fix debug msg

vgteam · Apr 12, 2024 · 69fc397 · 69fc397 · adamnovak · Apr 12, 2024
1 parent 54712e1
commit 69fc397
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Showing 2 changed files with 7 additions and 3 deletions.
diff --git a/src/rgfa.cpp b/src/rgfa.cpp
@@ -689,8 +689,12 @@ bool RGFACover::add_interval(vector<pair<step_handle_t, step_handle_t>>& thread_
 #ifdef debug
 #pragma omp critical(cerr)
                     cerr << "next interval found" << graph->get_path_name(graph->get_path_handle_of_step(next_interval.first))
-                         << ":" << graph->get_id(graph->get_handle_of_step(next_interval.first))
-                         << "-" << graph->get_id(graph->get_handle_of_step(next_interval.second)) << endl;
+                         << ":" << graph->get_id(graph->get_handle_of_step(next_interval.first));
+                    if (next_interval.second == graph->path_end(graph->get_path_handle_of_step(next_interval.second))) {
+                        cerr << "PATH_END" << endl;
+                    } else {
+                         cerr << "-" << graph->get_id(graph->get_handle_of_step(next_interval.second)) << endl;
+                    }
 #endif
                     next_interval.first = new_interval.first;
                     merged = true;

diff --git a/src/subcommand/paths_main.cpp b/src/subcommand/paths_main.cpp
@@ -42,7 +42,7 @@ void help_paths(char** argv) {
          << "    -r, --retain-paths       output a graph with only the selected paths retained" << endl
          << "  rGFA cover" << endl
          << "    -f, --rgfa-min-length N  add rGFA cover to graph, using seleciton from -Q/-S as rank-0 backbone, only adding fragments >= Nbp (default:-1=disabled)" << endl
-         << "    -s, --snarls FILE        snarls (from vg snarls) to avoid recomputing. snarls only used for rgfa cover (-R)." << endl
+         << "    -s, --snarls FILE        snarls (from vg snarls) to avoid recomputing. snarls only used for rgfa cover." << endl
          << "    -t, --threads N          use up to N threads when computing rGFA cover (default: all available)" << endl
          << "        --rgfa-vcf FILE      add rGFA cover tags to VCF (which must be called on rGFA cover in graph from -f)" << endl
          << "  output path data:" << endl