Method readCopyNumber

src/GenomeCopyNumber.cpp:42–72

bool GenomeCopyNumber::isMappUsed() {return isMappUsed_;}

void GenomeCopyNumber::readCopyNumber(std::string const& mateFileName ,std::string const& inputFormat, std::string const& matesOrientation, std::string const& chrLenFileName, float coefficientOfVariation ) {
	//first get the number of reads and the genome size
	//long genomeSize = 0;
	long readNumber = 0;
	int windowSize;
	//reading the file with genome information
	std::vector<std::string> names;
	std::vector<int> lengths;
	readFileWithGenomeInfo(chrLenFileName, names, lengths);
	refGenomeSize_ = sum(lengths);
	cout << "\t total genome size:\t" << refGenomeSize_ << "\n";
	if ((inputFormat.compare("pileup")==0 || inputFormat.compare("SAMtools pileup")==0)) {
        	readNumber = getReadNumberFromPileup(mateFileName);
	} else {
	  readNumber = getLineNumber(mateFileName, pathToReference_, pathToSamtools_, pathToSambamba_, SambambaThreads_);
	}
	cout << "\t read number:\t" << readNumber << "\n";
	cout << "\t coefficientOfVariation:\t" << coefficientOfVariation << "\n";
	windowSize = round_f(float(1./(coefficientOfVariation*coefficientOfVariation)/readNumber*refGenomeSize_));
	cout << "\t evaluated window size:\t" << windowSize << "\n";
	for (int i = 0; i < (int) names.size(); i++) {
		ChrCopyNumber chrCopyNumber(windowSize, lengths[i],names[i]);
		chromosomesInd_.insert(pair<string, int> (names[i],i));
		chrCopyNumber_.push_back(chrCopyNumber);
	}
	//cout << "data structure created";
	//read mateFileName and calculate copyNumber

	GenomeCopyNumber::fillMyHash(mateFileName ,inputFormat, matesOrientation, windowSize, windowSize);

}

long GenomeCopyNumber::getNormalNumberOfPairs(void) {
	return normalNumberOfPairs_;