Method run

src/rnabloom/RNABloom.java:1816–1932

()

        }
        
        @Override
        public void run() {
            try {
                int fragKmersDist = graph.getFragPairedKmerDistance();
                int maxEdgeClipLength = minPolyATailLengthRequired > 0 ? 0 : maxTipLength;
                boolean keepBluntEndArtifact = keepArtifact;
                
                String fragment;
                while ((fragment = fin.next()) != null) {
                    ++numParsed;
//                    String seq = "";
//                    ArrayList<Kmer> kmers2 = graph.getKmers(seq);
//                    printPairedKmersPositions(kmers2, graph);
                    
                    ArrayList<Kmer> kmers = graph.getKmers(fragment);

                    if (!kmers.isEmpty()) {
                        if ( (!extendBranchFreeFragmentsOnly || isBranchFree(kmers, graph, maxTipLength)) &&
                             !represented(kmers,
                                            graph,
                                            screeningBf,
                                            lookahead,
                                            maxIndelSize,
                                            maxEdgeClipLength,
                                            percentIdentity) &&
                             (keepChimera || !isChimera(kmers, graph, screeningBf, lookahead)) &&
                             (keepBluntEndArtifact || !isBluntEndArtifact(kmers, graph, screeningBf, maxEdgeClipLength)) ) {

                            int[] originalFragRange;

                            if (haveFragKmers) {
                                originalFragRange = extendPE(kmers, graph, maxTipLength, minKmerCov);
                            }
                            else {
                                originalFragRange = extendSE(kmers, graph, maxTipLength, minKmerCov);
                            }

                            int[] currentRange = new int[]{0, kmers.size()};

                            if (haveFragKmers) {
                                if (kmers.size() >= fragKmersDist) {
                                    ArrayDeque<int[]> ranges = breakWithFragPairedKmers(kmers, graph, minNumKmerPairs);
                                    int numFragSegs = ranges.size();

                                    if (numFragSegs == 1) {
                                        currentRange = ranges.peekFirst();
                                    }
                                    else if (numFragSegs > 1) {
                                        int bestOverlap = 0;
                                        int[] bestRange = null;
                                        for (int[] range : ranges) {
                                            int overlap = intervalOverlapSize(range, originalFragRange);
                                            if (overlap > bestOverlap) {
                                                bestOverlap = overlap;
                                                bestRange = range;
                                            }
                                        }