Method process

src/seprocessor.cpp:65–172

}

bool SingleEndProcessor::process(){
    if(!mOptions->split.enabled)
        initOutput();

    mInputLists = new SingleProducerSingleConsumerList<ReadPack*>*[mOptions->thread];

    ThreadConfig** configs = new ThreadConfig*[mOptions->thread];
    for(int t=0; t<mOptions->thread; t++){
        mInputLists[t] = new SingleProducerSingleConsumerList<ReadPack*>();
        configs[t] = new ThreadConfig(mOptions, t, false);
        configs[t]->setInputList(mInputLists[t]);
        initConfig(configs[t]);
    }

    std::thread readerThread(std::bind(&SingleEndProcessor::readerTask, this));

    std::thread** threads = new thread*[mOptions->thread];
    for(int t=0; t<mOptions->thread; t++){
        threads[t] = new std::thread(std::bind(&SingleEndProcessor::processorTask, this, configs[t]));
    }

    std::thread* leftWriterThread = NULL;
    std::thread* failedWriterThread = NULL;
    if(mLeftWriter)
        leftWriterThread = new std::thread(std::bind(&SingleEndProcessor::writerTask, this, mLeftWriter));
    if(mFailedWriter)
        failedWriterThread = new std::thread(std::bind(&SingleEndProcessor::writerTask, this, mFailedWriter));

    readerThread.join();
    for(int t=0; t<mOptions->thread; t++){
        threads[t]->join();
    }

    if(!mOptions->split.enabled) {
        if(leftWriterThread)
            leftWriterThread->join();
        if(failedWriterThread)
            failedWriterThread->join();
    }

    if(mOptions->verbose)
        loginfo("start to generate reports\n");

    // merge stats and read filter results
    vector<Stats*> preStats;
    vector<Stats*> postStats;
    vector<FilterResult*> filterResults;
    for(int t=0; t<mOptions->thread; t++){
        preStats.push_back(configs[t]->getPreStats1());
        postStats.push_back(configs[t]->getPostStats1());
        filterResults.push_back(configs[t]->getFilterResult());
    }
    Stats* finalPreStats = Stats::merge(preStats);
    finalPreStats->calcLengthHistogram();
    Stats* finalPostStats = Stats::merge(postStats);
    finalPostStats->calcLengthHistogram();
    FilterResult* finalFilterResult = FilterResult::merge(filterResults);