Method populateGraphHelper

src/rnabloom/RNABloom.java:1178–1246

(String path,
                            int numThreads,
                            boolean reverseComplement,
                            boolean addCountsOnly,
                            boolean storeReadKmerPairs)

    }
    
    private long populateGraphHelper(String path,
                            int numThreads,
                            boolean reverseComplement,
                            boolean addCountsOnly,
                            boolean storeReadKmerPairs) throws IOException, InterruptedException {
        Timer timer = new Timer();
        timer.start();
        System.out.println("Parsing `" + path + "`...");
        long numReads = 0;
        
        if (FastaReader.isCorrectFormat(path)) {
            Thread[] threads = new Thread[numThreads];

            FastaReader fr = new FastaReader(path);
            FastaToGraphWorker[] workers = new FastaToGraphWorker[numThreads];

            for (int i=0; i<numThreads; ++i) {
                FastaToGraphWorker worker = new FastaToGraphWorker(fr, reverseComplement, addCountsOnly, storeReadKmerPairs);
                workers[i] = worker;
                threads[i] = new Thread(worker);
                threads[i].start();
            }

            //System.out.println("Initialized " + numThreads + " worker(s).");

            for (Thread t : threads) {
                t.join();
            }

            fr.close();
            
            for (FastaToGraphWorker w : workers) {
                numReads += w.getReadCount();
            }
        }
        else if (FastqReader.isCorrectFormat(path)) {
            Thread[] threads = new Thread[numThreads];

            FastqReader fr = minAvgBaseQual > 0 ? new FastqFilteredReader(path, minAvgBaseQual) : new FastqReader(path);
            
            FastqToGraphWorker[] workers = new FastqToGraphWorker[numThreads];

            for (int i=0; i<numThreads; ++i) {
                FastqToGraphWorker worker = new FastqToGraphWorker(fr, reverseComplement, addCountsOnly, storeReadKmerPairs);
                workers[i] = worker;
                threads[i] = new Thread(worker);
                threads[i].start();
            }

            //System.out.println("Initialized " + numThreads + " worker(s).");

            for (Thread t : threads) {
                t.join();
            }

            fr.close();
            
            for (FastqToGraphWorker w : workers) {