allow thread safe use of add_paths_to_graph (i_wt select limitation)

Per caching in sdsl-lite: simongog/sdsl-lite#263.

This allows the calling context to decide whether or not to use the
add_paths_to_graph functionality that is often not necessary and is also not
thread safe.

xg.cpp

@@ -1026,7 +1026,7 @@ void XG::neighborhood(int64_t id, size_t steps, Graph& g) const {
     expand_context(g, steps);
 }
 
-void XG::expand_context(Graph& g, size_t steps) const {
+void XG::expand_context(Graph& g, size_t steps, bool add_paths) const {
     map<int64_t, Node*> nodes;
     map<pair<Side, Side>, Edge*> edges;
     set<int64_t> to_visit;
@@ -1088,7 +1088,9 @@ void XG::expand_context(Graph& g, size_t steps) const {
             *np = node(t);
         }
     }
-    add_paths_to_graph(nodes, g);
+    if (add_paths) {
+        add_paths_to_graph(nodes, g);
+    }
 }
 
 
@@ -1231,7 +1233,11 @@ size_t XG::node_position_in_path(int64_t id, const string& name) const {
         cerr << "warning: path " << name << " contains a loop" << endl;
     }
     auto& path = *paths[path_rank(name)-1];
-    return path.positions[path.ids.select(1, id_to_rank(id))];
+    auto rank = id_to_rank(id);
+    size_t node_rank_in_path;
+#pragma omp critical (path_ids)
+    node_rank_in_path = path.ids.select(1, rank);
+    return path.positions[node_rank_in_path];
 }
 
 int64_t XG::node_at_path_position(const string& name, size_t pos) const {

xg.hpp

@@ -97,7 +97,10 @@ class XG {
     void neighborhood(int64_t id, size_t steps, Graph& g) const;
     //void for_path_range(string& name, int64_t start, int64_t stop, function<void(Node)> lambda);
     void get_path_range(string& name, int64_t start, int64_t stop, Graph& g) const;
-    void expand_context(Graph& g, size_t steps) const;
+    // basic method to query regions of the graph
+    // add_paths flag allows turning off the (potentially costly, and thread-locking) addition of paths
+    // when these are not necessary
+    void expand_context(Graph& g, size_t steps, bool add_paths = true) const;
     void get_connected_nodes(Graph& g) const;
     void get_id_range(int64_t id1, int64_t id2, Graph& g) const;