vidjil.cpp: D e-value depends on actual number of representatives.

Discussed in #2003. The e-value depends on the number of (segmented) representatives,
not the total number of clones.

algo/core/tools.h

@@ -17,7 +17,7 @@
                                   many Ns in the sequence and the
                                   corresponding subsequence should be
                                   trimmed */
-
+#define MIN(x,y) ((x) < (y) ? (x) : (y))
 
 #include <sstream>
 #include <iostream>

algo/vidjil.cpp

@@ -1410,10 +1410,12 @@ int main (int argc, char **argv)
 
 
         // FineSegmenter
-        FineSegmenter seg(representative, segmented_germline, segment_cost, expected_value, sort_clones.size());
+        size_t nb_fine_segmented = (size_t) max_clones; // When -1, it will become the max value.
+        nb_fine_segmented = MIN(nb_fine_segmented, sort_clones.size());
+        FineSegmenter seg(representative, segmented_germline, segment_cost, expected_value, nb_fine_segmented);
 	
         if (segmented_germline->seg_method == SEG_METHOD_543)
-	  seg.FineSegmentD(segmented_germline, several_D, expected_value_D, sort_clones.size());
+	  seg.FineSegmentD(segmented_germline, several_D, expected_value_D, nb_fine_segmented);
 
         if (detect_CDR3)
           seg.findCDR3();