- d -

• dag_and_non_dag_snarl_count() : vg::ZipCodeTree
• DagifiedGraph() : vg::DagifiedGraph
• dagify() : vg::VG
• data_size() : vg::SmallBitset
• decode_rgfa_tags() : vg::algorithms::GFAParser
• decoder_length() : vg::ZipCode
• decoder_t() : vg::ZipCode::decoder_t
• decompose_alignments() : vg::MultipathAlignmentGraph
• decompose_genotype_fast() : vg::WindowedVcfBuffer
• 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_build_jobs() : GBWTConfig
• default_context_length() : GBWTConfig
• default_distance() : vg::WFAExtender::ErrorModel
• default_gap_length() : vg::WFAExtender::ErrorModel
• default_gaps() : vg::WFAExtender::ErrorModel
• default_merge_jobs() : GBWTConfig
• default_mismatches() : vg::WFAExtender::ErrorModel
• default_num_paths() : GBWTConfig
• default_num_paths_local() : GBWTConfig
• default_sort_zipcodes() : vg::ZipCodeForest
• deflect_to_matrix() : vg::BandedGlobalAligner< IntType >::AltTracebackStack
• Deflection() : vg::BandedGlobalAligner< IntType >::AltTracebackStack::Deflection
• del_predecessor() : vg::WFATree
• delete_haplotype() : vg::GenomeState
• delete_variant_index() : vg::VCFTraversalFinder
• deletion_filter() : vg::Filter
• DeletionAligner() : vg::DeletionAligner
• density() : vg::truncated_normal_distribution< T >
• dependency_order() : vg::IndexRegistry
• dependents() : vg::IndexingPlan
• depth() : vg::ZipCodeTree::reverse_iterator
• depth_filter() : vg::Filter
• describe() : vg::io::VPKG
• deserialize() : handlegraph::Serializable , handlegraph::TriviallySerializable , vg::GAFSorterRecord , vg::VG , vg::ZipCodeCollection
• deserialize_members() : handlegraph::Serializable , xg::XG
• 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
• DiagramExplainer() : vg::DiagramExplainer
• DinucleotideMachine() : vg::DinucleotideMachine
• discard_bytes() : vg::io::StreamMultiplexer
• discard_to_breakpoint() : vg::io::StreamMultiplexer
• 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::MultipathMapper
• distance_between() : vg::MinimizerMapper , vg::MultipathMapper
• distance_between_positions() : vg::Filter
• distance_to_annotation() : vg::MinimizerMapper
• 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_fragmenting_on_trees() : vg::MinimizerMapper
• do_poa() : vg::DozeuInterface
• do_rescue_alignment() : vg::MultipathMapper
• DotDumpExplainer() : vg::DotDumpExplainer< T >
• downsample_chunks() : vg::Surjector
• DozeuPinningOverlay() : vg::DozeuPinningOverlay
• DPScoreComparator() : vg::MEMClusterer::DPScoreComparator
• draw() : vg::Viz
• draw_graph() : vg::Viz
• drop_prefix() : vg::BitString
• 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
• duplication_filter() : vg::Filter