SeqAn3  3.0.3
The Modern C++ library for sequence analysis.
seqan3::alignment_file_header< ref_ids_type > Struct Template Reference

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

+ Inheritance diagram for seqan3::alignment_file_header< ref_ids_type >:

Additional Inherited Members

- Public Member Functions inherited from seqan3::sam_file_header< std::deque< std::string > >
ref_ids_type & ref_ids ()
 The range of reference ids. More...
 sam_file_header ()=default
 Default constructor is defaulted.
 sam_file_header (sam_file_header const &)=default
 Copy construction is defaulted.
 sam_file_header (sam_file_header &&)=default
 Move construction is defaulted.
 sam_file_header (ref_ids_type &ref_ids)
 Construct from a range of reference ids which redirects the ref_ids_ptr member (non-owning). More...
 sam_file_header (ref_ids_type &&ref_ids)
 Construct from a rvalue range of reference ids which is moved into the ref_ids_ptr (owning). More...
sam_file_headeroperator= (sam_file_header const &)=default
 Copy assignment is defaulted.
sam_file_headeroperator= (sam_file_header &&)=default
 Move assignment is defaulted.
 ~sam_file_header ()=default
 Destructor is defaulted.
- Public Attributes inherited from seqan3::sam_file_header< std::deque< std::string > >
std::vector< std::stringcomments
 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). More...
std::unordered_map< key_type, int32_t, std::hash< key_type >, 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) More...
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_-]+)+.

Detailed Description

template<std::ranges::forward_range ref_ids_type = std::deque<std::string>>
struct seqan3::alignment_file_header< ref_ids_type >

Use seqan3::sam_file_header instead.

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