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

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 = 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 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 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...
 

Static Public Attributes

static detail::min_viable_uint_t< size > constexpr 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.
 

Static Protected Attributes

static std::array< rank_type, 256 > constexpr char_to_rank
 Char to rank conversion table.
 
static std::array< rank_type, 256 > constexpr phred_to_rank
 Phred to rank conversion table.
 
static std::array< char_type, alphabet_size > constexpr rank_to_char
 Rank to char conversion table.
 
static std::array< phred_type, alphabet_size > constexpr rank_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...
 
Requirements for std::totally_ordered

You can expect these functions on all types that implement std::totally_ordered.

bool operator< (type const &lhs, type const &rhs)
 Less-than, greater-than and -or-equal comparisons. More...
 
bool operator<= (type const &lhs, type const &rhs)
 Less-than, greater-than and -or-equal comparisons. More...
 
bool operator> (type const &lhs, type const &rhs)
 Less-than, greater-than and -or-equal comparisons. More...
 
bool operator>= (type const &lhs, type const &rhs)
 Less-than, greater-than and -or-equal comparisons. More...
 
Requirements for std::equality_comparable

You can expect these functions on all types that implement std::Equality_comparable.

bool operator== (type const &lhs, type const &rhs)
 (In-)Equality comparison. More...
 
bool operator!= (type const &lhs, type const &rhs)
 (In-)Equality comparison. More...
 
Requirements for std::swappable

You can expect these functions on all types that implement std::swappable.

void swap (t &lhs, t &rhs)
 Swaps the contents of two objects. 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)
inlinenoexceptinherited

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)
inlinenoexceptinherited

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)
inlinenoexceptinherited

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 ( ) const
inlinenoexceptinherited

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 ( ) const
inlinenoexceptinherited

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]

constexpr phred42 operator""_phred42 ( char const  c)
related

The seqan3::phred42 char literal.

Returns
seqan3::phred42

◆ operator""_phred42() [2/2]

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) << std::endl; // prints 1 (true)
}

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