Method processRead

src/GenomeCopyNumber.cpp:3793–4129

*/

int GenomeCopyNumber::processRead(InputFormat inputFormat, MateOrientation matesOrientation, const char* line_buffer, int & prevInd,std::string targetBed, std::string mateFileName)
{

    int read_Size =150; // in case it is not initialized (e.g. for Pileup files)

    if (!*line_buffer) {
        return 0;
    }

    int valueToReturn = 0;

    if (inputFormat == SAM_INPUT_FORMAT && matesOrientation != SINGLE_END_SORTED_SAM) {
        if (line_buffer[0] == '@')
            return 0;
        if (WESanalysis == true)  {
            string chr1, chr2;
            char orient1, orient2;
            int left,right, insert_size;

            if (getSAMinfo(line_buffer,chr1,chr2,orient1,orient2,left,right, insert_size)) {
                char orient1_2_str[] = {orient1, orient2, 0};
                char orient2_1_str[] = {orient2, orient1, 0};
                MateOrientation orient1_2 = getMateOrientation(orient1_2_str);
                MateOrientation orient2_1 = getMateOrientation(orient2_1_str);
                if ((matesOrientation == orient1_2 && right-left>0) || (matesOrientation == orient2_1 && right-left<0)) {
                    left = min(left, right);
                    right  = left + abs(insert_size);
                    int index = findIndex(chr1);
                    if (index!=NA && chrCopyNumber_[index].getExons_Countchr() != 0) {
                        bool leftIsInTheWindow = false;
                        int l = 0;
                       // try around this value first
                        for (l=prevInd-1; l<=prevInd+30 && l<chrCopyNumber_[index].getExons_Countchr();l++ ) {
                            if ((left - 1 < chrCopyNumber_[index].getEndAtBin(l) && (left > (chrCopyNumber_[index].getCoordinateAtBin(l) - insert_size)))) {
                                leftIsInTheWindow = true;
                                prevInd=l;
                                break;
                            }
                        }
                        if (!leftIsInTheWindow) {
                             //start from the beginning of the chromosome
                            for (l=0; left>=chrCopyNumber_[index].getCoordinateAtBin(l)- 30*insert_size && l<chrCopyNumber_[index].getExons_Countchr();l++ ) {
                                if ((left - 1 < chrCopyNumber_[index].getEndAtBin(l) && (left > (chrCopyNumber_[index].getCoordinateAtBin(l) - insert_size)))) {
                                    leftIsInTheWindow = true;
                                    prevInd=l;
                                    break;
                                }
                            }
                        }
                        if (leftIsInTheWindow == false)   {
                            valueToReturn = 0;
                            return valueToReturn;
                        }
                        if ((right >  chrCopyNumber_[index].getCoordinateAtBin(l)) && (leftIsInTheWindow == true))   {
                            step_ = chrCopyNumber_[index].getEndAtBin(l) - chrCopyNumber_[index].getCoordinateAtBin(l) + insert_size +1;
                            chrCopyNumber_[index].mappedPlusOneAtI(left,step_, l);
                            valueToReturn = 1;
                            step_ = 0;