SeqAn3  3.2.0-rc.1
The Modern C++ library for sequence analysis.
header.hpp
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1 // -----------------------------------------------------------------------------------------------------
2 // Copyright (c) 2006-2022, Knut Reinert & Freie Universität Berlin
3 // Copyright (c) 2016-2022, 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 <ranges>
17 #include <unordered_map>
18 #include <vector>
19 
23 
24 namespace seqan3
25 {
26 
32 template <std::ranges::forward_range ref_ids_type = std::deque<std::string>>
34 {
35 public:
40  sam_file_header() = default;
42  sam_file_header(sam_file_header const &) = default;
50  ~sam_file_header() = default;
51 
55  sam_file_header(ref_ids_type & ref_ids) : ref_ids_ptr{&ref_ids, ref_ids_deleter_noop}
56  {}
57 
61  sam_file_header(ref_ids_type && ref_ids) :
62  ref_ids_ptr{new ref_ids_type{std::move(ref_ids)}, ref_ids_deleter_default}
63  {}
65 
68  {
75  };
76 
82 
84 
86 
87 private:
89  using ref_ids_ptr_t = std::unique_ptr<ref_ids_type, std::function<void(ref_ids_type *)>>;
91  static void ref_ids_deleter_noop(ref_ids_type *)
92  {}
94  static void ref_ids_deleter_default(ref_ids_type * ptr)
95  {
96  delete ptr;
97  }
100  std::span<range_innermost_value_t<ref_ids_type> const>,
101  type_reduce_t<std::ranges::range_reference_t<ref_ids_type>>>;
103  ref_ids_ptr_t ref_ids_ptr{new ref_ids_type{}, ref_ids_deleter_default};
104 
106  struct key_hasher
107  {
109  template <typename key_t>
110  size_t operator()(key_t && key) const noexcept
111  {
112  using char_t = std::ranges::range_value_t<key_t>;
113  size_t result{0};
114  std::hash<char_t> h{};
115  for (char_t character : key)
116  {
117  result *= 0x8F3F73B5CF1C9ADE;
118  result += h(character);
119  }
120  return result;
121  }
122  };
123 
124 public:
143  ref_ids_type & ref_ids()
144  {
145  return *ref_ids_ptr;
146  }
147 
180 
183 
219 };
220 
221 } // namespace seqan3
Core alphabet concept and free function/type trait wrappers.
Stores the header information of alignment files.
Definition: header.hpp:34
sam_file_header(sam_file_header const &)=default
Copy construction is defaulted.
sam_file_header & operator=(sam_file_header &&)=default
Move assignment 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).
Definition: header.hpp:55
std::vector< std::pair< std::string, std::string > > read_groups
The Read Group Dictionary (used by the SAM/BAM format).
Definition: header.hpp:218
std::string sorting
The sorting of the file. SAM: [unknown, unsorted, queryname, coordinate].
Definition: header.hpp:78
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::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.
Definition: header.hpp:182
std::vector< std::tuple< int32_t, std::string > > ref_id_info
The reference information. (used by the SAM/BAM format)
Definition: header.hpp:179
std::string format_version
The file format version. Note: this is overwritten by our formats on output.
Definition: header.hpp:77
~sam_file_header()=default
Destructor is defaulted.
ref_ids_type & ref_ids()
The range of reference ids.
Definition: header.hpp:143
std::vector< std::string > comments
The list of comments.
Definition: header.hpp:85
sam_file_header()=default
Default constructor is defaulted.
std::string grouping
The grouping of the file. SAM: [none, query, reference].
Definition: header.hpp:81
std::string subsorting
The sub-sorting of the file. SAM: [unknown, unsorted, queryname, coordinate](:[A-Za-z0-9_-]+)+.
Definition: header.hpp:80
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:61
std::vector< program_info_t > program_infos
The list of program information.
Definition: header.hpp:83
Auxiliary functions for the alignment IO.
The main SeqAn3 namespace.
Definition: aligned_sequence_concept.hpp:29
SeqAn specific customisations in the standard namespace.
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:68
std::string name
The official name.
Definition: header.hpp:70
std::string version
The program/tool version.
Definition: header.hpp:74
std::string previous
The id of the previous program if program calls were chained.
Definition: header.hpp:72
std::string command_line_call
The command line call that produces the file.
Definition: header.hpp:71
std::string description
A description of the program and/or program call.
Definition: header.hpp:73
std::string id
A unique (file scope) id.
Definition: header.hpp:69
Provides seqan3::views::type_reduce.