Quality type for PacBio Phred scores of HiFi reads. More...

#include <seqan3/alphabet/quality/phred94.hpp>

Inheritance diagram for seqan3::phred94:

Public Member Functions
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.

Public Member Functions inherited from seqan3::phred_base< phred94, 94 >
constexpr phred_type	to_phred () const noexcept
	Return the alphabet's value in Phred score representation.

constexpr phred94 &	assign_phred (phred_type const p) noexcept
	Assign from the numeric Phred score value.

constexpr	phred_base (other_qual_type const &other) noexcept
	Allow explicit construction from any other quality type by means of the Phred score representation.

Public Member Functions inherited from seqan3::alphabet_base< derived_type, size, char_t >
constexpr	alphabet_base () noexcept=default
	Defaulted.

constexpr	alphabet_base (alphabet_base const &) noexcept=default
	Defaulted.

constexpr	alphabet_base (alphabet_base &&) noexcept=default
	Defaulted.

constexpr alphabet_base &	operator= (alphabet_base const &) noexcept=default
	Defaulted.

constexpr alphabet_base &	operator= (alphabet_base &&) noexcept=default
	Defaulted.

	~alphabet_base () noexcept=default
	Defaulted.

constexpr char_type	to_char () const noexcept
	Return the letter as a character of char_type.

constexpr rank_type	to_rank () const noexcept
	Return the letter's numeric value (rank in the alphabet).

constexpr derived_type &	assign_char (char_type const chr) noexcept
	Assign from a character, implicitly converts invalid characters.

constexpr derived_type &	assign_rank (rank_type const c) noexcept
	Assign from a numeric value.

Static Public Attributes
Member variables.
static constexpr phred_type	offset_phred {0}
	The projection offset between Phred and rank score representation.

static constexpr char_type	offset_char {'!'}
	The projection offset between char and rank score representation.

Static Public Attributes inherited from seqan3::alphabet_base< derived_type, size, char_t >
static constexpr detail::min_viable_uint_t< size >	alphabet_size = size
	The size of the alphabet, i.e. the number of different values it can take.

Private Types
using	base_t = phred_base< phred94, 94 >
	The base class.

Private Attributes
friend	base_t
	Befriend seqan3::phred_base.

Related Symbols
(Note that these are not member symbols.)
Quality literals
constexpr phred94	operator""_phred94 (char const c) noexcept
	The seqan3::phred94 char literal.

constexpr std::vector< phred94 >	operator""_phred94 (char const *s, std::size_t n)
	The seqan3::phred94 string literal.

Related Symbols inherited from semialphabet
template<cereal_output_archive archive_t, semialphabet alphabet_t>
alphabet_rank_t< alphabet_t >	save_minimal (archive_t const &, alphabet_t const &l)
	Save an alphabet letter to stream.

template<cereal_input_archive archive_t, typename wrapped_alphabet_t >
void	load_minimal (archive_t const &, wrapped_alphabet_t &&l, alphabet_rank_t< detail::strip_cereal_wrapper_t< wrapped_alphabet_t > > const &r)
	Restore an alphabet letter from a saved rank.

Additional Inherited Members
Public Types inherited from seqan3::phred_base< phred94, 94 >
using	phred_type = int8_t
	The integer representation of the quality score.

Protected Types inherited from seqan3::alphabet_base< derived_type, size, char_t >
using	char_type = std::conditional_t< std::same_as< char_t, void >, char, char_t >
	The char representation; conditional needed to make semi alphabet definitions legal.

using	rank_type = detail::min_viable_uint_t< size - 1 >
	The type of the alphabet when represented as a number (e.g. via to_rank()).

Detailed Description

Quality type for PacBio Phred scores of HiFi reads.

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.

// SPDX-FileCopyrightText: 2006-2025 Knut Reinert & Freie Universität Berlin
// SPDX-FileCopyrightText: 2016-2025 Knut Reinert & MPI für molekulare Genetik
// SPDX-License-Identifier: CC0-1.0
 
#include <seqan3/alphabet/quality/phred94.hpp>
#include <seqan3/core/debug_stream.hpp>
 
int main()
{
    using namespace seqan3::literals;
 
    seqan3::phred94 letter{'@'_phred94};
 
    letter.assign_char('!');
    seqan3::debug_stream << letter.to_phred() << '\n'; // prints "0"
    seqan3::debug_stream << letter.to_char() << '\n';  // prints "!"
 
    letter.assign_phred(99); // Values exceeding the maximum are implicitly limited to the maximum phred value.
    seqan3::debug_stream << letter.to_phred() << '\n'; // prints "93"
}

See also: quality, it contains a comprehensive overview over all Phred implementations and what a Phred score represents.

This entity is stable. Since version 3.1.

Friends And Related Symbol Documentation

◆ operator""_phred94() [1/2]

constexpr std::vector< phred94 > operator""_phred94	(	char const *	s,
		std::size_t	n
	)

Parameters

[in]	s	A pointer to the character sequence to assign from.
[in]	n	The length of the character sequence to assign from.

Returns: seqan3::std::vector<seqan3::phred94>

You can use this string literal to easily assign to std::vector<seqan3::phred94>:

// SPDX-FileCopyrightText: 2006-2025 Knut Reinert & Freie Universität Berlin
// SPDX-FileCopyrightText: 2016-2025 Knut Reinert & MPI für molekulare Genetik
// SPDX-License-Identifier: CC0-1.0
 
#include <seqan3/alphabet/quality/phred94.hpp>
 
int main()
{
    using namespace seqan3::literals;
 
    std::vector<seqan3::phred94> sequence1{"##!!##"_phred94};
    std::vector<seqan3::phred94> sequence2 = "##!!##"_phred94;
    auto sequence3 = "##!!##"_phred94;
}

This entity is stable. Since version 3.1.

◆ operator""_phred94() [2/2]

constexpr phred94 operator""_phred94 ( char const c )

Returns: seqan3::phred94

You can use this char literal to assign a seqan3::phred94 character:

// SPDX-FileCopyrightText: 2006-2025 Knut Reinert & Freie Universität Berlin
// SPDX-FileCopyrightText: 2016-2025 Knut Reinert & MPI für molekulare Genetik
// SPDX-License-Identifier: CC0-1.0
 
#include <seqan3/alphabet/quality/phred94.hpp>
 
int main()
{
    using namespace seqan3::literals;
 
    seqan3::phred94 letter1{'!'_phred94};
    auto letter2 = '!'_phred94;
}

This entity is stable. Since version 3.1.

Member Data Documentation

◆ offset_char

constexpr char_type seqan3::phred94::offset_char {'!'}

staticconstexpr

The projection offset between char and rank score representation.

This entity is stable. Since version 3.1.

◆ offset_phred

constexpr phred_type seqan3::phred94::offset_phred {0}

staticconstexpr

The projection offset between Phred and rank score representation.

This entity is stable. Since version 3.1.

The documentation for this class was generated from the following file:

phred94.hpp

Public Member Functions

Static Public Attributes

Private Types

Private Attributes

Related Symbols

Additional Inherited Members

Detailed Description

Friends And Related Symbol Documentation

◆ operator""_phred94() [1/2]

◆ operator""_phred94() [2/2]

Member Data Documentation

◆ offset_char

◆ offset_phred