Method run

src/rnabloom/RNABloom.java:4230–4288

()

        }
        
        @Override
        public void run() {
            try {
                while (true) {
                    Fragment frag = fragments.poll(10, TimeUnit.MICROSECONDS);

                    if (frag == null) {
                        if (!keepGoing) {
                            break;
                        }
                    }
                    else {
                        float minCov = frag.minCov;
                        
                        if (frag.isUnconnectedRead) {
                            ++readPairsNotConnected;

                            String seq = frag.left;
                            if (seq != null && seq.length() >= k) {
                                writers.writeUnconnected(seq, minCov);
                            }

                            seq = frag.right;
                            if (seq != null && seq.length() >= k) {
                                writers.writeUnconnected(seq, minCov);
                            }
                        }
                        else {
                            ++readPairsConnected;

                            int fragLen = frag.kmers.size()+ k - 1; // not using frag.length because it is the original length and frag may be extended
                            
                            if (fragLen >= shortestFragmentLengthAllowed && minCov > 0) {
                                ArrayList<Kmer> fragKmers = frag.kmers;
                                boolean hasAllKmers = lookupAndAddAllKmers(screeningBf, fragKmers);

                                if (fragLen < longFragmentLengthThreshold) {
                                    if (!hasAllKmers) {
                                        writers.writeShort(graph.assemble(fragKmers), minCov);
                                    }
                                }
                                else {
                                    boolean hasAllKmerPairs = graph.lookupAndAddAllPairedKmers(fragKmers);
                                    if (!hasAllKmers || !hasAllKmerPairs) {
                                        writers.writeLong(graph.assemble(fragKmers), minCov);
                                    }
                                }
                            }
                        }
                    }
                }
                
                writers.closeAll();
            }
            catch(Exception ex) {
                ex.printStackTrace();
                throw new RuntimeException(ex);
            }