Method populateGraphPairedKmersHelper

src/rnabloom/RNABloom.java:1248–1288

(String path,
                                    int numThreads,
                                    boolean existingKmersOnly)

    }
    
    public long populateGraphPairedKmersHelper(String path,
                                    int numThreads,
                                    boolean existingKmersOnly) 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);
            FastaPairedKmersToGraphWorker[] workers = new FastaPairedKmersToGraphWorker[numThreads];

            for (int i=0; i<numThreads; ++i) {
                FastaPairedKmersToGraphWorker worker = new FastaPairedKmersToGraphWorker(fr, existingKmersOnly);
                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 (FastaPairedKmersToGraphWorker w : workers) {
                numReads += w.getReadCount();
            }
        }
        else {
            throw new RuntimeException("Unsupported file format detected in input file `" + path + "`. Only FASTA format is supported.");
        }
        
        System.out.println("Parsed " + NumberFormat.getInstance().format(numReads) + " sequences in " + timer.elapsedDHMS());
        
        return numReads;
    }
    
    public void populateGraph2(Collection<String> forwardReadPaths,
                            Collection<String> reverseReadPaths,