SeqAn3 3.4.0-rc.1
The Modern C++ library for sequence analysis.
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sam_tag_dictionary.hpp
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1// -----------------------------------------------------------------------------------------------------
2// Copyright (c) 2006-2023, Knut Reinert & Freie Universität Berlin
3// Copyright (c) 2016-2023, 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 <concepts>
16#include <map>
17#include <variant>
18
22
23namespace seqan3::detail
24{
27using sam_tag_variant = std::variant<char,
28 int32_t,
29 float,
39
42constexpr char sam_tag_type_char[12] = {'A', 'i', 'f', 'Z', 'H', 'B', 'B', 'B', 'B', 'B', 'B', 'B'};
45constexpr char sam_tag_type_char_extra[12] = {'\0', '\0', '\0', '\0', '\0', 'c', 'C', 's', 'S', 'i', 'I', 'f'};
46} // namespace seqan3::detail
47
48namespace seqan3
49{
50
51inline namespace literals
52{
53
73template <small_string<2> str> // TODO: better handling if too large string is provided?
74constexpr uint16_t operator""_tag()
75{
76 static_assert(str.size() == 2, "Illegal SAM tag: Exactly two characters must be given.");
77
78 constexpr char char0 = str[0];
79 constexpr char char1 = str[1];
80
81 static_assert((is_alpha(char0) && is_alnum(char1)), "Illegal SAM tag: a SAM tag must match /[A-Za-z][A-Za-z0-9]/.");
82
83 return static_cast<uint16_t>(char0) * 256 + static_cast<uint16_t>(char1);
84}
86
87} // namespace literals
88
166template <uint16_t tag_value>
172
175template <uint16_t tag_value>
177
178// clang-format off
180template <> struct sam_tag_type<"AM"_tag> { using type = int32_t; };
181template <> struct sam_tag_type<"AS"_tag> { using type = int32_t; };
182template <> struct sam_tag_type<"BC"_tag> { using type = std::string; };
183template <> struct sam_tag_type<"BQ"_tag> { using type = std::string; };
184template <> struct sam_tag_type<"BZ"_tag> { using type = std::string; };
185template <> struct sam_tag_type<"CB"_tag> { using type = std::string; };
186template <> struct sam_tag_type<"CC"_tag> { using type = std::string; };
187template <> struct sam_tag_type<"CG"_tag> { using type = std::vector<int32_t>; };
188template <> struct sam_tag_type<"CM"_tag> { using type = int32_t; };
189template <> struct sam_tag_type<"CO"_tag> { using type = std::string; };
190template <> struct sam_tag_type<"CP"_tag> { using type = int32_t; };
191template <> struct sam_tag_type<"CQ"_tag> { using type = std::string; };
192template <> struct sam_tag_type<"CR"_tag> { using type = std::string; };
193template <> struct sam_tag_type<"CS"_tag> { using type = std::string; };
194template <> struct sam_tag_type<"CT"_tag> { using type = std::string; };
195template <> struct sam_tag_type<"CY"_tag> { using type = std::string; };
196template <> struct sam_tag_type<"E2"_tag> { using type = std::string; };
197template <> struct sam_tag_type<"FI"_tag> { using type = int32_t; };
198template <> struct sam_tag_type<"FS"_tag> { using type = std::string; };
199template <> struct sam_tag_type<"FZ"_tag> { using type = std::vector<uint16_t>; };
200
201// template <> struct sam_tag_type<"GC"_tag> {};
202// template <> struct sam_tag_type<"GQ"_tag> {};
203// template <> struct sam_tag_type<"GS"_tag> {};
204
205template <> struct sam_tag_type<"H0"_tag> { using type = int32_t; };
206template <> struct sam_tag_type<"H1"_tag> { using type = int32_t; };
207template <> struct sam_tag_type<"H2"_tag> { using type = int32_t; };
208template <> struct sam_tag_type<"HI"_tag> { using type = int32_t; };
209template <> struct sam_tag_type<"IH"_tag> { using type = int32_t; };
210template <> struct sam_tag_type<"LB"_tag> { using type = std::string; };
211template <> struct sam_tag_type<"MC"_tag> { using type = std::string; };
212template <> struct sam_tag_type<"MD"_tag> { using type = std::string; };
213
214// template <> struct sam_tag_type<"MF"_tag> {};
215
216template <> struct sam_tag_type<"MI"_tag> { using type = std::string; };
217template <> struct sam_tag_type<"MQ"_tag> { using type = int32_t; };
218template <> struct sam_tag_type<"NH"_tag> { using type = int32_t; };
219template <> struct sam_tag_type<"NM"_tag> { using type = int32_t; };
220template <> struct sam_tag_type<"OC"_tag> { using type = std::string; };
221template <> struct sam_tag_type<"OP"_tag> { using type = int32_t; };
222template <> struct sam_tag_type<"OQ"_tag> { using type = std::string; };
223template <> struct sam_tag_type<"OX"_tag> { using type = std::string; };
224template <> struct sam_tag_type<"PG"_tag> { using type = std::string; };
225template <> struct sam_tag_type<"PQ"_tag> { using type = int32_t; };
226template <> struct sam_tag_type<"PT"_tag> { using type = std::string; };
227template <> struct sam_tag_type<"PU"_tag> { using type = std::string; };
228template <> struct sam_tag_type<"Q2"_tag> { using type = std::string; };
229template <> struct sam_tag_type<"QT"_tag> { using type = std::string; };
230template <> struct sam_tag_type<"QX"_tag> { using type = std::string; };
231template <> struct sam_tag_type<"R2"_tag> { using type = std::string; };
232template <> struct sam_tag_type<"RG"_tag> { using type = std::string; };
233template <> struct sam_tag_type<"RT"_tag> { using type = std::string; };
234template <> struct sam_tag_type<"RX"_tag> { using type = std::string; };
235
236// template <> struct sam_tag_type<"S2"_tag> {};
237
238template <> struct sam_tag_type<"SA"_tag> { using type = std::string; };
239template <> struct sam_tag_type<"SM"_tag> { using type = int32_t; };
240
241// template <> struct sam_tag_type<"SQ"_tag> {};
242
243template <> struct sam_tag_type<"TC"_tag> { using type = int32_t; };
244template <> struct sam_tag_type<"U2"_tag> { using type = std::string; };
245template <> struct sam_tag_type<"UQ"_tag> { using type = int32_t; };
247// clang-format on
248
329class sam_tag_dictionary : public std::map<uint16_t, detail::sam_tag_variant>
330{
331private:
334
335public:
338
355 template <uint16_t tag>
356 requires (!std::same_as<sam_tag_type_t<tag>, variant_type>)
357 auto & get() &
358 {
359 if ((*this).count(tag) == 0)
360 (*this)[tag] = sam_tag_type_t<tag>{}; // set correct type if tag is not set yet on
361
362 return std::get<sam_tag_type_t<tag>>((*this)[tag]);
363 }
364
366 template <uint16_t tag>
367 requires (!std::same_as<sam_tag_type_t<tag>, variant_type>)
368 auto && get() &&
369 {
370 if ((*this).count(tag) == 0)
371 (*this)[tag] = sam_tag_type_t<tag>{}; // set correct type if tag is not set yet on
372
373 return std::get<sam_tag_type_t<tag>>(std::move((*this)[tag]));
374 }
375
378 template <uint16_t tag>
379 requires (!std::same_as<sam_tag_type_t<tag>, variant_type>)
380 auto const & get() const &
381 {
382 return std::get<sam_tag_type_t<tag>>((*this).at(tag));
383 }
384
387 template <uint16_t tag>
388 requires (!std::same_as<sam_tag_type_t<tag>, variant_type>)
389 auto const && get() const &&
390 {
391 return std::get<sam_tag_type_t<tag>>(std::move((*this).at(tag)));
392 }
394};
395
396} // namespace seqan3
The SAM tag dictionary class that stores all optional SAM fields.
Definition sam_tag_dictionary.hpp:330
detail::sam_tag_variant variant_type
The variant type defining all valid SAM tag field types.
Definition sam_tag_dictionary.hpp:337
auto && get() &&
Uses std::map::operator[] for access and default initializes new keys.
Definition sam_tag_dictionary.hpp:368
auto & get() &
Uses std::map::operator[] for access and default initializes new keys.
Definition sam_tag_dictionary.hpp:357
auto const && get() const &&
Uses std::map::at() for access and throws when the key is unknown.
Definition sam_tag_dictionary.hpp:389
auto const & get() const &
Uses std::map::at() for access and throws when the key is unknown.
Definition sam_tag_dictionary.hpp:380
constexpr auto is_alnum
Checks whether c is a alphanumeric character.
Definition predicate.hpp:197
constexpr auto is_alpha
Checks whether c is a alphabetical character.
Definition predicate.hpp:214
The main SeqAn3 namespace.
Definition aligned_sequence_concept.hpp:29
Provides character predicates for tokenisation.
A constexpr string implementation to manipulate string literals at compile time.
The generic base class.
Definition sam_tag_dictionary.hpp:168
detail::sam_tag_variant type
The type for all unknown tags with no extra overload defaults to a std::variant.
Definition sam_tag_dictionary.hpp:170
typename sam_tag_type< tag_value >::type sam_tag_type_t
Short cut helper for seqan3::sam_tag_type::type.
Definition sam_tag_dictionary.hpp:176
Provides type traits for working with templates.