Method assembleFragments

src/rnabloom/RNABloom.java:5407–5439

(RNABloom assembler, boolean forceOverwrite,
            String outdir, String name, FastxFilePair[] fqPairs,
            String[] forwardReadPaths, String[] reverseReadPaths,
            long sbfSize, long pkbfSize, int sbfNumHash, int pkbfNumHash, int numThreads,
            int bound, int minOverlap, int sampleSize, int maxErrCorrItr, boolean extendFragments,
            int minKmerCoverage, boolean keepArtifact)

    }
    
    private static void assembleFragments(RNABloom assembler, boolean forceOverwrite,
            String outdir, String name, FastxFilePair[] fqPairs,
            String[] forwardReadPaths, String[] reverseReadPaths,
            long sbfSize, long pkbfSize, int sbfNumHash, int pkbfNumHash, int numThreads,
            int bound, int minOverlap, int sampleSize, int maxErrCorrItr, boolean extendFragments,
            int minKmerCoverage, boolean keepArtifact) throws FileFormatException, IOException, InterruptedException {

        final File fragsDoneStamp = new File(outdir + File.separator + STAMP_FRAGMENTS_DONE);
        
        if (forceOverwrite || !fragsDoneStamp.exists()) {
            FragmentPaths fragPaths = new FragmentPaths(outdir, name);
            fragPaths.deleteAll();

            assembler.setupKmerScreeningBloomFilter(sbfSize, sbfNumHash);
            assembler.setupFragmentPairedKmersBloomFilter(pkbfSize, pkbfNumHash);

            Quartiles fragStats = assembler.assembleFragmentsMultiThreaded(fqPairs,
                    forwardReadPaths, reverseReadPaths, fragPaths,
                    bound, minOverlap, sampleSize, numThreads,
                    maxErrCorrItr, extendFragments, minKmerCoverage, keepArtifact);

            String fragStatsFile = outdir + File.separator + name + ".fragstats";
            String graphFile = outdir + File.separator + name + ".graph";
            
            assembler.updateGraphDesc(new File(graphFile));
            assembler.writeQuartilesToFile(fragStats, fragStatsFile);

            touch(fragsDoneStamp);
        }
        else {
            System.out.println("WARNING: Fragments were already assembled for \"" + name + "!");
        }
    }
    
    private static long[] splitFastaByLength(String inFasta, String outLongFasta, String outShortFasta, int lengthThreshold) throws IOException {
        FastaReader fin = new FastaReader(inFasta);