_collection(sequence_or_rc, germline->rep_3, true, false, &tag_plus_J, &del_plus_J, &del2, &beg,
&plus_length, &score_plus_J
Jstart = align_against_collection(sequence_or_rc, germline->rep_3, true, false, &best_J, &del_J, &del2, &beg,
&plus_length, &score_J
, segment_cost);
plus_length += plus_right - plus_left ;
plus_score=score_plus_V[0].first + score_plus_J[0].first ;
{
Vend = plus_left ;
Jstart = plus_right ;
best_V = tag_plus_V ;
best_J = tag_plus_J ;
del_V = del_plus_V ;
del_J = del_plus_J ;
score_V=score_plus_V;
score_J=score_plus_J;
}
plus_length += Jstart - Vend ;
/* E-values */
evalue_left = multiplier * sequence.size() * germline->rep_5.totalSize() * segment_cost.toPValue(score_V[0].first);
......
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