seqan3::phred63 Class Reference

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

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

Inheritance diagram for seqan3::phred63:

Public Member Functions
Constructors, destructor and assignment
constexpr	phred63 () noexcept=default
	Defaulted.
constexpr	phred63 (phred63 const &) noexcept=default
	Defaulted.
constexpr	phred63 (phred63 &&) noexcept=default
	Defaulted.
constexpr phred63 &	operator= (phred63 const &) noexcept=default
	Defaulted.
constexpr phred63 &	operator= (phred63 &&) noexcept=default
	Defaulted.
	~phred63 () noexcept=default
	Defaulted.
constexpr	phred63 (phred_type const p)
	Allow construction from the Phred score value. More...
Public Member Functions inherited from seqan3::phred_base< phred63, 63 >
constexpr phred_type	to_phred () const noexcept
	Return the alphabet's value in Phred score representation. More...
constexpr phred63 &	assign_phred (phred_type const p) noexcept
	Assign from the numeric Phred score value. More...
constexpr	phred_base (other_qual_type const &other) noexcept
	Allow explicit construction from any other quality type by means of the Phred score representation. More...
Public Member Functions inherited from seqan3::alphabet_base< derived_type, size, char_t >
constexpr	alphabet_base () noexcept=default
	Defaulted.
constexpr	alphabet_base (alphabet_base const &) noexcept=default
	Defaulted.
constexpr	alphabet_base (alphabet_base &&) noexcept=default
	Defaulted.
constexpr alphabet_base &	operator= (alphabet_base const &) noexcept=default
	Defaulted.
constexpr alphabet_base &	operator= (alphabet_base &&) noexcept=default
	Defaulted.
	~alphabet_base () noexcept=default
	Defaulted.
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...
constexpr derived_type &	assign_char (char_type const chr) 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
Member variables.
static constexpr phred_type	offset_phred {0}
	The projection offset between Phred and rank score representation. More...
static constexpr char_type	offset_char {'!'}
	The projection offset between char and rank score representation. More...
Static Public Attributes inherited from seqan3::alphabet_base< derived_type, size, char_t >
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...

Related Functions
(Note that these are not member functions.)
Quality literals
constexpr phred63	operator""_phred63 (char const c) noexcept
	The seqan3::phred63 char literal. More...
std::vector< phred63 >	operator""_phred63 (char const *s, std::size_t n)
	The seqan3::phred63 string literal. More...

Additional Inherited Members
Public Types inherited from seqan3::phred_base< phred63, 63 >
using	phred_type = int8_t
	The integer representation of the quality score. More...
Protected Types inherited from seqan3::alphabet_base< derived_type, size, char_t >
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...

Detailed Description

Quality type for traditional Sanger and modern Illumina Phred scores.

The phred63 Quality alphabet represents the zero-based Phred score range [0..62] mapped to the consecutive ASCII range ['!' .. '_']. It represents the Sanger and Illumina 1.8+ standard beyond the typical range of raw reads (0 to 41), namely seqan3::phred42. If you intend to use Phred scores exceeding 62, use the larger score type, namely seqan3::phred94. Via seqan3::qualified, you can combine a nucleotide alphabet with the Phred score to save space. All seqan3::dna4 and seqan3::rna4 combinations with seqan3::phred63 still fit into a single byte, e.g. seqan3::qualified<seqan3::dna4, seqan3::phred63> (4 * 63 = 252 values can be stored in a single byte which can contain up to 256 values).

#include <seqan3/alphabet/quality/phred63.hpp>
#include <seqan3/core/debug_stream.hpp>
 
int main()
{
    using namespace seqan3::literals;
 
    seqan3::phred63 letter{'@'_phred63};
 
    letter.assign_char('!');
    seqan3::debug_stream << letter.to_phred() << '\n'; // prints "0"
    seqan3::debug_stream << letter.to_char() << '\n';  // prints "!"
 
    letter.assign_phred(72); // Values exceeding the maximum are implicitly limited to the maximum phred value.
    seqan3::debug_stream << letter.to_phred() << '\n'; // prints "62"
}

See also

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

This entity is stable. Since version 3.1.

Constructor & Destructor Documentation

phred63()

constexpr seqan3::phred63::phred63 ( phred_type const  p )

inlineconstexpr

Allow construction from the Phred score value.

Deprecated:

This will be removed in 3.1.0. Please use seqan3::phred63::assign_phred() or '!'_phred63.

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]	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::phred63>

You can use this string literal to easily assign to std::vector<seqan3::phred63>:

#include <seqan3/alphabet/quality/phred63.hpp>
 
int main()
{
    using namespace seqan3::literals;
 
    std::vector<seqan3::phred63> sequence1{"##!!##"_phred63};
    std::vector<seqan3::phred63> sequence2 = "##!!##"_phred63;
    auto sequence3 = "##!!##"_phred63;
}

This entity is stable. Since version 3.1.

operator""_phred63() [2/2]

constexpr phred63 operator""_phred63 ( char const  c )

related

The seqan3::phred63 char literal.

Returns

seqan3::phred63

You can use this char literal to assign a seqan3::phred63 character:

#include <seqan3/alphabet/quality/phred63.hpp>
 
int main()
{
    using namespace seqan3::literals;
 
    seqan3::phred63 letter1{'!'_phred63};
    auto letter2 = '!'_phred63;
}

This entity is stable. Since version 3.1.

Member Data Documentation

offset_char

constexpr char_type seqan3::phred63::offset_char {'!'}

staticconstexpr

The projection offset between char and rank score representation.

This entity is stable. Since version 3.1.

offset_phred

constexpr phred_type seqan3::phred63::offset_phred {0}

staticconstexpr

The projection offset between Phred and rank score representation.

This entity is stable. Since version 3.1.

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

• seqan3/alphabet/quality/phred63.hpp