seqan3::sam_tag_type< tag_value > Struct Template Reference

The generic base class. More...

#include <seqan3/io/sam_file/sam_tag_dictionary.hpp>

Public Types
using	type = detail::sam_tag_variant
	The type for all unknown tags with no extra overload defaults to a std::variant.

Related Symbols
(Note that these are not member symbols.)
template<uint16_t tag_value>
using	sam_tag_type_t = typename sam_tag_type< tag_value >::type
	Short cut helper for seqan3::sam_tag_type::type.

Detailed Description

template<uint16_t tag_value>
struct seqan3::sam_tag_type< tag_value >

The generic base class.

Attention

This is a pure base class that needs to be specialized in order to be used.

How to specialize the type for your custom tag

All known tags of the SAM specifications already have a pre-defined type. If you want to specify the type of your custom tag (the SAM specifications recommend to use X?, Y? or Z?) you need to overload the seqan3::sam_tag_type struct in the following way: (take tag "XX" as an example)

#include <seqan3/io/sam_file/sam_tag_dictionary.hpp>
 
using namespace seqan3::literals;
 
template <>                           // no template parameter since the tag is known
struct seqan3::sam_tag_type<"XX"_tag> // here comes your tag
{
    using type = int32_t; // specify the type of your tag
};

Everything else, like the get and set functions and correct SAM output (XX:i:? in this case) is handled by the seqan3::sam_tag_dictionary.

The seqan3::sam_tag_type is overloaded the following SAM tags:

Tag Name	SeqAn Type Implementation
"AM"_tag	int32_t
"AS"_tag	int32_t
"BC"_tag	std::string
"BQ"_tag	std::string
"BZ"_tag	std::string
"CB"_tag	std::string
"CC"_tag	std::string
"CG"_tag	std::vector<int32_t>
"CM"_tag	int32_t
"CO"_tag	std::string
"CP"_tag	int32_t
"CQ"_tag	std::string
"CR"_tag	std::string
"CS"_tag	std::string
"CT"_tag	std::string
"CY"_tag	std::string
"E2"_tag	std::string
"FI"_tag	int32_t
"FS"_tag	std::string
"FZ"_tag	std::vector<uint16_t>
"H0"_tag	int32_t
"H1"_tag	int32_t
"H2"_tag	int32_t
"HI"_tag	int32_t
"IH"_tag	int32_t
"LB"_tag	std::string
"MC"_tag	std::string
"MD"_tag	std::string
"MI"_tag	std::string
"MQ"_tag	int32_t
"NH"_tag	int32_t
"NM"_tag	int32_t
"OC"_tag	std::string
"OP"_tag	int32_t
"OQ"_tag	std::string
"OX"_tag	std::string
"PG"_tag	std::string
"PQ"_tag	int32_t
"PT"_tag	std::string
"PU"_tag	std::string
"Q2"_tag	std::string
"QT"_tag	std::string
"QX"_tag	std::string
"R2"_tag	std::string
"RG"_tag	std::string
"RT"_tag	std::string
"RX"_tag	std::string
"SA"_tag	std::string
"SM"_tag	int32_t
"TC"_tag	int32_t
"U2"_tag	std::string
"UQ"_tag	int32_t

Remarks

For a complete overview, take a look at SAM File

---

The documentation for this struct was generated from the following file:

• sam_tag_dictionary.hpp