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>
Go to the source code of this file.
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. | |
Provides seqan3::alignment_file_input and corresponding traits classes.