vidjil.cpp, core/germline.{h,c}: remove (in)complete filtering mechanism that was used with -i.

This should fix #2153.

algo/core/germline.cpp

@@ -256,7 +256,7 @@ void MultiGermline::add_germline(Germline *germline)
   germlines.push_back(germline);
 }
 
-void MultiGermline::build_from_json(string path, string json_filename_and_filter, int filter, int max_indexing)
+void MultiGermline::build_from_json(string path, string json_filename_and_filter, int max_indexing)
 {
 
   //extract json_filename and systems_filter
@@ -309,19 +309,6 @@ void MultiGermline::build_from_json(string path, string json_filename_and_filter
           continue ;
       }
 
-    switch (filter) {
-    case GERMLINES_REGULAR:
-      if (code.find("+") != string::npos) continue ;
-      break ;
-
-    case GERMLINES_INCOMPLETE:
-      if (code.find("+") == string::npos) continue ;
-      break ;
-
-    default:
-      break ;
-    }
-
     map<string, string> seedMap;
     seedMap["13s"] = SEED_S13;
     seedMap["12s"] = SEED_S12;

algo/core/germline.h

@@ -119,11 +119,6 @@ class Germline {
 ostream &operator<<(ostream &out, const Germline &germline);
 
 
-
-enum GERMLINES_FILTER { GERMLINES_ALL,
-                        GERMLINES_REGULAR,
-                        GERMLINES_INCOMPLETE } ;
-
 class MultiGermline {
  private:
   IndexTypes indexType;
@@ -147,10 +142,9 @@ class MultiGermline {
    * Build from a json .g germline file
    *   path: path, such as 'germline/'
    *   json_filename_and_filter: filename, optionally embedding a filter, such as 'homo-sapiens.g:IGH,TRG'
-   *   filter: see GERMLINES_FILTER
    *   max_indexing:
    */
-  void build_from_json(string path, string json_filename_and_filter, int filter, int max_indexing);
+  void build_from_json(string path, string json_filename_and_filter, int max_indexing);
 
   /**
    * Finishes the construction of the multi germline so that it can be used

algo/vidjil.cpp

@@ -849,7 +849,7 @@ int main (int argc, char **argv)
           for (pair <string, string> path_file: multi_germline_paths_and_files)
             {
               try {
-                multigermline->build_from_json(path_file.first, path_file.second, GERMLINES_REGULAR, trim_sequences);
+                multigermline->build_from_json(path_file.first, path_file.second, trim_sequences);
               } catch (std::exception& e) {
                 cerr << ERROR_STRING << "Vidjil cannot properly read " << path_file.first << "/" << path_file.second << ": " << e.what() << endl;
                 exit(1);
@@ -897,10 +897,9 @@ int main (int argc, char **argv)
         multigermline->germlines.push_back(pseudo_u);
     }
 
-      // Should come after the initialization of regular (and possibly pseudo) germlines
+      // Should come after the initialization of all germlines
     {
       for (pair <string, string> path_file: multi_germline_paths_and_files)
-        multigermline->build_from_json(path_file.first, path_file.second, GERMLINES_INCOMPLETE, trim_sequences);
       if ((! multigermline->one_index_per_germline) && (command != CMD_GERMLINES)) {
         multigermline->insert_in_one_index(multigermline->index, true);
       }