C++ SuffixArray::get方法代码示例

// Validate the sampled suffix array values are correct
void SampledSuffixArray::validate(const std::string filename, const BWT* pBWT)
{
    ReadTable* pRT = new ReadTable(filename);
    SuffixArray* pSA = new SuffixArray(pRT, 1);
    
    std::cout << "Validating sampled suffix array entries\n";

    for(size_t i = 0; i < pSA->getSize(); ++i)
    {
        SAElem calc = calcSA(i, pBWT);
        SAElem real = pSA->get(i);
        if(calc.getID() != real.getID() || calc.getPos() != real.getPos())
        {
            std::cout << "Error SA elements do not match for " << i << "\n";
            std::cout << "Calc: " << calc << "\n";
            std::cout << "Real: " << real << "\n";
            exit(1);
        }
    }
    
    std::cout << "All calculate SA values are correct\n";

    delete pRT;
    delete pSA;
}

void cluster()
{
    BWT* pBWT = new BWT(opt::prefix + BWT_EXT);
    BWT* pRBWT = new BWT(opt::prefix + RBWT_EXT);
    OverlapAlgorithm* pOverlapper = new OverlapAlgorithm(pBWT, pRBWT,opt::errorRate, opt::seedLength, opt::seedStride, true);

    pOverlapper->setExactModeOverlap(opt::errorRate < 0.001f);
    pOverlapper->setExactModeIrreducible(opt::errorRate < 0.001f);

    BitVector markedReads(pBWT->getNumStrings());

    std::string preclustersFile = opt::outFile + ".preclusters";
    std::ostream* pPreWriter = createWriter(preclustersFile);
    ClusterPostProcess postProcessor(pPreWriter, opt::minSize, &markedReads);
    
    // Set the cluster parameters
    ClusterParameters parameters;
    parameters.pOverlapper = pOverlapper;
    parameters.minOverlap = opt::minOverlap;
    parameters.maxClusterSize = opt::maxSize;
    parameters.maxIterations = opt::maxIterations;
    parameters.pMarkedReads = &markedReads;

    // Read the limit kmer sequences, if provided
    std::set<std::string>* pLimitKmers = NULL;

    if(!opt::limitFile.empty())
    {
        // Read in the limit sequences
        pLimitKmers = new std::set<std::string>;
        readLimitKmers(pLimitKmers);
        parameters.pLimitKmers = pLimitKmers;
        parameters.limitK = opt::limitKmer;
    }
    else
    {
        parameters.pLimitKmers = NULL;
        parameters.limitK = 0;
    }

    // Make pre-clusters from the reads
    if(opt::numThreads <= 1)
    {
        printf("[%s] starting serial-mode read clustering\n", PROGRAM_IDENT);
        ClusterProcess processor(parameters);
        
        // If the extend file is empty, build new clusters
        if(opt::extendFile.empty())
        {
            PROCESS_CLUSTER_SERIAL(opt::readsFile, &processor, &postProcessor);
        }
        else
        {
            // Process a set of preexisting clusters
            ClusterReader clusterReader(opt::extendFile);
            PROCESS_EXTEND_SERIAL(clusterReader, &processor, &postProcessor);
        }
    }
    else
    {
        printf("[%s] starting parallel-mode read clustering computation with %d threads\n", PROGRAM_IDENT, opt::numThreads);
        
        std::vector<ClusterProcess*> processorVector;
        for(int i = 0; i < opt::numThreads; ++i)
        {
            ClusterProcess* pProcessor = new ClusterProcess(parameters);
            processorVector.push_back(pProcessor);
        }
        
        if(opt::extendFile.empty())
        {
            PROCESS_CLUSTER_PARALLEL(opt::readsFile, processorVector, &postProcessor);
        }
        else
        {
            ClusterReader clusterReader(opt::extendFile);
            PROCESS_EXTEND_PARALLEL(clusterReader, processorVector, &postProcessor);
        }
        
        for(size_t i = 0; i < processorVector.size(); ++i)
        {
            delete processorVector[i];
            processorVector[i] = NULL;
        }
    }
    delete pPreWriter;
    delete pBWT;
    delete pRBWT;
    delete pOverlapper;

    // Deallocate limit kmers
    if(pLimitKmers != NULL)
        delete pLimitKmers;

    // Open the preclusters file and convert them to read names
    SuffixArray* pFwdSAI = new SuffixArray(opt::prefix + SAI_EXT);
    ReadInfoTable* pRIT = new ReadInfoTable(opt::readsFile, pFwdSAI->getNumStrings());

    size_t seedIdx = 0;
    std::istream* pPreReader = createReader(preclustersFile);
//.........这里部分代码省略.........