Use the germline filter object in segment.cpp

Since the filter methods are now in the Filter object stored in the Germline,
the segment.cpp file needs to use the Germline's Filter object in order to
filter its BioReader.

For more informations see #3283.

algo/core/segment.cpp

@@ -1050,7 +1050,8 @@ FineSegmenter::FineSegmenter(Sequence seq, Germline *germline, Cost segment_c,
 
   /* Regular 53 Segmentation */
   if(kmer_threshold != NO_LIMIT_VALUE){
-	  BioReader filtered = filterBioReaderWithACAutomaton(germline->automaton_5, germline->rep_5, sequence_or_rc, kmer_threshold);
+	  FilterWithACAutomaton* f = germline->getFilter();
+    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);
   }else{