Method calculateBAFBreakpoints

src/ChrCopyNumber.cpp:692–701

}

int ChrCopyNumber::calculateBAFBreakpoints(double threshold, int normalChrLength, int breakPointType) {
    // bpfinal_ should already contain copy number breakpoints
    std::vector <int> bpBAF;
 	//find breakpoints in the BAF profile
 	int chrLen = calculateBreakpoints_general(threshold,length_,BAF_,bpBAF,normalChrLength,breakPointType, getChromosome());
 	//add detected breakpoints to the breakpoints detected using copy number profiles
 	bpfinal_ = merge_no_dups(bpfinal_, bpBAF);
 	sort (bpfinal_.begin(), bpfinal_.end());
 	return chrLen;
}

int ChrCopyNumber::getCoveredPart(int breakPointStart, int breakPointEnd) { //for exome-seq: get length of the genome covered by the targeted region (from breakPointStart to breakPointEnd)
    int lengthCovered = 0;