Method run

src/rnabloom/RNABloom.java:451–515

()

        }
        
        @Override
        public void run() {
            System.out.println("[" + id + "] Parsing `" + path + "`...");
            
            try {
                Matcher mSeq = seqPattern.matcher("");

                if (FastaReader.isCorrectFormat(path)) {
                    FastaReader fr = new FastaReader(path);

                    String seq;

                    long[] lHashVals = pitr.hValsL;
                    long[] rHashVals = pitr.hValsR;
                    long[] pHashVals = pitr.hValsP;

                    if (existingKmersOnly) {
                        while (fr.hasNext()) {
                            seq = fr.next();
                            mSeq.reset(seq);

                            while (mSeq.find()) {
                                if (pitr.start(seq, mSeq.start(), mSeq.end())) {
                                    while (pitr.hasNext()) {
                                        pitr.next();
                                        if (graph.contains(lHashVals) && graph.contains(rHashVals)) {
                                            graph.addReadSingleKmerPair(pHashVals);
                                        }
                                    }
                                }
                            }

                            ++numReads;
                        }
                    }
                    else {
                        while (fr.hasNext()) {
                            seq = fr.next();
                            mSeq.reset(seq);

                            while (mSeq.find()) {
                                if (pitr.start(seq, mSeq.start(), mSeq.end())) {
                                    while (pitr.hasNext()) {
                                        pitr.next();
                                        graph.addReadSingleKmerPair(pHashVals);
                                    }
                                }
                            }

                            ++numReads;
                        }
                    }
                    
                    fr.close();
                }
                else {
                    throw new RuntimeException("Unsupported file format detected in input file `" + path + "`. Only FASTA format is supported.");
                }