// 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);
std::ostream* pClusterWriter = createWriter(opt::outFile);
std::string line;
while(getline(*pPreReader,line))
{
std::stringstream parser(line);
std::string clusterName;
std::string readSequence;
size_t clusterSize;
int64_t lowIdx;
int64_t highIdx;
parser >> clusterName >> clusterSize >> readSequence >> lowIdx >> highIdx;
if(lowIdx > highIdx)
{
// This is an extra read that is not present in the FM-index
// Output a record with a fake read ID
*pClusterWriter << clusterName << "\t" << clusterSize << "\tseed-" << seedIdx++ << "\t" << readSequence << "\n";
}
else
{
for(int64_t i = lowIdx; i <= highIdx; ++i)
{
const ReadInfo& targetInfo = pRIT->getReadInfo(pFwdSAI->get(i).getID());
std::string readName = targetInfo.id;
*pClusterWriter << clusterName << "\t" << clusterSize << "\t" << readName << "\t" << readSequence << "\n";
}
}
}
unlink(preclustersFile.c_str());
delete pFwdSAI;
delete pRIT;
delete pPreReader;
delete pClusterWriter;
}