[cudapoa] Add optional graph output in GFA format.

Adds methods for outputting the graph structure generated
during partial order alignment in GFA format and corresponding
optional command line arguments in main.cpp

common/base/include/claraparabricks/genomeworks/utils/graph.hpp

@@ -160,6 +160,19 @@ class Graph
         }
     }
 
+    ///
+    /// \brief Generates a GFA S(sequence) line from a node's label and sequence.
+    ///
+    /// \param gfa_str An output stringstream to write S lines to.
+    void node_labels_to_gfa(std::ostringstream& gfa_str) const
+    {
+        for (auto& iter : node_labels_)
+        {
+            gfa_str << "S"
+                    << "\t" << iter.first << "\t" << iter.second << std::endl;
+        }
+    }
+
     /// \brief Serialize edges to dot format
     ///
     /// \param dot_str Output string stream to serialize labels to
@@ -175,6 +188,27 @@ class Graph
         }
     }
 
+    ///
+    /// \brief Serialize edges to GFA (v1) format
+    ///
+    /// \param gfa_str An output stringstream to write output to.
+    void edges_to_gfa(std::ostringstream& gfa_str) const
+    {
+        for (auto& iter : edges_)
+        {
+            const edge_t& edge          = iter.first;
+            const node_id_t edge_source = edge.first;
+            const node_id_t edge_sink   = edge.second;
+            gfa_str << "L"
+                    << "\t" << edge_source << "\t"
+                    << "+"
+                    << "\t" << edge_sink << "\t"
+                    << "+"
+                    << "\t"
+                    << "*" << std::endl;
+        }
+    }
+
     /// List of adjacent nodes per node ID
     std::unordered_map<node_id_t, std::vector<node_id_t>> adjacent_nodes_;
 
@@ -214,6 +248,17 @@ class DirectedGraph : public Graph
         }
     }
 
+    std::string serialize_to_gfa() const
+    {
+        std::ostringstream gfa_str;
+        gfa_str << "H"
+                << "\t"
+                << "VN:Z:1.0" << std::endl;
+        node_labels_to_gfa(gfa_str);
+        edges_to_gfa(gfa_str);
+        return gfa_str.str();
+    }
+
     /// \brief Serialize graph structure to dot format
     ///
     /// \return A string encoding the graph in dot format

cudapoa/src/application_parameters.cpp

@@ -40,6 +40,7 @@ ApplicationParameters::ApplicationParameters(int argc, char* argv[])
         {"band-mode", required_argument, 0, 'b'},
         {"band-width", required_argument, 0, 'w'},
         {"dot", required_argument, 0, 'd'},
+        {"gfa", required_argument, 0, 'G'},
         {"max-groups", required_argument, 0, 'M'},
         {"gpu-mem-alloc", required_argument, 0, 'R'},
         {"match", required_argument, 0, 'm'},
@@ -49,7 +50,7 @@ ApplicationParameters::ApplicationParameters(int argc, char* argv[])
         {"help", no_argument, 0, 'h'},
     };
 
-    std::string optstring = "i:ab:w:d:M:R:m:n:g:vh";
+    std::string optstring = "i:ab:w:d:G:M:R:m:n:g:vh";
 
     int32_t argument = 0;
     while ((argument = getopt_long(argc, argv, optstring.c_str(), options, nullptr)) != -1)
@@ -75,6 +76,10 @@ ApplicationParameters::ApplicationParameters(int argc, char* argv[])
         case 'd':
             graph_output_path = std::string(optarg);
             break;
+        case 'G':
+            graph_output_path = std::string(optarg);
+            output_gfa        = true;
+            break;
         case 'M':
             max_groups = std::stoi(optarg);
             break;
@@ -188,6 +193,9 @@ void ApplicationParameters::help(int32_t exit_code)
         -d, --dot <file>
             output path for printing graph in DOT format [disabled])"
               << R"(
+        -G, --gfa <file>
+            output path for printing graph in GFA format [disabled])"
+              << R"(
         -M, --max-groups  <int>
             maximum number of POA groups to create from file (-1 for all, > 0 for limited) [-1]
             repeats groups if less groups are present than specified)"

cudapoa/src/application_parameters.hpp

@@ -39,6 +39,7 @@ class ApplicationParameters
 
     std::vector<std::string> input_paths;
     std::string graph_output_path;
+    bool output_gfa           = false;
     bool all_fasta            = true;
     bool msa                  = false; // consensus by default
     BandMode band_mode        = BandMode::adaptive_band;

cudapoa/src/main.cpp

@@ -235,7 +235,14 @@ int main(int argc, char* argv[])
                         batch->get_graphs(graph, graph_status);
                         for (auto& g : graph)
                         {
-                            graph_output << g.serialize_to_dot() << std::endl;
+                            if (parameters.output_gfa)
+                            {
+                                graph_output << g.serialize_to_gfa() << std::endl;
+                            }
+                            else
+                            {
+                                graph_output << g.serialize_to_dot() << std::endl;
+                            }
                         }
                     }