core/segment.{h, cpp}: DEFAULT_MINIMIZE_WIDTH, DEFAULT_MINIMIZE_ONE_MARGIN

algo/core/segment.cpp

@@ -477,12 +477,11 @@ KmerSegmenter::KmerSegmenter(Sequence seq, Germline *germline, double threshold,
         return ;
       }
 
+    int pos = kaa.minimize(kmer, DEFAULT_MINIMIZE_ONE_MARGIN, DEFAULT_MINIMIZE_WIDTH);
+
     segmented = true ;
     because = reversed ? SEG_MINUS : SEG_PLUS ;
 
-    // 30 should be more than half of the window. Should we run this during getJunction(), once w is known ?
-    int pos = kaa.minimize(kmer, 30, 8);
-
     info = "=" + string_of_int(c) + " @" + string_of_int(pos) ;
 
     // getJunction() will be centered on pos

algo/core/segment.h

@@ -46,6 +46,9 @@
                                     be overriden by the command line by
                                     providing a shorter -w*/
 
+#define DEFAULT_MINIMIZE_WIDTH       12
+
+#define DEFAULT_MINIMIZE_ONE_MARGIN  20
 
 using namespace std;
 using json = nlohmann::json;