From ed3d7216e678d85e2ffed0dcf2cfe9bd99ee4cb7 Mon Sep 17 00:00:00 2001 From: Svenja Mehringer Date: Tue, 29 Aug 2023 08:45:19 +0200 Subject: [PATCH 1/8] [MISC] Move include/hibf/detail/layout/ -> include/hibf/layout --- include/hibf/detail/build/compute_kmers.hpp | 2 +- include/hibf/detail/build/initialise_build_tree.hpp | 2 +- include/hibf/detail/build/insert_into_ibf.hpp | 2 +- include/hibf/detail/build/node_data.hpp | 2 +- .../hibf/detail/build/update_content_node_data.hpp | 2 +- .../hibf/detail/build/update_header_node_data.hpp | 2 +- include/hibf/detail/build/update_user_bins.hpp | 2 +- include/hibf/detail/data_store.hpp | 2 +- .../{detail => }/layout/compute_fpr_correction.hpp | 0 include/hibf/{detail => }/layout/compute_layout.hpp | 4 ++-- include/hibf/{detail => }/layout/execute.hpp | 0 .../{detail => }/layout/hierarchical_binning.hpp | 0 include/hibf/{detail => }/layout/layout.hpp | 0 include/hibf/{detail => }/layout/print_matrix.hpp | 0 include/hibf/{detail => }/layout/simple_binning.hpp | 0 src/CMakeLists.txt | 12 ++++++------ src/detail/build/compute_kmers.cpp | 2 +- src/detail/build/initialise_build_tree.cpp | 2 +- src/detail/build/insert_into_ibf.cpp | 2 +- src/detail/build/update_content_node_data.cpp | 2 +- src/detail/build/update_header_node_data.cpp | 2 +- src/hierarchical_interleaved_bloom_filter.cpp | 6 +++--- src/{detail => }/layout/compute_fpr_correction.cpp | 4 ++-- src/{detail => }/layout/compute_layout.cpp | 7 ++++--- src/{detail => }/layout/execute.cpp | 9 +++++---- src/{detail => }/layout/hierarchical_binning.cpp | 6 +++--- src/{detail => }/layout/layout.cpp | 2 +- src/{detail => }/layout/simple_binning.cpp | 4 ++-- test/unit/hibf/detail/layout/fpr_correction_test.cpp | 2 +- .../hibf/detail/layout/hierarchical_binning_test.cpp | 6 +++--- test/unit/hibf/detail/layout/layout_test.cpp | 2 +- test/unit/hibf/detail/layout/simple_binning_test.cpp | 4 ++-- util/fpr_quality.cpp | 2 +- 33 files changed, 49 insertions(+), 47 deletions(-) rename include/hibf/{detail => }/layout/compute_fpr_correction.hpp (100%) rename include/hibf/{detail => }/layout/compute_layout.hpp (86%) rename include/hibf/{detail => }/layout/execute.hpp (100%) rename include/hibf/{detail => }/layout/hierarchical_binning.hpp (100%) rename include/hibf/{detail => }/layout/layout.hpp (100%) rename include/hibf/{detail => }/layout/print_matrix.hpp (100%) rename include/hibf/{detail => }/layout/simple_binning.hpp (100%) rename src/{detail => }/layout/compute_fpr_correction.cpp (86%) rename src/{detail => }/layout/compute_layout.cpp (90%) rename src/{detail => }/layout/execute.cpp (85%) rename src/{detail => }/layout/hierarchical_binning.cpp (98%) rename src/{detail => }/layout/layout.cpp (99%) rename src/{detail => }/layout/simple_binning.cpp (96%) diff --git a/include/hibf/detail/build/compute_kmers.hpp b/include/hibf/detail/build/compute_kmers.hpp index ecb3cd31..1b7af412 100644 --- a/include/hibf/detail/build/compute_kmers.hpp +++ b/include/hibf/detail/build/compute_kmers.hpp @@ -16,7 +16,7 @@ #include // for unordered_flat_set #include // for build_data -#include // for layout +#include // for layout namespace seqan::hibf { diff --git a/include/hibf/detail/build/initialise_build_tree.hpp b/include/hibf/detail/build/initialise_build_tree.hpp index 87bebd04..d217844e 100644 --- a/include/hibf/detail/build/initialise_build_tree.hpp +++ b/include/hibf/detail/build/initialise_build_tree.hpp @@ -15,7 +15,7 @@ #include // for ListDigraph #include // for node_data -#include // for layout +#include // for layout namespace seqan::hibf { diff --git a/include/hibf/detail/build/insert_into_ibf.hpp b/include/hibf/detail/build/insert_into_ibf.hpp index a139b845..ae21e8cd 100644 --- a/include/hibf/detail/build/insert_into_ibf.hpp +++ b/include/hibf/detail/build/insert_into_ibf.hpp @@ -12,7 +12,7 @@ #include // for unordered_flat_set #include // for build_data -#include // for layout +#include // for layout #include // for concurrent, timer #include // for interleaved_bloom_filter diff --git a/include/hibf/detail/build/node_data.hpp b/include/hibf/detail/build/node_data.hpp index 6dcd2d93..916d2a70 100644 --- a/include/hibf/detail/build/node_data.hpp +++ b/include/hibf/detail/build/node_data.hpp @@ -14,7 +14,7 @@ #include // for tie, operator==, tuple #include // for vector -#include // for operator==, layout +#include // for operator==, layout namespace seqan::hibf { diff --git a/include/hibf/detail/build/update_content_node_data.hpp b/include/hibf/detail/build/update_content_node_data.hpp index 4931d6f4..f3860c83 100644 --- a/include/hibf/detail/build/update_content_node_data.hpp +++ b/include/hibf/detail/build/update_content_node_data.hpp @@ -17,7 +17,7 @@ #include // for vector #include // for node_data -#include // for layout +#include // for layout namespace seqan::hibf { diff --git a/include/hibf/detail/build/update_header_node_data.hpp b/include/hibf/detail/build/update_header_node_data.hpp index 4dae3225..ee1023bc 100644 --- a/include/hibf/detail/build/update_header_node_data.hpp +++ b/include/hibf/detail/build/update_header_node_data.hpp @@ -17,7 +17,7 @@ #include // for vector #include // for node_data -#include // for layout +#include // for layout namespace seqan::hibf { diff --git a/include/hibf/detail/build/update_user_bins.hpp b/include/hibf/detail/build/update_user_bins.hpp index 56e29d64..3287dfe8 100644 --- a/include/hibf/detail/build/update_user_bins.hpp +++ b/include/hibf/detail/build/update_user_bins.hpp @@ -11,7 +11,7 @@ #include // for int64_t #include // for vector -#include // for layout +#include // for layout namespace seqan::hibf { diff --git a/include/hibf/detail/data_store.hpp b/include/hibf/detail/data_store.hpp index d1a08ada..a6209ae6 100644 --- a/include/hibf/detail/data_store.hpp +++ b/include/hibf/detail/data_store.hpp @@ -8,7 +8,7 @@ #include // for string #include // for vector -#include // for layout +#include // for layout #include // for hyperloglog namespace seqan::hibf diff --git a/include/hibf/detail/layout/compute_fpr_correction.hpp b/include/hibf/layout/compute_fpr_correction.hpp similarity index 100% rename from include/hibf/detail/layout/compute_fpr_correction.hpp rename to include/hibf/layout/compute_fpr_correction.hpp diff --git a/include/hibf/detail/layout/compute_layout.hpp b/include/hibf/layout/compute_layout.hpp similarity index 86% rename from include/hibf/detail/layout/compute_layout.hpp rename to include/hibf/layout/compute_layout.hpp index 050e941b..68571db1 100644 --- a/include/hibf/detail/layout/compute_layout.hpp +++ b/include/hibf/layout/compute_layout.hpp @@ -3,8 +3,8 @@ #include // for size_t #include // for vector -#include // for config -#include // for layout +#include // for config +#include // for layout #include // for hyperloglog namespace seqan::hibf::layout diff --git a/include/hibf/detail/layout/execute.hpp b/include/hibf/layout/execute.hpp similarity index 100% rename from include/hibf/detail/layout/execute.hpp rename to include/hibf/layout/execute.hpp diff --git a/include/hibf/detail/layout/hierarchical_binning.hpp b/include/hibf/layout/hierarchical_binning.hpp similarity index 100% rename from include/hibf/detail/layout/hierarchical_binning.hpp rename to include/hibf/layout/hierarchical_binning.hpp diff --git a/include/hibf/detail/layout/layout.hpp b/include/hibf/layout/layout.hpp similarity index 100% rename from include/hibf/detail/layout/layout.hpp rename to include/hibf/layout/layout.hpp diff --git a/include/hibf/detail/layout/print_matrix.hpp b/include/hibf/layout/print_matrix.hpp similarity index 100% rename from include/hibf/detail/layout/print_matrix.hpp rename to include/hibf/layout/print_matrix.hpp diff --git a/include/hibf/detail/layout/simple_binning.hpp b/include/hibf/layout/simple_binning.hpp similarity index 100% rename from include/hibf/detail/layout/simple_binning.hpp rename to include/hibf/layout/simple_binning.hpp diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt index a1f76fab..ec424ae2 100644 --- a/src/CMakeLists.txt +++ b/src/CMakeLists.txt @@ -1,12 +1,12 @@ set (HIBF_SOURCE_FILES hierarchical_interleaved_bloom_filter.cpp config.cpp - detail/layout/simple_binning.cpp - detail/layout/layout.cpp - detail/layout/execute.cpp - detail/layout/compute_fpr_correction.cpp - detail/layout/compute_layout.cpp - detail/layout/hierarchical_binning.cpp + layout/simple_binning.cpp + layout/layout.cpp + layout/execute.cpp + layout/compute_fpr_correction.cpp + layout/compute_layout.cpp + layout/hierarchical_binning.cpp detail/sketch/toolbox.cpp detail/sketch/hyperloglog.cpp detail/build/initialise_build_tree.cpp diff --git a/src/detail/build/compute_kmers.cpp b/src/detail/build/compute_kmers.cpp index 3b6c396d..4843b3b1 100644 --- a/src/detail/build/compute_kmers.cpp +++ b/src/detail/build/compute_kmers.cpp @@ -18,7 +18,7 @@ #include // for unordered_flat_set #include // for build_data #include // for compute_kmers -#include // for layout +#include // for layout #include // for concurrent, timer namespace seqan::hibf diff --git a/src/detail/build/initialise_build_tree.cpp b/src/detail/build/initialise_build_tree.cpp index a03bcce2..9c836f6c 100644 --- a/src/detail/build/initialise_build_tree.cpp +++ b/src/detail/build/initialise_build_tree.cpp @@ -19,7 +19,7 @@ #include // for node_data #include // for update_content_node_data #include // for update_header_node_data -#include // for layout +#include // for layout namespace seqan::hibf { diff --git a/src/detail/build/insert_into_ibf.cpp b/src/detail/build/insert_into_ibf.cpp index 6ef1724c..6d7457a1 100644 --- a/src/detail/build/insert_into_ibf.cpp +++ b/src/detail/build/insert_into_ibf.cpp @@ -18,7 +18,7 @@ #include // for operator| #include // for build_data #include // for insert_into_ibf -#include // for layout +#include // for layout #include // for concurrent, timer #include // for interleaved_bloom_filter, bin_index diff --git a/src/detail/build/update_content_node_data.cpp b/src/detail/build/update_content_node_data.cpp index 5b1bb724..1d0ad110 100644 --- a/src/detail/build/update_content_node_data.cpp +++ b/src/detail/build/update_content_node_data.cpp @@ -22,7 +22,7 @@ #include // for node_data #include // for update_content_node_data -#include // for layout +#include // for layout namespace seqan::hibf { diff --git a/src/detail/build/update_header_node_data.cpp b/src/detail/build/update_header_node_data.cpp index 91ce2b31..e35054f3 100644 --- a/src/detail/build/update_header_node_data.cpp +++ b/src/detail/build/update_header_node_data.cpp @@ -23,7 +23,7 @@ #include // for node_data #include // for update_header_node_data -#include // for layout +#include // for layout namespace seqan::hibf { diff --git a/src/hierarchical_interleaved_bloom_filter.cpp b/src/hierarchical_interleaved_bloom_filter.cpp index 8116c49b..afdba6c8 100644 --- a/src/hierarchical_interleaved_bloom_filter.cpp +++ b/src/hierarchical_interleaved_bloom_filter.cpp @@ -28,9 +28,9 @@ #include // for node_data #include // for update_parent_kmers #include // for update_user_bins -#include // for compute_fpr_correction -#include // for compute_layout -#include // for layout +#include // for compute_fpr_correction +#include // for compute_layout +#include // for layout #include // for hierarchical_interleaved_bloom_filter #include // for interleaved_bloom_filter #include // for user_bins_type diff --git a/src/detail/layout/compute_fpr_correction.cpp b/src/layout/compute_fpr_correction.cpp similarity index 86% rename from src/detail/layout/compute_fpr_correction.cpp rename to src/layout/compute_fpr_correction.cpp index 440169ef..befbc3f3 100644 --- a/src/detail/layout/compute_fpr_correction.cpp +++ b/src/layout/compute_fpr_correction.cpp @@ -3,8 +3,8 @@ #include // for size_t #include // for vector -#include // for compute_fpr_correction -#include // for next_multiple_of_64 +#include // for compute_fpr_correction +#include // for next_multiple_of_64 namespace seqan::hibf::layout { diff --git a/src/detail/layout/compute_layout.cpp b/src/layout/compute_layout.cpp similarity index 90% rename from src/detail/layout/compute_layout.cpp rename to src/layout/compute_layout.cpp index e61acd34..23a9c80c 100644 --- a/src/detail/layout/compute_layout.cpp +++ b/src/layout/compute_layout.cpp @@ -9,9 +9,10 @@ #include // for config #include // for unordered_flat_set #include // for data_store -#include // for compute_layout -#include // for execute -#include // for layout +#include // for compute_layout +#include // for data_store +#include // for execute +#include // for layout #include // for estimate_kmer_counts #include // for hyperloglog diff --git a/src/detail/layout/execute.cpp b/src/layout/execute.cpp similarity index 85% rename from src/detail/layout/execute.cpp rename to src/layout/execute.cpp index 72318f59..a1218e05 100644 --- a/src/detail/layout/execute.cpp +++ b/src/layout/execute.cpp @@ -7,10 +7,11 @@ #include // for config #include // for data_store -#include // for compute_fpr_correction -#include // for execute -#include // for hierarchical_binning -#include // for next_multiple_of_64 +#include // for compute_fpr_correction +#include // for data_store +#include // for execute +#include // for hierarchical_binning +#include // for next_multiple_of_64 namespace seqan::hibf { diff --git a/src/detail/layout/hierarchical_binning.cpp b/src/layout/hierarchical_binning.cpp similarity index 98% rename from src/detail/layout/hierarchical_binning.cpp rename to src/layout/hierarchical_binning.cpp index 5c32438f..62b485aa 100644 --- a/src/detail/layout/hierarchical_binning.cpp +++ b/src/layout/hierarchical_binning.cpp @@ -11,9 +11,9 @@ #include // for config #include // for data_store -#include // for hierarchical_binning -#include // for layout -#include // for simple_binning +#include // for hierarchical_binning +#include // for layout +#include // for simple_binning #include // for toolbox #include // for next_multiple_of_64 #include // for HIBF_WORKAROUND_GCC_BOGUS_MEMCPY diff --git a/src/detail/layout/layout.cpp b/src/layout/layout.cpp similarity index 99% rename from src/detail/layout/layout.cpp rename to src/layout/layout.cpp index 79189014..b2f1387e 100644 --- a/src/detail/layout/layout.cpp +++ b/src/layout/layout.cpp @@ -10,7 +10,7 @@ #include #include -#include +#include #include namespace seqan::hibf::layout diff --git a/src/detail/layout/simple_binning.cpp b/src/layout/simple_binning.cpp similarity index 96% rename from src/detail/layout/simple_binning.cpp rename to src/layout/simple_binning.cpp index a7544136..db182964 100644 --- a/src/detail/layout/simple_binning.cpp +++ b/src/layout/simple_binning.cpp @@ -5,8 +5,8 @@ #include // for vector #include // for data_store -#include // for layout -#include // for simple_binning +#include // for layout +#include // for simple_binning namespace seqan::hibf::layout { diff --git a/test/unit/hibf/detail/layout/fpr_correction_test.cpp b/test/unit/hibf/detail/layout/fpr_correction_test.cpp index 26fc09fe..0bfebaa6 100644 --- a/test/unit/hibf/detail/layout/fpr_correction_test.cpp +++ b/test/unit/hibf/detail/layout/fpr_correction_test.cpp @@ -3,7 +3,7 @@ #include // for size_t #include // for vector, allocator -#include // for compute_fpr_correction +#include // for compute_fpr_correction TEST(fp_correction_test, one_bin) { diff --git a/test/unit/hibf/detail/layout/hierarchical_binning_test.cpp b/test/unit/hibf/detail/layout/hierarchical_binning_test.cpp index 7a84f73e..8ad85979 100644 --- a/test/unit/hibf/detail/layout/hierarchical_binning_test.cpp +++ b/test/unit/hibf/detail/layout/hierarchical_binning_test.cpp @@ -5,9 +5,9 @@ #include // for config #include // for data_store -#include // for compute_fpr_correction -#include // for hierarchical_binning -#include // for layout +#include // for compute_fpr_correction +#include // for hierarchical_binning +#include // for layout #include // for expect_range_eq, EXPECT_RANGE_EQ TEST(hierarchical_binning_test, small_example) diff --git a/test/unit/hibf/detail/layout/layout_test.cpp b/test/unit/hibf/detail/layout/layout_test.cpp index aeddbe3b..1b2868e8 100644 --- a/test/unit/hibf/detail/layout/layout_test.cpp +++ b/test/unit/hibf/detail/layout/layout_test.cpp @@ -6,7 +6,7 @@ #include // for operator<< #include // for vector -#include // for layout, operator<< +#include // for layout, operator<< #include // for expect_range_eq, EXPECT_RANGE_EQ TEST(layout_test, printing_max_bins) diff --git a/test/unit/hibf/detail/layout/simple_binning_test.cpp b/test/unit/hibf/detail/layout/simple_binning_test.cpp index 0038f6cf..6673b5c1 100644 --- a/test/unit/hibf/detail/layout/simple_binning_test.cpp +++ b/test/unit/hibf/detail/layout/simple_binning_test.cpp @@ -5,8 +5,8 @@ #include // for allocator, vector #include // for data_store -#include // for layout -#include // for simple_binning +#include // for layout +#include // for simple_binning #include // for expect_range_eq, EXPECT_RANGE_EQ TEST(simple_binning_test, small_example) diff --git a/util/fpr_quality.cpp b/util/fpr_quality.cpp index 9e0d2ccb..043f265d 100644 --- a/util/fpr_quality.cpp +++ b/util/fpr_quality.cpp @@ -10,7 +10,7 @@ #include #include -#include +#include #include #include From 3170b67200bc5c15ced85795302ae75f4685a395 Mon Sep 17 00:00:00 2001 From: Svenja Mehringer Date: Tue, 29 Aug 2023 08:46:37 +0200 Subject: [PATCH 2/8] [MISC] mv include/hibf/detail/build/ -> include/hibf/build --- .../{detail => }/build/bin_size_in_bits.hpp | 0 .../hibf/{detail => }/build/build_data.hpp | 6 +++--- .../build/chopper_pack_record.hpp | 0 .../hibf/{detail => }/build/compute_kmers.hpp | 6 +++--- .../hibf/{detail => }/build/construct_ibf.hpp | 2 +- .../build/initialise_build_tree.hpp | 2 +- .../{detail => }/build/insert_into_ibf.hpp | 4 ++-- include/hibf/{detail => }/build/node_data.hpp | 0 .../build/update_content_node_data.hpp | 2 +- .../build/update_header_node_data.hpp | 2 +- .../build/update_parent_kmers.hpp | 0 .../{detail => }/build/update_user_bins.hpp | 0 src/CMakeLists.txt | 12 +++++------ src/{detail => }/build/compute_kmers.cpp | 10 +++++----- src/{detail => }/build/construct_ibf.cpp | 20 +++++++++---------- .../build/initialise_build_tree.cpp | 8 ++++---- src/{detail => }/build/insert_into_ibf.cpp | 6 +++--- .../build/update_content_node_data.cpp | 4 ++-- .../build/update_header_node_data.cpp | 4 ++-- src/hierarchical_interleaved_bloom_filter.cpp | 19 ++++++++---------- util/fpr_quality.cpp | 3 +-- 21 files changed, 53 insertions(+), 57 deletions(-) rename include/hibf/{detail => }/build/bin_size_in_bits.hpp (100%) rename include/hibf/{detail => }/build/build_data.hpp (89%) rename include/hibf/{detail => }/build/chopper_pack_record.hpp (100%) rename include/hibf/{detail => }/build/compute_kmers.hpp (83%) rename include/hibf/{detail => }/build/construct_ibf.hpp (95%) rename include/hibf/{detail => }/build/initialise_build_tree.hpp (94%) rename include/hibf/{detail => }/build/insert_into_ibf.hpp (92%) rename include/hibf/{detail => }/build/node_data.hpp (100%) rename include/hibf/{detail => }/build/update_content_node_data.hpp (94%) rename include/hibf/{detail => }/build/update_header_node_data.hpp (94%) rename include/hibf/{detail => }/build/update_parent_kmers.hpp (100%) rename include/hibf/{detail => }/build/update_user_bins.hpp (100%) rename src/{detail => }/build/compute_kmers.cpp (79%) rename src/{detail => }/build/construct_ibf.cpp (77%) rename src/{detail => }/build/initialise_build_tree.cpp (81%) rename src/{detail => }/build/insert_into_ibf.cpp (94%) rename src/{detail => }/build/update_content_node_data.cpp (95%) rename src/{detail => }/build/update_header_node_data.cpp (94%) diff --git a/include/hibf/detail/build/bin_size_in_bits.hpp b/include/hibf/build/bin_size_in_bits.hpp similarity index 100% rename from include/hibf/detail/build/bin_size_in_bits.hpp rename to include/hibf/build/bin_size_in_bits.hpp diff --git a/include/hibf/detail/build/build_data.hpp b/include/hibf/build/build_data.hpp similarity index 89% rename from include/hibf/detail/build/build_data.hpp rename to include/hibf/build/build_data.hpp index 6e0ea2d9..8a49ceb4 100644 --- a/include/hibf/detail/build/build_data.hpp +++ b/include/hibf/build/build_data.hpp @@ -13,9 +13,9 @@ #include // for size_t #include // for vector -#include // for config -#include // for node_data -#include // for concurrent, timer +#include // for node_data +#include // for config +#include // for concurrent, timer namespace seqan::hibf { diff --git a/include/hibf/detail/build/chopper_pack_record.hpp b/include/hibf/build/chopper_pack_record.hpp similarity index 100% rename from include/hibf/detail/build/chopper_pack_record.hpp rename to include/hibf/build/chopper_pack_record.hpp diff --git a/include/hibf/detail/build/compute_kmers.hpp b/include/hibf/build/compute_kmers.hpp similarity index 83% rename from include/hibf/detail/build/compute_kmers.hpp rename to include/hibf/build/compute_kmers.hpp index 1b7af412..77823588 100644 --- a/include/hibf/detail/build/compute_kmers.hpp +++ b/include/hibf/build/compute_kmers.hpp @@ -14,9 +14,9 @@ #include // for uint64_t -#include // for unordered_flat_set -#include // for build_data -#include // for layout +#include // for build_data +#include // for unordered_flat_set +#include // for layout namespace seqan::hibf { diff --git a/include/hibf/detail/build/construct_ibf.hpp b/include/hibf/build/construct_ibf.hpp similarity index 95% rename from include/hibf/detail/build/construct_ibf.hpp rename to include/hibf/build/construct_ibf.hpp index 7599e070..3c982c05 100644 --- a/include/hibf/detail/build/construct_ibf.hpp +++ b/include/hibf/build/construct_ibf.hpp @@ -12,8 +12,8 @@ #include // for uint64_t #include // for size_t +#include // for build_data #include // for unordered_flat_set -#include // for build_data #include // for interleaved_bloom_filter namespace seqan::hibf diff --git a/include/hibf/detail/build/initialise_build_tree.hpp b/include/hibf/build/initialise_build_tree.hpp similarity index 94% rename from include/hibf/detail/build/initialise_build_tree.hpp rename to include/hibf/build/initialise_build_tree.hpp index d217844e..8e0abb3e 100644 --- a/include/hibf/detail/build/initialise_build_tree.hpp +++ b/include/hibf/build/initialise_build_tree.hpp @@ -14,7 +14,7 @@ #include // for ListDigraph -#include // for node_data +#include // for node_data #include // for layout namespace seqan::hibf diff --git a/include/hibf/detail/build/insert_into_ibf.hpp b/include/hibf/build/insert_into_ibf.hpp similarity index 92% rename from include/hibf/detail/build/insert_into_ibf.hpp rename to include/hibf/build/insert_into_ibf.hpp index ae21e8cd..85a1d1d6 100644 --- a/include/hibf/detail/build/insert_into_ibf.hpp +++ b/include/hibf/build/insert_into_ibf.hpp @@ -10,11 +10,11 @@ #include // for uint64_t #include // for size_t +#include // for build_data #include // for unordered_flat_set -#include // for build_data -#include // for layout #include // for concurrent, timer #include // for interleaved_bloom_filter +#include // for layout namespace seqan::hibf { diff --git a/include/hibf/detail/build/node_data.hpp b/include/hibf/build/node_data.hpp similarity index 100% rename from include/hibf/detail/build/node_data.hpp rename to include/hibf/build/node_data.hpp diff --git a/include/hibf/detail/build/update_content_node_data.hpp b/include/hibf/build/update_content_node_data.hpp similarity index 94% rename from include/hibf/detail/build/update_content_node_data.hpp rename to include/hibf/build/update_content_node_data.hpp index f3860c83..8691544d 100644 --- a/include/hibf/detail/build/update_content_node_data.hpp +++ b/include/hibf/build/update_content_node_data.hpp @@ -16,7 +16,7 @@ #include // for vector -#include // for node_data +#include // for node_data #include // for layout namespace seqan::hibf diff --git a/include/hibf/detail/build/update_header_node_data.hpp b/include/hibf/build/update_header_node_data.hpp similarity index 94% rename from include/hibf/detail/build/update_header_node_data.hpp rename to include/hibf/build/update_header_node_data.hpp index ee1023bc..ab4a923c 100644 --- a/include/hibf/detail/build/update_header_node_data.hpp +++ b/include/hibf/build/update_header_node_data.hpp @@ -16,7 +16,7 @@ #include // for vector -#include // for node_data +#include // for node_data #include // for layout namespace seqan::hibf diff --git a/include/hibf/detail/build/update_parent_kmers.hpp b/include/hibf/build/update_parent_kmers.hpp similarity index 100% rename from include/hibf/detail/build/update_parent_kmers.hpp rename to include/hibf/build/update_parent_kmers.hpp diff --git a/include/hibf/detail/build/update_user_bins.hpp b/include/hibf/build/update_user_bins.hpp similarity index 100% rename from include/hibf/detail/build/update_user_bins.hpp rename to include/hibf/build/update_user_bins.hpp diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt index ec424ae2..6ee38773 100644 --- a/src/CMakeLists.txt +++ b/src/CMakeLists.txt @@ -9,12 +9,12 @@ set (HIBF_SOURCE_FILES layout/hierarchical_binning.cpp detail/sketch/toolbox.cpp detail/sketch/hyperloglog.cpp - detail/build/initialise_build_tree.cpp - detail/build/insert_into_ibf.cpp - detail/build/compute_kmers.cpp - detail/build/update_header_node_data.cpp - detail/build/construct_ibf.cpp - detail/build/update_content_node_data.cpp) + build/initialise_build_tree.cpp + build/insert_into_ibf.cpp + build/compute_kmers.cpp + build/update_header_node_data.cpp + build/construct_ibf.cpp + build/update_content_node_data.cpp) add_library (hibf STATIC ${HIBF_SOURCE_FILES}) add_library (seqan::hibf ALIAS hibf) diff --git a/src/detail/build/compute_kmers.cpp b/src/build/compute_kmers.cpp similarity index 79% rename from src/detail/build/compute_kmers.cpp rename to src/build/compute_kmers.cpp index 4843b3b1..47d45952 100644 --- a/src/detail/build/compute_kmers.cpp +++ b/src/build/compute_kmers.cpp @@ -14,12 +14,12 @@ #include // for function #include // for inserter -#include // for config -#include // for unordered_flat_set -#include // for build_data -#include // for compute_kmers +#include // for build_data +#include // for compute_kmers +#include // for config +#include // for unordered_flat_set +#include // for concurrent, timer #include // for layout -#include // for concurrent, timer namespace seqan::hibf { diff --git a/src/detail/build/construct_ibf.cpp b/src/build/construct_ibf.cpp similarity index 77% rename from src/detail/build/construct_ibf.cpp rename to src/build/construct_ibf.cpp index 2049e528..e4d255e6 100644 --- a/src/detail/build/construct_ibf.cpp +++ b/src/build/construct_ibf.cpp @@ -13,16 +13,16 @@ #include // for size_t #include // for vector -#include // for config -#include // for unordered_flat_set -#include // for bin_size_in_bits -#include // for build_data -#include // for construct_ibf -#include // for insert_into_ibf -#include // for node_data -#include // for update_parent_kmers -#include // for concurrent, timer -#include // for interleaved_bloom_filter, bin_count, bin_size, hash_fun... +#include // for bin_size_in_bits +#include // for build_data +#include // for construct_ibf +#include // for insert_into_ibf +#include // for node_data +#include // for update_parent_kmers +#include // for config +#include // for unordered_flat_set +#include // for concurrent, timer +#include // for interleaved_bloom_filter, bin_count, bin_size, hash_fun... namespace seqan::hibf { diff --git a/src/detail/build/initialise_build_tree.cpp b/src/build/initialise_build_tree.cpp similarity index 81% rename from src/detail/build/initialise_build_tree.cpp rename to src/build/initialise_build_tree.cpp index 9c836f6c..6ffbe8c3 100644 --- a/src/detail/build/initialise_build_tree.cpp +++ b/src/build/initialise_build_tree.cpp @@ -15,10 +15,10 @@ #include // for move -#include // for initialise_build_tree -#include // for node_data -#include // for update_content_node_data -#include // for update_header_node_data +#include // for initialise_build_tree +#include // for node_data +#include // for update_content_node_data +#include // for update_header_node_data #include // for layout namespace seqan::hibf diff --git a/src/detail/build/insert_into_ibf.cpp b/src/build/insert_into_ibf.cpp similarity index 94% rename from src/detail/build/insert_into_ibf.cpp rename to src/build/insert_into_ibf.cpp index 6d7457a1..b0b745f7 100644 --- a/src/detail/build/insert_into_ibf.cpp +++ b/src/build/insert_into_ibf.cpp @@ -12,15 +12,15 @@ #include // for inserter, counted_iterator #include // for all_t, operator== +#include // for build_data +#include // for insert_into_ibf #include // for config #include // for unordered_flat_set #include // for chunk_view, operator==, chunk, chunk_fn #include // for operator| -#include // for build_data -#include // for insert_into_ibf -#include // for layout #include // for concurrent, timer #include // for interleaved_bloom_filter, bin_index +#include // for layout namespace seqan::hibf { diff --git a/src/detail/build/update_content_node_data.cpp b/src/build/update_content_node_data.cpp similarity index 95% rename from src/detail/build/update_content_node_data.cpp rename to src/build/update_content_node_data.cpp index 1d0ad110..187cc44b 100644 --- a/src/detail/build/update_content_node_data.cpp +++ b/src/build/update_content_node_data.cpp @@ -20,8 +20,8 @@ #include // for move #include // for vector -#include // for node_data -#include // for update_content_node_data +#include // for node_data +#include // for update_content_node_data #include // for layout namespace seqan::hibf diff --git a/src/detail/build/update_header_node_data.cpp b/src/build/update_header_node_data.cpp similarity index 94% rename from src/detail/build/update_header_node_data.cpp rename to src/build/update_header_node_data.cpp index e35054f3..88cd0eae 100644 --- a/src/detail/build/update_header_node_data.cpp +++ b/src/build/update_header_node_data.cpp @@ -21,8 +21,8 @@ #include // for move #include // for vector -#include // for node_data -#include // for update_header_node_data +#include // for node_data +#include // for update_header_node_data #include // for layout namespace seqan::hibf diff --git a/src/hierarchical_interleaved_bloom_filter.cpp b/src/hierarchical_interleaved_bloom_filter.cpp index afdba6c8..8bb1cca1 100644 --- a/src/hierarchical_interleaved_bloom_filter.cpp +++ b/src/hierarchical_interleaved_bloom_filter.cpp @@ -18,19 +18,16 @@ #include // for move #include // for vector +#include // for build_data +#include // for compute_kmers +#include // for construct_ibf +#include // for initialise_build_tree +#include // for insert_into_ibf +#include // for node_data +#include // for update_parent_kmers +#include // for update_user_bins #include // for config #include // for unordered_flat_set -#include // for build_data -#include // for compute_kmers -#include // for construct_ibf -#include // for initialise_build_tree -#include // for insert_into_ibf -#include // for node_data -#include // for update_parent_kmers -#include // for update_user_bins -#include // for compute_fpr_correction -#include // for compute_layout -#include // for layout #include // for hierarchical_interleaved_bloom_filter #include // for interleaved_bloom_filter #include // for user_bins_type diff --git a/util/fpr_quality.cpp b/util/fpr_quality.cpp index 043f265d..5589c6a1 100644 --- a/util/fpr_quality.cpp +++ b/util/fpr_quality.cpp @@ -8,9 +8,8 @@ #include #include +#include #include -#include -#include #include #include From a3abb5862db5fd7eaf9bf17ebad3541fc9857caf Mon Sep 17 00:00:00 2001 From: Svenja Mehringer Date: Tue, 29 Aug 2023 08:51:04 +0200 Subject: [PATCH 3/8] [TEST] mv test/unit/hibf/detail/layout/ -> test/unit/hibf/layout/ --- src/hierarchical_interleaved_bloom_filter.cpp | 3 +++ test/unit/hibf/{detail => }/layout/CMakeLists.txt | 0 test/unit/hibf/{detail => }/layout/fpr_correction_test.cpp | 0 .../hibf/{detail => }/layout/hierarchical_binning_test.cpp | 3 ++- test/unit/hibf/{detail => }/layout/layout_test.cpp | 2 +- test/unit/hibf/{detail => }/layout/simple_binning_test.cpp | 2 +- util/fpr_quality.cpp | 1 + 7 files changed, 8 insertions(+), 3 deletions(-) rename test/unit/hibf/{detail => }/layout/CMakeLists.txt (100%) rename test/unit/hibf/{detail => }/layout/fpr_correction_test.cpp (100%) rename test/unit/hibf/{detail => }/layout/hierarchical_binning_test.cpp (98%) rename test/unit/hibf/{detail => }/layout/layout_test.cpp (98%) rename test/unit/hibf/{detail => }/layout/simple_binning_test.cpp (96%) diff --git a/src/hierarchical_interleaved_bloom_filter.cpp b/src/hierarchical_interleaved_bloom_filter.cpp index 8bb1cca1..ec97e47f 100644 --- a/src/hierarchical_interleaved_bloom_filter.cpp +++ b/src/hierarchical_interleaved_bloom_filter.cpp @@ -30,6 +30,9 @@ #include // for unordered_flat_set #include // for hierarchical_interleaved_bloom_filter #include // for interleaved_bloom_filter +#include // for compute_fpr_correction +#include // for compute_layout +#include // for layout #include // for user_bins_type namespace seqan::hibf diff --git a/test/unit/hibf/detail/layout/CMakeLists.txt b/test/unit/hibf/layout/CMakeLists.txt similarity index 100% rename from test/unit/hibf/detail/layout/CMakeLists.txt rename to test/unit/hibf/layout/CMakeLists.txt diff --git a/test/unit/hibf/detail/layout/fpr_correction_test.cpp b/test/unit/hibf/layout/fpr_correction_test.cpp similarity index 100% rename from test/unit/hibf/detail/layout/fpr_correction_test.cpp rename to test/unit/hibf/layout/fpr_correction_test.cpp diff --git a/test/unit/hibf/detail/layout/hierarchical_binning_test.cpp b/test/unit/hibf/layout/hierarchical_binning_test.cpp similarity index 98% rename from test/unit/hibf/detail/layout/hierarchical_binning_test.cpp rename to test/unit/hibf/layout/hierarchical_binning_test.cpp index 8ad85979..e9b0781d 100644 --- a/test/unit/hibf/detail/layout/hierarchical_binning_test.cpp +++ b/test/unit/hibf/layout/hierarchical_binning_test.cpp @@ -6,9 +6,10 @@ #include // for config #include // for data_store #include // for compute_fpr_correction +#include // for data_store #include // for hierarchical_binning #include // for layout -#include // for expect_range_eq, EXPECT_RANGE_EQ +#include // for expect_range_eq, EXPECT_RANGE_EQ TEST(hierarchical_binning_test, small_example) { diff --git a/test/unit/hibf/detail/layout/layout_test.cpp b/test/unit/hibf/layout/layout_test.cpp similarity index 98% rename from test/unit/hibf/detail/layout/layout_test.cpp rename to test/unit/hibf/layout/layout_test.cpp index 1b2868e8..b615da50 100644 --- a/test/unit/hibf/detail/layout/layout_test.cpp +++ b/test/unit/hibf/layout/layout_test.cpp @@ -6,7 +6,7 @@ #include // for operator<< #include // for vector -#include // for layout, operator<< +#include // for layout, operator<< #include // for expect_range_eq, EXPECT_RANGE_EQ TEST(layout_test, printing_max_bins) diff --git a/test/unit/hibf/detail/layout/simple_binning_test.cpp b/test/unit/hibf/layout/simple_binning_test.cpp similarity index 96% rename from test/unit/hibf/detail/layout/simple_binning_test.cpp rename to test/unit/hibf/layout/simple_binning_test.cpp index 6673b5c1..5db5ff8d 100644 --- a/test/unit/hibf/detail/layout/simple_binning_test.cpp +++ b/test/unit/hibf/layout/simple_binning_test.cpp @@ -7,7 +7,7 @@ #include // for data_store #include // for layout #include // for simple_binning -#include // for expect_range_eq, EXPECT_RANGE_EQ +#include // for expect_range_eq, EXPECT_RANGE_EQ TEST(simple_binning_test, small_example) { diff --git a/util/fpr_quality.cpp b/util/fpr_quality.cpp index 5589c6a1..a56fa619 100644 --- a/util/fpr_quality.cpp +++ b/util/fpr_quality.cpp @@ -11,6 +11,7 @@ #include #include #include +#include #include From 0cca455c22d9f65ab7369b4e374a694b4dd49e7c Mon Sep 17 00:00:00 2001 From: Svenja Mehringer Date: Tue, 29 Aug 2023 08:53:23 +0200 Subject: [PATCH 4/8] [MISC] mv detail/sketch/ -> sketch/ --- include/hibf/detail/data_store.hpp | 2 +- include/hibf/layout/compute_layout.hpp | 2 +- include/hibf/{detail => }/sketch/estimate_kmer_counts.hpp | 2 +- include/hibf/{detail => }/sketch/hyperloglog.hpp | 0 include/hibf/{detail => }/sketch/toolbox.hpp | 4 ++-- src/CMakeLists.txt | 4 ++-- src/layout/compute_layout.cpp | 4 ++-- src/layout/hierarchical_binning.cpp | 6 +++--- src/{detail => }/sketch/hyperloglog.cpp | 2 +- src/{detail => }/sketch/toolbox.cpp | 6 +++--- test/unit/hibf/detail/sketch/estimate_kmer_counts_test.cpp | 4 ++-- test/unit/hibf/detail/sketch/hyperloglog_test.cpp | 2 +- test/unit/hibf/detail/sketch/toolbox_test.cpp | 4 ++-- 13 files changed, 21 insertions(+), 21 deletions(-) rename include/hibf/{detail => }/sketch/estimate_kmer_counts.hpp (87%) rename include/hibf/{detail => }/sketch/hyperloglog.hpp (100%) rename include/hibf/{detail => }/sketch/toolbox.hpp (98%) rename src/{detail => }/sketch/hyperloglog.cpp (99%) rename src/{detail => }/sketch/toolbox.cpp (98%) diff --git a/include/hibf/detail/data_store.hpp b/include/hibf/detail/data_store.hpp index a6209ae6..7b474dcd 100644 --- a/include/hibf/detail/data_store.hpp +++ b/include/hibf/detail/data_store.hpp @@ -9,7 +9,7 @@ #include // for vector #include // for layout -#include // for hyperloglog +#include // for hyperloglog namespace seqan::hibf { diff --git a/include/hibf/layout/compute_layout.hpp b/include/hibf/layout/compute_layout.hpp index 68571db1..7e3d4e32 100644 --- a/include/hibf/layout/compute_layout.hpp +++ b/include/hibf/layout/compute_layout.hpp @@ -5,7 +5,7 @@ #include // for config #include // for layout -#include // for hyperloglog +#include // for hyperloglog namespace seqan::hibf::layout { diff --git a/include/hibf/detail/sketch/estimate_kmer_counts.hpp b/include/hibf/sketch/estimate_kmer_counts.hpp similarity index 87% rename from include/hibf/detail/sketch/estimate_kmer_counts.hpp rename to include/hibf/sketch/estimate_kmer_counts.hpp index 5e6bbcfa..e32e9a62 100644 --- a/include/hibf/detail/sketch/estimate_kmer_counts.hpp +++ b/include/hibf/sketch/estimate_kmer_counts.hpp @@ -3,7 +3,7 @@ #include // for size_t #include // for vector -#include // for hyperloglog +#include // for hyperloglog namespace seqan::hibf::sketch { diff --git a/include/hibf/detail/sketch/hyperloglog.hpp b/include/hibf/sketch/hyperloglog.hpp similarity index 100% rename from include/hibf/detail/sketch/hyperloglog.hpp rename to include/hibf/sketch/hyperloglog.hpp diff --git a/include/hibf/detail/sketch/toolbox.hpp b/include/hibf/sketch/toolbox.hpp similarity index 98% rename from include/hibf/detail/sketch/toolbox.hpp rename to include/hibf/sketch/toolbox.hpp index bfd5162b..63f4af2e 100644 --- a/include/hibf/detail/sketch/toolbox.hpp +++ b/include/hibf/sketch/toolbox.hpp @@ -7,8 +7,8 @@ #include // for priority_queue #include // for vector -#include // for unordered_flat_map -#include // for hyperloglog +#include // for unordered_flat_map +#include // for hyperloglog namespace seqan::hibf::sketch::toolbox { diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt index 6ee38773..dccbd3a6 100644 --- a/src/CMakeLists.txt +++ b/src/CMakeLists.txt @@ -7,8 +7,8 @@ set (HIBF_SOURCE_FILES layout/compute_fpr_correction.cpp layout/compute_layout.cpp layout/hierarchical_binning.cpp - detail/sketch/toolbox.cpp - detail/sketch/hyperloglog.cpp + sketch/toolbox.cpp + sketch/hyperloglog.cpp build/initialise_build_tree.cpp build/insert_into_ibf.cpp build/compute_kmers.cpp diff --git a/src/layout/compute_layout.cpp b/src/layout/compute_layout.cpp index 23a9c80c..db942779 100644 --- a/src/layout/compute_layout.cpp +++ b/src/layout/compute_layout.cpp @@ -13,8 +13,8 @@ #include // for data_store #include // for execute #include // for layout -#include // for estimate_kmer_counts -#include // for hyperloglog +#include // for estimate_kmer_counts +#include // for hyperloglog namespace seqan::hibf::layout { diff --git a/src/layout/hierarchical_binning.cpp b/src/layout/hierarchical_binning.cpp index 62b485aa..ece86686 100644 --- a/src/layout/hierarchical_binning.cpp +++ b/src/layout/hierarchical_binning.cpp @@ -14,9 +14,9 @@ #include // for hierarchical_binning #include // for layout #include // for simple_binning -#include // for toolbox -#include // for next_multiple_of_64 -#include // for HIBF_WORKAROUND_GCC_BOGUS_MEMCPY +#include // for next_multiple_of_64 +#include // for HIBF_WORKAROUND_GCC_BOGUS_MEMCPY +#include // for toolbox namespace seqan::hibf::layout { diff --git a/src/detail/sketch/hyperloglog.cpp b/src/sketch/hyperloglog.cpp similarity index 99% rename from src/detail/sketch/hyperloglog.cpp rename to src/sketch/hyperloglog.cpp index 295c426c..9f359a96 100644 --- a/src/detail/sketch/hyperloglog.cpp +++ b/src/sketch/hyperloglog.cpp @@ -13,7 +13,7 @@ #include // for aligned_allocator #include // for XXH_INLINE_XXH3_64bits, XXH3_64bits -#include // for hyperloglog +#include // for hyperloglog #include // for simde_mm256_add_ps, simde_mm256_set_ps, simde__m256i, simde_mm... #include // for simde_mm256_max_epu8 diff --git a/src/detail/sketch/toolbox.cpp b/src/sketch/toolbox.cpp similarity index 98% rename from src/detail/sketch/toolbox.cpp rename to src/sketch/toolbox.cpp index 860d15c3..d5b8546a 100644 --- a/src/detail/sketch/toolbox.cpp +++ b/src/sketch/toolbox.cpp @@ -10,9 +10,9 @@ #include // for swap, move #include // for vector -#include // for unordered_flat_map, pair -#include // for hyperloglog -#include // for clustering_node, entry, neighbor, prio_queue, distance_matrix +#include // for unordered_flat_map, pair +#include // for hyperloglog +#include // for clustering_node, entry, neighbor, prio_queue, distance_matrix namespace seqan::hibf::sketch::toolbox { diff --git a/test/unit/hibf/detail/sketch/estimate_kmer_counts_test.cpp b/test/unit/hibf/detail/sketch/estimate_kmer_counts_test.cpp index d7b64543..345d7d58 100644 --- a/test/unit/hibf/detail/sketch/estimate_kmer_counts_test.cpp +++ b/test/unit/hibf/detail/sketch/estimate_kmer_counts_test.cpp @@ -6,8 +6,8 @@ #include // for string_view #include // for allocator, vector -#include // for estimate_kmer_counts -#include // for hyperloglog +#include // for estimate_kmer_counts +#include // for hyperloglog TEST(estimate_kmer_counts_test, small_example) { diff --git a/test/unit/hibf/detail/sketch/hyperloglog_test.cpp b/test/unit/hibf/detail/sketch/hyperloglog_test.cpp index 9ab3f893..7115b3d3 100644 --- a/test/unit/hibf/detail/sketch/hyperloglog_test.cpp +++ b/test/unit/hibf/detail/sketch/hyperloglog_test.cpp @@ -11,7 +11,7 @@ #include // for unordered_set #include // for vector -#include // for hyperloglog +#include // for hyperloglog #include // for operator/, sandboxed_path #include // for tmp_directory diff --git a/test/unit/hibf/detail/sketch/toolbox_test.cpp b/test/unit/hibf/detail/sketch/toolbox_test.cpp index e98081a2..c1bcec2f 100644 --- a/test/unit/hibf/detail/sketch/toolbox_test.cpp +++ b/test/unit/hibf/detail/sketch/toolbox_test.cpp @@ -10,8 +10,8 @@ #include // for vector #include // for unordered_flat_map -#include // for hyperloglog -#include // for clustering_node, entry, precompute_union_estimates_for, cluste... +#include // for hyperloglog +#include // for clustering_node, entry, precompute_union_estimates_for, cluste... #include // for expect_range_eq, EXPECT_RANGE_EQ // inherits from toolbox to test private members From c922fc3a08e78b7c6a4a705c2cc780e3571cf0a5 Mon Sep 17 00:00:00 2001 From: Svenja Mehringer Date: Tue, 29 Aug 2023 08:54:04 +0200 Subject: [PATCH 5/8] [TEST] mv test/unit/hibf/detail/sketch/ -> test/unit/hibf/sketch/ --- test/unit/hibf/detail/CMakeLists.txt | 1 - test/unit/hibf/{detail => }/sketch/CMakeLists.txt | 0 .../{detail => }/sketch/estimate_kmer_counts_test.cpp | 0 test/unit/hibf/{detail => }/sketch/hyperloglog_test.cpp | 6 +++--- test/unit/hibf/{detail => }/sketch/toolbox_test.cpp | 8 ++++---- 5 files changed, 7 insertions(+), 8 deletions(-) delete mode 100644 test/unit/hibf/detail/CMakeLists.txt rename test/unit/hibf/{detail => }/sketch/CMakeLists.txt (100%) rename test/unit/hibf/{detail => }/sketch/estimate_kmer_counts_test.cpp (100%) rename test/unit/hibf/{detail => }/sketch/hyperloglog_test.cpp (97%) rename test/unit/hibf/{detail => }/sketch/toolbox_test.cpp (97%) diff --git a/test/unit/hibf/detail/CMakeLists.txt b/test/unit/hibf/detail/CMakeLists.txt deleted file mode 100644 index 9ddf96d3..00000000 --- a/test/unit/hibf/detail/CMakeLists.txt +++ /dev/null @@ -1 +0,0 @@ -add_subdirectories () diff --git a/test/unit/hibf/detail/sketch/CMakeLists.txt b/test/unit/hibf/sketch/CMakeLists.txt similarity index 100% rename from test/unit/hibf/detail/sketch/CMakeLists.txt rename to test/unit/hibf/sketch/CMakeLists.txt diff --git a/test/unit/hibf/detail/sketch/estimate_kmer_counts_test.cpp b/test/unit/hibf/sketch/estimate_kmer_counts_test.cpp similarity index 100% rename from test/unit/hibf/detail/sketch/estimate_kmer_counts_test.cpp rename to test/unit/hibf/sketch/estimate_kmer_counts_test.cpp diff --git a/test/unit/hibf/detail/sketch/hyperloglog_test.cpp b/test/unit/hibf/sketch/hyperloglog_test.cpp similarity index 97% rename from test/unit/hibf/detail/sketch/hyperloglog_test.cpp rename to test/unit/hibf/sketch/hyperloglog_test.cpp index 7115b3d3..6b5e068b 100644 --- a/test/unit/hibf/detail/sketch/hyperloglog_test.cpp +++ b/test/unit/hibf/sketch/hyperloglog_test.cpp @@ -11,9 +11,9 @@ #include // for unordered_set #include // for vector -#include // for hyperloglog -#include // for operator/, sandboxed_path -#include // for tmp_directory +#include // for hyperloglog +#include // for operator/, sandboxed_path +#include // for tmp_directory TEST(hyperloglog, bit_widths) { diff --git a/test/unit/hibf/detail/sketch/toolbox_test.cpp b/test/unit/hibf/sketch/toolbox_test.cpp similarity index 97% rename from test/unit/hibf/detail/sketch/toolbox_test.cpp rename to test/unit/hibf/sketch/toolbox_test.cpp index c1bcec2f..c361905d 100644 --- a/test/unit/hibf/detail/sketch/toolbox_test.cpp +++ b/test/unit/hibf/sketch/toolbox_test.cpp @@ -9,10 +9,10 @@ #include // for tie, make_tuple #include // for vector -#include // for unordered_flat_map -#include // for hyperloglog -#include // for clustering_node, entry, precompute_union_estimates_for, cluste... -#include // for expect_range_eq, EXPECT_RANGE_EQ +#include // for unordered_flat_map +#include // for hyperloglog +#include // for clustering_node, entry, precompute_union_estimates_for, cluste... +#include // for expect_range_eq, EXPECT_RANGE_EQ // inherits from toolbox to test private members struct toolbox_test : public ::testing::Test From 943bea595adcfe7aaefd0bc9117bd645a8aeaff0 Mon Sep 17 00:00:00 2001 From: Svenja Mehringer Date: Tue, 29 Aug 2023 08:56:02 +0200 Subject: [PATCH 6/8] [MISC] include/hibf/detail/cereal/ -> include/hibf/cereal/ --- include/hibf/{detail => }/cereal/concepts.hpp | 0 include/hibf/{detail => }/cereal/path.hpp | 0 include/hibf/config.hpp | 2 +- include/hibf/hierarchical_interleaved_bloom_filter.hpp | 2 +- include/hibf/interleaved_bloom_filter.hpp | 2 +- 5 files changed, 3 insertions(+), 3 deletions(-) rename include/hibf/{detail => }/cereal/concepts.hpp (100%) rename include/hibf/{detail => }/cereal/path.hpp (100%) diff --git a/include/hibf/detail/cereal/concepts.hpp b/include/hibf/cereal/concepts.hpp similarity index 100% rename from include/hibf/detail/cereal/concepts.hpp rename to include/hibf/cereal/concepts.hpp diff --git a/include/hibf/detail/cereal/path.hpp b/include/hibf/cereal/path.hpp similarity index 100% rename from include/hibf/detail/cereal/path.hpp rename to include/hibf/cereal/path.hpp diff --git a/include/hibf/config.hpp b/include/hibf/config.hpp index 24ed511d..451707c5 100644 --- a/include/hibf/config.hpp +++ b/include/hibf/config.hpp @@ -14,8 +14,8 @@ #include // for ostream #include // for insert_iterator +#include // IWYU pragma: keep #include // for unordered_flat_set -#include // IWYU pragma: keep #include #include // for access diff --git a/include/hibf/hierarchical_interleaved_bloom_filter.hpp b/include/hibf/hierarchical_interleaved_bloom_filter.hpp index af2911ea..2a394858 100644 --- a/include/hibf/hierarchical_interleaved_bloom_filter.hpp +++ b/include/hibf/hierarchical_interleaved_bloom_filter.hpp @@ -17,8 +17,8 @@ #include // for addressof #include // for vector +#include // for cereal_archive #include // for config -#include // for cereal_archive #include // for interleaved_bloom_filter #include // for user_bins_type diff --git a/include/hibf/interleaved_bloom_filter.hpp b/include/hibf/interleaved_bloom_filter.hpp index d6f9d07f..6cf1fac3 100644 --- a/include/hibf/interleaved_bloom_filter.hpp +++ b/include/hibf/interleaved_bloom_filter.hpp @@ -27,7 +27,7 @@ #include // for addressof #include // for vector -#include // for cereal_archive +#include // for cereal_archive #include // for CEREAL_SERIALIZE_FUNCTION_NAME #include // for bit_vector From e9078da11dc4aa1a113e9fa0518483308254786b Mon Sep 17 00:00:00 2001 From: Svenja Mehringer Date: Tue, 29 Aug 2023 08:57:38 +0200 Subject: [PATCH 7/8] [MISC] mv include/hibf/detail/data_store.hpp -> include/hibf/layout/ --- include/hibf/{detail => layout}/data_store.hpp | 0 include/hibf/layout/execute.hpp | 2 +- include/hibf/layout/hierarchical_binning.hpp | 2 +- include/hibf/layout/simple_binning.hpp | 2 +- src/layout/compute_layout.cpp | 5 ++--- src/layout/execute.cpp | 3 +-- src/layout/hierarchical_binning.cpp | 4 ++-- src/layout/simple_binning.cpp | 2 +- test/unit/hibf/layout/hierarchical_binning_test.cpp | 3 +-- test/unit/hibf/layout/simple_binning_test.cpp | 2 +- 10 files changed, 11 insertions(+), 14 deletions(-) rename include/hibf/{detail => layout}/data_store.hpp (100%) diff --git a/include/hibf/detail/data_store.hpp b/include/hibf/layout/data_store.hpp similarity index 100% rename from include/hibf/detail/data_store.hpp rename to include/hibf/layout/data_store.hpp diff --git a/include/hibf/layout/execute.hpp b/include/hibf/layout/execute.hpp index afff8f97..3cc018c9 100644 --- a/include/hibf/layout/execute.hpp +++ b/include/hibf/layout/execute.hpp @@ -3,7 +3,7 @@ #include // for size_t #include // for config -#include // for data_store +#include // for data_store namespace seqan::hibf { diff --git a/include/hibf/layout/hierarchical_binning.hpp b/include/hibf/layout/hierarchical_binning.hpp index 9ff1ab8f..4bdae223 100644 --- a/include/hibf/layout/hierarchical_binning.hpp +++ b/include/hibf/layout/hierarchical_binning.hpp @@ -7,7 +7,7 @@ #include // for vector #include // for config -#include // for data_store +#include // for data_store #include // for HIBF_WORKAROUND_GCC_BOGUS_MEMCPY namespace seqan::hibf::layout diff --git a/include/hibf/layout/simple_binning.hpp b/include/hibf/layout/simple_binning.hpp index e2f9445a..d7d25e3a 100644 --- a/include/hibf/layout/simple_binning.hpp +++ b/include/hibf/layout/simple_binning.hpp @@ -6,7 +6,7 @@ #include // for addressof #include // for vector -#include // for data_store +#include // for data_store #include // for next_multiple_of_64 namespace seqan::hibf::layout diff --git a/src/layout/compute_layout.cpp b/src/layout/compute_layout.cpp index db942779..35068a68 100644 --- a/src/layout/compute_layout.cpp +++ b/src/layout/compute_layout.cpp @@ -6,9 +6,8 @@ #include // for addressof #include // for vector -#include // for config -#include // for unordered_flat_set -#include // for data_store +#include // for config +#include // for unordered_flat_set #include // for compute_layout #include // for data_store #include // for execute diff --git a/src/layout/execute.cpp b/src/layout/execute.cpp index a1218e05..af6830b6 100644 --- a/src/layout/execute.cpp +++ b/src/layout/execute.cpp @@ -5,8 +5,7 @@ #include // for invalid_argument #include // for vector -#include // for config -#include // for data_store +#include // for config #include // for compute_fpr_correction #include // for data_store #include // for execute diff --git a/src/layout/hierarchical_binning.cpp b/src/layout/hierarchical_binning.cpp index ece86686..25d2aa81 100644 --- a/src/layout/hierarchical_binning.cpp +++ b/src/layout/hierarchical_binning.cpp @@ -9,8 +9,8 @@ #include // for pair, addressof #include // for vector -#include // for config -#include // for data_store +#include // for config +#include // for data_store #include // for hierarchical_binning #include // for layout #include // for simple_binning diff --git a/src/layout/simple_binning.cpp b/src/layout/simple_binning.cpp index db182964..e85fb81b 100644 --- a/src/layout/simple_binning.cpp +++ b/src/layout/simple_binning.cpp @@ -4,7 +4,7 @@ #include // for numeric_limits #include // for vector -#include // for data_store +#include // for data_store #include // for layout #include // for simple_binning diff --git a/test/unit/hibf/layout/hierarchical_binning_test.cpp b/test/unit/hibf/layout/hierarchical_binning_test.cpp index e9b0781d..3e378415 100644 --- a/test/unit/hibf/layout/hierarchical_binning_test.cpp +++ b/test/unit/hibf/layout/hierarchical_binning_test.cpp @@ -3,8 +3,7 @@ #include // for size_t #include // for vector, allocator -#include // for config -#include // for data_store +#include // for config #include // for compute_fpr_correction #include // for data_store #include // for hierarchical_binning diff --git a/test/unit/hibf/layout/simple_binning_test.cpp b/test/unit/hibf/layout/simple_binning_test.cpp index 5db5ff8d..10042401 100644 --- a/test/unit/hibf/layout/simple_binning_test.cpp +++ b/test/unit/hibf/layout/simple_binning_test.cpp @@ -4,7 +4,7 @@ #include // for runtime_error #include // for allocator, vector -#include // for data_store +#include // for data_store #include // for layout #include // for simple_binning #include // for expect_range_eq, EXPECT_RANGE_EQ From 30cfc9cd7a6baa699ee28fb9a88216b6ea37cba1 Mon Sep 17 00:00:00 2001 From: Svenja Mehringer Date: Tue, 29 Aug 2023 08:58:45 +0200 Subject: [PATCH 8/8] [MISC] mv include/hibf/detail/prefixes.hpp -> include/hibf/layout/ --- include/hibf/layout/layout.hpp | 2 +- include/hibf/{detail => layout}/prefixes.hpp | 0 src/config.cpp | 2 +- src/layout/layout.cpp | 2 +- 4 files changed, 3 insertions(+), 3 deletions(-) rename include/hibf/{detail => layout}/prefixes.hpp (100%) diff --git a/include/hibf/layout/layout.hpp b/include/hibf/layout/layout.hpp index 93ea8978..05957f15 100644 --- a/include/hibf/layout/layout.hpp +++ b/include/hibf/layout/layout.hpp @@ -6,7 +6,7 @@ #include // for ostream #include // for vector, operator== -#include // for header, merged_bin +#include // for header, merged_bin #include namespace seqan::hibf::layout diff --git a/include/hibf/detail/prefixes.hpp b/include/hibf/layout/prefixes.hpp similarity index 100% rename from include/hibf/detail/prefixes.hpp rename to include/hibf/layout/prefixes.hpp diff --git a/src/config.cpp b/src/config.cpp index 477b1431..30ae6f42 100644 --- a/src/config.cpp +++ b/src/config.cpp @@ -10,7 +10,7 @@ #include #include -#include +#include #include diff --git a/src/layout/layout.cpp b/src/layout/layout.cpp index b2f1387e..f1ef13d0 100644 --- a/src/layout/layout.cpp +++ b/src/layout/layout.cpp @@ -11,7 +11,7 @@ #include #include -#include +#include namespace seqan::hibf::layout {