integrated new log_gbwt_changes.

Robin-Rounthwaite · Dec 23, 2023 · 9c3e01d · 9c3e01d
1 parent 7a89e20
commit 9c3e01d
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Showing 2 changed files with 6 additions and 5 deletions.
diff --git a/src/algorithms/0_oo_normalize_snarls.cpp b/src/algorithms/0_oo_normalize_snarls.cpp
@@ -329,9 +329,9 @@ std::vector<vg::RebuildJob::mapping_type> SnarlNormalizer::parallel_normalizatio
         pair<handle_t, handle_t> new_left_right = integrate_snarl(get<0>(snarl), *get<1>(snarl), get<2>(snarl), get<3>(snarl), get<4>(snarl), get<5>(snarl));
         // make a subhandlegraph of the normalized snarl to find the new gbwt paths in the graph.
         // cerr << "extraction" << endl;
-        SubHandleGraph integrated_snarl = extract_subgraph(_graph, _graph.get_id(new_left_right.first), _graph.get_id(new_left_right.second));
+        // SubHandleGraph integrated_snarl = extract_subgraph(_graph, _graph.get_id(new_left_right.first), _graph.get_id(new_left_right.second));
         // cerr << "log changes" << endl;
-        log_gbwt_changes(get<6>(snarl), integrated_snarl);
+        log_gbwt_changes(get<6>(snarl), new_left_right);
 
     }
     auto integration_time = std::chrono::high_resolution_clock::now();
@@ -1657,9 +1657,9 @@ vector<int> SnarlNormalizer::normalize_snarl(const id_t source_id, const id_t si
         _unskipped_snarls.emplace(make_pair(leftmost_id, rightmost_id));
 
         // make a subhandlegraph of the normalized snarl to find the new gbwt paths in the graph.
-        SubHandleGraph integrated_snarl = extract_subgraph(_graph, _graph.get_id(new_left_right.first), _graph.get_id(new_left_right.second));
+        // SubHandleGraph integrated_snarl = extract_subgraph(_graph, _graph.get_id(new_left_right.first), _graph.get_id(new_left_right.second));
 
-        log_gbwt_changes(source_to_sink_gbwt_paths, integrated_snarl);
+        log_gbwt_changes(source_to_sink_gbwt_paths, new_left_right);
 
         // integrated_snarl.for_each_handle([&](const handle_t handle) {
         //     if (integrated_snarl.get_id(handle) == 2605470)

diff --git a/src/algorithms/0_oo_normalize_snarls.hpp b/src/algorithms/0_oo_normalize_snarls.hpp
@@ -137,7 +137,8 @@ class SnarlNormalizer {
 
     handle_t overwrite_node_id(const id_t old_node_id, const id_t new_node_id);
 
-    void log_gbwt_changes(const vector<pair<vector<gbwt::vector_type::value_type>, string>>& source_to_sink_gbwt_paths, const HandleGraph &new_snarl);
+    void log_gbwt_changes(const vector<pair<gbwt::vector_type, string>>& source_to_sink_gbwt_paths, const pair<handle_t, handle_t> left_and_right_id);
+    // void log_gbwt_changes(const vector<pair<vector<gbwt::vector_type::value_type>, string>>& source_to_sink_gbwt_paths, const HandleGraph &new_snarl);
 
     bool source_and_sink_handles_map_properly(
         const HandleGraph &graph, const id_t new_source_id, const id_t new_sink_id,