Merge pull request #196 from vgteam/less-parallel-overlays

Make overlay construction less parallel and lookup hopefully faster

bdsg/include/bdsg/overlays/packed_path_position_overlay.hpp

@@ -34,7 +34,7 @@ class PackedPositionOverlay : public PathPositionHandleGraph, public ExpandingOv
     /// Make a new PackedPositionOverlay, on the given graph. Glom short paths
     /// together to make internal indexes each over at least the given number
     /// of steps.
-    PackedPositionOverlay(const PathHandleGraph* graph, size_t steps_per_index = 1000000);
+    PackedPositionOverlay(const PathHandleGraph* graph, size_t steps_per_index = 20000000);
     PackedPositionOverlay() = default;
     PackedPositionOverlay(const PackedPositionOverlay& other) = default;
     PackedPositionOverlay(PackedPositionOverlay&& other) = default;

bdsg/include/bdsg/overlays/packed_reference_path_overlay.hpp

@@ -29,7 +29,7 @@ class PackedReferencePathOverlay : public PackedPositionOverlay {
 
     /// Make a PackedReferencePathOverlay. Do the indexing and compute the
     /// additional indexes that the base class doesn't have.
-    PackedReferencePathOverlay(const PathHandleGraph* graph, size_t steps_per_index = 1000000);
+    PackedReferencePathOverlay(const PathHandleGraph* graph, size_t steps_per_index = 20000000);
 
     // We assume that tracing out a path is fast in the backing graph, but
     // finding visits on nodes is slow. We override the reverse lookups to go

bdsg/src/packed_path_position_overlay.cpp

@@ -252,6 +252,7 @@ void PackedPositionOverlay::index_path_positions() {
 
     // And this will be the cumulative path length of all the paths in each collection.
     std::vector<size_t> path_set_steps;
+    size_t total_length = 0;
     size_t accumulated_length = 0;
     for (size_t i = 0; i < path_handles.size(); i++) {
         if (accumulated_length >= steps_per_index) {
@@ -264,20 +265,22 @@ void PackedPositionOverlay::index_path_positions() {
 #endif
 
             path_set_steps.push_back(accumulated_length);
+            total_length += accumulated_length;
             accumulated_length = 0;
         }
         // Remember that this path's steps went into this index.
         accumulated_length += path_lengths[i];
     }
     bounds.push_back(path_handles.size());
     path_set_steps.push_back(accumulated_length);
+    total_length += accumulated_length;
 
     // Now we know how many indexes we need
     this->set_index_count(path_set_steps.size());
 
 #ifdef debug
         #pragma omp critical (cerr)
-        std::cerr << "Using " << indexes.size() << " indexes" << std::endl;
+        std::cerr << "Using " << indexes.size() << " indexes for " << total_length << " total steps" << std::endl;
 #endif
 
     #pragma omp parallel for