option -X <nb> added : segments nb clones then stop

algo/core/windowExtractor.cpp

@@ -3,10 +3,9 @@
 
 WindowExtractor::WindowExtractor(): out_segmented(NULL), out_unsegmented(NULL), out_affects(NULL){}
                                     
-
 WindowsStorage *WindowExtractor::extract(OnlineFasta *reads, MultiGermline *multigermline,
 					 size_t w,
-                                         map<string, string> &windows_labels) {
+                                         map<string, string> &windows_labels, int stop_after) {
   init_stats();
 
   WindowsStorage *windowsStorage = new WindowsStorage(windows_labels);
@@ -16,10 +15,12 @@ WindowsStorage *WindowExtractor::extract(OnlineFasta *reads, MultiGermline *mult
       Germline *germline = *it ;
       nb_reads_germline[germline->code] = 0;
     }
-  
-  while (reads->hasNext()) {
+
+  int stop=0;
+  while (reads->hasNext() && stop < stop_after) {
     reads->next();
     nb_reads++;
+    stop++;
 
     if (out_affects) {
       *out_affects << reads->getSequence();

algo/core/windowExtractor.h

@@ -46,7 +46,7 @@ class WindowExtractor {
    */
   WindowsStorage *extract(OnlineFasta *reads, MultiGermline *multigermline,
                           size_t w,
-                          map<string, string> &windows_labels);
+                          map<string, string> &windows_labels, int stop_after);
 
   /**
    * @return the average length of sequences whose segmentation has been classified as seg

algo/vidjil.cpp

@@ -188,6 +188,9 @@ void usage(char *progname)
        << "  -y <nb>       maximal number of clones computed with a representative ('" << NO_LIMIT << "': no limit) (default: " << DEFAULT_MAX_REPRESENTATIVES << ")" << endl
        << "  -z <nb>       maximal number of clones to be segmented ('" << NO_LIMIT << "': no limit, do not use) (default: " << DEFAULT_MAX_CLONES << ")" << endl
        << "  -A            reports and segments all clones (-r 0 -% 0 -y " << NO_LIMIT << " -z " << NO_LIMIT << "), to be used only on very small datasets" << endl
+       ////MODIF_TAT
+       << "  -X <nb>       number of clones segmented, have to be combined with -A ('" << NO_LIMIT << "' : no limit) (default: " <<WARN_MAX_CLONES << ")" << endl
+       /////END_TAT
        << endl
 
        << "Fine segmentation options (second pass, see warning in doc/algo.org)" << endl
@@ -284,6 +287,10 @@ int main (int argc, char **argv)
   float ratio_reads_clone = DEFAULT_RATIO_READS_CLONE;
   // int average_deletion = 4;     // Average number of deletion in V or J
 
+  ///MODIF_TAT
+  int max_clones_segmented = WARN_MAX_CLONES;
+  /// END_TAT
+
   float ratio_representative = DEFAULT_RATIO_REPRESENTATIVE;
   unsigned int max_auditionned = DEFAULT_MAX_AUDITIONED;
 
@@ -313,7 +320,9 @@ int main (int argc, char **argv)
 
   //$$ options: getopt
 
-  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:uUK3")) != EOF)
+
+  //// MODIF_TAT : ajouter X:  dans c
+  while ((c = getopt(argc, argv, "AX:haiIg:G:V:D:J:k:r:vw:e:C:f:l:c:m:M:N:s:b:Sn:o:L%:y:z:uUK3")) != EOF)
 
     switch (c)
       {
@@ -472,6 +481,12 @@ int main (int argc, char **argv)
 	max_clones = -1 ;
 	break ;
 
+  ////MODIF_TAT
+      case 'X':
+  max_clones_segmented = atoi(optarg);
+  break;
+  ///END_TAT
+
       case 'l':
 	windows_labels_file = optarg; 
 	break;
@@ -880,8 +895,9 @@ int main (int argc, char **argv)
       we.setAffectsOutput(out_affects);
     }
 
-
-    WindowsStorage *windowsStorage = we.extract(reads, multigermline, w, windows_labels);
+////MODIF_TAT : + max-clone-segmented
+    WindowsStorage *windowsStorage = we.extract(reads, multigermline, w, windows_labels, max_clones_segmented);
+///END_TAT
     windowsStorage->setIdToAll();
     size_t nb_total_reads = we.getNbReads();