SeqAn3
3.2.0
The Modern C++ library for sequence analysis.
- 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::custom::alphabet< char_type >
,
seqan3::custom::alphabet< uint_type >
,
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_header< ref_ids_type >::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_header< ref_ids_type >::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 -
hit_variant :
seqan3::search_cfg::hit
- i -
id :
seqan3::align_cfg::min_score
,
seqan3::sam_file_header< ref_ids_type >::program_info_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_header< ref_ids_type >::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_header< ref_ids_type >::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 >
result_buffer :
seqan3::interleaved_bloom_filter< data_layout_mode_ >::counting_agent_type< value_t >
,
seqan3::interleaved_bloom_filter< data_layout_mode_ >::membership_agent_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
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
- v -
value :
seqan3::bin_literal
,
seqan3::ungapped
version :
seqan3::argument_parser_meta_data
,
seqan3::sam_file_header< ref_ids_type >::program_info_t
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