code: public int addReference(NucleotideSequence sequence) {
          if (sequence.containWildcards())
              throw new IllegalArgumentException("Reference sequences with wildcards not supported.");
          int id = mapper.addReference(sequence);
          assert sequences.size() == id;
          sequences.add(sequence);
          return id;
      }
docs: Adds new reference sequence to the base of this mapper and returns index assigned to it.
  
  @param sequence sequence
  @return index assigned to the sequence