Method getMaxCoveragePath

src/rnabloom/util/GraphUtils.java:1591–1675

@param graph @param left @param right @param bound @param lookahead @param minKmerCov @return

(BloomFilterDeBruijnGraph graph, Kmer left, Kmer right, int bound, int lookahead, float minKmerCov)

     * @return 
     */
    public static ArrayDeque<Kmer> getMaxCoveragePath(BloomFilterDeBruijnGraph graph, Kmer left, Kmer right, int bound, int lookahead, float minKmerCov) {
               
        int k = graph.getK();
        int numHash = graph.getMaxNumHash();
        
        HashSet<Kmer> leftPathKmers = new HashSet<>(bound);
        
        /* greedy extend right */
        ArrayDeque<Kmer> leftPath = new ArrayDeque<>(bound);
        Kmer best;
        
        best = left;

        for (int depth=0; depth < bound; ++depth) {
            best = best.getMaxCovSuccessor(k, numHash, graph, minKmerCov);
            if (best == null) {
                break;
            }
            else {
                if (best.equals(right)) {
                    return leftPath;
                }
                else {
                    if (leftPathKmers.contains(best)) {
                        break;
                    }
                    else {
                        leftPathKmers.add(best);
                        leftPath.add(best);
                    }
                }
            }
        }
        
        HashSet<Kmer> rightPathKmers = new HashSet<>(bound);
        
        /* not connected, search from right */
        ArrayDeque<Kmer> rightPath = new ArrayDeque<>(bound);
        best = right;
        for (int depth=0; depth < bound; ++depth) {
            best = best.getMaxCovPredecessor(k, numHash, graph, minKmerCov);
            
            if (best == null) {
                break;
            }
            else {
                if (best.equals(left)) {
                    return rightPath;
                }
                else {
                    if (rightPathKmers.contains(best)) {
                        return null;
                    }
                    else if (leftPathKmers.contains(best)) {
                        /* right path intersects the left path */
                        
                        if (isLowComplexityShort(best.toString())) {
                            return null;