Method printRatio

src/GenomeCopyNumber.cpp:1670–1716

	return chrCopyNumber_[index];
}
void GenomeCopyNumber::printRatio(std::string const& outFile, bool ifBedGraphOutPut, bool printNA) {
    std::ofstream file (outFile.c_str());
    map<string,int>::iterator it;

    if (ifBedGraphOutPut==false) {
        file << "Chromosome\tStart\tRatio\tMedianRatio\tCopyNumber";


        if (hasBAF_==1){
            file << "\tBAF\testimatedBAF\tGenotype\tUncertaintyOfGT";
        }
        if (WESanalysis == true)
            {
            file << "\tGene";
            }
        if (SeekingSubc_ == true)
            {
            file << "\tSubclone_CN\tSubclone_Population";
            }
        file << "\n";
        for ( it=chromosomesInd_.begin() ; it != chromosomesInd_.end(); it++ ) {
            printRatio((*it).first,file,printNA);
        }

    } else {
        //print a track for LOH if hasBAF_
        if (hasBAF_) {
            file << "track type=bedGraph name=\"copy neutral LOH from "<<outFile<<"\" description=\"Copy Neutral LOH\" color=100,100,100\n";
            for ( it=chromosomesInd_.begin() ; it != chromosomesInd_.end(); it++ ) {
                printRatioBedGraph((*it).first,file, "LOH");
            }
        }
        file << "track type=bedGraph name=\"gains from "<<outFile<<"\" description=\"Gains\" color=255,40,20\n";
        for ( it=chromosomesInd_.begin() ; it != chromosomesInd_.end(); it++ ) {
            printRatioBedGraph((*it).first,file, "gain");
        }
        file << "track type=bedGraph name=\"losses from "<<outFile<<"\" description=\"Losses\" color=20,40,255\n";
        for ( it=chromosomesInd_.begin() ; it != chromosomesInd_.end(); it++ ) {
            printRatioBedGraph((*it).first,file, "loss");
        }
        file << "track type=bedGraph name=\"neutral copy number from "<<outFile<<"\" description=\"Neutral Copy Number\" color=20,255,40\n";
        for ( it=chromosomesInd_.begin() ; it != chromosomesInd_.end(); it++ ) {
            printRatioBedGraph((*it).first,file, "normal");
        }
    }
    file.close();
}

void GenomeCopyNumber::printBAF(std::string const& outFile, SNPinGenome& snpingenome, std::string const& matefile) {
    string myName = outFile;