SeqAn3  3.0.2
The Modern C++ library for sequence analysis.
seqan3::phred63 Class Reference

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

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

+ Inheritance diagram for seqan3::phred63:

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 phred63assign_char (char_type const c) noexcept
 Assign from a character, implicitly converts invalid characters. More...
 
constexpr phred63assign_rank (rank_type const c) noexcept
 Assign from a numeric value. More...
 
Constructors, destructor and assignment
constexpr phred63 () noexcept=default
 Defaulted.
 
constexpr phred63 (phred63 const &) noexcept=default
 Defaulted.
 
constexpr phred63 (phred63 &&) noexcept=default
 Defaulted.
 
constexpr phred63operator= (phred63 const &) noexcept=default
 Defaulted.
 
constexpr phred63operator= (phred63 &&) noexcept=default
 Defaulted.
 
 ~phred63 () noexcept=default
 Defaulted.
 
constexpr phred63 (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 phred63assign_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 phred63assign_char (char_type const c) noexcept
 Assign from a character, implicitly converts invalid characters. More...
 
constexpr phred63assign_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 phred63assign_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 phred63assign_char (char_type const c) noexcept
 Assign from a character, implicitly converts invalid characters. More...
 
constexpr phred63assign_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 phred63 operator""_phred63 (char const c) noexcept
 The seqan3::phred63 char literal. More...
 
std::vector< phred63operator""_phred63 (char const *s, std::size_t n)
 The seqan3::phred63 string literal. More...
 

Detailed Description

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

The phred63 quality alphabet represents the zero-based phred score range [0..62] mapped to the ASCII range ['!' .. '~']. It represents the Sanger and Illumina 1.8+ standard beyond the typical range of raw reads (0 to 41).

int main()
{
phred.assign_rank(2); // wrapper for assign_phred(2)
seqan3::debug_stream << static_cast<int>(phred.to_phred()) << "\n"; // 2
seqan3::debug_stream << phred.to_char() << "\n"; // '#'
seqan3::debug_stream << static_cast<int>(phred.to_rank()) << "\n"; // 2
seqan3::phred63 another_phred{49};
seqan3::debug_stream << another_phred.to_phred() << "\n"; // 49
// we need to cast to (int) for human readable console output
}

Member Function Documentation

◆ assign_char()

constexpr phred63 & seqan3::alphabet_base< phred63 , 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 phred63 & seqan3::quality_base< phred63 , 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 phred63 & seqan3::alphabet_base< phred63 , 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< phred63 , 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< phred63 , 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""_phred63() [1/2]

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>:

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)
}

◆ operator""_phred63() [2/2]

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

The seqan3::phred63 char literal.

Returns
seqan3::phred63

The documentation for this class was generated from the following file:
debug_stream.hpp
Provides seqan3::debug_stream and related types.
seqan3::phred63
Quality type for traditional Sanger and modern Illumina Phred scores (full range).
Definition: phred63.hpp:41
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::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
phred63.hpp
Provides seqan3::phred63 quality scores.
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