Method run

src/rnabloom/RNABloom.java:1961–2035

()

        }
        
        @Override
        public void run() {
            try {
                ArrayList<String> segments;
                while((segments = rin.nextSegments()) != null) {
                    ++numParsed;
                    
                    if (reverseComplement) {
                        int numSegments = segments.size();

                        if (numSegments > 1) {
                            Collections.reverse(segments);
                        }

                        for (int i=0; i<numSegments; ++i) {
                            segments.set(i, reverseComplement(segments.get(i)));
                        }
                    }
                    
                    String seq = connect(segments, graph, lookahead);
                    
                    if (seq.length() >= this.readLengthThreshold) {
                        if (!isLowComplexityShort(seq)) {
                            ArrayList<Kmer> kmers = graph.getKmers(seq);
                            
                            if (!kmers.isEmpty()) {
                                ArrayList<Kmer> corrected = null;
                                
                                if (errorCorrectionIterations > 0) {
                                    corrected = correctErrorsSE(kmers,
                                                                graph, 
                                                                lookahead, 
                                                                maxIndelSize, 
                                                                maxCovGradient, 
                                                                covFPR,
                                                                percentIdentity,
                                                                minKmerCov);
                                    if (corrected != null && !corrected.isEmpty()) {
                                        kmers = corrected;
                                    }
                                }
                            
                                if (kmers.size() >= lookahead) {
                                    float minCov = Float.MAX_VALUE;
                                    boolean hasComplexKmer = false;

                                    for (Kmer kmer : kmers) {
                                        if (kmer.count < minCov) {
                                            minCov = kmer.count;
                                        }

                                        if (!hasComplexKmer && !graph.isRepeatKmer(kmer)) {
                                            hasComplexKmer = true;
                                        }
                                    }

                                    if (hasComplexKmer) {
                                        if (corrected != null && !corrected.isEmpty()) {