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[MISC] Move counting_vector into separate header
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| // SPDX-FileCopyrightText: 2006-2023, Knut Reinert & Freie Universität Berlin | ||
| // SPDX-FileCopyrightText: 2016-2023, Knut Reinert & MPI für molekulare Genetik | ||
| // SPDX-License-Identifier: BSD-3-Clause | ||
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| /*!\file | ||
| * \author Enrico Seiler <enrico.seiler AT fu-berlin.de> | ||
| * \brief Provides seqan::hibf::counting_vector. | ||
| */ | ||
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| #pragma once | ||
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| #include <algorithm> // for fill | ||
| #include <array> // for array | ||
| #include <bit> // for countr_zero | ||
| #include <cassert> // for assert | ||
| #include <cinttypes> // for uint64_t, uint16_t | ||
| #include <concepts> // for integral, same_as, unsigned_integral | ||
| #include <cstring> // for size_t | ||
| #include <functional> // for plus | ||
| #include <ranges> // for range, forward_range, input_range, range_reference_t, range_value_t | ||
| #include <type_traits> // for remove_cvref_t | ||
| #include <utility> // for addressof | ||
| #include <vector> // for vector | ||
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| #include <hibf/cereal/concepts.hpp> // for cereal_archive | ||
| #include <hibf/config.hpp> // for config | ||
| #include <hibf/contrib/aligned_allocator.hpp> // for aligned_allocator | ||
| #include <hibf/misc/bit_vector.hpp> // for bit_vector | ||
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| #include <cereal/macros.hpp> // for CEREAL_SERIALIZE_FUNCTION_NAME | ||
| #include <cereal/types/base_class.hpp> // for base_class | ||
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| namespace seqan::hibf | ||
| { | ||
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| /*!\brief A data structure that behaves like a std::vector and can be used to consolidate the results of multiple calls | ||
| * to seqan::hibf::interleaved_bloom_filter::membership_agent_type::bulk_contains. | ||
| * \ingroup ibf | ||
| * \tparam value_t The type of the count. Must model std::integral. | ||
| * | ||
| * \details | ||
| * | ||
| * When using the seqan::hibf::interleaved_bloom_filter::membership_agent_type::bulk_contains operation, a common use | ||
| * case is to add up, for example, the results for all k-mers in a query. This yields, for each bin, the number of | ||
| * k-mers of a query that are in the respective bin. Such information can be used to apply further filtering or | ||
| * abundance estimation based on the k-mer counts. | ||
| * | ||
| * The seqan::hibf::counting_vector offers an easy way to add up the individual | ||
| * seqan::hibf::bit_vector by offering an `+=` operator. | ||
| * | ||
| * The `value_t` template parameter should be chosen in a way that no overflow occurs if all calls to `bulk_contains` | ||
| * return a hit for a specific bin. For example, `uint8_t` will suffice when processing short Illumina reads, whereas | ||
| * long reads will require at least `uint32_t`. | ||
| * | ||
| * ### Example | ||
| * | ||
| * \include test/snippet/ibf/counting_vector.cpp | ||
| */ | ||
| template <std::integral value_t> | ||
| class counting_vector : public std::vector<value_t> | ||
| { | ||
| private: | ||
| //!\brief The base type. | ||
| using base_t = std::vector<value_t>; | ||
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| public: | ||
| /*!\name Constructors, destructor and assignment | ||
| * \{ | ||
| */ | ||
| counting_vector() = default; //!< Defaulted. | ||
| counting_vector(counting_vector const &) = default; //!< Defaulted. | ||
| counting_vector & operator=(counting_vector const &) = default; //!< Defaulted. | ||
| counting_vector(counting_vector &&) = default; //!< Defaulted. | ||
| counting_vector & operator=(counting_vector &&) = default; //!< Defaulted. | ||
| ~counting_vector() = default; //!< Defaulted. | ||
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| using base_t::base_t; | ||
| //!\} | ||
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| /*!\brief Bin-wise adds the bits of a seqan::hibf::bit_vector. | ||
| * \param bit_vector The seqan::hibf::bit_vector. | ||
| * \attention The counting_vector must be at least as big as `bit_vector`. | ||
| * | ||
| * \details | ||
| * | ||
| * ### Example | ||
| * | ||
| * \include test/snippet/ibf/counting_vector.cpp | ||
| */ | ||
| counting_vector & operator+=(bit_vector const & bit_vector) | ||
| { | ||
| for_each_set_bin(bit_vector, | ||
| [this](size_t const bin) | ||
| { | ||
| ++(*this)[bin]; | ||
| }); | ||
| return *this; | ||
| } | ||
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| /*!\brief Bin-wise subtracts the bits of a seqan::hibf::bit_vector. | ||
| * \param bit_vector The seqan::hibf::bit_vector. | ||
| * \attention The counting_vector must be at least as big as `bit_vector`. | ||
| */ | ||
| counting_vector & operator-=(bit_vector const & bit_vector) | ||
| { | ||
| for_each_set_bin(bit_vector, | ||
| [this](size_t const bin) | ||
| { | ||
| assert((*this)[bin] > 0); | ||
| --(*this)[bin]; | ||
| }); | ||
| return *this; | ||
| } | ||
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| /*!\brief Bin-wise addition of two `seqan::hibf::counting_vector`s. | ||
| * \param rhs The other seqan::hibf::counting_vector. | ||
| * \attention The seqan::hibf::counting_vector must be at least as big as `rhs`. | ||
| * | ||
| * \details | ||
| * | ||
| * ### Example | ||
| * | ||
| * \include test/snippet/ibf/counting_vector.cpp | ||
| */ | ||
| counting_vector & operator+=(counting_vector const & rhs) | ||
| { | ||
| assert(this->size() >= rhs.size()); // The counting vector may be bigger than what we need. | ||
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| std::transform(this->begin(), this->end(), rhs.begin(), this->begin(), std::plus<value_t>()); | ||
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| return *this; | ||
| } | ||
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| /*!\brief Bin-wise substraction of two `seqan::hibf::counting_vector`s. | ||
| * \param rhs The other seqan::hibf::counting_vector. | ||
| * \attention The seqan::hibf::counting_vector must be at least as big as `rhs`. | ||
| */ | ||
| counting_vector & operator-=(counting_vector const & rhs) | ||
| { | ||
| assert(this->size() >= rhs.size()); // The counting vector may be bigger than what we need. | ||
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| std::transform(this->begin(), | ||
| this->end(), | ||
| rhs.begin(), | ||
| this->begin(), | ||
| [](auto a, auto b) | ||
| { | ||
| assert(a >= b); | ||
| return a - b; | ||
| }); | ||
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| return *this; | ||
| } | ||
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| private: | ||
| //!\brief Enumerates all bins of a seqan::hibf::bit_vector. | ||
| template <typename on_bin_fn_t> | ||
| void for_each_set_bin(bit_vector const & bit_vector, on_bin_fn_t && on_bin_fn) | ||
| { | ||
| assert(this->size() >= bit_vector.size()); // The counting vector may be bigger than what we need. | ||
| size_t const words = (bit_vector.size() + 63u) >> 6; | ||
| uint64_t const * const bitvector_raw = bit_vector.data(); | ||
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| // Jump to the next 1 and return the number of places jumped in the bit_sequence | ||
| auto jump_to_next_1bit = [](uint64_t & x) | ||
| { | ||
| auto const zeros = std::countr_zero(x); | ||
| x >>= zeros; // skip number of zeros | ||
| return zeros; | ||
| }; | ||
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| // Each iteration can handle 64 bits | ||
| for (size_t batch = 0; batch < words; ++batch) | ||
| { | ||
| // get 64 bits starting at position `bit_pos` | ||
| uint64_t bit_sequence = bitvector_raw[batch]; | ||
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| // process each relative bin inside the bit_sequence | ||
| for (size_t bin = batch << 6; bit_sequence != 0u; ++bin, bit_sequence >>= 1) | ||
| { | ||
| // Jump to the next 1 and | ||
| bin += jump_to_next_1bit(bit_sequence); | ||
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| on_bin_fn(bin); | ||
| } | ||
| } | ||
| } | ||
| }; | ||
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| } // namespace seqan::hibf |