connect end to start diag

Author: marcelm

src/nam.cpp

@@ -163,16 +163,16 @@ void merge_nearby_nams(std::vector<Nam>& nams) {
         }
         // by diagonal
         // TODO make branchless
-        return (a.diagonal() < b.diagonal()) || ((a.diagonal() == b.diagonal()) && (a.ref_start < b.ref_start));
+        return (a.start_diagonal() < b.start_diagonal()) || ((a.start_diagonal() == b.start_diagonal()) && (a.ref_start < b.ref_start));
     });
     if (nams.empty()) {
         return;
     }
 
     size_t j = 0;
     for (size_t i = 1; i < nams.size(); i++) {
-        if (nams[j].ref_id == nams[i].ref_id && nams[j].diagonal() == nams[i].diagonal() && nams[j].is_rc == nams[i].is_rc
-            && nams[j].query_end + 100 <= nams[i].query_start
+        if (nams[j].ref_id == nams[i].ref_id && nams[j].end_diagonal() == nams[i].start_diagonal() && nams[j].is_rc == nams[i].is_rc
+            && nams[j].query_end + 10 <= nams[i].query_start
         ) {
             assert(nams[j].is_rc == nams[i].is_rc);
             // merge // TODO turn into method

src/nam.hpp

@@ -34,9 +34,13 @@ struct Nam {
         return std::max(0, ref_start - query_start);
     }
 
-    int diagonal() const {
+    int start_diagonal() const {
         return ref_start - query_start;
     }
+
+    int end_diagonal() const {
+        return ref_end - query_end;
+    }
 };
 
 void merge_nearby_nams(std::vector<Nam>& nams);