23 namespace seqan3::detail
42 constexpr
char sam_tag_type_char[12] = {
'A',
'i',
'f',
'Z',
'H',
'B',
'B',
'B',
'B',
'B',
'B',
'B'};
45 constexpr
char sam_tag_type_char_extra[12] = {
'\0',
'\0',
'\0',
'\0',
'\0',
'c',
'C',
's',
'S',
'i',
'I',
'f'};
51 inline namespace literals
74 #ifdef __cpp_nontype_template_parameter_class
75 template <small_
string<2> str>
76 constexpr uint16_t
operator""_tag()
79 # pragma GCC diagnostic push
80 # pragma GCC diagnostic ignored "-Wpedantic"
81 template <
typename char_t, char_t... s>
82 constexpr uint16_t
operator""_tag()
84 static_assert(std::same_as<char_t, char>,
"Illegal SAM tag: Type must be char.");
86 # pragma GCC diagnostic pop
89 static_assert(str.size() == 2,
"Illegal SAM tag: Exactly two characters must be given.");
91 constexpr
char char0 = str[0];
92 constexpr
char char1 = str[1];
94 static_assert((
is_alpha(char0) &&
is_alnum(char1)),
"Illegal SAM tag: a SAM tag must match /[A-Za-z][A-Za-z0-9]/.");
96 return static_cast<uint16_t
>(char0) * 256 +
static_cast<uint16_t
>(char1);
179 template <u
int16_t tag_value>
188 template <u
int16_t tag_value>
194 template <>
struct sam_tag_type<"AS"_tag> {
using type = int32_t; };
195 template <>
struct sam_tag_type<"BC"_tag> {
using type =
std::string; };
196 template <>
struct sam_tag_type<"BQ"_tag> {
using type =
std::string; };
197 template <>
struct sam_tag_type<"BZ"_tag> {
using type =
std::string; };
198 template <>
struct sam_tag_type<"CB"_tag> {
using type =
std::string; };
199 template <>
struct sam_tag_type<"CC"_tag> {
using type =
std::string; };
201 template <>
struct sam_tag_type<"CM"_tag> {
using type = int32_t; };
202 template <>
struct sam_tag_type<"CO"_tag> {
using type =
std::string; };
203 template <>
struct sam_tag_type<"CP"_tag> {
using type = int32_t; };
204 template <>
struct sam_tag_type<"CQ"_tag> {
using type =
std::string; };
205 template <>
struct sam_tag_type<"CR"_tag> {
using type =
std::string; };
206 template <>
struct sam_tag_type<"CS"_tag> {
using type =
std::string; };
207 template <>
struct sam_tag_type<"CT"_tag> {
using type =
std::string; };
208 template <>
struct sam_tag_type<"CY"_tag> {
using type =
std::string; };
209 template <>
struct sam_tag_type<"E2"_tag> {
using type =
std::string; };
210 template <>
struct sam_tag_type<"FI"_tag> {
using type = int32_t; };
211 template <>
struct sam_tag_type<"FS"_tag> {
using type =
std::string; };
218 template <>
struct sam_tag_type<"H0"_tag> {
using type = int32_t; };
219 template <>
struct sam_tag_type<"H1"_tag> {
using type = int32_t; };
220 template <>
struct sam_tag_type<"H2"_tag> {
using type = int32_t; };
221 template <>
struct sam_tag_type<"HI"_tag> {
using type = int32_t; };
222 template <>
struct sam_tag_type<"IH"_tag> {
using type = int32_t; };
223 template <>
struct sam_tag_type<"LB"_tag> {
using type =
std::string; };
224 template <>
struct sam_tag_type<"MC"_tag> {
using type =
std::string; };
225 template <>
struct sam_tag_type<"MD"_tag> {
using type =
std::string; };
229 template <>
struct sam_tag_type<"MI"_tag> {
using type =
std::string; };
230 template <>
struct sam_tag_type<"MQ"_tag> {
using type = int32_t; };
231 template <>
struct sam_tag_type<"NH"_tag> {
using type = int32_t; };
232 template <>
struct sam_tag_type<"NM"_tag> {
using type = int32_t; };
233 template <>
struct sam_tag_type<"OC"_tag> {
using type =
std::string; };
234 template <>
struct sam_tag_type<"OP"_tag> {
using type = int32_t; };
235 template <>
struct sam_tag_type<"OQ"_tag> {
using type =
std::string; };
236 template <>
struct sam_tag_type<"OX"_tag> {
using type =
std::string; };
237 template <>
struct sam_tag_type<"PG"_tag> {
using type =
std::string; };
238 template <>
struct sam_tag_type<"PQ"_tag> {
using type = int32_t; };
239 template <>
struct sam_tag_type<"PT"_tag> {
using type =
std::string; };
240 template <>
struct sam_tag_type<"PU"_tag> {
using type =
std::string; };
241 template <>
struct sam_tag_type<"Q2"_tag> {
using type =
std::string; };
242 template <>
struct sam_tag_type<"QT"_tag> {
using type =
std::string; };
243 template <>
struct sam_tag_type<"QX"_tag> {
using type =
std::string; };
244 template <>
struct sam_tag_type<"R2"_tag> {
using type =
std::string; };
245 template <>
struct sam_tag_type<"RG"_tag> {
using type =
std::string; };
246 template <>
struct sam_tag_type<"RT"_tag> {
using type =
std::string; };
247 template <>
struct sam_tag_type<"RX"_tag> {
using type =
std::string; };
251 template <>
struct sam_tag_type<"SA"_tag> {
using type =
std::string; };
252 template <>
struct sam_tag_type<"SM"_tag> {
using type = int32_t; };
256 template <>
struct sam_tag_type<"TC"_tag> {
using type = int32_t; };
257 template <>
struct sam_tag_type<"U2"_tag> {
using type =
std::string; };
258 template <>
struct sam_tag_type<"UQ"_tag> {
using type = int32_t; };
368 template <u
int16_t tag>
372 if ((*this).count(tag) == 0)
373 (*this)[tag] = sam_tag_type_t<tag>{};
375 return std::get<sam_tag_type_t<tag>>((*this)[tag]);
379 template <u
int16_t tag>
383 if ((*this).count(tag) == 0)
384 (*this)[tag] = sam_tag_type_t<tag>{};
386 return std::get<sam_tag_type_t<tag>>(std::move((*
this)[tag]));
391 template <u
int16_t tag>
393 auto const &
get() const &
395 return std::get<sam_tag_type_t<tag>>((*this).at(tag));
400 template <u
int16_t tag>
402 auto const &&
get() const &&
404 return std::get<sam_tag_type_t<tag>>(std::move((*this).at(tag)));
The SAM tag dictionary class that stores all optional SAM fields.
Definition: sam_tag_dictionary.hpp:343
requires(!std::same_as< sam_tag_type_t< tag >, variant_type >) auto const &&get() const &&
Uses std::map::at() for access and throws when the key is unknown.
Definition: sam_tag_dictionary.hpp:401
requires(!std::same_as< sam_tag_type_t< tag >, variant_type >) auto &get() &
Uses std::map::operator[] for access and default initializes new keys.
Definition: sam_tag_dictionary.hpp:369
requires(!std::same_as< sam_tag_type_t< tag >, variant_type >) auto &&get() &&
Uses std::map::operator[] for access and default initializes new keys.
Definition: sam_tag_dictionary.hpp:380
requires(!std::same_as< sam_tag_type_t< tag >, variant_type >) auto const &get() const &
Uses std::map::at() for access and throws when the key is unknown.
Definition: sam_tag_dictionary.hpp:392
Implements a small string that can be used for compile time computations.
Definition: small_string.hpp:44
The <concepts> header from C++20's standard library.
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
constexpr auto const & get(configuration< configs_t... > const &config) noexcept
This is an overloaded member function, provided for convenience. It differs from the above function o...
Definition: configuration.hpp:415
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:181
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:189
Provides type traits for working with templates.