[FEATURE] Allow empty bins in layout

include/hibf/config.hpp

@@ -40,6 +40,7 @@ namespace seqan::hibf
  * | General | seqan::hibf::config::threads                  | 1       | [RECOMMENDED_TO_ADAPT] |
  * | Layout  | seqan::hibf::config::sketch_bits              | 12      |                        |
  * | Layout  | seqan::hibf::config::tmax                     | 0       | 0 indicates unset      |
+ * | Layout  | seqan::hibf::config::empty_bin_fraction       | 0.0     | Dynamic Layout         |
  * | Layout  | seqan::hibf::config::max_rearrangement_ratio  | 0.5     |                        |
  * | Layout  | seqan::hibf::config::alpha                    | 1.2     |                        |
  * | Layout  | seqan::hibf::config::disable_estimate_union   | false   |                        |
@@ -228,6 +229,9 @@ struct config
      */
     size_t tmax{};
 
+    //!\brief The percentage of empty bins in the layout.
+    double empty_bin_fraction{};
+
     /*!\brief A scaling factor to influence the amount of merged bins produced by the layout algorithm.
      *
      * The layout algorithm optimizes the space consumption of the resulting HIBF, but currently has no means of
@@ -300,6 +304,7 @@ struct config
      *   * seqan::hibf::config::threads must be greater than `0`.
      *   * seqan::hibf::config::sketch_bits must be in `[5,32]`.
      *   * seqan::hibf::config::tmax must be at most `18446744073709551552`.
+     *   * seqan::hibf::config::empty_bin_fraction must be in `[0.0,1.0)`.
      *   * seqan::hibf::config::alpha must be positive.
      *   * seqan::hibf::config::max_rearrangement_ratio must be in `[0.0,1.0]`.
      *
@@ -322,6 +327,7 @@ struct config
                threads == other.threads &&
                sketch_bits == other.sketch_bits &&
                tmax == other.tmax &&
+               empty_bin_fraction == other.empty_bin_fraction &&
                alpha == other.alpha &&
                max_rearrangement_ratio == other.max_rearrangement_ratio &&
                disable_estimate_union == other.disable_estimate_union &&
@@ -332,11 +338,13 @@ struct config
 private:
     friend class cereal::access;
 
+    static constexpr uint32_t version{2};
+
     template <typename archive_t>
     void serialize(archive_t & archive)
     {
-        uint32_t version{1};
-        archive(CEREAL_NVP(version));
+        uint32_t parsed_version{version};
+        archive(cereal::make_nvp("version", parsed_version));
 
         archive(CEREAL_NVP(number_of_user_bins));
         archive(CEREAL_NVP(number_of_hash_functions));
@@ -346,6 +354,10 @@ struct config
 
         archive(CEREAL_NVP(sketch_bits));
         archive(CEREAL_NVP(tmax));
+
+        if (parsed_version > 1u)
+            archive(CEREAL_NVP(empty_bin_fraction));
+
         archive(CEREAL_NVP(alpha));
         archive(CEREAL_NVP(max_rearrangement_ratio));
         archive(CEREAL_NVP(disable_estimate_union));

include/hibf/layout/hierarchical_binning.hpp

@@ -117,7 +117,8 @@ class hierarchical_binning
         config{config_},
         data{std::addressof(data_)},
         num_user_bins{data->positions.size()},
-        num_technical_bins{data->previous.empty() ? config.tmax : needed_technical_bins(num_user_bins)}
+        num_technical_bins{data->previous.empty() ? config.tmax
+                                                  : std::min<size_t>(needed_technical_bins(num_user_bins), config.tmax)}
     {
         assert(data != nullptr);
     }

include/hibf/misc/empty_bins_by_fraction.hpp

@@ -0,0 +1,26 @@
+// SPDX-FileCopyrightText: 2006-2024, Knut Reinert & Freie Universität Berlin
+// SPDX-FileCopyrightText: 2016-2024, Knut Reinert & MPI für molekulare Genetik
+// SPDX-License-Identifier: BSD-3-Clause
+
+#pragma once
+
+#include <algorithm>
+#include <cstddef>
+
+#include <hibf/platform.hpp>
+
+namespace seqan::hibf
+{
+
+/*!\brief Returns the number of empty bins that should be created by a given fraction of the total number of bins.
+ * \param[in] tmax     The total number of bins.
+ * \param[in] fraction The fraction of the total number of bins that should be empty.
+ * \ingroup hibf
+ * \sa https://godbolt.org/z/cMjbM39vj
+ */
+[[nodiscard]] constexpr size_t empty_bins_by_fraction(size_t const tmax, double const fraction) noexcept
+{
+    return std::clamp<size_t>(tmax * fraction, 1, tmax - 1) - (fraction == 0.0);
+}
+
+} // namespace seqan::hibf

src/config.cpp

@@ -14,9 +14,10 @@
 #include <cereal/archives/json.hpp> // for JSONInputArchive, JSONOutputArchive
 #include <cereal/cereal.hpp>        // for make_nvp, InputArchive, OutputArchive
 
-#include <hibf/config.hpp>                   // for config
-#include <hibf/layout/prefixes.hpp>          // for meta_header, meta_hibf_config_end, meta_hibf_config_start
-#include <hibf/misc/next_multiple_of_64.hpp> // for next_multiple_of_64
+#include <hibf/config.hpp>                      // for config
+#include <hibf/layout/prefixes.hpp>             // for meta_header, meta_hibf_config_end, meta_hibf_config_start
+#include <hibf/misc/empty_bins_by_fraction.hpp> // for empty_bins_by_fraction
+#include <hibf/misc/next_multiple_of_64.hpp>    // for next_multiple_of_64
 
 namespace seqan::hibf
 {
@@ -107,6 +108,11 @@ void config::validate_and_set_defaults()
                   << "anyway, so we increased your number of technical bins to " << tmax << ".\n";
     }
 
+    if (empty_bin_fraction < 0.0 || empty_bin_fraction >= 1.0)
+        throw std::invalid_argument{"[HIBF CONFIG ERROR] config::empty_bin_fraction must be in [0.0,1.0)."};
+
+    tmax -= empty_bins_by_fraction(tmax, empty_bin_fraction);
+
     if (alpha < 0.0)
         throw std::invalid_argument{"[HIBF CONFIG ERROR] config::alpha must be positive."};
 

src/layout/hierarchical_binning.cpp

@@ -17,6 +17,7 @@
 #include <hibf/layout/layout.hpp>               // for layout
 #include <hibf/layout/simple_binning.hpp>       // for simple_binning
 #include <hibf/misc/divide_and_ceil.hpp>        // for divide_and_ceil
+#include <hibf/misc/empty_bins_by_fraction.hpp> // for empty_bins_by_fraction
 #include <hibf/misc/next_multiple_of_64.hpp>    // for next_multiple_of_64
 #include <hibf/misc/timer.hpp>                  // for concurrent_timer
 #include <hibf/platform.hpp>                    // for HIBF_WORKAROUND_GCC_BOGUS_MEMCPY
@@ -77,12 +78,13 @@ size_t hierarchical_binning::execute()
 
 [[nodiscard]] size_t hierarchical_binning::needed_technical_bins(size_t const requested_num_ub) const
 {
-    return std::min<size_t>(next_multiple_of_64(requested_num_ub), config.tmax);
+    size_t const next_multiple = next_multiple_of_64(requested_num_ub);
+    return next_multiple - empty_bins_by_fraction(next_multiple, config.empty_bin_fraction);
 }
 
 [[nodiscard]] size_t hierarchical_binning::max_merge_levels(size_t const num_ubs_in_merge) const
 {
-    size_t const lower_lvl_tbs = needed_technical_bins(num_ubs_in_merge);
+    size_t const lower_lvl_tbs = std::min<size_t>(needed_technical_bins(num_ubs_in_merge), config.tmax);
     double const levels = std::log(num_ubs_in_merge) / std::log(lower_lvl_tbs);
     return static_cast<size_t>(std::ceil(levels));
 }
@@ -405,16 +407,19 @@ void hierarchical_binning::update_libf_data(data_store & libf_data, size_t const
 
 size_t hierarchical_binning::add_lower_level(data_store & libf_data) const
 {
+    size_t const number_of_user_bins = libf_data.positions.size();
+
     // now do the binning for the low-level IBF:
-    if (libf_data.positions.size() > config.tmax)
+    if (number_of_user_bins > config.tmax)
     {
         // recursively call hierarchical binning if there are still too many UBs
         return hierarchical_binning{libf_data, config}.execute(); // return id of maximum technical bin
     }
     else
     {
         // use simple binning to distribute remaining UBs
-        return simple_binning{libf_data, 0}.execute(); // return id of maximum technical bin
+        size_t const number_of_technical_bins = needed_technical_bins(number_of_user_bins);
+        return simple_binning{libf_data, number_of_technical_bins}.execute(); // return id of maximum technical bin
     }
 }
 

test/unit/hibf/config_test.cpp

@@ -37,14 +37,15 @@ TEST(config_test, write_to)
     std::string const expected_file{"@HIBF_CONFIG\n"
                                     "@{\n"
                                     "@    \"hibf_config\": {\n"
-                                    "@        \"version\": 1,\n"
+                                    "@        \"version\": 2,\n"
                                     "@        \"number_of_user_bins\": 123456789,\n"
                                     "@        \"number_of_hash_functions\": 4,\n"
                                     "@        \"maximum_fpr\": 0.0001,\n"
                                     "@        \"relaxed_fpr\": 0.3,\n"
                                     "@        \"threads\": 31,\n"
                                     "@        \"sketch_bits\": 8,\n"
                                     "@        \"tmax\": 128,\n"
+                                    "@        \"empty_bin_fraction\": 0.0,\n"
                                     "@        \"alpha\": 1.0,\n"
                                     "@        \"max_rearrangement_ratio\": 0.333,\n"
                                     "@        \"disable_estimate_union\": true,\n"
@@ -57,6 +58,45 @@ TEST(config_test, write_to)
 }
 
 TEST(config_test, read_from)
+{
+    std::stringstream ss{"@HIBF_CONFIG\n"
+                         "@{\n"
+                         "@    \"hibf_config\": {\n"
+                         "@        \"version\": 2,\n"
+                         "@        \"number_of_user_bins\": 123456789,\n"
+                         "@        \"number_of_hash_functions\": 4,\n"
+                         "@        \"maximum_fpr\": 0.0001,\n"
+                         "@        \"relaxed_fpr\": 0.3,\n"
+                         "@        \"threads\": 31,\n"
+                         "@        \"sketch_bits\": 8,\n"
+                         "@        \"tmax\": 128,\n"
+                         "@        \"empty_bin_fraction\": 0.5,\n"
+                         "@        \"alpha\": 1.0,\n"
+                         "@        \"max_rearrangement_ratio\": 0.333,\n"
+                         "@        \"disable_estimate_union\": true,\n"
+                         "@        \"disable_rearrangement\": false\n"
+                         "@    }\n"
+                         "@}\n"
+                         "@HIBF_CONFIG_END\n"};
+
+    seqan::hibf::config configuration;
+    configuration.read_from(ss);
+
+    EXPECT_EQ(configuration.number_of_user_bins, 123456789);
+    EXPECT_EQ(configuration.number_of_hash_functions, 4);
+    EXPECT_EQ(configuration.maximum_fpr, 0.0001);
+    EXPECT_EQ(configuration.relaxed_fpr, 0.3);
+    EXPECT_EQ(configuration.threads, 31);
+    EXPECT_EQ(configuration.sketch_bits, 8);
+    EXPECT_EQ(configuration.tmax, 128);
+    EXPECT_EQ(configuration.empty_bin_fraction, 0.5);
+    EXPECT_EQ(configuration.alpha, 1.0);
+    EXPECT_EQ(configuration.max_rearrangement_ratio, 0.333);
+    EXPECT_EQ(configuration.disable_estimate_union, true);
+    EXPECT_EQ(configuration.disable_rearrangement, false);
+}
+
+TEST(config_test, read_from_v1)
 {
     std::stringstream ss{"@HIBF_CONFIG\n"
                          "@{\n"
@@ -87,6 +127,7 @@ TEST(config_test, read_from)
     EXPECT_EQ(configuration.threads, 31);
     EXPECT_EQ(configuration.sketch_bits, 8);
     EXPECT_EQ(configuration.tmax, 128);
+    EXPECT_EQ(configuration.empty_bin_fraction, 0.0);
     EXPECT_EQ(configuration.alpha, 1.0);
     EXPECT_EQ(configuration.max_rearrangement_ratio, 0.333);
     EXPECT_EQ(configuration.disable_estimate_union, true);
@@ -272,6 +313,17 @@ TEST(config_test, validate_and_set_defaults)
                   "increased your number of technical bins to 64.\n");
     }
 
+    // empty_bin_fraction must be in [0.0,1.0)
+    {
+        seqan::hibf::config configuration{.input_fn = dummy_input_fn,
+                                          .number_of_user_bins = 1u,
+                                          .empty_bin_fraction = -0.1};
+        check_error_message(configuration, "[HIBF CONFIG ERROR] config::empty_bin_fraction must be in [0.0,1.0).");
+
+        configuration.empty_bin_fraction = 1.0;
+        check_error_message(configuration, "[HIBF CONFIG ERROR] config::empty_bin_fraction must be in [0.0,1.0).");
+    }
+
     // alpha must be positive
     {
         seqan::hibf::config configuration{.input_fn = dummy_input_fn, .number_of_user_bins = 1u, .alpha = -0.1};

test/unit/hibf/layout/hierarchical_binning_test.cpp

@@ -45,6 +45,40 @@ TEST(hierarchical_binning_test, small_example)
     EXPECT_RANGE_EQ(hibf_layout.user_bins, expected_user_bins);
 }
 
+TEST(hierarchical_binning_test, small_example_with_empty_bins)
+{
+    seqan::hibf::config config;
+    config.tmax = 4;
+    config.disable_estimate_union = true; // also disables rearrangement
+    config.empty_bin_fraction = 0.001;
+
+    seqan::hibf::layout::layout hibf_layout{};
+    std::vector<size_t> kmer_counts{500, 1000, 500, 500, 500, 500, 500, 500};
+
+    seqan::hibf::layout::data_store data{.hibf_layout = &hibf_layout, .kmer_counts = &kmer_counts};
+
+    data.fpr_correction =
+        seqan::hibf::layout::compute_fpr_correction({.fpr = 0.05, .hash_count = 2, .t_max = config.tmax});
+    seqan::hibf::layout::hierarchical_binning algo{data, config};
+    EXPECT_EQ(algo.execute(), 3u); // #HIGH_LEVEL_IBF max_bin_id:3
+
+    std::vector<seqan::hibf::layout::layout::max_bin> expected_max_bins{{{1}, 0}, {{2}, 0}};
+
+    // clang-format off
+    std::vector<seqan::hibf::layout::layout::user_bin> expected_user_bins{{{},       0,      1, 7},
+                                                                          {{1},      0, 22 - 1, 4},
+                                                                          {{1}, 22 - 1,     21, 5},
+                                                                          {{1}, 43 - 1,     21, 6},
+                                                                          {{2},      0, 22 - 1, 0},
+                                                                          {{2}, 22 - 1,     21, 2},
+                                                                          {{2}, 43 - 1,     21, 3},
+                                                                          {{},       3,      1, 1}};
+    // clang-format on
+
+    EXPECT_RANGE_EQ(hibf_layout.max_bins, expected_max_bins);
+    EXPECT_RANGE_EQ(hibf_layout.user_bins, expected_user_bins);
+}
+
 TEST(hierarchical_binning_test, another_example)
 {
     seqan::hibf::config config;