core/windowExtractor.{h,cpp}: only_labeled_windows, keeps only windows from windows_label

Hey, could windows labels (-l) be used for another thing ?

algo/core/windowExtractor.cpp

@@ -9,7 +9,7 @@ WindowExtractor::WindowExtractor(): out_segmented(NULL), out_unsegmented(NULL),
                                     
 WindowsStorage *WindowExtractor::extract(OnlineFasta *reads, MultiGermline *multigermline,
 					 size_t w,
-                                         map<string, string> &windows_labels,
+                                         map<string, string> &windows_labels, bool only_labeled_windows,
                                          int stop_after, int only_nth_read, bool keep_unsegmented_as_clone,
                                          double nb_expected, int nb_reads_for_evalue) {
   init_stats();
@@ -57,6 +57,10 @@ WindowsStorage *WindowExtractor::extract(OnlineFasta *reads, MultiGermline *mult
     stats[seg->getSegmentationStatus()].insert(read_length);
 
     if (seg->isSegmented()) {
+
+      // Filter
+      if (!only_labeled_windows || (windows_labels.find(junc) != windows_labels.end()))
+
       // Store the window
       windowsStorage->add(junc, reads->getSequence(), seg->getSegmentationStatus(), seg->segmented_germline);
 

algo/core/windowExtractor.h

@@ -39,6 +39,7 @@ class WindowExtractor {
    * @param multigermline: the multigermline
    * @param w: length of the window
    * @param windows_labels: Windows that must be kept and registered as such.
+   * @param only_labeled_windows: remember only windows from windows_labels
    * @param nb_expected: maximal e-value of the segmentation
    * @param nb_reads_for_evalue: number of reads, used for e-value computation. Can be approximate or faked.
    * @return a pointer to a WindowsStorage that will contain all the windows.
@@ -48,7 +49,7 @@ class WindowExtractor {
    */
   WindowsStorage *extract(OnlineFasta *reads, MultiGermline *multigermline,
                           size_t w,
-                          map<string, string> &windows_labels,
+                          map<string, string> &windows_labels, bool only_labeled_windows=false,
                           int stop_after=-1, int only_nth_reads=1, bool keep_unsegmented_as_clone=false,
                           double nb_expected = THRESHOLD_NB_EXPECTED, int nb_reads_for_evalue = 1);
 

algo/vidjil.cpp

@@ -331,6 +331,7 @@ int main (int argc, char **argv)
   string forced_edges = "" ;
 
   string windows_labels_file = "" ;
+  bool only_labeled_windows = false ;
 
   char c ;
 
@@ -954,7 +955,9 @@ int main (int argc, char **argv)
       we.setAffectsOutput(out_affects);
     }
 
-    WindowsStorage *windowsStorage = we.extract(reads, multigermline, w, windows_labels, max_reads_processed, only_nth_read, keep_unsegmented_as_clone,
+    WindowsStorage *windowsStorage = we.extract(reads, multigermline, w,
+                                                windows_labels, only_labeled_windows,
+                                                max_reads_processed, only_nth_read, keep_unsegmented_as_clone,
                                                 expected_value, nb_reads_for_evalue);
     windowsStorage->setIdToAll();
     size_t nb_total_reads = we.getNbReads();