Here is a list of all documented variables with links to the class documentation for each member:

- s -

• sam_require_header : seqan3::sam_file_output_options
• scheme : seqan3::align_cfg::scoring_scheme< scoring_scheme_t >
• score : seqan3::align_cfg::min_score, seqan3::detail::alignment_optimum< score_t >, seqan3::detail::alignment_result_value_type< sequence1_id_t, sequence2_id_t, score_t, end_positions_t, begin_positions_t, alignment_t, score_debug_matrix_t, trace_debug_matrix_t >
• score_debug_matrix : seqan3::detail::alignment_algorithm< config_t, algorithm_policies_t >, seqan3::detail::alignment_result_value_type< sequence1_id_t, sequence2_id_t, score_t, end_positions_t, begin_positions_t, alignment_t, score_debug_matrix_t, trace_debug_matrix_t >
• score_for_padding_symbol : seqan3::detail::simd_matrix_scoring_scheme< simd_score_t, alphabet_t, alignment_t >
• score_mask : seqan3::detail::edit_distance_unbanded< database_t, query_t, align_config_t, edit_traits >
• score_matrix : seqan3::detail::alignment_matrix_policy< alignment_algorithm_t, score_matrix_t, trace_matrix_t >, seqan3::detail::combined_score_and_trace_matrix< score_matrix_t, trace_matrix_t >
• score_matrix_it : seqan3::detail::combined_score_and_trace_matrix< score_matrix_t, trace_matrix_t >::iterator
• score_matrix_iter : seqan3::detail::alignment_matrix_policy< alignment_algorithm_t, score_matrix_t, trace_matrix_t >
• score_matrix_sentinel : seqan3::detail::combined_score_and_trace_matrix< score_matrix_t, trace_matrix_t >::sentinel
• score_offset : seqan3::detail::simd_global_alignment_state< simd_t >
• scoring_scheme : seqan3::detail::policy_scoring_scheme< alignment_configuration_t, scoring_scheme_t >, seqan3::detail::scoring_scheme_policy< alignment_algorithm_t, scoring_scheme_t >
• scoring_scheme_data : seqan3::detail::simd_matrix_scoring_scheme< simd_score_t, alphabet_t, alignment_t >
• screenWidth : seqan3::detail::format_help::console_layout_struct
• search_all_best_hits : seqan3::detail::search_traits< search_configuration_t >
• search_all_hits : seqan3::detail::search_traits< search_configuration_t >
• search_single_best_hit : seqan3::detail::search_traits< search_configuration_t >
• search_strata_hits : seqan3::detail::search_traits< search_configuration_t >
• sec_rng : seqan3::detail::aligned_sequence_builder< fst_sequence_t, sec_sequence_t >
• second : seqan3::detail::advanceable_alignment_coordinate< state >
• second_it : seqan3::detail::pairwise_combine_view< underlying_range_type >::basic_iterator< range_type >
• second_range_is_given : seqan3::detail::minimiser_view< urng1_t, urng2_t >
• second_sequence_slice_positions : seqan3::detail::aligned_sequence_builder< fst_sequence_t, sec_sequence_t >::result_type
• secondary_stream : 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::structure_file_input< traits_type_, selected_field_ids_, valid_formats_ >, seqan3::structure_file_output< selected_field_ids_, valid_formats_ >
• selected_frames : seqan3::detail::view_translate< urng_t >, seqan3::detail::view_translate_join< urng_t >
• seq1_slice_offset : seqan3::detail::alignment_matrix_policy< alignment_algorithm_t, score_matrix_t, trace_matrix_t >
• seq2_slice_offset : seqan3::detail::alignment_matrix_policy< alignment_algorithm_t, score_matrix_t, trace_matrix_t >
• seqan3_alphabet_tuple_like : seqan3::alphabet_tuple_base< derived_type, component_types >
• sequence1_id : seqan3::detail::alignment_result_value_type< sequence1_id_t, sequence2_id_t, score_t, end_positions_t, begin_positions_t, alignment_t, score_debug_matrix_t, trace_debug_matrix_t >
• sequence2_id : seqan3::detail::alignment_result_value_type< sequence1_id_t, sequence2_id_t, score_t, end_positions_t, begin_positions_t, alignment_t, score_debug_matrix_t, trace_debug_matrix_t >
• shape_ : seqan3::detail::kmer_hash_view< urng_t >::basic_iterator< const_range >, seqan3::detail::kmer_hash_view< urng_t >
• short_copyright : seqan3::argument_parser_meta_data
• short_description : seqan3::argument_parser_meta_data
• show_advanced_options : seqan3::detail::format_help_base< derived_type >
• sigma : seqan3::bi_fm_index_cursor< index_t >, seqan3::detail::kmer_hash_view< urng_t >::basic_iterator< const_range >, seqan3::fm_index_cursor< index_t >
• single_value : seqan3::detail::repeat_view< value_t >
• size : seqan3::dynamic_bitset< bit_capacity >::bitfield, seqan3::fields< fs >
• size_in_bits : seqan3::bloom_filter< data_layout_mode_ >
• skills : seqan3::detail::strong_type< value_t, derived_t, skills_ >
• soft_back : seqan3::cigar_clipped_bases
• soft_front : seqan3::cigar_clipped_bases
• sorting : seqan3::sam_file_header< ref_ids_type >
• state : seqan3::detail::execution_handler_parallel
• state_ptr : seqan3::detail::async_input_buffer_view< urng_t >, seqan3::detail::single_pass_input_view< urng_t >
• step_size : seqan3::detail::view_interleave< urng_t, inserted_rng_t >
• storage : seqan3::detail::two_dimensional_matrix< value_t, allocator_t, order >
• stratum : seqan3::detail::search_scheme_algorithm< configuration_t, index_t, policies_t >, seqan3::detail::unidirectional_search_algorithm< configuration_t, index_t, policies_t >, seqan3::search_cfg::hit_strata
• stream : seqan3::debug_stream_type< char_t >
• stream_buf : seqan3::detail::fast_istreambuf_iterator< char_t, traits_t >, seqan3::detail::fast_ostreambuf_iterator< char_t, traits_t >
• stream_buffer : 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::structure_file_input< traits_type_, selected_field_ids_, valid_formats_ >, seqan3::structure_file_output< selected_field_ids_, valid_formats_ >
• string_buffer : seqan3::format_bam
• sub_parser : seqan3::argument_parser
• subcommands : seqan3::argument_parser
• subsorting : seqan3::sam_file_header< ref_ids_type >
• substitution : seqan3::detail::policy_max_error, seqan3::detail::search_param
• synopsis : seqan3::argument_parser_meta_data
• sz : seqan3::small_vector< value_type_, capacity_ >