Method correctLongReadsMultithreaded

src/rnabloom/RNABloom.java:3948–4025

(String[] inputFastxPaths,
                                                FastaWriter longSeqWriter,
                                                FastaWriter shortSeqWriter,
                                                FastaWriter repeatsSeqWriter,
                                                Writer polyAReadNamesWriter,
                                                String sampleReadLengthsPath,
                                                int minKmerCov,
                                                int maxErrCorrItr,
                                                int numThreads,
                                                int maxSampleSize,
                                                int minSeqLen,
                                                boolean reverseComplement,
                                                boolean trimArtifact,
                                                boolean storeReads)

    */
    
    public ArrayList<BitSequence> correctLongReadsMultithreaded(String[] inputFastxPaths,
                                                FastaWriter longSeqWriter,
                                                FastaWriter shortSeqWriter,
                                                FastaWriter repeatsSeqWriter,
                                                Writer polyAReadNamesWriter,
                                                String sampleReadLengthsPath,
                                                int minKmerCov,
                                                int maxErrCorrItr,
                                                int numThreads,
                                                int maxSampleSize,
                                                int minSeqLen,
                                                boolean reverseComplement,
                                                boolean trimArtifact,
                                                boolean storeReads) throws InterruptedException, IOException, Exception {

        int minNumSolidKmers = Math.max(0, (int) Math.floor(minSeqLen/100.0));
        //int minNumSolidKmers = Math.max(0, (int) Math.floor((minSeqLen-k+1) * percentIdentity / k));
        
        long numReads = 0;
        ArrayBlockingQueue<Sequence2> outputQueue = new ArrayBlockingQueue<>(maxSampleSize);
                
        LongReadCorrectionWorker[] correctionWorkers = new LongReadCorrectionWorker[numThreads];
        Thread[] threads = new Thread[numThreads];
        
        FastxSequenceIterator itr = new FastxSequenceIterator(inputFastxPaths, minAvgBaseQual, false);
        
        for (int i=0; i<numThreads; ++i) {
            LongReadCorrectionWorker worker = new LongReadCorrectionWorker(itr, outputQueue, maxErrCorrItr, minKmerCov,
                    minNumSolidKmers, reverseComplement, trimArtifact);
            correctionWorkers[i] = worker;
            threads[i] = new Thread(worker);
            threads[i].start();
        }
        //System.out.println("Initialized " + numThreads + " worker(s).");
        
        CorrectedLongReadsWriterWorker2 writerWorker = new CorrectedLongReadsWriterWorker2(outputQueue, 
                longSeqWriter, shortSeqWriter, repeatsSeqWriter, polyAReadNamesWriter, sampleReadLengthsPath,
                maxSampleSize, minSeqLen, storeReads);
        Thread writerThread = new Thread(writerWorker);
        writerThread.start();
        //System.out.println("Initialized writer.");
        
        for (Thread t : threads) {
            t.join();
        }

        writerWorker.terminateWhenInputExhausts();
        writerThread.join();
        
        // check for errors
        if (!writerWorker.isSucessful()) {
            throw writerWorker.getExceptionCaught();
        }
                
        long numArtifacts = 0;
        long numDiscarded = 0;
        for (LongReadCorrectionWorker worker : correctionWorkers) {
            if (!worker.isSucessful()) {