SeqAn3
3.4.0-rc.4
The Modern C++ library for sequence analysis.
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Welcome
Setup
Quick Setup (using CMake)
Tutorial
First steps with SeqAn
Parsing command line arguments with Sharg
C++ Concepts
Alphabets in SeqAn
Ranges
Minimisers
Sequence File Input and Output
Pairwise Alignment
Indexing and searching with SeqAn
SAM Input and Output in SeqAn
Implementing your own read mapper with SeqAn
How-To
Porting from SeqAn2
How to write an argument parser with subcommands
How to serialise SeqAn data structures
How to write a view
How to write your own alphabet
Cookbook
About
Stability and long-term promises
Citing
Customisation
Changelog
Copyright
Code of Conduct
Contributing
API Reference
API Reference (details)
Namespace List
Namespace List
Class List
Class List
Class Index
Class Hierarchy
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Class Index
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W
A
aa10li
(
seqan3
)
aa10murphy
(
seqan3
)
aa20
(
seqan3
)
aa27
(
seqan3
)
advanceable_alignment_coordinate_printer
(
seqan3
)
advanceable_alignment_coordinate_printer< detail::advanceable_alignment_coordinate< state_t > >
(
seqan3
)
algorithm_result_generator_range::algorithm_range_iterator
(
seqan3
)
algorithm_result_generator_range
(
seqan3
)
aligned_allocator
(
seqan3
)
aligned_sequence
(
seqan3
)
alignment_matrix_printer
(
seqan3
)
alignment_matrix_printer< alignment_matrix_t >
(
seqan3
)
alignment_printer
(
seqan3
)
alignment_printer< alignment_t >
(
seqan3
)
alignment_result
(
seqan3
)
alignment_result_printer
(
seqan3
)
alignment_result_printer< alignment_result< result_value_t > >
(
seqan3
)
alphabet
(
seqan3
)
alphabet
(
seqan3::custom
)
alphabet< char_type >
(
seqan3::custom
)
alphabet< uint_type >
(
seqan3::custom
)
alphabet_base
(
seqan3
)
alphabet_printer
(
seqan3
)
alphabet_printer< alphabet_t >
(
seqan3
)
alphabet_proxy
(
seqan3
)
alphabet_tuple_base
(
seqan3
)
alphabet_variant
(
seqan3
)
aminoacid_alphabet
(
seqan3
)
aminoacid_base
(
seqan3
)
aminoacid_empty_base
(
seqan3
)
aminoacid_scoring_scheme
(
seqan3
)
argument_parser
(
seqan3
)
argument_parser_compatible_option
(
seqan3
)
argument_parser_error
(
seqan3
)
argument_parser_meta_data
(
seqan3
)
argument_parsing
(
seqan3::custom
)
arithmetic
(
seqan3
)
arithmetic_range_validator
(
seqan3
)
B
band_fixed_size
(
seqan3::align_cfg
)
bi_fm_index
(
seqan3
)
bi_fm_index_cursor
(
seqan3
)
bin_count
(
seqan3
)
bin_index
(
seqan3
)
bin_literal
(
seqan3
)
bin_size
(
seqan3
)
interleaved_bloom_filter::membership_agent_type::binning_bitvector
(
seqan3
)
bitpacked_sequence
(
seqan3
)
bloom_filter
(
seqan3
)
builtin_character
(
seqan3
)
C
cereal_archive
(
seqan3
)
cereal_input_archive
(
seqan3
)
cereal_output_archive
(
seqan3
)
cereal_text_archive
(
seqan3
)
cerealisable
(
seqan3
)
char_sequence_printer
(
seqan3
)
char_sequence_printer< char_sequence_t >
(
seqan3
)
cigar
(
seqan3
)
cigar_clipped_bases
(
seqan3
)
cigar_operation
(
seqan3::exposition_only
)
cigar_printer
(
seqan3
)
cigar_printer< cigar >
(
seqan3
)
concatenated_sequences
(
seqan3
)
configuration
(
seqan3
)
const_iterable_range
(
seqan3
)
container
(
seqan3
)
interleaved_bloom_filter::counting_agent_type
(
seqan3
)
counting_vector
(
seqan3
)
D
debug_stream_printer
(
seqan3
)
debug_stream_printer< value_t >
(
seqan3
)
debug_stream_type
(
seqan3
)
deep
(
seqan3::views
)
default_printer
(
seqan3
)
design_error
(
seqan3
)
dna15
(
seqan3
)
dna16sam
(
seqan3
)
dna3bs
(
seqan3
)
dna4
(
seqan3
)
dna5
(
seqan3
)
dot_bracket3
(
seqan3
)
dssp9
(
seqan3
)
dynamic_bitset
(
seqan3
)
dynamic_bitset_printer
(
seqan3
)
dynamic_bitset_printer< dynamic_bitset< bit_capacity > >
(
seqan3
)
E
enum_bitwise_operators
(
seqan3
)
enumeration_printer
(
seqan3
)
enumeration_printer< enum_t >
(
seqan3
)
error_count
(
seqan3::search_cfg
)
error_rate
(
seqan3::search_cfg
)
explicitly_convertible_to
(
seqan3
)
extension_score
(
seqan3::align_cfg
)
F
fields
(
seqan3
)
file_open_error
(
seqan3
)
file_validator_base
(
seqan3
)
fm_index
(
seqan3
)
fm_index_cursor
(
seqan3
)
format_bam
(
seqan3
)
format_embl
(
seqan3
)
format_error
(
seqan3
)
format_fasta
(
seqan3
)
format_fastq
(
seqan3
)
format_genbank
(
seqan3
)
format_sam
(
seqan3
)
format_vienna
(
seqan3
)
free_end_gaps_sequence1_leading
(
seqan3::align_cfg
)
free_end_gaps_sequence1_trailing
(
seqan3::align_cfg
)
free_end_gaps_sequence2_leading
(
seqan3::align_cfg
)
free_end_gaps_sequence2_trailing
(
seqan3::align_cfg
)
function_traits< std::function< return_t(args_t...)> >
(
seqan3
)
G
gap
(
seqan3
)
gap_cost_affine
(
seqan3::align_cfg
)
gap_decorator
(
seqan3
)
gap_erase_failure
(
seqan3
)
H
hamming_scoring_scheme
(
seqan3
)
hash< alphabet_t >
(
std
)
hash< seqan3::dynamic_bitset< cap > >
(
std
)
hash< urng_t >
(
std
)
hash_function_count
(
seqan3
)
hit
(
seqan3::search_cfg
)
hit_all
(
seqan3::search_cfg
)
hit_all_best
(
seqan3::search_cfg
)
hit_single_best
(
seqan3::search_cfg
)
hit_strata
(
seqan3::search_cfg
)
I
implicitly_convertible_to
(
seqan3
)
input_directory_validator
(
seqan3
)
input_file_validator
(
seqan3
)
input_range_printer
(
seqan3
)
input_range_printer< rng_t >
(
seqan3
)
input_stream_over
(
seqan3
)
integer_sequence_printer
(
seqan3
)
integer_sequence_printer< integer_sequence_t >
(
seqan3
)
integral_printer
(
seqan3
)
integral_printer< integral_t >
(
seqan3
)
interleaved_bloom_filter
(
seqan3
)
invalid_alignment_configuration
(
seqan3
)
invalid_char_assignment
(
seqan3
)
io_error
(
seqan3
)
is_constexpr_default_constructible
(
seqan3
)
L
lower_diagonal
(
seqan3::align_cfg
)
M
mask
(
seqan3
)
mask_printer
(
seqan3
)
mask_printer< mask_t >
(
seqan3
)
masked
(
seqan3
)
match_score
(
seqan3
)
max_error_deletion
(
seqan3::search_cfg
)
max_error_insertion
(
seqan3::search_cfg
)
max_error_substitution
(
seqan3::search_cfg
)
max_error_total
(
seqan3::search_cfg
)
interleaved_bloom_filter::membership_agent_type
(
seqan3
)
method_global
(
seqan3::align_cfg
)
method_local
(
seqan3::align_cfg
)
min_score
(
seqan3::align_cfg
)
mismatch_score
(
seqan3
)
N
named_enumeration
(
seqan3
)
no_printer_found
(
seqan3
)
nonrecursive_range
(
seqan3
)
nucleotide_alphabet
(
seqan3
)
nucleotide_base
(
seqan3
)
nucleotide_scoring_scheme
(
seqan3
)
O
on_result
(
seqan3::search_cfg
)
on_result
(
seqan3::align_cfg
)
open_score
(
seqan3::align_cfg
)
option_declared_multiple_times
(
seqan3
)
optional_printer
(
seqan3
)
optional_printer< std::nullopt_t >
(
seqan3
)
optional_printer< std::optional< T > >
(
seqan3
)
output_alignment
(
seqan3::align_cfg
)
output_begin_position
(
seqan3::align_cfg
)
output_directory_validator
(
seqan3
)
output_end_position
(
seqan3::align_cfg
)
output_file_validator
(
seqan3
)
output_index_cursor
(
seqan3::search_cfg
)
output_query_id
(
seqan3::search_cfg
)
output_reference_begin_position
(
seqan3::search_cfg
)
output_reference_id
(
seqan3::search_cfg
)
output_score
(
seqan3::align_cfg
)
output_sequence1_id
(
seqan3::align_cfg
)
output_sequence2_id
(
seqan3::align_cfg
)
output_stream_over
(
seqan3
)
P
pair_like
(
seqan3
)
parse_error
(
seqan3
)
phred42
(
seqan3
)
phred63
(
seqan3
)
phred68solexa
(
seqan3
)
phred94
(
seqan3
)
phred_base
(
seqan3
)
pipeable_config_element
(
seqan3
)
pod_tuple
(
seqan3
)
pod_tuple< type0 >
(
seqan3
)
pod_tuple< type0, types... >
(
seqan3
)
printable_with
(
seqan3
)
printer_order
(
seqan3
)
pseudo_random_access_iterator
(
seqan3
)
pseudo_random_access_range
(
seqan3
)
Q
qualified
(
seqan3
)
quality_alphabet
(
seqan3
)
R
random_access_container
(
seqan3
)
range_innermost_value
(
seqan3
)
aligned_allocator::rebind
(
seqan3
)
record
(
seqan3
)
ref_info_not_given
(
seqan3
)
regex_validator
(
seqan3
)
remove_rvalue_reference
(
seqan3
)
required_option_missing
(
seqan3
)
reservible_container
(
seqan3
)
result_type
(seqan3::align_cfg::detail)
result_type
(seqan3::search_cfg::detail)
rna15
(
seqan3
)
rna4
(
seqan3
)
rna5
(
seqan3
)
rna_structure_alphabet
(
seqan3
)
S
sam_file_header
(
seqan3
)
sam_file_input
(
seqan3
)
sam_file_input_default_traits
(
seqan3
)
sam_file_input_format
(
seqan3
)
sam_file_input_options
(
seqan3
)
sam_file_input_traits
(
seqan3
)
sam_file_output
(
seqan3
)
sam_file_output_format
(
seqan3
)
sam_file_output_options
(
seqan3
)
sam_file_program_info_t
(
seqan3
)
sam_flag_printer
(
seqan3
)
sam_flag_printer< sam_flag >
(
seqan3
)
sam_record
(
seqan3
)
sam_tag_dictionary
(
seqan3
)
sam_tag_type
(
seqan3
)
score_type
(
seqan3::align_cfg
)
scoring_scheme
(
seqan3::align_cfg
)
scoring_scheme_base
(
seqan3
)
scoring_scheme_for
(
seqan3
)
search_result
(
seqan3
)
search_result_printer
(
seqan3
)
search_result_printer< search_result< specs_t... > >
(
seqan3
)
seed
(
seqan3
)
semialphabet
(
seqan3
)
semialphabet_any
(
seqan3
)
sequence
(
seqan3
)
sequence_container
(
seqan3
)
sequence_file_input
(
seqan3
)
sequence_file_input_default_traits_aa
(
seqan3
)
sequence_file_input_default_traits_dna
(
seqan3
)
sequence_file_input_format
(
seqan3
)
sequence_file_input_options
(
seqan3
)
sequence_file_input_traits
(
seqan3
)
sequence_file_output
(
seqan3
)
sequence_file_output_format
(
seqan3
)
sequence_file_output_options
(
seqan3
)
sequence_printer
(
seqan3
)
sequence_printer< sequence_t >
(
seqan3
)
sequence_record
(
seqan3
)
shape
(
seqan3
)
simd_printer
(
seqan3
)
small_string
(
seqan3
)
small_vector
(
seqan3
)
standard_layout
(
seqan3
)
std_byte_printer
(
seqan3
)
std_byte_printer< std::byte >
(
seqan3
)
std_printer
(
seqan3
)
std_printer< type_t >
(
seqan3
)
std_variant_printer
(
seqan3
)
std_variant_printer< std::variant< variant_ts... > >
(
seqan3
)
strong_type_printer
(
seqan3
)
structure_file_input
(
seqan3
)
structure_file_input_default_traits_aa
(
seqan3
)
structure_file_input_default_traits_rna
(
seqan3
)
structure_file_input_format
(
seqan3
)
structure_file_input_options
(
seqan3
)
structure_file_input_traits
(
seqan3
)
structure_file_output
(
seqan3
)
structure_file_output_format
(
seqan3
)
structure_file_output_options
(
seqan3
)
structure_record
(
seqan3
)
structured_aa
(
seqan3
)
structured_rna
(
seqan3
)
suffix_array_interval
(
seqan3
)
T
too_few_arguments
(
seqan3
)
too_many_arguments
(
seqan3
)
trace_directions_printer
(
seqan3
)
trace_directions_printer< detail::trace_directions >
(
seqan3
)
transformation_trait
(
seqan3
)
trivial
(
seqan3
)
trivially_copyable
(
seqan3
)
trivially_destructible
(
seqan3
)
tuple_element< elem_no, seqan3::sam_record< field_types, field_ids > >
(
std
)
tuple_element< elem_no, seqan3::sequence_record< field_types, field_ids > >
(
std
)
tuple_element< elem_no, seqan3::structure_record< field_types, field_ids > >
(
std
)
tuple_element< i, t< types... > >
(
std
)
tuple_element< i, tuple_t >
(
std
)
tuple_like
(
seqan3
)
tuple_printer
(
seqan3
)
tuple_printer< tuple_t >
(
seqan3
)
tuple_size< seqan3::sam_record< field_types, field_ids > >
(
std
)
tuple_size< seqan3::sequence_record< field_types, field_ids > >
(
std
)
tuple_size< seqan3::structure_record< field_types, field_ids > >
(
std
)
tuple_size< t< types... > >
(
std
)
tuple_size< tuple_t >
(
std
)
type_list
(
seqan3
)
U
unary_type_trait
(
seqan3
)
unexpected_end_of_input
(
seqan3
)
ungapped
(
seqan3
)
unhandled_extension_error
(
seqan3
)
unknown_option
(
seqan3
)
upper_diagonal
(
seqan3::align_cfg
)
user_input_error
(
seqan3
)
V
validation_error
(
seqan3
)
validator
(
seqan3
)
value_list_validator
(
seqan3
)
vectorised
(
seqan3::align_cfg
)
W
weakly_assignable_from
(
seqan3
)
window_size
(
seqan3
)
writable_aligned_sequence
(
seqan3
)
writable_alphabet
(
seqan3
)
writable_quality_alphabet
(
seqan3
)
writable_semialphabet
(
seqan3
)
wuss
(
seqan3
)
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