SeqAn3
header.hpp
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2 // SeqAn - The Library for Sequence Analysis
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34 
40 #pragma once
41 
42 #include <unordered_map>
43 #include <vector>
44 
45 #include <seqan3/core/platform.hpp>
46 
47 namespace seqan3
48 {
49 
53 {
56  {
57  std::string id;
58  std::string name;
59  std::string command_line_call;
60  std::string previous;
61  std::string description;
62  std::string version;
63  };
64 
65  std::string format_version;
66  std::string sorting{"unknown"};
67  std::string grouping{"none"};
68 
69  std::vector<program_info_t> program_infos;
70 
71  std::vector<std::string> comments;
72 
110  std::unordered_map<std::string, std::tuple<uint32_t, std::string>> ref_dict;
111 
151  std::vector<std::pair<std::string, std::string>> read_groups;
152 };
153 
154 } // namespace seqan3
std::string sorting
The sorting state of the file. SAM: [unknown, unsorted, queryname, coordinate].
Definition: header.hpp:66
std::vector< std::string > comments
The list of comments.
Definition: header.hpp:71
Contains platform and dependency checks.
std::string name
The official name.
Definition: header.hpp:58
std::unordered_map< std::string, std::tuple< uint32_t, std::string > > ref_dict
The Reference Dictionary. (used by the SAM/BAM format)
Definition: header.hpp:110
The main SeqAn3 namespace.
Definition: aligned_sequence_concept.hpp:58
std::string version
The program/tool version.
Definition: header.hpp:62
std::vector< std::pair< std::string, std::string > > read_groups
The Read Group Dictionary. (used by the SAM/BAM format)
Definition: header.hpp:151
std::string id
A unique (file scope) id.
Definition: header.hpp:57
std::vector< program_info_t > program_infos
The list of program information.
Definition: header.hpp:69
std::string grouping
The grouping state of the file. SAM: [none, query, reference].
Definition: header.hpp:67
std::string description
A description of the program and/or program call.
Definition: header.hpp:61
std::string previous
The id of the previous program if program calls were chained.
Definition: header.hpp:60
Stores the header information of alignment files.
Definition: header.hpp:52
std::string command_line_call
The command line call that produces the file.
Definition: header.hpp:59
Stores information of the program/tool that was used to create the file.
Definition: header.hpp:55
std::string format_version
The file format version. Note: this is overwritten by our formats on output.
Definition: header.hpp:65