Method recalculateRatio

src/GenomeCopyNumber.cpp:425–440

}

void GenomeCopyNumber::recalculateRatio (float contamination) {
	if (contamination >= 1 || contamination <= 0) {
        cerr << "contamination should be between 0 and 1\n";
        exit(-1);
	}
	vector<ChrCopyNumber>::iterator it;

    for ( it=chrCopyNumber_.begin() ; it != chrCopyNumber_.end(); it++ ) {
        if (sex_.compare("XY")==0 && (it->getChromosome().find("X")!=string::npos || it->getChromosome().find("Y")!=string::npos)) {
            //should take into account that normally one has only one copy of X and Y..
            it->recalculateRatioWithContam(contamination,0.5, isRatioLogged_);
	    } else
            it->recalculateRatioWithContam(contamination,1, isRatioLogged_);
	}

}

void GenomeCopyNumber::recalculateRatioUsingCG (int degree, bool intercept, float minExpectedGC, float maxExpectedGC) {