bool CheckCanRemap(const Sequence& old_s, const Sequence& new_s) const {
if(!CheckAllDifferent(old_s, new_s))
return false;
size_t old_length = old_s.size() - k_ + 1;
size_t new_length = new_s.size() - k_ + 1;
UniformPositionAligner aligner(old_s.size() - k_ + 1,
new_s.size() - k_ + 1);
Kmer old_kmer = old_s.start<Kmer>(k_);
old_kmer >>= 0;
for (size_t i = k_ - 1; i < old_s.size(); ++i) {
old_kmer <<= old_s[i];
size_t old_kmer_offset = i - k_ + 1;
size_t new_kmer_offest = aligner.GetPosition(old_kmer_offset);
if(old_kmer_offset * 2 + 1 == old_length && new_length % 2 == 0) {
Kmer middle(k_ - 1, new_s, new_length / 2);
if (typename Kmer::less2()(middle, !middle)) {
new_kmer_offest = new_length - 1 - new_kmer_offest;
}
}
Kmer new_kmer(k_, new_s, new_kmer_offest);
auto it = mapping_.find(new_kmer);
if (it != mapping_.end()) {
if (Substitute(new_kmer) != old_kmer) {
return false;
}
}
}
return true;
}
void RemapKmers(const Sequence& old_s, const Sequence& new_s) {
VERIFY(this->IsAttached());
size_t old_length = old_s.size() - k_ + 1;
size_t new_length = new_s.size() - k_ + 1;
UniformPositionAligner aligner(old_s.size() - k_ + 1,
new_s.size() - k_ + 1);
Kmer old_kmer = old_s.start<Kmer>(k_);
for (size_t i = k_ - 1; i < old_s.size(); ++i) {
// Instead of shifting right
if (i != k_ - 1) {
old_kmer <<= old_s[i];
}
size_t old_kmer_offset = i - k_ + 1;
size_t new_kmer_offest = aligner.GetPosition(old_kmer_offset);
if(old_kmer_offset * 2 + 1 == old_length && new_length % 2 == 0) {
Kmer middle(unsigned(k_ - 1), new_s, new_length / 2);
if(typename Kmer::less2()(middle, !middle)) {
new_kmer_offest = new_length - 1 - new_kmer_offest;
}
}
Kmer new_kmer(unsigned(k_), new_s, new_kmer_offest);
auto it = mapping_.find(new_kmer);
if (it != mapping_.end()) {
if(verification_on_)
VERIFY(Substitute(new_kmer) == old_kmer);
mapping_.erase(it);
}
if(old_kmer != new_kmer)
mapping_[old_kmer] = new_kmer;
}
}
void
checkKmers(DnaString const & kmer,
TVertexDescriptor const & starting_vertex,
TVertexDescriptor const & source_vertex,
TGraph const & graph,
std::vector<VertexLabels> & vertex_vector,
boost::unordered_set<TVertexDescriptor> const & free_nodes,
boost::unordered_map< std::pair<TVertexDescriptor, TVertexDescriptor>, boost::dynamic_bitset<> > & edge_ids,
boost::dynamic_bitset<> const & id_bits,
TKmerMap & kmer_map,
std::size_t const & kmer_size
)
{
if (id_bits.none())
return;
if (length(kmer) == kmer_size)
{
KmerLabels new_kmer_label =
{
starting_vertex,
source_vertex,
id_bits
};
if (kmer_map.count(kmer) == 0)
{
std::vector<KmerLabels> new_vector(1, new_kmer_label);
kmer_map[kmer] = new_vector;
}
else
{
kmer_map[kmer].push_back(new_kmer_label);
}
return;
}
for (Iterator<TGraph, OutEdgeIterator>::Type out_edge_iterator (graph, source_vertex) ; !atEnd(out_edge_iterator) ; ++out_edge_iterator)
{
DnaString new_kmer(kmer);
TVertexDescriptor const & target_vertex = targetVertex(out_edge_iterator);
boost::dynamic_bitset<> new_id_bits(id_bits);
if (free_nodes.count(target_vertex) == 0)
{
seqan::appendValue(new_kmer, vertex_vector[target_vertex].dna);
std::pair<TVertexDescriptor, TVertexDescriptor> edge_pair(source_vertex, target_vertex);
if (edge_ids.count(edge_pair) == 1)
{
new_id_bits = id_bits & edge_ids[edge_pair];
}
}
checkKmers(new_kmer, starting_vertex, target_vertex, graph, vertex_vector, free_nodes, edge_ids, new_id_bits, kmer_map, kmer_size);
}
}
void
check_kmers_simple(DnaString const & kmer,
TGraph const & graph,
TVertexDescriptor const & source_vertex,
std::vector<VertexLabels> & vertex_vector,
boost::unordered_set<TVertexDescriptor> const & free_nodes,
boost::unordered_map< std::pair<TVertexDescriptor, TVertexDescriptor>, boost::dynamic_bitset<> > & edge_ids,
boost::dynamic_bitset<> const & id_bits,
TKmerMapSimple & kmer_map,
std::size_t const & kmer_size
)
{
if (id_bits.none())
return;
if (length(kmer) == kmer_size)
{
if (id_bits.all())
return;
if (kmer_map.count(kmer) == 0)
{
kmer_map[kmer] = id_bits;
}
else
{
kmer_map[kmer] |= id_bits;
}
return;
}
for (Iterator<TGraph, OutEdgeIterator>::Type out_edge_iterator (graph, source_vertex) ; !atEnd(out_edge_iterator) ; ++out_edge_iterator)
{
DnaString new_kmer(kmer);
TVertexDescriptor const & target_vertex = targetVertex(out_edge_iterator);
// std::cout << source_vertex << " -> " << target_vertex << std::endl;
boost::dynamic_bitset<> new_id_bits(id_bits);
if (free_nodes.count(target_vertex) == 0)
{
seqan::appendValue(new_kmer, vertex_vector[target_vertex].dna);
std::pair<TVertexDescriptor, TVertexDescriptor> edge_pair(source_vertex, target_vertex);
if (edge_ids.count(edge_pair) == 1)
{
new_id_bits = id_bits & edge_ids[edge_pair];
}
}
check_kmers_simple(new_kmer, graph, target_vertex, vertex_vector, free_nodes, edge_ids, new_id_bits, kmer_map, kmer_size);
}
}
