sam_file_input_traits Interface Reference

The requirements a traits_type for seqan3::sam_file_input must meet. More...

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

Inheritance diagram for sam_file_input_traits:

Related Symbols
(Note that these are not member symbols.)
Requirements for seqan3::sam_file_input_traits
You can expect these member types of all types that model seqan3::sam_file_input_traits.
using	sequence_alphabet
	Alphabet of the characters for the seqan3::field::seq; must model seqan3::alphabet.
using	sequence_legal_alphabet
	Intermediate alphabet for seqan3::field::seq; must model seqan3::alphabet and be convertible to sequence_alphabet.
using	sequence_container
	Type template of the seqan3::field::seq, a container template over sequence_alphabet; must model seqan3::sequence_container.
using	id_container
	Type template of the seqan3::field::id, a container template over char; must model seqan3::sequence_container.
using	quality_alphabet
	Alphabet of the characters for the seqan3::field::qual; must model seqan3::writable_quality_alphabet.
using	quality_container
	Type template of the seqan3::field::qual, a container template over quality_alphabet; must model seqan3::sequence_container.
using	ref_sequences
	The type of range over reference sequences; must model std::ranges::forward_range, the value_type must also model std::ranges::forward_range, and the value type of the value type must model seqan3::alphabet (e.g. std::vector<std::vector<dna4>>).
using	ref_ids
	The type of range over reference sequences; must model std::ranges::forward_range, the value_type must also model std::ranges::forward_range, and the value type of the value type must model seqan3::alphabet (e.g. std::vector<string>).

Detailed Description

The requirements a traits_type for seqan3::sam_file_input must meet.

Friends And Related Symbol Documentation

ref_ids()

using ref_ids

related

The type of range over reference sequences; must model std::ranges::forward_range, the value_type must also model std::ranges::forward_range, and the value type of the value type must model seqan3::alphabet (e.g. std::vector<string>).

Attention

This type is the second template parameter of seqan3::sam_file_input_default_traits and should not be manually configured in order to allow for automatic type deduction from reference information input on construction.

ref_sequences()

using ref_sequences

related

The type of range over reference sequences; must model std::ranges::forward_range, the value_type must also model std::ranges::forward_range, and the value type of the value type must model seqan3::alphabet (e.g. std::vector<std::vector<dna4>>).

Attention

This type is the first template parameter of seqan3::sam_file_input_default_traits and should not be manually configured in order to allow for automatic type deduction from reference information input on construction.

sequence_legal_alphabet()

using sequence_legal_alphabet

related

Intermediate alphabet for seqan3::field::seq; must model seqan3::alphabet and be convertible to sequence_alphabet.

This alphabet can be a superset of sequence_alphabet to allow conversion of some characters without producing an error, e.g. if this is set to seqan3::dna15 and sequence_alphabet is set to seqan3::dna5, 'M' will be an accepted character and automatically converted to 'N', while 'Z' will still be an illegal character and produce an error.

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

• sam_file/input.hpp