Merge pull request #206 from pangenome/fix_path_embedding

Fix path embedding
pangenome · Mar 18, 2024 · 52a81b7 · 52a81b7
2 parents ea36234 + 45314a0
commit 52a81b7
Showing 1 changed file with 12 additions and 4 deletions.
diff --git a/src/main.cpp b/src/main.cpp
@@ -411,6 +411,7 @@ int main(int argc, char **argv) {
 
             uint64_t block_count;
 
+            uint64_t number_of_paths_in_the_original_graph;
             {
                 auto graph = std::make_unique<XG>();
 
@@ -441,6 +442,8 @@ int main(int argc, char **argv) {
                     }
                 }
 
+                number_of_paths_in_the_original_graph = graph->get_path_count();
+
                 auto *blockset = new smoothxg::blockset_t();
                 smoothxg::smoothable_blocks(*graph,
                                             *blockset,
@@ -680,10 +683,8 @@ int main(int argc, char **argv) {
                             prec_i = i;
                         }
                     }
-                    if (path_mapping.size() == 1 || prec_i != path_mapping.size() - 1) {
-                        smoothed->create_path_handle(path_handle_2_name_and_length[prec_path].first);
-                        path_handle_2_start_and_end_in_path_mapping[prec_path] = std::make_pair(prec_i, path_mapping.size() - 1);
-                    }
+                    smoothed->create_path_handle(path_handle_2_name_and_length[prec_path].first);
+                    path_handle_2_start_and_end_in_path_mapping[prec_path] = std::make_pair(prec_i, path_mapping.size() - 1);
                 }
 
                 // then for each path, ensure that it's embedded in the graph by walking through
@@ -792,6 +793,13 @@ int main(int argc, char **argv) {
                     validate_progress.finish();
                 }
 
+                if (number_of_paths_in_the_original_graph != smoothed->get_path_count()) {
+                    std::cerr << smoothxg_iter << "] error! path count mismatch between input (" 
+                            << number_of_paths_in_the_original_graph << ") and smoothed graph (" 
+                            << smoothed->get_path_count() << ")" << std::endl;
+                    exit(1);
+                }
+
                 if (!consensus_mapping.empty()) {
                     std::cerr << smoothxg_iter << "::smooth_and_lace] sorting consensus" << std::endl;