Add getter for filter attribute in germline

The filter attribute has now a getter function. This way the filter attribute
can be used outside of the germline class.

For more informations see #3283.

algo/core/germline.cpp

@@ -208,6 +208,10 @@ void Germline::override_rep5_rep3_from_labels(KmerAffect left, KmerAffect right)
   rep_3 = index->getLabel(right);
 }
 
+FilterWithACAutomaton* Germline::getFilter(){
+  return this->filter;
+}
+
 Germline::~Germline()
 {
   if(automaton_5){

algo/core/germline.h

@@ -115,11 +115,13 @@ class Germline {
   string affect_5 ;
   string affect_4 ;
   string affect_3 ;
-  
+
   BioReader  rep_5 ;
   BioReader  rep_4 ;
   BioReader  rep_3 ;
   IKmerStore<KmerAffect> *index;
+
+  FilterWithACAutomaton* getFilter();
 };
 
 ostream &operator<<(ostream &out, const Germline &germline);