code: private static List<Contig> getContigsInVariantSet(String variantSetId,
        SexChromosomeFilter sexChromosomeFilter, OfflineAuth auth) throws IOException {
      List<Contig> contigs = Lists.newArrayList();
      for (ReferenceBound bound : GenomicsUtils.getReferenceBounds(variantSetId, auth)) {
        if (sexChromosomeFilter == SexChromosomeFilter.EXCLUDE_XY
            && SEX_CHROMOSOME_REGEXP.matcher(bound.getReferenceName()).matches()) {
          // X and Y can skew some analysis results
          continue;
        }
        contigs.add(new Contig(bound.getReferenceName(), 0, bound.getUpperBound()));
      }
      return contigs;
    }
docs: Retrieve the list of all the reference names and their start=0/end positions for the variantSet.
  
  Note that start is hardcoded to zero since the referenceBounds only include the upper bound.
  
  @param variantSetId - The id of the variantSet to query.
  @param sexChromosomeFilter - An enum value indicating how sex chromosomes should be
  handled in the result.
  @return The list of all references in the variantSet.
  @throws IOException