seqan · smehringer · Nov 9, 2023 · Nov 28, 2023 · Dec 4, 2023 · Dec 4, 2023
diff --git a/include/chopper/configuration.hpp b/include/chopper/configuration.hpp
@@ -19,8 +19,18 @@
 namespace chopper
 {
 
+enum partitioning_scheme
+{
+    blocked,
+    sorted,
+    folded,
+    weighted_fold,
+    similarity
+};
+
 struct configuration
 {
+    int partitioning_approach{};
     /*!\name General Configuration
      * \{
      */
@@ -46,6 +56,16 @@ struct configuration
     bool precomputed_files{false};
     //!\}
 
+    /*!\name Partitioned HIBF configuration
+     * \{
+     */
+    //!\brief The maximum index size that the HIBF should not exceed. number_of_paritions will be set accordingly.
+    size_t maximum_index_size{0};
+
+    //!\brief The number of partitions for the HIBF index.
+    size_t number_of_partitions{0};
+    //!\}
+
     /*!\name Configuration of size estimates
      * \{
      */
@@ -93,6 +113,9 @@ struct configuration
         archive(CEREAL_NVP(disable_sketch_output));
         archive(CEREAL_NVP(precomputed_files));
 
+        archive(CEREAL_NVP(maximum_index_size));
+        archive(CEREAL_NVP(number_of_partitions));
+
         archive(CEREAL_NVP(output_filename));
         archive(CEREAL_NVP(determine_best_tmax));
         archive(CEREAL_NVP(force_all_binnings));

diff --git a/include/chopper/layout/input.hpp b/include/chopper/layout/input.hpp
@@ -20,7 +20,8 @@ namespace chopper::layout
 {
 
 std::vector<std::vector<std::string>> read_filenames_from(std::istream & stream);
-std::tuple<std::vector<std::vector<std::string>>, configuration, seqan::hibf::layout::layout>
-read_layout_file(std::istream & stream);
+
+std::tuple<std::vector<std::vector<std::string>>, configuration, std::vector<seqan::hibf::layout::layout>>
+read_layouts_file(std::istream & stream);
 
 } // namespace chopper::layout
diff --git a/lib/hibf b/lib/hibf
+2 −7		.github/workflows/ci_iwyu.yml
+3 −4		README.md
+6 −3		include/hibf/contrib/aligned_allocator.hpp
+6 −5		include/hibf/hierarchical_interleaved_bloom_filter.hpp
+24 −160		include/hibf/interleaved_bloom_filter.hpp
+2 −0		include/hibf/layout/compute_layout.hpp
+1 −2		include/hibf/layout/data_store.hpp
+3 −4		include/hibf/layout/graph.hpp
+2 −1		include/hibf/layout/hierarchical_binning.hpp
+5 −6		include/hibf/layout/layout.hpp
+1 −1		include/hibf/layout/simple_binning.hpp
+7 −0		include/hibf/misc/bit_vector.hpp
+300 −0		include/hibf/misc/counting_vector.hpp
+1 −2		include/hibf/misc/insert_iterator.hpp
+61 −0		include/hibf/misc/partition.hpp
+2 −2		include/hibf/misc/print.hpp
+13 −1		include/hibf/platform.hpp
+5 −0		include/hibf/sketch/compute_sketches.hpp
+2 −3		include/hibf/sketch/estimate_kmer_counts.hpp
+0 −1		include/hibf/sketch/hyperloglog.hpp
+0 −1		include/hibf/sketch/toolbox.hpp
+4 −5		src/config.cpp
+9 −0		src/hierarchical_interleaved_bloom_filter.cpp
+25 −5		src/layout/compute_layout.cpp
+2 −2		src/layout/graph.cpp
+4 −2		src/layout/layout.cpp
+4 −4		src/misc/print.cpp
+34 −3		src/sketch/compute_sketches.cpp
+4 −3		src/sketch/hyperloglog.cpp
+11 −12		src/sketch/toolbox.cpp
+8 −8		test/documentation/DoxygenLayout.xml
+21 −1		test/documentation/doxygen-awesome/doxygen-awesome-tabs.js
+225 −78		test/documentation/doxygen-awesome/doxygen-awesome.css
+4 −4		test/documentation/hibf-doxygen-layout.cmake
+2 −2		test/documentation/hibf-doxygen.cmake
+1 −1		test/documentation/hibf_doxygen_cfg.in
+2 −0		test/include/hibf/test/bytes.hpp
+2 −2		test/include/hibf/test/sandboxed_path.hpp
+2 −3		test/include/hibf/test/tmp_directory.hpp
+3 −4		test/include/hibf/test/type_name_as_string.hpp
+0 −19		test/iwyu/mappings/gcc.stl.headers.imp
+0 −11		test/iwyu/mappings/gcc.symbols.imp
+5 −0		test/iwyu/mappings/iwyu.imp
+51 −21		test/iwyu/mappings/libcxx.imp
+28 −0		test/iwyu/mappings/stl.public.imp
+1 −2		test/performance/ibf/bit_vector_benchmark.cpp
+128 −96		test/performance/ibf/interleaved_bloom_filter_benchmark.cpp
+0 −1		test/performance/sketch/hyperloglog_benchmark.cpp
+1 −2		test/snippet/ibf/counting_agent.cpp
+2 −1		test/snippet/ibf/counting_vector.cpp
+3 −4		test/snippet/readme.cpp
+1 −2		test/snippet/test/tmp_directory.cpp
+3 −0		test/unit/hibf/CMakeLists.txt
+18 −0		test/unit/hibf/bit_vector_test.cpp
+0 −2		test/unit/hibf/build/bin_size_in_bits_test.cpp
+7 −0		test/unit/hibf/counting_vector_avx512_test.cpp
+197 −0		test/unit/hibf/counting_vector_test.cpp
+1 −1		test/unit/hibf/hierarchical_interleaved_bloom_filter_test.cpp
+7 −0		test/unit/hibf/interleaved_bloom_filter_avx512_test.cpp
+16 −10		test/unit/hibf/interleaved_bloom_filter_test.cpp
+15 −2		test/unit/hibf/layout/compute_layout_test.cpp
+50 −6		test/unit/hibf/layout/layout_test.cpp
+1 −2		test/unit/hibf/path_test.cpp
+4 −4		test/unit/hibf/print_test.cpp
+8 −8		test/unit/hibf/sketch/toolbox_test.cpp
+0 −1		test/unit/hibf/timer_test.cpp
+2 −2		test/unit/test/expect_range_eq_test.cpp
+1 −1		test/unit/test/expect_same_type_test.cpp
+2 −3		test/unit/test/file_access_test.cpp
+2 −3		test/unit/test/temporary_snippet_file_test.cpp