Method correctLongReads

src/rnabloom/RNABloom.java:5255–5284

(RNABloom assembler, 
            String[] inFastxList, String outLongFasta, String outShortFasta, String outRepeatsFasta,
            String polyAReadNamesPath, String sampleReadLengthsPath,
            int maxErrCorrItr, int minKmerCov, int numThreads, int sampleSize, int minSeqLen, 
            boolean reverseComplement, boolean trimArtifact, boolean storeReads)

    */
    
    private static ArrayList<BitSequence> correctLongReads(RNABloom assembler, 
            String[] inFastxList, String outLongFasta, String outShortFasta, String outRepeatsFasta,
            String polyAReadNamesPath, String sampleReadLengthsPath,
            int maxErrCorrItr, int minKmerCov, int numThreads, int sampleSize, int minSeqLen, 
            boolean reverseComplement, boolean trimArtifact, boolean storeReads) throws InterruptedException, IOException, Exception {
        
        FastaWriter longWriter = new FastaWriter(outLongFasta, false);
        FastaWriter shortWriter = new FastaWriter(outShortFasta, false);
        FastaWriter repeatsWriter = new FastaWriter(outRepeatsFasta, false);
        Writer polyAReadNamesWriter = getTextFileWriter(polyAReadNamesPath, false);

        ArrayList<BitSequence> longReads = assembler.correctLongReadsMultithreaded(inFastxList,
                                                longWriter, shortWriter, repeatsWriter, polyAReadNamesWriter,
                                                sampleReadLengthsPath,
                                                minKmerCov,
                                                maxErrCorrItr,
                                                numThreads,
                                                sampleSize,
                                                minSeqLen,
                                                reverseComplement,
                                                trimArtifact,
                                                storeReads);
        
        longWriter.close();
        shortWriter.close();
        repeatsWriter.close();
        polyAReadNamesWriter.close();
        
        return longReads;
    }
    
    /*
    private static void clusterLongReads(RNABloom assembler,