Here is a list of all class members with links to the classes they belong to:

- d -

• dag_and_non_dag_snarl_count() : vg::ZipCodeTree
• DagifiedGraph() : vg::DagifiedGraph
• dagify() : vg::VG
• 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_size() : vg::SmallBitset
• data_width : vg::Packer
• dead_end : vg::WFANode
• debug : vg::BaseMapper
• Debug : vg::IndexingParameters
• decode_rgfa_tags() : vg::algorithms::GFAParser
• decoder : vg::ZipCode
• decoder_length() : vg::ZipCode
• decoder_t() : vg::ZipCode::decoder_t
• decompose_alignments() : vg::MultipathAlignmentGraph
• decompose_genotype_fast() : vg::WindowedVcfBuffer
• decomposition_source_t : handlegraph::BuildableSnarlDecomposition
• deconstruct() : vg::Deconstructor
• deconstruct_graph() : vg::Deconstructor
• deconstruct_graph_top_down() : vg::Deconstructor
• deconstruct_site() : vg::Deconstructor
• Deconstructor() : vg::Deconstructor
• decrement_node_ids() : vg::VG
• deduplicate_alt_alns() : vg::MultipathAlignmentGraph
• deduplicate_cluster_pairs() : vg::MEMClusterer
• deep_contents() : vg::SnarlManager
• default_align_from_chains : vg::MinimizerMapper
• default_batch_size : GiraffeMainOptions
• default_build_jobs() : GBWTConfig
• 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_context_length() : GBWTConfig
• default_distance() : vg::WFAExtender::ErrorModel
• 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_length() : vg::WFAExtender::ErrorModel
• default_gap_scale : vg::MinimizerMapper
• default_gapless_extension_limit : vg::MinimizerMapper
• default_gaps() : vg::WFAExtender::ErrorModel
• 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_merge_jobs() : GBWTConfig
• 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_mismatches() : vg::WFAExtender::ErrorModel
• default_num_bp_per_min : vg::MinimizerMapper
• default_num_paths() : GBWTConfig
• default_num_paths_local() : GBWTConfig
• 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_sort_zipcodes() : vg::ZipCodeForest
• 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
• deflect_to_matrix() : vg::BandedGlobalAligner< IntType >::AltTracebackStack
• Deflection() : vg::BandedGlobalAligner< IntType >::AltTracebackStack::Deflection
• defray : vg::Counts
• defray_all : vg::Counts
• defray_count : vg::ReadFilter< Read >
• defray_length : vg::ReadFilter< Read >
• del_predecessor() : vg::WFATree
• delete_haplotype() : vg::GenomeState
• delete_variant_index() : vg::VCFTraversalFinder
• deleted_prior_logprob : vg::Genotyper
• deletion : vg::WFAAlignment
• deletion_aligner : vg::GSSWAligner
• deletion_filter() : vg::Filter
• DeletionAligner() : vg::DeletionAligner
• deletions : vg::DeleteHaplotypeCommand , vg::ReplaceLocalHaplotypeCommand
• DELETIONS : vg::WFANode
• delim1 : vg::Packer
• delim2 : vg::Packer
• dense_to_sparse : vg::SparseUnionFind
• density() : vg::truncated_normal_distribution< T >
• dependency_order() : vg::IndexRegistry
• dependents() : vg::IndexingPlan
• depth : vg::ZipCodeForest::interval_state_t , vg::ZipCodeTree::reverse_iterator
• depth_err : vg::PoissonSupportSnarlCaller::PoissonCallInfo
• depth_filter() : vg::Filter
• depth_index : vg::PoissonSupportSnarlCaller
• depth_padding_factor : vg::PoissonSupportSnarlCaller
• describe() : vg::io::VPKG
• description : vg::BaseOption< Value, Parser > , vg::subcommand::Subcommand
• deserialize() : handlegraph::Serializable , handlegraph::TriviallySerializable , vg::GAFSorterRecord , vg::VG , vg::ZipCodeCollection
• deserialize_members() : handlegraph::Serializable , xg::XG
• dest : vg::subcommand::ArgSpec< T, Receiver >
• destroy_edge() : handlegraph::DeletableHandleGraph , vg::VG
• destroy_handle() : handlegraph::DeletableHandleGraph , vg::VG
• destroy_node() : vg::VG
• destroy_path() : handlegraph::MutablePathHandleGraph , vg::VG
• destroy_paths() : handlegraph::MutablePathHandleGraph
• destroy_progress() : vg::Progressive
• determine_distance_correlation() : vg::MultipathMapper
• dfs() : vg::FlowSort , vg::VG
• dfs_gbwt() : vg::MinimizerMapper
• diagonal : vg::WFAPoint
• DiagramExplainer() : vg::DiagramExplainer
• difference_type : vg::count_back_inserter< T > , vg::VectorView< Item >::const_iterator
• dinuc_machine : vg::MultipathMapper
• DinucleotideMachine() : vg::DinucleotideMachine
• diploid_prior_logprob : vg::Genotyper
• diploid_sampling : vg::Recombinator::Parameters
• directed_acyclic_net_graph : vg::Snarl
• dirnames : vg::temp_file::Handler
• discard_bytes() : vg::io::StreamMultiplexer
• discard_overlaps : vg::HaplotypeIndexer
• discard_to_breakpoint() : vg::io::StreamMultiplexer
• discordant_insert_size : vg::Alignment
• discrete_distribution() : vg::discrete_distribution< T >
• discrete_uniform_sample() : vg::SnarlManager
• disjoint() : haplo::int_itvl_t
• display() : vg::AlignmentChainModel , vg::MEMChainModel
• display_dot() : vg::AlignmentChainModel , vg::MEMChainModel
• dissociate() : handlegraph::TriviallySerializable
• distance() : vg::Haplotypes::Subchain , vg::MatchPos , vg::MEMClusterer::HitEdge , vg::MultipathMapper , vg::WFAExtender::ErrorModel , vg::ZipCodeTree::seed_result_t
• distance_between() : vg::MinimizerMapper , vg::MultipathMapper
• distance_between_positions() : vg::Filter
• 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
• distance_to_annotation() : vg::MinimizerMapper
• distances : vg::ZipCodeForest::child_info_t
• divide_handle() : handlegraph::MutableHandleGraph , vg::VG
• divide_mapping() : vg::Paths
• divide_node() : vg::VG
• divide_path() : vg::VG
• do_alignment_on_chains() : vg::MinimizerMapper
• do_chaining_on_fragments() : vg::MinimizerMapper
• do_dp : vg::MinimizerMapper
• do_fragmenting_on_trees() : vg::MinimizerMapper
• do_poa() : vg::DozeuInterface
• do_remap : vg::Filter
• do_rescue_alignment() : vg::MultipathMapper
• do_spliced_alignment : vg::MultipathMapper
• do_svs : vg::Constructor
• dominated_path_chunk_diff : vg::Surjector
• DotDumpExplainer() : vg::DotDumpExplainer< T >
• Double : vg::multipath_alignment_t
• doubling_steps : vg::VariantAdder
• downsample_chunks() : vg::Surjector
• 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
• DozeuPinningOverlay() : vg::DozeuPinningOverlay
• DP_column : haplo::haplo_DP
• dp_score : vg::MEMClusterer::HitNode
• DPScoreComparator() : vg::MEMClusterer::DPScoreComparator
• draw() : vg::Viz
• draw_graph() : vg::Viz
• drop_chain : vg::Mapper
• drop_hairpin_paths : vg::SmallSnarlSimplifier
• drop_prefix() : vg::BitString
• drop_split : vg::ReadFilter< Read >
• dry_run : vg::RebuildParameters
• dump() : vg::GenomeState , vg::SnarlState , vg::ZipCode
• dump_chaining_problem() : vg::MinimizerMapper
• dump_debug_clustering() : vg::MinimizerMapper
• dump_debug_dotplot() : vg::MinimizerMapper
• dump_debug_extension_set() : vg::MinimizerMapper
• dump_debug_graph() : vg::MinimizerMapper
• dump_debug_minimizers() : vg::MinimizerMapper
• dump_debug_query() : vg::MinimizerMapper
• dump_debug_seeds() : vg::MinimizerMapper
• dump_debug_sequence() : vg::MinimizerMapper
• dump_to_stream() : xg::XG
• dup() : vg::ZipCodeTree::reverse_iterator
• duplicated_handles : vg::DozeuPinningOverlay
• duplication_filter() : vg::Filter
• duration : vg::Funnel::Stage , vg::Watchdog
• dynamic : vg::GBWTHandler
• dynamic_max_alt_alns : vg::MultipathMapper
• dz : vg::DozeuInterface