Method assembleSingleEndReads

src/rnabloom/RNABloom.java:4844–4884

(String[] forwardReadPaths,
                                    String[] reverseReadPaths,
                                    String outFasta,
                                    String outFastaShort,
                                    int numThreads,
                                    int minTranscriptLength,
                                    boolean keepArtifact,
                                    boolean keepChimera,
                                    String txptNamePrefix,
                                    float minKmerCov,
                                    boolean writeUracil)

    }
    
    public void assembleSingleEndReads(String[] forwardReadPaths,
                                    String[] reverseReadPaths,
                                    String outFasta,
                                    String outFastaShort,
                                    int numThreads,
                                    int minTranscriptLength,
                                    boolean keepArtifact,
                                    boolean keepChimera,
                                    String txptNamePrefix,
                                    float minKmerCov,
                                    boolean writeUracil) throws IOException, InterruptedException {

        //boolean assemblePolya = minPolyATailLengthRequired > 0;
        /*@TODO support prioritized assembly of polya reads */
                
        boolean includeNaiveExtensions = true;
        boolean extendBranchFreeFragmentsOnly = false;

        FastaWriter fout = new FastaWriter(outFasta, false, writeUracil);
        FastaWriter foutShort = new FastaWriter(outFastaShort, false, writeUracil);
        TranscriptWriter writer = new TranscriptWriter(fout, foutShort, minTranscriptLength, maxTipLength, writeUracil);
        
        SingleEndReadsIterator readsItr = new SingleEndReadsIterator(forwardReadPaths, reverseReadPaths);
        
        TranscriptAssemblyWorker[] workers = new TranscriptAssemblyWorker[numThreads];
        Thread[] threads = new Thread[numThreads];
        for (int i=0; i<numThreads; ++i) {
            workers[i] = new TranscriptAssemblyWorker(readsItr, writer, includeNaiveExtensions, extendBranchFreeFragmentsOnly, keepArtifact, keepChimera, false, minKmerCov);
            threads[i] = new Thread(workers[i]);
            threads[i].start();
        }

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

        fout.close();
        foutShort.close();
        
        System.out.println("Parsed " + NumberFormat.getInstance().format(readsItr.numReadsParsed) + " reads.");
    }
    
    public void assembleTranscriptsMultiThreaded(FragmentPaths fragPaths,
                                                String outFasta,