Get back singletons

      uint64_t value = kh_value(lookup_table_, khash_iterator);

      uint32_t read_position = minimizers[mi].second >> 1;

      if (kh_key(lookup_table_, khash_iterator) & 1) { // singleton

        //uint64_t reference_id = value >> 33;

        //uint32_t reference_position = value >> 1;

        //// Check whether the strands of reference minimizer and read minimizer are the same

        //// Later, we can play some tricks with 0,1 here to make it faster.

        //if (((minimizers[mi].second & 1) ^ (value & 1)) == 0) { // same

        //  if (direction == kPositive) {

        //    uint32_t candidate_position = reference_position - read_position;// > 0 ? reference_position - read_position : 0;

        //    // ok, for now we can't see the reference here. So let us don't do the check.

        //    // Instead, we do it later some time when we check the candidates.

        //    uint64_t candidate = (reference_id << 32) | candidate_position;

        //    hits->push_back(candidate);

        //  }

        //} else if (direction == kNegative) {

        //  uint32_t candidate_position = reference_position + read_position - kmer_size_ + 1;// < reference_length ? reference_position - read_position : 0;

        //  uint64_t candidate = (reference_id << 32) | candidate_position;

        //  hits->push_back(candidate);

        //}

        uint64_t reference_id = value >> 33;

        uint32_t reference_position = value >> 1;

        // Check whether the strands of reference minimizer and read minimizer are the same

        // Later, we can play some tricks with 0,1 here to make it faster.

        if (((minimizers[mi].second & 1) ^ (value & 1)) == 0) { // same

          if (direction == kPositive) {

            uint32_t candidate_position = reference_position - read_position;// > 0 ? reference_position - read_position : 0;

            // ok, for now we can't see the reference here. So let us don't do the check.

            // Instead, we do it later some time when we check the candidates.

            uint64_t candidate = (reference_id << 32) | candidate_position;

            hits->push_back(candidate);

          }

        } else if (direction == kNegative) {

          uint32_t candidate_position = reference_position + read_position - kmer_size_ + 1;// < reference_length ? reference_position - read_position : 0;

          uint64_t candidate = (reference_id << 32) | candidate_position;

          hits->push_back(candidate);

        }

      } else {

        uint32_t offset = value >> 32;

        uint32_t num_occurrences = value;