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::path_handle_t
, handlegraph::step_handle_t
, vg::SmallBitset
, vg::SpliceMotifs
- data_size()
: vg::SmallBitset
- data_width
: vg::Packer
- db
: vg::Index
- db_options
: vg::Index
- debug
: vg::BaseMapper
- decode()
: vg::MIPayload
- decode_nucleotide()
: bdsg::PackedGraph
- decode_path_name()
: bdsg::PackedGraph
- decode_traversal()
: bdsg::PackedGraph
- decompose_genotype_fast()
: vg::WindowedVcfBuffer
- deconstruct()
: vg::Deconstructor
- deconstruct_site()
: vg::Deconstructor
- Deconstructor()
: vg::Deconstructor
- decrement_node_ids()
: vg::VG
- decrement_rank()
: bdsg::ODGI
- deduplicate_cluster_pairs()
: vg::MEMClusterer
- deep_contents()
: vg::SnarlManager
- DEFAULT_PATH_WEIGHT
: vg::FlowSort
- default_sequence_quality
: vg::Genotyper
- default_value
: vg::BaseOption< Value, Parser >
- defining_path
: vg::PathSubgraph
- deflect_to_matrix()
: vg::BandedGlobalAligner< IntType >::AltTracebackStack
- Deflection()
: vg::BandedGlobalAligner< IntType >::AltTracebackStack::Deflection
- defrag_factor
: bdsg::PackedGraph
- defragment()
: bdsg::PackedGraph
- defragment_path()
: bdsg::PackedGraph
- defray
: vg::ReadFilter::Counts
- defray_all
: vg::ReadFilter::Counts
- defray_count
: vg::ReadFilter
- defray_length
: vg::ReadFilter
- delete_haplotype()
: vg::GenomeState
- delete_variant_index()
: vg::VCFTraversalFinder
- deleted_bases
: bdsg::PackedGraph
- deleted_edge_records
: bdsg::PackedGraph
- deleted_membership_records
: bdsg::PackedGraph
- deleted_node_bv
: bdsg::ODGI
- deleted_node_records
: bdsg::PackedGraph
- deleted_prior_logprob
: vg::Genotyper
- deleted_reversing_self_edge_records
: bdsg::PackedGraph
- deletion_filter()
: vg::Filter
- deletions
: vg::DeleteHaplotypeCommand
, vg::ReplaceLocalHaplotypeCommand
- delim1
: vg::Packer
- delim2
: vg::Packer
- depth
: vg::MinimumDistanceIndex::SnarlIndex
, vg::SRPE
- depth_err
: vg::PoissonSupportSnarlCaller::PoissonCallInfo
- depth_filter()
: vg::Filter
- depth_index
: vg::PoissonSupportSnarlCaller
- depth_padding_factor
: vg::PoissonSupportSnarlCaller
- DepthMap()
: vg::DepthMap
- depths
: vg::DepthMap
- describe()
: vg::io::VPKG
- description
: vg::BaseOption< Value, Parser >
, vg::subcommand::Subcommand
- deserialize()
: bdsg::HashGraph::node_t
, bdsg::HashGraph::path_t
, handlegraph::SerializableHandleGraph
, vg::VG
- deserialize_members()
: bdsg::HashGraph
, bdsg::ODGI
, bdsg::PackedGraph
, handlegraph::SerializableHandleGraph
, xg::XG
- destroy_edge()
: bdsg::HashGraph
, bdsg::ODGI
, bdsg::PackedGraph
, handlegraph::DeletableHandleGraph
, vg::VG
- destroy_handle()
: bdsg::HashGraph
, bdsg::ODGI
, bdsg::PackedGraph
, handlegraph::DeletableHandleGraph
, vg::VG
- destroy_node()
: vg::VG
- destroy_path()
: bdsg::HashGraph
, bdsg::ODGI
, bdsg::PackedGraph
, handlegraph::MutablePathHandleGraph
, vg::VG
- destroy_path_handle_records()
: bdsg::ODGI
- destroy_progress()
: vg::Progressive
- destroy_step()
: bdsg::ODGI
- dfs()
: vg::FlowSort
, vg::VG
- dfs_gbwt()
: vg::MinimizerMapper
- dice_nodes()
: vg::VG
- dinuc_machine
: vg::MultipathMapper
- DinucleotideMachine()
: vg::DinucleotideMachine
- diploid_prior_logprob
: vg::Genotyper
- directed_acyclic_net_graph
: vg::Snarl
- discard_bytes()
: vg::io::StreamMultiplexer
- discard_overlaps
: vg::HaplotypeIndexer
- discard_to_breakpoint()
: vg::io::StreamMultiplexer
- discordance_score()
: vg::SRPE
- discordant_insert_size
: vg::Alignment
- discrete_distribution()
: vg::discrete_distribution< T >
- discrete_uniform_sample()
: vg::SnarlManager
- disjoint()
: haplo::int_itvl_t
- disjoint_subgraphs()
: vg::VG
- display()
: bdsg::ODGI
, vg::AlignmentChainModel
, vg::MEMChainModel
- display_dot()
: vg::AlignmentChainModel
, vg::MEMChainModel
- dist_index
: vg::SnarlSeedClusterer
- dist_to_common_ancestor()
: vg::MinimumDistanceIndex
- dist_to_ends()
: vg::MinimumDistanceIndex::SnarlIndex
- distance
: vg::IndexManager
, vg::MEMClusterer::HitEdge
, vg::MultipathMapper
- distance_between()
: vg::MinimizerMapper
, vg::MultipathMapper
- distance_between_positions()
: vg::Filter
- distance_from_start()
: vg::IncrementalSubgraph
- distance_index
: vg::MinDistanceClusterer
, vg::MinimizerMapper
, vg::MultipathMapper
, vg::SnarlMinDistance
, vg::SnarlOrientedDistanceMeasurer
, vg::TipAnchoredMaxDistance
- distance_limit
: vg::MinimizerMapper
- distance_measurer
: vg::OrientedDistanceClusterer
- distance_override
: vg::IndexManager
- distances
: vg::MinimumDistanceIndex::SnarlIndex
- divide_handle()
: bdsg::HashGraph
, bdsg::ODGI
, bdsg::PackedGraph
, 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_spliced_alignment
: vg::MultipathMapper
- do_svs
: vg::Constructor
- Double
: vg::multipath_alignment_t
- doubling_steps
: vg::VariantAdder
- downsample_probability
: vg::ReadFilter
- downsample_seed_mask
: vg::ReadFilter
- 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
- dump()
: vg::GenomeState
, vg::Index
, vg::SnarlState
- dump_debug_extension_set()
: vg::MinimizerMapper
- dump_debug_minimizers()
: vg::MinimizerMapper
- dump_debug_sequence()
: vg::MinimizerMapper
- dump_to_stream()
: xg::XG
- duplicated_handles
: vg::DozeuPinningOverlay
- duplication_filter()
: vg::Filter
- duration
: vg::Watchdog
- dynamic_max_alt_alns
: vg::MultipathMapper
- dz
: vg::DozeuInterface