Method correctErrorHelper

src/rnabloom/util/GraphUtils.java:3711–3912

(ArrayList<Kmer> kmers,
                                                    BloomFilterDeBruijnGraph graph, 
                                                    int lookahead,
                                                    int maxIndelSize,
                                                    float covThreshold,
                                                    float percentIdentity,
                                                    float minKmerCov)

    }
    
    public static ArrayList<Kmer> correctErrorHelper(ArrayList<Kmer> kmers,
                                                    BloomFilterDeBruijnGraph graph, 
                                                    int lookahead,
                                                    int maxIndelSize,
                                                    float covThreshold,
                                                    float percentIdentity,
                                                    float minKmerCov) {
        
        
        boolean corrected = false;
        int numKmers = kmers.size();
        
        int k = graph.getK();
        int numHash = graph.getMaxNumHash();
        int expectedGapSize = k;
        
        ArrayList<Kmer> kmers2 = new ArrayList<>(numKmers + maxIndelSize);
        int numBadKmersSince = 0;
        Kmer kmer;
        for (int i=0; i<numKmers; ++i) {
            kmer = kmers.get(i);
            
            if (kmer.count >= covThreshold) {
                
                if (numBadKmersSince > 0) {
                    if (kmers2.isEmpty()) {
                        // check left edge
                        ArrayDeque<Kmer> leftVars = kmers.get(i-1).getLeftVariants(k, numHash, graph, minKmerCov);
                        if (leftVars.isEmpty()) {
                            // no branches found
                            for (int j=0; j<i; ++j) {
                                kmers2.add(kmers.get(j));
                            }
                        }
                        else if (numBadKmersSince >= lookahead) {
                            // calculate median cov of edge kmers
                            float[] tipCovs = new float[numBadKmersSince];
                            for (int j=0; j<i; ++j) {
                                tipCovs[j] = kmers.get(j).count;
                            }
                            float tipMedCov = getMedian(tipCovs);
                            
                            ArrayDeque<Kmer> greedyTipKmers = greedyExtendLeft(graph, kmer, lookahead, numBadKmersSince);
                            if (greedyTipKmers.size() == numBadKmersSince && getMedianKmerCoverage(greedyTipKmers) > tipMedCov) {
                                if (getPercentIdentity(graph.assemble(greedyTipKmers), graph.assemble(kmers, 0, i)) >= percentIdentity){
                                    corrected = true;
                                    kmers2.addAll(greedyTipKmers);
                                }
                                else if (!kmers.get(0).hasPredecessors(k, numHash, graph) && numBadKmersSince < k) {
                                    // this is blunt end in graph
                                    // do not add its kmers
                                    corrected = true;
                                }
                                else {
                                    // use original sequence
                                    for (int j=0; j<i; ++j) {
                                        kmers2.add(kmers.get(j));
                                    }