Method correctErrorHelper2

src/rnabloom/util/GraphUtils.java:2196–2423

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

    }
    
    private static ArrayList<Kmer> correctErrorHelper2(final ArrayList<Kmer> kmers,
                                                    final BloomFilterDeBruijnGraph graph, 
                                                    final int lookahead,
                                                    final int maxIndelSize,
                                                    final float covThreshold,
                                                    final float percentIdentity) {
        
        /**@TODO Need to be debugged*/
        
        final int numKmers = kmers.size();
        final int k = graph.getK();
        final int numHash = graph.getMaxNumHash();
        final int snvBubbleLength = k;
        final int minIslandSize = 3;
        
        ArrayList<Kmer> kmers2 = new ArrayList<>(numKmers + maxIndelSize);
        
        boolean corrected = false;
                
        int start = -1; // left edge of kmer island
        int end = -1;   // right edge of kmer island
        
        for (int i=0; i<numKmers; ++i) {
            if (start < 0) {
                // the left edge of kmer island has not been defined yet
                boolean enoughKmers = true;
                for (int j=i; j<i+minIslandSize; ++j) {
                    if (kmers.get(j).count < covThreshold) {
                        enoughKmers = false;
                        break;
                    }
                }
                
                if (enoughKmers) {
                    start = i;
                    
                    // attempt to correct bad kmers to the left of island
                    
                    if (end < 0) {
                        if (start > 0) {
                            // correct left edge

                            ArrayDeque<Kmer> leftVars = kmers.get(start-1).getLeftVariants(k, numHash, graph);
                            
                            if (leftVars.isEmpty()) {
                                // no branches found
                                for (int j=0; j<start; ++j) {
                                    kmers2.add(kmers.get(j));
                                }
                            }
                            else if (start >= lookahead) {
                                // calculate median cov of edge kmers
                                float[] tipCovs = new float[start];
                                for (int j=0; j<start; ++j) {
                                    tipCovs[j] = kmers.get(j).count;
                                }
                                float tipMedCov = getMedian(tipCovs);