Commit 936075ea authored by Cyprien Borée's avatar Cyprien Borée Committed by Mikaël Salson

Replace "filter" with "filter_5" in germline and functions calls

Since the filter operates only on the bioreader n°5, its name has been changed.

For more informations, see #3283.
parent 66243b83
......@@ -24,7 +24,7 @@ void Germline::init(string _code, char _shortcut,
affect_5 = string(1, toupper(shortcut)) + "-" + code + "V";
affect_4 = string(1, 14 + shortcut) + "-" + code + "D";
affect_3 = string(1, tolower(shortcut)) + "-" + code + "J";
filter = build_automaton ? new FilterWithACAutomaton(rep_5, seed) : nullptr;
filter_5 = build_automaton ? new FilterWithACAutomaton(rep_5, seed) : nullptr;
}
......@@ -208,14 +208,14 @@ void Germline::override_rep5_rep3_from_labels(KmerAffect left, KmerAffect right)
rep_3 = index->getLabel(right);
}
FilterWithACAutomaton* Germline::getFilter(){
return this->filter;
FilterWithACAutomaton* Germline::getFilter_5(){
return this->filter_5;
}
Germline::~Germline()
{
if(filter){
delete filter;
if(filter_5){
delete filter_5;
}
if (index)
{
......
......@@ -41,7 +41,7 @@ using json = nlohmann::json;
class Germline {
private:
FilterWithACAutomaton* filter;
FilterWithACAutomaton* filter_5;
int max_indexing;
......@@ -121,7 +121,7 @@ class Germline {
BioReader rep_3 ;
IKmerStore<KmerAffect> *index;
FilterWithACAutomaton* getFilter();
FilterWithACAutomaton* getFilter_5();
};
ostream &operator<<(ostream &out, const Germline &germline);
......
......@@ -1050,7 +1050,7 @@ FineSegmenter::FineSegmenter(Sequence seq, Germline *germline, Cost segment_c,
/* Regular 53 Segmentation */
if(kmer_threshold != NO_LIMIT_VALUE){
FilterWithACAutomaton* f = germline->getFilter();
FilterWithACAutomaton* f = germline->getFilter_5();
BioReader filtered = f->filterBioReaderWithACAutomaton(germline->rep_5, sequence_or_rc, kmer_threshold);
align_against_collection(sequence_or_rc, filtered, NO_FORBIDDEN_ID, reverse_V, reverse_V, false,
box_V, segment_cost);
......
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