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Merged
eseiler merged 1 commit into from
Feb 3, 2025
Merged

[MISC] IWYU #265

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2 changes: 1 addition & 1 deletion include/hibf/build/compute_kmers.hpp
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#pragma once

#include <cinttypes> // for uint64_t
#include <cstdint> // for uint64_t

#include <hibf/build/build_data.hpp> // for build_data
#include <hibf/contrib/robin_hood.hpp> // for unordered_flat_set
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6 changes: 3 additions & 3 deletions include/hibf/build/construct_ibf.hpp
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#pragma once

#include <cinttypes> // for uint64_t
#include <cstddef> // for size_t
#include <cstddef> // for size_t
#include <cstdint> // for uint64_t

#include <hibf/build/build_data.hpp> // for build_data
#include <hibf/contrib/robin_hood.hpp> // for unordered_flat_set
#include <hibf/interleaved_bloom_filter.hpp> // for interleaved_bloom_filter
#include <hibf/layout/graph.hpp>
#include <hibf/layout/graph.hpp> // for graph

namespace seqan::hibf::build
{
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6 changes: 3 additions & 3 deletions include/hibf/build/insert_into_ibf.hpp
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#pragma once

#include <cinttypes> // for uint64_t
#include <cstddef> // for size_t
#include <cstddef> // for size_t
#include <cstdint> // for uint64_t

#include <hibf/build/build_data.hpp> // for build_data
#include <hibf/contrib/robin_hood.hpp> // for unordered_flat_set
#include <hibf/interleaved_bloom_filter.hpp> // for interleaved_bloom_filter
#include <hibf/layout/layout.hpp> // for layout
#include <hibf/misc/timer.hpp> // for concurrent, timer
#include <hibf/misc/timer.hpp> // for concurrent_timer

namespace seqan::hibf::build
{
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2 changes: 1 addition & 1 deletion include/hibf/build/update_parent_kmers.hpp
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*/
#pragma once

#include <cinttypes> // for uint64_t
#include <cstdint> // for uint64_t
#include <functional> // for equal_to

#include <hibf/contrib/robin_hood.hpp> // for unordered_flat_set, hash
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2 changes: 1 addition & 1 deletion include/hibf/build/update_user_bins.hpp
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#pragma once

#include <algorithm> // for fill_n
#include <cinttypes> // for int64_t
#include <cstdint> // for uint64_t
#include <vector> // for vector

#include <hibf/layout/layout.hpp> // for layout
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6 changes: 4 additions & 2 deletions include/hibf/cereal/concepts.hpp
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#pragma once

#include <cereal/details/helpers.hpp> // for InputArchiveBase, OutputArchiveBase
#include <cereal/details/traits.hpp> // for InputArchiveBase, OutputArchiveBase
#include <type_traits> // for is_base_of_v

#include <cereal/details/helpers.hpp> // for OutputArchiveBase, InputArchiveBase, BinaryInputArchive, BinaryOutputA...
#include <cereal/details/traits.hpp> // for TextArchive

#include <hibf/platform.hpp>

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2 changes: 1 addition & 1 deletion include/hibf/config.hpp
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#pragma once

#include <cinttypes> // for uint32_t, uint8_t
#include <cstddef> // for size_t
#include <cstdint> // for uint32_t, uint8_t
#include <functional> // for function
#include <iosfwd> // for istream, ostream

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2 changes: 1 addition & 1 deletion include/hibf/hierarchical_interleaved_bloom_filter.hpp
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#include <algorithm> // for __fn, fill, sort
#include <cassert> // for assert
#include <cinttypes> // for uint64_t, uint16_t, uint32_t
#include <concepts> // for integral, unsigned_integral
#include <cstddef> // for size_t
#include <cstdint> // for uint64_t, uint16_t, uint32_t
#include <limits> // for numeric_limits
#include <memory> // for addressof
#include <ranges> // for forward_range, range_value_t, range
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2 changes: 1 addition & 1 deletion include/hibf/interleaved_bloom_filter.hpp
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#include <algorithm> // for fill
#include <array> // for array
#include <cassert> // for assert
#include <cinttypes> // for uint32_t, uint16_t, uint64_t
#include <concepts> // for integral, same_as, unsigned_integral
#include <cstdint> // for uint32_t, uint16_t, uint64_t
#include <cstring> // for size_t
#include <memory> // for addressof
#include <ranges> // for range, range_reference_t, range_value_t, forward_range, input_...
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12 changes: 6 additions & 6 deletions include/hibf/layout/data_store.hpp
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#pragma once

#include <cassert> // for assert
#include <cinttypes> // for uint64_t
#include <cstddef> // for size_t
#include <numeric> // for iota
#include <string> // for string
#include <vector> // for vector
#include <cassert> // for assert
#include <cstddef> // for size_t
#include <cstdint> // for uint64_t
#include <numeric> // for iota
#include <string> // for basic_string, string
#include <vector> // for vector

#include <hibf/layout/layout.hpp> // for layout
#include <hibf/misc/timer.hpp> // for concurrent_timer
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6 changes: 3 additions & 3 deletions include/hibf/misc/bit_vector.hpp
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#include <algorithm> // for __fn, for_each, all_of, any_of, copy, fill
#include <bit> // for countr_zero
#include <cassert> // for assert
#include <cinttypes> // for uint64_t
#include <climits> // for CHAR_BIT
#include <compare> // for strong_ordering, operator==
#include <concepts> // for assignable_from
#include <cstddef> // for size_t, ptrdiff_t
#include <cstdint> // for uint64_t
#include <initializer_list> // for initializer_list
#include <iterator> // for iter_reference_t, __fn, back_inserter, distance, iter_differen...
#include <memory> // for allocator, assume_aligned, allocator_traits, __compressed_pair
#include <memory> // for allocator, allocator_traits, assume_aligned, __compressed_pair
#include <ranges> // for __fn, begin, end
#include <stdexcept> // for out_of_range
#include <string> // for char_traits, operator+, to_string, operator""s
#include <string> // for char_traits, operator+, to_string, operator""s, basic_string
#include <type_traits> // for conditional_t
#include <utility> // for swap
#include <vector> // for vector
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4 changes: 2 additions & 2 deletions include/hibf/misc/counting_vector.hpp
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#include <algorithm> // for transform
#include <bit> // for countr_zero
#include <cassert> // for assert
#include <cinttypes> // for uint64_t
#include <climits> // for CHAR_BIT
#include <concepts> // for integral
#include <cstdint> // for uint64_t, uint8_t
#include <cstring> // for size_t
#include <functional> // for minus, plus
#include <type_traits> // for conditional_t
#include <type_traits> // for conditional, conditional_t
#include <vector> // for vector

#include <hibf/contrib/aligned_allocator.hpp> // for aligned_allocator
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2 changes: 1 addition & 1 deletion include/hibf/misc/insert_iterator.hpp
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#pragma once

#include <cassert> // for assert
#include <cinttypes> // for uint64_t, uint8_t
#include <cstddef> // for size_t, ptrdiff_t
#include <cstdint> // for uint64_t, uint8_t
#include <functional> // for function, equal_to
#include <iterator> // for output_iterator_tag
#include <memory> // for addressof
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6 changes: 3 additions & 3 deletions include/hibf/misc/print.hpp
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#pragma once

#include <cinttypes> // for int64_t, int16_t, int32_t, int8_t, uint16_t, uint32_t, uint64_t
#include <iostream> // for cout, ostream
#include <vector> // for vector
#include <cstdint> // for uint64_t, int16_t, int32_t, int64_t, int8_t, uint16_t, uint32_t
#include <iostream> // for cout, ostream
#include <vector> // for vector

#include <hibf/misc/bit_vector.hpp> // for bit_vector
#include <hibf/misc/counting_vector.hpp> // for counting_vector
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2 changes: 1 addition & 1 deletion include/hibf/misc/timer.hpp
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#include <atomic> // for atomic, __atomic_base, memory_order_relaxed
#include <cassert> // for assert
#include <chrono> // for duration, time_point, operator-, operator<=>, steady_clock
#include <cinttypes> // for uint64_t
#include <compare> // for operator>=, strong_ordering
#include <concepts> // for same_as
#include <cstdint> // for uint64_t

#include <hibf/platform.hpp>

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10 changes: 5 additions & 5 deletions include/hibf/sketch/hyperloglog.hpp
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#pragma once

#include <array> // for array
#include <cinttypes> // for uint64_t, uint8_t, uint32_t
#include <cstddef> // for size_t
#include <iosfwd> // for istream, ostream
#include <vector> // for vector
#include <array> // for array
#include <cstddef> // for size_t
#include <cstdint> // for uint64_t, uint8_t, uint32_t
#include <iosfwd> // for istream, ostream
#include <vector> // for vector

#include <cereal/access.hpp> // for access
#include <cereal/cereal.hpp> // for make_nvp, CEREAL_NVP
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2 changes: 1 addition & 1 deletion include/hibf/sketch/toolbox.hpp
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#pragma once

#include <cinttypes> // for uint64_t, int64_t
#include <cstddef> // for size_t
#include <cstdint> // for uint64_t, int64_t
#include <functional> // for greater
#include <queue> // for priority_queue
#include <vector> // for vector
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4 changes: 2 additions & 2 deletions include/hibf/version.hpp
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// IWYU pragma: always_keep

#include <cinttypes> // for uint8_t
#include <cstddef> // for size_t
#include <cstddef> // for size_t
#include <cstdint> // for uint8_t

/*!\file
* \brief Provides version macros and global variables.
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4 changes: 2 additions & 2 deletions src/build/compute_kmers.cpp
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* \author Enrico Seiler <enrico.seiler AT fu-berlin.de>
*/

#include <cinttypes> // for uint64_t
#include <cstdint> // for uint64_t
#include <functional> // for function

#include <hibf/build/build_data.hpp> // for build_data
#include <hibf/build/compute_kmers.hpp> // for compute_kmers
#include <hibf/config.hpp> // for config, insert_iterator
#include <hibf/config.hpp> // for insert_iterator, config
#include <hibf/contrib/robin_hood.hpp> // for unordered_flat_set
#include <hibf/layout/layout.hpp> // for layout
#include <hibf/misc/timer.hpp> // for serial_timer, concurrent_timer
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2 changes: 1 addition & 1 deletion src/build/construct_ibf.cpp
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// SPDX-License-Identifier: BSD-3-Clause

#include <cassert> // for assert
#include <cinttypes> // for uint64_t
#include <cmath> // for ceil
#include <cstddef> // for size_t
#include <cstdint> // for uint64_t
#include <functional> // for equal_to
#include <vector> // for vector

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3 changes: 2 additions & 1 deletion src/build/insert_into_ibf.cpp
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#include <algorithm> // for __fn, all_of, fill_n
#include <cassert> // for assert
#include <cinttypes> // for uint64_t
#include <cstddef> // for size_t
#include <cstdint> // for uint64_t
#include <functional> // for equal_to, function
#include <iterator> // for counted_iterator
#include <ranges> // for subrange
#include <vector> // for vector

#include <hibf/build/build_data.hpp> // for build_data
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14 changes: 7 additions & 7 deletions src/hierarchical_interleaved_bloom_filter.cpp
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#include <algorithm> // for shuffle, __fn, none_of
#include <cassert> // for assert
#include <cinttypes> // for uint64_t, int64_t
#include <cstddef> // for size_t
#include <cstdint> // for uint64_t
#include <functional> // for equal_to
#include <mutex> // for mutex, lock_guard
#include <numeric> // for iota
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#include <hibf/build/update_user_bins.hpp> // for update_user_bins
#include <hibf/config.hpp> // for config
#include <hibf/contrib/robin_hood.hpp> // for unordered_flat_set, hash
#include <hibf/hierarchical_interleaved_bloom_filter.hpp> // for hierarchical_interleaved_bloom_filter
#include <hibf/hierarchical_interleaved_bloom_filter.hpp> // for hierarchical_interleaved_bloom_filter, merged
#include <hibf/interleaved_bloom_filter.hpp> // for interleaved_bloom_filter
#include <hibf/layout/compute_fpr_correction.hpp> // for compute_fpr_correction
#include <hibf/layout/compute_layout.hpp> // for compute_layout
#include <hibf/layout/graph.hpp> // for graph
#include <hibf/layout/layout.hpp> // for layout
#include <hibf/misc/divide_and_ceil.hpp> // for divide_and_ceil
#include <hibf/misc/iota_vector.hpp>
#include <hibf/misc/timer.hpp> // for concurrent_timer
#include <hibf/sketch/compute_sketches.hpp> // for compute_sketches
#include <hibf/sketch/estimate_kmer_counts.hpp>
#include <hibf/sketch/hyperloglog.hpp> // for hyperloglog
#include <hibf/misc/iota_vector.hpp> // for iota_vector
#include <hibf/misc/timer.hpp> // for concurrent_timer
#include <hibf/sketch/compute_sketches.hpp> // for compute_sketches
#include <hibf/sketch/estimate_kmer_counts.hpp> // for estimate_kmer_counts
#include <hibf/sketch/hyperloglog.hpp> // for hyperloglog

namespace seqan::hibf
{
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2 changes: 1 addition & 1 deletion src/interleaved_bloom_filter.cpp
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#include <array> // for array
#include <bit> // for bit_ceil, countl_zero
#include <cassert> // for assert
#include <cinttypes> // for uint64_t
#include <cstdint> // for uint64_t
#include <cstring> // for size_t, memcpy
#include <functional> // for equal_to, function
#include <stdexcept> // for logic_error, invalid_argument
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4 changes: 2 additions & 2 deletions src/misc/print.cpp
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// SPDX-FileCopyrightText: 2016-2024, Knut Reinert & MPI für molekulare Genetik
// SPDX-License-Identifier: BSD-3-Clause

#include <cinttypes> // for uint16_t, int16_t, int64_t, int8_t, uint8_t, int32_t, uint32_t, uin...
#include <cstddef> // for size_t
#include <iostream> // for ostream, operator<<, basic_ostream
#include <cstdint> // for uint16_t, int16_t, int8_t, uint64_t, uint8_t, int32_t, int64_t, uin...
#include <iostream> // for ostream, basic_ostream, operator<<
#include <ranges> // for range_value_t, empty
#include <type_traits> // for conditional
#include <vector> // for vector
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6 changes: 3 additions & 3 deletions src/sketch/compute_sketches.cpp
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// SPDX-FileCopyrightText: 2016-2024, Knut Reinert & MPI für molekulare Genetik
// SPDX-License-Identifier: BSD-3-Clause

#include <algorithm> // for __fn, sort_heap, fill, make_heap
#include <algorithm> // for __fn, sort_heap, all_of, fill, make_heap
#include <atomic> // for atomic_flag
#include <cassert> // for assert
#include <cinttypes> // for uint64_t
#include <cstddef> // for size_t
#include <cstdint> // for uint64_t, uint8_t
#include <functional> // for equal_to, function
#include <limits> // for numeric_limits
#include <span> // for span
#include <stdexcept> // for runtime_error
#include <string> // for allocator, char_traits, operator+, to_string
#include <string> // for operator+, allocator, char_traits, to_string, basic_string
#include <utility> // for move
#include <vector> // for vector

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2 changes: 1 addition & 1 deletion src/sketch/hyperloglog.cpp
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#include <array> // for array
#include <bit> // for countl_zero
#include <cassert> // for assert
#include <cinttypes> // for uint64_t, uint8_t, uint32_t
#include <cmath> // for log
#include <cstddef> // for size_t
#include <cstdint> // for uint64_t, uint8_t, uint32_t
#include <iostream> // for basic_ostream, basic_istream, istream, ostream
#include <memory> // for addressof
#include <stdexcept> // for runtime_error, invalid_argument
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2 changes: 1 addition & 1 deletion src/sketch/minhashes.cpp
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#include <algorithm> // for __fn, is_sorted, all_of, find, pop_heap, push_heap
#include <cassert> // for assert
#include <cinttypes> // for uint64_t
#include <cstdint> // for uint64_t
#include <span> // for span
#include <vector> // for vector

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2 changes: 1 addition & 1 deletion src/sketch/toolbox.cpp
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#include <algorithm> // for sort
#include <cassert> // for assert
#include <cinttypes> // for uint64_t, int64_t
#include <cmath> // for floor, sqrt
#include <cstddef> // for size_t
#include <cstdint> // for uint64_t, int64_t
#include <functional> // for equal_to
#include <limits> // for numeric_limits
#include <omp.h> // for omp_get_thread_num
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5 changes: 3 additions & 2 deletions test/include/hibf/test/cereal.hpp
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#pragma once

#include <gtest/gtest.h> // for AssertionResult, EXPECT_TRUE, Message, TestPartResult
#include <gtest/gtest.h> // for AssertionResult, Message, EXPECT_TRUE, TestPartResult

#include <fstream> // for basic_ios, ios, basic_ifstream, basic_ofstream, ifstream, ofs...
#include <fstream> // for basic_ifstream, basic_ios, basic_ofstream, ios, ifstream, ofs...
#include <string> // for basic_string
#include <type_traits> // for remove_cvref_t

#include <cereal/archives/binary.hpp> // for BinaryInputArchive, BinaryOutputArchive
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