Free memory in Filter and Germline

Since the Germline now contains a Filter object instead of an automaton
and respectively Filter contains the automaton. Both of them have to
free the memory allocated correctly.

For more informations, see #3283.

algo/core/filter.cpp

@@ -5,7 +5,8 @@ FilterWithACAutomaton::FilterWithACAutomaton(BioReader &origin, string seed){
 }
 
 FilterWithACAutomaton::~FilterWithACAutomaton(){
-
+  delete p->first;
+  delete p->second;
 }
 
 void FilterWithACAutomaton::buildACAutomatonToFilterBioReader

algo/core/germline.cpp

@@ -214,14 +214,8 @@ FilterWithACAutomaton* Germline::getFilter(){
 
 Germline::~Germline()
 {
-  if(automaton_5){
-    if(automaton_5->first){
-      delete automaton_5->first;
-    }
-    if(automaton_5->second){
-      delete automaton_5->second;
-    }
-    delete automaton_5;
+  if(filter){
+    delete filter;
   }
   if (index)
     {

algo/tests/unit-tests/testFilter.cpp

@@ -247,9 +247,7 @@ void testAutomatonBuilderFilteringBioReader(){
       TEST_LABEL_ERROR);
     }
   }
-  delete pair1->first; delete pair1->second; delete pair1;
-  delete pair2->first; delete pair2->second; delete pair2;
-  delete pair3->first; delete pair3->second; delete pair3;
+  delete f1; delete f2; delete f3;
 }
 
 void testFilterBioReaderWithACAutomaton(){
@@ -337,10 +335,7 @@ void testFilterBioReaderWithACAutomaton(){
               TEST_FILTER_BIOREADER_WITH_AC_AUTOMATON, GENES_ERROR);
     }
   }
-
-  delete pair1->first, delete pair1->second; delete pair1;
-  delete pair2->first; delete pair2->second; delete pair2;
-  delete pair3->first; delete pair3->second; delete pair3;
+  delete f1; delete f2; delete f3;
 }
 
 void testGetNSignicativeKmers(){
@@ -364,6 +359,7 @@ void testGetNSignicativeKmers(){
     Sequence seq = germline.rep_5.read(i);
     FilterWithACAutomaton *f = germline.getFilter();
     filtered = f->filterBioReaderWithACAutomaton(germline.rep_5, seq.sequence, 1);
+    delete f;
     int j = 0;
     while(j < filtered.size()){
       if(extractGeneName(filtered.label(j)) == extractGeneName(seq.label)){