Add conjugate links during GFA I/O

src/common/assembly_graph/core/graph.hpp

@@ -148,6 +148,8 @@ class DeBruijnGraph: public omnigraph::ObservableGraph<DeBruijnDataMaster> {
     auto links() { return adt::make_range(link_begin(), link_end()); }
     auto links() const { return adt::make_range(link_begin(), link_end()); }
 
+    size_t link_size() const {return link_storage_.size(); }
+
     using base::AddVertex;
     using base::AddEdge;
 

src/common/io/graph/gfa_reader.cpp

@@ -120,6 +120,8 @@ static void HandleLink(Links &links,
         e2 = g.conjugate(e2);
 
     links.emplace_back(e1, e2, record.overlap);
+    if (e1 != g.conjugate(e2))
+        links.emplace_back(g.conjugate(e2), g.conjugate(e1), record.overlap);
 }
 
 static void HandlePath(std::vector<GFAReader::GFAPath> &paths,
@@ -175,10 +177,7 @@ 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) {

src/test/debruijn/graph_fragments/v_overlaps/conjugate_bone.fasta

@@ -0,0 +1,4 @@
+>path1
+ACATGCTCGATATAACGGTTGCTCACCGGAGAGACGACTTTATAGTTCTTGTAATGGGACTGGCGGGAGGAGAGTTACTACGTGTGGTATATCGGGGTTGGATCAGAGTAATCTGAAACAAAGAAGGTAAGATGTTAGACGGGCGGCATCTATATATATAGGGATACAGTTAGAAGAATAATTGGGATGTATGGTACCTCGTCTGTTGCGGCGTCGAAGTAGCGGTTCCATTTATCGCTGCCGTGCGAAATTAAACTGCGTGGATGCTCTCTTTCCGAGCTCCAACTTCTGTCTTGGCCAGGCGGCATCACTGCGGATCCCCCTTTTTGTGAGGGCCAGTTCCGACCCGTTCACTACAAGACTAGACTGTTCACGTGGCAACCTAGATCCCCAGGCGTACGAGGTCAACTCCTCTCGGAACACCGAAGATGCCGTGGTTGCCACTTAGAAGGCTCTATGACTTTGCACCTATTTTTTGAGAGAGTTATGTCTTGCATCGA
+>path2
+GGTACCTTGGAGGGACAATTCGGTTACGGATTCATTCATCTTAAGGCAAGACGTTTCCGCGTGTCGCTGTGGTGGCTCTCCCTCGCGTAGTTTCTATACGGATCAGAGTAATCTGAAACAAAGAAGGTAAGATGTTAGACGGGCGGCATCTATATATATAGGGATACAGTTAGAAGAATAATTGGGATGTATGGTACCTCCGGGACTGTTGGTCTTCCCCAAGGGTTCACACGCCCACTTGCGACTGGAGCACGAAATTGTCCAGAATGGCTGCGCTTATGAGACTGGACCCTATCCTCGCGGATTTACGTAATGTTCTACGTACCTATTCCGGCGCCACCAGGTCATGTCCGGCTTGCGCACTTAATTGCGCTATGATGTCCGGAGGCAGCCGACCCAG

src/test/debruijn/graph_fragments/v_overlaps/conjugate_bone.gfa

@@ -0,0 +1,11 @@
+H	VN:Z:1.0
+S	edge1	ACATGCTCGATATAACGGTTGCTCACCGGAGAGACGACTTTATAGTTCTTGTAATGGGACTGGCGGGAGGAGAGTTACTACGTGTGGTATATCGGGGTTGGATCAGAGTAATCTGAAACAAAGAAGGTAAGATGTTAGACGGGCGGCATCTATATATATAGGGATACAGTTAGAAGAATAATTGGGATGTATGGTACCTC
+S	edge2	GGTACCTTGGAGGGACAATTCGGTTACGGATTCATTCATCTTAAGGCAAGACGTTTCCGCGTGTCGCTGTGGTGGCTCTCCCTCGCGTAGTTTCTATACGGATCAGAGTAATCTGAAACAAAGAAGGTAAGATGTTAGACGGGCGGCATCTATATATATAGGGATACAGTTAGAAGAATAATTGGGATGTATGGTACCTC
+S	edge3	GATCAGAGTAATCTGAAACAAAGAAGGTAAGATGTTAGACGGGCGGCATCTATATATATAGGGATACAGTTAGAAGAATAATTGGGATGTATGGTACCTCGTCTGTTGCGGCGTCGAAGTAGCGGTTCCATTTATCGCTGCCGTGCGAAATTAAACTGCGTGGATGCTCTCTTTCCGAGCTCCAACTTCTGTCTTGGCCAGGCGGCATCACTGCGGATCCCCCTTTTTGTGAGGGCCAGTTCCGACCCGTTCACTACAAGACTAGACTGTTCACGTGGCAACCTAGATCCCCAGGCGTACGAGGTCAACTCCTCTCGGAACACCGAAGATGCCGTGGTTGCCACTTAGAAGGCTCTATGACTTTGCACCTATTTTTTGAGAGAGTTATGTCTTGCATCGA
+S	edge4	GATCAGAGTAATCTGAAACAAAGAAGGTAAGATGTTAGACGGGCGGCATCTATATATATAGGGATACAGTTAGAAGAATAATTGGGATGTATGGTACCTCCGGGACTGTTGGTCTTCCCCAAGGGTTCACACGCCCACTTGCGACTGGAGCACGAAATTGTCCAGAATGGCTGCGCTTATGAGACTGGACCCTATCCTCGCGGATTTACGTAATGTTCTACGTACCTATTCCGGCGCCACCAGGTCATGTCCGGCTTGCGCACTTAATTGCGCTATGATGTCCGGAGGCAGCCGACCCAG
+L	edge1	+	edge3	+	100M
+L	edge4	-	edge1	-	100M
+L	edge3	-	edge2	-	100M
+L	edge4	-	edge2	-	100M
+P	path1	edge1+,edge3+	100M
+P	path2	edge2+,edge4+	100M

src/test/debruijn/graph_fragments/v_overlaps/conjugate_bone.graph

@@ -0,0 +1,21 @@
+bone
+4
+edge1	200
+edge2	200
+edge3	400
+edge4	300
+1
+vertex1	100
+4
+edge1	vertex1
+edge2	vertex1
+vertex1	edge3
+vertex1	edge4
+4
+edge1	edge3	100
+edge1	edge4	100
+edge2	edge3	100
+edge2	edge4	100
+2
+path1	edge1	edge3
+path2	edge2	edge4

src/test/debruijn/graph_fragments/v_overlaps/conjugate_bone.ops

@@ -0,0 +1,5 @@
+1
+split edge1	edge3
+2
+path1	2   edge1	edge3
+path2	2   edge2	edge4

src/test/debruijn/graph_fragments/v_overlaps/conjugate_triple.fasta

@@ -0,0 +1,4 @@
+>path1
+GCGGATAGACTTGTGGCAAAAGATGTAAGCTTCATTGTCTGCTAAAGCAGTTCTCAGAACGCCGAAACAGTACCAAAGCCAATGTGCTTCGGTATACACGGGCCTGAGCGGGCCGCACACTCGACAACGGTCGAACTAGTTATCGTATGAGGTCACTCGAGGATAAGCGTAATACGAGTGTCTCTTACGACCACCATGGGTGAGGGGGCCCCGTCGTGGACAAATTTTCTTGGTTTACCCGGAACTAGAAATTAAGTCACGCTTATGTGATAGCTATTGATCTGTAGGATCTTACCGTGTCTTATAGAACCACTCTACATGGGTATTGGGCAGGGTTGAGTTCAACTGTCCTCGGCGGACAGGTATTCTGACGCGGTAAAAGTCCTATCCTCCTCTATGTTGATATGGGACAGGCACGCAGCGAGATATACTGATTAGAGGTATTACACTGACATCAGGAAACATCACAGAATAGGGCCCAGGAGAATACGAGAAAGACAGAAGCAGAATTCAGTTTACAAACCCCGACAACCTGCTTCCGAAAGCGTTCTGCCGGAAAGCTTAGTTCGCGATCAAAGTAAGGCTGTGTGAAGCAAATTCATAAGTGGCCTTTCATGCGCCGTTTGAAGTGTCACAATGAGTCGGGACAGCTCGCACGAAGCTGAATCAATTATGCTAAACCGTGAGACGATATCCTAAGAAGGAATGCAAGGCCGAATGGAATCCTCCGTACTATTCATGTCTTCCCCAGACTGATCGTGACAACCTGGAGGTACTTTTTTGCATCAGTAGAGTTTTGC
+>path2
+AACCCGGAGAGAACCCAACTTGAAGAGAGAGCCAGGATGTCGGTCAAACAGTTTTCCCTGTTTTCACCCGCGACGAAACGAATCCAGCTCGTAAAATGAGTCAATGGGGAACCACGAAAATGTTCTGACAAAATACGGAACCGCTTGCTACAGGGAGGGAACTAAACGATAAGCATATTTGAACGACAGCTACCAGTAAATGAGGGGGCCCCGTCGTGGACAAATTTTCTTGGTTTACCCGGAACTAGAAATTAAGTCACGCTTATGTGATAGCTATTGATCTGTAGGATCTTACCGTGTCTTATAGAACCACTCTACATGGGTATTGGGCAGGGTTGAGTTCAACTGTCCTCGGCGGACAGGTATTCTGACGCGGTAAAAGTCCTATCCTCCTCTATGTGGCACCGACGACACCTTAGGCACCTGGAATAGAGTAGCATTTGGTGGCCATGCAATCCGCTTGTTCTACACCCCGTACGTCATTGCACATTTCCCTGGAGTATTATTTTATCGTCGCCGGATGGATCCTGCGGTGTTCGTTGCCAAGCGGAGAGCATCGACGGGTGCTGAGGTTCCCTGAGGCTTACAATGTGTCGGTGCTCACCCCGTGAATTATAGAAAACCTGTTTGGTGGGACACATCTTACGGGGATGTATCATAAACAATTCTGCAGATGAAGCACTGCCTAATCACCATCCGCTGATATGGGACAGGCACGCAGCGAGATATACTGATTAGAGGTATTACACTGACATCAGGAAACATCACAGAATAGGGCCCAGGAGAATACGAGAAAGACA

src/test/debruijn/graph_fragments/v_overlaps/conjugate_triple.gfa

@@ -0,0 +1,15 @@
+H	VN:Z:1.0
+S	edge1_in	GCGGATAGACTTGTGGCAAAAGATGTAAGCTTCATTGTCTGCTAAAGCAGTTCTCAGAACGCCGAAACAGTACCAAAGCCAATGTGCTTCGGTATACACGGGCCTGAGCGGGCCGCACACTCGACAACGGTCGAACTAGTTATCGTATGAGGTCACTCGAGGATAAGCGTAATACGAGTGTCTCTTACGACCACCATGGGTGAGGGGGCCCCGTCGTGGACAAATTTTCTTGGTTTACCCGGAACTAGAAATTAAGTCACGCTTATGTGATAGCTATTGATCTGTAGGATCTTACCGTGTCTTATAGAACCACTCTACATGGGTATTGGGCAGGGTTGAGTTCAACTGTCCTCGGCGGACAGGTATTCTGACGCGGTAAAAGTCCTATCCTCCTCTATGT
+S	edge2_in	AACCCGGAGAGAACCCAACTTGAAGAGAGAGCCAGGATGTCGGTCAAACAGTTTTCCCTGTTTTCACCCGCGACGAAACGAATCCAGCTCGTAAAATGAGTCAATGGGGAACCACGAAAATGTTCTGACAAAATACGGAACCGCTTGCTACAGGGAGGGAACTAAACGATAAGCATATTTGAACGACAGCTACCAGTAAATGAGGGGGCCCCGTCGTGGACAAATTTTCTTGGTTTACCCGGAACTAGAAATTAAGTCACGCTTATGTGATAGCTATTGATCTGTAGGATCTTACCGTGTCTTATAGAACCACTCTACATGGGTATTGGGCAGGGTTGAGTTCAACTGTCCTCGGCGGACAGGTATTCTGACGCGGTAAAAGTCCTATCCTCCTCTATGT
+S	edge1_mid	TGAGGGGGCCCCGTCGTGGACAAATTTTCTTGGTTTACCCGGAACTAGAAATTAAGTCACGCTTATGTGATAGCTATTGATCTGTAGGATCTTACCGTGTCTTATAGAACCACTCTACATGGGTATTGGGCAGGGTTGAGTTCAACTGTCCTCGGCGGACAGGTATTCTGACGCGGTAAAAGTCCTATCCTCCTCTATGTTGATATGGGACAGGCACGCAGCGAGATATACTGATTAGAGGTATTACACTGACATCAGGAAACATCACAGAATAGGGCCCAGGAGAATACGAGAAAGACA
+S	edge2_mid	TGAGGGGGCCCCGTCGTGGACAAATTTTCTTGGTTTACCCGGAACTAGAAATTAAGTCACGCTTATGTGATAGCTATTGATCTGTAGGATCTTACCGTGTCTTATAGAACCACTCTACATGGGTATTGGGCAGGGTTGAGTTCAACTGTCCTCGGCGGACAGGTATTCTGACGCGGTAAAAGTCCTATCCTCCTCTATGTGGCACCGACGACACCTTAGGCACCTGGAATAGAGTAGCATTTGGTGGCCATGCAATCCGCTTGTTCTACACCCCGTACGTCATTGCACATTTCCCTGGAGTATTATTTTATCGTCGCCGGATGGATCCTGCGGTGTTCGTTGCCAAGCGGAGAGCATCGACGGGTGCTGAGGTTCCCTGAGGCTTACAATGTGTCGGTGCTCACCCCGTGAATTATAGAAAACCTGTTTGGTGGGACACATCTTACGGGGATGTATCATAAACAATTCTGCAGATGAAGCACTGCCTAATCACCATCCGCTGATATGGGACAGGCACGCAGCGAGATATACTGATTAGAGGTATTACACTGACATCAGGAAACATCACAGAATAGGGCCCAGGAGAATACGAGAAAGACA
+S	edge3_in	ATTCCTCTGTACAGGACGCCTGCCCTTCCGTGTTAGCAATTTAGTTCGGATTTCGCTTTGGGAGAGCAACCTTCAGCTCAGGCATCATACGAAAATATTTAAAACGTTCCCCAAAGCACTACTTAGTACCTTTTACTGGTAAAAGGGGGCGGAAGTAACCGCCCTTTGCTTAGGCGTGCCAGATAGTCGCGTTAGACAGATATAACCACATGAGCTATACGAAGACAACGTTCTCAGTTTGGGTCGTTATATCCACCGGCGGCCTAAACGGGCCTATATTAATGGCGGGCGAGGGCGAGTCCTTTCGTCCGTTGGCTGCCTGGAGTGGAAGGGTACCACTGGGTCCTTGGGCCTCTCTTCGCTGGCCTATTAGGGTGTTGGCTGACCGGTCACAGAACTGTGATATGGGACAGGCACGCAGCGAGATATACTGATTAGAGGTATTACACTGACATCAGGAAACATCACAGAATAGGGCCCAGGAGAATACGAGAAAGACA
+S	edge1_out	TGATATGGGACAGGCACGCAGCGAGATATACTGATTAGAGGTATTACACTGACATCAGGAAACATCACAGAATAGGGCCCAGGAGAATACGAGAAAGACAGAAGCAGAATTCAGTTTACAAACCCCGACAACCTGCTTCCGAAAGCGTTCTGCCGGAAAGCTTAGTTCGCGATCAAAGTAAGGCTGTGTGAAGCAAATTCATAAGTGGCCTTTCATGCGCCGTTTGAAGTGTCACAATGAGTCGGGACAGCTCGCACGAAGCTGAATCAATTATGCTAAACCGTGAGACGATATCCTAAGAAGGAATGCAAGGCCGAATGGAATCCTCCGTACTATTCATGTCTTCCCCAGACTGATCGTGACAACCTGGAGGTACTTTTTTGCATCAGTAGAGTTTTGC
+S	edge2_out	TGATATGGGACAGGCACGCAGCGAGATATACTGATTAGAGGTATTACACTGACATCAGGAAACATCACAGAATAGGGCCCAGGAGAATACGAGAAAGACAGTATTTGTACGAGCGGTGTGAAGAAACAACGTGCACGTTCCTGTGCTTAAGGAGACGTGTCCATTTTGGGCTTGTCTTATCAAGTATATATTTTTATCTCATAGCTCATTTAGACGGAAGTCTAGTGCACATCGCTGCAGCCCTTCGAAACCTCGTCCAGTATCCCGCGCAGATGACTGGCACTAAGGTAAGCGTGTTGGTCTGTGGCAAAACGTAACCAGTTGGCGAAGCTTGGTATCCTACTGCGCCAATTTTCTCGGCAGTCTTACCCTTTCCAACCTCGCATGATCTCGGTCGTGTTTTTGCTCAATCTGGCTCGTACTGGTATTAAGCCGCATCCCAAGATTCTCGCGCGACTGAATTGACGGGGCGCAAGCGTAAACGGGAAAGAACATCTCCA
+S	edge3_out	TGATATGGGACAGGCACGCAGCGAGATATACTGATTAGAGGTATTACACTGACATCAGGAAACATCACAGAATAGGGCCCAGGAGAATACGAGAAAGACAAGGATGCCTCATAGCTTACTGCACACTAAGAATCCATTGAACCTGAAAACTCGCAATTCCGACGCGACGTTGGGCGATGTCTAGCGCATGCTACCAATGGTACAATTCAATCAGACTTCCGGGTATAACGGTTATCAGCGTATGAACAATAGTTTTTCGTTTGATTGGTGACGTGCTAATACCCCAGGAGCCAGTGAGAGC
+L	edge1_mid	-	edge1_in	-	200M
+L	edge2_in	+	edge2_mid	+	200M
+L	edge1_out	-	edge1_mid	-	100M
+L	edge3_in	+	edge3_out	+	100M
+P	path1	edge1_in+,edge1_mid+,edge1_out+	200M,100M
+P	path2	edge2_in+,edge2_mid+	200M

src/test/debruijn/graph_fragments/v_overlaps/conjugate_triple.graph

@@ -0,0 +1,32 @@
+triple_repeat
+8
+edge1_in	400
+edge2_in	400
+edge1_mid  300
+edge2_mid   600
+edge3_in	500
+edge1_out   400
+edge2_out   500
+edge3_out   301
+2
+vertex1    200
+vertex2   100
+10
+edge1_in    vertex1
+edge2_in    vertex1
+vertex1 edge1_mid
+vertex1 edge2_mid
+edge1_mid   vertex2
+edge2_mid   vertex2
+edge3_in    vertex2
+vertex2 edge1_out
+vertex2 edge2_out
+vertex2 edge3_out
+4
+edge1_in    edge1_mid  200
+edge2_in    edge2_mid  200
+edge1_mid   edge1_out   100
+edge3_in    edge3_out   100
+2
+path1   edge1_in    edge1_mid  edge1_out
+path2   edge2_in    edge2_mid

src/test/debruijn/graph_fragments/v_overlaps/conjugate_triple.ops

@@ -0,0 +1,6 @@
+2
+split edge1_in	edge1_mid
+split edge1_mid    edge1_out
+2
+path1	3   edge1_in    edge1_mid  edge1_out
+path2	2   edge2_in    edge2_mid

src/test/debruijn/v_overlaps.cpp

@@ -82,29 +82,42 @@ std::unordered_map<VertexId, std::string> CheckStructure(std::ifstream &graph_st
 void CheckLinks(std::ifstream &graph_stream, const Graph &graph, const IdMapper &id_mapper) {
     int num_links;
     graph_stream >> num_links;
-    size_t checked_links = 0;
+    bool is_complex = false;
     for (int i = 0; i < num_links; ++i) {
         std::string first_edge_name, second_edge_name;
         int overlap;
         graph_stream >> first_edge_name >> second_edge_name >> overlap;
-        EdgeId first_edge = id_mapper[first_edge_name];
-        EdgeId second_edge = id_mapper[second_edge_name];
-        VertexId vertex = graph.EdgeEnd(first_edge);
-        EXPECT_EQ(vertex, graph.EdgeStart(second_edge));
+        EdgeId in_edge = id_mapper[first_edge_name];
+        EdgeId out_edge = id_mapper[second_edge_name];
+        EdgeId in_conjugate = graph.conjugate(in_edge);
+        EdgeId out_conjugate = graph.conjugate(out_edge);
+        VertexId vertex = graph.EdgeEnd(in_edge);
+        EXPECT_EQ(vertex, graph.EdgeStart(out_edge));
+        EXPECT_EQ(graph.conjugate(vertex), graph.EdgeEnd(out_conjugate));
         if (graph.is_complex(vertex)) {
             bool link_found = false;
+            bool conj_link_found = false;
             for (const auto &link: graph.links(vertex)) {
-                if (graph.link(link).link.first == first_edge and graph.link(link).link.second == second_edge) {
+                auto link_in_edge = graph.link(link).link.first;
+                auto link_out_edge = graph.link(link).link.second;
+                if (link_in_edge == in_edge and link_out_edge == out_edge) {
                     link_found = true;
                 }
             }
-            EXPECT_TRUE(link_found);
-            ++checked_links;
-        } else {
-            checked_links++;
+            for (const auto &link: graph.links(graph.conjugate(vertex))) {
+                auto link_in_edge = graph.link(link).link.first;
+                auto link_out_edge = graph.link(link).link.second;
+                if (link_in_edge == out_conjugate and link_out_edge == in_conjugate) {
+                    conj_link_found = true;
+                }
+            }
+            EXPECT_TRUE(link_found && conj_link_found);
+            is_complex = true;
         }
     }
-    EXPECT_EQ(num_links, checked_links);
+    if (is_complex) {
+        EXPECT_EQ(num_links * 2, graph.link_size());
+    }
 }
 
 void PerformSplits(debruijn_graph::Graph &graph, std::ifstream &ops_stream, const IdMapper &id_mapper) {
@@ -216,5 +229,7 @@ void CheckGraphWithPaths(const std::filesystem::path &graph_basename) {
 
 TEST(VariableOverlaps, BasicOperations) {
     CheckGraphWithPaths("src/test/debruijn/graph_fragments/v_overlaps/bone");
+    CheckGraphWithPaths("src/test/debruijn/graph_fragments/v_overlaps/conjugate_bone");
+    CheckGraphWithPaths("src/test/debruijn/graph_fragments/v_overlaps/conjugate_triple");
     CheckGraphWithPaths("src/test/debruijn/graph_fragments/v_overlaps/triple_repeat");
 }