fixes a bug introduced by partial hits: several full seeds can have t…

…he same partial base seed (identical query and ref coordinates. Such partial seeds got added to the same NAM and thus increased the score (through incrementing n_hits several times)

src/nam.cpp

@@ -62,6 +62,11 @@ inline void add_to_hits_per_ref_partial(
     }
 }
 
+    bool operator==(const Hit& lhs, const Hit& rhs)
+    {
+        return (lhs.query_start == rhs.query_start) && (lhs.query_end == rhs.query_end) && (lhs.ref_start == rhs.ref_start) && (lhs.ref_end == rhs.ref_end);
+    }
+
 void merge_hits_into_nams(
     robin_hood::unordered_map<unsigned int, std::vector<Hit>>& hits_per_ref,
     int k,
@@ -80,7 +85,11 @@ void merge_hits_into_nams(
 
         std::vector<Nam> open_nams;
         unsigned int prev_q_start = 0;
+        auto prev_hit = Hit{0,0,0,0};
         for (auto &h : hits) {
+            if (prev_hit == h) {
+                continue;
+            }
             bool is_added = false;
             for (auto & o : open_nams) {
 
@@ -152,6 +161,7 @@ void merge_hits_into_nams(
                 open_nams.erase(std::remove_if(open_nams.begin(), open_nams.end(), predicate), open_nams.end());
                 prev_q_start = h.query_start;
             }
+            prev_hit = h;
         }
 
         // Add all current open_matches to final NAMs