void IterateHashGraph(AssemblyInfo &assembly_info, int new_kmer_size, int min_support, HashGraph &hash_graph, deque<Sequence> &old_contigs)
{
int old_kmer_size = hash_graph.kmer_size();
deque<ShortSequence> &reads = assembly_info.reads;
deque<Sequence> &long_reads = assembly_info.long_reads;
vector<bool> &read_flags = assembly_info.read_flags;
vector<bool> &long_read_flags = assembly_info.long_read_flags;
#pragma omp parallel for schedule(static, 1)
for (int64_t i = 0; i < (int64_t)old_contigs.size(); ++i)
hash_graph.InsertUncountKmers(old_contigs[i]);
hash_graph.AddAllEdges();
deque<Sequence> contigs;
hash_graph.Assemble(contigs);
hash_graph.clear();
uint64_t sum = 0;
int d = new_kmer_size - old_kmer_size;
for (unsigned i = 0; i < contigs.size(); ++i)
{
if ((int)contigs[i].size() - old_kmer_size + 1 >= 2*d + 2)
sum += 2*d + 2;
else if ((int)contigs[i].size() >= old_kmer_size)
sum += contigs[i].size() - old_kmer_size + 1;
}
HashGraph old_hash_graph(old_kmer_size);
old_hash_graph.reserve(sum);
#pragma omp parallel for schedule(static, 1)
for (int64_t i = 0; i < (int64_t)contigs.size(); ++i)
{
Sequence seq;
seq.Assign(contigs[i], 0, min(new_kmer_size, (int)contigs[i].size()));
old_hash_graph.InsertKmers(seq);
seq.Assign(contigs[i], max(0, (int)contigs[i].size() - new_kmer_size), min(new_kmer_size, (int)contigs[i].size()));
old_hash_graph.InsertKmers(seq);
}
//cout << "old kmer " << old_hash_graph.num_vertices() << endl;
hash_graph.set_kmer_size(new_kmer_size);
#pragma omp parallel for
for (int64_t i = 0; i < (int64_t)reads.size(); ++i)
{
if (!read_flags[i])
continue;
Sequence seq(reads[i]);
InsertIterativeKmers(old_hash_graph, seq, hash_graph);
}
#pragma omp parallel for schedule(static, 1)
for (int64_t i = 0; i < (int64_t)long_reads.size(); ++i)
{
if (!long_read_flags[i])
continue;
InsertIterativeKmers(old_hash_graph, long_reads[i], hash_graph);
}
#pragma omp parallel for schedule(static, 1)
for (int64_t i = 0; i < (int64_t)assembly_info.ref_contigs.size(); ++i)
InsertIterativeKmers(old_hash_graph, assembly_info.ref_contigs[i], hash_graph);
old_hash_graph.clear();
{
HashGraph tmp_hash_graph;
tmp_hash_graph.swap(old_hash_graph);
}
hash_graph.RefreshVertices(min_support);
#pragma omp parallel for schedule(static, 1)
for (int64_t i = 0; i < (int64_t)old_contigs.size(); ++i)
hash_graph.InsertUncountKmers(old_contigs[i]);
hash_graph.ClearCount();
InsertExistKmers(assembly_info, hash_graph);
}
