SeqAn3  3.1.0
The Modern C++ library for sequence analysis.
header.hpp
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1 // -----------------------------------------------------------------------------------------------------
2 // Copyright (c) 2006-2021, Knut Reinert & Freie Universität Berlin
3 // Copyright (c) 2016-2021, Knut Reinert & MPI für molekulare Genetik
4 // This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License
5 // shipped with this file and also available at: https://github.com/seqan/seqan3/blob/master/LICENSE.md
6 // -----------------------------------------------------------------------------------------------------
7 
13 #pragma once
14 
15 #include <deque>
16 #include <seqan3/std/ranges>
17 #include <unordered_map>
18 #include <vector>
19 
24 
25 namespace seqan3
26 {
27 
33 template <std::ranges::forward_range ref_ids_type = std::deque<std::string>>
35 {
36 public:
41  sam_file_header() = default;
43  sam_file_header(sam_file_header const &) = default;
51  ~sam_file_header() = default;
52 
56  sam_file_header(ref_ids_type & ref_ids) :
57  ref_ids_ptr{&ref_ids, ref_ids_deleter_noop}
58  {}
59 
63  sam_file_header(ref_ids_type && ref_ids) :
64  ref_ids_ptr{new ref_ids_type{std::move(ref_ids)}, ref_ids_deleter_default}
65  {}
67 
70  {
77  };
78 
83 
85 
87 
88 private:
90  using ref_ids_ptr_t = std::unique_ptr<ref_ids_type, std::function<void(ref_ids_type*)>>;
92  static void ref_ids_deleter_noop(ref_ids_type *) {}
94  static void ref_ids_deleter_default(ref_ids_type * ptr) { delete ptr; }
97  std::span<range_innermost_value_t<ref_ids_type> const>,
98  type_reduce_t<std::ranges::range_reference_t<ref_ids_type>>>;
100  ref_ids_ptr_t ref_ids_ptr{new ref_ids_type{}, ref_ids_deleter_default};
101 
102 public:
121  ref_ids_type & ref_ids()
122  {
123  return *ref_ids_ptr;
124  }
125 
158 
161 
197 };
198 
199 } // namespace seqan3
Core alphabet concept and free function/type trait wrappers.
Stores the header information of alignment files.
Definition: header.hpp:35
sam_file_header(sam_file_header const &)=default
Copy construction is defaulted.
sam_file_header & operator=(sam_file_header &&)=default
Move assignment is defaulted.
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.
Definition: header.hpp:160
sam_file_header(ref_ids_type &ref_ids)
Construct from a range of reference ids which redirects the ref_ids_ptr member (non-owning).
Definition: header.hpp:56
std::vector< std::pair< std::string, std::string > > read_groups
The Read Group Dictionary (used by the SAM/BAM format).
Definition: header.hpp:196
std::string sorting
The sorting of the file. SAM: [unknown, unsorted, queryname, coordinate].
Definition: header.hpp:80
sam_file_header & operator=(sam_file_header const &)=default
Copy assignment is defaulted.
sam_file_header(sam_file_header &&)=default
Move construction is defaulted.
std::vector< std::tuple< int32_t, std::string > > ref_id_info
The reference information. (used by the SAM/BAM format)
Definition: header.hpp:157
std::string format_version
The file format version. Note: this is overwritten by our formats on output.
Definition: header.hpp:79
~sam_file_header()=default
Destructor is defaulted.
ref_ids_type & ref_ids()
The range of reference ids.
Definition: header.hpp:121
std::vector< std::string > comments
The list of comments.
Definition: header.hpp:86
sam_file_header()=default
Default constructor is defaulted.
std::string grouping
The grouping of the file. SAM: [none, query, reference].
Definition: header.hpp:82
std::string subsorting
The sub-sorting of the file. SAM: [unknown, unsorted, queryname, coordinate](:[A-Za-z0-9_-]+)+.
Definition: header.hpp:81
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).
Definition: header.hpp:63
std::vector< program_info_t > program_infos
The list of program information.
Definition: header.hpp:84
Auxiliary functions for the alignment IO.
The main SeqAn3 namespace.
Definition: aligned_sequence_concept.hpp:29
SeqAn specific customisations in the standard namespace.
Provides overloads for std::hash.
The <ranges> header from C++20's standard library.
Stores information of the program/tool that was used to create the file.
Definition: header.hpp:70
std::string name
The official name.
Definition: header.hpp:72
std::string version
The program/tool version.
Definition: header.hpp:76
std::string previous
The id of the previous program if program calls were chained.
Definition: header.hpp:74
std::string command_line_call
The command line call that produces the file.
Definition: header.hpp:73
std::string description
A description of the program and/or program call.
Definition: header.hpp:75
std::string id
A unique (file scope) id.
Definition: header.hpp:71
Provides seqan3::views::type_reduce.