The seqan3::cigar semialphabet pairs a counter with a seqan3::cigar::operation letter. More...
#include <seqan3/alphabet/cigar/cigar.hpp>
Public Types | |
using | operation = exposition_only::cigar_operation |
The (extended) cigar operation alphabet of M,D,I,H,N,P,S,X,=. More... | |
Public Member Functions | |
Constructors, destructor and assignment | |
constexpr | cigar () noexcept=default |
Defaulted. | |
constexpr | cigar (cigar const &) noexcept=default |
Defaulted. | |
constexpr | cigar (cigar &&) noexcept=default |
Defaulted. | |
constexpr cigar & | operator= (cigar const &) noexcept=default |
Defaulted. | |
constexpr cigar & | operator= (cigar &&) noexcept=default |
Defaulted. | |
~cigar () noexcept=default | |
Defaulted. | |
constexpr | cigar (component_type const alph) noexcept |
Construction via a value of one of the components. More... | |
constexpr cigar & | operator= (component_type const alph) noexcept |
Assignment via a value of one of the components. More... | |
Read functions | |
small_string< 11 > | to_string () const noexcept |
Return the string representation. | |
Write functions | |
cigar & | assign_string (small_string< 11 > const s) noexcept |
Assign from the string representation. | |
Get functions | |
template<size_t index> | |
constexpr auto | get (cigar &l) noexcept |
Tuple-like access to the contained components. More... | |
template<typename type > | |
constexpr auto | get (cigar &l) noexcept |
Tuple-like access to the contained components. More... | |
Read functions | |
All read operations are constant complexity. | |
constexpr | operator type () const noexcept |
Implicit cast to a single letter. Works only if the type is unique in the type list. | |
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 cigar & | assign_char (char_type const c) noexcept |
Assign from a character, implicitly converts invalid characters. More... | |
constexpr cigar & | 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. More... | |
Protected Types | |
Member types | |
using | char_type = std::conditional_t< std::same_as< void, void >, char, void > |
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... | |
Related Functions | |
(Note that these are not member functions.) | |
Literals | |
cigar::operation | operator""_cigar_operation (char const c) noexcept |
The seqan3::cigar::operation char literal. More... | |
The seqan3::cigar semialphabet pairs a counter with a seqan3::cigar::operation letter.
This semialphabet represents a unit in a CIGAR string, typically found in the SAM and BAM formats. It consists of a number and a seqan3::cigar::operation symbol.
It has a "visual representation", but since this is a string and not a char, the type only models seqan3::writable_semialphabet and not seqan3::writable_alphabet. Members for reading/writing the string are provided.
To avoid confusion between string and char literal, this alphabet has no user defined literal operators. Always assign from a pair of uint32_t and seqan3::cigar::operation.
OP | Description |
---|---|
M | Alignment match (can be a sequence match or mismatch, used only in basic CIGAR representations) |
I | Insertion to the reference |
D | Deletion from the reference |
N | Skipped region from the reference |
S | Soft clipping (clipped sequences present in seqan3::sam_record::sequence) |
H | Hard clipping (clipped sequences NOT present in seqan3::sam_record::sequence) |
P | Padding (silent deletion from padded reference) |
= | Sequence match |
X | Sequence mismatch |
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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.
The (extended) cigar operation alphabet of M,D,I,H,N,P,S,X,=.
The CIGAR string can be either basic or extended. The only difference in the extended cigar alphabet is that aligned bases are classified as an actual match ('=') or mismatch ('X'). In contrast, the basic cigar alphabet only indicated the aligned status with an 'M', without further information if the bases are actually equal or not.
The main purpose of the seqan3::cigar::operation alphabet is to be used in the seqan3::cigar composition, where a cigar operation is paired with a count value.
OP | Description |
---|---|
M | Alignment match (can be a sequence match or mismatch, used only in basic CIGAR representations) |
I | Insertion to the reference |
D | Deletion from the reference |
N | Skipped region from the reference |
S | Soft clipping (clipped sequences present in seqan3::sam_record::sequence) |
H | Hard clipping (clipped sequences NOT present in seqan3::sam_record::sequence) |
P | Padding (silent deletion from padded reference) |
= | Sequence match |
X | Sequence mismatch |
Example usage:
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protectedinherited |
The type of the alphabet when represented as a number (e.g. via to_rank()).
|
inlineconstexprnoexcept |
Construction via a value of one of the components.
component_type | One of the component types; must be uniquely contained in the type list of the composite. |
[in] | alph | The value of a component that should be assigned. |
|
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.
|
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.
|
inlineconstexprnoexcept |
Tuple-like access to the contained components.
index | Return the i-th element. |
|
inlineconstexprnoexcept |
Tuple-like access to the contained components.
type | Return the element of specified type; only available if the type is unique in the set of components. |
|
inlineconstexprnoexcept |
Assignment via a value of one of the components.
component_type | One of the component types; must be uniquely contained in the type list of the composite. |
[in] | alph | The value of a component that should be assigned. |
|
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.
|
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::cigar::operation char literal.
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staticconstexprinherited |
The size of the alphabet, i.e. the number of different values it can take.