The alignment base format. More...

#include <seqan3/io/sam_file/detail/format_sam_base.hpp>

Inheritance diagram for seqan3::detail::format_sam_base:

Protected Member Functions
template<typename ref_id_type , typename ref_id_tmp_type , typename header_type , typename ref_seqs_type >
void	check_and_assign_ref_id (ref_id_type &ref_id, ref_id_tmp_type &ref_id_tmp, header_type &header, ref_seqs_type &)
	Checks for known reference ids or adds a new reference is and assigns a reference id to `ref_id`.

template<arithmetic arithmetic_target_type>
void	read_arithmetic_field (std::string_view const &str, arithmetic_target_type &arithmetic_target)
	Reads arithmetic fields using std::from_chars.

template<std::ranges::forward_range target_range_type>
void	read_forward_range_field (std::string_view const str, target_range_type &target)
	Reads from `str` to `target`, converting values with seqan3::views::char_to.

template<typename stream_view_type , std::ranges::forward_range target_range_type>
void	read_forward_range_field (stream_view_type &&stream_view, target_range_type &target)
	Reads a range by copying from stream_view to target, converting values with seqan3::views::char_to.

template<typename stream_view_type , typename ref_ids_type , typename ref_seqs_type >
void	read_header (stream_view_type &&stream_view, sam_file_header< ref_ids_type > &hdr, ref_seqs_type &)
	Reads the SAM header.

int32_t	soft_clipping_at_front (std::vector< cigar > const &cigar_vector) const
	Returns the soft clipping value at the front of the `cigar_vector` or 0 if none present.

template<typename stream_t , typename header_type >
void	write_header (stream_t &stream, sam_file_output_options const &options, header_type &header)
	Writes the SAM header.

Constructors, destructor and assignment
	format_sam_base ()=default
	Defaulted.

	format_sam_base (format_sam_base const &)=default
	Defaulted.

format_sam_base &	operator= (format_sam_base const &)=default
	Defaulted.

	format_sam_base (format_sam_base &&)=default
	Defaulted.

format_sam_base &	operator= (format_sam_base &&)=default
	Defaulted.

	~format_sam_base ()=default
	Defaulted.

Protected Attributes
std::array< char, 316 >	arithmetic_buffer {}
	A buffer used when parsing arithmetic values with std::from_chars.

bool	header_was_written {false}
	A variable that tracks whether the content of header has been written or not.

bool	ref_info_present_in_header {false}
	Tracks whether reference information (@SQ tag) were found in the SAM header.

Static Protected Attributes
static constexpr std::array	format_version {'1', '.', '6'}
	The format version string.

Detailed Description

The alignment base format.

Since the SAM and BAM format share a lot of functionality, this abstract base class defines common member variables and functions that are used in both formats.

Member Function Documentation

◆ check_and_assign_ref_id()

template<typename ref_id_type , typename ref_id_tmp_type , typename header_type , typename ref_seqs_type >

void seqan3::detail::format_sam_base::check_and_assign_ref_id	(	ref_id_type &	ref_id,
		ref_id_tmp_type &	ref_id_tmp,
		header_type &	header,
		ref_seqs_type &
	)

inlineprotected

Checks for known reference ids or adds a new reference is and assigns a reference id to ref_id.

Template Parameters

ref_id_type	The type of the reference id (usually a views::type_reduce over ref_id_tmp_type).
ref_id_tmp_type	The type of the temporary parsed id (same_as type as reference ids in header).
header_type	The type of the alignment header.
ref_seqs_type	A tag whether the reference information were given or not (std::ignore or not).

Parameters

[out]	ref_id	The reference id to be filled.
[in]	ref_id_tmp	The temporary of the parsed reference id.
[in,out]	header	The header object that stores the reference id information.

◆ read_arithmetic_field()

template<arithmetic arithmetic_target_type>

void seqan3::detail::format_sam_base::read_arithmetic_field	(	std::string_view const &	str,
		arithmetic_target_type &	arithmetic_target
	)

inlineprotected

Reads arithmetic fields using std::from_chars.

Template Parameters

arithmetic_target_type The type of value to parse from input; must model seqan3::arithmetic.

Parameters

[in,out]	str	The string_view to parse.
[out]	arithmetic_target	The arithmetic value object to store the parsed value.

Exceptions

seqan3::format_error if the character sequence in str cannot be successfully converted to a value of type arithmetic_target_type.

◆ read_forward_range_field() [1/2]

template<std::ranges::forward_range target_range_type>

void seqan3::detail::format_sam_base::read_forward_range_field	(	std::string_view const	str,
		target_range_type &	target
	)

inlineprotected

Reads from str to target, converting values with seqan3::views::char_to.

Template Parameters

target_range_type The type of range to parse from input; must model std::ranges::forward_range.

Parameters

[in,out]	str	The string_view to parse.
[out]	target	The range to store the parsed sequence.

◆ read_forward_range_field() [2/2]

template<typename stream_view_type , std::ranges::forward_range target_range_type>

void seqan3::detail::format_sam_base::read_forward_range_field	(	stream_view_type &&	stream_view,
		target_range_type &	target
	)

inlineprotected

Reads a range by copying from stream_view to target, converting values with seqan3::views::char_to.

Template Parameters

stream_view_type	The type of the stream as a view.
target_range_type	The type of range to parse from input; must model std::ranges::forward_range.

Parameters

[in,out]	stream_view	The stream view to iterate over.
[out]	target	The range to store the parsed sequence.

◆ read_header()

template<typename stream_view_type , typename ref_ids_type , typename ref_seqs_type >

void seqan3::detail::format_sam_base::read_header	(	stream_view_type &&	stream_view,
		sam_file_header< ref_ids_type > &	hdr,
		ref_seqs_type &
	)

inlineprotected

Reads the SAM header.

Template Parameters

stream_view_type The type of the stream as a view.

Parameters

[in,out]	stream_view	The stream view to iterate over.
[in,out]	hdr	The header (as a pointer) to store the parsed values.

Exceptions

seqan3::format_error if any unexpected character or format is encountered.

Reading the header format is done according to the official SAM format specifications.

The function throws a seqan3::format_error if the format is not in a correct state (e.g. required fields are not given), but throwing might occur downstream of the actual error.

Any user-defined tags are not checked for correctness ([TAG]:[VALUE]) and are stored as strings:

◆ soft_clipping_at_front()

int32_t seqan3::detail::format_sam_base::soft_clipping_at_front ( std::vector< cigar > const & cigar_vector ) const

inlineprotected

Returns the soft clipping value at the front of the cigar_vector or 0 if none present.

Parameters

[in] cigar_vector The cigar information to parse for soft-clipping.

◆ write_header()

template<typename stream_t , typename header_type >

void seqan3::detail::format_sam_base::write_header	(	stream_t &	stream,
		sam_file_output_options const &	options,
		header_type &	header
	)

inlineprotected

Writes the SAM header.

Template Parameters

stream_t The stream type.

Parameters

[in,out]	stream	The stream to print to.
[in]	options	The options to alter printing.
[in]	header	The header to print.

Exceptions

seqan3::format_error if the header object contains the wrong information or the contents are ill-formed.

Before writing the header, the contents are checked for correctness according to the rules of the official SAM format specifications.

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

format_sam_base.hpp

Protected Member Functions

Protected Attributes

Static Protected Attributes

Detailed Description

Member Function Documentation

◆ check_and_assign_ref_id()

◆ read_arithmetic_field()

◆ read_forward_range_field() [1/2]

◆ read_forward_range_field() [2/2]

◆ read_header()

◆ soft_clipping_at_front()

◆ write_header()