input.hpp File Reference

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

#include <cassert>
#include <fstream>
#include <string>
#include <variant>
#include <vector>
#include <seqan3/alphabet/adaptation/char.hpp>
#include <seqan3/alphabet/aminoacid/aa27.hpp>
#include <seqan3/alphabet/cigar/cigar.hpp>
#include <seqan3/alphabet/nucleotide/dna5.hpp>
#include <seqan3/alphabet/nucleotide/dna15.hpp>
#include <seqan3/alphabet/quality/phred42.hpp>
#include <seqan3/alphabet/quality/qualified.hpp>
#include <seqan3/core/concept/tuple.hpp>
#include <seqan3/core/type_list/traits.hpp>
#include <seqan3/core/type_traits/transformation_trait_or.hpp>
#include <seqan3/io/alignment_file/input_format_concept.hpp>
#include <seqan3/io/alignment_file/format_bam.hpp>
#include <seqan3/io/alignment_file/format_sam.hpp>
#include <seqan3/io/alignment_file/misc.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/exception.hpp>
#include <seqan3/io/record.hpp>
#include <seqan3/io/stream/concept.hpp>
#include <seqan3/range/decorator/gap_decorator.hpp>
#include <seqan3/range/views/repeat_n.hpp>
#include <seqan3/range/views/slice.hpp>
#include <seqan3/std/concepts>
#include <seqan3/std/filesystem>
#include <seqan3/std/ranges>

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Classes
class	seqan3::alignment_file_input< traits_type_, selected_field_ids_, valid_formats_ >
	A class for reading alignment files, e.g. SAM, BAM, BLAST ... More...
struct	seqan3::alignment_file_input_default_traits< ref_sequences_t, ref_ids_t >
	The default traits for seqan3::alignment_file_input. More...
struct	std::tuple_element< elem_no, seqan3::alignment_file_input< traits_type, selected_field_ids, valid_formats > >
	Obtains the type of the specified element. More...
struct	std::tuple_size< seqan3::alignment_file_input< traits_type, selected_field_ids, valid_formats > >
	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::alignment_file_input and corresponding traits classes.

Author

Svenja Mehringer <svenja.mehringer AT fu-berlin.de>