bio::alphabet::phred42 Class Reference

Quality type for traditional Sanger and modern Illumina Phred scores (typical range).. More...

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

Inheritance diagram for bio::alphabet::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 value.
Read functions
constexpr phred_type	to_phred () const noexcept
	Return the alphabet's value in phred representation.
Write functions
constexpr phred42 &	assign_phred (phred_type const p) noexcept
	Assign from the numeric phred value.
Read functions
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).
Write functions
constexpr derived_type &	assign_char (char_type const c) 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
static constexpr size_t	alphabet_size = size
	The size of the alphabet, i.e. the number of different values it can take.
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.
using	rank_type = meta::detail::min_viable_uint_t< size - 1 >
	The type of the alphabet when represented as a number (e.g. via to_rank()).

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.

Related Functions
(Note that these are not member functions.)
Literals
consteval phred42	operator""_phred42 (char const c)
	The bio::alphabet::phred42 char literal.
template<meta::detail::literal_buffer_string str>
constexpr std::vector< phred42 >	operator""_phred42 ()
	The bio::alphabet::phred42 string literal.

Detailed Description

Quality type for traditional Sanger and modern Illumina Phred scores (typical range).

.

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 type, namely bio::alphabet::phred63, otherwise on construction exceeding scores are mapped to 41.

#include <bio/alphabet/quality/phred42.hpp>
#include <bio/alphabet/fmt.hpp>
 
int main()
{
    bio::alphabet::phred42 phred;
    phred.assign_rank(2); // wrapper for assign_phred(2)
    fmt::print("{}\n", (int) phred.to_phred()); // 2
    fmt::print("{}\n", phred.to_char());        // '#'
    fmt::print("{}\n", (int) phred.to_rank());  // 2
 
    bio::alphabet::phred42 another_phred;
    another_phred.assign_phred(49); // converted down to 41
    fmt::print("{}\n", another_phred.to_phred()); // 41
    // we need to cast to(int)for human readable console output
}

Member Function Documentation

assign_char()

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

constexpr derived_type & bio::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 bio::alphabet::assign_char_to, required to model bio::alphabet::alphabet.

Complexity

Constant.

Exceptions

Guaranteed not to throw.

assign_phred()

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

inlineconstexprnoexceptinherited

Assign from the numeric phred value.

Satisfies the bio::alphabet::writable_quality::assign_phred() requirement via the bio::alphabet::assign_rank() wrapper.

Complexity

Constant.

assign_rank()

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

constexpr derived_type & bio::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 bio::alphabet::assign_rank_to, required to model bio::alphabet::semialphabet.

Complexity

Constant.

Exceptions

Guaranteed not to throw.

to_char()

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

constexpr char_type bio::alphabet::base< derived_type, size, char_t >::to_char ( ) const

inlineconstexprnoexceptinherited

Return the letter as a character of char_type.

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

Complexity

Constant.

Exceptions

Guaranteed not to throw.

to_rank()

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

constexpr rank_type bio::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 bio::alphabet::to_rank, required to model bio::alphabet::semialphabet.

Complexity

Constant.

Exceptions

Guaranteed not to throw.

Friends And Related Function Documentation

operator""_phred42() [1/2]

template<meta::detail::literal_buffer_string str>

constexpr std::vector< phred42 > operator""_phred42 ( )

related

The bio::alphabet::phred42 string literal.

Returns

std::vector<bio::alphabet::phred42>

You can use this string literal to easily create a std::vector<bio::alphabet::phred42>:

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

operator""_phred42() [2/2]

consteval phred42 operator""_phred42 ( char const  c )

related

The bio::alphabet::phred42 char literal.

Returns

bio::alphabet::phred42

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

• bio/alphabet/quality/phred42.hpp