Here is a list of all variables with links to the classes they belong to:
- d -
- 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_width : vg::Packer
- dead_end : vg::WFANode
- debug : vg::BaseMapper
- default_align_from_chains : vg::MinimizerMapper
- 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_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_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_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_num_bp_per_min : vg::MinimizerMapper
- 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
- defray_count : vg::ReadFilter< Read >
- defray_length : vg::ReadFilter< Read >
- deleted_prior_logprob : vg::Genotyper
- deletion_aligner : vg::GSSWAligner
- deletions : vg::DeleteHaplotypeCommand, vg::ReplaceLocalHaplotypeCommand
- DELETIONS : vg::WFANode
- delim1 : vg::Packer
- delim2 : vg::Packer
- dense_to_sparse : vg::SparseUnionFind
- depth_err : vg::PoissonSupportSnarlCaller::PoissonCallInfo
- depth_index : vg::PoissonSupportSnarlCaller
- depth_padding_factor : vg::PoissonSupportSnarlCaller
- description : vg::BaseOption< Value, Parser >, vg::subcommand::Subcommand
- dest : vg::subcommand::ArgSpec< T, Receiver >
- diagonal : vg::WFAPoint
- dinuc_machine : vg::MultipathMapper
- diploid_prior_logprob : vg::Genotyper
- diploid_sampling : vg::Recombinator::Parameters
- directed_acyclic_net_graph : vg::Snarl
- dirnames : vg::temp_file::Handler
- discard_overlaps : vg::HaplotypeIndexer
- discordant_insert_size : vg::Alignment
- distance : vg::MEMClusterer::HitEdge, vg::WFAExtender::ErrorModel
- 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
- do_dp : vg::MinimizerMapper
- do_remap : vg::Filter
- do_spliced_alignment : vg::MultipathMapper
- do_svs : vg::Constructor
- dominated_path_chunk_diff : vg::Surjector
- doubling_steps : vg::VariantAdder
- downsample_context_length : vg::IndexingParameters
- downsample_coverage : vg::Surjector
- downsample_probability : vg::ReadFilter< Read >
- downsample_seed_mask : vg::ReadFilter< Read >
- downsample_threshold : vg::IndexingParameters
- DP_column : haplo::haplo_DP
- dp_score : vg::MEMClusterer::HitNode
- drop_chain : vg::Mapper
- drop_hairpin_paths : vg::SmallSnarlSimplifier
- drop_split : vg::ReadFilter< Read >
- dry_run : vg::RebuildParameters
- duplicated_handles : vg::DozeuPinningOverlay
- duration : vg::Funnel::Stage
- dynamic : vg::GBWTHandler
- dynamic_max_alt_alns : vg::MultipathMapper
- dz : vg::DozeuInterface