Merge pull request #509 from pangenome/polite_odgi_heaps

`odgi heaps`: avoid missing groups
pangenome · Jun 14, 2023 · c54f98d · c54f98d
2 parents 2d58cd8 + 892d090
commit c54f98d
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Showing 2 changed files with 5 additions and 33 deletions.
diff --git a/src/subcommand/heaps_main.cpp b/src/subcommand/heaps_main.cpp
@@ -128,6 +128,11 @@ int main_heaps(int argc, char **argv) {
                 auto vals = split(path_name, '#');
                 path_groups_map[vals.front()].push_back(p);
             });
+        } else {
+            // no groups
+            graph.for_each_path_handle([&](const path_handle_t& p) {
+                path_groups_map[graph.get_path_name(p)].push_back(p);
+            });
         }
         path_groups.reserve(path_groups_map.size());
         for (auto& g : path_groups_map) {

diff --git a/src/subcommand/overlap_main.cpp b/src/subcommand/overlap_main.cpp
@@ -125,39 +125,6 @@ namespace odgi {
             }
         }
 
-        auto get_graph_pos = [](const odgi::graph_t &graph,
-                                const path_pos_t &pos) {
-            auto path_end = graph.path_end(pos.path);
-            uint64_t walked = 0;
-            for (step_handle_t s = graph.path_begin(pos.path);
-                 s != path_end; s = graph.get_next_step(s)) {
-                handle_t h = graph.get_handle_of_step(s);
-                uint64_t node_length = graph.get_length(h);
-                if (walked + node_length > pos.offset) {
-                    return make_pos_t(graph.get_id(h), graph.get_is_reverse(h), pos.offset - walked);
-                }
-                walked += node_length;
-            }
-
-#pragma omp critical (cout)
-            std::cerr << "[odgi::overlap] warning: position " << graph.get_path_name(pos.path) << ":" << pos.offset
-                      << " outside of path" << std::endl;
-            return make_pos_t(0, false, 0);
-        };
-
-        auto get_offset_in_path = [](const odgi::graph_t &graph,
-                                     const path_handle_t &path, const step_handle_t &target) {
-            auto path_end = graph.path_end(path);
-            uint64_t walked = 0;
-            step_handle_t s = graph.path_begin(path);
-            for (; s != target; s = graph.get_next_step(s)) {
-                handle_t h = graph.get_handle_of_step(s);
-                walked += graph.get_length(h);
-            }
-            assert(s != path_end);
-            return walked;
-        };
-
         if (!path_ranges.empty()) {
             std::cout << "#path\tstart\tend\tpath.touched" << std::endl;