diff --git a/src/clip.cpp b/src/clip.cpp index f3c59486fb..a8c2af99b4 100644 --- a/src/clip.cpp +++ b/src/clip.cpp @@ -123,7 +123,7 @@ void visit_contained_snarls(const PathPositionHandleGraph* graph, const vector 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 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& ref_prefixes, int64_t min_fragment_len, bool verbose) { unordered_set 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; diff --git a/src/rare_variant_simplifier.cpp b/src/rare_variant_simplifier.cpp index abbbe0eb2d..9cce1a48bb 100644 --- a/src/rare_variant_simplifier.cpp +++ b/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 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 diff --git a/src/subcommand/clip_main.cpp b/src/subcommand/clip_main.cpp index 7f1a4fb88e..9929c8e22c 100644 --- a/src/subcommand/clip_main.cpp +++ b/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); diff --git a/src/subcommand/deconstruct_main.cpp b/src/subcommand/deconstruct_main.cpp index 844dcbf417..beef23ab90 100644 --- a/src/subcommand/deconstruct_main.cpp +++ b/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); diff --git a/src/subcommand/depth_main.cpp b/src/subcommand/depth_main.cpp index b109f81049..c4988c881c 100644 --- a/src/subcommand/depth_main.cpp +++ b/src/subcommand/depth_main.cpp @@ -222,7 +222,7 @@ int main_depth(int argc, char** argv) { map, string> ref_paths; unordered_set 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); diff --git a/src/subcommand/simplify_main.cpp b/src/subcommand/simplify_main.cpp index 983422ef5d..782ea52b66 100644 --- a/src/subcommand/simplify_main.cpp +++ b/src/subcommand/simplify_main.cpp @@ -243,7 +243,7 @@ int main_simplify(int argc, char** argv) { if (!keep_nonref_paths) { vector 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); } diff --git a/src/traversal_finder.cpp b/src/traversal_finder.cpp index b011cfe51f..7327faacd1 100644 --- a/src/traversal_finder.cpp +++ b/src/traversal_finder.cpp @@ -72,7 +72,7 @@ vector PathBasedTraversalFinder::find_traversals(const Snarl& si regex alt_str ("(_alt_)"); regex back ("(_[0-9]*)"); set 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)); });