void ReadContainer::addUpstreamRead ( const Genome& genome, const chr_num_t chr, const chr_pos_t pos ) {
  assume(pos <= 0, "3' ends need to be given as negative numbers!");
  int ipos = pos - 1; // fix difference in one-based offsets
  auto upstr = genome.getReadAt(chr, ipos); // 3' ends are linked at negative indices
  if (upstr != nullptr) {

    // check if this is a multistrand splice junction
    if (genome.multistrand != nullptr &&
	(upstr->chromosome != chromosome || (upstr->flags & MULTISTRAND) == MULTISTRAND)) {
      upstr->flags |= MULTISTRAND;
      flags |= MULTISTRAND;
      genome.multistrand->insert(shared_from_this());
      genome.multistrand->insert(upstr);
    }
    
    int link = findLink(upstr, false); // search link  upstr <= this
    int backLink = upstr->findLink(shared_from_this()); // search link upstr => this

    if (link == -1) { // upstr <= this unknown yet
      fivePrimeRead->push_back(upstr);
    }

    if (backLink >= 0) { // upstr => this known
      upstr->threePrimeRefs->at(backLink)++;
    }
    else { // upstr => this new
      upstr->threePrimeRead->push_back(shared_from_this());
      upstr->threePrimeRefs->push_back(1);
    }
  }
}
void ReadContainer::addDownstreamRead ( const Genome& genome, const chr_num_t chr, const chr_pos_t pos ) {
  auto dnstr = genome.getReadAt(chr, pos);
  if (dnstr != nullptr) {
    // check if this is a multistrand splice junction
    if (dnstr->chromosome != chromosome && !(dnstr->flags & MULTISTRAND) ) {
      flags |= MULTISTRAND;
      genome.multistrand->insert(shared_from_this());    // adding one multistrand seed suffices
    }

    int link = findLink(dnstr); // search link this => dnstr
    int backLink = dnstr->findLink(shared_from_this(), false); // search link this <= dnstr

    if (link == -1) { // this => dnstr unknown yet
      threePrimeRead->push_back(dnstr);
      threePrimeRefs->push_back(1);
    }
    else { // this => dnstr known
      threePrimeRefs->at(link)++;
    }
    if (backLink == -1) { // this <= dnstr unknown yet
      dnstr->fivePrimeRead->push_back(shared_from_this());
    }
  }
}