Quality type for PacBio Phred scores of HiFi reads. More...
#include <seqan3/alphabet/quality/phred94.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 | phred94 () noexcept=default |
Defaulted. | |
constexpr | phred94 (phred94 const &) noexcept=default |
Defaulted. | |
constexpr | phred94 (phred94 &&) noexcept=default |
Defaulted. | |
constexpr phred94 & | operator= (phred94 const &) noexcept=default |
Defaulted. | |
constexpr phred94 & | operator= (phred94 &&) noexcept=default |
Defaulted. | |
~phred94 () noexcept=default | |
Defaulted. | |
constexpr | phred94 (phred_type const p) |
Construct from Phred score value. | |
Read functions | |
constexpr phred_type | to_phred () const noexcept |
Return the alphabet's value in Phred score representation. More... | |
Write functions | |
constexpr phred94 & | assign_phred (phred_type const p) noexcept |
Assign from the numeric Phred score 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 derived_type & | assign_char (char_type const c) 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 | |
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... | |
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_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... | |
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. | |
Private Types | |
using | base_t = quality_base< phred94, 94 > |
The base class. | |
Private Attributes | |
friend | base_t |
Befriend seqan3::quality_base. | |
friend | derived_type |
Befriend the derived_type so it can instantiate. | |
rank_type | rank {} |
The value of the alphabet letter is stored as the rank. | |
Related Functions | |
(Note that these are not member functions.) | |
Literals | |
constexpr phred94 | operator""_phred94 (char const c) noexcept |
The seqan3::phred94 char literal. More... | |
std::vector< phred94 > | operator""_phred94 (char const *s, std::size_t n) |
The seqan3::phred94 string literal. More... | |
Generic serialisation functions for all seqan3::semialphabet | |
All types that satisfy seqan3::semialphabet can be serialised via Cereal. | |
template<cereal_output_archive archive_t, semialphabet alphabet_t> | |
alphabet_rank_t< alphabet_t > | save_minimal (archive_t const &, alphabet_t const &l) |
Save an alphabet letter to stream. More... | |
Quality type for PacBio Phred scores of HiFi reads.
The phred94 quality alphabet represents the zero-based Phred score range [0..93] mapped to the ASCII range '!' .. '~'. It is typically used for HiFi reads produced by PacBio. For Sanger and Illumina Phred scores of raw reads the range is typically (0 to 41), represented as seqan3::phred42. If you expect only slightly larger score types you can use seqan3::phred63 (0 to 62) which still has memory advantages when used with seqan3::qualified.
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protectedinherited |
The char representation; conditional needed to make semi alphabet definitions legal.
We need a return type for seqan3::alphabet_base::to_char and seqan3::alphabet_base::assign_char other than void to make these in-class definitions valid when char_t
is void.
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protectedinherited |
The type of the alphabet when represented as a number (e.g. via to_rank()).
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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 score 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 alphabet's value in Phred score representation.
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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::phred94 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::phred94>:
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related |
The seqan3::phred94 char literal.
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related |
Save an alphabet letter to stream.
archive_t | Must satisfy seqan3::cereal_output_archive. |
alphabet_t | Type of l; must satisfy seqan3::semialphabet. |
l | The alphabet letter. |
Delegates to seqan3::to_rank.
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staticconstexprinherited |
The size of the alphabet, i.e. the number of different values it can take.