seqan3::alignment_file_input_default_traits< ref_sequences_t, ref_ids_t > Struct Template Reference

The default traits for seqan3::alignment_file_input. More...

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

Inheritance diagram for seqan3::alignment_file_input_default_traits< ref_sequences_t, ref_ids_t >:

Public Types
Member types
Definitions to model seqan3::AlignmentFileInputTraits.
using	sequence_alphabet = dna5
	The sequence alphabet is seqan3::dna5.
using	sequence_legal_alphabet = dna15
	The legal sequence alphabet for parsing is seqan3::dna15.
template<typename _sequence_alphabet >
using	sequence_container = std::vector< _sequence_alphabet >
	The container for a sequence is std::vector.
using	id_alphabet = char
	The alphabet for an identifier string is char.
template<typename _id_alphabet >
using	id_container = std::basic_string< _id_alphabet >
	The string type for an identifier is std::basic_string.
using	quality_alphabet = phred42
	The alphabet for a quality annotation is seqan3::phred42.
template<typename _quality_alphabet >
using	quality_container = std::vector< _quality_alphabet >
	The string type for a quality annotation is std::vector.
using	ref_sequences = ref_sequences_t
	The type of the reference sequences is deduced on construction.
using	ref_ids = ref_ids_t
	The type of the reference identifiers is deduced on construction.

Detailed Description

template<typename ref_sequences_t = ref_info_not_given, typename ref_ids_t = std::deque<std::string>>
struct seqan3::alignment_file_input_default_traits< ref_sequences_t, ref_ids_t >

The default traits for seqan3::alignment_file_input.

Template Parameters

ref_sequences_t	A range over reference sequences. This type is automatically deduced on construction.
ref_ids_t	A range over reference ids. This type is automatically deduced on construction.

If you wish to change a single or a few types from the default, just inherit from this class and "overwrite" the respective type definitions.

This example will make the file read into a smaller alphabet and a compressed container:

#include <seqan3/alphabet/nucleotide/dna4.hpp>
#include <seqan3/io/alignment_file/all.hpp>
#include <seqan3/range/container/bitcompressed_vector.hpp>

using namespace seqan3;

struct my_traits : alignment_file_input_default_traits<>
{
    using sequence_alphabet = dna4;                        // instead of dna5

    template <typename alph>
    using sequence_container = bitcompressed_vector<alph>; // must be defined as a template!
};

// ... within main you can then use:

alignment_file_input<my_traits> fin{"/tmp/my.sam"};

// ...

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

• seqan3/io/alignment_file/input.hpp