update path storage to linked lists

Resolves #30

.gitmodules

@@ -1,6 +1,6 @@
 [submodule "pb2json"]
 	path = pb2json
-	url = https://github.com/shafreeck/pb2json.git
+	url = https://github.com/ekg/pb2json.git
 [submodule "vcflib"]
 	path = vcflib
 	url = https://github.com/ekg/vcflib.git

index.cpp

@@ -536,7 +536,7 @@ void Index::load_graph(VG& graph) {
 
 void Index::load_paths(VG& graph) {
     graph.destroy_progress();
-    graph.create_progress("indexing paths of " + graph.name, graph.paths._paths->size());
+    graph.create_progress("indexing paths of " + graph.name, graph.paths._paths.size());
     store_paths(graph);
     graph.destroy_progress();
 }
@@ -608,9 +608,10 @@ int64_t Index::get_path_id(const string& name) {
 }
 
 void Index::store_paths(VG& graph) {
-    for (auto& path : *graph.paths._paths) {
+    function<void(Path&)> lambda = [this, &graph](Path& path) {
         store_path(graph, path);
-    }
+    };
+    graph.paths.for_each(lambda);
 }
 
 void Index::store_path(VG& graph, Path& path) {

main.cpp

@@ -332,8 +332,10 @@ void help_mod(char** argv) {
          << "Modifies graph, outputs modified on stdout." << endl
          << endl
          << "options:" << endl
-         << "    -k, --keep-path NAME  keep only nodes and edges in the path" << endl
-         << "    -o, --remove-orphans  remove orphan edges from graph (edge specified but node missing)" << endl;
+         << "    -i, --include-aln FILE  include the paths implied by alignments in the graph" << endl
+         << "    -c, --compact-ids       should we sort and compact the id space? (default false)" << endl
+         << "    -k, --keep-path NAME    keep only nodes and edges in the path" << endl
+         << "    -o, --remove-orphans    remove orphan edges from graph (edge specified but node missing)" << endl;
 }
 
 int main_mod(int argc, char** argv) {
@@ -345,20 +347,24 @@ int main_mod(int argc, char** argv) {
 
     string path_name;
     bool remove_orphans = false;
+    string aln_file;
+    bool compact_ids = false;
 
     int c;
     optind = 2; // force optind past command positional argument
     while (true) {
         static struct option long_options[] =
             {
                 {"help", no_argument, 0, 'h'},
+                {"include-aln", required_argument, 0, 'i'},
+                {"compact-ids", no_argument, 0, 'c'},
                 {"keep-path", required_argument, 0, 'k'},
                 {"remove-orphans", no_argument, 0, 'o'},
                 {0, 0, 0, 0}
             };
 
         int option_index = 0;
-        c = getopt_long (argc, argv, "hk:o",
+        c = getopt_long (argc, argv, "hk:oi:c",
                          long_options, &option_index);
 
         // Detect the end of the options.
@@ -368,6 +374,14 @@ int main_mod(int argc, char** argv) {
         switch (c)
         {
 
+        case 'i':
+            aln_file = optarg;
+            break;
+
+        case 'c':
+            compact_ids = true;
+            break;
+
         case 'k':
             path_name = optarg;
             break;
@@ -405,6 +419,24 @@ int main_mod(int argc, char** argv) {
         graph->remove_orphan_edges();
     }
 
+    if (!aln_file.empty()) {
+        function<void(Alignment&)> lambda = [&graph](Alignment& aln) {
+            const Path& path = aln.path();
+            graph->include(path);
+        };
+        if (aln_file == "-") {
+            stream::for_each(std::cin, lambda);
+        } else {
+            ifstream in;
+            in.open(aln_file.c_str());
+            stream::for_each(in, lambda);
+        }
+        if (compact_ids) {
+            graph->sort();
+            graph->compact_ids();
+        }
+    }
+
     graph->serialize_to_ostream(std::cout);
 
     delete graph;
@@ -2554,7 +2586,7 @@ void vg_help(char** argv) {
          << "  -- concat        concatenate graphs tail-to-head" << endl
          << "  -- kmers         enumerate kmers of the graph" << endl
          << "  -- sim           simulate reads from the graph" << endl
-         << "  -- mod           filter and transform the graph" << endl
+         << "  -- mod           filter, transform, and edit the graph" << endl
          << "  -- surject       map alignments onto specific paths" << endl;
 }