Commit 8de7558d authored by Cyprien Borée's avatar Cyprien Borée Committed by Mikaël Salson

segment.{h,cpp}: filters BioReader with automaton before calling align_against_collection

See #920 and #3190.

(squashed from earlier commits)
parent baed6fcd
......@@ -29,7 +29,10 @@
#include <cstring>
#include <string>
#include "windowExtractor.h"
#include <set>
#include "automaton.h"
#include <map>
#include <string>
#define NO_FORBIDDEN_ID (-1)
AlignBox::AlignBox(string _key, string _color) {
......@@ -1046,12 +1049,11 @@ FineSegmenter::FineSegmenter(Sequence seq, Germline *germline, Cost segment_c,
/* Regular 53 Segmentation */
align_against_collection(sequence_or_rc, germline->rep_5, NO_FORBIDDEN_ID, reverse_V, reverse_V, false,
BioReader filtered = filterBioReaderWithACAutomaton(germline->pair_automaton, germline->rep_5, sequence_or_rc);
align_against_collection(sequence_or_rc, filtered, NO_FORBIDDEN_ID, reverse_V, reverse_V, false,
box_V, segment_cost);
align_against_collection(sequence_or_rc, germline->rep_3, NO_FORBIDDEN_ID, reverse_J, !reverse_J, false,
box_J, segment_cost);
// 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 ;
......
......@@ -12,6 +12,7 @@
#include "kmeraffect.h"
#include "affectanalyser.h"
#include "../lib/json.hpp"
#include "filter.h"
// #define DEBUG_EVALUE
......
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