Method recalcFlanksForIndeces

src/ChrCopyNumber.cpp:1341–1378

}

void ChrCopyNumber::recalcFlanksForIndeces (int i_start, int i_end) {
        vector <float> data;
        int notNA = 0;
        int totalCount = 0;
        int breakPointStart = 0;
        int breakPointEnd = 0;
        for (int i = i_start; i<=i_end; i++) { //collect data points:
            breakPointStart = 0;
            if (i>0)
                breakPointStart = bpfinal_[i-1]+1;
            breakPointEnd = bpfinal_[i];
            for (int j = breakPointStart; j <= breakPointEnd; j++)
                if (ratio_[j] != NA) {
                    data.push_back(ratio_[j]);
                    notNA++;
                }
            totalCount += breakPointEnd-breakPointStart+1;
        }
        float median;
        if (notNA==0 ||(notNA == 1 && totalCount>2)) {
           // median = get_median(data);
            median = NA;
        } else {
            median = get_median(data); //including the last point!!!!
        }
        float sd_local = sd(data,median);

        for (int i = i_start; i<=i_end; i++) {
            medianValues_[i] = median;
            sd_[i] = sd_local;
        }

        breakPointStart = 0;
        if (i_start>0)
                breakPointStart = bpfinal_[i_start-1]+1;
        for (int j = breakPointStart; j<= breakPointEnd; j++)
            medianProfile_[j] = median;
}

void ChrCopyNumber::clearCGcontent () {
	GCprofile_.clear ();