vidjil.cpp, germline.{h,cpp}: Use default behaviour for delta_min (if not redefined by CLI)

We use the same constant as the ones that were defined in vidjil.cpp rather
than relying on hard-coded values.

See #2156

algo/core/germline.cpp

@@ -105,11 +105,12 @@ Germline::Germline(string _code, char _shortcut,
 Germline::Germline(string code, char shortcut, string path, json json_recom,
                    int delta_min, string seed, int max_indexing)
 {
-    
-  int delta_min = -10;
+  if (delta_min == ~0) {
+    delta_min = DEFAULT_DELTA_MIN;
   
-  if (json_recom.find("4") != json_recom.end()) {
-      delta_min = 0;
+    if (json_recom.find("4") != json_recom.end()) {
+      delta_min = DEFAULT_DELTA_MIN_D;
+    }
   }
   
   init(code, shortcut, delta_min, seed, max_indexing);

algo/core/germline.h

@@ -13,6 +13,10 @@
 #include "kmerstorefactory.hpp"
 #include "bioreader.hpp"
 
+#define DEFAULT_DELTA_MIN  -10
+#define DEFAULT_DELTA_MIN_D  0
+
+
 enum SEGMENTATION_METHODS {
   SEG_METHOD_53,      // Regular or incomplete germlines, 5'-3'
   SEG_METHOD_543,     // Regular or incomplete germlines, 5'-3', with an additional middle gene (such a D gene)

algo/vidjil.cpp

@@ -107,10 +107,6 @@ enum { CMD_WINDOWS, CMD_CLONES, CMD_SEGMENT, CMD_GERMLINES } ;
 #define DEFAULT_W      50
 #define DEFAULT_SEED   ""
 
-#define DEFAULT_DELTA_MIN  -10
-
-#define DEFAULT_DELTA_MIN_D  0
-
 #define DEFAULT_MAX_AUDITIONED 2000
 #define DEFAULT_RATIO_REPRESENTATIVE 0.5