code: protected static String getReferenceBase(String chromosome, int from, int to, Map<Integer, Character> referenceAlleles) {
          int length = to - from;
          if (length < 0) {
              throw new IllegalStateException(
                      "Sequence length is negative: chromosome " + chromosome + " from " + from + " to " + to);
          }
          StringBuilder sb = new StringBuilder(length);
          for (int i = from; i < to; i++) {
              sb.append(referenceAlleles.getOrDefault(i, 'N'));
          }
          return sb.toString();
      //        return StringUtils.repeat('N', length); // current return default base TODO load reference sequence
      }
docs: Get bases from reference sequence.
  
  @param chromosome        Chromosome
  @param from              Start ( inclusive) position
  @param to                End (exclusive) position
  @param referenceAlleles  Reference alleles
  @return String Reference sequence of length to - from