From 2a7b4f588a2b78f54d29b79aff86d566310b36bb Mon Sep 17 00:00:00 2001
From: Marcel Martin <marcel.martin@scilifelab.se>
Date: Wed, 29 Jan 2025 23:12:56 +0100
Subject: [PATCH] PartialHit is no longer needed

---
 src/nam.cpp | 32 --------------------------------
 1 file changed, 32 deletions(-)

diff --git a/src/nam.cpp b/src/nam.cpp
index 9bcd55b0..266ee6d5 100644
--- a/src/nam.cpp
+++ b/src/nam.cpp
@@ -13,19 +13,6 @@ bool operator==(const Match& lhs, const Match& 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);
 }
 
-/*
- * A partial hit is a hit where not the full randstrobe hash could be found in
- * the index but only the "main" hash (only the first aux_len bits).
- */
-struct PartialHit {
-    randstrobe_hash_t hash;
-    unsigned int start;  // position in strobemer index
-    bool is_reverse;
-    bool operator==(const PartialHit& rhs) const {
-        return (hash == rhs.hash) && (start == rhs.start) && (is_reverse == rhs.is_reverse);
-    }
-};
-
 inline void add_to_matches_map_full(
     robin_hood::unordered_map<unsigned int, std::vector<Match>>& matches_map,
     int query_start,
@@ -223,10 +210,6 @@ 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);
@@ -243,22 +226,15 @@ std::tuple<float, int, std::vector<Nam>> find_nams(
             add_to_matches_map_full(matches_map[q.is_revcomp], 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_revcomp], q.start, q.start + index.k(), index, partial_pos);
             }
-            partial_queried.push_back(ph);
         }
     }
 
@@ -306,8 +282,6 @@ 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::array<std::vector<RescueHit>, 2> hits;
     matches_map[0].reserve(100);
@@ -323,18 +297,12 @@ std::pair<int, std::vector<Nam>> find_nams_rescue(
             hits[qr.is_revcomp].push_back(rh);
         }
         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);
                 RescueHit rh{partial_pos, partial_count, qr.start, qr.start + index.k(), true};
                 hits[qr.is_revcomp].push_back(rh);
             }
-            partial_queried.push_back(ph);
         }
     }