seqan3::cigar Class Reference

The seqan3::cigar semialphabet pairs a counter with a seqan3::cigar::operation letter. More...

#include <seqan3/alphabet/cigar/cigar.hpp>

Inheritance diagram for seqan3::cigar:

Public Types
using	operation = exposition_only::cigar_operation
	The (extended) cigar operation alphabet of M,D,I,H,N,P,S,X,=.

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.
constexpr cigar &	operator= (component_type const alph) noexcept
	Assignment via a value of one of the components.
Read functions
small_string< 11 >	to_string () const noexcept
	Return the string representation.
Write functions
cigar &	assign_string (std::string_view const input) noexcept
	Assign from a std::string_view.
Public Member Functions inherited from seqan3::alphabet_tuple_base< cigar, uint32_t, exposition_only::cigar_operation >
constexpr	alphabet_tuple_base (component_types... components) noexcept
	Construction from initialiser-list.
constexpr	alphabet_tuple_base (component_type const alph) noexcept
	Construction via a value of one of the components.
constexpr	alphabet_tuple_base (indirect_component_type const alph) noexcept
	Construction via a value of a subtype that is assignable to one of the components.
constexpr cigar &	operator= (component_type const alph) noexcept
	Assignment via a value of one of the components.
constexpr cigar &	operator= (indirect_component_type const alph) noexcept
	Assignment via a value of a subtype that is assignable to one of the components.
constexpr	operator type () const noexcept
	Implicit cast to a single letter. Works only if the type is unique in the type list.
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_base &	operator= (alphabet_base const &) noexcept=default
	Defaulted.
constexpr alphabet_base &	operator= (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.

Friends
Get functions
template<size_t index>
constexpr auto	get (cigar &l) noexcept
	Tuple-like access to the contained components.
template<typename type >
constexpr auto	get (cigar &l) noexcept
	Tuple-like access to the contained components.
Friends inherited from seqan3::alphabet_tuple_base< cigar, uint32_t, exposition_only::cigar_operation >
Comparison operators

Related Symbols
(Note that these are not member symbols.)
Other literals
constexpr cigar::operation	operator""_cigar_operation (char const c) noexcept
	The seqan3::cigar::operation char literal.

Additional Inherited Members
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.
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

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

Example

// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin
// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik
// SPDX-License-Identifier: CC0-1.0
 
#include <seqan3/alphabet/cigar/cigar.hpp>
#include <seqan3/core/debug_stream.hpp>
 
int main()
{
    using namespace seqan3::literals;
 
    seqan3::cigar letter{12, 'M'_cigar_operation};
 
    letter.assign_string("10D");
    seqan3::debug_stream << letter << '\n'; // prints "10D"
 
    letter.assign_string("20Z");            // Unknown strings are implicitly converted to 0P.
    seqan3::debug_stream << letter << '\n'; // prints "0P"
}

See also

https://samtools.github.io/hts-specs/SAMv1.pdf#page=8

Member Typedef Documentation

operation

using seqan3::cigar::operation = exposition_only::cigar_operation

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:

// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin
// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik
// SPDX-License-Identifier: CC0-1.0
 
#include <seqan3/alphabet/cigar/cigar.hpp>
#include <seqan3/core/debug_stream.hpp>
 
int main()
{
    using namespace seqan3::literals;
 
    seqan3::cigar::operation letter{'M'_cigar_operation};
 
    letter.assign_char('D');
    seqan3::debug_stream << letter << '\n'; // prints "D"
 
    letter.assign_char('Z');                // Unknown characters are implicitly converted to M.
    seqan3::debug_stream << letter << '\n'; // prints "M"
}

Note

Usually you do not want to manipulate cigar elements and vectors on your own but convert an alignment to a cigar and back. See seqan3::cigar_from_alignment for how to convert two aligned sequences into a cigar_vector.

See also

https://samtools.github.io/hts-specs/SAMv1.pdf#page=8

This entity is stable. Since version 3.1.

Constructor & Destructor Documentation

cigar()

constexpr seqan3::cigar::cigar ( component_type const  alph )

inlineconstexprnoexcept

Construction via a value of one of the components.

Template Parameters

component_type

One of the component types; must be uniquely contained in the type list of the composite.

Parameters

[in]

alph

The value of a component that should be assigned.

// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin
// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik
// SPDX-License-Identifier: CC0-1.0
 
#include <seqan3/alphabet/cigar/cigar.hpp>
#include <seqan3/core/debug_stream.hpp>
 
int main()
{
    using namespace seqan3::literals;
 
    // creates 10M, as the cigar_op field is not provided.
    seqan3::cigar letter1{10};
    seqan3::debug_stream << "letter1: " << letter1 << '\n'; // 10M
 
    // creates 0I, as the integer field is not provided.
    seqan3::cigar letter2{'I'_cigar_operation};
    seqan3::debug_stream << "letter2: " << letter2 << '\n'; // 0I
 
    // creates 10I, as both fields are explicitly given.
    seqan3::cigar letter3{10, 'I'_cigar_operation};
    seqan3::debug_stream << "letter3: " << letter3 << '\n'; // 10I
}

This entity is stable. Since version 3.1.

Member Function Documentation

assign_string()

cigar & seqan3::cigar::assign_string ( std::string_view const  input )

inlinenoexcept

Assign from a std::string_view.

In order to avoid unnecessary copies, you can initialise a seqan3::cigar from a std::string_view that contains the cigar string.

// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin
// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik
// SPDX-License-Identifier: CC0-1.0
 
#include <seqan3/alphabet/cigar/cigar.hpp>
#include <seqan3/core/debug_stream.hpp>
 
int main()
{
    std::string cigar_str{"4S134M"}; // input
 
    seqan3::cigar letter1{};
    seqan3::cigar letter2{};
 
    // Assign from string
    // convenient but creates an unnecessary string copy "4S"
    letter1.assign_string(cigar_str.substr(0, 2));
    letter2.assign_string(cigar_str.substr(2, 4));
    seqan3::debug_stream << letter1 << '\n'; // prints 4S
    seqan3::debug_stream << letter2 << '\n'; // prints 134M
 
    // Assign from std::string_view (No extra string copies)
    // Version 1
    letter1.assign_string(std::string_view{cigar_str}.substr(0, 2));
    letter2.assign_string(std::string_view{cigar_str}.substr(2, 4));
    seqan3::debug_stream << letter1 << '\n'; // prints 4S
    seqan3::debug_stream << letter2 << '\n'; // prints 134M
    // No extra string copiesersion 2
    letter1.assign_string(/*std::string_view*/ {cigar_str.data(), 2});
    letter2.assign_string(/*std::string_view*/ {cigar_str.data() + 2, 4});
    seqan3::debug_stream << letter1 << '\n'; // prints 4S
    seqan3::debug_stream << letter2 << '\n'; // prints 134M
 
    // Assign from char array
    letter2.assign_string("40S");
    seqan3::debug_stream << letter2 << '\n'; // prints 40S
 
    // Assign from seqan3::small_string
    letter2.assign_string(letter1.to_string());
    seqan3::debug_stream << letter2 << '\n'; // prints 4S
}

This entity is experimental and subject to change in the future. Experimental since version 3.2.

operator=()

constexpr cigar & seqan3::cigar::operator= ( component_type const  alph )

inlineconstexprnoexcept

Assignment via a value of one of the components.

Template Parameters

component_type

One of the component types; must be uniquely contained in the type list of the composite.

Parameters

[in]

alph

The value of a component that should be assigned.

// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin
// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik
// SPDX-License-Identifier: CC0-1.0
 
#include <seqan3/alphabet/cigar/cigar.hpp>
#include <seqan3/core/debug_stream.hpp>
 
int main()
{
    using namespace seqan3::literals;
 
    seqan3::cigar letter{10, 'I'_cigar_operation};
    seqan3::debug_stream << "letter: " << letter << '\n'; // 10I
 
    letter = 'D'_cigar_operation;
    seqan3::debug_stream << "letter: " << letter << '\n'; // 10D
 
    letter = 20;
    seqan3::debug_stream << "letter: " << letter << '\n'; // 20D
}

This entity is stable. Since version 3.1.

to_string()

small_string< 11 > seqan3::cigar::to_string ( ) const

inlinenoexcept

Return the string representation.

This entity is experimental and subject to change in the future. Experimental since version 3.1.

Friends And Related Symbol Documentation

get [1/2]

template<size_t index>

constexpr auto get ( cigar &  l )

friend

Tuple-like access to the contained components.

Template Parameters

index

Return the i-th element.

Returns

A proxy to the contained element that models the same alphabets concepts and supports assignment.

This entity is stable. Since version 3.1.

// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin
// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik
// SPDX-License-Identifier: CC0-1.0
 
#include <seqan3/alphabet/cigar/cigar.hpp>
#include <seqan3/core/debug_stream.hpp>
 
int main()
{
    using seqan3::get;
    using namespace seqan3::literals;
 
    seqan3::cigar letter{10, 'M'_cigar_operation};
 
    // Note that this is equivalent to get<uint32_t>(letter)
    uint32_t size{get<0>(letter)};
 
    // Note that this is equivalent to get<seqan3::cigar::operation>(letter)
    seqan3::cigar::operation cigar_char{get<1>(letter)};
 
    seqan3::debug_stream << "Size is " << size << '\n';
    seqan3::debug_stream << "Cigar char is " << cigar_char << '\n'; // seqan3::debug_stream converts to char on the fly.
}

This entity is stable. Since version 3.1.

get [2/2]

template<typename type >

constexpr auto get ( cigar &  l )

friend

Tuple-like access to the contained components.

Template Parameters

type	Return the element of specified type; only available if the type is unique in the set of components.

Returns

A proxy to the contained element that models the same alphabet concepts and supports assignment.

// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin
// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik
// SPDX-License-Identifier: CC0-1.0
 
#include <seqan3/alphabet/cigar/cigar.hpp>
#include <seqan3/core/debug_stream.hpp>
 
int main()
{
    using seqan3::get;
    using namespace seqan3::literals;
 
    seqan3::cigar letter{10, 'M'_cigar_operation};
 
    // Note that this is equivalent to get<0>(letter)
    uint32_t size{get<uint32_t>(letter)};
 
    // Note that this is equivalent to get<1>(letter)
    seqan3::cigar::operation cigar_char{get<seqan3::cigar::operation>(letter)};
 
    seqan3::debug_stream << "Size is " << size << '\n';
    seqan3::debug_stream << "Cigar char is " << cigar_char << '\n'; // seqan3::debug_stream converts to char on the fly.
}

This entity is stable. Since version 3.1.

operator""_cigar_operation()

constexpr cigar::operation operator""_cigar_operation ( char const  c )

related

The seqan3::cigar::operation char literal.

Returns

seqan3::cigar::operation

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

// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin
// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik
// SPDX-License-Identifier: CC0-1.0
 
#include <seqan3/alphabet/cigar/cigar.hpp>
 
int main()
{
    using namespace seqan3::literals;
 
    seqan3::cigar::operation letter1{'M'_cigar_operation};
    auto letter2 = 'M'_cigar_operation;
}

This entity is stable. Since version 3.1.

---

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

• alphabet/cigar/cigar.hpp