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merge contiguous rgfa fragments
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@glennhickey
glennhickey committed Mar 27, 2024
1 parent f23e65a commit 6ebd95f
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Showing 2 changed files with 65 additions and 12 deletions.
70 changes: 58 additions & 12 deletions src/rgfa.cpp
View file
Original file line number Diff line number Diff line change
Expand Up @@ -146,7 +146,9 @@ void RGFACover::compute(const PathHandleGraph* graph,
vector<pair<step_handle_t, step_handle_t>>& thread_rgfa_intervals = rgfa_intervals_vector[omp_get_thread_num()];
unordered_map<nid_t, int64_t>& thread_node_to_interval = node_to_interval_vector[omp_get_thread_num()];

vector<const Snarl*> queue = {snarl};
vector<const Snarl*> queue = {snarl};

cerr << "top level snarl " << pb2json(*snarl) << endl;

while(!queue.empty()) {
const Snarl* cur_snarl = queue.back();
Expand Down Expand Up @@ -576,19 +578,13 @@ void RGFACover::compute_snarl(const Snarl& snarl, PathTraversalFinder& path_trav
}
continue;
}

// add the interval to the local (thread safe) structures
step_handle_t step = trav[uncovered_interval.first];
int64_t interval_length = uncovered_interval.second - uncovered_interval.first;
pair<step_handle_t, step_handle_t> new_interval = make_pair(trav.at(uncovered_interval.first),
graph->get_next_step(trav.at(uncovered_interval.second - 1)));
#ifdef debug
int64_t interval_length = uncovered_interval.second - uncovered_interval.first;
cerr << "adding interval with length " << interval_length << endl;
#endif
for (int64_t i = 0; i < interval_length; ++i) {
thread_node_to_interval[graph->get_id(graph->get_handle_of_step(step))] = thread_rgfa_intervals.size();
step = graph->get_next_step(step);
}
thread_rgfa_intervals.push_back(make_pair(trav.at(uncovered_interval.first),
graph->get_next_step(trav.at(uncovered_interval.second - 1))));
add_interval(thread_rgfa_intervals, thread_node_to_interval, new_interval);
}
}

Expand Down Expand Up @@ -621,6 +617,54 @@ vector<pair<int64_t, int64_t>> RGFACover::get_uncovered_intervals(const vector<s
return intervals;
}

bool RGFACover::add_interval(vector<pair<step_handle_t, step_handle_t>>& thread_rgfa_intervals,
unordered_map<nid_t, int64_t>& thread_node_to_interval,
const pair<step_handle_t, step_handle_t>& new_interval) {

bool merged = false;
path_handle_t path_handle = graph->get_path_handle_of_step(new_interval.first);

// check the before-first step. if it's in an interval then it must be immediately
// preceeding so we merge the new interval to the end of the found interval
step_handle_t before_first_step = graph->get_previous_step(new_interval.first);
if (before_first_step != graph->path_front_end(graph->get_path_handle_of_step(before_first_step))) {
nid_t prev_node_id = graph->get_id(graph->get_handle_of_step(before_first_step));
if (thread_node_to_interval.count(prev_node_id)) {
pair<step_handle_t, step_handle_t>& prev_interval = thread_rgfa_intervals[thread_node_to_interval[prev_node_id]];
if (graph->get_path_handle_of_step(prev_interval.first) == path_handle) {
assert(prev_interval.second == new_interval.first);
prev_interval.second = new_interval.second;
merged = true;
}
}
}

// check the end step. if it's in an interval then it must be immediately
// following we merge the new interval to the front of the found interval
if (new_interval.second != graph->path_end(graph->get_path_handle_of_step(new_interval.second))) {
nid_t next_node_id = graph->get_id(graph->get_handle_of_step(new_interval.second));
if (thread_node_to_interval.count(next_node_id)) {
pair<step_handle_t, step_handle_t>& next_interval = thread_rgfa_intervals[thread_node_to_interval[next_node_id]];
path_handle_t next_path = graph->get_path_handle_of_step(next_interval.first);
if (graph->get_path_handle_of_step(next_interval.first) == path_handle) {
assert(next_interval.first == new_interval.second);
next_interval.first = new_interval.first;
merged = true;
}
}
}

// add the interval to the local (thread safe) structures
if (!merged) {
for (step_handle_t step = new_interval.first; step != new_interval.second; step = graph->get_next_step(step)) {
thread_node_to_interval[graph->get_id(graph->get_handle_of_step(step))] = thread_rgfa_intervals.size();
}
thread_rgfa_intervals.push_back(new_interval);
}

return !merged;
}

int64_t RGFACover::get_coverage(const vector<step_handle_t>& trav, const pair<int64_t, int64_t>& uncovered_interval) {
path_handle_t path_handle = graph->get_path_handle_of_step(trav.front());
int64_t coverage = 0;
Expand All @@ -635,7 +679,9 @@ int64_t RGFACover::get_coverage(const vector<step_handle_t>& trav, const pair<in

return coverage;
}




// copied pretty much verbatem from
// https://github.com/ComparativeGenomicsToolkit/hal2vg/blob/v1.1.2/clip-vg.cpp#L809-L880
void RGFACover::forwardize_rgfa_paths(MutablePathMutableHandleGraph* mutable_graph) {
Expand Down
7 changes: 7 additions & 0 deletions src/rgfa.hpp
View file
Original file line number Diff line number Diff line change
Expand Up @@ -101,6 +101,13 @@ class RGFACover {
vector<pair<int64_t, int64_t>> get_uncovered_intervals(const vector<step_handle_t>& trav,
const unordered_map<nid_t, int64_t>& thread_node_to_interval);

// add a new interval into the rgfa_intervals veector and update the node_to_interval map
// if the interval can be merged into an existing, contiguous interval, do that instead
// returns true if a new interval was added, false if an existing interval was updated
bool add_interval(vector<pair<step_handle_t, step_handle_t>>& thread_rgfa_intervals,
unordered_map<nid_t, int64_t>& thread_node_to_interval,
const pair<step_handle_t, step_handle_t>& new_interval);

// get the total coverage of a traversal (sum of step lengths)
int64_t get_coverage(const vector<step_handle_t>& trav, const pair<int64_t, int64_t>& uncovered_interval);

Expand Down

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vg CI tests complete for branch rgfa2. View the full report here.

16 tests passed, 0 tests failed and 0 tests skipped in 16991 seconds

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