diff --git a/src/algorithms/0_oo_normalize_snarls.cpp b/src/algorithms/0_oo_normalize_snarls.cpp index a80fdbc9af2..13df5e73d23 100644 --- a/src/algorithms/0_oo_normalize_snarls.cpp +++ b/src/algorithms/0_oo_normalize_snarls.cpp @@ -329,9 +329,9 @@ std::vector SnarlNormalizer::parallel_normalizatio pair 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 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 index 896df37015c..10505d8eed5 100644 --- 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, string>>& source_to_sink_gbwt_paths, const HandleGraph &new_snarl); + void log_gbwt_changes(const vector>& source_to_sink_gbwt_paths, const pair left_and_right_id); + // void log_gbwt_changes(const vector, 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,