Method assembleTranscriptsNR

src/rnabloom/RNABloom.java:5515–5544

(RNABloom assembler, String outdir, String name, boolean forceOverwrite,
            int numThreads, boolean keepArtifact, boolean usePacBioPreset, String minimapOptions)

    }
    
    private static void assembleTranscriptsNR(RNABloom assembler, String outdir, String name, boolean forceOverwrite,
            int numThreads, boolean keepArtifact, boolean usePacBioPreset, String minimapOptions) throws IOException {
        
        final File nrTxptsDoneStamp = new File(outdir + File.separator + STAMP_TRANSCRIPTS_NR_DONE);

        if (forceOverwrite || !nrTxptsDoneStamp.exists()) {
            String transcriptsFasta        = outdir + File.separator + name + ".transcripts" + FASTA_EXT;
            String nrTranscriptsFasta      = outdir + File.separator + name + ".transcripts.nr" + FASTA_EXT;

            deleteIfExists(nrTranscriptsFasta);

            System.out.println("Reducing redundancy in assembled transcripts...");
            Timer timer = new Timer();
            timer.start();

            boolean ok = assembler.generateNonRedundantTranscripts(transcriptsFasta,
                    nrTranscriptsFasta, numThreads, !keepArtifact, usePacBioPreset, minimapOptions);

            if (ok) {
                System.out.println("Redundancy reduced in " + timer.elapsedDHMS());
                touch(nrTxptsDoneStamp);
            }
            else {
                exitOnError("Error during redundancy reduction!");
            }
        }
        else {
            System.out.println("WARNING: Redundancy reduction had completed previously for \"" + name + "\"!");
        } 
    }
    
    private static void assembleTranscriptsSE(RNABloom assembler, boolean forceOverwrite,
            String outdir, String name, String txptNamePrefix,