From 80317ef437110ccfd0f946908ed6d841948506a9 Mon Sep 17 00:00:00 2001
From: Evelin <evelin.aasna@fu-berlin.de>
Date: Fri, 11 Oct 2024 16:17:51 +0200
Subject: [PATCH] Dismiss low entropy patterns

---
 include/raptor/threshold/threshold.hpp   |  2 ++
 include/valik/search/local_prefilter.hpp | 25 ++++++++++++++++--------
 src/raptor/threshold/threshold.cpp       |  5 +++++
 3 files changed, 24 insertions(+), 8 deletions(-)

diff --git a/include/raptor/threshold/threshold.hpp b/include/raptor/threshold/threshold.hpp
index 2a06acd1..658ceec6 100644
--- a/include/raptor/threshold/threshold.hpp
+++ b/include/raptor/threshold/threshold.hpp
@@ -32,6 +32,8 @@ class threshold
 
     size_t get(size_t const minimiser_count) const noexcept;
 
+    size_t mean_number_of_minimizers() const noexcept;
+
 private:
     enum class threshold_kinds
     {
diff --git a/include/valik/search/local_prefilter.hpp b/include/valik/search/local_prefilter.hpp
index cf1e9889..fefbf8a0 100644
--- a/include/valik/search/local_prefilter.hpp
+++ b/include/valik/search/local_prefilter.hpp
@@ -67,10 +67,10 @@ struct pattern_bounds
  * @return pattern_bounds The interval of minimisers corresponding to the pattern.
  */
 template <typename span_vec_t>
-pattern_bounds make_pattern_bounds(size_t const & begin,
-                                   search_arguments const & arguments,
-                                   span_vec_t const & window_span_begin,
-                                   raptor::threshold::threshold const & thresholder)
+std::optional<pattern_bounds> make_pattern_bounds(size_t const & begin,
+                                                  search_arguments const & arguments,
+                                                  span_vec_t const & window_span_begin,
+                                                  raptor::threshold::threshold const & thresholder)
 {
     assert(window_span_begin.size() >= 1);
     assert(window_span_begin[0] == 0);
@@ -91,8 +91,16 @@ pattern_bounds make_pattern_bounds(size_t const & begin,
 
     size_t const minimiser_count = pattern.end_position - pattern.begin_position;
 
-    pattern.threshold = thresholder.get(minimiser_count);
-    return pattern;
+    if (arguments.keep_all_repeats ||
+        (arguments.keep_best_repeats && 
+        (minimiser_count >= (thresholder.mean_number_of_minimizers()))))  
+        // ignore low entropy repeat patterns 
+    {   
+        pattern.threshold = thresholder.get(minimiser_count);
+        return pattern;
+    }
+    else
+        return std::nullopt;
 }
 
 /**
@@ -205,8 +213,9 @@ void local_prefilter(
         std::unordered_map<size_t, size_t> sequence_hits{};
         pattern_begin_positions(seq.size(), arguments.pattern_size, arguments.query_every, [&](size_t const begin)
         {
-            pattern_bounds const pattern = make_pattern_bounds(begin, arguments, window_span_begin, thresholder);
-            find_pattern_bins(pattern, bin_count, counting_table, sequence_hits, pattern_hits);
+            auto const pattern = make_pattern_bounds(begin, arguments, window_span_begin, thresholder);
+            if (pattern)
+                find_pattern_bins(*pattern, bin_count, counting_table, sequence_hits, pattern_hits);
         });
 
         result_cb(record, sequence_hits, pattern_hits);
diff --git a/src/raptor/threshold/threshold.cpp b/src/raptor/threshold/threshold.cpp
index 1d57418c..5d669280 100644
--- a/src/raptor/threshold/threshold.cpp
+++ b/src/raptor/threshold/threshold.cpp
@@ -60,5 +60,10 @@ size_t threshold::get(size_t const minimiser_count) const noexcept
     }
     }
 }
+ 
+size_t threshold::mean_number_of_minimizers() const noexcept
+{
+    return (size_t) std::round((maximal_number_of_minimizers - minimal_number_of_minimizers) / 2.0);
+}
 
 } // namespace raptor::threshold