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check the GFA while reading it #591

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merged 1 commit into from
Sep 18, 2024
Merged

check the GFA while reading it #591

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57 changes: 42 additions & 15 deletions src/gfa_to_handle.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -45,9 +45,14 @@ void gfa_to_handle(const string& gfa_filename,
gg.for_each_sequence_line_in_file(
filename,
[&](gfak::sequence_elem s) {
uint64_t id = stol(s.name);
min_id = std::min(min_id, id);
max_id = std::max(max_id, id);
try {
uint64_t id = stol(s.name);
min_id = std::min(min_id, id);
max_id = std::max(max_id, id);
} catch (const std::exception& e) {
std::cerr << "[odgi::gfa_to_handle] Error parsing segment '" << s.name << "': " << e.what() << std::endl;
exit(1);
}
});
});
line_counts = gfa_line_counts(filename);
Expand All @@ -67,8 +72,13 @@ void gfa_to_handle(const string& gfa_filename,
gg.for_each_sequence_line_in_file(
filename,
[&](const gfak::sequence_elem& s) {
uint64_t id = stol(s.name);
graph->create_handle(s.sequence, id - id_increment);
try {
uint64_t id = stol(s.name);
graph->create_handle(s.sequence, id - id_increment);
} catch (const std::exception& e) {
std::cerr << "[odgi::gfa_to_handle] Error creating node '" << s.name << ": " << e.what() << std::endl;
exit(1);
}
if (progress) progress_meter->increment(1);
});
if (progress) {
Expand All @@ -86,9 +96,22 @@ void gfa_to_handle(const string& gfa_filename,
filename,
[&](const gfak::edge_elem& e) {
if (e.source_name.empty()) return;
handlegraph::handle_t a = graph->get_handle(stol(e.source_name) - id_increment, !e.source_orientation_forward);
handlegraph::handle_t b = graph->get_handle(stol(e.sink_name) - id_increment, !e.sink_orientation_forward);
graph->create_edge(a, b);
try {
uint64_t source_id = stol(e.source_name) - id_increment;
uint64_t sink_id = stol(e.sink_name) - id_increment;
if (graph->has_node(source_id) && graph->has_node(sink_id)) {
handlegraph::handle_t a = graph->get_handle(stol(e.source_name) - id_increment, !e.source_orientation_forward);
handlegraph::handle_t b = graph->get_handle(stol(e.sink_name) - id_increment, !e.sink_orientation_forward);
graph->create_edge(a, b);
} else {
std::cerr << "[odgi::gfa_to_handle] Error creating edge '" << e.source_name << " <--> " << e.sink_name << "' due to missing node(s)" << std::endl;
exit(1);
}
} catch (const std::exception& exc) {
std::cerr << "[odgi::gfa_to_handle] Error creating edge '" << e.source_name << " <--> " << e.sink_name << "': " << exc.what() << std::endl;
exit(1);
}

if (progress) progress_meter->increment(1);
});
if (progress) {
Expand Down Expand Up @@ -116,17 +139,21 @@ void gfa_to_handle(const string& gfa_filename,
uint64_t id = 0;
try {
id = std::stoull(s) - id_increment;
if (graph->has_node(id)) {
graph->append_step(p->path,
graph->get_handle(id,
// in gfak, true == +
!p->gfak.orientations[i++]));
} else {
std::cerr << "[odgi::gfa_to_handle] Error creating path '" << graph->get_path_name(p->path) << "' due to missing node '" << s << "'" << std::endl;
exit(1);
}
} catch (...) {
std::cerr << std::endl // pad
<< "[odgi::gfa_to_handle] id parsing failure for path "
std::cerr << "[odgi::gfa_to_handle] id parsing failure for path "
<< graph->get_path_name(p->path)
<< " attempting to parse node id from '" << s << "'" << std::endl;
throw;
exit(1);
}
graph->append_step(p->path,
graph->get_handle(id,
// in gfak, true == +
!p->gfak.orientations[i++]));
}
delete p;
if (progress) progress_meter->increment(1);
Expand Down