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.

constexpr	phred63 (phred_type const p)
	Construct from Phred score value.

Public Member Functions inherited from seqan3::quality_base< phred63, 63 >
constexpr phred_type	to_phred () const noexcept
	Return the alphabet's value in Phred score representation. More...

constexpr phred63 &	assign_phred (phred_type const p) noexcept
	Assign from the numeric Phred score value. More...

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

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. More...

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

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

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

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

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

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. More...

Private Types
using	base_t = quality_base< phred63, 63 >
	The base class.

Private Attributes
friend	base_t
	Befriend seqan3::quality_base.

Related Functions
(Note that these are not member functions.)
Literals
constexpr phred63	operator""_phred63 (char const c) noexcept
	The seqan3::phred63 char literal. More...

std::vector< phred63 >	operator""_phred63 (char const *s, std::size_t n)
	The seqan3::phred63 string literal. More...

Related Functions 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. More...

Additional Inherited Members
Public Types inherited from seqan3::quality_base< phred63, 63 >
using	phred_type = int8_t
	The integer representation of the quality score. More...

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. More...

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()). More...

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).

#include <seqan3/alphabet/nucleotide/dna4.hpp>
#include <seqan3/alphabet/quality/phred63.hpp>
#include <seqan3/alphabet/quality/qualified.hpp>
#include <seqan3/core/debug_stream.hpp>
 
using seqan3::operator""_dna4;
using seqan3::operator""_phred63;
 
int main()
{
    seqan3::phred63 phred;
    phred.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
 
    seqan3::phred63 another_phred{49};
    seqan3::debug_stream << another_phred.to_phred() << "\n"; // 49
 
    seqan3::phred63 a_third_phred;
    another_phred.assign_phred(75); // converted down to 62
    seqan3::debug_stream << another_phred.to_phred() << "\n"; // 62
 
    std::vector<seqan3::qualified<seqan3::dna4, seqan3::phred63>> query{{'A'_dna4, '!'_phred63},
                                                                        {'C'_dna4, 'A'_phred63},
                                                                        {'G'_dna4, '6'_phred63},
                                                                        {'T'_dna4, '&'_phred63}};
}

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 Function Documentation

◆ operator""_phred63() [1/2]

std::vector< phred63 > operator""_phred63	(	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::phred63>

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

#include <seqan3/alphabet/quality/phred63.hpp>
#include <seqan3/core/debug_stream.hpp>
#include <seqan3/std/algorithm>
 
int main()
{
    using seqan3::operator""_phred63;
 
    // directly assign to a std::vector<phred63> using a string literal
    std::vector<seqan3::phred63> qual_vec = "###!"_phred63;
 
    // This is the same as a sequence of char literals:
    std::vector<seqan3::phred63> qual_vec2 = {'#'_phred63, '#'_phred63, '#'_phred63, '!'_phred63};
 
    seqan3::debug_stream << std::ranges::equal(qual_vec, qual_vec2) << '\n'; // prints 1 (true)
}

This entity is stable. Since version 3.1.

◆ operator""_phred63() [2/2]

constexpr phred63 operator""_phred63 ( char const c )

Returns: seqan3::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:

seqan3/alphabet/quality/phred63.hpp

Public Member Functions

Static Public Attributes

Private Types

Private Attributes

Related Functions

Additional Inherited Members

Detailed Description

Friends And Related Function Documentation

◆ operator""_phred63() [1/2]

◆ operator""_phred63() [2/2]

Member Data Documentation

◆ offset_char

◆ offset_phred