void PathIndex::apply_translations(const vector<Translation>& translations) {
// Convert from normal to partitioning translations
// For each original node ID, we keep a vector of pairs of from mapping and
// to mapping. We only keep pairs where the from mapping isn't empty.
map<id_t, vector<pair<Mapping, Mapping>>> collated;
for (auto& t : translations) {
if (t.from().mapping_size() < 1 || t.to().mapping_size() != 1) {
// Ensure the translations are the format we expect. They always have
// at least one from mapping (but maybe an insert too) and exactly 1
// to mapping.
cerr << "error:[vg::PathIndex] Bad translation: " << pb2json(t) << endl;
throw runtime_error("Translation not in VG::edit() format");
}
if (mapping_from_length(t.from().mapping(0)) == 0) {
// This is a novel node and can't be on our path
continue;
}
if (t.from().mapping(0).position().is_reverse()) {
// Wait for the forward-orientation version
continue;
}
// Stick the from and to mappings in the list for the from node
collated[t.from().mapping(0).position().node_id()].push_back(make_pair(t.from().mapping(0), t.to().mapping(0)));
}
for (auto& kv : collated) {
// For every original node and its replacement nodes
// Sort the replacement mappings
std::sort(kv.second.begin(), kv.second.end(), [](const pair<Mapping, Mapping>& a, const pair<Mapping, Mapping>& b) {
// Return true if the a pair belongs before the b pair along the path through the original node
return a.first.position().offset() <= b.first.position().offset();
});
// Make a new translation to cover the original node
Translation covering;
for (auto mapping_pair : kv.second) {
// Split across these parts of new nodes
*(covering.mutable_to()->add_mapping()) = mapping_pair.second;
}
// Just assume we take up the whole original node
auto* from_mapping = covering.mutable_from()->add_mapping();
from_mapping->mutable_position()->set_node_id(kv.first);
// Give it a full length perfect match
auto* from_edit = from_mapping->add_edit();
from_edit->set_from_length(path_from_length(covering.to()));
from_edit->set_to_length(from_edit->from_length());
// Apply this (single node) translation.
// TODO: batch up a bit?
apply_translation(covering);
}
}
size_t from_length_before_pos(const Alignment& aln, const Position& pos) {
return path_from_length(cut_path(aln.path(), pos).first);
}
size_t from_length_after_pos(const Alignment& aln, const Position& pos) {
return path_from_length(cut_path(aln.path(), pos).second);
}
