Method breakWithFragPairedKmers

src/rnabloom/util/GraphUtils.java:4312–4374

(ArrayList<Kmer> kmers, BloomFilterDeBruijnGraph graph, int numPairsRequired)

    }
    
    public static ArrayDeque<int[]> breakWithFragPairedKmers(ArrayList<Kmer> kmers, BloomFilterDeBruijnGraph graph, int numPairsRequired) {
        int interlockDistance = 0;
        
        ArrayDeque<int[]> segments = new ArrayDeque<>();
        
        int d = graph.getFragPairedKmerDistance();
        int lastIndex = kmers.size() - 1 - d;
        
        int start = -1;
        int end = -1;
        
        if (numPairsRequired == 1) {
            for (int i=0; i<=lastIndex; ++i) {
                if (graph.lookupFragmentKmerPair(kmers.get(i), kmers.get(i+d))) {
                    if (start < 0) {
                        start = i;
                    }

                    end = i+d;
                }
                else if (start >= 0 && i >= end-interlockDistance) {
                    segments.add(new int[]{start, end+1});

                    start = -1;
                    end = -1;
                }
            }

            if (start >= 0) {
                segments.add(new int[]{start, end+1});
            }
        }
        else {
            int numPreviousKmerPairs = 0;
            for (int i=0; i<=lastIndex; ++i) {
                if (graph.lookupFragmentKmerPair(kmers.get(i), kmers.get(i+d))) {
                    if (++numPreviousKmerPairs >= numPairsRequired) {
                        if (start < 0) {
                            start = i-numPairsRequired+1;
                        }
                        
                        end = i+d;
                    }
                }
                else {
                    if (start >= 0 && i >= end-interlockDistance) {
                        segments.add(new int[]{start, end+1});

                        start = -1;
                        end = -1;
                    }
                    
                    numPreviousKmerPairs = 0;
                }
            }
            
            if (start >= 0) {
                segments.add(new int[]{start, end+1});