Method splitFastaByLength

src/rnabloom/RNABloom.java:5441–5471

(String inFasta, String outLongFasta, String outShortFasta, int lengthThreshold)

    }
    
    private static long[] splitFastaByLength(String inFasta, String outLongFasta, String outShortFasta, int lengthThreshold) throws IOException {
        FastaReader fin = new FastaReader(inFasta);
        FastaWriter foutLong = new FastaWriter(outLongFasta, false);
        FastaWriter foutShort = new FastaWriter(outShortFasta, false);
        long numLong = 0;
        long numShort = 0;
        while(fin.hasNext()) {
            String[] nameCommentSeq = fin.nextWithComment();
            
            String header = nameCommentSeq[0];
            if (!nameCommentSeq[1].isEmpty()) {
                header += " " + nameCommentSeq[1];
            }
            
            String seq = nameCommentSeq[2];
            
            if (seq.length() >= lengthThreshold) {
                foutLong.write(header, seq);
                ++numLong;
            }
            else {
                foutShort.write(header, seq);
                ++numShort;
            }
        }
        foutLong.close();
        foutShort.close();
        fin.close();
        
        return new long[]{numShort, numLong};
    }
    
    private static boolean mergePooledAssemblies(RNABloom assembler, 
            String outdir, String assemblyName, String[] sampleNames,