Method populateGraph2

src/rnabloom/RNABloom.java:1290–1346

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

    }
    
    public void populateGraph2(Collection<String> forwardReadPaths,
                            Collection<String> reverseReadPaths,
                            Collection<String> longReadPaths,
                            Collection<String> refTranscriptsPaths,
                            boolean reverseComplementLong,
                            int numThreads,
                            boolean addCountsOnly,
                            boolean storeReadKmerPairs) throws IOException, InterruptedException {        
        long numReads = 0;
        int numReadFiles = 0;
           
        for (String path : forwardReadPaths) {
            ++numReadFiles;
            numReads += populateGraphHelper(path, numThreads, false,
                            addCountsOnly, storeReadKmerPairs);
        }

        for (String path : reverseReadPaths) {
            ++numReadFiles;
            numReads += populateGraphHelper(path, numThreads, true,
                            addCountsOnly, storeReadKmerPairs);
        }
        
        for (String path : longReadPaths) {
            ++numReadFiles;
            numReads += populateGraphHelper(path, numThreads, reverseComplementLong,
                            addCountsOnly, false);
        }
        
        if (numReadFiles > 1) {
            System.out.println("Parsed " + NumberFormat.getInstance().format(numReads) + " sequences from " + numReadFiles + " files.");
        }
        
        if (!refTranscriptsPaths.isEmpty()) {
            System.out.println("Augmenting graph with reference transcripts...");
            long numRefs = 0;
            int numRefFiles = 0;
            for (String path : refTranscriptsPaths) {
                ++numRefFiles;
                populateGraphPairedKmersHelper(path, numThreads, true);
            }
            
            if (numRefFiles > 1) {
                System.out.println("Parsed " + NumberFormat.getInstance().format(numRefs) + " sequences from " + numRefFiles + " reference files.");
            }
        }
        
        dbgFPR = graph.getDbgbf().getFPR();
        covFPR = graph.getCbf().getFPR();
        
        System.out.println("DBG Bloom filter FPR:                 " + convertToRoundedPercent(dbgFPR) + " %");
        System.out.println("Counting Bloom filter FPR:            " + convertToRoundedPercent(covFPR) + " %");
        
        if (graph.getReadPairedKmerDistance() > 0) {
            System.out.println("Reads paired k-mers Bloom filter FPR: " + convertToRoundedPercent(graph.getRpkbf().getFPR()) + " %");
        }
    }