SeqAn3
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:
[legend]

Public Types

using char_type = char_t
 The type of the alphabet when converted to char (e.g. via to_char()).
 
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 phred63 ()
 
constexpr phred63 (phred63 const &)=default
 
constexpr phred63 (phred63 &&)=default
 
constexpr phred63operator= (phred63 const &)=default
 
constexpr phred63operator= (phred63 &&)=default
 
 ~phred63 ()=default
 
constexpr phred63 (phred_type const p)
 Construct from phred value.
 
Read functions
constexpr char_type to_char () const noexcept
 Return the letter as a character of char_type. More...
 
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 rank_type to_rank () const noexcept
 Return the letter's numeric value (rank in the alphabet). More...
 
Write functions
constexpr phred63assign_char (std::conditional_t< std::Same< char_type, void >, char, char_type > const c) noexcept
 Assign from a character. More...
 
constexpr phred63assign_rank (rank_type const c) noexcept
 Assign from a numeric value. More...
 

Static Public Attributes

static detail::min_viable_uint_t< size > constexpr value_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.
 

Related Functions

(Note that these are not member functions.)

Requirements for seqan3::alphabet_concept

You can expect these functions on all types that implement seqan3::alphabet_concept.

template<typename alphabet_type >
using underlying_char_t = typename underlying_char< alphabet_type >::type
 The char_type of the alphabet. [type metafunction shortcut]. More...
 
char_type to_char (alphabet_concept const alph)
 Returns the alphabet letter's value in character representation. More...
 
alphabet_concept && assign_char (alphabet_concept &&alph, char_type const chr)
 Returns the alphabet letter's value in character representation. More...
 
Requirements for seqan3::semi_alphabet_concept

You can expect these functions on all types that implement seqan3::semi_alphabet_concept.

template<typename semi_alphabet_type >
using underlying_rank_t = typename underlying_rank< semi_alphabet_type >::type
 The rank_type of the semi_alphabet. [type metafunction shortcut]. More...
 
template<typename alphabet_type >
constexpr auto alphabet_size_v = alphabet_size<alphabet_type>::value
 The size of the alphabet. [value metafunction shortcut]. More...
 
rank_type to_rank (semi_alphabet_concept const alph)
 Returns the alphabet letter's value in rank representation. More...
 
semi_alphabet_concept && assign_rank (semi_alphabet_concept &&alph, rank_type const rank)
 Returns the alphabet letter's value in rank representation. 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...
 
Requirements for std::EqualityComparable

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::StrictTotallyOrdered

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

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...
 

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).

// doesn't work:
// phred = 2;
// works:
phred63 phred;
phred.assign_rank(2); // wrapper for assign_phred(2)
debug_stream << (int) phred.to_phred() << "\n"; // 2
debug_stream << phred.to_char() << "\n"; // '#'
debug_stream << (int) phred.to_rank() << "\n"; // 2
// phred = 75; // <- throws assertion
// doesn't work:
// phred63{4};
// works:
phred63 another_phred{49};
debug_stream << (int) 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 ( std::conditional_t< std::Same< char_type, void >, char, char_type > const  c)
inlinenoexceptinherited

Assign from a character.

Satisfies the seqan3::alphabet_concept::assign_char() requirement via the seqan3::assign_char() wrapper.

Complexity

Constant.

Exceptions

Guaranteed not to throw.

◆ assign_phred()

constexpr phred63 & seqan3::quality_base< phred63 , size >::assign_phred ( phred_type const  p)
inlinenoexceptinherited

Assign from the numeric phred value.

Satisfies the seqan3::quality_concept::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)
inlinenoexceptinherited

Assign from a numeric value.

Satisfies the seqan3::semi_alphabet_concept::assign_rank() requirement via the seqan3::assign_rank() wrapper.

Complexity

Constant.

Exceptions

Guaranteed not to throw.

◆ to_char()

constexpr char_type seqan3::quality_base< phred63 , size >::to_char ( ) const
inlinenoexceptinherited

Return the letter as a character of char_type.

Satisfies the seqan3::alphabet_concept::to_char() requirement via the seqan3::to_char() wrapper.

Complexity

Constant.

Exceptions

Guaranteed not to throw.

◆ to_rank()

constexpr rank_type seqan3::alphabet_base< phred63 , size, char >::to_rank ( ) const
inlinenoexceptinherited

Return the letter's numeric value (rank in the alphabet).

Satisfies the seqan3::semi_alphabet_concept::to_rank() requirement via the to_rank() wrapper.

Complexity

Constant.

Exceptions

Guaranteed not to throw.


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