Method isTemplateSwitch2

src/rnabloom/util/GraphUtils.java:8305–8432

(ArrayList<Kmer> seqKmers, BloomFilterDeBruijnGraph graph, BloomFilter assembledKmers, int lookahead, float minPercentIdentity)

    }
        
    public static boolean isTemplateSwitch2(ArrayList<Kmer> seqKmers, BloomFilterDeBruijnGraph graph, BloomFilter assembledKmers, int lookahead, float minPercentIdentity) {
        int numKmers = seqKmers.size();
        int k = graph.getK();
        int maxNumKmersInLoop = 2*k;
        
        if (assembledKmers.lookup(seqKmers.get(numKmers-1).getHash())) {
            int start = Math.max(0, numKmers-2);
            for (; start>=0; --start) {
                if (!assembledKmers.lookup(seqKmers.get(start).getHash())) {
                    if (start-k >=0) {
                        ArrayDeque<Kmer> path = getMaxCoveragePath(graph, 
                                                    seqKmers.get(start-k), 
                                                    seqKmers.get(start+1),
                                                    k+1, 
                                                    lookahead, 
                                                    assembledKmers);
                        if (path != null) {
                            start -= k; 
                            continue;
                        }
                    }
                    
                    ++start;
                    break;
                }
            }
            
            if (start < k) {
                // no unassembled kmers
                return false;
            }
            
            float medCoverage = getMedianKmerCoverage(seqKmers, start, numKmers);

            int backBoneKmerIndex = -1;
            for (int i=start; i<numKmers; ++i) {
                if (seqKmers.get(i).count >= medCoverage) {
                    backBoneKmerIndex = i;
                    break;
                }
            }

            if (backBoneKmerIndex >= 0) {
                Kmer backBoneKmer = seqKmers.get(backBoneKmerIndex);

                ArrayDeque<Kmer> extension = greedyExtendLeft(graph, backBoneKmer, lookahead, 1000, assembledKmers);
                extension.add(backBoneKmer);
                extension.addAll(greedyExtendRight(graph, backBoneKmer, lookahead, 1000, assembledKmers));
                
                String backBone = graph.assemble(extension);

                String tipRC = reverseComplement(graph.assemble(seqKmers, 0, Math.max(1, start-maxNumKmersInLoop)));

                if (backBone.contains(tipRC)) {
                    return true;
                }

//                if (found) {