Method calculateBAFBreakpoints

src/GenomeCopyNumber.cpp:236–268

}

void GenomeCopyNumber::calculateBAFBreakpoints(double breakPointThreshold, int breakPointType) {
	cout << "..Calculating breakpoints for BAF, breakPointThreshold = " <<breakPointThreshold<<"\n";
#if 1
	ThreadPool* thrPool = ThreadPoolManager::getInstance()->newThreadPool("ChrCopyNumber_calculateBAFBreakpoint");
	for (vector<ChrCopyNumber>::iterator it = chrCopyNumber_.begin(); it != chrCopyNumber_.end(); it++) {
	  ChrCopyNumber& chrCopyNumber = *it;
	  ChrCopyNumberCalculateBreakpointArgWrapper* bkpArg = new ChrCopyNumberCalculateBreakpointArgWrapper(chrCopyNumber, breakPointThreshold, breakPointType);
	  thrPool->addThread(ChrCopyNumber_calculateBAFBreakpoint_wrapper, bkpArg);
	}

	thrPool->run();
	delete thrPool;
#else
	vector<ChrCopyNumber>::iterator it=chrCopyNumber_.begin();
	//calculate breakpoints for the first chromosome and get its length to normalize other graphs
	int firstChromLen = 0; //we don't know it
    if (it != chrCopyNumber_.end()) {
        cout << "..processing chromosome " <<it->getChromosome()<<"\n";
		firstChromLen = it->calculateBAFBreakpoints(breakPointThreshold, firstChromLen,breakPointType);
		if (firstChromLen == 0) {
            cerr << "..failed to run segmentation on chr" << it->getChromosome() << "\n..no chromosome length normalization will be performed\n";
		}
    }
    it++;
	for (  ; it != chrCopyNumber_.end(); it++ ) {
		cout << "..processing chromosome " <<it->getChromosome()<<"\n";
		int result = it->calculateBAFBreakpoints(breakPointThreshold, firstChromLen,breakPointType);
		if (result == 0) {
            cerr << "..failed to run segmentation on chr" << it->getChromosome() << "\n";
		}
	}
#endif
}

void GenomeCopyNumber::fillMyHash(std::string const& mateFileName ,std::string const& inputFormat_str, std::string const& matesOrientation_str, int windowSize , int step, std::string targetBed) {
	//read mateFileName and calculate copyNumber