Method correctErrorsSE

src/rnabloom/util/GraphUtils.java:3998–4049

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

    }
            
    public static ArrayList<Kmer> correctErrorsSE(ArrayList<Kmer> kmers,
                                    BloomFilterDeBruijnGraph graph, 
                                    int lookahead,
                                    int maxIndelSize,
                                    float maxCovGradient, 
                                    float covFPR,
                                    float percentIdentity,
                                    float minKmerCov) {
        
        if (!kmers.isEmpty()) {
            int numKmers = kmers.size();
            
            // sort coverage in ascending order
            float[] covs = new float[numKmers];
            for (int i=0; i<numKmers; ++i) {
                covs[i] = kmers.get(i).count;
            }
            Arrays.sort(covs);

            boolean thresholdFound = false;

            int numFalsePositivesAllowed = (int) Math.round(numKmers * covFPR);
            int startIndex = numKmers - 1 - numFalsePositivesAllowed;

            float covThreshold = 0;

            if (startIndex >= 0) {
                covThreshold = covs[startIndex];
                float c = -1;
                for (int i=startIndex-1; i>=0; --i) {
                    c = covs[i];
                    if (covThreshold * maxCovGradient > c) {
                        thresholdFound = true;
                        break;
                    }
                    covThreshold = c;
                }
            }

            if (thresholdFound) {
                return correctErrorHelper(kmers,
                                            graph, 
                                            lookahead,
                                            maxIndelSize,
                                            covThreshold,
                                            percentIdentity,
                                            minKmerCov);
            }
        }

        return null;
    }
    
    public static ReadPair correctErrorsPE(ArrayList<Kmer> leftKmers, 
                                            ArrayList<Kmer> rightKmers,