Method initCopyNumber

src/GenomeCopyNumber.cpp:175–211

}

void GenomeCopyNumber::initCopyNumber(std::string const& chrLenFileName, int windowSize , int step, std::string targetBed) {

  ThreadPoolManager::getInstance()->lock();
  if (WESanalysis == false)  {
    if (step == NA) {
	  step = windowSize;
	}
    //check if steo value is correct:
    if (step <= 0 || step > windowSize) {
        cerr << "step  should be a positive interger value less than or equal to the window size\n";
        exit(-1);
    }
    step_=step;
	windowSize_ = windowSize;
	//reading the file with genome information
	std::vector<std::string> names;
	std::vector<int> lengths;
	readFileWithGenomeInfo(chrLenFileName, names, lengths);
	refGenomeSize_ = sum(lengths);
	for (int i = 0; i < (int) names.size(); i++) {
		ChrCopyNumber chrCopyNumber(windowSize, lengths[i],names[i], step);
		chromosomesInd_.insert(pair<string, int> (names[i],i));
		chrCopyNumber_.push_back(chrCopyNumber);
	}
   }   else   {
    std::vector<std::string> names;
	std::vector<int> lengths;
	readFileWithGenomeInfo(chrLenFileName, names, lengths);
	refGenomeSize_ = sum(lengths);
	for (int i = 0; i < (int) names.size(); i++) {
		ChrCopyNumber chrCopyNumber(windowSize, lengths[i],names[i], step, targetBed);
		chromosomesInd_.insert(pair<string, int> (names[i],i));
		chrCopyNumber_.push_back(chrCopyNumber);
    }
   }
   ThreadPoolManager::getInstance()->unlock();
}

void GenomeCopyNumber::finishCopyNumber(long normalCount) {
	totalNumberOfPairs_ = normalCount;