input.hpp File Reference

Provides seqan3::sequence_file_input and corresponding traits classes. More...

#include <cassert>
#include <fstream>
#include <string>
#include <variant>
#include <vector>
#include <range/v3/algorithm/equal.hpp>
#include <seqan3/alphabet/adaptation/char.hpp>
#include <seqan3/alphabet/aminoacid/aa27.hpp>
#include <seqan3/alphabet/nucleotide/all.hpp>
#include <seqan3/alphabet/quality/phred42.hpp>
#include <seqan3/alphabet/quality/qualified.hpp>
#include <seqan3/core/type_traits/basic.hpp>
#include <seqan3/io/stream/concept.hpp>
#include <seqan3/io/exception.hpp>
#include <seqan3/std/filesystem>
#include <seqan3/io/record.hpp>
#include <seqan3/io/detail/in_file_iterator.hpp>
#include <seqan3/io/detail/misc_input.hpp>
#include <seqan3/io/detail/record.hpp>
#include <seqan3/io/sequence_file/input_format_concept.hpp>
#include <seqan3/io/sequence_file/format_embl.hpp>
#include <seqan3/io/sequence_file/format_fasta.hpp>
#include <seqan3/io/sequence_file/format_fastq.hpp>
#include <seqan3/io/sequence_file/format_genbank.hpp>
#include <seqan3/io/sequence_file/format_sam.hpp>
#include <seqan3/range/container/concatenated_sequences.hpp>

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Classes
class	seqan3::sequence_file_input< traits_type_, selected_field_ids_, valid_formats_, stream_char_type_ >
	A class for reading sequence files, e.g. FASTA, FASTQ ... More...
struct	seqan3::sequence_file_input_default_traits_aa
	A traits type that specifies input as amino acids. More...
struct	seqan3::sequence_file_input_default_traits_dna
	The default traits for seqan3::sequence_file_input. More...
struct	std::tuple_element< elem_no, seqan3::sequence_file_input< traits_type, selected_field_ids, valid_formats, stream_char_t > >
	Obtains the type of the specified element. More...
struct	std::tuple_size< seqan3::sequence_file_input< traits_type, selected_field_ids, valid_formats, stream_char_t > >
	Provides access to the number of elements in a tuple as a compile-time constant expression. More...

Namespaces
	seqan3
	The main SeqAn3 namespace.
	std
	SeqAn specific customisations in the standard namespace.

Detailed Description

Provides seqan3::sequence_file_input and corresponding traits classes.

Author

Hannes Hauswedell <hannes.hauswedell AT fu-berlin.de>