Quality type for traditional Sanger and modern Illumina Phred scores (typical range). More...
#include <seqan3/alphabet/quality/phred42.hpp>
Public Types | |
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 phred42 & | operator= (phred42 const &) noexcept=default |
Defaulted. | |
constexpr phred42 & | operator= (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 phred42 & | assign_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 phred42 & | assign_char (char_type const c) noexcept |
Assign from a character, implicitly converts invalid characters. More... | |
constexpr phred42 & | assign_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()). | |
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_size > | rank_to_char |
Rank to char conversion table. | |
static constexpr std::array< phred_type, alphabet_size > | 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< phred42 > | operator""_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... | |
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.
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inlineconstexprnoexceptinherited |
Assign from a character, implicitly converts invalid characters.
c | The character to be assigned. |
Provides an implementation for seqan3::assign_char_to, required to model seqan3::alphabet.
Constant.
Guaranteed not to throw.
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inlineconstexprnoexceptinherited |
Assign from the numeric phred value.
Satisfies the seqan3::writable_quality_alphabet::assign_phred() requirement via the seqan3::assign_rank() wrapper.
Constant.
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inlineconstexprnoexceptinherited |
Assign from a numeric value.
c | The rank to be assigned. |
Provides an implementation for seqan3::assign_rank_to, required to model seqan3::semialphabet.
Constant.
Guaranteed not to throw.
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inlineconstexprnoexceptinherited |
Return the letter as a character of char_type.
Provides an implementation for seqan3::to_char, required to model seqan3::alphabet.
Constant.
Guaranteed not to throw.
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inlineconstexprnoexceptinherited |
Return the letter's numeric value (rank in the alphabet).
Provides an implementation for seqan3::to_rank, required to model seqan3::semialphabet.
Constant.
Guaranteed not to throw.
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related |
The seqan3::phred42 string literal.
[in] | s | A pointer to the character sequence to assign from. |
[in] | n | The length of the character sequence to assign from. |
You can use this string literal to easily assign to std::vector<seqan3::phred42>:
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related |
The seqan3::phred42 char literal.