Quick fix to process conjugate overlaps

ablab · Sep 26, 2024 · 2468e6e · 2468e6e
1 parent 91e6772
commit 2468e6e
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Showing 3 changed files with 11 additions and 6 deletions.
diff --git a/src/common/assembly_graph/core/debruijn_data.hpp b/src/common/assembly_graph/core/debruijn_data.hpp
@@ -110,20 +110,20 @@ class DeBruijnVertexData {
         return overlap_.get<ExplicitOverlap>();
     }
 
-    auto &links() {
+    [[nodiscard]] auto &links() {
         return overlap_.get<ComplexOverlap>()->links();
     }
 
-    auto links() const {
+    [[nodiscard]] auto links() const {
         return overlap_.get<ComplexOverlap>()->links();
     }
 
-    auto move_links() {
+    [[nodiscard]] auto move_links() {
         return overlap_.get<ComplexOverlap>()->move();
     }
 
-    auto clear_links() {
-        return overlap_.get<ComplexOverlap>()->clear();
+    void clear_links() {
+        overlap_.get<ComplexOverlap>()->clear();
     }
 
     void add_link(LinkId link) {

diff --git a/src/common/assembly_graph/core/graph.hpp b/src/common/assembly_graph/core/graph.hpp
@@ -90,7 +90,7 @@ class DeBruijnGraph: public omnigraph::ObservableGraph<DeBruijnDataMaster> {
     }
 
     auto move_links(VertexId v) {
-        data(v).move_links();
+        return data(v).move_links();
     }
 
     auto clear_links(VertexId v) {

diff --git a/src/common/io/graph/gfa_reader.cpp b/src/common/io/graph/gfa_reader.cpp
@@ -159,6 +159,8 @@ static std::pair<unsigned, bool> ProcessLinks(DeBruijnGraph &g, const Links &lin
         }
     }
 
+    INFO("Overlaps: " << (simple ? "simple" : "complex"));
+
     auto helper = g.GetConstructionHelper();
     for (const auto &link: links) {
         EdgeId e1 = std::get<0>(link), e2 = std::get<1>(link);
@@ -173,7 +175,10 @@ static std::pair<unsigned, bool> ProcessLinks(DeBruijnGraph &g, const Links &lin
         if (simple) {
             g.set_overlap(v1, ovl);
             g.set_overlap(v2, ovl);
+            g.set_overlap(g.conjugate(v1), ovl);
+            g.set_overlap(g.conjugate(v2), ovl);
         } else {
+            // FIXME: Correctly add conjugate links
             LinkId link_idx = g.add_link(e1, e2, ovl);
             g.add_link(v1, link_idx);
             if (v1 != v2) {