merge - two commits updating the '-g' option

algo/core/germline.cpp

@@ -109,10 +109,10 @@ void MultiGermline::insert(Germline *germline)
   germlines.push_back(germline);
 }
 
-void MultiGermline::load_default_set()
+void MultiGermline::load_default_set(string path)
 {
-  germlines.push_back(new Germline("TRG", 'G', "germline/TRGV.fa", "",                 "germline/TRGJ.fa", "#####-#####",   -10, 20));
-  germlines.push_back(new Germline("IGH", 'H', "germline/IGHV.fa", "germline/IGHD.fa", "germline/IGHJ.fa", "######-######",   0, 80));
+  germlines.push_back(new Germline("TRG", 'G', path + "/TRGV.fa", "",                path + "/TRGJ.fa", "#####-#####",   -10, 20));
+  germlines.push_back(new Germline("IGH", 'H', path + "/IGHV.fa", path + "/IGHD.fa", path + "/IGHJ.fa", "######-######",   0, 80));
 }
 
 

algo/core/germline.h

@@ -68,7 +68,7 @@ class MultiGermline {
   ~MultiGermline();
 
   void insert(Germline *germline);
-  void load_default_set();
+  void load_default_set(string path);
 
   void out_stats(ostream &out);
 };

algo/vidjil.cpp

@@ -147,7 +147,7 @@ void usage(char *progname)
        << "  -D <file>     D germline multi-fasta file (automatically implies -d)" << endl
        << "  -J <file>     J germline multi-fasta file" << endl
        << "  -G <prefix>   prefix for V (D) and J repertoires (shortcut for -V <prefix>V.fa -D <prefix>D.fa -J <prefix>J.fa)" << endl
-       << "  -g            multiple germlines (experimental)" << endl
+       << "  -g <path>     multiple germlines (experimental)" << endl
        << endl
 
        << "Window prediction" << endl
@@ -279,6 +279,7 @@ int main (int argc, char **argv)
   bool output_segmented = false;
   bool output_unsegmented = false;
   bool multi_germline = false;
+  string multi_germline_file = "";
 
   string forced_edges = "" ;
 
@@ -294,7 +295,7 @@ int main (int argc, char **argv)
 
   //$$ options: getopt
 
-  while ((c = getopt(argc, argv, "AhagG:V:D:J:k:r:vw:e:C:t:l:dc:m:M:N:s:p:Sn:o:L%:Z:y:z:uU")) != EOF)
+  while ((c = getopt(argc, argv, "Ahag:G:V:D:J:k:r:vw:e:C:t:l:dc:m:M:N:s:p:Sn:o:L%:Z:y:z:uU")) != EOF)
 
     switch (c)
       {
@@ -355,7 +356,8 @@ int main (int argc, char **argv)
 	break;
 
       case 'g':
-	multi_germline = true ;
+	multi_germline = true;
+	multi_germline_file = string(optarg);
 	break;
 	
       case 'G':
@@ -747,9 +749,6 @@ int main (int argc, char **argv)
   if (!segment_D) // TODO: add other constructor to Fasta, and do not load rep_D in this case
     f_rep_D = "";
 
-  Fasta rep_V(f_rep_V, 2, "|", cout);
-  Fasta rep_D(f_rep_D, 2, "|", cout);
-  Fasta rep_J(f_rep_J, 2, "|", cout);
 
   OnlineFasta *reads;
 
@@ -785,10 +784,14 @@ int main (int argc, char **argv)
 
     if (multi_germline)
       {
-	multigermline->load_default_set();
+	multigermline->load_default_set(multi_germline_file);
       }
     else
       {
+	Fasta rep_V(f_rep_V, 2, "|", cout);
+	Fasta rep_D(f_rep_D, 2, "|", cout);
+	Fasta rep_J(f_rep_J, 2, "|", cout);
+
 	Germline *germline;
 	germline = new Germline(germline_system, 'X',
                 rep_V, rep_D, rep_J, seed,
@@ -1309,6 +1312,11 @@ int main (int argc, char **argv)
          << "* They should be checked with other softwares such as IgBlast, iHHMune-align or IMGT/V-QUEST." << endl
       ;
 
+
+    Fasta rep_V(f_rep_V, 2, "|", cout);
+    Fasta rep_D(f_rep_D, 2, "|", cout);
+    Fasta rep_J(f_rep_J, 2, "|", cout);
+
     Germline *germline;
 
     // Here, it could be run without building the index