Method statRead

src/stats.cpp:191–291

}

void Stats::statRead(Read* r) {
    int len = r->length();

    mLengthSum += len;

    if(mBufLen < len) {
        extendBuffer(max(len + 100, (int)(len * 1.5)));
    }
    const char* seqstr = r->mSeq->c_str();
    const char* qualstr = r->mQuality->c_str();

    int kmer = 0;
    bool needFullCompute = true;
    for(int i=0; i<len; i++) {
        char base = seqstr[i];
        char qual = qualstr[i];
        // get last 3 bits
        char b = base & 0x07;

        const char q20 = '5';
        const char q30 = '?';

        mBaseQualHistogram[qual]++;

        if(qual >= q30) {
            mCycleQ30Bases[b][i]++;
            mCycleQ20Bases[b][i]++;
        } else if(qual >= q20) {
            mCycleQ20Bases[b][i]++;
        }

        mCycleBaseContents[b][i]++;
        mCycleBaseQual[b][i] += (qual-33);

        mCycleTotalBase[i]++;
        mCycleTotalQual[i] += (qual-33);

        if(base == 'N'){
            needFullCompute = true;
            continue;
        }

        // 5 bases required for kmer computing
        if(i<4)
            continue;

        // calc 5 KMER
        // 0x3FC == 0011 1111 1100
        if(!needFullCompute){
            int val = base2val(base);
            if(val < 0){
                needFullCompute = true;
                continue;
            } else {
                kmer = ((kmer<<2) & 0x3FC ) | val;
                mKmer[kmer]++;
            }
        } else {