Method extendRightPE

src/rnabloom/util/GraphUtils.java:6206–6309

(ArrayList<Kmer> kmers, 
                                            BloomFilterDeBruijnGraph graph,
                                            int maxTipLen,
                                            float minKmerCov)

    }
    
    private static ArrayDeque<Kmer> extendRightPE(ArrayList<Kmer> kmers, 
                                            BloomFilterDeBruijnGraph graph,
                                            int maxTipLen,
                                            float minKmerCov) {
        final int k = graph.getK();
        final int numHash = graph.getMaxNumHash();
        final int readPairedKmersDist = graph.getReadPairedKmerDistance();
        final int fragPairedKmersDist = graph.getFragPairedKmerDistance();        
        final int numKmers = kmers.size();
        int maxExtensionLength = fragPairedKmersDist - 2; // -1 for candidate k-mer; -1 for partner kmer on current sequence
        
        ArrayDeque<Kmer> candidates = kmers.get(numKmers-1).getSuccessors(k, numHash, graph);
        
        if (candidates.size() == 1) {
            Kmer c = candidates.peek();
            ArrayDeque<Kmer> e = naiveExtendRightNoBackChecks(c, graph, maxTipLen, maxExtensionLength, minKmerCov);
            e.addFirst(c);
            return e;
        }
    
        for (int i=numKmers-1; i>=0; --i) {
            if (graph.isRepeatKmer(kmers.get(i))) {
                --maxExtensionLength;
            }
            else {
               break;
            }
        }
        
        final float pathMinCov = getMinimumKmerCoverage(kmers, Math.max(numKmers - fragPairedKmersDist, 0), numKmers);        
        float bestScore = 0;
        float bestCov = 0;
        ArrayDeque<Kmer> bestExtension = null;
        int[] result = new int[3];
        
        for (Kmer candidate : candidates) {
            ArrayDeque<Kmer> e = naiveExtendRightNoBackChecks(candidate, graph, maxTipLen, maxExtensionLength, minKmerCov);
            e.addFirst(candidate);
            
            countKmerPairsPE(kmers, e, 0, graph, result);
            
            int lastPartneredKmerIndex = result[2];
            
            if (lastPartneredKmerIndex >= 0 && result[0] > 0 && result[1] > 0) {
                float cov = getMedianKmerCoverage(e);
                float score = Math.min(pathMinCov, cov) * (result[0] + result[1]) / (lastPartneredKmerIndex+1);
//                System.out.println(score + ": " + graph.assemble(e));
                if (score > bestScore || (score == bestScore && cov > bestCov)) {
                    bestScore = score;
                    bestCov = cov;
                    bestExtension = e;
                    
                    Iterator<Kmer> itr = e.descendingIterator();
                    for (int i=e.size()-1; i>lastPartneredKmerIndex; --i) {
                        itr.next();
                        itr.remove();
                    }
                }