23namespace seqan3::detail
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'};
51inline namespace literals
74#ifdef __cpp_nontype_template_parameter_class
75template <small_
string<2> str>
76constexpr uint16_t
operator""_tag()
79# pragma GCC diagnostic push
80# pragma GCC diagnostic ignored "-Wpedantic"
81template <
typename char_t, char_t... s>
82constexpr 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);
179template <u
int16_t tag_value>
188template <u
int16_t tag_value>
194template <>
struct sam_tag_type<"AS"_tag> {
using type = int32_t; };
195template <>
struct sam_tag_type<"BC"_tag> {
using type =
std::string; };
196template <>
struct sam_tag_type<"BQ"_tag> {
using type =
std::string; };
197template <>
struct sam_tag_type<"BZ"_tag> {
using type =
std::string; };
198template <>
struct sam_tag_type<"CB"_tag> {
using type =
std::string; };
199template <>
struct sam_tag_type<"CC"_tag> {
using type =
std::string; };
201template <>
struct sam_tag_type<"CM"_tag> {
using type = int32_t; };
202template <>
struct sam_tag_type<"CO"_tag> {
using type =
std::string; };
203template <>
struct sam_tag_type<"CP"_tag> {
using type = int32_t; };
204template <>
struct sam_tag_type<"CQ"_tag> {
using type =
std::string; };
205template <>
struct sam_tag_type<"CR"_tag> {
using type =
std::string; };
206template <>
struct sam_tag_type<"CS"_tag> {
using type =
std::string; };
207template <>
struct sam_tag_type<"CT"_tag> {
using type =
std::string; };
208template <>
struct sam_tag_type<"CY"_tag> {
using type =
std::string; };
209template <>
struct sam_tag_type<"E2"_tag> {
using type =
std::string; };
210template <>
struct sam_tag_type<"FI"_tag> {
using type = int32_t; };
211template <>
struct sam_tag_type<"FS"_tag> {
using type =
std::string; };
218template <>
struct sam_tag_type<"H0"_tag> {
using type = int32_t; };
219template <>
struct sam_tag_type<"H1"_tag> {
using type = int32_t; };
220template <>
struct sam_tag_type<"H2"_tag> {
using type = int32_t; };
221template <>
struct sam_tag_type<"HI"_tag> {
using type = int32_t; };
222template <>
struct sam_tag_type<"IH"_tag> {
using type = int32_t; };
223template <>
struct sam_tag_type<"LB"_tag> {
using type =
std::string; };
224template <>
struct sam_tag_type<"MC"_tag> {
using type =
std::string; };
225template <>
struct sam_tag_type<"MD"_tag> {
using type =
std::string; };
229template <>
struct sam_tag_type<"MI"_tag> {
using type =
std::string; };
230template <>
struct sam_tag_type<"MQ"_tag> {
using type = int32_t; };
231template <>
struct sam_tag_type<"NH"_tag> {
using type = int32_t; };
232template <>
struct sam_tag_type<"NM"_tag> {
using type = int32_t; };
233template <>
struct sam_tag_type<"OC"_tag> {
using type =
std::string; };
234template <>
struct sam_tag_type<"OP"_tag> {
using type = int32_t; };
235template <>
struct sam_tag_type<"OQ"_tag> {
using type =
std::string; };
236template <>
struct sam_tag_type<"OX"_tag> {
using type =
std::string; };
237template <>
struct sam_tag_type<"PG"_tag> {
using type =
std::string; };
238template <>
struct sam_tag_type<"PQ"_tag> {
using type = int32_t; };
239template <>
struct sam_tag_type<"PT"_tag> {
using type =
std::string; };
240template <>
struct sam_tag_type<"PU"_tag> {
using type =
std::string; };
241template <>
struct sam_tag_type<"Q2"_tag> {
using type =
std::string; };
242template <>
struct sam_tag_type<"QT"_tag> {
using type =
std::string; };
243template <>
struct sam_tag_type<"QX"_tag> {
using type =
std::string; };
244template <>
struct sam_tag_type<"R2"_tag> {
using type =
std::string; };
245template <>
struct sam_tag_type<"RG"_tag> {
using type =
std::string; };
246template <>
struct sam_tag_type<"RT"_tag> {
using type =
std::string; };
247template <>
struct sam_tag_type<"RX"_tag> {
using type =
std::string; };
251template <>
struct sam_tag_type<"SA"_tag> {
using type =
std::string; };
252template <>
struct sam_tag_type<"SM"_tag> {
using type = int32_t; };
256template <>
struct sam_tag_type<"TC"_tag> {
using type = int32_t; };
257template <>
struct sam_tag_type<"U2"_tag> {
using type =
std::string; };
258template <>
struct sam_tag_type<"UQ"_tag> {
using type = int32_t; };
368 template <u
int16_t tag>
369 requires (!std::same_as<sam_tag_type_t<tag>,
variant_type>)
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>
380 requires (!std::same_as<sam_tag_type_t<tag>, variant_type>)
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>
392 requires (!std::same_as<sam_tag_type_t<tag>, variant_type>)
393 auto const &
get()
const &
395 return std::get<sam_tag_type_t<tag>>((*this).at(tag));
400 template <u
int16_t tag>
401 requires (!std::same_as<sam_tag_type_t<tag>, variant_type>)
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
auto && get() &&
Uses std::map::operator[] for access and default initializes new keys.
Definition: sam_tag_dictionary.hpp:381
auto & get() &
Uses std::map::operator[] for access and default initializes new keys.
Definition: sam_tag_dictionary.hpp:370
auto const && get() const &&
Uses std::map::at() for access and throws when the key is unknown.
Definition: sam_tag_dictionary.hpp:402
auto const & get() const &
Uses std::map::at() for access and throws when the key is unknown.
Definition: sam_tag_dictionary.hpp:393
Implements a small string that can be used for compile time computations.
Definition: small_string.hpp:44
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: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.