Method populateGraphFromFragments

src/rnabloom/RNABloom.java:1541–1572

(Collection<String> fragPaths, Collection<String> refFastas, boolean loadPairedKmers, int numThreads)

    }
    
    public void populateGraphFromFragments(Collection<String> fragPaths, Collection<String> refFastas, boolean loadPairedKmers, int numThreads) throws InterruptedException {        
        ExecutorService service = Executors.newFixedThreadPool(numThreads);
        
        int threadId = 0;
        
        for (String path : fragPaths) {
            service.submit(new FragmentsToGraphWorker(++threadId, path, loadPairedKmers));
        }
                
        service.shutdown();
        service.awaitTermination(Long.MAX_VALUE, TimeUnit.NANOSECONDS);
        
        if (!refFastas.isEmpty()) {
            System.out.println("Augmenting graph with reference transcripts...");
            
            service = Executors.newFixedThreadPool(numThreads);
            
            for (String path : refFastas) {
                service.submit(new PairedKmersToGraphWorker(++threadId, path, true));
            }
            
            service.shutdown();
            service.awaitTermination(Long.MAX_VALUE, TimeUnit.NANOSECONDS);
        }
        
        dbgFPR = graph.getDbgbfFPR();

        System.out.println("DBG Bloom filter FPR:                     " + convertToRoundedPercent(dbgFPR) + " %");
        System.out.println("Reads paired k-mers Bloom filter FPR:     " + convertToRoundedPercent(graph.getRpkbf().getFPR()) + " %");
        System.out.println("Fragments paired k-mers Bloom filter FPR: " + convertToRoundedPercent(graph.getFpkbf().getFPR()) + " %");
//        covFPR = graph.getCbfFPR();
    }
        
    public static class ReadPair {
        ArrayList<Kmer> leftKmers;