Project: s41467-024-52886-2 | Function: callThisConsensus (cpp)

system: You are an expert C++ programmer implementing algorithms from scientific papers.
Complete the masked function based on the algorithm description.
Follow C++ best practices and maintain consistent code style.
Return **only** the complete C++ function code.

user: Complete this C++ function:

**DESCRIPTION:** Identifies transcript errors by comparing CircSeq consensus sequences to reference genome, applying quality thresholds and depth filters to distinguish true errors from sequencing artifacts

**KEY TERMS:** {
  "csBase": "consensus base from CircSeq",
  "gBase": "genomic reference base",
  "minDepth": "minimum coverage depth threshold",
  "minConsensusQual": "minimum quality difference threshold",
  "nbPosDiff": "number of positions with differences",
  "CS_Candidate": "transcript error candidate",
  "vStatus_csPositions": "positions passing quality filters"
}

**CONTEXT CODE:** 
    int posBreakPoint1 = posBreakPoint;
    if( mappedRC == true ){
      seqan::reverseComplement(seq1);
      seqan::reverse(qual1);
      posBreakPoint1 = ( length(seq1) % csLg ) + posBreakPoint;
    }

    int posBreakPoint2 = (ppos.second + posBreakPoint) % csLg;
    if( pairedFile == true ){
      if( (reverseCptSeq2 == true && mappedRC == false) || (reverseCptSeq2==false && mappedRC==true)  ){
	//std::cerr<<"REVERSE!\n";
	seqan::reverseComplement(seq2);
	seqan::reverse(qual2);
      }

      if( mappedRC == true ){
	posBreakPoint2 = ( (length(seq2) - ppos.second) + posBreakPoint) % csLg;
      }
      
      vSeq[1] = std::string(seqan::toCString(seq2));
      vQual[1] = std::string(seqan::toCString(qual2));
      vPosFirstBreakPoint[1] = posBreakPoint2;
    }
      
    //std::cerr<<"seq2:'"<<seq2<<"'\n";
    vSeq[0] = std::string(seqan::toCString(seq1));
    vQual[0] = std::string(seqan::toCString(qual1));
    vPosFirstBreakPoint[0] = posBreakPoint1;

    /*
    std::cerr<<"seq1:"<<seq1<<'\n';
    std::cerr<<"seq2:"<<seq2<<'\n';
    std::cerr<<"ppos: "    <<ppos.first<<" - "<<ppos.second<<'\n';
    std::cerr<<"BP1:"<<posBreakPoint<<'\n';
    std::cerr<<"BP2:"<<posBreakPoint2<<'\n';
    */
    //auto start1 = high_resolution_clock::now();
    CS_Consensus cs(vSeq, vQual, csLg, vPosFirstBreakPoint, BI, illuminaMinScore);
    int nbMatch, nbMismatch;
    double csPrctMM = cs.getPrctMismatchesInsideConsensus(&nbMatch, &nbMismatch);
    outPrct<<readID<<'\t'<<csPrctMM<<"\n";
    if( csPrctMM > max_csPrctMM )
      continue;

    //auto stop1 = high_resolution_clock::now();
    //auto duration1 = duration_cast<nanoseconds>(stop1 - start1);
    //std::cerr<<"Building the consensus: "<<duration1.count()<<'\n';

    //auto start2 = high_resolution_clock::now();
    int nbPosDiff = callThisConsensus(cs,
				      nbExcludeStart, nbExcludeEnd,
				      record,
				      chrID, tStrand, mappedRC, strandSpecific,
				      ChrSeq, gt, vTtoG,
				      cobCalls, cobObs,
				      minDepth, allowAlternativeCalls, maxAltQual, minConsensusQual, nbMaxMMperCs,
				      BI, oneBased);

    if( nbPosDiff < 0 ){
      std::cerr<<"ERROR: nbPosDiff<0 --> Printing the structure for '"<<transcriptID<<"'\n";
      mTranscripts[transcriptID].printStructure(std::cerr);
      std::flush(std::cerr);
      exit(1);
    }
    
    //auto stop2 = high_resolution_clock::now();
    //auto duration2 = duration_cast<nanoseconds>(stop2 - start2);
    //std::cerr<<"Making the calls: "<<duration2.count()<<'\n';


    //std::cerr<<readID<<"\t"<<nbPosDiff<<'\n';
    //cs.printDetails(std::cout, BI);
    //std::cerr<<cs.getConsensus()<<'\n';   
  }
  
  cobCalls.print(outCalls, true, false, false, combineStrands, ChrSeq, BI, oneBased);
  cobObs.print(outObs, true, false, false, combineStrands, ChrSeq, BI, oneBased);

  boost::iostreams::close(outbufCalls);
  boost::iostreams::close(outbufObs);
  boost::iostreams::close(outbufPrct);
  ofsCalls.close();
  ofsObs.close();
  ofsPrct.close();
  
  return 0;
}



int callThisConsensus(CS_Consensus &cs,
		      int nbExcludeStart, int nbExcludeEnd,
		      seqan::BamAlignmentRecord &record,
		      std::string &chrID, char tStrand, bool mappedRC, bool strandSpecific,
		      seqan::CharString &ChrSeq,
		      GFFtranscriptCoordinates &gt,
		      std::vector<int> &vTtoG,
		      CS_ScaffoldObservations &cobCalls, CS_ScaffoldObservations &cobObs,
		      int minDepth, int allowAlternativeCalls, int maxAltQual, int minConsensusQual,
		      int nbMaxMMperCs, // How many divergent base calls are allowed per consensus?
		      BasesIndices &BI,
		      int oneBased
		      ){
    std::cerr << "Function callThisConsensus has been masked" << std::endl;
    throw std::runtime_error("Function implementation has been masked");
    return -1;
}


Complete the function implementation replacing "throw std::runtime_error("Not implemented");".