Method join

src/rnabloom/util/GraphUtils.java:892–1147

(BloomFilterDeBruijnGraph graph, 
                                        ArrayList<Kmer> leftKmers, 
                                        ArrayList<Kmer> rightKmers, 
                                        int bound, 
                                        int lookahead, 
                                        float maxCovGradient,
                                        int maxTipLen,
                                        int maxIndelLen,
                                        float minPercentIdentity,
                                        float minKmerCov)

    }
    
    public static ArrayList<Kmer> join(BloomFilterDeBruijnGraph graph, 
                                        ArrayList<Kmer> leftKmers, 
                                        ArrayList<Kmer> rightKmers, 
                                        int bound, 
                                        int lookahead, 
                                        float maxCovGradient,
                                        int maxTipLen,
                                        int maxIndelLen,
                                        float minPercentIdentity,
                                        float minKmerCov) {
        int k = graph.getK();
        int numHash = graph.getMaxNumHash();
        //int pkd = graph.getReadPairedKmerDistance();
        
        HashSet<Kmer> leftKmersSet = new HashSet<>(leftKmers);
        HashSet<Kmer> rightKmersSet = new HashSet<>(rightKmers);
        

        Kmer right = rightKmers.get(0);
        
        float leftCoverageThreshold = Math.max(minKmerCov, getMinimumKmerCoverage(leftKmers) * maxCovGradient);
        
        ArrayList<Kmer> leftPath = new ArrayList<>(leftKmers);
        
        int maxSize = bound + leftPath.size();
        while (leftPath.size() < maxSize) {            
            ArrayDeque<Kmer> neighbors = leftPath.get(leftPath.size()-1).getSuccessors(k, numHash, graph, minKmerCov);

            // filter by coverage
            if (neighbors.isEmpty()) {
                break;
            }
            else {
                Kmer best = null;

                if (neighbors.size() == 1) {
                    best = neighbors.pop();
                    leftCoverageThreshold = Math.max(minKmerCov, Math.min(leftCoverageThreshold, best.count*maxCovGradient));
                }
                else {
                    Iterator<Kmer> itr = neighbors.iterator();
                    while (itr.hasNext()) {
                        if (itr.next().count < leftCoverageThreshold) {
                            itr.remove();
                        }
                    }

                    if (neighbors.size() == 1) {
                        best = neighbors.pop();
                        leftCoverageThreshold = Math.max(minKmerCov, Math.min(leftCoverageThreshold, best.count*maxCovGradient));
                    }
                }

                if (best != null) {                    
                    if (rightKmersSet.contains(best)) {
                        if (best.equals(right)) {
                            leftPath.addAll(rightKmers);
                            return leftPath;