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

- d -

dag_and_cyclic_snarl_count() : vg::ZipCodeTree
DagifiedGraph() : vg::DagifiedGraph
dagify() : vg::VG
dagify_steps : vg::Genotyper
data : vg::kff_recoding_t, vg::SmallBitset, vg::varint_vector_t
data_bytes : vg::ParallelKFFReader
data_size() : vg::SmallBitset
data_width : vg::Packer
dead_end : vg::WFANode
Debug : vg::IndexingParameters
debug : vg::BaseMapper
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
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_find_supplementaries : 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_haplotype_positions : vg::MinimizerMapper
default_hard_hit_cap : vg::MinimizerMapper
default_hit_cap : vg::MinimizerMapper
default_item_bonus : vg::MinimizerMapper
DEFAULT_ITERATIONS : vg::MinimizerIndexParameters
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_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_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_supplementary_overlap : vg::MinimizerMapper
default_max_supplementary_separation : vg::MinimizerMapper
default_max_supplementary_uncovered_end : vg::MinimizerMapper
default_max_tail_dp_length : vg::MinimizerMapper
default_max_tail_gap : vg::MinimizerMapper
default_max_tail_length : 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_extension_sets : vg::MinimizerMapper
default_min_extensions : vg::MinimizerMapper
default_min_indel_avoid_bases : vg::MinimizerMapper
default_min_mapq0_score : vg::MinimizerMapper
default_min_supplementary_filter_size_proportion : vg::MinimizerMapper
default_min_supplementary_read_coverage : vg::MinimizerMapper
default_min_supplementary_score_fraction : vg::MinimizerMapper
default_min_supplementary_size : 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_prune_low_cplx : GiraffeMainOptions
default_rec_consistency_bonus : vg::MinimizerMapper
default_rec_penalty : vg::MinimizerMapper
default_rec_penalty_aln : 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_softclip_penalty : vg::MinimizerMapper
default_sort_by_chain_score : vg::MinimizerMapper
default_sort_zipcodes() : vg::ZipCodeForest
DEFAULT_SUBGRAPH_LIMIT : vg::Surjector
default_target_alignment_attempts : vg::MinimizerMapper
DEFAULT_THRESHOLD : vg::MinimizerIndexParameters
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_variant_index() : vg::VCFTraversalFinder
deleted_prior_logprob : vg::Genotyper
deletion : vg::WFAAlignment
deletion_aligner : vg::GSSWAligner
DeletionAligner() : vg::DeletionAligner
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::distance_iterator
depth_err : vg::PoissonSupportSnarlCaller::PoissonCallInfo
depth_index : vg::PoissonSupportSnarlCaller
depth_padding_factor : vg::PoissonSupportSnarlCaller
description : vg::BaseOption< Value, Parser >, vg::subcommand::Subcommand
deserialize() : vg::GAFSorterRecord, vg::VG, vg::ZipCodeCollection
dest : vg::subcommand::ArgSpec< T, Receiver >
destroy_edge() : vg::VG
destroy_handle() : vg::VG
destroy_node() : vg::VG
destroy_path() : vg::VG
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
direct_numeric_lookup : vg::algorithms::GFAIDMapInfo
dirnames : vg::temp_file::Handler
discard_overlaps : vg::HaplotypeIndexer
discrete_distribution() : vg::discrete_distribution< T >
discrete_uniform_sample() : vg::SnarlManager
disjoint() : haplo::int_itvl_t
disjoint_interval_allowable_overlap : vg::Surjector
display() : vg::AlignmentChainModel, vg::MEMChainModel
display_dot() : vg::AlignmentChainModel, vg::MEMChainModel
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_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_iterator() : vg::ZipCodeTree::distance_iterator, vg::ZipCodeTree::seed_iterator
distance_left : vg::SnarlDistanceIndexClusterer::ClusterHead, vg::SnarlDistanceIndexClusterer::SeedCache
distance_limit : vg::MinimizerMapper, vg::ZipCodeForest::forest_growing_state_t, vg::ZipCodeTree::distance_iterator
distance_measurer : vg::OrientedDistanceClusterer
distance_name : HaplotypesConfig, MinimizerConfig
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
distinct_snarls_with_fragments : vg::GrefCover::TopLevelSnarlStats
divergence : vg::LoggedGapAlignmentScorer
divide_handle() : vg::VG
divide_mapping() : vg::Paths
divide_node() : vg::VG
divide_path() : vg::VG
do_alignment_on_chains() : vg::MinimizerMapper
do_chaining_on_trees() : vg::MinimizerMapper
do_dp : vg::MinimizerMapper
do_poa() : vg::DozeuInterface
do_rescue_alignment() : vg::MultipathMapper
do_spliced_alignment : vg::MultipathMapper
do_svs : vg::Constructor
dominated_path_chunk_diff : vg::Surjector
done() : vg::ZipCodeTree::distance_iterator
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_aligner : vg::Surjector
DP_column : haplo::haplo_DP
dp_gap_open_extra_cost : vg::Surjector
dp_score : vg::MEMClusterer::HitNode
dp_score_scale : vg::Surjector
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::ZipCode
dump_chaining_problem() : vg::MinimizerMapper
dump_debug_chains() : 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
dup() : vg::ZipCodeTree::distance_iterator
duplicated_handles : vg::DozeuPinningOverlay
duration : vg::Funnel::Stage, vg::Watchdog
dynamic : vg::GBWTHandler
dynamic_max_alt_alns : vg::MultipathMapper
dz : vg::DozeuInterface