Implement has_edges() and get_degree() to avoid clang bus errors / se…

…gfaults

gbwtgraph.cpp

@@ -312,6 +312,39 @@ GBWTGraph::for_each_handle_impl(const std::function<bool(const handle_t&)>& iter
   return true;
 }
 
+size_t
+GBWTGraph::get_degree(const handle_t& handle, bool go_left) const
+{
+  // Cache the node.
+  gbwt::node_type curr = handle_to_node(handle);
+  if(go_left) { curr = gbwt::Node::reverse(curr); }
+  gbwt::CachedGBWT cache(*(this->index), true);
+  gbwt::size_type cache_index = cache.findRecord(curr);
+
+  // The outdegree reported by GBWT might account for the endmarker, which is
+  // always the first successor.
+  size_t result = cache.outdegree(cache_index);
+  if(result > 0 && cache.successor(cache_index, 0) == gbwt::ENDMARKER) { result--; }
+  return result;
+}
+
+bool
+GBWTGraph::has_edge(const handle_t& left, const handle_t& right) const
+{
+  // Cache the node.
+  gbwt::node_type curr = handle_to_node(left);
+  gbwt::CachedGBWT cache(*(this->index), true);
+  gbwt::size_type cache_index = cache.findRecord(curr);
+
+  for(gbwt::rank_type outrank = 0; outrank < cache.outdegree(cache_index); outrank++)
+  {
+    gbwt::node_type next = cache.successor(cache_index, outrank);
+    if(node_to_handle(next) == right) { return true; }
+  }
+
+  return false;
+}
+
 //------------------------------------------------------------------------------
 
 void

gfa.cpp

@@ -63,12 +63,12 @@ struct GFAFile
     }
     this->file_size = st.st_size;
 
-		void* temp_ptr = ::mmap(nullptr, file_size, PROT_READ, MAP_FILE | MAP_SHARED, this->fd, 0);
-		if(temp_ptr == MAP_FAILED)
-		{
+    void* temp_ptr = ::mmap(nullptr, file_size, PROT_READ, MAP_FILE | MAP_SHARED, this->fd, 0);
+    if(temp_ptr == MAP_FAILED)
+    {
       std::cerr << "GFAFile::GFAFile(): Cannot memory map file " << filename << std::endl;
       return;
-		}
+    }
     this->ptr = static_cast<char*>(temp_ptr);
   }
 
@@ -215,7 +215,7 @@ gfa_to_gbwt(const std::string& gfa_filename, gbwt::size_type node_width, gbwt::s
 
   // Index the paths. Adjust batch size down if we are dealing with a small file.
   gbwt::Verbosity::set(gbwt::Verbosity::SILENT);
-	if(gfa_file.size() < batch_size) { batch_size = gfa_file.size(); }
+  if(gfa_file.size() < batch_size) { batch_size = gfa_file.size(); }
   gbwt::GBWTBuilder builder(node_width, batch_size, sample_interval);
   SequenceSource* source = new SequenceSource();
   gbwt::vector_type current_path;

include/gbwtgraph/gbwtgraph.h

@@ -144,6 +144,21 @@ class GBWTGraph : public HandleGraph, public SerializableHandleGraph
   // stopped early.
   virtual bool for_each_handle_impl(const std::function<bool(const handle_t&)>& iteratee, bool parallel = false) const;
 
+public:
+
+  /*
+    Reimplementations to avoid weird segfaults / bus errors when calling lambdas
+    on clang.
+  */
+
+  /// Get the number of edges on the right (go_left = false) or left (go_left
+  /// = true) side of the given handle.
+  virtual size_t get_degree(const handle_t& handle, bool go_left) const;
+
+  /// Returns true if there is an edge that allows traversal from the left
+  /// handle to the right handle.
+  virtual bool has_edge(const handle_t& left, const handle_t& right) const;
+
 //------------------------------------------------------------------------------
 
   /*