Commit 46538a57 authored by Mikaël Salson's avatar Mikaël Salson

Germline: Create Aho-Corasick automaton rather than kmer index

parent d7d99079
#include "germline.h" #include "germline.h"
#include "automaton.hpp"
#include <fstream> #include <fstream>
#include <ctype.h> #include <ctype.h>
...@@ -154,7 +155,7 @@ void Germline::new_index() ...@@ -154,7 +155,7 @@ void Germline::new_index()
assert(! seed.empty()); assert(! seed.empty());
bool rc = true ; bool rc = true ;
index = KmerStoreFactory::createIndex<KmerAffect>(seed, rc); index = new PointerACAutomaton<KmerAffect>(seed, rc);
index->refs = 1; index->refs = 1;
update_index(); update_index();
...@@ -310,7 +311,7 @@ void MultiGermline::insert_in_one_index(IKmerStore<KmerAffect> *_index, bool set ...@@ -310,7 +311,7 @@ void MultiGermline::insert_in_one_index(IKmerStore<KmerAffect> *_index, bool set
void MultiGermline::build_with_one_index(string seed, bool set_index) void MultiGermline::build_with_one_index(string seed, bool set_index)
{ {
bool rc = true ; bool rc = true ;
index = KmerStoreFactory::createIndex<KmerAffect>(seed, rc); index = new PointerACAutomaton<KmerAffect>(seed, rc);
insert_in_one_index(index, set_index); insert_in_one_index(index, set_index);
} }
......
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