Revert path sense filtering in clip, depth, simplify and traversal_fi…

src/clip.cpp

@@ -123,7 +123,7 @@ void visit_contained_snarls(const PathPositionHandleGraph* graph, const vector<R
         path_name_set.insert(region.seq);
     }
     unordered_set<string> graph_path_name_set;
-    graph->for_each_path_of_sense({PathSense::REFERENCE, PathSense::GENERIC}, [&](path_handle_t path_handle) {
+    graph->for_each_path_handle([&](path_handle_t path_handle) {
             string graph_path_name = graph->get_path_name(path_handle);
             if (path_name_set.count(Paths::strip_subrange(graph_path_name))) {
                 graph_path_name_set.insert(graph_path_name);
@@ -614,7 +614,7 @@ void clip_low_depth_nodes_and_edges_generic(MutablePathMutableHandleGraph* graph
     bdsg::PackedVector<> edge_depths;
     edge_depths.resize(edge_count + 1);
 
-    graph->for_each_path_of_sense({PathSense::REFERENCE, PathSense::GENERIC}, [&](path_handle_t path_handle) {
+    graph->for_each_path_handle([&](path_handle_t path_handle) {
             bool is_ref_path = check_prefixes(graph->get_path_name(path_handle));
             handle_t prev_handle;
             bool first = true;
@@ -1053,7 +1053,7 @@ void clip_deletion_edges(MutablePathMutableHandleGraph* graph, int64_t max_delet
 
     // load up the reference paths and their ids
     unordered_set<path_handle_t> ref_paths;
-    graph->for_each_path_of_sense({PathSense::REFERENCE, PathSense::GENERIC}, [&](path_handle_t path_handle) {
+    graph->for_each_path_handle([&](path_handle_t path_handle) {
             string path_name = graph->get_path_name(path_handle);
             for (const string& ref_prefix : ref_prefixes) {
                 if (path_name.compare(0, ref_prefix.length(), ref_prefix) == 0) {
@@ -1312,7 +1312,7 @@ void clip_contained_stubs(MutablePathMutableHandleGraph* graph, PathPositionHand
 void stubbify_ref_paths(MutablePathMutableHandleGraph* graph, const vector<string>& ref_prefixes, int64_t min_fragment_len, bool verbose) {
     unordered_set<edge_t> edges_to_delete;
     int64_t stubbified_path_count = 0; // just for logging
-    graph->for_each_path_of_sense({PathSense::REFERENCE, PathSense::GENERIC}, [&](path_handle_t path_handle) {
+    graph->for_each_path_handle([&](path_handle_t path_handle) {
         string path_name = graph->get_path_name(path_handle);
         for (const string& ref_prefix : ref_prefixes) {
             bool was_stubbified = false;

src/rare_variant_simplifier.cpp

@@ -12,11 +12,11 @@ void RareVariantSimplifier::simplify() {
     // This holds the IDs of all the nodes we want to keep around
     unordered_set<id_t> to_keep;
 
-    graph.for_each_path_of_sense({PathSense::REFERENCE, PathSense::GENERIC}, [&](const path_handle_t& path) {
+    graph.for_each_path_handle([&](const path_handle_t& path) {
         // For each path
-        
+
         if (!Paths::is_alt(graph.get_path_name(path))) {
-            // If it isn't an alt or haplotype path, we want to trace it
+            // If it isn't an alt path, we want to trace it
 
             // For each occurrence from start to end
             // Put the ID of the node we are visiting in the to-keep set

src/subcommand/clip_main.cpp

@@ -300,7 +300,7 @@ int main_clip(int argc, char** argv) {
             for (const Region& region : bed_regions) {
                 contig_set.insert(region.seq);
             }
-            graph->for_each_path_of_sense({PathSense::REFERENCE, PathSense::GENERIC}, [&] (path_handle_t path_handle) {
+            graph->for_each_path_handle([&] (path_handle_t path_handle) {
                     string base_name = Paths::strip_subrange(graph->get_path_name(path_handle));
                     if (contig_set.count(base_name)) {
                         // todo: should take into account coordinate comp
@@ -329,7 +329,7 @@ int main_clip(int argc, char** argv) {
             assert(need_pp);
             assert(!ref_prefixes.empty());
             // load the BED regions from the reference path prefix
-            pp_graph->for_each_path_of_sense({PathSense::REFERENCE, PathSense::GENERIC}, [&](path_handle_t path_handle) {
+            pp_graph->for_each_path_handle([&](path_handle_t path_handle) {
                     string path_name = pp_graph->get_path_name(path_handle);
                     subrange_t subrange;
                     path_name = Paths::strip_subrange(path_name, &subrange);

src/subcommand/deconstruct_main.cpp

@@ -339,7 +339,6 @@ int main_deconstruct(int argc, char** argv) {
     }
 
     // process the prefixes to find ref paths
-    // Altpaths are included (priority given to non-altpaths in deconstructor.cpp)
     if (!refpath_prefixes.empty()) {
         graph->for_each_path_of_sense({PathSense::REFERENCE, PathSense::GENERIC}, [&](const path_handle_t& path_handle) {
             string path_name = graph->get_path_name(path_handle);

src/subcommand/depth_main.cpp

@@ -222,7 +222,7 @@ int main_depth(int argc, char** argv) {
         map<pair<string, int64_t>, string> ref_paths;
         unordered_set<string> base_path_set;
 
-        graph->for_each_path_of_sense({PathSense::REFERENCE, PathSense::GENERIC}, [&](path_handle_t path_handle) {
+        graph->for_each_path_handle([&](path_handle_t path_handle) {
                 string path_name = graph->get_path_name(path_handle);
                 subrange_t subrange;
                 string base_name = Paths::strip_subrange(path_name, &subrange);

src/subcommand/simplify_main.cpp

@@ -243,7 +243,7 @@ int main_simplify(int argc, char** argv) {
 
         if (!keep_nonref_paths) {
             vector<path_handle_t> to_destroy;
-            graph->for_each_path_of_sense({PathSense::REFERENCE, PathSense::GENERIC}, [&](const path_handle_t path_handle) {
+            graph->for_each_path_handle([&](const path_handle_t path_handle) {
                 if (graph->get_path_name(path_handle).compare(0, ref_path_prefix.length(), ref_path_prefix) != 0) {
                     to_destroy.push_back(path_handle);
                 }

src/traversal_finder.cpp

@@ -72,7 +72,7 @@ vector<SnarlTraversal> PathBasedTraversalFinder::find_traversals(const Snarl& si
     regex alt_str ("(_alt_)");
     regex back ("(_[0-9]*)");
     set<string> gpath_names;
-    graph.for_each_path_of_sense({PathSense::REFERENCE, PathSense::GENERIC}, [&](const path_handle_t& path_handle) {
+    graph.for_each_path_handle([&](const path_handle_t& path_handle) {
         gpath_names.insert(graph.get_path_name(path_handle));
     });