SeqAn3  3.0.2
The Modern C++ library for sequence analysis.
seqan3::sam_tag_type< tag_value > Struct Template Reference

The generic base class. More...

#include <seqan3/io/alignment_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 an std::variant.
 

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)

using seqan3::operator""_tag;
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

The documentation for this struct was generated from the following file:
sam_tag_dictionary.hpp
Provides the seqan3::sam_tag_dictionary class and auxiliaries.
seqan3::sam_tag_type
The generic base class.
Definition: sam_tag_dictionary.hpp:166
seqan3::sam_tag_type::type
detail::sam_tag_variant type
The type for all unknown tags with no extra overload defaults to an std::variant.
Definition: sam_tag_dictionary.hpp:169