vidjil.cpp: experimental -I option, ignore common k-mers between different germlines

This option is sponsored by UPMC.

algo/vidjil.cpp

@@ -154,6 +154,7 @@ void usage(char *progname)
        << "  -G <prefix>   prefix for V (D) and J repertoires (shortcut for -V <prefix>V.fa -D <prefix>D.fa -J <prefix>J.fa) (basename gives germline code)" << endl
        << "  -g <path>     multiple germlines (in the path <path>, takes TRA, TRB, TRG, TRD, IGH and IGL and sets window prediction parameters)" << endl
        << "  -i            multiple germlines, also incomplete rearrangements (experimental, must be used with -g)" << endl
+       << "  -I            ignore k-mers common to different germline systems (experimental, must be used with -g, do not use)" << endl
        << endl
 
        << "Window prediction" << endl
@@ -288,6 +289,7 @@ int main (int argc, char **argv)
   bool output_unsegmented = false;
   bool multi_germline = false;
   bool multi_germline_incomplete = false;
+  bool multi_germline_mark = false;
   string multi_germline_file = DEFAULT_MULTIGERMLINE;
 
   string forced_edges = "" ;
@@ -303,7 +305,7 @@ int main (int argc, char **argv)
 
   //$$ options: getopt
 
-  while ((c = getopt(argc, argv, "Ahaig:G:V:D:J:k:r:vw:e:C:f:l:c:m:M:N:s:b:Sn:o:L%:y:z:uU")) != EOF)
+  while ((c = getopt(argc, argv, "AhaiIg:G:V:D:J:k:r:vw:e:C:f:l:c:m:M:N:s:b:Sn:o:L%:y:z:uU")) != EOF)
 
     switch (c)
       {
@@ -355,6 +357,10 @@ int main (int argc, char **argv)
 	multi_germline_incomplete = true;
 	break;
 
+      case 'I':
+        multi_germline_mark = true;
+	break;
+        
       case 'G':
 	germline_system = string(optarg);
 	f_reps_V.push_back((germline_system + "V.fa").c_str()) ;
@@ -720,6 +726,9 @@ int main (int argc, char **argv)
 
     cout << endl ;
 
+    if (multi_germline_mark)
+      multigermline->mark_cross_germlines_as_ambiguous();
+    
     cout << "Germlines loaded" << endl ;
     cout << *multigermline ;
     cout << endl ;