vidjil.cpp, core/germline.cpp: simplify handling of '-g' option

Defers to core/germline.cpp the possible failure in opening the file.
Completes the previous commit to fix #2134.

algo/core/germline.cpp

@@ -269,12 +269,22 @@ void MultiGermline::build_from_json(string path, string json_filename_and_filter
     systems_filter = "," + json_filename_and_filter.substr(pos_lastcolon+1) + "," ;
   }
 
-  //parse .g file
-  ifstream germline_data(path + "/" + json_filename);
-  string content( (std::istreambuf_iterator<char>(germline_data) ),
-                  (std::istreambuf_iterator<char>()    ) );
 
-  json germlines = json::parse(content);
+  //open and parse .g file
+  json germlines ;
+
+  try {
+    ifstream germline_data(path + "/" + json_filename);
+
+    string content( (std::istreambuf_iterator<char>(germline_data) ),
+                    (std::istreambuf_iterator<char>()    ) );
+
+    germlines = json::parse(content);
+
+  } catch (const invalid_argument e) {
+    cerr << ERROR_STRING << "Vidjil cannot open .g file " << path + "/" + json_filename << ": " << e.what() << endl;
+    exit(1);
+  }
 
   species = germlines["species"].get<std::string>();
   species_taxon_id = germlines["species_taxon_id"];

algo/vidjil.cpp

@@ -451,6 +451,7 @@ int main (int argc, char **argv)
 
       case 'g':
 	multi_germline = true;
+        germline_system = "multi" ;
         {
           string arg = string(optarg);
           struct stat buffer;
@@ -460,20 +461,14 @@ int main (int argc, char **argv)
                 {
                   // argument is a directory
                   multi_germline_paths_and_files.push_back(make_pair(arg, DEFAULT_MULTI_GERMLINE_FILE)) ;
-                }
-              else
-                {
-                  multi_germline_paths_and_files.push_back(make_pair(extract_dirname(arg), extract_basename(arg, false)));
+                  break ;
                 }
             }
-          else
-             {
-               cerr << ERROR_STRING << "A path or a file must be given with -g" << endl ;
-               exit(1);
-             }
+
+          // argument is not a directory (and basename can include ':' with a filter)
+          multi_germline_paths_and_files.push_back(make_pair(extract_dirname(arg), extract_basename(arg, false)));
+          break ;
         }
-	germline_system = "multi" ;
-	break;
 
       case 'd':
         several_D = true;