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SeqAn3
3.0.3
The Modern C++ library for sequence analysis.
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SeqAn3
3.0.3
The Modern C++ library for sequence analysis.
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| ▼ doc | |
| ► fragments | |
| cigar_operation_table.hpp | |
| dna15_implicit_conversion_from_rna15.hpp | |
| dna4_implicit_conversion_from_rna4.hpp | |
| dna5_implicit_conversion_from_rna5.hpp | |
| readme.hpp | |
| rna15_implicit_conversion_from_dna15.hpp | |
| rna4_implicit_conversion_from_dna4.hpp | |
| rna5_implicit_conversion_from_dna5.hpp | |
| ► howto | |
| ► use_cereal | |
| load.hpp | |
| store.hpp | |
| ► tutorial | |
| ► search | |
| cleanup.hpp | |
| ▼ seqan3 | |
| ► alignment | |
| ► aligned_sequence | |
| aligned_sequence_concept.hpp | Includes the aligned_sequence and the related insert_gap and erase_gap functions to enable stl container support |
| all.hpp | Meta-header for the aligned sequence in the alignment module |
| debug_stream_alignment.hpp | The seqan3::debug_stream_type overload in order to print alignments |
| ► band | |
| all.hpp | [DEPRECATED] Meta-header for the band implementations |
| static_band.hpp | [DEPRECATED] Provides seqan3::band_static |
| ► configuration | |
| align_config_band.hpp | Provides seqan3::detail::align_config_band |
| align_config_debug.hpp | Provides seqan3::align_cfg::detail::debug |
| align_config_edit.hpp | Provides seqan3::align_cfg::edit_scheme |
| align_config_gap_cost_affine.hpp | Provides seqan3::align_config::gap_cost_affine |
| align_config_method.hpp | Provides global and local alignment configurations |
| align_config_min_score.hpp | Provides seqan3::align_cfg::min_score configuration |
| align_config_on_result.hpp | Provides seqan3::align_cfg::on_result |
| align_config_output.hpp | Provides configuration for alignment output |
| align_config_parallel.hpp | Provides seqan3::align_cfg::parallel configuration |
| align_config_result_type.hpp | Provides seqan3::align_cfg::detail::result_type |
| align_config_score_type.hpp | Provides alignment configuration seqan3::align_cfg::score_type |
| align_config_scoring_scheme.hpp | Provides seqan3::align_cfg::scoring_scheme |
| align_config_vectorised.hpp | Provides seqan3::align_cfg::vectorised configuration |
| all.hpp | Meta-header for the alignment configuration module |
| detail.hpp | Provides some utility functions for the alignment configurations |
| ► decorator | |
| gap_decorator.hpp | Provides seqan3::gap_decorator |
| ► detail | |
| pairwise_alignment_concept.hpp | Provides seqan3::detail::pairwise_alignment and seqan3::detail::writable_pairwise_alignment |
| ► matrix | |
| ► detail | |
| advanceable_alignment_coordinate.hpp | Provides seqan3::detail::advanceable_alignment_coordinate |
| affine_cell_proxy.hpp | Provides seqan3::detail::affine_cell_proxy |
| aligned_sequence_builder.hpp | Provides seqan3::detail::aligned_sequence_builder |
| alignment_matrix_column_major_range_base.hpp | Provides seqan3::detail::alignment_matrix_column_major_range_base |
| alignment_score_matrix_one_column.hpp | Provides seqan3::detail::alignment_score_matrix_one_column |
| alignment_score_matrix_one_column_banded.hpp | Provides seqan3::detail::alignment_score_matrix_one_column_banded |
| alignment_score_matrix_one_column_base.hpp | Provides seqan3::detail::alignment_score_matrix_one_column_base |
| alignment_score_matrix_proxy.hpp | Provides seqan3::detail::alignment_score_matrix_proxy |
| alignment_trace_matrix_base.hpp | Provides seqan3::detail::alignment_trace_matrix_base |
| alignment_trace_matrix_full.hpp | Provides seqan3::detail::alignment_trace_matrix_full |
| alignment_trace_matrix_full_banded.hpp | Provides seqan3::detail::alignment_trace_matrix_full_banded |
| alignment_trace_matrix_proxy.hpp | Provides seqan3::detail::alignment_trace_matrix_proxy |
| all.hpp | Meta-header for the detail block of the matrix sub-module |
| combined_score_and_trace_matrix.hpp | Provides seqan3::detail::combined_score_and_trace_matrix |
| coordinate_matrix.hpp | Provides seqan3::detail::coordinate_matrix |
| matrix_coordinate.hpp | Provides seqan3::detail::matrix_index, seqan3::detail::matrix_coordinate and associated strong types |
| score_matrix_single_column.hpp | Provides seqan3::detail::score_matrix_single_column |
| trace_iterator.hpp | Provides seqan3::detail::trace_iterator |
| trace_iterator_banded.hpp | Provides seqan3::detail::trace_iterator_banded |
| trace_iterator_base.hpp | Provides seqan3::detail::trace_iterator_base |
| trace_matrix_full.hpp | Provides seqan3::detail::trace_matrix_full |
| two_dimensional_matrix.hpp | Provides seqan3::detail::two_dimensional_matrix |
| two_dimensional_matrix_iterator_base.hpp | Provides seqan3::detail::two_dimensional_matrix_iterator_base |
| two_dimensional_matrix_iterator_concept.hpp | Provides seqan3::detail::two_dimensional_matrix_iterator |
| alignment_coordinate.hpp | [DEPRECATED] Provides seqan3::alignment_coordinate |
| alignment_optimum.hpp | Provides seqan3::detail::alignment_optimum |
| all.hpp | Meta-header for the matrix sub-module |
| debug_matrix.hpp | Provides the declaration of seqan3::detail::debug_matrix |
| edit_distance_score_matrix_full.hpp | Provides seqan3::detail::edit_distance_score_matrix_full |
| edit_distance_trace_matrix_full.hpp | Provides seqan3::detail::edit_distance_trace_matrix_full |
| matrix_concept.hpp | Provides seqan3::detail::matrix |
| row_wise_matrix.hpp | Provides seqan3::detail::row_wise_matrix |
| trace_directions.hpp | Provides the declaration of seqan3::detail::trace_directions |
| ► pairwise | |
| ► detail | |
| alignment_algorithm_state.hpp | Provides seqan3::detail::alignment_algorithm_state |
| concept.hpp | Provides concepts needed internally for the alignment algorithms |
| pairwise_alignment_algorithm.hpp | Provides seqan3::detail::pairwise_alignment_algorithm |
| pairwise_alignment_algorithm_banded.hpp | Provides seqan3::detail::pairwise_alignment_algorithm |
| policy_affine_gap_recursion.hpp | Provides seqan3::detail::policy_affine_gap_recursion |
| policy_affine_gap_recursion_banded.hpp | Provides seqan3::detail::policy_affine_gap_recursion_banded |
| policy_affine_gap_with_trace_recursion.hpp | Provides seqan3::detail::policy_affine_gap_with_trace_recursion |
| policy_affine_gap_with_trace_recursion_banded.hpp | Provides seqan3::detail::policy_affine_gap_with_trace_recursion_banded |
| policy_alignment_matrix.hpp | Provides seqan3::detail::policy_alignment_matrix |
| policy_alignment_result_builder.hpp | Provides seqan3::detail::policy_alignment_result_builder |
| policy_optimum_tracker.hpp | Provides seqan3::detail::policy_optimum_tracker |
| policy_optimum_tracker_simd.hpp | Provides seqan3::detail::policy_optimum_tracker_simd |
| policy_scoring_scheme.hpp | Provides seqan3::detail::policy_scoring_scheme |
| type_traits.hpp | Provides helper type traits for the configuration and execution of the alignment algorithm |
| ► policy | |
| affine_gap_init_policy.hpp | Provides seqan3::detail::affine_gap_init_policy |
| affine_gap_policy.hpp | Provides seqan3::detail::affine_gap_policy |
| alignment_matrix_policy.hpp | Provides seqan3::detail::alignment_matrix_policy |
| all.hpp | |
| find_optimum_policy.hpp | Provides seqan3::detail::find_optimum_policy |
| scoring_scheme_policy.hpp | Provides seqan3::detail::scoring_scheme_policy |
| simd_affine_gap_policy.hpp | Provides seqan3::detail::simd_affine_gap_policy |
| simd_find_optimum_policy.hpp | Provides seqan3::detail::simd_find_optimum_policy |
| align_pairwise.hpp | Provides pairwise alignment function |
| align_result_selector.hpp | Provides seqan3::detail::align_result_selector |
| alignment_algorithm.hpp | Provides seqan3::detail::alignment_algorithm |
| alignment_configurator.hpp | Provides seqan3::detail::alignment_selector |
| alignment_result.hpp | Provides seqan3::alignment_result |
| all.hpp | Meta-header for the pairwise submodule |
| edit_distance_algorithm.hpp | Provides seqan3::detail::edit_distance_algorithm |
| edit_distance_fwd.hpp | Forwards for seqan3::edit_distance_unbanded related types |
| edit_distance_unbanded.hpp | Provides a pairwise alignment algorithm for edit distance but without band |
| ► scoring | |
| ► detail | |
| simd_match_mismatch_scoring_scheme.hpp | Provides seqan3::detail::simd_match_mismatch_scoring_scheme |
| simd_matrix_scoring_scheme.hpp | Provides seqan3::detail::simd_matrix_scoring_scheme |
| all.hpp | Meta-header for the Scoring sub-module |
| aminoacid_scoring_scheme.hpp | Provides seqan3::aminoacid_scoring_scheme |
| gap_scheme.hpp | Provides seqan3::gap_scheme |
| nucleotide_scoring_scheme.hpp | Provides seqan3::nucleotide_scoring_scheme |
| scoring_scheme_base.hpp | Provides seqan3::scoring_scheme_base |
| scoring_scheme_concept.hpp | Provides seqan3::scoring_scheme_for |
| all.hpp | Meta-header for the alignment module |
| exception.hpp | Includes customized exception types for the alignment module |
| ► alphabet | |
| ► adaptation | |
| all.hpp | Meta-header for the adaptation submodule; includes all headers from alphabet/adaptation/ |
| char.hpp | Provides alphabet adaptations for standard char types |
| uint.hpp | Provides alphabet adaptations for standard uint types |
| ► aminoacid | |
| aa10li.hpp | Provides seqan3::aa10li, container aliases and string literals |
| aa10murphy.hpp | Provides seqan3::aa10murphy, container aliases and string literals |
| aa20.hpp | Provides seqan3::aa20, container aliases and string literals |
| aa27.hpp | Provides seqan3::aa27, container aliases and string literals |
| all.hpp | Meta-header for the aminoacid submodule; includes all headers from alphabet/aminoacid/ |
| aminoacid_base.hpp | Provides seqan3::aminoacid_base |
| concept.hpp | Provides seqan3::aminoacid_alphabet |
| translation.hpp | Provides functions for translating a triplet of nucleotides into an amino acid |
| translation_details.hpp | Provides translation details for nucleotide to aminoacid translation |
| translation_genetic_code.hpp | Genetic codes used for translating a triplet of nucleotides into an amino acid |
| ► cigar | |
| ► exposition_only | |
| cigar_operation.hpp | Introduces the seqan3::exposition_only::cigar_operation alphabet |
| all.hpp | Meta-header for the cigar submodule; includes all headers from alphabet/cigar/ |
| cigar.hpp | Provides the seqan3::cigar alphabet |
| cigar_op.hpp | [DEPRECATED] Introduces the seqan3::cigar_op alphabet |
| ► composite | |
| all.hpp | Meta-header for the composite submodule; includes all headers from alphabet/composite/ |
| alphabet_tuple_base.hpp | Provides seqan3::alphabet_tuple_base |
| alphabet_variant.hpp | Provides seqan3::alphabet_variant |
| detail.hpp | Provides implementation detail for seqan3::alphabet_variant and seqan3::alphabet_tuple_base |
| semialphabet_any.hpp | Provides seqan3::semialphabet_any |
| ► container | |
| bitpacked_sequence.hpp | Provides seqan3::bitpacked_sequence |
| concatenated_sequences.hpp | Provides seqan3::concatenated_sequences |
| ► detail | |
| alphabet_proxy.hpp | Provides seqan3::alphabet_proxy |
| convert.hpp | |
| debug_stream_alphabet.hpp | Provides seqan3::debug_stream and related types |
| ► gap | |
| all.hpp | Meta-header for the gap submodule; includes all headers from alphabet/gap/ |
| gap.hpp | Provides seqan3::gap |
| gapped.hpp | Provides seqan3::gapped |
| ► mask | |
| all.hpp | Meta-header for the mask submodule; includes all headers from alphabet/mask/ |
| mask.hpp | Create a mask composite which can be applied with another alphabet |
| masked.hpp | Extends a given alphabet with the mask alphabet |
| ► nucleotide | |
| all.hpp | Meta-header for the nucleotide submodule; includes all headers from alphabet/nucleotide/ |
| concept.hpp | Provides seqan3::nucleotide_alphabet |
| dna15.hpp | Provides seqan3::dna15, container aliases and string literals |
| dna16sam.hpp | Provides seqan3::dna16sam |
| dna3bs.hpp | Provides seqan3::dna3bs, container aliases and string literals |
| dna4.hpp | Provides seqan3::dna4, container aliases and string literals |
| dna5.hpp | Provides seqan3::dna5, container aliases and string literals |
| nucleotide_base.hpp | Provides seqan3::nucleotide_base |
| rna15.hpp | Provides seqan3::rna15, container aliases and string literals |
| rna4.hpp | Provides seqan3::rna4, container aliases and string literals |
| rna5.hpp | Provides seqan3::rna5, container aliases and string literals |
| sam_dna16.hpp | [DEPRECATED] Provides seqan3::dna16sam |
| ► quality | |
| aliases.hpp | Provides aliases for qualified |
| all.hpp | Meta-header that includes all headers from alphabet/quality/ |
| concept.hpp | Quality alphabet concept |
| phred42.hpp | Provides seqan3::phred42 quality scores |
| phred63.hpp | Provides seqan3::phred63 quality scores |
| phred68legacy.hpp | [DEPRECATED] Provides seqan3::phred68solexa quality scores |
| phred68solexa.hpp | Provides seqan3::phred68solexa quality scores |
| phred94.hpp | Provides seqan3::phred94 quality scores |
| phred_base.hpp | Provides seqan3::phred42 quality scores |
| qualified.hpp | Provides quality alphabet composites |
| quality_base.hpp | [DEPRECATED] Provides seqan3::phred42 quality scores |
| ► range | |
| hash.hpp | Provides overloads for std::hash |
| sequence.hpp | Additional non-standard concepts for ranges |
| ► structure | |
| all.hpp | Meta-header for the structure module. It includes all headers from alphabet/structure/ |
| concept.hpp | Provides seqan3::rna_structure_alphabet |
| dot_bracket3.hpp | Provides the dot bracket format for RNA structure |
| dssp9.hpp | Provides the dssp format for protein structure |
| structured_aa.hpp | Provides the composite of aminoacid with structure alphabets |
| structured_rna.hpp | Provides the composite of nucleotide with structure alphabets |
| wuss.hpp | Provides the WUSS format for RNA structure |
| ► views | |
| all.hpp | Meta-header for alphabet-related views |
| char_to.hpp | Provides seqan3::views::char_to |
| complement.hpp | Provides seqan3::views::complement |
| rank_to.hpp | Provides seqan3::views::rank_to |
| to_char.hpp | Provides seqan3::views::to_char |
| to_rank.hpp | Provides seqan3::views::to_rank |
| translate.hpp | Provides seqan3::views::translate and seqan3::views::translate_single |
| translate_join.hpp | Provides seqan3::views::translate_join |
| trim_quality.hpp | Provides seqan3::views::trim_quality |
| all.hpp | Meta-header for the alphabet module |
| alphabet_base.hpp | Provides seqan3::alphabet_base |
| concept.hpp | Core alphabet concept and free function/type trait wrappers |
| exception.hpp | Exceptions thrown by entities in the alphabet module |
| hash.hpp | Provides overloads for std::hash |
| ► argument_parser | |
| ► detail | |
| format_base.hpp | Provides the format_base struct containing all helper functions that are needed in all formats |
| format_help.hpp | Provides the format_help struct that print the help page to the command line and the two child formats (format_version, format_short_help) that print short help messages to the command line |
| format_html.hpp | Provides the format_html struct and its helper functions |
| format_man.hpp | Provides the format_man struct and its helper functions |
| format_parse.hpp | Provides the format_parse class |
| terminal.hpp | Checks if program is run interactively and retrieves dimensions of terminal (Transferred from seqan2) |
| version_check.hpp | Provides the version check functionality |
| all.hpp | Meta-Header for the argument parser module |
| argument_parser.hpp | Provides seqan3::argument_parser class |
| auxiliary.hpp | Provides auxiliary information |
| exceptions.hpp | Provides parser related exceptions |
| validators.hpp | Provides some standard validators for (positional) options |
| ► contrib | |
| ► charconv | |
| charconv_pre.hpp | |
| ► parallel | |
| buffer_queue.hpp | Provides seqan3::buffer_queue |
| serialised_resource_pool.hpp | Provides helper structs from SeqAn2 for the bgzf_ostream |
| suspendable_queue.hpp | Provides seqan suspendable queue |
| ► stream | |
| bgzf_istream.hpp | |
| bgzf_ostream.hpp | |
| bgzf_stream_util.hpp | Provides stream compression utilities |
| bz2_istream.hpp | |
| bz2_ostream.hpp | |
| gz_istream.hpp | |
| gz_ostream.hpp | |
| ► core | |
| ► algorithm | |
| ► detail | |
| algorithm_executor_blocking.hpp | Provides seqan3::detail::algorithm_executor_blocking |
| all.hpp | Meta-header for the detail functionality of core algorithm |
| execution_handler_parallel.hpp | Provides seqan3::detail::execution_handler_parallel |
| execution_handler_sequential.hpp | Provides seqan3::detail::execution_handler_sequential |
| algorithm_result_generator_range.hpp | Provides seqan3::detail::algorithm_result_generator_range |
| all.hpp | Meta-Header for components of the algorithm submodule |
| bound.hpp | [DEPRECATED] Provides seqan3::lower_bound and seqan3::upper_bound |
| concept.hpp | [DEPRECATED] Provides concepts for the configuration classes |
| configuration.hpp | [DEPRECATED] Provides seqan3::configuration and utility functions |
| configuration_element_debug_mode.hpp | [DEPRECATED] Provides seqan3::detail::debug_mode |
| configuration_element_parallel_mode.hpp | [DEPRECATED] Provides seqan3::detail::parallel_mode |
| configuration_utility.hpp | [DEPRECATED] Provides various auxiliary functions with which parts of the configurations can be checked |
| pipeable_config_element.hpp | [DEPRECATED] Provides seqan3::pipeable_config_element |
| ► char_operations | |
| all.hpp | [DEPRECATED] Provides Char predicates for tokenization |
| predicate.hpp | [DEPRECATED] Provides character predicates for tokenisation |
| predicate_detail.hpp | [DEPRECATED] Provides parse conditions for tokenization |
| pretty_print.hpp | [DEPRECATED] Provides pretty printing for chars |
| transform.hpp | [DEPRECATED] Provides utilities for modifying characters |
| ► concept | |
| all.hpp | Meta-include for custom concepts |
| cereal.hpp | Adaptions of concepts from the Cereal library |
| core_language.hpp | [DEPRECATED] Provides concepts for core language types and relations that don't have concepts in C++20 (yet) |
| tuple.hpp | [DEPRECATED] Provides seqan3::tuple_like |
| ► configuration | |
| ► detail | |
| all.hpp | Meta-header for the detail functionality of configuration |
| concept.hpp | Provides concepts for the configuration classes |
| configuration_element_debug_mode.hpp | Provides seqan3::detail::debug_mode |
| configuration_element_parallel_mode.hpp | Provides seqan3::detail::parallel_mode |
| configuration_utility.hpp | Provides various auxiliary functions with which parts of the configurations can be checked |
| all.hpp | Meta-Header for components of the configuration submodule |
| configuration.hpp | Provides seqan3::configuration and utility functions |
| pipeable_config_element.hpp | Provides seqan3::pipeable_config_element |
| ► debug_stream | |
| ► detail | |
| to_string.hpp | Auxiliary for pretty printing of exception messages |
| byte.hpp | Provides seqan3::debug_stream and related types |
| debug_stream_type.hpp | Provides seqan3::debug_stream and related types |
| optional.hpp | Provides seqan3::debug_stream and related types |
| range.hpp | Provides seqan3::debug_stream and related types |
| tuple.hpp | Provides seqan3::debug_stream and related types |
| variant.hpp | Provides seqan3::debug_stream and related types |
| ► detail | |
| all.hpp | Meta-header for implementation details in the core module |
| customisation_point.hpp | Helper utilities for defining customisation point objects (CPOs) |
| debug_stream_alphabet.hpp | [DEPRECATED] Provides seqan3::debug_stream and related types |
| debug_stream_byte.hpp | [DEPRECATED] Provides seqan3::debug_stream and related types |
| debug_stream_optional.hpp | [DEPRECATED] Provides seqan3::debug_stream and related types |
| debug_stream_range.hpp | [DEPRECATED] Provides seqan3::debug_stream and related types |
| debug_stream_tuple.hpp | [DEPRECATED] Provides seqan3::debug_stream and related types |
| debug_stream_type.hpp | [DEPRECATED] Provides seqan3::debug_stream and related types |
| debug_stream_variant.hpp | [DEPRECATED] Provides seqan3::debug_stream and related types |
| deferred_crtp_base.hpp | Provides seqan3::detail::deferred_crtp_base |
| empty_type.hpp | Provides seqan3::detail::empty_type |
| endian.hpp | [DEPRECATED] Provides seqan3::detail::endian |
| int_types.hpp | [DEPRECATED] Provides metaprogramming utilities for integer types |
| is_class_template_declarable.hpp | Provides a type trait for verifying valid template declarations |
| iterator_traits.hpp | Provides various transformation traits for use on iterators |
| pack_algorithm.hpp | Provides algorithms for meta programming, parameter packs and seqan3::type_list |
| persist_view.hpp | Provides seqan3::detail::persist |
| strong_type.hpp | Provides basic data structure for strong types |
| template_inspection.hpp | Provides type traits for working with templates |
| test_accessor.hpp | Forward declares seqan3::detail::test_accessor |
| to_string.hpp | [DEPRECATED] Auxiliary for pretty printing of exception messages |
| transfer_type_modifier_onto.hpp | Provides type traits seqan3::detail::transfer_type_modifier_onto |
| type_inspection.hpp | [DEPRECATED] Provides traits to inspect some information of a type, for example its name |
| ► parallel | |
| ► detail | |
| latch.hpp | [DEPRECATED] Provides seqan3::detail::latch |
| reader_writer_manager.hpp | [DEPRECATED] Provides seqan3::detail::reader_writer_manager |
| spin_delay.hpp | [DEPRECATED] Provides seqan3::detail::spin_delay |
| all.hpp | [DEPRECATED] Meta-header for the parallel module. |
| execution.hpp | [DEPRECATED] Provides execution policies |
| ► range | |
| ► detail | |
| adaptor_base.hpp | Provides seqan3::detail::adaptor_base and seqan3::detail::combined_adaptor |
| adaptor_for_view_without_args.hpp | Provides seqan3::detail::adaptor_for_view_without_args |
| adaptor_from_functor.hpp | Provides seqan3::detail::adaptor_from_functor |
| inherited_iterator_base.hpp | Provides the seqan3::detail::inherited_iterator_base template |
| misc.hpp | Provides various utility functions |
| random_access_iterator.hpp | Provides the seqan3::detail::random_access_iterator class |
| type_traits.hpp | Provides various transformation traits used by the range module |
| ► simd | |
| ► detail | |
| builtin_simd.hpp | Provides seqan3::detail::builtin_simd, seqan3::detail::is_builtin_simd and seqan3::simd::simd_traits<builtin_simd_t> |
| builtin_simd_intrinsics.hpp | [DEPRECATED] Provides intrinsics include for builtin simd |
| default_simd_backend.hpp | [DEPRECATED] Provides seqan3::detail::default_simd_backend |
| default_simd_length.hpp | [DEPRECATED] Provides seqan3::detail::default_simd_length and seqan3::detail::default_simd_max_length |
| simd_algorithm_avx2.hpp | [DEPRECATED] Provides specific algorithm implementations for AVX2 instruction set |
| simd_algorithm_avx512.hpp | [DEPRECATED] Provides specific algorithm implementations for AVX512 instruction set |
| simd_algorithm_sse4.hpp | [DEPRECATED] Provides specific algorithm implementations for SSE4 instruction set |
| all.hpp | [DEPRECATED] Meta-header for the simd module |
| concept.hpp | [DEPRECATED] Provides seqan3::simd::simd_concept |
| debug_stream_simd.hpp | [DEPRECATED] Provides seqan3::debug_stream overload for seqan3::simd::simd_type |
| simd.hpp | [DEPRECATED] Provides seqan3::simd::simd_type |
| simd_algorithm.hpp | [DEPRECATED] Provides algorithms to modify seqan3::simd::simd_type |
| simd_traits.hpp | [DEPRECATED] Provides seqan3::simd::simd_traits |
| view_iota_simd.hpp | [DEPRECATED] Provides seqan3::detail::counted_simd_iterator and seqan3::views::iota_simd |
| view_to_simd.hpp | [DEPRECATED] Provides seqan3::detail::to_simd view |
| ► type_list | |
| all.hpp | [DEPRECATED] Provides seqan3::type_list and metaprogramming utilities |
| traits.hpp | [DEPRECATED] Provides traits for seqan3::type_list |
| type_list.hpp | [DEPRECATED] Provides seqan3::type_list |
| ► type_traits | |
| all.hpp | [DEPRECATED] Provides various type traits |
| basic.hpp | [DEPRECATED] Provides various type traits on generic types |
| concept.hpp | [DEPRECATED] Provides the concepts seqan3::transformation_trait and seqan3::unary_type_trait |
| deferred_crtp_base.hpp | [DEPRECATED] Provides seqan3::detail::deferred_crtp_base |
| function.hpp | [DEPRECATED] Provides various type traits for use on functions |
| iterator.hpp | [DEPRECATED] Provides various transformation traits for use on iterators |
| lazy.hpp | [DEPRECATED] Provides lazy template instantiation traits |
| pack.hpp | [DEPRECATED] Provides unary type traits on a set of types, usually provided as template argument pack |
| pre.hpp | [DEPRECATED] Provides various transformation trait base templates and shortcuts |
| range.hpp | [DEPRECATED] Provides various transformation traits used by the range module |
| template_inspection.hpp | [DEPRECATED] Provides seqan3::type_list and auxiliary type traits |
| transformation_trait_or.hpp | [DEPRECATED] Provides seqan3::detail::transformation_trait_or |
| add_enum_bitwise_operators.hpp | Provides seqan3::add_enum_bitwise_operators |
| all.hpp | Meta-header for the core module |
| bit_manipulation.hpp | [DEPRECATED] Provides utility functions for bit twiddling |
| common_tuple.hpp | [DEPRECATED] Provides seqan3::common_tuple and seqan3::common_pair |
| debug_stream.hpp | Provides seqan3::debug_stream and related types |
| math.hpp | [DEPRECATED] Provides math related functionality |
| platform.hpp | Provides platform and dependency checks |
| pod_tuple.hpp | [DEPRECATED] Provides seqan3::pod_tuple |
| semiregular_box.hpp | Provides seqan3::semiregular_box |
| tuple_utility.hpp | [DEPRECATED] Provides utility functions for tuple like interfaces |
| ► io | |
| ► alignment_file | |
| all.hpp | [DEPRECATED] Meta-include for the alignment IO submodule |
| detail.hpp | [DEPRECATED] Auxiliary functions for the alignment IO |
| format_bam.hpp | [DEPRECATED] Provides the seqan3::format_bam |
| format_sam.hpp | [DEPRECATED] Provides the seqan3::format_sam |
| format_sam_base.hpp | [DEPRECATED] Provides the seqan3::format_sam_base that can be inherited from |
| header.hpp | [DEPRECATED] Provides the seqan3::alignment_file_header class |
| input.hpp | [DEPRECATED] Provides seqan3::sam_file_input and corresponding traits classes |
| input_format_concept.hpp | [DEPRECATED] Provides seqan3::alignment_file_input_format and auxiliary classes |
| input_options.hpp | [DEPRECATED] Provides seqan3::sam_file_input_options |
| misc.hpp | [DEPRECATED] Provides helper data structures for the seqan3::sam_file_output |
| output.hpp | [DEPRECATED] Provides seqan3::sam_file_output and corresponding traits classes |
| output_format_concept.hpp | [DEPRECATED] Provides seqan3::alignment_file_output_format and auxiliary classes |
| output_options.hpp | [DEPRECATED] Provides seqan3::sam_file_output_options |
| sam_tag_dictionary.hpp | [DEPRECATED] Provides the seqan3::sam_tag_dictionary class and auxiliaries |
| ► detail | |
| ignore_output_iterator.hpp | Provides seqan3::detail::ignore_output_iterator for writing to null stream |
| in_file_iterator.hpp | Provides the seqan3::detail::in_file_iterator class template |
| istreambuf_view.hpp | Provides seqan3::detail::istreambuf |
| magic_header.hpp | Provides seqan3::detail::magic_header |
| misc.hpp | Provides various utility functions |
| misc_input.hpp | Provides various utility functions required only for input |
| misc_output.hpp | Provides various utility functions required only for output |
| out_file_iterator.hpp | Provides the seqan3::detail::out_file_iterator class template |
| record.hpp | |
| record_like.hpp | Provides seqan3::detail::record_like |
| safe_filesystem_entry.hpp | Provides seqan3::detail::safe_filesystem_entry |
| take_exactly_view.hpp | Provides seqan3::views::take_exactly and seqan3::views::take_exactly_or_throw |
| take_line_view.hpp | Provides seqan3::detail::take_line and seqan3::detail::take_line_or_throw |
| take_until_view.hpp | Provides seqan3::views::take_until and seqan3::views::take_until_or_throw |
| take_view.hpp | [DEPRECATED] Provides seqan3::views::take |
| ► sam_file | |
| ► detail | |
| cigar.hpp | Auxiliary functions for the alignment IO |
| format_sam_base.hpp | Provides the seqan3::format_sam_base that can be inherited from |
| all.hpp | Meta-include for the SAM IO submodule |
| format_bam.hpp | Provides the seqan3::format_bam |
| format_sam.hpp | Provides the seqan3::format_sam |
| header.hpp | Provides the seqan3::sam_file_header class |
| input.hpp | Provides seqan3::sam_file_input and corresponding traits classes |
| input_format_concept.hpp | Provides seqan3::sam_file_input_format and auxiliary classes |
| input_options.hpp | Provides seqan3::sam_file_input_options |
| output.hpp | Provides seqan3::sam_file_output and corresponding traits classes |
| output_format_concept.hpp | Provides seqan3::sam_file_output_format and auxiliary classes |
| output_options.hpp | Provides seqan3::sam_file_output_options |
| record.hpp | Provides seqan3::sam_record |
| sam_flag.hpp | Provides helper data structures for the seqan3::sam_file_output |
| sam_tag_dictionary.hpp | Provides the seqan3::sam_tag_dictionary class and auxiliaries |
| ► sequence_file | |
| all.hpp | Meta-include for the sequence IO submodule |
| format_embl.hpp | |
| format_fasta.hpp | |
| format_fastq.hpp | |
| format_genbank.hpp | Provides the seqan3::sequence_file_format_genbank class |
| input.hpp | Provides seqan3::sequence_file_input and corresponding traits classes |
| input_format_concept.hpp | Provides seqan3::sequence_file_input_format and auxiliary classes |
| input_options.hpp | Provides seqan3::sequence_file_input_options |
| output.hpp | Provides seqan3::sequence_file_output and corresponding traits classes |
| output_format_concept.hpp | Provides seqan3::sequence_file_output_format and auxiliary classes |
| output_options.hpp | Provides seqan3::sequence_file_output_options |
| record.hpp | Provides seqan3::sequence_record |
| ► stream | |
| ► detail | |
| fast_istreambuf_iterator.hpp | Provides seqan3::detail::fast_istreambuf_iterator |
| fast_ostreambuf_iterator.hpp | Provides seqan3::detail::fast_ostreambuf_iterator |
| stream_buffer_exposer.hpp | Provides seqan3::detail::stream_buffer_exposer |
| all.hpp | Meta-header for all stream related functionality |
| concept.hpp | Stream concepts |
| iterator.hpp | Provides seqan3::detail::fast_istreambuf_iterator and seqan3::detail::fast_ostreambuf_iterator |
| ► structure_file | |
| all.hpp | Meta-include for the structure IO submodule |
| detail.hpp | Helper functions (e.g. conversions) for the structure IO submodule |
| format_vienna.hpp | Provides the seqan3::format_vienna |
| input.hpp | Provides seqan3::structure_file_input and corresponding traits classes |
| input_format_concept.hpp | Provides seqan3::structure_file_input_format |
| input_options.hpp | Provides seqan3::structure_file_input_options |
| output.hpp | Provides seqan3::structure_file_output and corresponding traits classes |
| output_format_concept.hpp | Provides seqan3::structure_file_output_format and auxiliary classes |
| output_options.hpp | Provides seqan3::structure_file_output_options |
| record.hpp | Provides seqan3::structure_record |
| ► views | |
| async_input_buffer.hpp | Provides seqan3::views::async_input_buffer |
| all.hpp | Meta-header for all IO related functionality |
| exception.hpp | Provides exceptions used in the I/O module |
| record.hpp | Provides the seqan3::record template and the seqan3::field enum |
| ► range | |
| ► container | |
| aligned_allocator.hpp | Provides seqan3::aligned_allocator |
| all.hpp | Meta-header for the container submodule |
| bitcompressed_vector.hpp | Provides seqan3::bitpacked_sequence |
| concatenated_sequences.hpp | [DEPRECATED] Provides seqan3::concatenated_sequences |
| concept.hpp | [DEPRECATED] Adaptations of concepts from the standard library |
| dynamic_bitset.hpp | A constexpr bitset implementation with dynamic size at compile time |
| small_string.hpp | A constexpr string implementation to manipulate string literals at compile time |
| small_vector.hpp | [DEPRECATED] A constexpr vector implementation with dynamic size at compile time |
| ► decorator | |
| all.hpp | Meta-header for the decorator submodule |
| gap_decorator.hpp | [DEPRECATED] Provides seqan3::gap_decorator |
| ► detail | |
| inherited_iterator_base.hpp | [DEPRECATED] Provides the seqan3::detail::inherited_iterator_base template |
| misc.hpp | [DEPRECATED] Provides various utility functions |
| random_access_iterator.hpp | [DEPRECATED] Provides the seqan3::detail::random_access_iterator class |
| ► views | |
| all.hpp | Meta-header for the views submodule |
| as_const.hpp | [DEPRECATED] Provides seqan3::views::as_const |
| async_input_buffer.hpp | [DEPRECATED] Provides seqan3::views::async_input_buffer |
| char_to.hpp | [DEPRECATED] Provides seqan3::views::char_to |
| chunk.hpp | [DEPRECATED] Provides seqan3::views::chunk |
| complement.hpp | [DEPRECATED] Provides seqan3::views::complement |
| convert.hpp | [DEPRECATED] Provides seqan3::views::convert |
| deep.hpp | [DEPRECATED] Provides seqan3::views::deep |
| detail.hpp | [DEPRECATED] Auxiliary header for the views submodule |
| drop.hpp | [DEPRECATED] Provides seqan3::views::drop |
| enforce_random_access.hpp | [DEPRECATED] Provides seqan3::views::enforce_random_access |
| get.hpp | [DEPRECATED] Provides seqan3::views::get |
| interleave.hpp | [DEPRECATED] Provides seqan3::views::interleave |
| istreambuf.hpp | [DEPRECATED] Provides seqan3::detail::istreambuf |
| join.hpp | [DEPRECATED] Provides seqan3::views::join |
| kmer_hash.hpp | [DEPRECATED] Provides seqan3::views::kmer_hash |
| minimiser.hpp | [DEPRECATED] Provides seqan3::views::minimiser |
| minimiser_hash.hpp | [DEPRECATED] Provides seqan3::views::minimiser_hash |
| move.hpp | [DEPRECATED] Provides seqan3::views::move |
| pairwise_combine.hpp | [DEPRECATED] Provides seqan3::views::pairwise_combine |
| persist.hpp | [DEPRECATED] Provides seqan3::views::persist |
| rank_to.hpp | [DEPRECATED] Provides seqan3::views::rank_to |
| repeat.hpp | [DEPRECATED] Provides the seqan3::views::repeat |
| repeat_n.hpp | [DEPRECATED] Provides seqan3::views::repeat_n |
| single_pass_input.hpp | [DEPRECATED] Provides seqan3::views::single_pass_input |
| slice.hpp | [DEPRECATED] Provides seqan3::views::slice |
| take.hpp | [DEPRECATED] Provides seqan3::views::take |
| take_exactly.hpp | [DEPRECATED] Provides seqan3::views::take_exactly and seqan3::views::take_exactly_or_throw |
| take_line.hpp | [DEPRECATED] Provides seqan3::views::take_line and seqan3::views::take_line_or_throw |
| take_until.hpp | [DEPRECATED] Provides seqan3::views::take_until |
| to.hpp | [DEPRECATED] Provides seqan3::views::to |
| to_char.hpp | [DEPRECATED] Provides seqan3::views::to_char |
| to_lower.hpp | [DEPRECATED] Provides seqan3::views::to_lower |
| to_rank.hpp | [DEPRECATED] Provides seqan3::views::to_rank |
| to_upper.hpp | [DEPRECATED] Provides seqan3::views::to_upper |
| translate.hpp | [DEPRECATED] Provides seqan3::views::translate and seqan3::views::translate_single |
| translate_join.hpp | [DEPRECATED] Provides seqan3::views::translate_join |
| trim_quality.hpp | [DEPRECATED] Provides seqan3::views::trim_quality |
| type_reduce.hpp | [DEPRECATED] Provides seqan3::views::type_reduce |
| zip.hpp | [DEPRECATED] Provides seqan3::views::zip |
| all.hpp | Meta-header for the range module |
| concept.hpp | [DEPRECATED] Additional non-standard concepts for ranges |
| hash.hpp | Provides overloads for std::hash |
| shortcuts.hpp | [DEPRECATED] Provides various shortcuts for common std::ranges functions |
| ► search | |
| ► configuration | |
| all.hpp | Meta-header for the search configuration module |
| default_configuration.hpp | Provides the default configuration for the seqan3::search() interface |
| detail.hpp | Provides compatibility matrix for search configurations |
| hit.hpp | Provides the configuration to define the hit strategies "hit_strata", "hit_all", "hit_all_best", "hit_single_best" |
| max_error.hpp | Provides the configuration for maximum number of errors for all error types |
| max_error_common.hpp | Provides the error types for maximum number of errors |
| on_result.hpp | Provides seqan3::search_cfg::on_result |
| output.hpp | Provides the configuration for the content of the search result |
| parallel.hpp | Provides seqan3::search_cfg::parallel configuration |
| result_type.hpp | Provides seqan3::search_cfg::detail::result_type |
| ► detail | |
| policy_max_error.hpp | Provides the seqan3::detail::policy_max_error |
| policy_search_result_builder.hpp | Provides the seqan3::detail::policy_search_result_builder |
| search_common.hpp | Provides data structures used by different search algorithms |
| search_configurator.hpp | Provides seqan3::detail::search_configurator |
| search_scheme_algorithm.hpp | Provides the algorithm to search in an index using search schemes |
| search_scheme_precomputed.hpp | Provides the data structures and precomputed instances for (optimum) search schemes |
| search_traits.hpp | Provides seqan3::detail::search_traits |
| unidirectional_search_algorithm.hpp | Provides an approximate string matching algorithm based on simple backtracking. This should only be used as a reference for unit testing |
| ► dream_index | |
| all.hpp | Meta-header for the DREAM index module |
| interleaved_bloom_filter.hpp | Provides seqan3::interleaved_bloom_filter |
| ► fm_index | |
| ► detail | |
| fm_index_cursor.hpp | Provides the internal representation of a node of the seqan3::fm_index_cursor |
| all.hpp | Meta-header for the FM index module |
| bi_fm_index.hpp | Provides the bidirectional seqan3::bi_fm_index |
| bi_fm_index_cursor.hpp | Provides the seqan3::bi_fm_index_cursor for searching in the bidirectional seqan3::bi_fm_index |
| concept.hpp | Provides the concept for seqan3::detail::sdsl_index |
| fm_index.hpp | Provides the unidirectional seqan3::fm_index |
| fm_index_cursor.hpp | Provides the seqan3::fm_index_cursor for searching in the unidirectional seqan3::fm_index |
| ► kmer_index | |
| all.hpp | Meta-header for the kmer_index module |
| shape.hpp | Provides seqan3::shape |
| ► views | |
| kmer_hash.hpp | Provides seqan3::views::kmer_hash |
| minimiser.hpp | Provides seqan3::views::minimiser |
| minimiser_hash.hpp | Provides seqan3::views::minimiser_hash |
| all.hpp | Meta-header for the search module |
| search.hpp | Provides the public interface for search algorithms |
| search_result.hpp | Provides seqan3::search_result |
| ► std | |
| algorithm | Adaptations of algorithms from the Ranges TS |
| bit | Provides the C++20 <bit> header if it is not already available |
| charconv | Provides std::from_chars and std::to_chars if not defined in the stdlib <charconv> header |
| concepts | The Concepts library |
| filesystem | This header includes C++17 filesystem support and imports it into namespace std::filesystem (independent of whether it is marked as "experimental") |
| iterator | Provides C++20 additions to the <iterator> header |
| memory | Provides C++20 additions to the <memory> header |
| new | Provides C++17/20 additions to the <new> header, if they are not already available |
| ranges | Adaptations of concepts from the Ranges TS |
| span | Provides std::span from the C++20 standard library |
| type_traits | Provides C++20 additions to the type_traits header |
| ► utility | |
| ► char_operations | |
| all.hpp | Provides Char predicates for tokenization |
| predicate.hpp | Provides character predicates for tokenisation |
| predicate_detail.hpp | Provides parse conditions for tokenization |
| pretty_print.hpp | Provides seqan3::detail::make_printable which converts non printable characters (e.g. a tab) to a std::string |
| transform.hpp | Provides utilities for modifying characters |
| ► container | |
| aligned_allocator.hpp | Provides seqan3::aligned_allocator |
| concept.hpp | Adaptations of concepts from the standard library |
| dynamic_bitset.hpp | A constexpr bitset implementation with dynamic size at compile time |
| small_string.hpp | A constexpr string implementation to manipulate string literals at compile time |
| small_vector.hpp | A constexpr vector implementation with dynamic size at compile time |
| ► detail | |
| bits_of.hpp | Provides utility functions for bit twiddling |
| exposition_only_concept.hpp | Provides concepts for core language types and relations that don't have concepts in C++20 (yet) |
| integer_traits.hpp | Provides metaprogramming utilities for integer types |
| multi_invocable.hpp | Provides a type that combines multiple invocables |
| to_little_endian.hpp | Provides utility functions for bit twiddling |
| type_name_as_string.hpp | Provides traits to inspect some information of a type, for example its name |
| ► parallel | |
| ► detail | |
| all.hpp | Provides implementation relevant helper objects and functions |
| latch.hpp | Provides seqan3::detail::latch |
| reader_writer_manager.hpp | Provides seqan3::detail::reader_writer_manager |
| spin_delay.hpp | Provides seqan3::detail::spin_delay |
| all.hpp | Meta-header for the parallel module |
| ► range | |
| concept.hpp | Additional non-standard concepts for ranges |
| ► simd | |
| ► detail | |
| builtin_simd.hpp | Provides seqan3::detail::builtin_simd, seqan3::detail::is_builtin_simd and seqan3::simd::simd_traits<builtin_simd_t> |
| builtin_simd_intrinsics.hpp | Provides intrinsics include for builtin simd |
| debug_stream_simd.hpp | Provides seqan3::debug_stream overload for seqan3::simd::simd_type |
| default_simd_backend.hpp | Provides seqan3::detail::default_simd_backend |
| default_simd_length.hpp | Provides seqan3::detail::default_simd_length and seqan3::detail::default_simd_max_length |
| simd_algorithm_avx2.hpp | Provides specific algorithm implementations for AVX2 instruction set |
| simd_algorithm_avx512.hpp | Provides specific algorithm implementations for AVX512 instruction set |
| simd_algorithm_sse4.hpp | Provides specific algorithm implementations for SSE4 instruction set |
| ► views | |
| iota_simd.hpp | Provides seqan3::detail::counted_simd_iterator and seqan3::views::iota_simd |
| to_simd.hpp | Provides seqan3::detail::to_simd view |
| algorithm.hpp | Provides algorithms to modify seqan3::simd::simd_type |
| all.hpp | Meta-header for the simd module |
| concept.hpp | Provides seqan3::simd::simd_concept |
| simd.hpp | Provides seqan3::simd::simd_type |
| simd_traits.hpp | Provides seqan3::simd::simd_traits |
| ► tuple | |
| all.hpp | Meta-include for tuple utilities: concept |
| common_tuple.hpp | Provides seqan3::common_tuple and seqan3::common_pair |
| concept.hpp | Provides seqan3::tuple_like |
| pod_tuple.hpp | Provides seqan3::pod_tuple |
| pop_front.hpp | Provides seqan3::tuple_pop_front |
| split.hpp | Provides seqan3::tuple_split |
| ► type_list | |
| all.hpp | Provides seqan3::type_list and associated metaprogramming utilities |
| traits.hpp | Provides traits for seqan3::type_list |
| type_list.hpp | Provides seqan3::type_list |
| ► type_pack | |
| all.hpp | Provides metaprogramming utilities for template parameter packs |
| traits.hpp | Provides various traits for template packs |
| ► type_traits | |
| ► detail | |
| transformation_trait_or.hpp | Provides seqan3::detail::transformation_trait_or |
| all.hpp | Provides various type traits |
| basic.hpp | Provides various type traits on generic types |
| concept.hpp | Provides the concepts seqan3::transformation_trait and seqan3::unary_type_trait |
| function_traits.hpp | Provides various type traits for use on functions |
| lazy_conditional.hpp | Provides lazy template instantiation traits |
| pre.hpp | Provides various transformation trait base templates and shortcuts |
| ► views | |
| chunk.hpp | Provides seqan3::views::chunk |
| convert.hpp | Provides seqan3::views::convert |
| deep.hpp | Provides seqan3::views::deep |
| elements.hpp | Provides seqan3::views::elements |
| enforce_random_access.hpp | Provides seqan3::views::enforce_random_access |
| interleave.hpp | Provides seqan3::views::interleave |
| join_with.hpp | Provides seqan3::views::join_with |
| pairwise_combine.hpp | Provides seqan3::views::pairwise_combine |
| repeat.hpp | Provides the seqan3::views::repeat |
| repeat_n.hpp | Provides seqan3::views::repeat_n |
| single_pass_input.hpp | Provides seqan3::views::single_pass_input |
| slice.hpp | Provides seqan3::views::slice |
| to.hpp | Provides seqan3::views::to |
| type_reduce.hpp | Provides seqan3::views::type_reduce |
| zip.hpp | Provides seqan3::views::zip |
| all.hpp | Meta-header for the utility module , which provides useful, stand-alone features that are not strongly coupled with SeqAn3 |
| math.hpp | Provides math related functionality |
| version.hpp | Provides SeqAn version macros and global variables |
1.9.1