seqan3::phred42 Class Reference

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

#include <seqan3/alphabet/quality/phred42.hpp>

Inheritance diagram for seqan3::phred42:

Public Types
Member types
using	phred_type = int8_t
	The integer representation of a quality score assignable with =operator.

Public Member Functions
Constructors, destructor and assignment
constexpr	phred42 () noexcept=default
	Defaulted.
constexpr	phred42 (phred42 const &) noexcept=default
	Defaulted.
constexpr	phred42 (phred42 &&) noexcept=default
	Defaulted.
constexpr phred42 &	operator= (phred42 const &) noexcept=default
	Defaulted.
constexpr phred42 &	operator= (phred42 &&) noexcept=default
	Defaulted.
	~phred42 () noexcept=default
	Defaulted.
constexpr	phred42 (phred_type const p)
	Construct from Phred score value.
Read functions
constexpr phred_type	to_phred () const noexcept
	Return the alphabet's value in Phred score representation. More...
Write functions
constexpr phred42 &	assign_phred (phred_type const p) noexcept
	Assign from the numeric Phred score value. More...
Read functions
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...
Write functions
constexpr derived_type &	assign_char (char_type const c) 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
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...
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.

Protected Types
Member types
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...

Static Protected Attributes
static constexpr std::array< rank_type, 256 >	char_to_rank
	Char to rank conversion table.
static constexpr std::array< rank_type, 256 >	phred_to_rank
	Phred to rank conversion table.
static constexpr std::array< char_type, alphabet_size >	rank_to_char
	Rank to char conversion table.
static constexpr std::array< phred_type, alphabet_size >	rank_to_phred
	Rank to phred conversion table.

Private Types
using	base_t = quality_base< phred42, 42 >
	The base class.

Private Attributes
friend	base_t
	Befriend seqan3::quality_base.
friend	derived_type
	Befriend the derived_type so it can instantiate.
rank_type	rank {}
	The value of the alphabet letter is stored as the rank.

Related Functions
(Note that these are not member functions.)
Literals
constexpr phred42	operator""_phred42 (char const c) noexcept
	The seqan3::phred42 char literal. More...
std::vector< phred42 >	operator""_phred42 (char const *s, std::size_t n)
	The seqan3::phred42 string literal. More...
Generic serialisation functions for all seqan3::semialphabet
All types that satisfy seqan3::semialphabet can be serialised via Cereal.
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...

Detailed Description

Quality type for traditional Sanger and modern Illumina Phred scores.

The phred42 Quality alphabet represents the zero-based Phred score range [0..41] mapped to the consecutive ASCII range ['!' .. 'J']. It therefore can represent the Illumina 1.8+ standard and the original Sanger score. If you intend to use Phred scores exceeding 41, use the larger score types, namely seqan3::phred63 or seqan3::phred94, otherwise on construction exceeding scores are mapped to 41. Via seqan3::qualified, you can combine a nucleotide alphabet with the Phred score to save space. All dna and rna combinations with seqan3::phred42 still fit into a single byte, e.g. seqan3::qualified<seqan3::dna4, seqan3::phred42> (4 * 42 = 168 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/phred42.hpp>
#include <seqan3/alphabet/quality/qualified.hpp>
#include <seqan3/core/debug_stream.hpp>
 
using seqan3::operator""_dna4;
using seqan3::operator""_phred42;
 
int main()
{
    seqan3::phred42 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::phred42 another_phred;
    another_phred.assign_phred(49); // converted down to 41
    seqan3::debug_stream << another_phred.to_phred() << "\n"; // 41
 
    std::vector<seqan3::qualified<seqan3::dna4, seqan3::phred42>> query{{'A'_dna4, '!'_phred42},
                                                                        {'C'_dna4, 'A'_phred42},
                                                                        {'G'_dna4, '6'_phred42},
                                                                        {'T'_dna4, '&'_phred42}};
}

See also

Quality, it contains a comprehensive overview over all Phred implementations and what a Phred score represents.

Member Typedef Documentation

char_type

template<typename derived_type , size_t size, typename char_t = char>

using seqan3::alphabet_base< derived_type, size, char_t >::char_type = std::conditional_t<std::same_as<char_t, void>, char, char_t>

protectedinherited

The char representation; conditional needed to make semi alphabet definitions legal.

We need a return type for seqan3::alphabet_base::to_char and seqan3::alphabet_base::assign_char other than void to make these in-class definitions valid when char_t is void.

This entity is stable. Since version 3.1.

rank_type

template<typename derived_type , size_t size, typename char_t = char>

using seqan3::alphabet_base< derived_type, size, char_t >::rank_type = detail::min_viable_uint_t<size - 1>

protectedinherited

The type of the alphabet when represented as a number (e.g. via to_rank()).

This entity is stable. Since version 3.1.

Member Function Documentation

assign_char()

template<typename derived_type , size_t size, typename char_t = char>

constexpr derived_type& seqan3::alphabet_base< derived_type, size, char_t >::assign_char ( char_type const  c )

inlineconstexprnoexceptinherited

Assign from a character, implicitly converts invalid characters.

Parameters

c	The character to be assigned.

Provides an implementation for seqan3::assign_char_to, required to model seqan3::alphabet.

Complexity

Constant.

Exceptions

Guaranteed not to throw.

This entity is stable. Since version 3.1.

assign_phred()

constexpr phred42 & seqan3::quality_base< phred42 , size >::assign_phred ( phred_type const  p )

inlineconstexprnoexceptinherited

Assign from the numeric Phred score value.

Satisfies the seqan3::writable_quality_alphabet::assign_phred() requirement via the seqan3::assign_rank() wrapper.

See also

Quality

Complexity

Constant.

assign_rank()

template<typename derived_type , size_t size, typename char_t = char>

constexpr derived_type& seqan3::alphabet_base< derived_type, size, char_t >::assign_rank ( rank_type const  c )

inlineconstexprnoexceptinherited

Assign from a numeric value.

Parameters

c	The rank to be assigned.

Provides an implementation for seqan3::assign_rank_to, required to model seqan3::semialphabet.

Complexity

Constant.

Exceptions

Guaranteed not to throw.

This entity is stable. Since version 3.1.

to_char()

template<typename derived_type , size_t size, typename char_t = char>

constexpr char_type seqan3::alphabet_base< derived_type, size, char_t >::to_char ( ) const

inlineconstexprnoexceptinherited

Return the letter as a character of char_type.

Provides an implementation for seqan3::to_char, required to model seqan3::alphabet.

Complexity

Constant.

Exceptions

Guaranteed not to throw.

This entity is stable. Since version 3.1.

to_phred()

constexpr phred_type seqan3::quality_base< phred42 , size >::to_phred ( ) const

inlineconstexprnoexceptinherited

Return the alphabet's value in Phred score representation.

See also

Quality

to_rank()

template<typename derived_type , size_t size, typename char_t = char>

constexpr rank_type seqan3::alphabet_base< derived_type, size, char_t >::to_rank ( ) const

inlineconstexprnoexceptinherited

Return the letter's numeric value (rank in the alphabet).

Provides an implementation for seqan3::to_rank, required to model seqan3::semialphabet.

Complexity

Constant.

Exceptions

Guaranteed not to throw.

This entity is stable. Since version 3.1.

Friends And Related Function Documentation

operator""_phred42() [1/2]

std::vector< phred42 > operator""_phred42 ( char const *  s, std::size_t  n  )

related

The seqan3::phred42 string literal.

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::phred42>

You can use this string literal to easily assign to std::vector<seqan3::phred42>:

#include <seqan3/alphabet/quality/phred42.hpp>
#include <seqan3/core/debug_stream.hpp>
#include <seqan3/std/algorithm>
 
int main()
{
    using seqan3::operator""_phred42;
 
    // directly assign to a std::vector<phred42> using a string literal
    std::vector<seqan3::phred42> qual_vec = "###!"_phred42;
 
    // This is the same as a sequence of char literals:
    std::vector<seqan3::phred42> qual_vec2 = {'#'_phred42, '#'_phred42, '#'_phred42, '!'_phred42};
 
    seqan3::debug_stream << std::ranges::equal(qual_vec, qual_vec2) << '\n'; // prints 1 (true)
}

operator""_phred42() [2/2]

constexpr phred42 operator""_phred42 ( char const  c )

related

The seqan3::phred42 char literal.

Returns

seqan3::phred42

save_minimal()

template<cereal_output_archive archive_t, semialphabet alphabet_t>

alphabet_rank_t< alphabet_t > save_minimal ( archive_t const &  , alphabet_t const &  l  )

related

Save an alphabet letter to stream.

Template Parameters

archive_t	Must satisfy seqan3::cereal_output_archive.
alphabet_t	Type of l; must satisfy seqan3::semialphabet.

Parameters

l	The alphabet letter.

Delegates to seqan3::to_rank.

Attention

These functions are never called directly, see the Alphabet module on how to use serialisation.

This entity is stable. Since version 3.1.

Member Data Documentation

alphabet_size

template<typename derived_type , size_t size, typename char_t = char>

constexpr detail::min_viable_uint_t<size> seqan3::alphabet_base< derived_type, size, char_t >::alphabet_size = size

staticconstexprinherited

The size of the alphabet, i.e. the number of different values it can take.

This entity is stable. Since version 3.1.

---

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

• seqan3/alphabet/quality/phred42.hpp