Option to write .gg in simple-sds format

include/gbwtgraph/gbz.h

@@ -105,10 +105,12 @@ class GBZ
   // Returns the size of the serialized structure in elements.
   size_t simple_sds_size() const;
 
-  // Serialize the GBWT (simple-sds format) and the GBWTGraph (SDSL format) to separate files.
-  void serialize_to_files(const std::string& gbwt_name, const std::string& graph_name) const;
+  // Serialize the GBWT (simple-sds format) and the GBWTGraph to separate files.
+  // Default graph format is libhandlegraph / SDSL.
+  void serialize_to_files(const std::string& gbwt_name, const std::string& graph_name, bool simple_sds_graph = false) const;
 
-  // Loads the GBWT (simple-sds format) and the GBWTGraph (SDSL format) from separate.
+  // Loads the GBWT (simple-sds format) and the GBWTGraph from separate files.
+  // Graph format is libhandlegraph / SDSL; the simple-sds format cannot be read.
   void load_from_files(const std::string& gbwt_name, const std::string& graph_name);
 
 private:

src/gbz.cpp

@@ -236,10 +236,11 @@ GBZ::simple_sds_size() const
 }
 
 void
-GBZ::serialize_to_files(const std::string& gbwt_name, const std::string& graph_name) const
+GBZ::serialize_to_files(const std::string& gbwt_name, const std::string& graph_name, bool simple_sds_graph) const
 {
   sdsl::simple_sds::serialize_to(this->index, gbwt_name);
-  this->graph.serialize(graph_name);
+  if(simple_sds_graph) { sdsl::simple_sds::serialize_to(this->graph, graph_name); }
+  else { this->graph.serialize(graph_name); }
 }
 
 void

src/gfa2gbwt.cpp

@@ -28,6 +28,7 @@ struct Config
 
   bool translation = false;
   bool show_progress = false;
+  bool simple_sds_graph = false;
 };
 
 const std::string tool_name = "GFA to GBWTGraph";
@@ -129,11 +130,16 @@ printUsage(int exit_code)
   std::cerr << "  -p, --progress          show progress information" << std::endl;
   std::cerr << "  -t, --translation       write translation table into a " << SequenceSource::TRANSLATION_EXTENSION << " file" << std::endl;
   std::cerr << std::endl;
+  std::cerr << "Other options:" << std::endl;
+  std::cerr << "  -s, --simple-sds-graph  serialize " << GBWTGraph::EXTENSION << " in simple-sds format instead of libhandlegraph format" << std::endl;
+  std::cerr << "                          (this tool cannot read simple-sds graphs)" << std::endl;
+  std::cerr << std::endl;
   std::cerr << "GFA parsing parameters:" << std::endl;
   std::cerr << "  -m, --max-node N        break > N bp segments into multiple nodes (default " << MAX_NODE_LENGTH << ")" << std::endl;
   std::cerr << "                          (minimizer index requires nodes of length <= 1024 bp)" << std::endl;
   std::cerr << "  -r, --path-regex STR    parse path names using regex STR (default " << GFAParsingParameters::DEFAULT_REGEX << ")" << std::endl;
   std::cerr << "  -f, --path-fields STR   map the submatches to fields STR (default " << GFAParsingParameters::DEFAULT_FIELDS << ")" << std::endl;
+  std::cerr << "                          (the first submatch is the entire path name)" << std::endl;
   std::cerr << std::endl;
   std::cerr << "Fields (case insensitive):" << std::endl;
   std::cerr << "  S      sample name" << std::endl;
@@ -164,13 +170,14 @@ Config::Config(int argc, char** argv)
     { "decompress-graph", no_argument, 0, 'D' },
     { "progress", no_argument, 0, 'p' },
     { "translation", no_argument, 0, 't' },
+    { "simple-sds-graph", no_argument, 0, 's' },
     { "max-node", required_argument, 0, 'm' },
     { "path-regex", required_argument, 0, 'r' },
     { "path-fields", required_argument, 0, 'f' },
   };
 
   // Process options.
-  while((c = getopt_long(argc, argv, "becdCDptm:r:f:", long_options, &option_index)) != -1)
+  while((c = getopt_long(argc, argv, "becdCDptsm:r:f:", long_options, &option_index)) != -1)
   {
     switch(c)
     {
@@ -207,6 +214,10 @@ Config::Config(int argc, char** argv)
       this->translation = true;
       break;
 
+    case 's':
+      this->simple_sds_graph = true;
+      break;
+
     case 'm':
       try { this->parameters.max_node_length = std::stoul(optarg); }
       catch(const std::invalid_argument&)
@@ -322,7 +333,7 @@ write_graph(const GBZ& gbz, const Config& config)
   {
     std::cerr << "Writing GBWT and GBWTGraph to " << gbwt_name << " and " << graph_name << std::endl;
   }
-  gbz.serialize_to_files(gbwt_name, graph_name);
+  gbz.serialize_to_files(gbwt_name, graph_name, config.simple_sds_graph);
 }
 
 //------------------------------------------------------------------------------