vidjil.cpp: outputs also the representative in 'out/seq/sequences.fa-*'

algo/vidjil.cpp

@@ -1128,7 +1128,7 @@ int main (int argc, char **argv)
 	//$$ There is one representative, FineSegmenter
 
 
-          representative.label = string_of_int(it->second) + "-" 
+          representative.label = string_of_int(it->second) + "--" 
             + representative.label;
 	  FineSegmenter seg(representative, rep_V, rep_J, delta_min, delta_max, segment_cost);
 	
@@ -1323,11 +1323,27 @@ int main (int argc, char **argv)
 
 	// Output all sequences
 
+
+        Sequence representative 
+          = windowsStorage->getRepresentative(it->first, seed, 
+                                             min_cover_representative,
+                                             ratio_representative,
+                                             max_auditionned);
+
+
+        if (representative != NULL_SEQUENCE) {
+          representative.label = string_of_int(it->second) + "--" 
+            + representative.label;
+
+
 	if (output_sequences_by_cluster)
 	  {
 	    out_sequences << ">" << it->second << "--window--" << num_seq << " " << windows_labels[it->first] << endl ;
 	    out_sequences << it->first << endl;
 
+	    if (representative != NULL_SEQUENCE) 
+	      out_sequences << representative ;
+
 	    list<Sequence> &sequences = windowsStorage->getReads(it->first);
 	    
 	    for (list<Sequence>::const_iterator itt = sequences.begin(); itt != sequences.end(); ++itt)
@@ -1336,17 +1352,6 @@ int main (int argc, char **argv)
 	      }
 	  }
 
-        Sequence representative 
-          = windowsStorage->getRepresentative(it->first, seed, 
-                                             min_cover_representative,
-                                             ratio_representative,
-                                             max_auditionned);
-
-
-        if (representative != NULL_SEQUENCE) {
-          representative.label = string_of_int(it->second) + "-" 
-            + representative.label;
-
           FineSegmenter seg(representative, rep_V, rep_J, delta_min, delta_max, segment_cost);
 
           if (segment_D)