inline void Unitigging::removeTransitiveEdges() {
layout::BetterReadSet brs(reads_, 1);
for (size_t i = 0; i < no_contains_->size(); ++i) {
auto better_overlap = (*no_contains_)[i];
auto overlap = better_overlap->overlap();
brs[overlap->read_one]->AddOverlap(better_overlap);
brs[overlap->read_two]->AddOverlap(better_overlap);
}
brs.Finalize();
// for o1(x, y) and o2(x, a), o3(y, a)
std::vector< size_t > erased;
erased.reserve(no_contains_->size());
for (size_t i = 0; i < no_contains_->size(); ++i) {
auto better_overlap = (*no_contains_)[i];
auto overlap = better_overlap->overlap();
// TODO(brahle): izdvoji ovo u zasebnu klasu iterator
auto v1 = brs[overlap->read_one]->overlaps();
auto v2 = brs[overlap->read_two]->overlaps();
auto it1 = v1.begin();
auto it2 = v2.begin();
bool done = false;
while (!done && it1 != v1.end() && it2 != v2.end()) {
if (it1->first == overlap->read_one || it1->first == overlap->read_two) {
++it1;
continue;
}
if (it2->first == overlap->read_one || it2->first == overlap->read_two) {
++it2;
continue;
}
if (it1->first == it2->first) {
if (isTransitive(better_overlap, it1->second, it2->second)) {
(*reads_)[overlap->read_one]->addCoverage(
static_cast<double> (better_overlap->Length()) /
(*reads_)[overlap->read_one]->size());
(*reads_)[it1->first]->addCoverage(
static_cast<double> (better_overlap->Length()) /
(*reads_)[it1->first]->size());
erased.emplace_back(i);
const auto& o = better_overlap->overlap();
const auto& o1 = it1->second->overlap();
const auto& o2 = it2->second->overlap();
fprintf(stderr,
"Removing overlap (%d, %d) as transitive of (%d, %d), (%d, %d)\n",
(*reads_)[o->read_one]->orig_id(),
(*reads_)[o->read_two]->orig_id(),
(*reads_)[o1->read_one]->orig_id(),
(*reads_)[o1->read_two]->orig_id(),
(*reads_)[o2->read_one]->orig_id(),
(*reads_)[o2->read_two]->orig_id()
);
done = true;
}
++it1;
++it2;
} else if (it1->first < it2->first) {
++it1;
} else {
++it2;
}
}
}
no_transitives_ = BetterOverlapSetPtr(new BetterOverlapSet(reads_));
size_t idx = 0;
for (size_t i = 0; i < no_contains_->size(); ++i) {
if (idx < erased.size() && i == erased[idx]) {
++idx;
continue;
}
auto better_overlap = (*no_contains_)[i];
no_transitives_->Add(new BetterOverlap(better_overlap));
}
int transitive_edge_count = no_contains_->size() - no_transitives_->size();
fprintf(
stderr,
"Transitive edges = %d (%.2lf%%)\n",
transitive_edge_count,
(transitive_edge_count * 100.0) / no_contains_->size());
}
bool BinaryRelation::isEquivalence() const {
return(isReflexive() && isSymmetric() && isTransitive());
}
