Method calculateCopyNumberProbs_and_genomeLength

src/GenomeCopyNumber.cpp:2122–2498

}

void GenomeCopyNumber::calculateCopyNumberProbs_and_genomeLength(int breakPointType) {
	estimationOfGenomeSize_ = 0;

	vector<ChrCopyNumber>::iterator it;
	unsigned long long count = 0;
    int min_fragment= telo_centromeric_flanks_/step_;
	int endsSize=0;
	string NormalBAF,NormalBAF_XY;
    float normalXYploidy=ploidy_*0.5; //will only use it when the genome is male

    if (hasBAF_) {
            NormalBAF = getNormalBAFforPloidy(ploidy_);
            NormalBAF_XY=getXYBAFforPloidy(ploidy_);//will only use it when the genome is male
    }

    CNVs_.clear();
    copyNumberProbs_.clear();

    //check it they are empty:
    cout << "copyNumberProbs_ contains:\n";
    map<int, double>::iterator itProb;
    for ( itProb=copyNumberProbs_.begin() ; itProb != copyNumberProbs_.end(); itProb++ )
    cout << (*itProb).first << " => " << (*itProb).second << "\n";

	for ( it=chrCopyNumber_.begin() ; it != chrCopyNumber_.end(); it++ ) {
		float previousLevel = NA;
		int lengthOfPreviousLevel = 0;
		float nextLevel = NA;
		int lengthOfNextLevel = 0;
		it->setIsSmoothed(true);
		string chr = it->getChromosome();
		cout << "..Annotation of CNVs for "<< chr <<"\n";
		//will use these three variables to collect CNVs:
		int start = 0;
		int end = NA;
		int cnumber = NA;
		string BAFSym = "-";
        string BAFprev = "-";
        string BAFnext = "-";
        string lBAF = "-";

        float lUncertainty = NA;
        float BAFUncertainty = NA;

        float normalLevel=1;
        if (sex_.compare("XY")==0 && (it->getChromosome().find("X")!=string::npos || it->getChromosome().find("Y")!=string::npos)) {
            normalLevel = 0.5;
        }

		for (int i = 0; i<(int)it->getMedianValues().size(); i++) {
			float level = it->getLevelAt(i, ploidy_);
			int fragmentLength =  it->getFragmentLengths()[i];
            if (hasBAF_) {
                BAFSym = it->getBAFsymbPerFrg(i);
                BAFUncertainty = it->getEstimatedBAFuncertaintyAtBin(i);
//                cout << "..Control: read "<< BAFSym << "\n";
            }