SeqAn3
3.4.0-rc.4
The Modern C++ library for sequence analysis.
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Parsing command line arguments with Sharg
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Alphabets in SeqAn
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Pairwise Alignment
Indexing and searching with SeqAn
SAM Input and Output in SeqAn
Implementing your own read mapper with SeqAn
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Here is a list of all documented functions with links to the class documentation for each member:
- o -
off_type() :
input_stream_over
,
output_stream_over
offset() :
seqan3::bi_fm_index_cursor< index_t >
,
seqan3::fm_index_cursor< index_t >
offset_type() :
structure_file_input_traits
on_column_iterator_creation() :
seqan3::detail::alignment_matrix_column_major_range_base< derived_t >
,
seqan3::detail::alignment_score_matrix_one_column< score_t >
,
seqan3::detail::alignment_score_matrix_one_column_banded< score_t >
on_hit() :
seqan3::detail::edit_distance_unbanded< database_t, query_t, align_config_t, edit_traits >
on_result() :
seqan3::align_cfg::on_result< callback_t >
,
seqan3::search_cfg::on_result< callback_t >
on_update() :
seqan3::alphabet_tuple_base< derived_type, component_types >::component_proxy< alphabet_type, index >
,
seqan3::bitpacked_sequence< alphabet_type >::reference_proxy_type
operator alphabet_type() :
seqan3::alphabet_proxy< derived_type, alphabet_type >
operator bool() :
seqan3::dynamic_bitset< bit_capacity >::reference_proxy_type
operator matrix_column_value_t() :
seqan3::detail::trace_matrix_full< trace_t >::iterator::column_proxy
operator other_alph_t() :
seqan3::semialphabet_any< size >
operator other_t() :
seqan3::alphabet_proxy< derived_type, alphabet_type >
operator std::pair< first_index_t, second_index_t >() :
seqan3::detail::matrix_index< index_t >
operator std::string() :
seqan3::small_string< capacity_ >
operator std::string_view() :
seqan3::small_string< capacity_ >
operator type() :
seqan3::alphabet_tuple_base< derived_type, component_types >
operator value_t() :
seqan3::detail::strong_type< value_t, derived_t, skills_ >
operator value_t &() :
seqan3::detail::proxy_reference< value_t >
operator!() :
seqan3::detail::char_predicate_base< derived_t >
,
seqan3::detail::strong_type< value_t, derived_t, skills_ >
operator!=() :
seqan3::aligned_allocator< value_t, alignment_v >
,
seqan3::bi_fm_index< alphabet_t, text_layout_mode_, sdsl_index_type_ >
,
seqan3::bi_fm_index_cursor< index_t >
,
seqan3::bitpacked_sequence< alphabet_type >
,
seqan3::concatenated_sequences< underlying_container_type, data_delimiters_type >
,
seqan3::detail::alignment_matrix_column_major_range_base< derived_t >::alignment_column_type::iterator_type
,
seqan3::detail::alignment_matrix_column_major_range_base< derived_t >::iterator_type
,
seqan3::detail::basic_iterator< single_pass_input_view< view_type > >
,
seqan3::detail::fm_index_cursor_node< index_t >
,
seqan3::detail::in_file_iterator< file_type >
,
seqan3::detail::inherited_iterator_base< derived_t, base_t >
,
seqan3::detail::matrix< matrix_t >
,
seqan3::detail::out_file_iterator< file_type >
,
seqan3::detail::pairwise_combine_view< underlying_range_type >::basic_iterator< range_type >
,
seqan3::detail::random_access_iterator_base< range_type, derived_t_template, args_t >
,
seqan3::detail::repeat_view< value_t >::basic_iterator< parent_type >
,
seqan3::detail::strong_type< value_t, derived_t, skills_ >
,
seqan3::detail::two_dimensional_matrix_iterator_base< derived_t, order >
,
seqan3::detail::view_take_exactly< urng_t, or_throw >::basic_iterator< const_range >
,
seqan3::detail::view_take_until< urng_t, fun_t, or_throw, and_consume >::basic_consume_iterator< const_range >
,
seqan3::detail::view_to_simd< urng_t, simd_t >::iterator_type
,
seqan3::fm_index< alphabet_t, text_layout_mode_, sdsl_index_type_ >
,
seqan3::fm_index_cursor< index_t >
,
seqan3::hamming_scoring_scheme
,
seqan3::pod_tuple< type0 >
,
seqan3::pod_tuple< type0, types... >
,
seqan3::scoring_scheme_base< derived_t, alphabet_t, score_t >
operator""_aa10li() :
seqan3::aa10li
operator""_aa10murphy() :
seqan3::aa10murphy
operator""_aa20() :
seqan3::aa20
operator""_aa27() :
seqan3::aa27
operator""_cigar_operation() :
seqan3::cigar
operator""_db3() :
seqan3::dot_bracket3
operator""_dna15() :
seqan3::dna15
operator""_dna16sam() :
seqan3::dna16sam
operator""_dna3bs() :
seqan3::dna3bs
operator""_dna4() :
seqan3::dna4
operator""_dna5() :
seqan3::dna5
operator""_dssp9() :
seqan3::dssp9
operator""_phred42() :
seqan3::phred42
operator""_phred63() :
seqan3::phred63
operator""_phred68solexa() :
seqan3::phred68solexa
operator""_phred94() :
seqan3::phred94
operator""_rna15() :
seqan3::rna15
operator""_rna4() :
seqan3::rna4
operator""_rna5() :
seqan3::rna5
operator""_shape() :
seqan3::shape
operator""_tag() :
seqan3::sam_tag_dictionary
operator""_wuss51() :
seqan3::wuss< SIZE >
operator%() :
seqan3::detail::strong_type< value_t, derived_t, skills_ >
operator&() :
enum_bitwise_operators
,
seqan3::detail::strong_type< value_t, derived_t, skills_ >
operator&&() :
seqan3::detail::strong_type< value_t, derived_t, skills_ >
operator&=() :
enum_bitwise_operators
,
seqan3::dynamic_bitset< bit_capacity >
,
seqan3::dynamic_bitset< bit_capacity >::reference_proxy_type
operator()() :
char_predicate
,
seqan3::advanceable_alignment_coordinate_printer< detail::advanceable_alignment_coordinate< state_t > >
,
seqan3::alignment_matrix_printer< alignment_matrix_t >
,
seqan3::alignment_printer< alignment_t >
,
seqan3::alignment_result_printer< alignment_result< result_value_t > >
,
seqan3::alphabet_printer< alphabet_t >
,
seqan3::arithmetic_range_validator< option_value_t >
,
seqan3::char_sequence_printer< char_sequence_t >
,
seqan3::cigar_printer< cigar >
,
seqan3::debug_stream_printer< value_t >
,
seqan3::default_printer
,
seqan3::detail::access_restrictor_fn
,
seqan3::detail::adaptor_base< derived_type, stored_args_ts >
,
seqan3::detail::adl_only::assign_char_strictly_to_fn
,
seqan3::detail::aligned_sequence_builder< fst_sequence_t, sec_sequence_t >
,
seqan3::detail::alignment_algorithm< config_t, algorithm_policies_t >
,
seqan3::detail::async_input_buffer_fn
,
seqan3::detail::char_predicate_base< derived_t >
,
seqan3::detail::coordinate_matrix< index_t >::convert_to_matrix_coordinate
,
seqan3::detail::customisation_point_object< derived_t, max_priority >
,
seqan3::detail::default_validator< option_value_t >
,
seqan3::detail::edit_distance_algorithm< config_t, traits_t >
,
seqan3::detail::edit_distance_unbanded< database_t, query_t, align_config_t, edit_traits >
,
seqan3::detail::interleave_fn
,
seqan3::detail::iota_simd_view_fn< index_simd_t >
,
seqan3::detail::istreambuf_fn
,
seqan3::detail::kmer_hash_fn
,
seqan3::detail::max_score_banded_updater
,
seqan3::detail::max_score_updater
,
seqan3::detail::max_score_updater_simd_global
,
seqan3::detail::minimiser_fn
,
seqan3::detail::minimiser_hash_fn
,
seqan3::detail::pairwise_alignment_algorithm< alignment_configuration_t, policies_t >
,
seqan3::detail::pairwise_alignment_algorithm_banded< alignment_configuration_t, policies_t >
,
seqan3::detail::repeat_fn
,
seqan3::detail::repeat_n_fn
,
seqan3::detail::search_scheme_algorithm< configuration_t, index_t, policies_t >
,
seqan3::detail::slice_fn
,
seqan3::detail::take_exactly_fn< or_throw >
,
seqan3::detail::take_until_fn< or_throw, and_consume >
,
seqan3::detail::to_simd_fn< simd_t >
,
seqan3::detail::translate_fn< single >
,
seqan3::detail::translate_join_fn
,
seqan3::detail::trim_fn
,
seqan3::detail::unidirectional_search_algorithm< configuration_t, index_t, policies_t >
,
seqan3::detail::validator_chain_adaptor< validator1_type, validator2_type >
,
seqan3::detail::version_checker
,
seqan3::detail::view_equality_fn
,
seqan3::dynamic_bitset_printer< dynamic_bitset< bit_capacity > >
,
seqan3::enumeration_printer< enum_t >
,
seqan3::file_validator_base
,
seqan3::input_directory_validator
,
seqan3::input_file_validator< file_t >
,
seqan3::input_range_printer< rng_t >
,
seqan3::integral_printer< integral_t >
,
seqan3::mask_printer< mask_t >
,
seqan3::optional_printer< std::nullopt_t >
,
seqan3::optional_printer< std::optional< T > >
,
seqan3::output_directory_validator
,
seqan3::output_file_validator< file_t >
,
seqan3::regex_validator
,
seqan3::sam_file_header< ref_ids_type >::key_hasher
,
seqan3::sam_flag_printer< sam_flag >
,
seqan3::search_result_printer< search_result< specs_t... > >
,
seqan3::sequence_printer< sequence_t >
,
seqan3::simd_printer< simd_t >
,
seqan3::std_byte_printer< std::byte >
,
seqan3::std_printer< type_t >
,
seqan3::std_variant_printer< std::variant< variant_ts... > >
,
seqan3::strong_type_printer< strong_type_t >
,
seqan3::trace_directions_printer< detail::trace_directions >
,
seqan3::tuple_printer< tuple_t >
,
seqan3::value_list_validator< option_value_t >
,
seqan3::views::deep< underlying_adaptor_t >
,
std::hash< alphabet_t >
,
std::hash< seqan3::dynamic_bitset< cap > >
,
std::hash< urng_t >
,
validator
operator*() :
seqan3::algorithm_result_generator_range< algorithm_executor_type >::algorithm_range_iterator
,
seqan3::detail::alignment_matrix_column_major_range_base< derived_t >::alignment_column_type::iterator_type
,
seqan3::detail::alignment_matrix_column_major_range_base< derived_t >::iterator_type
,
seqan3::detail::async_input_buffer_view< urng_t >::iterator
,
seqan3::detail::basic_iterator< single_pass_input_view< view_type > >
,
seqan3::detail::combined_score_and_trace_matrix< score_matrix_t, trace_matrix_t >::iterator
,
seqan3::detail::coordinate_matrix< index_t >::iterator
,
seqan3::detail::counted_simd_iterator< index_simd_t >
,
seqan3::detail::edit_distance_trace_matrix_full< word_t, is_semi_global, use_max_errors >::trace_path_iterator
,
seqan3::detail::fast_istreambuf_iterator< char_t, traits_t >
,
seqan3::detail::fast_ostreambuf_iterator< char_t, traits_t >
,
seqan3::detail::ignore_output_iterator
,
seqan3::detail::in_file_iterator< file_type >
,
seqan3::detail::inherited_iterator_base< derived_t, base_t >
,
seqan3::detail::kmer_hash_view< urng_t >::basic_iterator< const_range >
,
seqan3::detail::minimiser_view< urng1_t, urng2_t >::basic_iterator< const_range >
,
seqan3::detail::out_file_iterator< file_type >
,
seqan3::detail::pairwise_combine_view< underlying_range_type >::basic_iterator< range_type >
,
seqan3::detail::random_access_iterator_base< range_type, derived_t_template, args_t >
,
seqan3::detail::score_matrix_single_column< score_t >::matrix_iterator
,
seqan3::detail::strong_type< value_t, derived_t, skills_ >
,
seqan3::detail::trace_iterator_base< derived_t, matrix_iter_t >
,
seqan3::detail::trace_matrix_full< trace_t >::iterator
,
seqan3::detail::two_dimensional_matrix_iterator_base< derived_t, order >
,
seqan3::detail::view_to_simd< urng_t, simd_t >::iterator_type
,
seqan3::gap_decorator< inner_type >::basic_iterator< bool >
operator+() :
seqan3::detail::advanceable_alignment_coordinate< state >
,
seqan3::detail::inherited_iterator_base< derived_t, base_t >
,
seqan3::detail::kmer_hash_view< urng_t >::basic_iterator< const_range >
,
seqan3::detail::pairwise_combine_view< underlying_range_type >::basic_iterator< range_type >
,
seqan3::detail::random_access_iterator_base< range_type, derived_t_template, args_t >
,
seqan3::detail::strong_type< value_t, derived_t, skills_ >
,
seqan3::detail::two_dimensional_matrix_iterator< iter_t >
,
seqan3::detail::two_dimensional_matrix_iterator_base< derived_t, order >
,
seqan3::gap_decorator< inner_type >::basic_iterator< bool >
operator++() :
seqan3::algorithm_result_generator_range< algorithm_executor_type >::algorithm_range_iterator
,
seqan3::detail::advanceable_alignment_coordinate< state >
,
seqan3::detail::alignment_matrix_column_major_range_base< derived_t >::alignment_column_type::iterator_type
,
seqan3::detail::alignment_matrix_column_major_range_base< derived_t >::iterator_type
,
seqan3::detail::async_input_buffer_view< urng_t >::iterator
,
seqan3::detail::basic_iterator< single_pass_input_view< view_type > >
,
seqan3::detail::combined_score_and_trace_matrix< score_matrix_t, trace_matrix_t >::iterator
,
seqan3::detail::coordinate_matrix< index_t >::iterator
,
seqan3::detail::counted_simd_iterator< index_simd_t >
,
seqan3::detail::edit_distance_trace_matrix_full< word_t, is_semi_global, use_max_errors >::trace_path_iterator
,
seqan3::detail::fast_istreambuf_iterator< char_t, traits_t >
,
seqan3::detail::fast_ostreambuf_iterator< char_t, traits_t >
,
seqan3::detail::ignore_output_iterator
,
seqan3::detail::in_file_iterator< file_type >
,
seqan3::detail::inherited_iterator_base< derived_t, base_t >
,
seqan3::detail::kmer_hash_view< urng_t >::basic_iterator< const_range >
,
seqan3::detail::minimiser_view< urng1_t, urng2_t >::basic_iterator< const_range >
,
seqan3::detail::out_file_iterator< file_type >
,
seqan3::detail::pairwise_combine_view< underlying_range_type >::basic_iterator< range_type >
,
seqan3::detail::random_access_iterator_base< range_type, derived_t_template, args_t >
,
seqan3::detail::score_matrix_single_column< score_t >::matrix_iterator
,
seqan3::detail::strong_type< value_t, derived_t, skills_ >
,
seqan3::detail::trace_iterator_base< derived_t, matrix_iter_t >
,
seqan3::detail::trace_matrix_full< trace_t >::iterator
,
seqan3::detail::two_dimensional_matrix_iterator_base< derived_t, order >
,
seqan3::detail::view_take_exactly< urng_t, or_throw >::basic_iterator< const_range >
,
seqan3::detail::view_take_until< urng_t, fun_t, or_throw, and_consume >::basic_consume_iterator< const_range >
,
seqan3::detail::view_to_simd< urng_t, simd_t >::iterator_type
,
seqan3::gap_decorator< inner_type >::basic_iterator< bool >
operator+=() :
seqan3::counting_vector< value_t >
,
seqan3::detail::advanceable_alignment_coordinate< state >
,
seqan3::detail::inherited_iterator_base< derived_t, base_t >
,
seqan3::detail::kmer_hash_view< urng_t >::basic_iterator< const_range >
,
seqan3::detail::pairwise_combine_view< underlying_range_type >::basic_iterator< range_type >
,
seqan3::detail::random_access_iterator_base< range_type, derived_t_template, args_t >
,
seqan3::detail::two_dimensional_matrix< value_t, allocator_t, order >::basic_iterator< const_range >
,
seqan3::detail::two_dimensional_matrix_iterator< iter_t >
,
seqan3::detail::two_dimensional_matrix_iterator_base< derived_t, order >
,
seqan3::detail::view_take_exactly< urng_t, or_throw >::basic_iterator< const_range >
,
seqan3::gap_decorator< inner_type >::basic_iterator< bool >
operator-() :
seqan3::detail::advanceable_alignment_coordinate< state >
,
seqan3::detail::counted_simd_iterator< index_simd_t >
,
seqan3::detail::inherited_iterator_base< derived_t, base_t >
,
seqan3::detail::kmer_hash_view< urng_t >::basic_iterator< const_range >
,
seqan3::detail::pairwise_combine_view< underlying_range_type >::basic_iterator< range_type >
,
seqan3::detail::random_access_iterator_base< range_type, derived_t_template, args_t >
,
seqan3::detail::strong_type< value_t, derived_t, skills_ >
,
seqan3::detail::two_dimensional_matrix_iterator< iter_t >
,
seqan3::detail::two_dimensional_matrix_iterator_base< derived_t, order >
,
seqan3::detail::view_enforce_random_access< urng_t >::basic_iterator< underlying_iter_t >
,
seqan3::gap_decorator< inner_type >::basic_iterator< bool >
operator--() :
seqan3::detail::advanceable_alignment_coordinate< state >
,
seqan3::detail::inherited_iterator_base< derived_t, base_t >
,
seqan3::detail::kmer_hash_view< urng_t >::basic_iterator< const_range >
,
seqan3::detail::pairwise_combine_view< underlying_range_type >::basic_iterator< range_type >
,
seqan3::detail::random_access_iterator_base< range_type, derived_t_template, args_t >
,
seqan3::detail::strong_type< value_t, derived_t, skills_ >
,
seqan3::detail::two_dimensional_matrix_iterator_base< derived_t, order >
,
seqan3::detail::view_take_exactly< urng_t, or_throw >::basic_iterator< const_range >
,
seqan3::gap_decorator< inner_type >::basic_iterator< bool >
operator-=() :
seqan3::counting_vector< value_t >
,
seqan3::detail::advanceable_alignment_coordinate< state >
,
seqan3::detail::inherited_iterator_base< derived_t, base_t >
,
seqan3::detail::kmer_hash_view< urng_t >::basic_iterator< const_range >
,
seqan3::detail::pairwise_combine_view< underlying_range_type >::basic_iterator< range_type >
,
seqan3::detail::random_access_iterator_base< range_type, derived_t_template, args_t >
,
seqan3::detail::two_dimensional_matrix_iterator< iter_t >
,
seqan3::detail::two_dimensional_matrix_iterator_base< derived_t, order >
,
seqan3::detail::view_take_exactly< urng_t, or_throw >::basic_iterator< const_range >
,
seqan3::gap_decorator< inner_type >::basic_iterator< bool >
operator->() :
seqan3::algorithm_result_generator_range< algorithm_executor_type >::algorithm_range_iterator
,
seqan3::detail::async_input_buffer_view< urng_t >::iterator
,
seqan3::detail::basic_iterator< single_pass_input_view< view_type > >
,
seqan3::detail::inherited_iterator_base< derived_t, base_t >
,
seqan3::detail::random_access_iterator_base< range_type, derived_t_template, args_t >
,
seqan3::detail::trace_iterator_base< derived_t, matrix_iter_t >
,
seqan3::detail::two_dimensional_matrix_iterator_base< derived_t, order >
operator/() :
seqan3::detail::strong_type< value_t, derived_t, skills_ >
operator<() :
seqan3::bitpacked_sequence< alphabet_type >
,
seqan3::concatenated_sequences< underlying_container_type, data_delimiters_type >
,
seqan3::detail::inherited_iterator_base< derived_t, base_t >
,
seqan3::detail::pairwise_combine_view< underlying_range_type >::basic_iterator< range_type >
,
seqan3::detail::random_access_iterator_base< range_type, derived_t_template, args_t >
,
seqan3::detail::two_dimensional_matrix_iterator_base< derived_t, order >
,
seqan3::pod_tuple< type0 >
,
seqan3::pod_tuple< type0, types... >
operator<<() :
output_stream_over
,
seqan3::debug_stream_type< char_t >
,
seqan3::detail::strong_type< value_t, derived_t, skills_ >
,
seqan3::dynamic_bitset< bit_capacity >
operator<<=() :
seqan3::dynamic_bitset< bit_capacity >
operator<=() :
seqan3::bitpacked_sequence< alphabet_type >
,
seqan3::concatenated_sequences< underlying_container_type, data_delimiters_type >
,
seqan3::detail::inherited_iterator_base< derived_t, base_t >
,
seqan3::detail::pairwise_combine_view< underlying_range_type >::basic_iterator< range_type >
,
seqan3::detail::random_access_iterator_base< range_type, derived_t_template, args_t >
,
seqan3::detail::two_dimensional_matrix_iterator_base< derived_t, order >
,
seqan3::pod_tuple< type0 >
,
seqan3::pod_tuple< type0, types... >
operator=() :
seqan3::aa10li
,
seqan3::aa10murphy
,
seqan3::aa20
,
seqan3::aa27
,
seqan3::algorithm_result_generator_range< algorithm_executor_type >::algorithm_range_iterator
,
seqan3::algorithm_result_generator_range< algorithm_executor_type >
,
seqan3::align_cfg::band_fixed_size
,
seqan3::align_cfg::detail::result_type< alignment_result_t >
,
seqan3::align_cfg::gap_cost_affine
,
seqan3::align_cfg::method_global
,
seqan3::align_cfg::method_local
,
seqan3::align_cfg::min_score
,
seqan3::align_cfg::on_result< callback_t >
,
seqan3::align_cfg::output_alignment
,
seqan3::align_cfg::output_begin_position
,
seqan3::align_cfg::output_end_position
,
seqan3::align_cfg::output_score
,
seqan3::align_cfg::output_sequence1_id
,
seqan3::align_cfg::output_sequence2_id
,
seqan3::align_cfg::score_type< score_t >
,
seqan3::align_cfg::scoring_scheme< scoring_scheme_t >
,
seqan3::align_cfg::vectorised
,
seqan3::aligned_allocator< value_t, alignment_v >
,
seqan3::alignment_result< alignment_result_value_t >
,
seqan3::alphabet_base< derived_type, size, char_t >
,
seqan3::alphabet_proxy< derived_type, alphabet_type >
,
seqan3::alphabet_tuple_base< derived_type, component_types >::component_proxy< alphabet_type, index >
,
seqan3::alphabet_tuple_base< derived_type, component_types >
,
seqan3::alphabet_variant< alternative_types >
,
seqan3::aminoacid_base< derived_type, size >
,
seqan3::argument_parser
,
seqan3::bi_fm_index< alphabet_t, text_layout_mode_, sdsl_index_type_ >
,
seqan3::bi_fm_index_cursor< index_t >
,
seqan3::bitpacked_sequence< alphabet_type >
,
seqan3::bitpacked_sequence< alphabet_type >::reference_proxy_type
,
seqan3::bloom_filter< data_layout_mode_ >
,
seqan3::cigar
,
seqan3::concatenated_sequences< underlying_container_type, data_delimiters_type >
,
seqan3::configuration< configs_t >
,
seqan3::counting_vector< value_t >
,
seqan3::debug_stream_type< char_t >
,
seqan3::detail::adaptor_base< derived_type, stored_args_ts >
,
seqan3::detail::adaptor_for_view_without_args< view_type >
,
seqan3::detail::adaptor_from_functor< functor_type, stored_args_ts >
,
seqan3::detail::advanceable_alignment_coordinate< state >
,
seqan3::detail::affine_cell_proxy< tuple_t >
,
seqan3::detail::affine_gap_init_policy< alignment_algorithm_t >
,
seqan3::detail::affine_gap_policy< alignment_algorithm_t, score_t, align_local_t >
,
seqan3::detail::algorithm_executor_blocking< resource_t, algorithm_t, algorithm_result_t, execution_handler_t >
,
seqan3::detail::aligned_sequence_builder< fst_sequence_t, sec_sequence_t >
,
seqan3::detail::alignment_algorithm< config_t, algorithm_policies_t >
,
seqan3::detail::alignment_matrix_column_major_range_base< derived_t >::alignment_column_type::iterator_type
,
seqan3::detail::alignment_matrix_column_major_range_base< derived_t >::alignment_column_type
,
seqan3::detail::alignment_matrix_column_major_range_base< derived_t >::iterator_type
,
seqan3::detail::alignment_matrix_column_major_range_base< derived_t >
,
seqan3::detail::alignment_matrix_policy< alignment_algorithm_t, score_matrix_t, trace_matrix_t >
,
seqan3::detail::alignment_score_matrix_one_column< score_t >
,
seqan3::detail::alignment_score_matrix_one_column_banded< score_t >
,
seqan3::detail::alignment_trace_matrix_full< trace_t, coordinate_only >
,
seqan3::detail::alignment_trace_matrix_full_banded< trace_t, coordinate_only >
,
seqan3::detail::async_input_buffer_view< urng_t >::iterator
,
seqan3::detail::async_input_buffer_view< urng_t >
,
seqan3::detail::basic_iterator< single_pass_input_view< view_type > >
,
seqan3::detail::combined_adaptor< left_adaptor_t, right_adaptor_t >
,
seqan3::detail::combined_score_and_trace_matrix< score_matrix_t, trace_matrix_t >::iterator
,
seqan3::detail::combined_score_and_trace_matrix< score_matrix_t, trace_matrix_t >
,
seqan3::detail::combined_score_and_trace_matrix< score_matrix_t, trace_matrix_t >::sentinel
,
seqan3::detail::coordinate_matrix< index_t >::iterator
,
seqan3::detail::coordinate_matrix< index_t >
,
seqan3::detail::counted_simd_iterator< index_simd_t >
,
seqan3::detail::customisation_point_object< derived_t, max_priority >
,
seqan3::detail::debug_matrix< matrix_t, first_sequence_t, second_sequence_t >
,
seqan3::detail::debug_mode< wrapped_config_id_t >
,
seqan3::detail::edit_distance_algorithm< config_t, traits_t >
,
seqan3::detail::edit_distance_score_matrix_full< word_t, score_t, is_semi_global, use_max_errors >
,
seqan3::detail::edit_distance_trace_matrix_full< word_t, is_semi_global, use_max_errors >
,
seqan3::detail::edit_distance_unbanded< database_t, query_t, align_config_t, edit_traits >
,
seqan3::detail::edit_distance_unbanded_global_policy< derived_t, edit_traits >
,
seqan3::detail::edit_distance_unbanded_max_errors_policy< derived_t, edit_traits >
,
seqan3::detail::edit_distance_unbanded_score_matrix_policy< derived_t, edit_traits >
,
seqan3::detail::edit_distance_unbanded_semi_global_policy< derived_t, edit_traits >
,
seqan3::detail::edit_distance_unbanded_trace_matrix_policy< derived_t, edit_traits >
,
seqan3::detail::execution_handler_parallel::internal_state
,
seqan3::detail::execution_handler_parallel
,
seqan3::detail::fast_istreambuf_iterator< char_t, traits_t >
,
seqan3::detail::fast_ostreambuf_iterator< char_t, traits_t >
,
seqan3::detail::find_optimum_policy< alignment_algorithm_t >
,
seqan3::detail::format_help
,
seqan3::detail::format_help_base< derived_type >
,
seqan3::detail::format_html
,
seqan3::detail::format_man
,
seqan3::detail::format_parse
,
seqan3::detail::format_sam_base
,
seqan3::detail::ignore_output_iterator
,
seqan3::detail::in_file_iterator< file_type >
,
seqan3::detail::inherited_iterator_base< derived_t, base_t >
,
seqan3::detail::iota_simd_view< index_simd_t >
,
seqan3::detail::kmer_hash_view< urng_t >::basic_iterator< const_range >
,
seqan3::detail::kmer_hash_view< urng_t >
,
seqan3::detail::latch
,
seqan3::detail::matrix_index< index_t >
,
seqan3::detail::minimiser_view< urng1_t, urng2_t >::basic_iterator< const_range >
,
seqan3::detail::minimiser_view< urng1_t, urng2_t >
,
seqan3::detail::non_propagating_cache< T >
,
seqan3::detail::out_file_iterator< file_type >
,
seqan3::detail::pairwise_alignment_algorithm< alignment_configuration_t, policies_t >
,
seqan3::detail::pairwise_alignment_algorithm_banded< alignment_configuration_t, policies_t >
,
seqan3::detail::pairwise_combine_view< underlying_range_type >::basic_iterator< range_type >
,
seqan3::detail::pairwise_combine_view< underlying_range_type >
,
seqan3::detail::parallel_mode< wrapped_config_id_t >
,
seqan3::detail::policy_affine_gap_recursion< alignment_configuration_t >
,
seqan3::detail::policy_affine_gap_recursion_banded< alignment_configuration_t >
,
seqan3::detail::policy_affine_gap_with_trace_recursion< alignment_configuration_t >
,
seqan3::detail::policy_affine_gap_with_trace_recursion_banded< alignment_configuration_t >
,
seqan3::detail::policy_alignment_matrix< traits_t, alignment_matrix_t >
,
seqan3::detail::policy_alignment_result_builder< alignment_configuration_t >
,
seqan3::detail::policy_max_error
,
seqan3::detail::policy_optimum_tracker< alignment_configuration_t, optimum_updater_t >
,
seqan3::detail::policy_optimum_tracker_simd< alignment_configuration_t, optimum_updater_t >
,
seqan3::detail::policy_scoring_scheme< alignment_configuration_t, scoring_scheme_t >
,
seqan3::detail::policy_search_result_builder< search_configuration_t >
,
seqan3::detail::proxy_reference< value_t >
,
seqan3::detail::random_access_iterator_base< range_type, derived_t_template, args_t >
,
seqan3::detail::reader_writer_manager
,
seqan3::detail::reader_writer_manager::scoped_reader_type
,
seqan3::detail::reader_writer_manager::scoped_writer_type
,
seqan3::detail::repeat_view< value_t >::basic_iterator< parent_type >
,
seqan3::detail::repeat_view< value_t >
,
seqan3::detail::safe_filesystem_entry
,
seqan3::detail::score_matrix_single_column< score_t >::matrix_iterator
,
seqan3::detail::score_matrix_single_column< score_t >
,
seqan3::detail::scoring_scheme_policy< alignment_algorithm_t, scoring_scheme_t >
,
seqan3::detail::search_scheme_algorithm< configuration_t, index_t, policies_t >
,
seqan3::detail::simd_affine_gap_policy< alignment_algorithm_t, score_t, align_local_t >
,
seqan3::detail::simd_find_optimum_policy< alignment_algorithm_t, simd_t >
,
seqan3::detail::simd_match_mismatch_scoring_scheme< simd_score_t, alphabet_t, alignment_t >
,
seqan3::detail::simd_matrix_scoring_scheme< simd_score_t, alphabet_t, alignment_t >
,
seqan3::detail::single_pass_input_view< urng_t >
,
seqan3::detail::spin_delay
,
seqan3::detail::strong_type< value_t, derived_t, skills_ >
,
seqan3::detail::trace_iterator< matrix_iter_t >
,
seqan3::detail::trace_iterator_banded< matrix_iter_t >
,
seqan3::detail::trace_iterator_base< derived_t, matrix_iter_t >
,
seqan3::detail::trace_matrix_full< trace_t >::iterator::column_proxy
,
seqan3::detail::trace_matrix_full< trace_t >::iterator
,
seqan3::detail::trace_matrix_full< trace_t >
,
seqan3::detail::two_dimensional_matrix< value_t, allocator_t, order >::basic_iterator< const_range >
,
seqan3::detail::two_dimensional_matrix< value_t, allocator_t, order >
,
seqan3::detail::two_dimensional_matrix_iterator_base< derived_t, order >
,
seqan3::detail::unidirectional_search_algorithm< configuration_t, index_t, policies_t >
,
seqan3::detail::validator_chain_adaptor< validator1_type, validator2_type >
,
seqan3::detail::version_checker
,
seqan3::detail::view_enforce_random_access< urng_t >::basic_iterator< underlying_iter_t >
,
seqan3::detail::view_enforce_random_access< urng_t >
,
seqan3::detail::view_interleave< urng_t, inserted_rng_t >
,
seqan3::detail::view_take_exactly< urng_t, or_throw >::basic_iterator< const_range >
,
seqan3::detail::view_take_exactly< urng_t, or_throw >
,
seqan3::detail::view_take_until< urng_t, fun_t, or_throw, and_consume >::basic_consume_iterator< const_range >
,
seqan3::detail::view_take_until< urng_t, fun_t, or_throw, and_consume >::basic_sentinel< const_range >
,
seqan3::detail::view_take_until< urng_t, fun_t, or_throw, and_consume >
,
seqan3::detail::view_to_simd< urng_t, simd_t >::iterator_type
,
seqan3::detail::view_to_simd< urng_t, simd_t >
,
seqan3::detail::view_translate< urng_t >
,
seqan3::detail::view_translate_join< urng_t >
,
seqan3::detail::view_translate_single< urng_t >
,
seqan3::dna15
,
seqan3::dna16sam
,
seqan3::dna3bs
,
seqan3::dna4
,
seqan3::dna5
,
seqan3::dot_bracket3
,
seqan3::dssp9
,
seqan3::dynamic_bitset< bit_capacity >
,
seqan3::dynamic_bitset< bit_capacity >::reference_proxy_type
,
seqan3::exposition_only::cigar_operation
,
seqan3::file_validator_base
,
seqan3::fm_index< alphabet_t, text_layout_mode_, sdsl_index_type_ >
,
seqan3::fm_index_cursor< index_t >
,
seqan3::format_bam
,
seqan3::format_embl
,
seqan3::format_fasta
,
seqan3::format_fastq
,
seqan3::format_genbank
,
seqan3::format_sam
,
seqan3::format_vienna
,
seqan3::gap
,
seqan3::gap_decorator< inner_type >::basic_iterator< bool >
,
seqan3::gap_decorator< inner_type >
,
seqan3::hamming_scoring_scheme
,
seqan3::input_directory_validator
,
seqan3::input_file_validator< file_t >
,
seqan3::interleaved_bloom_filter< data_layout_mode_ >::counting_agent_type< value_t >
,
seqan3::interleaved_bloom_filter< data_layout_mode_ >::membership_agent_type::binning_bitvector
,
seqan3::interleaved_bloom_filter< data_layout_mode_ >::membership_agent_type
,
seqan3::interleaved_bloom_filter< data_layout_mode_ >
,
seqan3::mask
,
seqan3::masked< sequence_alphabet_t >
,
seqan3::nucleotide_base< derived_type, size >
,
seqan3::output_directory_validator
,
seqan3::output_file_validator< file_t >
,
seqan3::phred42
,
seqan3::phred63
,
seqan3::phred68solexa
,
seqan3::phred94
,
seqan3::phred_base< derived_type, size >
,
seqan3::pod_tuple< type0, types... >
,
seqan3::qualified< sequence_alphabet_t, quality_alphabet_t >
,
seqan3::record< field_types, field_ids >
,
seqan3::rna15
,
seqan3::rna4
,
seqan3::rna5
,
seqan3::sam_file_header< ref_ids_type >
,
seqan3::sam_file_input< traits_type_, selected_field_ids_, valid_formats_ >
,
seqan3::sam_file_output< selected_field_ids_, valid_formats_, ref_ids_type >
,
seqan3::sam_record< field_types, field_ids >
,
seqan3::scoring_scheme_base< derived_t, alphabet_t, score_t >
,
seqan3::search_cfg::detail::result_type< search_result_t >
,
seqan3::search_cfg::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::max_error_deletion
,
seqan3::search_cfg::max_error_insertion
,
seqan3::search_cfg::max_error_substitution
,
seqan3::search_cfg::max_error_total
,
seqan3::search_cfg::on_result< callback_t >
,
seqan3::search_cfg::output_index_cursor
,
seqan3::search_cfg::output_query_id
,
seqan3::search_cfg::output_reference_begin_position
,
seqan3::search_cfg::output_reference_id
,
seqan3::search_result< query_id_type, cursor_type, reference_id_type, reference_begin_position_type >
,
seqan3::semialphabet_any< size >
,
seqan3::sequence_file_input< traits_type_, selected_field_ids_, valid_formats_ >
,
seqan3::sequence_file_input< traits_type_, selected_field_ids_, valid_formats_ >::selected_sequence_format< format_t >
,
seqan3::sequence_file_input< traits_type_, selected_field_ids_, valid_formats_ >::sequence_format_base
,
seqan3::sequence_file_output< selected_field_ids_, valid_formats_ >
,
seqan3::sequence_record< field_types, field_ids >
,
seqan3::shape
,
seqan3::small_string< capacity_ >
,
seqan3::small_vector< value_type_, capacity_ >
,
seqan3::structure_file_input< traits_type_, selected_field_ids_, valid_formats_ >
,
seqan3::structure_file_output< selected_field_ids_, valid_formats_ >
,
seqan3::structure_record< field_types, field_ids >
,
seqan3::structured_aa< sequence_alphabet_t, structure_alphabet_t >
,
seqan3::structured_rna< sequence_alphabet_t, structure_alphabet_t >
,
seqan3::value_list_validator< option_value_t >
,
seqan3::views::deep< underlying_adaptor_t >
,
seqan3::wuss< SIZE >
operator==() :
seqan3::aligned_allocator< value_t, alignment_v >
,
seqan3::bi_fm_index< alphabet_t, text_layout_mode_, sdsl_index_type_ >
,
seqan3::bi_fm_index_cursor< index_t >
,
seqan3::bitpacked_sequence< alphabet_type >
,
seqan3::concatenated_sequences< underlying_container_type, data_delimiters_type >
,
seqan3::detail::alignment_matrix_column_major_range_base< derived_t >::alignment_column_type::iterator_type
,
seqan3::detail::alignment_matrix_column_major_range_base< derived_t >::iterator_type
,
seqan3::detail::basic_iterator< single_pass_input_view< view_type > >
,
seqan3::detail::fm_index_cursor_node< index_t >
,
seqan3::detail::in_file_iterator< file_type >
,
seqan3::detail::inherited_iterator_base< derived_t, base_t >
,
seqan3::detail::matrix< matrix_t >
,
seqan3::detail::out_file_iterator< file_type >
,
seqan3::detail::pairwise_combine_view< underlying_range_type >::basic_iterator< range_type >
,
seqan3::detail::random_access_iterator_base< range_type, derived_t_template, args_t >
,
seqan3::detail::repeat_view< value_t >::basic_iterator< parent_type >
,
seqan3::detail::strong_type< value_t, derived_t, skills_ >
,
seqan3::detail::two_dimensional_matrix_iterator_base< derived_t, order >
,
seqan3::detail::view_take_exactly< urng_t, or_throw >::basic_iterator< const_range >
,
seqan3::detail::view_take_until< urng_t, fun_t, or_throw, and_consume >::basic_consume_iterator< const_range >
,
seqan3::detail::view_to_simd< urng_t, simd_t >::iterator_type
,
seqan3::fm_index< alphabet_t, text_layout_mode_, sdsl_index_type_ >
,
seqan3::fm_index_cursor< index_t >
,
seqan3::hamming_scoring_scheme
,
seqan3::pod_tuple< type0 >
,
seqan3::pod_tuple< type0, types... >
,
seqan3::scoring_scheme_base< derived_t, alphabet_t, score_t >
operator>() :
seqan3::bitpacked_sequence< alphabet_type >
,
seqan3::concatenated_sequences< underlying_container_type, data_delimiters_type >
,
seqan3::detail::inherited_iterator_base< derived_t, base_t >
,
seqan3::detail::pairwise_combine_view< underlying_range_type >::basic_iterator< range_type >
,
seqan3::detail::random_access_iterator_base< range_type, derived_t_template, args_t >
,
seqan3::detail::two_dimensional_matrix_iterator_base< derived_t, order >
,
seqan3::pod_tuple< type0 >
,
seqan3::pod_tuple< type0, types... >
operator>=() :
seqan3::bitpacked_sequence< alphabet_type >
,
seqan3::concatenated_sequences< underlying_container_type, data_delimiters_type >
,
seqan3::detail::inherited_iterator_base< derived_t, base_t >
,
seqan3::detail::pairwise_combine_view< underlying_range_type >::basic_iterator< range_type >
,
seqan3::detail::random_access_iterator_base< range_type, derived_t_template, args_t >
,
seqan3::detail::two_dimensional_matrix_iterator_base< derived_t, order >
,
seqan3::pod_tuple< type0 >
,
seqan3::pod_tuple< type0, types... >
operator>>() :
input_stream_over
,
seqan3::detail::strong_type< value_t, derived_t, skills_ >
,
seqan3::dynamic_bitset< bit_capacity >
operator>>=() :
seqan3::dynamic_bitset< bit_capacity >
operator[]() :
seqan3::bitpacked_sequence< alphabet_type >
,
seqan3::concatenated_sequences< underlying_container_type, data_delimiters_type >
,
seqan3::detail::inherited_iterator_base< derived_t, base_t >
,
seqan3::detail::kmer_hash_view< urng_t >::basic_iterator< const_range >
,
seqan3::detail::pairwise_combine_view< underlying_range_type >::basic_iterator< range_type >
,
seqan3::detail::random_access_iterator_base< range_type, derived_t_template, args_t >
,
seqan3::detail::repeat_view< value_t >
,
seqan3::detail::two_dimensional_matrix< value_t, allocator_t, order >
,
seqan3::detail::two_dimensional_matrix_iterator_base< derived_t, order >
,
seqan3::detail::view_interleave< urng_t, inserted_rng_t >
,
seqan3::detail::view_take_exactly< urng_t, or_throw >::basic_iterator< const_range >
,
seqan3::detail::view_translate< urng_t >
,
seqan3::detail::view_translate_join< urng_t >
,
seqan3::detail::view_translate_single< urng_t >
,
seqan3::dynamic_bitset< bit_capacity >
,
seqan3::gap_decorator< inner_type >::basic_iterator< bool >
,
seqan3::gap_decorator< inner_type >
,
seqan3::interleaved_bloom_filter< data_layout_mode_ >::membership_agent_type::binning_bitvector
,
seqan3::small_vector< value_type_, capacity_ >
operator^() :
enum_bitwise_operators
,
seqan3::detail::strong_type< value_t, derived_t, skills_ >
operator^=() :
enum_bitwise_operators
,
seqan3::dynamic_bitset< bit_capacity >
,
seqan3::dynamic_bitset< bit_capacity >::reference_proxy_type
operator|() :
enum_bitwise_operators
,
seqan3::configuration< configs_t >
,
seqan3::detail::constexpr_pseudo_bitset< N >
,
seqan3::detail::strong_type< value_t, derived_t, skills_ >
operator|=() :
enum_bitwise_operators
,
seqan3::dynamic_bitset< bit_capacity >
,
seqan3::dynamic_bitset< bit_capacity >::reference_proxy_type
operator||() :
seqan3::detail::char_predicate_base< derived_t >
,
seqan3::detail::strong_type< value_t, derived_t, skills_ >
operator~() :
enum_bitwise_operators
,
seqan3::detail::constexpr_pseudo_bitset< N >
,
seqan3::detail::strong_type< value_t, derived_t, skills_ >
,
seqan3::dynamic_bitset< bit_capacity >
,
seqan3::dynamic_bitset< bit_capacity >::reference_proxy_type
option_declared_multiple_times() :
seqan3::option_declared_multiple_times
option_type_and_list_info() :
seqan3::detail::format_base
option_value_type() :
validator
out_file_iterator() :
seqan3::detail::out_file_iterator< file_type >
output_alignment() :
seqan3::align_cfg::output_alignment
output_begin_position() :
seqan3::align_cfg::output_begin_position
output_directory_validator() :
seqan3::output_directory_validator
output_end_position() :
seqan3::align_cfg::output_end_position
output_file_validator() :
seqan3::output_file_validator< file_t >
output_index_cursor() :
seqan3::search_cfg::output_index_cursor
output_query_id() :
seqan3::search_cfg::output_query_id
output_reference_begin_position() :
seqan3::search_cfg::output_reference_begin_position
output_reference_id() :
seqan3::search_cfg::output_reference_id
output_score() :
seqan3::align_cfg::output_score
output_sequence1_id() :
seqan3::align_cfg::output_sequence1_id
output_sequence2_id() :
seqan3::align_cfg::output_sequence2_id
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