SeqAn3  3.0.2
The Modern C++ library for sequence analysis.
seqan3::phred42 Class Reference

Quality type for traditional Sanger and modern Illumina Phred scores (typical range). 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.
 
Member types
using phred_type = int8_t
 The integer representation of a quality score assignable with =operator.
 

Public Member Functions

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 phred42assign_char (char_type const c) noexcept
 Assign from a character, implicitly converts invalid characters. More...
 
constexpr phred42assign_rank (rank_type const c) noexcept
 Assign from a numeric value. More...
 
Constructors, destructor and assignment
constexpr phred42 () noexcept=default
 Defaulted.
 
constexpr phred42 (phred42 const &) noexcept=default
 Defaulted.
 
constexpr phred42 (phred42 &&) noexcept=default
 Defaulted.
 
constexpr phred42operator= (phred42 const &) noexcept=default
 Defaulted.
 
constexpr phred42operator= (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 phred42assign_phred (phred_type const p) noexcept
 Assign from the numeric phred 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 phred42assign_char (char_type const c) noexcept
 Assign from a character, implicitly converts invalid characters. More...
 
constexpr phred42assign_rank (rank_type const c) noexcept
 Assign from a numeric value. More...
 
Read functions
constexpr phred_type to_phred () const noexcept
 Return the alphabet's value in phred representation.
 
Write functions
constexpr phred42assign_phred (phred_type const p) noexcept
 Assign from the numeric phred 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 phred42assign_char (char_type const c) noexcept
 Assign from a character, implicitly converts invalid characters. More...
 
constexpr phred42assign_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
 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, void >, char, char >
 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()).
 
Member types
using char_type = std::conditional_t< std::same_as< char, void >, char, char >
 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()).
 
Member types
using char_type = std::conditional_t< std::same_as< char, void >, char, char >
 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()).
 

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_sizerank_to_char
 Rank to char conversion table.
 
static constexpr std::array< phred_type, alphabet_sizerank_to_phred
 Rank to phred conversion table.
 

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< phred42operator""_phred42 (char const *s, std::size_t n)
 The seqan3::phred42 string literal. More...
 

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 seqan3::phred63, otherwise on construction exceeding scores are mapped to 41.

int main()
{
phred.assign_rank(2); // wrapper for assign_phred(2)
seqan3::debug_stream << (int) phred.to_phred() << "\n"; // 2
seqan3::debug_stream << phred.to_char() << "\n"; // '#'
seqan3::debug_stream << (int) 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
// we need to cast to(int)for human readable console output
}

Member Function Documentation

◆ assign_char()

constexpr phred42 & seqan3::alphabet_base< phred42 , size, char >::assign_char ( char_type const  c)
inlineconstexprnoexceptinherited

Assign from a character, implicitly converts invalid characters.

Parameters
cThe character to be assigned.

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

Complexity

Constant.

Exceptions

Guaranteed not to throw.

◆ assign_phred()

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

Assign from the numeric phred value.

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

Complexity

Constant.

◆ assign_rank()

constexpr phred42 & seqan3::alphabet_base< phred42 , size, char >::assign_rank ( rank_type const  c)
inlineconstexprnoexceptinherited

Assign from a numeric value.

Parameters
cThe rank to be assigned.

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

Complexity

Constant.

Exceptions

Guaranteed not to throw.

◆ to_char()

constexpr char_type seqan3::alphabet_base< phred42 , size, char >::to_char
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.

◆ to_rank()

constexpr rank_type seqan3::alphabet_base< phred42 , size, char >::to_rank
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.

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]sA pointer to the character sequence to assign from.
[in]nThe 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>:

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

The documentation for this class was generated from the following file:
debug_stream.hpp
Provides seqan3::debug_stream and related types.
seqan3::quality_base::assign_phred
constexpr derived_type & assign_phred(phred_type const p) noexcept
Assign from the numeric phred value.
Definition: quality_base.hpp:111
std::vector
seqan3::alphabet_base::to_char
constexpr char_type to_char() const noexcept
Return the letter as a character of char_type.
Definition: alphabet_base.hpp:96
algorithm
Adaptations of algorithms from the Ranges TS.
seqan3::quality_base::to_phred
constexpr phred_type to_phred() const noexcept
Return the alphabet's value in phred representation.
Definition: quality_base.hpp:91
seqan3::phred42
Quality type for traditional Sanger and modern Illumina Phred scores (typical range).
Definition: phred42.hpp:43
seqan3::debug_stream
debug_stream_type debug_stream
A global instance of seqan3::debug_stream_type.
Definition: debug_stream.hpp:42
seqan3::alphabet_base::assign_rank
constexpr derived_type & assign_rank(rank_type const c) noexcept
Assign from a numeric value.
Definition: alphabet_base.hpp:167
seqan3::alphabet_base::to_rank
constexpr rank_type to_rank() const noexcept
Return the letter's numeric value (rank in the alphabet).
Definition: alphabet_base.hpp:118
phred42.hpp
Provides seqan3::phred42 quality scores.