Method run

src/rnabloom/RNABloom.java:1475–1538

()

        }
        
        @Override
        public void run() {
            try {
                System.out.println("[" + id + "] Parsing `" + path + "`...");
                
                NTHashIterator itr = graph.getHashIterator(graph.getMaxNumHash());
                long[] hashVals = itr.hVals;

                PairedNTHashIterator readItr = graph.getPairedHashIterator(graph.getReadPairedKmerDistance());
                long[] readHashValsP = readItr.hValsP;

                PairedNTHashIterator fragItr = graph.getPairedHashIterator(graph.getFragPairedKmerDistance());
                long[] fragHashValsP = fragItr.hValsP;

                NucleotideBitsReader fin = new NucleotideBitsReader(path);

                if (loadPairedKmers) {
                    String seq = null;
                    while ((seq = fin.next()) != null) {
                        ++numSeqs;

                        if (itr.start(seq)) {
                            while (itr.hasNext()) {
                                itr.next();
                                graph.addDbgOnly(hashVals);
                            }

                            if (readItr.start(seq)) {
                                while (readItr.hasNext()) {
                                    readItr.next();
                                    graph.addReadSingleKmerPair(readHashValsP);
                                }

                                if (fragItr.start(seq)) {
                                    while (fragItr.hasNext()) {
                                        fragItr.next();
                                        graph.addFragmentSingleKmerPair(fragHashValsP);
                                    }
                                }
                            }
                        }
                    }
                }
                else {
                    String seq = null;
                    while ((seq = fin.next()) != null) {
                        ++numSeqs;

                        if (itr.start(seq)) {
                            while (itr.hasNext()) {
                                itr.next();
                                graph.addDbgOnly(hashVals);
                            }
                        }
                    }
                }

                fin.close();