seqan3::sam_file_header< ref_ids_type > Class Template Reference

Stores the header information of SAM/BAM files. More...

#include <seqan3/io/sam_file/header.hpp>

Public Types
using	program_info_t = sam_file_program_info_t
	Stores information of the program/tool that was used to create the file.

Public Member Functions
ref_ids_type &	ref_ids ()
	The range of reference ids.
Constructors, destructor and assignment
	sam_file_header ()=default
	Defaulted.
	sam_file_header (sam_file_header const &)=default
	Defaulted.
sam_file_header &	operator= (sam_file_header const &)=default
	Defaulted.
	sam_file_header (sam_file_header &&)=default
	Defaulted.
sam_file_header &	operator= (sam_file_header &&)=default
	Defaulted.
	~sam_file_header ()=default
	Defaulted.
	sam_file_header (ref_ids_type ref_ids)
	Construct from a range of reference ids.

Public Attributes
std::vector< std::string >	comments
	The list of comments.
std::string	format_version
	The file format version. Note: this is overwritten by our formats on output.
std::string	grouping
	The grouping of the file. SAM: [none, query, reference].
std::vector< program_info_t >	program_infos
	The list of program information.
std::vector< std::pair< std::string, std::string > >	read_groups
	The Read Group Dictionary (used by the SAM/BAM format).
std::unordered_map< key_type, int32_t, key_hasher, detail::view_equality_fn >	ref_dict {}
	The mapping of reference id to position in the ref_ids() range and the ref_id_info range.
std::vector< std::tuple< int32_t, std::string > >	ref_id_info {}
	The reference information. (used by the SAM/BAM format)
std::string	sorting
	The sorting of the file. SAM: [unknown, unsorted, queryname, coordinate].
std::string	subsorting
	The sub-sorting of the file. SAM: [unknown, unsorted, queryname, coordinate](:[A-Za-z0-9_-]+)+.
std::string	user_tags
	Additional user-defined tags.

Detailed Description

template<std::ranges::forward_range ref_ids_type = std::deque<std::string>>
class seqan3::sam_file_header< ref_ids_type >

Stores the header information of SAM/BAM files.

Remarks

For a complete overview, take a look at SAM File

Constructor & Destructor Documentation

sam_file_header()

template<std::ranges::forward_range ref_ids_type = std::deque<std::string>>

seqan3::sam_file_header< ref_ids_type >::sam_file_header ( ref_ids_type  ref_ids )

inline

Construct from a range of reference ids.

Parameters

[in]

ref_ids

The range over reference ids.

Member Function Documentation

ref_ids()

template<std::ranges::forward_range ref_ids_type = std::deque<std::string>>

ref_ids_type & seqan3::sam_file_header< ref_ids_type >::ref_ids ( )

inline

The range of reference ids.

This member function gives you access to the range of reference ids.

When reading a file, there are three scenarios: 1) Reference id information is provided on construction. In this case, no copy is made but this function gives you a reference to the provided range. When reading the header or the records, their reference information will be checked against the given input. 2) No reference information is provided on construction but the @SQ tags are present in the header. In this case, the reference id information is extracted from the header and this member function provides access to them. When reading the records, their reference id information will be checked against the header information. 3) No reference information is provided on construction an no @SQ tags are present in the header. In this case, the reference information is parsed from the records field::ref_id and stored in the header. This member function then provides access to the unique list of reference ids encountered in the records.

Member Data Documentation

read_groups

template<std::ranges::forward_range ref_ids_type = std::deque<std::string>>

std::vector<std::pair<std::string, std::string> > seqan3::sam_file_header< ref_ids_type >::read_groups

The Read Group Dictionary (used by the SAM/BAM format).

The read group dictionary stores the group id and additional information of each read group in the file. The record may store a RG tag information referencing one of the stored id's. The id information is required if the header is provided.

The additional information (2nd tuple entry) for the SAM format must follow the following formatting rules: The information is given in a tab separated TAG:VALUE format, where TAG must be one of [AH, AN, AS, m5, SP, UR]. The following information and rules apply for each tag (taken from the SAM specs):

• BC: Barcode sequence identifying the sample or library. This value is the expected barcode bases as read by the sequencing machine in the absence of errors. If there are several barcodes for the sample/library (e.g., one on each end of the template), the recommended implementation concatenates all the barcodes separating them with hyphens ('-').
• CN: Name of sequencing center producing the read.
• DS: Description. UTF-8 encoding may be used.
• DT: Date the run was produced (ISO8601 date or date/time).
• FO: Flow order. The array of nucleotide bases that correspond to the nucleotides used for each flow of each read. Multi-base flows are encoded in IUPAC format, and non-nucleotide flows by various other characters. Format : /*|[ACMGRSVTWYHKDBN]+/
• KS: The array of nucleotide bases that correspond to the key sequence of each read.
• LB: Library.
• PG: Programs used for processing the read group.
• PI: Predicted median insert size.
• PL: Platform/technology used to produce the reads. Valid values : CAPILLARY, LS454, ILLUMINA, SOLID, HELICOS, IONTORRENT, ONT, and PACBIO.
• PM: Platform model. Free-form text providing further details of the platform/technology used.
• PU: Platform unit (e.g. flowcell-barcode.lane for Illumina or slide for SOLiD). Unique identifier.
• SM: Sample. Use pool name where a pool is being sequenced.

ref_id_info

template<std::ranges::forward_range ref_ids_type = std::deque<std::string>>

std::vector<std::tuple<int32_t, std::string> > seqan3::sam_file_header< ref_ids_type >::ref_id_info {}

The reference information. (used by the SAM/BAM format)

The reference information store the length (@LN tag) and additional information of each reference sequence in the file. The record must then store only the index of the reference. The name and length information are required if the header is provided and each reference sequence that is referred to in any of the records must be present in the dictionary, otherwise a seqan3::format_error will be thrown upon reading or writing a file.

The additional information (2nd tuple entry) must model the following formatting rules: The information is given in a tab separated TAG:VALUE format, where TAG must be one of [AH, AN, AS, m5, SP, UR]. The following information and rules apply for each tag (taken from the SAM specs):

• AH: Indicates that this sequence is an alternate locus. The value is the locus in the primary assembly for which this sequence is an alternative, in the format 'chr:start-end', 'chr' (if known), or '*' (if unknown), where 'chr' is a sequence in the primary assembly. Must not be present on sequences in the primary assembly.
• AN: Alternative reference sequence names. A comma-separated list of alternative names that tools may use when referring to this reference sequence. These alternative names are not used elsewhere within the SAM file; in particular, they must not appear in SAM records’ RNAME or RNEXT fields. regular expression : name (, name )* where name is [0-9A-Za-z][0-9A-Za-z*+.@ |-]*
• AS: Genome assembly identifier.
• M5: MD5 checksum of the sequence. See Section 1.3.1
• SP: Species.
• UR: URI of the sequence. This value may start with one of the standard protocols, e.g http: or ftp:. If it does not start with one of these protocols, it is assumed to be a file-system path

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

• header.hpp