Add FilterWithACAutomaton object in Germline

The Germline class now contains a FilterWithACAutomaton pointer which is built
if the Germline constructor has TRUE for the boolean build_automaton.

For more informations see #3283.

algo/core/germline.cpp

-
+#include "filter.h"
 #include "germline.h"
 #include "automaton.hpp"
 #include <fstream>
@@ -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";
-  automaton_5 = build_automaton ? buildACAutomatonToFilterBioReader(rep_5, seed) : nullptr;
+  filter = build_automaton ? new FilterWithACAutomaton(rep_5, seed) : nullptr;
 }
 
 

algo/core/germline.h

@@ -41,6 +41,8 @@ using json = nlohmann::json;
 
 class Germline {
  private:
+  FilterWithACAutomaton* filter;
+
   int max_indexing;
 
   void init(string _code, char _shortcut,