keep paths in xg

Author: glennhickey

src/subcommand/benchmark_main.cpp

@@ -118,7 +118,7 @@ int main_benchmark(int argc, char** argv) {
 
     // Get an XG for it
     xg::XG xg_index;
-    xg_index.from_handle_graph(vg);
+    xg_index.from_path_handle_graph(vg);
 
     // And an IndexedVG
     auto filename = temp_file::create();

src/subcommand/msga_main.cpp

@@ -564,7 +564,7 @@ int main_msga(int argc, char** argv) {
 
         if (debug) cerr << "building xg index" << endl;
         xgidx = new xg::XG();
-        xgidx->from_handle_graph(*graph);
+        xgidx->from_path_handle_graph(*graph);
 
         if (debug) cerr << "building GCSA2 index" << endl;
         // Configure GCSA2 verbosity so it doesn't spit out loads of extra info

src/variant_adder.cpp

@@ -719,7 +719,7 @@ Alignment VariantAdder::smart_align(vg::VG& graph, pair<NodeSide, NodeSide> endp
 
                 // Generate an XG index
                 xg::XG xg_index;
-                xg_index.from_handle_graph(graph);
+                xg_index.from_path_handle_graph(graph);
 
                 // Generate a GCSA2 index
                 gcsa::GCSA* gcsa_index = nullptr;

src/variant_recall.cpp

@@ -73,7 +73,7 @@ void genotype_svs(VG* graph,
         augment(graph, direct_ins, &transls);
 
         XG xg_index;
-        xg_index.from_handle_graph(*graph); // Index the graph so deconstruct can get path positions
+        xg_index.from_path_handle_graph(*graph); // Index the graph so deconstruct can get path positions
         Deconstructor decon;
         CactusSnarlFinder finder(xg_index);
         SnarlManager snarl_manager = finder.find_snarls();