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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SAM Input and Output in SeqAn
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Here is a list of all documented class members with links to the class documentation for each member:
- d -
D :
seqan3::detail::edit_distance_trace_matrix_full< word_t, is_semi_global, use_max_errors >::trace_path_iterator
d0 :
seqan3::detail::edit_distance_unbanded< database_t, query_t, align_config_t, edit_traits >::compute_state
data :
seqan3::alignment_result< alignment_result_value_t >
,
seqan3::bitpacked_sequence< alphabet_type >
,
seqan3::bloom_filter< data_layout_mode_ >
,
seqan3::detail::alignment_trace_matrix_base< trace_t >
,
seqan3::detail::char_predicate_disjunction< condition_ts >
,
seqan3::detail::char_predicate_negator< condition_t >
,
seqan3::detail::is_char_type< char_v >
,
seqan3::detail::is_in_interval_type< interval_first, interval_last >
,
seqan3::detail::two_dimensional_matrix< value_t, allocator_t, order >
,
seqan3::dynamic_bitset< bit_capacity >
,
seqan3::interleaved_bloom_filter< data_layout_mode_ >
,
seqan3::interleaved_bloom_filter< data_layout_mode_ >::membership_agent_type::binning_bitvector
,
seqan3::small_vector< value_type_, capacity_ >
data_ :
seqan3::small_vector< value_type_, capacity_ >
data_delimiters :
seqan3::concatenated_sequences< underlying_container_type, data_delimiters_type >
data_layout_mode :
seqan3::bloom_filter< data_layout_mode_ >
,
seqan3::interleaved_bloom_filter< data_layout_mode_ >
data_t :
seqan3::detail::char_predicate_base< derived_t >
data_type :
seqan3::bitpacked_sequence< alphabet_type >
,
seqan3::bloom_filter< data_layout_mode_ >
,
seqan3::interleaved_bloom_filter< data_layout_mode_ >
,
seqan3::interleaved_bloom_filter< data_layout_mode_ >::membership_agent_type::binning_bitvector
data_values :
seqan3::concatenated_sequences< underlying_container_type, data_delimiters_type >
database :
seqan3::detail::edit_distance_unbanded< database_t, query_t, align_config_t, edit_traits >
database_it :
seqan3::detail::edit_distance_unbanded< database_t, query_t, align_config_t, edit_traits >
database_it_end :
seqan3::detail::edit_distance_unbanded< database_t, query_t, align_config_t, edit_traits >
database_iterator :
seqan3::detail::default_edit_distance_trait_type< database_t, query_t, align_config_t, is_semi_global_t, word_t >
database_type :
seqan3::detail::default_edit_distance_trait_type< database_t, query_t, align_config_t, is_semi_global_t, word_t >
date :
seqan3::argument_parser_meta_data
db :
seqan3::detail::edit_distance_unbanded< database_t, query_t, align_config_t, edit_traits >::compute_state_trace_matrix
,
seqan3::detail::edit_distance_unbanded_trace_matrix_policy< derived_t, edit_traits >
deallocate() :
seqan3::aligned_allocator< value_t, alignment_v >
debug_matrix() :
seqan3::detail::debug_matrix< matrix_t, first_sequence_t, second_sequence_t >
debug_mode() :
seqan3::detail::debug_mode< wrapped_config_id_t >
debug_score_matrix_type :
seqan3::detail::align_result_selector< first_range_t, second_range_t, configuration_t >
debug_stream_type() :
seqan3::debug_stream_type< char_t >
debug_trace_matrix_type :
seqan3::detail::align_result_selector< first_range_t, second_range_t, configuration_t >
decide_if_check_is_performed() :
seqan3::detail::version_checker
deep() :
seqan3::views::deep< underlying_adaptor_t >
default_extensions() :
seqan3::output_file_validator< file_t >
default_frames :
seqan3::detail::translate_fn< single >
default_header :
seqan3::format_sam
default_or() :
seqan3::format_sam
default_urng2_t :
seqan3::detail::minimiser_view< urng1_t, urng2_t >
defaultScreenWidth :
seqan3::detail::format_help::console_layout_struct
delegate :
seqan3::detail::unidirectional_search_algorithm< configuration_t, index_t, policies_t >
deletion :
seqan3::detail::policy_max_error
,
seqan3::detail::search_param
depth :
seqan3::bi_fm_index_cursor< index_t >
,
seqan3::detail::fm_index_cursor_node< index_t >
derived() :
seqan3::detail::trace_iterator_base< derived_t, matrix_iter_t >
derived_from() :
seqan3::detail::is_derived_from_record< record_t >
derived_t :
seqan3::detail::alignment_matrix_column_major_range_base< derived_t >
,
seqan3::detail::customisation_point_object< derived_t, max_priority >
,
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::format_help_base< derived_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 >
,
seqan3::scoring_scheme_base< derived_t, alphabet_t, score_t >
derived_type :
seqan3::alphabet_proxy< derived_type, alphabet_type >
,
seqan3::alphabet_tuple_base< derived_type, component_types >
,
seqan3::aminoacid_base< derived_type, size >
,
seqan3::detail::adaptor_base< derived_type, stored_args_ts >
,
seqan3::detail::format_help_base< derived_type >
,
seqan3::nucleotide_base< derived_type, size >
,
seqan3::phred_base< derived_type, size >
description :
seqan3::argument_parser_meta_data
,
seqan3::sam_file_program_info_t
design_error() :
seqan3::design_error
detail::policy_alignment_result_builder :
seqan3::alignment_result< alignment_result_value_t >
detail::random_access_iterator_base :
seqan3::detail::repeat_view< value_t >
,
seqan3::detail::view_interleave< urng_t, inserted_rng_t >
,
seqan3::detail::view_translate_join< urng_t >
determine_alignment_result_type() :
seqan3::detail::alignment_configuration_traits< configuration_t >
diagonal :
seqan3::detail::alignment_score_matrix_proxy< score_type >
,
seqan3::detail::edit_distance_trace_matrix_full< word_t, is_semi_global, use_max_errors >::trace_matrix_state
difference_type :
seqan3::algorithm_result_generator_range< algorithm_executor_type >::algorithm_range_iterator
,
seqan3::aligned_allocator< value_t, alignment_v >
,
seqan3::bitpacked_sequence< alphabet_type >
,
seqan3::concatenated_sequences< underlying_container_type, data_delimiters_type >
,
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::repeat_view< value_t >
,
seqan3::detail::score_matrix_single_column< score_t >::matrix_iterator
,
seqan3::detail::trace_iterator_base< derived_t, matrix_iter_t >
,
seqan3::detail::trace_matrix_full< trace_t >::iterator
,
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::view_interleave< urng_t, inserted_rng_t >
,
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::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::sam_file_input< traits_type_, selected_field_ids_, valid_formats_ >
,
seqan3::sam_file_output< selected_field_ids_, valid_formats_, ref_ids_type >
,
seqan3::sequence_file_input< traits_type_, selected_field_ids_, valid_formats_ >
,
seqan3::sequence_file_output< selected_field_ids_, valid_formats_ >
,
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_ >
disabled_type :
seqan3::detail::align_result_selector< first_range_t, second_range_t, configuration_t >
dna15() :
seqan3::dna15
dna15_vector :
seqan3::dna15
dna16sam() :
seqan3::dna16sam
dna16sam_vector :
seqan3::dna16sam
dna3bs() :
seqan3::dna3bs
dna3bs_vector :
seqan3::dna3bs
dna4() :
seqan3::dna4
dna4_vector :
seqan3::dna4
dna5() :
seqan3::dna5
dna5_vector :
seqan3::dna5
dot_bracket3() :
seqan3::dot_bracket3
dssp9() :
seqan3::dssp9
dummy :
seqan3::format_sam
dummy_ref_type :
seqan3::sam_file_input< traits_type_, selected_field_ids_, valid_formats_ >
dump_alignment_column() :
seqan3::detail::alignment_algorithm< config_t, algorithm_policies_t >
dynamic_bitset :
seqan3::dynamic_bitset< bit_capacity >
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