PufferfishContigStats

int getPufferfishContigStats(IndexT& pi) {
  //size_t k = pi.k();
  CanonicalKmer::k(pi.k());
  size_t found = 0;
  size_t notFound = 0;
  size_t correctPosCntr = 0;
  size_t incorrectPosCntr = 0;
  size_t numTrueTxp = 0;
  size_t numLostTxp = 0;
  std::ofstream out("contigInfo.txt");
  std::cerr << "store the contig info\n";
  uint64_t cid{0}, totalLength{0};
  while (totalLength < pi.getSeq().size()) {
    auto kmer = pi.getStartKmer(cid);
    auto clen = pi.getContigLen(cid);
    totalLength += clen;
    out << cid << "\t" << clen << "\t"; // contigId, contigLen
    float sumTxphits{0};
    std::unordered_map<uint64_t, uint64_t> txpCntMap;
    auto chits = pi.getRefPos(kmer) ;
    for (auto& rpos : chits.refRange) {
      if (txpCntMap.find(rpos.transcript_id()) == txpCntMap.end())
        txpCntMap[rpos.transcript_id()] = 0;
      txpCntMap[rpos.transcript_id()]++;
    }
    for (auto kv: txpCntMap) {
      sumTxphits += kv.second;
    }
    out << txpCntMap.size() << "\t" << (txpCntMap.size() > 0 ? sumTxphits/txpCntMap.size():0) << "\n"; // # of txps, avg of hits per txp
    cid++;
  }
}