further isolate snarl code

src/deconstructor.cpp

@@ -1027,6 +1027,48 @@ string Deconstructor::get_vcf_header() {
     return stream.str();
 }
 
+void Deconstructor::deconstruct_graph(SnarlManager* snarl_manager) {
+
+    vector<const Snarl*> snarls_todo;
+    // Do the top-level snarls in parallel
+    snarl_manager->for_each_top_level_snarl([&](const Snarl* snarl) {
+            vector<const Snarl*> todo(1, snarl);
+            vector<const Snarl*> next;
+            while (!todo.empty()) {
+                for (auto next_snarl : todo) {
+                    // if we can't make a variant from the snarl due to not finding
+                    // paths through it, we try again on the children
+                    // note: we may want to push the parallelism down a bit
+#pragma omp critical (snarls_todo)
+                    snarls_todo.push_back(next_snarl);
+                    if (include_nested) {
+                        // n.b. we no longer attempt to deconstruct the site to determine if we nest
+                        const vector<const Snarl*>& children = snarl_manager->children_of(next_snarl);
+                        next.insert(next.end(), children.begin(), children.end());
+                    }
+                }
+                swap(todo, next);
+                next.clear();
+            }
+        });
+
+//#pragma omp parallel
+//#pragma omp single
+    {
+#pragma omp parallel for schedule(dynamic,1)
+        for (size_t i = 0; i < snarls_todo.size(); i++) {
+//#pragma omp task firstprivate(i)
+            {
+                auto& snarl = snarls_todo[i];
+                deconstruct_site(graph->get_handle(snarl->start().node_id(), snarl->start().backward()),
+                                 graph->get_handle(snarl->end().node_id(), snarl->end().backward()));
+            }
+        }
+    }
+//#pragma omp taskwait
+
+}
+
 /**
  * Convenience wrapper function for deconstruction of multiple paths.
  */
@@ -1040,7 +1082,6 @@ void Deconstructor::deconstruct(vector<string> ref_paths, const PathPositionHand
                                 gbwt::GBWT* gbwt) {
 
     this->graph = graph;
-    this->snarl_manager = snarl_manager;
     this->ref_paths = set<string>(ref_paths.begin(), ref_paths.end());
     this->include_nested = include_nested;
     this->path_jaccard_window = context_jaccard_window;
@@ -1069,43 +1110,7 @@ void Deconstructor::deconstruct(vector<string> ref_paths, const PathPositionHand
         gbwt_trav_finder = unique_ptr<GBWTTraversalFinder>(new GBWTTraversalFinder(*graph, *gbwt));
     }
 
-    vector<const Snarl*> snarls_todo;
-    // Do the top-level snarls in parallel
-    snarl_manager->for_each_top_level_snarl([&](const Snarl* snarl) {
-            vector<const Snarl*> todo(1, snarl);
-            vector<const Snarl*> next;
-            while (!todo.empty()) {
-                for (auto next_snarl : todo) {
-                    // if we can't make a variant from the snarl due to not finding
-                    // paths through it, we try again on the children
-                    // note: we may want to push the parallelism down a bit
-#pragma omp critical (snarls_todo)
-                    snarls_todo.push_back(next_snarl);
-                    if (include_nested) {
-                        // n.b. we no longer attempt to deconstruct the site to determine if we nest
-                        const vector<const Snarl*>& children = snarl_manager->children_of(next_snarl);
-                        next.insert(next.end(), children.begin(), children.end());
-                    }
-                }
-                swap(todo, next);
-                next.clear();
-            }
-        });
-
-//#pragma omp parallel
-//#pragma omp single
-    {
-#pragma omp parallel for schedule(dynamic,1)
-        for (size_t i = 0; i < snarls_todo.size(); i++) {
-//#pragma omp task firstprivate(i)
-            {
-                auto& snarl = snarls_todo[i];
-                deconstruct_site(graph->get_handle(snarl->start().node_id(), snarl->start().backward()),
-                                 graph->get_handle(snarl->end().node_id(), snarl->end().backward()));
-            }
-        }
-    }
-//#pragma omp taskwait
+    deconstruct_graph(snarl_manager);
 
     // write variants in sorted order
     write_variants(cout, snarl_manager);

src/deconstructor.hpp

@@ -51,6 +51,8 @@ class Deconstructor : public VCFOutputCaller {
 
     // initialize the vcf and get the header 
     string get_vcf_header();
+
+    void deconstruct_graph(SnarlManager* snarl_manager);
 
     // write a vcf record for the given site.  returns true if a record was written
     // (need to have a path going through the site)
@@ -101,9 +103,6 @@ class Deconstructor : public VCFOutputCaller {
     // the graph
     const PathPositionHandleGraph* graph;
 
-    // the snarl manager
-    SnarlManager* snarl_manager;
-
     // the gbwt
     gbwt::GBWT* gbwt;