Ejemplos de BWT::printRunLengths en C++ (Cpp)

Ejemplo n.º 1

Archivo: stats.cpp Proyecto: Buttonwood/sga

//
// Main
//
int statsMain(int argc, char** argv)
{
    parseStatsOptions(argc, argv);
    Timer* pTimer = new Timer(PROGRAM_IDENT);

    BWT* pBWT = new BWT(opt::prefix + BWT_EXT, opt::sampleRate);
    BWT* pRBWT = new BWT(opt::prefix + RBWT_EXT, opt::sampleRate);

    if(opt::bPrintRunLengths)
    {
        pBWT->printInfo();
        pBWT->printRunLengths();
    }

    SeqReader reader(opt::readsFile);
    
    StatsPostProcess postProcessor(opt::bPrintKmerDist);
    if(opt::numThreads <= 1)
    {
        // Serial mode
        StatsProcess processor(pBWT, pRBWT, opt::kmerLength, opt::minOverlap, opt::branchCutoff, opt::bNoOverlap);

        SequenceProcessFramework::processSequencesSerial<SequenceWorkItem,
                                                         StatsResult, 
                                                         StatsProcess, 
                                                         StatsPostProcess>(reader, &processor, &postProcessor, opt::numReads);
    }
    else
    {
        // Parallel mode
        std::vector<StatsProcess*> processorVector;
        for(int i = 0; i < opt::numThreads; ++i)
        {
            StatsProcess* pProcessor = new StatsProcess(pBWT, pRBWT, opt::kmerLength, opt::minOverlap, opt::branchCutoff, opt::bNoOverlap);
            processorVector.push_back(pProcessor);
        }
        
        SequenceProcessFramework::processSequencesParallel<SequenceWorkItem,
                                                           StatsResult, 
                                                           StatsProcess, 
                                                           StatsPostProcess>(reader, processorVector, &postProcessor, opt::numReads);

        for(int i = 0; i < opt::numThreads; ++i)
        {
            delete processorVector[i];
        }
    }

    delete pBWT;
    delete pRBWT;
    delete pTimer;

    if(opt::numThreads > 1)
        pthread_exit(NULL);

    return 0;
}