Merge pull request #4400 from vgteam/path-normalize

Set snarl distance to 0 in path normalizer now that distance index is fixed.

src/traversal_clusters.cpp

@@ -384,8 +384,7 @@ void merge_equivalent_traversals_in_graph(MutablePathHandleGraph* graph, const u
     SnarlDistanceIndex distance_index;
     {
         IntegratedSnarlFinder snarl_finder(*graph);
-        // todo: why can't I pass in 0 below -- I don't want any dinstances!
-        fill_in_distance_index(&distance_index, graph, &snarl_finder, 1);
+        fill_in_distance_index(&distance_index, graph, &snarl_finder, 0);
     }
 
     // only consider embedded paths that span snarl

test/t/11_vg_paths.t

@@ -90,10 +90,10 @@ diff original.fa norm_x4.fa
 is $? 0 "path normalizer doesnt alter path sequences"
 
 # note: x3 is x4 in reverse, so we key on that
-grep x3 norm_x2.gfa | awk '{print $3}' > x4.path
-grep x3 norm_x2.gfa | awk '{print $3}' >> x4.path
-grep x3 norm_x2.gfa | awk '{print $3}'> x4.norm.path
-grep x5 norm_x2.gfa | awk '{print $3}' >> x4.norm.path
+grep x3 norm_x4.gfa | awk '{print $3}' > x4.path
+grep x3 norm_x4.gfa | awk '{print $3}' >> x4.path
+grep x3 norm_x4.gfa | awk '{print $3}'> x4.norm.path
+grep x5 norm_x4.gfa | awk '{print $3}' >> x4.norm.path
 diff x4.path x4.norm.path
 is $? 0 "path normalizere correctly snapped all equivalent paths to x4"