restructure

include/hibf/config.hpp

@@ -177,8 +177,6 @@ struct config
      */
     double relaxed_fpr{0.3};
 
-    double relaxed_fpr_correction_factor{};
-
     /*!\brief The number of threads to use during construction. [RECOMMENDED_TO_ADAPT]
      *
      * Using more threads increases the memory consumption during construction because the threads hold local

include/hibf/layout/hierarchical_binning.hpp

@@ -26,6 +26,8 @@ class hierarchical_binning
 private:
     //!\brief The user config passed down from the command line.
     seqan::hibf::config config{};
+    //!\brief The correction factor for merged bins which are allowed to have a relaxed FPR
+    double relaxed_fpr_correction_factor{};
     //!\brief Stores all data that is needed to compute the layout, e.g. the counts, sketches and the layout::layout.
     data_store * data{nullptr};
 
@@ -87,8 +89,8 @@ class hierarchical_binning
             std::log1p(-std::exp(std::log(config_.maximum_fpr) / config_.number_of_hash_functions));
         double const denominator =
             std::log1p(-std::exp(std::log(config_.relaxed_fpr) / config_.number_of_hash_functions));
-        config.relaxed_fpr_correction_factor = numerator / denominator;
-        assert(config.relaxed_fpr_correction_factor <= 1.0);
+        relaxed_fpr_correction_factor = numerator / denominator;
+        assert(relaxed_fpr_correction_factor <= 1.0);
         assert(data != nullptr);
     }
 

src/layout/hierarchical_binning.cpp

@@ -118,7 +118,7 @@ void hierarchical_binning::initialization(std::vector<std::vector<size_t>> & mat
         for (size_t j = 1; j < num_user_bins; ++j)
         {
             sum += (*data->kmer_counts)[data->positions[j]];
-            matrix[0][j] = data->union_estimates[j] * config.relaxed_fpr_correction_factor;
+            matrix[0][j] = data->union_estimates[j] * relaxed_fpr_correction_factor;
             ll_matrix[0][j] = max_merge_levels(j + 1) * sum;
             trace[0][j] = {0u, j - 1}; // unnecessary?
         }
@@ -130,7 +130,7 @@ void hierarchical_binning::initialization(std::vector<std::vector<size_t>> & mat
             assert(j < data->positions.size());
             assert(data->positions[j] < data->kmer_counts->size());
             sum += (*data->kmer_counts)[data->positions[j]];
-            matrix[0][j] = sum * config.relaxed_fpr_correction_factor;
+            matrix[0][j] = sum * relaxed_fpr_correction_factor;
             ll_matrix[0][j] = max_merge_levels(j + 1) * sum;
             trace[0][j] = {0u, j - 1}; // unnecessary?
         }
@@ -212,7 +212,7 @@ void hierarchical_binning::recursion(std::vector<std::vector<size_t>> & matrix,
                 // union_estimates[j_prime] is the union of {j_prime, ..., j}
                 // the + 1 is necessary because j_prime is decremented directly after weight is updated
                 size_t const uncorrected = config.disable_estimate_union ? weight : data->union_estimates[j_prime + 1];
-                return config.relaxed_fpr_correction_factor * uncorrected;
+                return relaxed_fpr_correction_factor * uncorrected;
             };
 
             // if the user bin j-1 was not split into multiple technical bins!
@@ -279,7 +279,7 @@ void hierarchical_binning::backtrack_merged_bin(size_t trace_j,
     if (!config.disable_estimate_union)
         kmer_count = sketch.estimate(); // overwrite kmer_count high_level_max_id/size bin
 
-    max_tracker.update_max(bin_id, kmer_count * config.relaxed_fpr_correction_factor);
+    max_tracker.update_max(bin_id, kmer_count * relaxed_fpr_correction_factor);
     // std::cout << "]: " << kmer_count << std::endl;
 }