Loading...
Searching...
No Matches
Here is a list of all documented variables with links to the class documentation for each member:

### - a -

- add_carriage_return : seqan3::sam_file_output_options, seqan3::sequence_file_output_options, seqan3::structure_file_output_options
- alignment : seqan3::aligned_allocator< value_t, alignment_v >
- alphabet_size : seqan3::alphabet_base< derived_type, size, char_t >, seqan3::alphabet_proxy< derived_type, alphabet_type >, seqan3::alphabet_tuple_base< derived_type, component_types >, seqan3::alphabet_variant< alternative_types >, seqan3::aminoacid_base< derived_type, size >, seqan3::custom::alphabet< char_type >, seqan3::custom::alphabet< uint_type >, seqan3::masked< sequence_alphabet_t >, seqan3::nucleotide_base< derived_type, size >, seqan3::phred_base< derived_type, size >, seqan3::qualified< sequence_alphabet_t, quality_alphabet_t >, seqan3::wuss< SIZE >
- app_name : seqan3::argument_parser_meta_data
- argument_count : seqan3::function_traits< std::function< return_t(args_t...)> >
- author : seqan3::argument_parser_meta_data

### - b -

- begin_position : seqan3::suffix_array_interval

### - c -

- callback : seqan3::align_cfg::on_result< callback_t >, seqan3::search_cfg::on_result< callback_t >
- char_to_rank : seqan3::masked< sequence_alphabet_t >
- citation : seqan3::argument_parser_meta_data
- command_line_call : seqan3::sam_file_program_info_t
- comments : seqan3::sam_file_header< ref_ids_type >

### - d -

- data_layout_mode : seqan3::bloom_filter< data_layout_mode_ >, seqan3::interleaved_bloom_filter< data_layout_mode_ >
- date : seqan3::argument_parser_meta_data
- description : seqan3::argument_parser_meta_data, seqan3::sam_file_program_info_t

### - e -

- email : seqan3::argument_parser_meta_data
- embl_genbank_complete_header : seqan3::sequence_file_input_options< sequence_legal_alphabet >, seqan3::sequence_file_output_options
- end_position : seqan3::suffix_array_interval
- error : seqan3::search_cfg::max_error_deletion, seqan3::search_cfg::max_error_insertion, seqan3::search_cfg::max_error_substitution, seqan3::search_cfg::max_error_total
- examples : seqan3::argument_parser_meta_data
- extension_score : seqan3::align_cfg::gap_cost_affine
- extensions : seqan3::file_validator_base

### - f -

- fasta_blank_before_id : seqan3::sequence_file_output_options
- fasta_ignore_blanks_before_id : seqan3::sequence_file_input_options< sequence_legal_alphabet >
- fasta_legacy_id_marker : seqan3::sequence_file_output_options
- fasta_letters_per_line : seqan3::sequence_file_output_options
- fastq_double_id : seqan3::sequence_file_output_options
- file_extensions : seqan3::format_bam, seqan3::format_embl, seqan3::format_fasta, seqan3::format_fastq, seqan3::format_genbank, seqan3::format_sam, seqan3::format_vienna
- format_version : seqan3::sam_file_header< ref_ids_type >
- free_end_gaps_sequence1_leading : seqan3::align_cfg::method_global
- free_end_gaps_sequence1_trailing : seqan3::align_cfg::method_global
- free_end_gaps_sequence2_leading : seqan3::align_cfg::method_global
- free_end_gaps_sequence2_trailing : seqan3::align_cfg::method_global

### - g -

- grouping : seqan3::sam_file_header< ref_ids_type >

### - h -

- hard_back : seqan3::cigar_clipped_bases
- hard_front : seqan3::cigar_clipped_bases
- hit_variant : seqan3::search_cfg::hit

### - i -

- id : seqan3::align_cfg::detail::result_type< alignment_result_t >, seqan3::align_cfg::min_score, seqan3::sam_file_program_info_t, seqan3::search_cfg::detail::result_type< search_result_t >
- info : seqan3::argument_parser
- is_compatible_with_value_type : seqan3::concatenated_sequences< underlying_container_type, data_delimiters_type >
- is_constexpr_default_constructible_v : seqan3::is_constexpr_default_constructible< t >
- iter_value_t_is_compatible_with_value_type : seqan3::concatenated_sequences< underlying_container_type, data_delimiters_type >

### - l -

- long_copyright : seqan3::argument_parser_meta_data
- lower_diagonal : seqan3::align_cfg::band_fixed_size

### - m -

- man_page_section : seqan3::argument_parser_meta_data
- man_page_title : seqan3::argument_parser_meta_data
- masked : seqan3::mask
- matrix_size : seqan3::scoring_scheme_base< derived_t, alphabet_t, score_t >
- max_pseudoknot_depth : seqan3::dot_bracket3, seqan3::structured_rna< sequence_alphabet_t, structure_alphabet_t >, seqan3::wuss< SIZE >

### - n -

- name : seqan3::sam_file_program_info_t

### - o -

- offset_char : seqan3::phred42, seqan3::phred63, seqan3::phred68solexa, seqan3::phred94
- offset_phred : seqan3::phred42, seqan3::phred63, seqan3::phred68solexa, seqan3::phred94
- open_score : seqan3::align_cfg::gap_cost_affine
- options : 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_ >
- other_alignment : seqan3::aligned_allocator< value_t, alignment_v >::rebind< new_value_type >

### - p -

- precision : seqan3::structure_file_output_options
- previous : seqan3::sam_file_program_info_t
- program_infos : seqan3::sam_file_header< ref_ids_type >

### - r -

- range_value_t_is_compatible_with_value_type : seqan3::concatenated_sequences< underlying_container_type, data_delimiters_type >
- rank_to_char : seqan3::masked< sequence_alphabet_t >
- read_groups : seqan3::sam_file_header< ref_ids_type >
- ref_dict : seqan3::sam_file_header< ref_ids_type >
- ref_id_info : seqan3::sam_file_header< ref_ids_type >

### - s -

- sam_require_header : seqan3::sam_file_output_options
- scheme : seqan3::align_cfg::scoring_scheme< scoring_scheme_t >
- score : seqan3::align_cfg::min_score
- short_copyright : seqan3::argument_parser_meta_data
- short_description : seqan3::argument_parser_meta_data
- soft_back : seqan3::cigar_clipped_bases
- soft_front : seqan3::cigar_clipped_bases
- sorting : seqan3::sam_file_header< ref_ids_type >
- stratum : seqan3::search_cfg::hit_strata
- subsorting : seqan3::sam_file_header< ref_ids_type >
- synopsis : seqan3::argument_parser_meta_data

### - t -

- text_layout_mode : seqan3::bi_fm_index< alphabet_t, text_layout_mode_, sdsl_index_type_ >, seqan3::fm_index< alphabet_t, text_layout_mode_, sdsl_index_type_ >
- truncate_ids : seqan3::sequence_file_input_options< sequence_legal_alphabet >, seqan3::structure_file_input_options< seq_legal_alphabet, structured_seq_combined >

### - u -

- unmasked : seqan3::mask
- upper_diagonal : seqan3::align_cfg::band_fixed_size
- url : seqan3::argument_parser_meta_data
- user_tags : seqan3::sam_file_header< ref_ids_type >, seqan3::sam_file_program_info_t

### - v -

- value : seqan3::bin_literal, seqan3::ungapped
- version : seqan3::argument_parser_meta_data, seqan3::sam_file_program_info_t

Hide me