Update stages

CMakeLists.txt

@@ -1,6 +1,6 @@
 cmake_minimum_required(VERSION 3.9)
 
-project(raven VERSION 1.1.3
+project(raven VERSION 1.1.4
               LANGUAGES CXX
               DESCRIPTION "Raven is a de novo genome assembler for long uncorrected reads.")
 

src/graph.cpp

@@ -843,7 +843,7 @@ void Graph::Construct(std::vector<std::unique_ptr<biosoup::Sequence>>& sequences
 }  // NOLINT
 
 void Graph::Assemble() {
-  if (stage_ > -1) {
+  if (stage_ < -3 || stage_ > -1) {
     return;
   }
 
@@ -1581,6 +1581,11 @@ void Graph::Polish(
     return;
   }
 
+  auto unitigs = GetUnitigs();
+  if (unitigs.empty()) {
+    return;
+  }
+
   double q = 0.;
   for (const auto& it : sequences) {
     if (it->quality.empty()) {
@@ -1608,8 +1613,6 @@ void Graph::Polish(
       cuda_banded_alignment,
       cuda_alignment_batches);
 
-  auto unitigs = GetUnitigs();
-
   while (stage_ < static_cast<std::int32_t>(num_rounds)) {
     polisher->Initialize(unitigs, sequences);
     auto polished = polisher->Polish(false);

src/graph.hpp

@@ -48,16 +48,6 @@ class Graph {
   // simplify with transitive reduction, tip prunning and bubble popping
   void Assemble();
 
-  // inspired by (Myers 1995) & (Myers 2005)
-  std::uint32_t RemoveTransitiveEdges();
-
-  std::uint32_t RemoveTips();
-
-  std::uint32_t RemoveBubbles();
-
-  // remove long edges in force directed layout
-  std::uint32_t RemoveLongEdges(std::uint32_t num_round);
-
   // Racon wrapper
   void Polish(
       const std::vector<std::unique_ptr<biosoup::Sequence>>& sequences,
@@ -91,6 +81,16 @@ class Graph {
   void Store() const;
 
  private:
+  // inspired by (Myers 1995) & (Myers 2005)
+  std::uint32_t RemoveTransitiveEdges();
+
+  std::uint32_t RemoveTips();
+
+  std::uint32_t RemoveBubbles();
+
+  // remove long edges in force directed layout
+  std::uint32_t RemoveLongEdges(std::uint32_t num_round);
+
   friend cereal::access;
 
   Graph() = default;  // needed for cereal