Method evaluateReadNum

src/evaluator.cpp:178–218

}

void Evaluator::evaluateReadNum(long& readNum) {
    FastqReader reader(mOptions->in1);

    const long READ_LIMIT = 512*1024;
    const long BASE_LIMIT = 151 * 512*1024;
    long records = 0;
    long bases = 0;
    size_t firstReadPos = 0;

    size_t bytesRead;
    size_t bytesTotal;

    bool reachedEOF = false;
    bool first = true;
    while(records < READ_LIMIT && bases < BASE_LIMIT) {
        Read* r = reader.read();
        if(!r) {
            reachedEOF = true;
            break;
        }
        if(first) {
            reader.getBytes(bytesRead, bytesTotal);
            firstReadPos = bytesRead;
            first = false;
        }
        records++;
        bases += r->length();
        delete r;
    }

    readNum = 0;
    if(reachedEOF){
        readNum = records;
    } else if(records>0) {
        // by the way, update readNum so we don't need to evaluate it if splitting output is enabled
        reader.getBytes(bytesRead, bytesTotal);
        double bytesPerRead = (double)(bytesRead - firstReadPos) / (double) records;
        // increase it by 1% since the evaluation is usually a bit lower due to bad quality causes lower compression rate
        readNum = (long) (bytesTotal*1.01 / bytesPerRead);
    }
}

string Evaluator::checkKnownAdapters(Read** reads, long num) {
    map<string, string> knownAdapters = getKnownAdapter();