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

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

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

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

Public Types
Member types
Definitions to model seqan3::sam_file_input_traits.
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.
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.

Additional Inherited Members
Related Symbols inherited from 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

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

The default traits for seqan3::sam_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:

// SPDX-FileCopyrightText: 2006-2026 Knut Reinert & Freie Universität Berlin
// SPDX-FileCopyrightText: 2016-2026 Knut Reinert & MPI für molekulare Genetik
// SPDX-License-Identifier: CC0-1.0
 
#include <sstream>
 
#include <seqan3/alphabet/container/bitpacked_sequence.hpp>
#include <seqan3/alphabet/nucleotide/dna4.hpp>
#include <seqan3/io/sam_file/input.hpp>
#include <seqan3/utility/type_list/type_list.hpp>
 
struct my_traits : seqan3::sam_file_input_default_traits<>
{
    using sequence_alphabet = seqan3::dna4; // instead of dna5
 
    template <typename alph>
    using sequence_container = seqan3::bitpacked_sequence<alph>; // must be defined as a template!
};
 
auto sam_file_raw = R"(@HD  VN:1.6  SO:coordinate   GO:none
@SQ SN:ref  LN:45
r001    99  ref 7   30  8M2I4M1D3M  =   37  39  TTAGATAAAGGATACTG   *
r003    0   ref 29  30  5S6M    *   0   0   GCCTAAGCTAA *   SA:Z:ref,29,-,6H5M,17,0;
r003    2064    ref 29  17  6H5M    *   0   0   TAGGC   *   SA:Z:ref,9,+,5S6M,30,1;
r001    147 ref 237 30  9M  =   7   -39 CAGCGGCAT   *   NM:i:1
)";
 
// ... within main you can then use:
int main()
{
    seqan3::sam_file_input<my_traits> fin{std::istringstream{sam_file_raw}, seqan3::format_sam{}};
}

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

• sam_file/input.hpp