PartialHit is no longer needed

Author: marcelm

src/nam.cpp

@@ -223,10 +223,6 @@ std::tuple<float, int, std::vector<Nam>> find_nams(
     const StrobemerIndex& index,
     bool use_mcs
 ) {
-    std::vector<PartialHit> partial_queried; // TODO: is a small set more efficient than linear search in a small vector?
-    if (use_mcs) {
-        partial_queried.reserve(10);
-    }
     std::array<robin_hood::unordered_map<unsigned int, std::vector<Match>>, 2> matches_map;
     matches_map[0].reserve(100);
     matches_map[1].reserve(100);
@@ -243,24 +239,18 @@ std::tuple<float, int, std::vector<Nam>> find_nams(
             add_to_matches_map_full(matches_map[q.is_reverse], q.start, q.end, index, position);
         }
         else if (use_mcs) {
-            PartialHit ph{q.hash & index.get_main_hash_mask(), q.start, q.is_reverse};
-            if (std::find(partial_queried.begin(), partial_queried.end(), ph) != partial_queried.end()) {
-                // already queried
-                continue;
-            }
             size_t partial_pos = index.find_partial(q.hash);
             if (partial_pos != index.end()) {
                 total_hits++;
                 if (index.is_partial_filtered(partial_pos)) {
-                    partial_queried.push_back(ph);
                     continue;
                 }
                 nr_good_hits++;
                 add_to_matches_map_partial(matches_map[q.is_reverse], q.start, q.start + index.k(), index, partial_pos);
             }
-            partial_queried.push_back(ph);
         }
     }
+
     float nonrepetitive_fraction = total_hits > 0 ? ((float) nr_good_hits) / ((float) total_hits) : 1.0;
     auto nams = merge_matches_into_nams_forward_and_reverse(matches_map, index.k(), use_mcs);
     return {nonrepetitive_fraction, nr_good_hits, nams};
@@ -290,8 +280,6 @@ std::pair<int, std::vector<Nam>> find_nams_rescue(
                 < std::tie(rhs.count, rhs.query_start, rhs.query_end);
         }
     };
-    std::vector<PartialHit> partial_queried;  // TODO: is a small set more efficient than linear search in a small vector?
-    partial_queried.reserve(10);
     std::array<robin_hood::unordered_map<unsigned int, std::vector<Match>>, 2> matches_map;
     std::vector<RescueHit> hits_fw;
     std::vector<RescueHit> hits_rc;
@@ -312,11 +300,6 @@ std::pair<int, std::vector<Nam>> find_nams_rescue(
             }
         }
         else if (use_mcs) {
-            PartialHit ph = {qr.hash & index.get_main_hash_mask(), qr.start, qr.is_reverse};
-            if (std::find(partial_queried.begin(), partial_queried.end(), ph) != partial_queried.end()) {
-                // already queried
-                continue;
-            }
             size_t partial_pos = index.find_partial(qr.hash);
             if (partial_pos != index.end()) {
                 unsigned int partial_count = index.get_count_partial(partial_pos);
@@ -327,7 +310,6 @@ std::pair<int, std::vector<Nam>> find_nams_rescue(
                     hits_fw.push_back(rh);
                 }
             }
-            partial_queried.push_back(ph);
         }
     }