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consider the mask when filling bp_length #601

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merged 1 commit into from
Jan 28, 2025
Merged

consider the mask when filling bp_length #601

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67 changes: 36 additions & 31 deletions src/subcommand/similarity_main.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -140,6 +140,36 @@ args::Group threading_opts(parser, "[ Threading ]");
});
}

// ska::flat_hash_map<std::pair<uint64_t, uint64_t>, uint64_t> leads to huge memory usage with deep graphs
// Load mask if specified
std::vector<bool> node_mask(graph.get_node_count(), true); // Default all nodes included
if (mask_file) {
std::ifstream mask_in(args::get(mask_file));
std::string line;
uint64_t line_count = 0;
while (std::getline(mask_in, line)) {
if (line_count >= graph.get_node_count()) {
std::cerr << "[odgi::similarity] error: mask file has more lines than graph nodes ("
<< graph.get_node_count() << ")" << std::endl;
return 1;
}
if (line == "0") {
node_mask[line_count] = false;
} else if (line == "1") {
node_mask[line_count] = true;
} else {
std::cerr << "[odgi::similarity] error: mask file should contain only 0 or 1 values, found: " << line << std::endl;
return 1;
}
line_count++;
}
if (line_count != graph.get_node_count()) {
std::cerr << "[odgi::similarity] error: mask file should have exactly " << graph.get_node_count()
<< " lines, found: " << line_count << std::endl;
return 1;
}
}

auto get_path_name
= (using_delim ?
(std::function<std::string(const uint32_t&)>)
Expand Down Expand Up @@ -186,7 +216,12 @@ args::Group threading_opts(parser, "[ Threading ]");
graph.for_each_step_in_path(
p,
[&](const step_handle_t& s) {
path_length += graph.get_length(graph.get_handle_of_step(s));
auto h = graph.get_handle_of_step(s);
// Skip masked-out nodes
if (!node_mask[graph.get_id(h) - 1]) {
return;
}
path_length += graph.get_length(h);
});
#pragma omp critical (bp_count)
bp_count[get_path_id(p)] += path_length;
Expand All @@ -199,36 +234,6 @@ args::Group threading_opts(parser, "[ Threading ]");
graph.get_node_count(), "[odgi::similarity] collecting path intersection lengths");
}

// ska::flat_hash_map<std::pair<uint64_t, uint64_t>, uint64_t> leads to huge memory usage with deep graphs
// Load mask if specified
std::vector<bool> node_mask(graph.get_node_count(), true); // Default all nodes included
if (mask_file) {
std::ifstream mask_in(args::get(mask_file));
std::string line;
uint64_t line_count = 0;
while (std::getline(mask_in, line)) {
if (line_count >= graph.get_node_count()) {
std::cerr << "[odgi::similarity] error: mask file has more lines than graph nodes ("
<< graph.get_node_count() << ")" << std::endl;
return 1;
}
if (line == "0") {
node_mask[line_count] = false;
} else if (line == "1") {
node_mask[line_count] = true;
} else {
std::cerr << "[odgi::similarity] error: mask file should contain only 0 or 1 values, found: " << line << std::endl;
return 1;
}
line_count++;
}
if (line_count != graph.get_node_count()) {
std::cerr << "[odgi::similarity] error: mask file should have exactly " << graph.get_node_count()
<< " lines, found: " << line_count << std::endl;
return 1;
}
}

ska::flat_hash_map<uint64_t, uint64_t> path_intersection_length;
graph.for_each_handle(
[&](const handle_t& h) {
Expand Down