Commit 4f6c817c authored by Cyprien Borée's avatar Cyprien Borée

store filtered bioreader in FineSegmenter

It is necessary to store this bioReader since the N best genes that will be
exported to the Json are based on it.

For more informations, see #1409.
parent 50331bad
......@@ -1050,9 +1050,9 @@ FineSegmenter::FineSegmenter(Sequence seq, Germline *germline, Cost segment_c,
/* Regular 53 Segmentation */
if(kmer_threshold != NO_LIMIT_VALUE){
FilterWithACAutomaton* f = germline->getFilter_5();
BioReader filtered = f->filterBioReaderWithACAutomaton(sequence_or_rc, kmer_threshold);
align_against_collection(sequence_or_rc, filtered, NO_FORBIDDEN_ID, reverse_V, reverse_V, false,
FilterWithACAutomaton* f = germline->getFilter_5();
this->filtered_rep_5 = f->filterBioReaderWithACAutomaton(sequence_or_rc, kmer_threshold);
align_against_collection(sequence_or_rc, this->filtered_rep_5, NO_FORBIDDEN_ID, reverse_V, reverse_V, false,
box_V, segment_cost, false, standardised_threshold_evalue);
align_against_collection(sequence_or_rc, germline->rep_5, NO_FORBIDDEN_ID, reverse_V, reverse_V, false,
......@@ -356,6 +356,7 @@ class KmerMultiSegmenter
class FineSegmenter : public Segmenter
BioReader filtered_rep_5;
int alternative_genes;
vector<pair<int, int> > score_V;
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