SeqAn3 3.4.0-rc.1
The Modern C++ library for sequence analysis.
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seqan3::phred63 Class Reference
Alphabet » Quality

Quality type for traditional Sanger and modern Illumina Phred scores. More...

#include <seqan3/alphabet/quality/phred63.hpp>

+ Inheritance diagram for seqan3::phred63:

Public Member Functions

Constructors, destructor and assignment
constexpr phred63 () noexcept=default
 Defaulted.
 
constexpr phred63 (phred63 const &) noexcept=default
 Defaulted.
 
constexpr phred63 (phred63 &&) noexcept=default
 Defaulted.
 
constexpr phred63 & operator= (phred63 const &) noexcept=default
 Defaulted.
 
constexpr phred63 & operator= (phred63 &&) noexcept=default
 Defaulted.
 
 ~phred63 () noexcept=default
 Defaulted.
 
- Public Member Functions inherited from seqan3::phred_base< phred63, 63 >
constexpr phred_type to_phred () const noexcept
 Return the alphabet's value in Phred score representation.
 
constexpr phred63 & 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.
 

Related Symbols

(Note that these are not member symbols.)

Quality literals
constexpr phred63 operator""_phred63 (char const c) noexcept
 The seqan3::phred63 char literal.
 
constexpr std::vector< phred63 > operator""_phred63 (char const *s, std::size_t n)
 The seqan3::phred63 string literal.
 

Additional Inherited Members

- Public Types inherited from seqan3::phred_base< phred63, 63 >
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 traditional Sanger and modern Illumina Phred scores.

The phred63 Quality alphabet represents the zero-based Phred score range [0..62] mapped to the consecutive ASCII range ['!' .. '_']. It represents the Sanger and Illumina 1.8+ standard beyond the typical range of raw reads (0 to 41), namely seqan3::phred42. If you intend to use Phred scores exceeding 62, use the larger score type, namely seqan3::phred94. Via seqan3::qualified, you can combine a nucleotide alphabet with the Phred score to save space. All seqan3::dna4 and seqan3::rna4 combinations with seqan3::phred63 still fit into a single byte, e.g. seqan3::qualified<seqan3::dna4, seqan3::phred63> (4 * 63 = 252 values can be stored in a single byte which can contain up to 256 values).

// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin
// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik
// SPDX-License-Identifier: CC0-1.0
#include <seqan3/alphabet/quality/phred63.hpp>
#include <seqan3/core/debug_stream.hpp>
int main()
{
using namespace seqan3::literals;
seqan3::phred63 letter{'@'_phred63};
letter.assign_char('!');
seqan3::debug_stream << letter.to_phred() << '\n'; // prints "0"
seqan3::debug_stream << letter.to_char() << '\n'; // prints "!"
letter.assign_phred(72); // Values exceeding the maximum are implicitly limited to the maximum phred value.
seqan3::debug_stream << letter.to_phred() << '\n'; // prints "62"
}
seqan3::debug_stream_type
A "pretty printer" for most SeqAn data structures and related types.
Definition debug_stream_type.hpp:79
seqan3::phred63
Quality type for traditional Sanger and modern Illumina Phred scores.
Definition phred63.hpp:44
debug_stream.hpp
Provides seqan3::debug_stream and related types.
seqan3::debug_stream
debug_stream_type debug_stream
A global instance of seqan3::debug_stream_type.
Definition debug_stream.hpp:37
seqan3::literals
The SeqAn namespace for literals.
phred63.hpp
Provides seqan3::phred63 quality scores.
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""_phred63() [1/2]

constexpr std::vector< phred63 > operator""_phred63 ( char const *  s,
std::size_t  n 
)
related

The seqan3::phred63 string literal.

Parameters
[in]sA pointer to the character sequence to assign from.
[in]nThe length of the character sequence to assign from.
Returns
seqan3::std::vector<seqan3::phred63>

You can use this string literal to easily assign to std::vector<seqan3::phred63>:

// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin
// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik
// SPDX-License-Identifier: CC0-1.0
#include <seqan3/alphabet/quality/phred63.hpp>
int main()
{
using namespace seqan3::literals;
std::vector<seqan3::phred63> sequence1{"##!!##"_phred63};
std::vector<seqan3::phred63> sequence2 = "##!!##"_phred63;
auto sequence3 = "##!!##"_phred63;
}

This entity is stable. Since version 3.1.

◆ operator""_phred63() [2/2]

constexpr phred63 operator""_phred63 ( char const  c)
related

The seqan3::phred63 char literal.

Returns
seqan3::phred63

You can use this char literal to assign a seqan3::phred63 character:

// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin
// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik
// SPDX-License-Identifier: CC0-1.0
#include <seqan3/alphabet/quality/phred63.hpp>
int main()
{
using namespace seqan3::literals;
seqan3::phred63 letter1{'!'_phred63};
auto letter2 = '!'_phred63;
}

This entity is stable. Since version 3.1.

Member Data Documentation

◆ offset_char

constexpr char_type seqan3::phred63::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::phred63::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:
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