//
// Main
//
int graphDiffMain(int argc, char** argv)
{
parseGraphDiffOptions(argc, argv);
// Create BWTS
std::string basePrefix = stripFilename(opt::baseFile);
BWT* pBaseBWT = new BWT(basePrefix + BWT_EXT, opt::sampleRate);
BWT* pBaseRevBWT = new BWT(basePrefix + RBWT_EXT, opt::sampleRate);
std::string variantPrefix = stripFilename(opt::variantFile);
BWT* pVariantBWT = new BWT(variantPrefix + BWT_EXT, opt::sampleRate);
BWT* pVariantRevBWT = new BWT(variantPrefix + RBWT_EXT, opt::sampleRate);
// Create the shared bit vector and shared results aggregator
BitVector* pSharedBitVector = new BitVector(pVariantBWT->getBWLen());
GraphCompareAggregateResults* pSharedResults = new GraphCompareAggregateResults(opt::outFile);
// Create interval caches to speed up k-mer lookups
BWTIntervalCache varBWTCache(opt::cacheLength, pVariantBWT);
BWTIntervalCache varRBWTCache(opt::cacheLength, pVariantRevBWT);
BWTIntervalCache baseBWTCache(opt::cacheLength, pBaseBWT);
BWTIntervalCache baseRBWTCache(opt::cacheLength, pBaseRevBWT);
// Set the parameters shared between all threads
GraphCompareParameters sharedParameters;
sharedParameters.pVariantBWT = pVariantBWT;
sharedParameters.pVariantRevBWT = pVariantRevBWT;
sharedParameters.pBaseBWT = pBaseBWT;
sharedParameters.pBaseRevBWT = pBaseRevBWT;
sharedParameters.kmer = opt::kmer;
sharedParameters.pBitVector = pSharedBitVector;
sharedParameters.kmerThreshold = 3;
sharedParameters.maxBranches = opt::maxBranches;
sharedParameters.pVarBWTCache = &varBWTCache;
sharedParameters.pVarRevBWTCache = &varRBWTCache;
sharedParameters.pBaseBWTCache = &baseBWTCache;
sharedParameters.pBaseRevBWTCache = &baseRBWTCache;
if(opt::numThreads <= 1)
{
printf("[%s] starting serial-mode graph diff\n", PROGRAM_IDENT);
GraphCompare graphCompare(sharedParameters);
PROCESS_GDIFF_SERIAL(opt::variantFile, &graphCompare, pSharedResults);
graphCompare.updateSharedStats(pSharedResults);
}
else
{
printf("[%s] starting parallel-mode graph diff with %d threads\n", PROGRAM_IDENT, opt::numThreads);
std::vector<GraphCompare*> processorVector;
for(int i = 0; i < opt::numThreads; ++i)
{
GraphCompare* pProcessor = new GraphCompare(sharedParameters);
processorVector.push_back(pProcessor);
}
PROCESS_GDIFF_PARALLEL(opt::variantFile, processorVector, pSharedResults);
for(size_t i = 0; i < processorVector.size(); ++i)
{
// Update the shared stats
processorVector[i]->updateSharedStats(pSharedResults);
delete processorVector[i];
processorVector[i] = NULL;
}
}
pSharedResults->printStats();
// Cleanup
delete pBaseBWT;
delete pBaseRevBWT;
delete pVariantBWT;
delete pVariantRevBWT;
delete pSharedBitVector;
delete pSharedResults;
if(opt::numThreads > 1)
pthread_exit(NULL);
return 0;
}
