Here is a list of all class members with links to the classes they belong to:
- d -
- 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
- data_bytes : vg::ParallelKFFReader
- data_size() : vg::SmallBitset
- data_width : vg::Packer
- dead_end : vg::WFANode
- debug : vg::BaseMapper
- Debug : vg::IndexingParameters
- decode() : vg::MIPayload
- decode_rgfa_tags() : vg::algorithms::GFAParser
- 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_build_jobs() : GBWTConfig
- default_chain_min_score : vg::MinimizerMapper
- default_chain_score_threshold : vg::MinimizerMapper
- default_chaining_cluster_distance : vg::MinimizerMapper
- default_cluster_coverage_threshold : vg::MinimizerMapper
- default_cluster_score_threshold : vg::MinimizerMapper
- 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_gap_length() : vg::WFAExtender::ErrorModel
- default_gaps() : vg::WFAExtender::ErrorModel
- default_hard_hit_cap : vg::MinimizerMapper
- default_hit_cap : vg::MinimizerMapper
- default_initial_lookback_threshold : vg::MinimizerMapper
- default_item_bonus : vg::MinimizerMapper
- DEFAULT_K : vg::Haplotypes::Header
- default_lookback_item_hard_cap : vg::MinimizerMapper
- default_lookback_scale_factor : vg::MinimizerMapper
- default_max_alignments : vg::MinimizerMapper
- default_max_chain_connection : vg::MinimizerMapper
- default_max_clusters_to_chain : vg::MinimizerMapper
- default_max_dozeu_cells : vg::MinimizerMapper
- default_max_dp_cells : vg::MinimizerMapper
- default_max_extensions : vg::MinimizerMapper
- default_max_fragment_length : vg::MinimizerMapper
- default_max_indel_bases : vg::MinimizerMapper
- default_max_local_extensions : vg::MinimizerMapper
- default_max_lookback_bases : vg::MinimizerMapper
- default_max_multimaps : vg::MinimizerMapper
- default_max_precluster_connections : vg::MinimizerMapper
- default_max_rescue_attempts : vg::MinimizerMapper
- default_max_tail_length : vg::MinimizerMapper
- default_max_unique_min : vg::MinimizerMapper
- default_merge_jobs() : GBWTConfig
- default_min_chains : vg::MinimizerMapper
- default_min_clusters_to_chain : vg::MinimizerMapper
- default_min_extension_sets : vg::MinimizerMapper
- default_min_extensions : vg::MinimizerMapper
- default_min_good_transition_score_per_base : vg::MinimizerMapper
- default_min_lookback_items : vg::MinimizerMapper
- default_min_precluster_connections : 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_paired_distance_stdevs : vg::MinimizerMapper
- default_paired_rescue_score_limit : vg::MinimizerMapper
- DEFAULT_PATH_WEIGHT : vg::FlowSort
- default_precluster_connection_coverage_threshold : vg::MinimizerMapper
- default_rescue_seed_limit : vg::MinimizerMapper
- default_rescue_subgraph_stdevs : vg::MinimizerMapper
- default_reseed_search_distance : vg::MinimizerMapper
- default_sequence_quality : vg::Genotyper
- default_show_work : vg::MinimizerMapper
- default_track_correctness : vg::MinimizerMapper
- default_track_provenance : vg::MinimizerMapper
- default_value : vg::BaseOption< Value, Parser >, vg::subcommand::ArgSpec< T, Receiver >
- default_watchdog_timeout : GiraffeMainOptions
- 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_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::VG
- 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::MatchPos, vg::MEMClusterer::HitEdge, vg::MultipathMapper, vg::WFAExtender::ErrorModel
- distance_between() : vg::MinimizerMapper, vg::MultipathMapper
- distance_between_positions() : vg::Filter
- distance_between_seeds() : vg::SnarlDistanceIndexClusterer
- distance_end_left : vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem
- distance_end_right : vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem
- distance_index : vg::HaplotypePartitioner, vg::MinDistanceClusterer, vg::MinimizerMapper, vg::MultipathMapper, vg::SnarlDistanceIndexClusterer, vg::SnarlMinDistance, vg::SnarlOrientedDistanceMeasurer, vg::TipAnchoredMaxDistance
- distance_left : vg::SnarlDistanceIndexClusterer::ClusterHead, vg::SnarlDistanceIndexClusterer::SeedCache
- distance_limit : vg::MinimizerMapper
- distance_measurer : vg::OrientedDistanceClusterer
- distance_name : HaplotypesConfig
- distance_right : vg::SnarlDistanceIndexClusterer::ClusterHead, vg::SnarlDistanceIndexClusterer::SeedCache
- distance_start_left : vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem
- distance_start_right : vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem
- distance_to_annotation() : vg::MinimizerMapper
- divide_handle() : handlegraph::MutableHandleGraph, vg::VG
- divide_mapping() : vg::Paths
- divide_node() : vg::VG
- divide_path() : vg::VG
- do_dp : 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
- 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
- dump_chaining_problem() : vg::MinimizerMapper
- dump_debug_clustering() : vg::MinimizerMapper
- dump_debug_extension_set() : 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
- 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