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Merge pull request #2290 from Irallia/feature/alphabet/add_phred94
[FEATURE] Alphabet: Add the quality alphabet seqan3::phred94
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| Original file line number | Diff line number | Diff line change |
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| // ----------------------------------------------------------------------------------------------------- | ||
| // Copyright (c) 2006-2020, Knut Reinert & Freie Universität Berlin | ||
| // Copyright (c) 2016-2020, Knut Reinert & MPI für molekulare Genetik | ||
| // This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License | ||
| // shipped with this file and also available at: https://github.com/seqan/seqan3/blob/master/LICENSE.md | ||
| // ----------------------------------------------------------------------------------------------------- | ||
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| /*!\file | ||
| * \author Lydia Buntrock <lydia.buntrock AT fu-berlin.de> | ||
| * \brief Provides seqan3::phred94 quality scores. | ||
| */ | ||
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| #pragma once | ||
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| #include <seqan3/alphabet/quality/quality_base.hpp> | ||
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| namespace seqan3 | ||
| { | ||
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| /*!\brief Quality type for PacBio Phred scores of HiFi reads. | ||
| * \implements seqan3::writable_quality_alphabet | ||
| * \if DEV \implements seqan3::detail::writable_constexpr_alphabet \endif | ||
| * \implements seqan3::trivially_copyable | ||
| * \implements seqan3::standard_layout | ||
| * \implements std::regular | ||
| * | ||
| * \ingroup quality | ||
| * | ||
| * \details | ||
| * | ||
| * The phred94 quality alphabet represents the zero-based phred score range [0..93] mapped to the ASCII range | ||
| * ['!' .. '~'] (Sanger, Illumina 1.8+ format). It is typically used for HiFi reads produced by PacBio. For Sanger and | ||
| * Illumina phred scores of raw reads the range is typically (0 to 41), represented as seqan3::phred42. If you expect | ||
| * only slightly larger score types you can use seqan3::phred63 (0 to 62) which still has memory advantages when used | ||
| * with seqan3::qualified. | ||
| * | ||
| * \include test/snippet/alphabet/quality/phred94.cpp | ||
| * | ||
| * You can find more information about the Phred scores in our \ref quality submodule \see quality submodule. | ||
| */ | ||
| class phred94 : public quality_base<phred94, 94> | ||
| { | ||
| private: | ||
| //!\brief The base class. | ||
| using base_t = quality_base<phred94, 94>; | ||
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| //!\brief Befriend seqan3::quality_base. | ||
| friend base_t; | ||
| //!\cond \brief Befriend seqan3::alphabet_base. | ||
| friend base_t::base_t; | ||
| //!\endcond | ||
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| public: | ||
| /*!\name Constructors, destructor and assignment | ||
| * \{ | ||
| */ | ||
| constexpr phred94() noexcept = default; //!< Defaulted. | ||
| constexpr phred94(phred94 const &) noexcept = default; //!< Defaulted. | ||
| constexpr phred94(phred94 &&) noexcept = default; //!< Defaulted. | ||
| constexpr phred94 & operator=(phred94 const &) noexcept = default; //!< Defaulted. | ||
| constexpr phred94 & operator=(phred94 &&) noexcept = default; //!< Defaulted. | ||
| ~phred94() noexcept = default; //!< Defaulted. | ||
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| //!\brief Construct from phred value. | ||
| constexpr phred94(phred_type const p) : base_t{p} {} | ||
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| // Inherit converting constructor | ||
| using base_t::base_t; | ||
| //!\} | ||
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| /*!\name Member variables. | ||
| * \{ | ||
| */ | ||
| //!\brief The projection offset between phred and rank score representation. | ||
| static constexpr phred_type offset_phred{0}; | ||
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| //!\brief The projection offset between char and rank score representation. | ||
| static constexpr char_type offset_char{'!'}; | ||
| //!\} | ||
| }; | ||
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| /*!\name Literals | ||
| * \{ | ||
| */ | ||
| /*!\brief The seqan3::phred94 char literal. | ||
| * \relates seqan3::phred94 | ||
| * \returns seqan3::phred94 | ||
| */ | ||
| constexpr phred94 operator""_phred94(char const c) noexcept | ||
| { | ||
| return phred94{}.assign_char(c); | ||
| } | ||
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| /*!\brief The seqan3::phred94 string literal. | ||
| * \param[in] s A pointer to the character sequence to assign from. | ||
| * \param[in] n The length of the character sequence to assign from. | ||
| * \relates seqan3::phred94 | ||
| * \returns seqan3::std::vector<seqan3::phred94> | ||
| * | ||
| * You can use this string literal to easily assign to std::vector<seqan3::phred94>: | ||
| * | ||
| * \include test/snippet/alphabet/quality/phred94_literal.cpp | ||
| */ | ||
| inline std::vector<phred94> operator""_phred94(char const * s, std::size_t n) | ||
| { | ||
| std::vector<phred94> r; | ||
| r.resize(n); | ||
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| for (size_t i = 0; i < n; ++i) | ||
| r[i].assign_char(s[i]); | ||
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| return r; | ||
| } | ||
| //!\} | ||
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| } // namespace seqan3 |
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,18 @@ | ||
| #include <seqan3/alphabet/quality/phred94.hpp> | ||
| #include <seqan3/core/debug_stream.hpp> | ||
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| int main() | ||
| { | ||
| seqan3::phred94 phred; | ||
| phred.assign_rank(2); // wrapper for assign_phred(2) | ||
| seqan3::debug_stream << phred.to_phred() << "\n"; // 2 | ||
| seqan3::debug_stream << phred.to_char() << "\n"; // '#' | ||
| seqan3::debug_stream << phred.to_rank() << "\n"; // 2 | ||
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| seqan3::phred94 another_phred{75}; | ||
| seqan3::debug_stream << another_phred.to_phred() << "\n"; // 75 | ||
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| seqan3::phred94 a_third_phred; | ||
| another_phred.assign_phred(105); // converted down to 93 | ||
| seqan3::debug_stream << another_phred.to_phred() << "\n"; // 93 | ||
| } |
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| @@ -0,0 +1,17 @@ | ||
| #include <seqan3/std/algorithm> | ||
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| #include <seqan3/alphabet/quality/phred94.hpp> | ||
| #include <seqan3/core/debug_stream.hpp> | ||
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| int main() | ||
| { | ||
| using seqan3::operator""_phred94; | ||
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| // directly assign to a std::vector<phred94> using a string literal | ||
| std::vector<seqan3::phred94> qual_vec = "###!"_phred94; | ||
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| // This is the same as a sequence of char literals: | ||
| std::vector<seqan3::phred94> qual_vec2 = {'#'_phred94, '#'_phred94, '#'_phred94, '!'_phred94}; | ||
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| seqan3::debug_stream << std::ranges::equal(qual_vec, qual_vec2) << '\n'; // prints 1 (true) | ||
| } |
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