- d -

• dagify_steps : vg::Genotyper
• data : handlegraph::handle_t , handlegraph::net_handle_t , handlegraph::path_handle_t , handlegraph::step_handle_t , vg::kff_recoding_t , vg::SmallBitset , vg::str_view , vg::varint_vector_t
• data_bytes : vg::ParallelKFFReader
• data_width : vg::Packer
• dead_end : vg::WFANode
• debug : vg::BaseMapper
• decoder : vg::ZipCode
• default_align_from_chains : vg::MinimizerMapper
• default_batch_size : GiraffeMainOptions
• default_chain_score_threshold : vg::MinimizerMapper
• default_cluster_coverage_threshold : vg::MinimizerMapper
• default_cluster_score_threshold : vg::MinimizerMapper
• DEFAULT_COMPRESSION_LEVEL : vg::zstd_compress_buf
• default_distance_limit : vg::MinimizerMapper
• default_do_dp : vg::MinimizerMapper
• default_error_model : vg::WFAExtender
• default_exclude_overlapping_min : vg::MinimizerMapper
• default_extension_score_threshold : vg::MinimizerMapper
• default_extension_set_min_score : vg::MinimizerMapper
• default_extension_set_score_threshold : vg::MinimizerMapper
• default_fragment_gap_scale : vg::MinimizerMapper
• default_fragment_max_graph_lookback_bases : vg::MinimizerMapper
• default_fragment_max_graph_lookback_bases_per_base : vg::MinimizerMapper
• default_fragment_max_indel_bases : vg::MinimizerMapper
• default_fragment_max_indel_bases_per_base : vg::MinimizerMapper
• default_fragment_max_min_score : vg::MinimizerMapper
• default_fragment_max_read_lookback_bases : vg::MinimizerMapper
• default_fragment_max_read_lookback_bases_per_base : vg::MinimizerMapper
• default_fragment_min_score : vg::MinimizerMapper
• default_fragment_points_per_possible_match : vg::MinimizerMapper
• default_fragment_score_fraction : vg::MinimizerMapper
• default_fragment_set_score_threshold : vg::MinimizerMapper
• default_gap_scale : vg::MinimizerMapper
• default_gapless_extension_limit : vg::MinimizerMapper
• default_hard_hit_cap : vg::MinimizerMapper
• default_hit_cap : vg::MinimizerMapper
• default_item_bonus : vg::MinimizerMapper
• default_item_scale : vg::MinimizerMapper
• DEFAULT_K : vg::Haplotypes::Header
• default_log_reads : GiraffeMainOptions
• default_mapq_score_scale : vg::MinimizerMapper
• default_mapq_score_window : vg::MinimizerMapper
• default_max_alignments : vg::MinimizerMapper
• default_max_chain_connection : vg::MinimizerMapper
• default_max_chaining_problems : vg::MinimizerMapper
• default_max_chains_per_tree : vg::MinimizerMapper
• default_max_direct_to_chain : vg::MinimizerMapper
• default_max_dozeu_cells : vg::MinimizerMapper
• default_max_dp_cells : vg::MinimizerMapper
• default_max_extension_mismatches : vg::MinimizerMapper
• default_max_extensions : vg::MinimizerMapper
• default_max_fragment_length : vg::MinimizerMapper
• default_max_fragments : vg::MinimizerMapper
• default_max_graph_lookback_bases : vg::MinimizerMapper
• default_max_graph_lookback_bases_per_base : vg::MinimizerMapper
• default_max_indel_bases : vg::MinimizerMapper
• default_max_indel_bases_per_base : vg::MinimizerMapper
• default_max_local_extensions : vg::MinimizerMapper
• default_max_middle_dp_length : vg::MinimizerMapper
• default_max_middle_gap : vg::MinimizerMapper
• default_max_min_chain_score : vg::MinimizerMapper
• default_max_multimaps : vg::MinimizerMapper
• default_max_read_lookback_bases : vg::MinimizerMapper
• default_max_read_lookback_bases_per_base : vg::MinimizerMapper
• default_max_rescue_attempts : vg::MinimizerMapper
• default_max_skipped_bases : vg::MinimizerMapper
• DEFAULT_MAX_SLIDE : vg::Surjector
• default_max_tail_dp_length : vg::MinimizerMapper
• default_max_tail_gap : vg::MinimizerMapper
• default_max_tail_length : vg::MinimizerMapper
• default_max_to_fragment : vg::MinimizerMapper
• default_max_unique_min : vg::MinimizerMapper
• default_min_chain_score_per_base : vg::MinimizerMapper
• default_min_chaining_problems : vg::MinimizerMapper
• default_min_chains : vg::MinimizerMapper
• default_min_extension_sets : vg::MinimizerMapper
• default_min_extensions : vg::MinimizerMapper
• default_min_to_fragment : vg::MinimizerMapper
• default_min_unique_node_fraction : vg::MinimizerMapper
• default_minimizer_coverage_flank : vg::MinimizerMapper
• default_minimizer_downsampling_max_window_length : vg::MinimizerMapper
• default_minimizer_downsampling_window_count : vg::MinimizerMapper
• default_minimizer_score_fraction : vg::MinimizerMapper
• default_num_bp_per_min : vg::MinimizerMapper
• default_pad_cluster_score_threshold : vg::MinimizerMapper
• default_pad_zipcode_tree_score_threshold : vg::MinimizerMapper
• default_paired_distance_stdevs : vg::MinimizerMapper
• default_paired_rescue_score_limit : vg::MinimizerMapper
• DEFAULT_PATH_WEIGHT : vg::FlowSort
• default_points_per_possible_match : vg::MinimizerMapper
• default_rescue_likelihood_limit : vg::MinimizerMapper
• default_rescue_seed_limit : vg::MinimizerMapper
• default_rescue_subgraph_stdevs : vg::MinimizerMapper
• default_sequence_quality : vg::Genotyper
• default_set_refpos : vg::MinimizerMapper
• default_show_work : vg::MinimizerMapper
• default_sort_by_chain_score : vg::MinimizerMapper
• DEFAULT_SUBGRAPH_LIMIT : vg::Surjector
• default_track_correctness : vg::MinimizerMapper
• default_track_position : vg::MinimizerMapper
• default_track_provenance : vg::MinimizerMapper
• default_use_explored_cap : vg::MinimizerMapper
• default_value : vg::BaseOption< Value, Parser > , vg::subcommand::ArgSpec< T, Receiver >
• default_watchdog_timeout : GiraffeMainOptions
• default_wfa_distance : vg::MinimizerMapper
• default_wfa_distance_per_base : vg::MinimizerMapper
• default_wfa_max_distance : vg::MinimizerMapper
• default_wfa_max_max_mismatches : vg::MinimizerMapper
• default_wfa_max_mismatches : vg::MinimizerMapper
• default_wfa_max_mismatches_per_base : vg::MinimizerMapper
• default_zipcode_tree_coverage_threshold : vg::MinimizerMapper
• default_zipcode_tree_scale : vg::MinimizerMapper
• default_zipcode_tree_score_threshold : vg::MinimizerMapper
• defining_path : vg::PathSubgraph
• defray_count : vg::ReadFilter< Read >
• defray_length : vg::ReadFilter< Read >
• deleted_prior_logprob : vg::Genotyper
• deletion_aligner : vg::GSSWAligner
• deletions : vg::DeleteHaplotypeCommand , vg::ReplaceLocalHaplotypeCommand
• DELETIONS : vg::WFANode
• delim1 : vg::Packer
• delim2 : vg::Packer
• dense_to_sparse : vg::SparseUnionFind
• depth : vg::ZipCodeForest::interval_state_t
• depth_err : vg::PoissonSupportSnarlCaller::PoissonCallInfo
• depth_index : vg::PoissonSupportSnarlCaller
• depth_padding_factor : vg::PoissonSupportSnarlCaller
• description : vg::BaseOption< Value, Parser > , vg::subcommand::Subcommand
• dest : vg::subcommand::ArgSpec< T, Receiver >
• diagonal : vg::WFAPoint
• dinuc_machine : vg::MultipathMapper
• diploid_prior_logprob : vg::Genotyper
• diploid_sampling : vg::Recombinator::Parameters
• directed_acyclic_net_graph : vg::Snarl
• dirnames : vg::temp_file::Handler
• discard_overlaps : vg::HaplotypeIndexer
• discordant_insert_size : vg::Alignment
• distance : vg::MEMClusterer::HitEdge , vg::WFAExtender::ErrorModel , vg::ZipCodeTree::seed_result_t
• distance_end_left : vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem , vg::ZipCode::snarl_code_t
• distance_end_right : vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem , vg::ZipCode::snarl_code_t
• distance_index : vg::HaplotypePartitioner , vg::MinDistanceClusterer , vg::MinimizerMapper , vg::MultipathMapper , vg::PrimerFinder , vg::SnarlDistanceIndexClusterer , vg::SnarlMinDistance , vg::SnarlOrientedDistanceMeasurer , vg::TipAnchoredMaxDistance , vg::ZipCodeForest::forest_growing_state_t
• distance_left : vg::SnarlDistanceIndexClusterer::ClusterHead , vg::SnarlDistanceIndexClusterer::SeedCache
• distance_limit : vg::MinimizerMapper , vg::ZipCodeForest::forest_growing_state_t , vg::ZipCodeTree::reverse_iterator
• distance_measurer : vg::OrientedDistanceClusterer
• distance_name : HaplotypesConfig
• distance_right : vg::SnarlDistanceIndexClusterer::ClusterHead , vg::SnarlDistanceIndexClusterer::SeedCache
• distance_start_left : vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem , vg::ZipCode::snarl_code_t
• distance_start_right : vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem , vg::ZipCode::snarl_code_t
• distances : vg::ZipCodeForest::child_info_t
• do_dp : vg::MinimizerMapper
• do_remap : vg::Filter
• do_spliced_alignment : vg::MultipathMapper
• do_svs : vg::Constructor
• dominated_path_chunk_diff : vg::Surjector
• doubling_steps : vg::VariantAdder
• downsample_context_length : vg::IndexingParameters
• downsample_coverage : vg::Surjector
• downsample_probability : vg::ReadFilter< Read >
• downsample_seed_mask : vg::ReadFilter< Read >
• downsample_threshold : vg::IndexingParameters
• dozeu_tail : vg::MinimizerMapper::aligner_stats_t::stat_set_t
• DP_column : haplo::haplo_DP
• dp_score : vg::MEMClusterer::HitNode
• drop_chain : vg::Mapper
• drop_hairpin_paths : vg::SmallSnarlSimplifier
• drop_split : vg::ReadFilter< Read >
• dry_run : vg::RebuildParameters
• duplicated_handles : vg::DozeuPinningOverlay
• duration : vg::Funnel::Stage
• dynamic : vg::GBWTHandler
• dynamic_max_alt_alns : vg::MultipathMapper
• dz : vg::DozeuInterface