API Reference

Here is a list of all topics with brief descriptions:

[detail level 123]

▼Sequence Alignment	The alignment module contains concepts, algorithms and classes that are related to the computation of pairwise and multiple sequence alignments
Aligned Sequence	Provides seqan3::aligned_sequence, as well as various ranges that model it
CIGAR Conversion	The CIGAR Conversion submodule contains utility functions to convert a CIGAR to an alignment or vice versa
Configuration	Provides configuration elements for the pairwise alignment configuration
Decorator	The decorator submodule contains special SeqAn decorators
Matrix	Provides data structures for representing alignment coordinates and alignments as a matrix
▼Pairwise Alignments	Provides the algorithmic components for the computation of pairwise alignments
Alignment policies	Provides policies for the alignment algorithm
Scoring	Provides the data structures used for scoring alphabets and sequences
▼Alphabet
Adaptation	Provides alphabet adaptions of some standard char and uint types
Aminoacid	Provides the amino acid alphabets and functionality for translation from nucleotide
CIGAR	Provides (semi-)alphabets for representing elements in CIGAR strings
Composite	Provides templates for combining existing alphabets into new alphabet types
Container	Alphabet related container
Gap	Provides the gap alphabet and functionality to make an alphabet a gapped alphabet
Mask	Provides the mask alphabet and functionality for creating masked composites
Nucleotide	Provides the different DNA and RNA alphabet types
Quality	Provides the various quality score types
Range	Alphabet related ranges
Structure	Provides types to represent single elements of RNA and protein structures
Views	Alphabet related views
Argument Parser
▼Core	Provides core functionality used by multiple modules
Algorithm	Provides core functionality used for algorithms
Concept	Provides core concepts
Configuration	Provides core functionality used to configure configurations
Debug Stream	Provides core functionality used to print seqan3 and std types
Range	Provides seqan3 general purpose range functionality
▼IO	The IO module provides stream handling formatted I/O
SAM File	Provides files and formats for handling read mapping data
Sequence File	Provides files and formats for handling sequence data
Stream	The stream sub-module contains data structures and functions for streaming and tokenization
Structure File	Provides files and formats for handling structure data
Views	IO related views
▼Search	Data structures and approximate string search algorithms for large collection of text (e.g. DNA)
Configuration	Data structures and utility functions for configuring search algorithm
DREAM Index	Provides seqan3::interleaved_bloom_filter
FM Index	Provides seqan3::fm_index and seqan3::bi_fm_index as well as respective cursors
k-mer Index	Implementation of shapes for a k-mer Index
Views	Search related views
▼std	A subset of the C++20 standard library made available in pre-C++20 contexts
charconv	The <charconv> header from C++17's standard library
new	The <new> header from C++17's standard library
▼Utility	Provides additional utility functionality used by multiple modules
Bloom Filter	Provides seqan3:bloom_filter
Builtin Character Operations	Provides various operations on character types
Concept	Provides various general purpose concepts
Container	Provides various general purpose container and concepts
Parallel	This module contains types and utilities for concurrent execution of algorithms in SeqAn
Range	The range module provides general purpose range concepts
▼SIMD	The simd module contains a unified interface to provide simd types and functions used in seqan3
Views	SIMD related views
Tuple	Additional helper utilities for "tuple" types like std::tuple, std::pair, seqan3::pod_tuple that are not specific to a SeqAn module
Type List	Provides seqan3::type_list and metaprogramming utilities for working on type lists
Type Pack	Provides metaprogramming utilities for working on template parameter packs
Type Traits	Provides various type traits and their shortcuts
Views	Views are "lazy range combinators" that offer modified views onto other ranges