From eee0cd876332fa1599795f676aea46120c8c0961 Mon Sep 17 00:00:00 2001
From: ksahlin <ksahlin@math.su.se>
Date: Fri, 19 Apr 2024 11:10:41 +0200
Subject: [PATCH] Fixes that the mcs implementation gave different results
 depending on the -b parameter value

---
 src/index.hpp       |  2 +-
 src/nam.cpp         | 10 +++++-----
 src/randstrobes.hpp |  2 +-
 3 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/src/index.hpp b/src/index.hpp
index 48b8124a..6ee9d631 100644
--- a/src/index.hpp
+++ b/src/index.hpp
@@ -110,7 +110,7 @@ struct StrobemerIndex {
                                     randstrobes.begin() + position_end,
                                     RefRandstrobe{key, 0, 0},
                                     cmp);
-        if (pos->hash == key) return pos - randstrobes.begin();
+        if (pos->hash >> aux_len == key_prefix) return pos - randstrobes.begin();
         return end();
     }
 
diff --git a/src/nam.cpp b/src/nam.cpp
index 6bccb41a..cded85e9 100644
--- a/src/nam.cpp
+++ b/src/nam.cpp
@@ -52,13 +52,13 @@ inline void add_to_hits_per_ref_partial(
             adj_ref_start = index.get_strobe1_position(position) + index.strobe2_offset(position);
         }
         adj_ref_end = adj_ref_start + index.k();
-        int diff = std::abs((query_end - query_start) - (adj_ref_end - adj_ref_start));
-        if (diff <= min_diff) {
+//        int diff = std::abs((query_end - query_start) - (adj_ref_end - adj_ref_start));
+//        if (diff <= min_diff) {
             hits_per_ref[index.reference_index(position)].push_back(
                 Hit{query_start, query_end, adj_ref_start, adj_ref_end}
             );
-            min_diff = diff;
-        }
+//            min_diff = diff;
+//        }
     }
 }
 
@@ -211,7 +211,7 @@ std::pair<float, std::vector<Nam>> find_nams(
             size_t partial_pos = index.partial_find(q.hash);
             if (partial_pos != index.end()) {
                 total_hits++;
-                if (index.is_partial_filtered(position)) {
+                if (index.is_partial_filtered(partial_pos)) {
                     continue;
                 }
                 nr_good_hits++;
diff --git a/src/randstrobes.hpp b/src/randstrobes.hpp
index 070b874b..cdd8d1da 100644
--- a/src/randstrobes.hpp
+++ b/src/randstrobes.hpp
@@ -58,7 +58,7 @@ struct RefRandstrobe {
     packed_t m_packed; // packed representation of ref_index and strobe offset
 
 public:
-    static constexpr uint32_t max_number_of_references = (1 << (32 - bit_alloc)) - 1;
+    static constexpr uint32_t max_number_of_references = (1 << (32 - bit_alloc - 1)) - 1; // bit_alloc - 1 because 1 bit to main_is_first()
 };
 
 struct QueryRandstrobe {