seqan3::detail::format_sam_base Class Reference

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 , typename seq_legal_alph_type >
void	read_header (stream_view_type &&stream_view, sam_file_header< ref_ids_type > &hdr, ref_seqs_type &, sam_file_input_options< seq_legal_alph_type > const &options)
	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 , typename seq_legal_alph_type >

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

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.
[in]	options	The options to alter the parsing process.

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.

If any unknown tag was encountered, a warning will be emitted to std::cerr. This can be configured with seqan3::sam_file_input_options::stream_warnings_to.

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.

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

• format_sam_base.hpp