Commit e2bff0aa authored by Mathieu Giraud's avatar Mathieu Giraud

core/segment.{h,cpp}: remember in AligBox the 'marked_pos' coming from the DP backtrack

parent 6e1d108c
......@@ -722,7 +722,8 @@ void align_against_collection(string &read, Fasta &rep, int forbidden_rep_id,
DynProg dp = DynProg(sequence_or_rc, rep.sequence(r),
dpMode, // DynProg::SemiGlobalTrans,
segment_cost, // DNA
reverse_both, reverse_both);
reverse_both, reverse_both,
rep.read(r).marked_pos);
bool onlyBottomTriangle = !local ;
int score = dp.compute(onlyBottomTriangle, BOTTOM_TRIANGLE_SHIFT);
......@@ -740,6 +741,10 @@ void align_against_collection(string &read, Fasta &rep, int forbidden_rep_id,
best_first_j = dp.first_j ;
box->ref_nb = r ;
box->ref_label = rep.label(r) ;
if (!local)
dp.backtrack();
box->marked_pos = dp.marked_pos_i ;
}
score_r.push_back(make_pair(score, r));
......
......@@ -91,6 +91,9 @@ class AlignBox
string ref_label;
string ref;
/* Marked position, for Cys104 and Phe118/Trp118 */
int marked_pos;
/* Identifiers and scores of other possible reference sequence */
vector<pair<int, int> > score;
};
......
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