Method populateGraph

src/rnabloom/RNABloom.java:1106–1176

(Collection<String> forwardReadPaths,
                            Collection<String> reverseReadPaths,
                            Collection<String> longReadPaths,
                            Collection<String> refTranscriptsPaths,
                            boolean reverseComplementLong,
                            int numThreads,
                            boolean addCountsOnly,
                            boolean storeReadKmerPairs)

    }
    
    public void populateGraph(Collection<String> forwardReadPaths,
                            Collection<String> reverseReadPaths,
                            Collection<String> longReadPaths,
                            Collection<String> refTranscriptsPaths,
                            boolean reverseComplementLong,
                            int numThreads,
                            boolean addCountsOnly,
                            boolean storeReadKmerPairs) throws IOException, InterruptedException {        
        
//        screeningBf = new BloomFilter(sbfNumBits, sbfNumHash, graph.getHashFunction());
        /** parse the reads */
        
        long numReads = 0;
        
        ExecutorService service = Executors.newFixedThreadPool(numThreads);
        
        ArrayList<SeqToGraphWorker> threadPool = new ArrayList<>();
        int threadId = 0;
           
        for (String path : forwardReadPaths) {
            SeqToGraphWorker t = new SeqToGraphWorker(++threadId, path, false, addCountsOnly, storeReadKmerPairs);
            service.submit(t);
            threadPool.add(t);
        }

        for (String path : reverseReadPaths) {
            SeqToGraphWorker t = new SeqToGraphWorker(++threadId, path, true, addCountsOnly, storeReadKmerPairs);
            service.submit(t);
            threadPool.add(t);
        }
        
        for (String path : longReadPaths) {
            SeqToGraphWorker t = new SeqToGraphWorker(++threadId, path, reverseComplementLong, addCountsOnly, false);
            service.submit(t);
            threadPool.add(t);
        }

        service.shutdown();
        service.awaitTermination(Long.MAX_VALUE, TimeUnit.NANOSECONDS);
        
        for (SeqToGraphWorker t : threadPool) {
            numReads += t.getReadCount();
        }

        System.out.println("Parsed " + NumberFormat.getInstance().format(numReads) + " reads in total.");
        
        if (!refTranscriptsPaths.isEmpty()) {
            System.out.println("Augmenting graph with reference transcripts...");

            service = Executors.newFixedThreadPool(numThreads);

            for (String path : refTranscriptsPaths) {
                PairedKmersToGraphWorker t = new PairedKmersToGraphWorker(++threadId, path, true);
                service.submit(t);
            }

            service.shutdown();
            service.awaitTermination(Long.MAX_VALUE, TimeUnit.NANOSECONDS);