SeqAn3 3.4.0-rc.1
The Modern C++ library for sequence analysis.
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seqan3::phred42 Class Reference

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

#include <seqan3/alphabet/quality/phred42.hpp>

+ Inheritance diagram for seqan3::phred42:

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.
 
- Public Member Functions inherited from seqan3::phred_base< phred42, 42 >
constexpr phred_type to_phred () const noexcept
 Return the alphabet's value in Phred score representation.
 
constexpr phred42assign_phred (phred_type const p) noexcept
 Assign from the numeric Phred score value.
 
constexpr phred_base (other_qual_type const &other) noexcept
 Allow explicit construction from any other quality type by means of the Phred score representation.
 
- 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_baseoperator= (alphabet_base const &) noexcept=default
 Defaulted.
 
constexpr alphabet_baseoperator= (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.
 
constexpr rank_type to_rank () const noexcept
 Return the letter's numeric value (rank in the alphabet).
 
constexpr derived_type & assign_char (char_type const chr) 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

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 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.
 

Related Functions

(Note that these are not member functions.)

Quality literals
constexpr phred42 operator""_phred42 (char const c) noexcept
 The seqan3::phred42 char literal.
 
constexpr std::vector< phred42operator""_phred42 (char const *s, std::size_t n)
 The seqan3::phred42 string literal.
 

Additional Inherited Members

- Public Types inherited from seqan3::phred_base< phred42, 42 >
using phred_type = int8_t
 The integer representation of the quality score.
 
- 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.
 
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()).
 

Detailed Description

Quality type for traditional Sanger and modern Illumina Phred scores.

.

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 types, namely seqan3::phred63 or seqan3::phred94, otherwise on construction exceeding scores are mapped to 41. Via seqan3::qualified, you can combine a nucleotide alphabet with the Phred score to save space. All dna and rna combinations with seqan3::phred42 still fit into a single byte, e.g. seqan3::qualified<seqan3::dna4, seqan3::phred42> (4 * 42 = 168 values can be stored in a single byte which can contain up to 256 values).

int main()
{
using namespace seqan3::literals;
seqan3::phred42 letter{'@'_phred42};
letter.assign_char('!');
seqan3::debug_stream << letter.to_phred() << '\n'; // prints "0"
seqan3::debug_stream << letter.to_char() << '\n'; // prints "!"
letter.assign_phred(49); // Values exceeding the maximum are implicitly limited to the maximum phred value.
seqan3::debug_stream << letter.to_phred() << '\n'; // prints "41"
}
constexpr derived_type & assign_char(char_type const chr) noexcept
Assign from a character, implicitly converts invalid characters.
Definition: alphabet_base.hpp:163
Quality type for traditional Sanger and modern Illumina Phred scores..
Definition: phred42.hpp:47
Provides seqan3::debug_stream and related types.
debug_stream_type debug_stream
A global instance of seqan3::debug_stream_type.
Definition: debug_stream.hpp:37
The SeqAn namespace for literals.
Provides seqan3::phred42 quality scores.
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.

Friends And Related Function Documentation

◆ operator""_phred42() [1/2]

constexpr 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 namespace seqan3::literals;
std::vector<seqan3::phred42> sequence1{"##!!##"_phred42};
std::vector<seqan3::phred42> sequence2 = "##!!##"_phred42;
auto sequence3 = "##!!##"_phred42;
}

This entity is stable. Since version 3.1.

◆ operator""_phred42() [2/2]

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

The seqan3::phred42 char literal.

Returns
seqan3::phred42

You can use this char literal to assign a seqan3::phred42 character:

int main()
{
using namespace seqan3::literals;
seqan3::phred42 letter1{'!'_phred42};
auto letter2 = '!'_phred42;
}

This entity is stable. Since version 3.1.

Member Data Documentation

◆ offset_char

constexpr char_type seqan3::phred42::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::phred42::offset_phred {0}
staticconstexpr

The projection offset between Phred and rank score representation.

This entity is stable. Since version 3.1.


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