Method assembleTranscriptsSE

src/rnabloom/RNABloom.java:5546–5590

(RNABloom assembler, boolean forceOverwrite,
            String outdir, String name, String txptNamePrefix,
            long sbfSize, int sbfNumHash, int numThreads, 
            String[] forwardReadPaths, String[] reverseReadPaths,
            int minTranscriptLength, boolean keepArtifact, boolean keepChimera,
            float minKmerCov, boolean reduceRedundancy, boolean writeUracil,
            boolean usePacBioPreset, String minimapOptions, boolean destroyBf)

    }
    
    private static void assembleTranscriptsSE(RNABloom assembler, boolean forceOverwrite,
            String outdir, String name, String txptNamePrefix,
            long sbfSize, int sbfNumHash, int numThreads, 
            String[] forwardReadPaths, String[] reverseReadPaths,
            int minTranscriptLength, boolean keepArtifact, boolean keepChimera,
            float minKmerCov, boolean reduceRedundancy, boolean writeUracil,
            boolean usePacBioPreset, String minimapOptions, boolean destroyBf) throws IOException, InterruptedException {

        final File txptsDoneStamp = new File(outdir + File.separator + STAMP_TRANSCRIPTS_DONE);
        final String transcriptsFasta      = outdir + File.separator + name + ".transcripts" + FASTA_EXT;
        final String shortTranscriptsFasta = outdir + File.separator + name + ".transcripts.short" + FASTA_EXT;
        
        if (forceOverwrite || !txptsDoneStamp.exists()) {
            Timer timer = new Timer();
            assembler.setupKmerScreeningBloomFilter(sbfSize, sbfNumHash);

            assembler.assembleSingleEndReads(forwardReadPaths,
                                    reverseReadPaths,
                                    transcriptsFasta,
                                    shortTranscriptsFasta,
                                    numThreads,
                                    minTranscriptLength,
                                    keepArtifact,
                                    keepChimera,
                                    txptNamePrefix,
                                    minKmerCov,
                                    writeUracil);
            System.out.println("Transcripts assembled in " + timer.elapsedDHMS());

            touch(txptsDoneStamp);

            System.out.println("Assembled transcripts at `" + transcriptsFasta + "`");
        }
        else {
            System.out.println("WARNING: Transcripts were already assembled for \"" + name + "\"!");
        }
        
        if (destroyBf) {
            assembler.destroyAllBf();
        }
        
        if (reduceRedundancy) {
            assembleTranscriptsNR(assembler, outdir, name, forceOverwrite, numThreads, keepArtifact, usePacBioPreset, minimapOptions);
        }
    }
    
    private static void assembleTranscriptsPE(RNABloom assembler, boolean forceOverwrite,
            String outdir, String name, String txptNamePrefix,