Commit 6391a287 authored by Mathieu Giraud's avatar Mathieu Giraud

core/segment.cpp: breaking refactor, no reverse conversion here

parent 20f017b9
...@@ -1089,10 +1089,6 @@ FineSegmenter::FineSegmenter(Sequence seq, Germline *germline, Cost segment_c, ...@@ -1089,10 +1089,6 @@ FineSegmenter::FineSegmenter(Sequence seq, Germline *germline, Cost segment_c,
} }
align_against_collection(sequence_or_rc, germline->rep_3, NO_FORBIDDEN_ID, reverse_J, !reverse_J, false, align_against_collection(sequence_or_rc, germline->rep_3, NO_FORBIDDEN_ID, reverse_J, !reverse_J, false,
box_J, segment_cost, false, standardised_threshold_evalue); box_J, segment_cost, false, standardised_threshold_evalue);
// J was run with '!reverseJ', we copy the box informations from right to left
// Should this directly be handled in align_against_collection() ?
box_J->start = box_J->end ;
box_J->del_left = box_J->del_right;
/* E-values */ /* E-values */
evalue_left = multiplier * sequence.size() * germline->rep_5.totalSize() * segment_cost.toPValue(box_V->score[0].first); evalue_left = multiplier * sequence.size() * germline->rep_5.totalSize() * segment_cost.toPValue(box_V->score[0].first);
......
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