#include <seqan3/io/alignment_file/header.hpp>
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_header & | operator= (sam_file_header const &)=default |
Copy assignment is defaulted. | |
sam_file_header & | operator= (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::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). 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_-]+)+. | |