diff --git a/algo/core/windowExtractor.cpp b/algo/core/windowExtractor.cpp
index 390b71191c99213d75f87645aaede08ae1167a46..af9962d35a4d12fcf3fbc2bab17aa647b8fa2121 100644
--- a/algo/core/windowExtractor.cpp
+++ b/algo/core/windowExtractor.cpp
@@ -5,9 +5,10 @@
 #define PROGRESS_POINT 25000
 #define PROGRESS_LINE 40
 
-WindowExtractor::WindowExtractor(): out_segmented(NULL), out_unsegmented(NULL), out_affects(NULL), max_reads_per_window(~0){}
+WindowExtractor::WindowExtractor(MultiGermline *multigermline): out_segmented(NULL), out_unsegmented(NULL), out_affects(NULL), max_reads_per_window(~0), multigermline(multigermline){
+}
                                     
-WindowsStorage *WindowExtractor::extract(OnlineFasta *reads, MultiGermline *multigermline,
+WindowsStorage *WindowExtractor::extract(OnlineFasta *reads,
 					 size_t w,
                                          map<string, string> &windows_labels, bool only_labeled_windows,
                                          int stop_after, int only_nth_read, bool keep_unsegmented_as_clone,
diff --git a/algo/core/windowExtractor.h b/algo/core/windowExtractor.h
index ac9d52ee2ccdbb3066fa14cf71156531db58c340..29a45f953ed808d6799b8cc48a63c6cfb1b0c9f7 100644
--- a/algo/core/windowExtractor.h
+++ b/algo/core/windowExtractor.h
@@ -27,16 +27,17 @@ class WindowExtractor {
 
   Stats stats[STATS_SIZE];
   size_t max_reads_per_window;
+
+  MultiGermline *multigermline;
  public:
 
-  WindowExtractor();
+  WindowExtractor(MultiGermline *multigermline);
 
   /**
    * Extract windows from the collection of input reads.
    * If (un)segmented sequences must be output, the functions 
    * set(Un)SegmentedOutput() must be called before.
    * @param reads: the collection of input reads
-   * @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
@@ -47,7 +48,7 @@ class WindowExtractor {
    * @post Statistics on segmentation will be provided through the getSegmentationStats() methods
    *       and getAverageSegmentationLength().
    */
-  WindowsStorage *extract(OnlineFasta *reads, MultiGermline *multigermline,
+  WindowsStorage *extract(OnlineFasta *reads,
                           size_t w,
                           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,
diff --git a/algo/tests/testSegment.cpp b/algo/tests/testSegment.cpp
index 1a98a1d7c1b39073487e6ee818e4ad8e1a3439a9..1b2736083fe0b292baa18ae84c778cb41c929e6d 100644
--- a/algo/tests/testSegment.cpp
+++ b/algo/tests/testSegment.cpp
@@ -220,14 +220,14 @@ void testExtractor() {
   multi = new MultiGermline();
   multi->insert(germline);
 
-  WindowExtractor we;
+  WindowExtractor we(multi);
   map<string, string> labels;
   ofstream out_seg("segmented.log");
   ofstream out_unseg("unsegmented.log");
   we.setSegmentedOutput(&out_seg);
   we.setUnsegmentedOutput(&out_unseg);
 
-  WindowsStorage *ws = we.extract(&data, multi, 30, labels);
+  WindowsStorage *ws = we.extract(&data, 30, labels);
   // we.out_stats(cout);
 
   TAP_TEST(we.getNbReads() == 13, TEST_EXTRACTOR_NB_READS, "");
diff --git a/algo/vidjil.cpp b/algo/vidjil.cpp
index e9c71ef913f10689025431eb21c36bbcd50f2453..e650284998b6de345c3eb9de525d50e47ddc0b15 100644
--- a/algo/vidjil.cpp
+++ b/algo/vidjil.cpp
@@ -951,7 +951,7 @@ int main (int argc, char **argv)
     ofstream *out_unsegmented = NULL;
     ofstream *out_affects = NULL;
  
-    WindowExtractor we;
+    WindowExtractor we(multigermline);
     if (! output_sequences_by_cluster)
       we.setMaximalNbReadsPerWindow(max_auditionned);
  
@@ -976,7 +976,7 @@ int main (int argc, char **argv)
       we.setAffectsOutput(out_affects);
     }
 
-    WindowsStorage *windowsStorage = we.extract(reads, multigermline, w,
+    WindowsStorage *windowsStorage = we.extract(reads, w,
                                                 windows_labels, only_labeled_windows,
                                                 max_reads_processed, only_nth_read, keep_unsegmented_as_clone,
                                                 expected_value, nb_reads_for_evalue);