Method extendRight

src/rnabloom/util/GraphUtils.java:7114–7241

(Kmer source,
                                            BloomFilterDeBruijnGraph graph, 
                                            int maxTipLength,
                                            int bound, 
                                            int maxIndelSize, 
                                            float percentIdentity,
                                            float minKmerCov)

    }
    
    public static ArrayDeque<Kmer> extendRight(Kmer source,
                                            BloomFilterDeBruijnGraph graph, 
                                            int maxTipLength,
                                            int bound, 
                                            int maxIndelSize, 
                                            float percentIdentity,
                                            float minKmerCov) {
        int k = graph.getK();
        int numHash = graph.getMaxNumHash();
        ArrayDeque<Kmer> result = new ArrayDeque<>();
        
        ArrayDeque<Kmer> neighbors = new ArrayDeque<>(4);
        source.getSuccessors(k, numHash, graph, neighbors, minKmerCov);
        Kmer best;
        
        while (!neighbors.isEmpty() && result.size() <= bound) {
            
            if (neighbors.size() == 1) {
                best = neighbors.pop();
                result.add(best);
                
                ArrayDeque<Kmer> b = naiveExtendRight(best, graph, maxTipLength, bound-result.size(), minKmerCov);
                
                if (b.isEmpty()) {
                    break;
                }
                else {
                    result.addAll(b);
                    best = result.peekLast();
                }
            }
            else {
                best = null;
                
                ArrayDeque<ArrayDeque<Kmer>> branches = new ArrayDeque<>(4);
                
                float maxCov = -1;
                while (!neighbors.isEmpty()) {
                    Kmer n = neighbors.pop();

                    if (n.hasDepthRight(k, numHash, graph, maxTipLength)) {
                        ArrayDeque<Kmer> b = naiveExtendRight(n, graph, maxTipLength, bound-result.size(), minKmerCov);
                        
                        if (b.size() < maxTipLength) {
                            // indicates too many branches; can't resolve
                            return result;
                        }
                        
                        b.addFirst(n);
                        
                        float c = getMedianKmerCoverage(b);
                        if (c > maxCov) {
                            maxCov = c;
                            branches.addFirst(b);
                        }
                        else {
                            branches.addLast(b);
                        }