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

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• A() : vg::truncated_normal_distribution< T >
• a() : vg::uniform_int_distribution< T > , vg::uniform_real_distribution< T >
• absent : vg::Recombinator
• ABSENT_SCORE : vg::Recombinator
• absent_score : vg::Recombinator::Parameters
• AbstractReadSampler() : vg::AbstractReadSampler
• accelerate_mem_query() : vg::BaseMapper
• accelerator : vg::BaseMapper
• accept_record() : vg::VcfRecordFilter
• access_mutex : vg::Watchdog::thread_state_t
• active_tree_index : vg::ZipCodeForest::forest_growing_state_t
• Adaptive : vg::Genotyper
• adaptive_diff_exponent : vg::BaseMapper
• adaptive_reseed_diff : vg::BaseMapper
• adaptive_reseed_length_memo : vg::BaseMapper
• add() : vg::Packer
• add_allele_path_to_info() : vg::VCFOutputCaller
• add_annotations() : vg::MinimizerMapper::aligner_stats_t , vg::MinimizerMapper::aligner_stats_t::stat_set_t , vg::MultipathAlignmentEmitter
• add_bv() : Vectorizer
• add_chain_child() : vg::NetGraph
• add_child_to_chain() : vg::ZipCodeForest
• add_connection() : vg::subpath_t
• add_contigs_to_vcf_header() : vg::Deconstructor
• add_decomposed_tail_alignments() : vg::MultipathAlignmentGraph
• add_edge() : vg::DiagramExplainer , vg::MEMClusterer::HitGraph , vg::VG
• add_edges() : vg::VG
• add_edit() : vg::path_mapping_t
• add_edited_transcript_paths() : vg::Transcriptome
• add_entry() : vg::subcommand::Preset
• add_exon() : vg::Transcriptome
• add_flag() : vg::subcommand::OptionGroup< Receiver >
• add_globals() : vg::DiagramExplainer
• add_group() : vg::StreamIndex< Message > , vg::StreamIndexBase , vg::subcommand::GroupedOptionGroup
• add_handle() : handlegraph::algorithms::SubHandleGraph , vg::SubHandleGraph
• add_haplotype() : vg::PhasedGenome
• add_haplotype_transcripts() : vg::Transcriptome
• add_intron_splice_junctions() : vg::Transcriptome
• add_mapping() : vg::path_t
• add_name() : Vectorizer
• add_name_mapping() : vg::NameMapper
• add_next() : vg::subpath_t
• add_node() : vg::algorithms::Graph , vg::DiagramExplainer , vg::VG
• add_nodes() : vg::VG
• add_one_byte() : vg::varint_vector_t
• add_option() : vg::subcommand::OptionGroup< Receiver >
• add_points() : vg::algorithms::TracedScore
• add_primer_pair() : vg::PrimerFinder
• add_range() : vg::subcommand::OptionGroup< Receiver >
• add_reachability_edges() : vg::MultipathAlignmentGraph
• add_reference_transcripts() : vg::Transcriptome
• add_seed_to_chain_problem() : vg::SnarlDistanceIndexClusterer
• add_snarl() : vg::SnarlManager
• add_snarl_distances() : vg::ZipCodeForest
• add_snarl_to_chain_problem() : vg::SnarlDistanceIndexClusterer
• add_splice_junction_edges() : vg::Transcriptome
• add_star_traversals() : vg::Deconstructor
• add_start() : vg::multipath_alignment_t
• add_start_end_markers() : vg::VG
• add_subpath() : vg::multipath_alignment_t
• add_transcripts_to_gbwt() : vg::Transcriptome
• add_traversals() : vg::ExhaustiveTraversalFinder
• add_unary_child() : vg::NetGraph
• add_value() : vg::varint_vector_t
• add_variant() : vg::VCFOutputCaller
• add_variants() : vg::VariantAdder
• added_fwd : vg::ExtraNodeGraph
• added_id : vg::ExtraNodeGraph
• added_rev : vg::ExtraNodeGraph
• additional_items : vg::MatchPos::PathList
• adjacent() : vg::VG
• adjacent_positions() : vg::Mapper
• adjust_alignments_for_base_quality : vg::AlignerClient
• adjust_diagonal_range() : vg::WFATree
• adjust_for_base_quality : vg::BandedGlobalAligner< IntType >
• advance() : vg::io::MessageIterator , vg::io::ProtobufIterator< T > , vg::NGSSimulator , vg::PathBranch
• advance_by_distance() : vg::NGSSimulator
• advance_on_graph() : vg::NGSSimulator
• advance_on_graph_by_distance() : vg::NGSSimulator
• advance_on_path() : vg::NGSSimulator
• advance_on_path_by_distance() : vg::NGSSimulator
• Affinity() : vg::Genotyper::Affinity
• affinity : vg::Genotyper::Affinity
• after : ReferenceInterval
• agglomerate() : vg::MultipathMapper
• agglomerate_alignment_pairs() : vg::MultipathMapper
• agglomerate_alignments() : vg::MultipathMapper
• agglomerate_multipath_alns : vg::MultipathMapper
• agglomeration_length : vg::MinimizerMapper::Minimizer
• agglomeration_start : vg::MinimizerMapper::Minimizer
• agglomeration_window_count() : vg::MinimizerMapper::Minimizer
• alg2name : vg::Genotyper
• AliasGraph() : vg::AliasGraph
• align() : vg::Aligner , vg::BandedGlobalAligner< IntType > , vg::BaseAligner , vg::DeletionAligner , vg::DozeuInterface , vg::Mapper , vg::MultipathAlignmentGraph , vg::QualAdjAligner , vg::SSWAligner , vg::VG
• align_banded() : vg::Mapper
• align_cluster() : vg::Mapper
• align_downward() : vg::DozeuInterface
• align_from_chains : vg::MinimizerMapper
• align_global_banded() : vg::Aligner , vg::GSSWAligner , vg::QualAdjAligner
• align_global_banded_multi() : vg::Aligner , vg::GSSWAligner , vg::QualAdjAligner
• align_internal() : vg::Aligner , vg::QualAdjAligner
• align_maybe_flip() : vg::Mapper
• align_mem_multi() : vg::Mapper
• align_multi() : vg::DeletionAligner , vg::Mapper
• align_multi_internal() : vg::Mapper
• align_ns() : vg::VariantAdder
• align_paired_multi() : vg::Mapper
• align_pinned() : vg::Aligner , vg::DozeuInterface , vg::GSSWAligner , vg::QualAdjAligner
• align_pinned_multi() : vg::Aligner , vg::GSSWAligner , vg::QualAdjAligner
• align_qual_adjusted() : vg::VG
• align_sequence_between() : vg::MinimizerMapper
• align_sequence_between_consistently() : vg::MinimizerMapper
• align_tails() : vg::MultipathAlignmentGraph
• align_to_cluster_graph_pairs() : vg::MultipathMapper
• align_to_cluster_graphs() : vg::MultipathMapper
• align_to_cluster_graphs_with_rescue() : vg::MultipathMapper
• align_to_graph() : vg::Mapper
• align_to_splice_candidates() : vg::MultipathMapper
• align_xdrop() : vg::Aligner , vg::GSSWAligner , vg::QualAdjAligner
• Aligner() : vg::Aligner
• aligner : vg::GaplessExtender , vg::VariantAdder , vg::WFAExtender
• AlignerClient() : vg::AlignerClient
• alignment : vg::alignment_index_t , vg::BandedGlobalAligner< IntType > , vg::BandedGlobalAligner< IntType >::BABuilder , vg::BandedGlobalAligner< IntType >::BAMatrix , vg::read_alignment_index_t , vg::Sampler
• alignment_emitter : vg::FlowCaller , vg::NestedFlowCaller
• alignment_end_matches() : vg::ReadFilter< Read >
• alignment_end_position() : vg::Mapper
• alignment_overhang() : vg::ReadFilter< Read >
• alignment_pair() : vg::Sampler
• alignment_qual_score() : vg::Genotyper
• alignment_score() : vg::WFAPoint
• alignment_score_partition_function() : vg::GSSWAligner
• alignment_seq() : vg::Sampler
• alignment_to_a_hot() : Vectorizer
• alignment_to_custom_score() : Vectorizer
• alignment_to_graph() : vg::Sampler
• alignment_to_identity_hot() : Vectorizer
• alignment_to_onehot() : Vectorizer
• alignment_to_path() : vg::Sampler
• alignment_with_error() : vg::Sampler
• AlignmentChainModel() : vg::AlignmentChainModel
• AlignmentChainModelVertex() : vg::AlignmentChainModelVertex
• alignments : vg::MSAConverter
• alignments_by_edge : vg::AugmentedGraph
• alignments_by_node : vg::AugmentedGraph
• alignments_consistent() : vg::Mapper
• all_children_trivial() : vg::SnarlManager
• all_finished() : vg::IndexRegistry
• all_groups() : vg::SparseUnionFind
• all_mapping_qualities_exact() : vg::GSSWAligner
• all_node_problems : vg::SnarlDistanceIndexClusterer::ClusteringProblem
• all_path_names() : vg::Paths
• all_seeds : vg::SnarlDistanceIndexClusterer::ClusteringProblem
• all_snarls : vg::Genotyper
• allele() : haplo::linear_haplo_structure::SNVvector , vg::Genotype , vg::Locus
• allele_ambiguity_log_probs() : vg::Genotyper
• allele_length_range : vg::FlowCaller
• allele_log_likelihood : vg::Locus
• alleles : haplo::linear_haplo_structure::SNVvector , vg::VG::Plan
• allow_duplicates : vg::PathRestrictedTraversalFinder
• allowed_vcf_names : vg::Constructor
• allowed_vcf_regions : vg::Constructor
• AllowsAliasing() : vg::io::BlockedGzipOutputStream
• aln : vg::AlignmentChainModelVertex
• aln_emitter : vg::ReadFilter< Read >
• aln_emitters : vg::MultipathAlignmentEmitter
• alphabet : vg::NGSSimulator
• also_merge_group() : vg::Funnel
• also_relevant() : vg::Funnel
• alt_alignments : vg::BandedGlobalAligner< IntType >
• alt_anchor_max_length_diff : vg::MultipathMapper
• alt_paths : vg::Constructor
• alt_proposal_sample() : vg::MCMCGenotyper
• alt_tracebacks : vg::BandedGlobalAligner< IntType >::AltTracebackStack
• alts_as_loci : vg::Constructor
• AltTracebackStack() : vg::BandedGlobalAligner< IntType >::AltTracebackStack , vg::BandedGlobalAligner< IntType >::BAMatrix
• always_check_population : vg::MultipathMapper
• always_rescue : vg::Mapper
• ambiguous_warned_sequences : vg::Constructor
• Anchor() : vg::algorithms::Anchor
• anchored_filter() : vg::Filter
• anno_type_t : vg::multipath_alignment_t
• annotate_mapped_alignment() : vg::Funnel
• annotate_with_all_path_scores : vg::Surjector
• annotate_with_minimizer_statistics() : vg::MinimizerMapper
• annotate_with_path_positions() : vg::AbstractReadSampler
• annotation : vg::Alignment , vg::Counts , vg::MultipathAlignment
• annotation_path_filter : vg::AbstractReadSampler
• annotation_t : vg::DiagramExplainer
• annotation_to_match : vg::ReadFilter< Read >
• append() : vg::Paths , vg::SnarlState , vg::VG , vg::WFAAlignment
• append_haplotype() : vg::GenomeState
• append_left() : vg::PhasedGenome::Haplotype
• append_mapping() : vg::Paths
• append_node() : vg::WFANode
• append_right() : vg::PhasedGenome::Haplotype
• append_step() : handlegraph::MutablePathHandleGraph , vg::VG
• apply() : vg::subcommand::BaseArgSpec< Receiver > , vg::subcommand::GroupedOptionGroup , vg::subcommand::OptionGroup< Receiver > , vg::subcommand::Preset , vg::subcommand::ValueArgSpec< T, Receiver, Holder >
• apply_aligned_base() : vg::NGSSimulator
• apply_deletion() : vg::NGSSimulator
• apply_edit() : vg::GraphSynchronizer::Lock
• apply_full_length_edit() : vg::GraphSynchronizer::Lock
• apply_haplotype_consistency_scores() : vg::BaseMapper
• apply_insertion() : vg::NGSSimulator
• apply_mask_sequences() : vg::Masker
• apply_max_reads() : vg::Counts
• apply_min_bp_edge_override() : vg::TraversalSupportFinder
• apply_N_mask() : vg::NGSSimulator
• apply_ordering() : handlegraph::MutableHandleGraph , vg::VG
• apply_orientation() : handlegraph::MutableHandleGraph , vg::VG
• apply_translation() : vg::PathIndex
• apply_translations() : vg::PathIndex
• approx_alignment_position() : vg::Mapper
• approx_distance() : vg::Mapper
• approx_fragment_length() : vg::Mapper
• approx_position() : vg::Mapper
• APPROXIMATE_JOBS : vg::HaplotypePartitioner
• approximate_jobs : vg::HaplotypePartitioner::Parameters
• arch_is_big_endian() : vg::endianness< IntType >
• are_consecutive_nodes_in_path() : vg::Paths
• are_consistent() : vg::MultipathMapper
• args : vg::subcommand::OptionGroup< Receiver >
• ArgSpec() : vg::subcommand::ArgSpec< T, Receiver >
• array_end() : vg::ProblemDumpExplainer
• array_start() : vg::ProblemDumpExplainer
• as_edge_table() : vg::Packer
• as_quality_table() : vg::Packer
• as_table() : vg::Packer , vg::Packers
• ASSEMBLY_OR_NAME_MATCH : handlegraph::PathMetadata
• assign_constructed() : vg::IndexFile
• assign_new_sequence_id() : vg::algorithms::GFAParser
• assign_reference_paths() : vg::Haplotypes
• assume_acyclic : vg::BaseMapper
• at() : vg::Option< vector< Item >, Parser > , vg::ZipCodeCollection
• at_dead_end() : vg::WFATree
• at_last_node() : vg::MatchPos
• at_next_deflection() : vg::BandedGlobalAligner< IntType >::AltTracebackStack
• at_or_after() : vg::BitString
• at_or_before() : vg::BitString
• at_position() : vg::PathIndex
• atomic_header : vg::HTSWriter
• attempt_rescue() : vg::MinimizerMapper , vg::MultipathMapper
• attempt_rescue_for_secondaries() : vg::MultipathMapper
• attempt_rescue_for_splice_segment() : vg::MultipathMapper
• attempt_unpaired_multipath_map_of_pair() : vg::MultipathMapper
• attributes : vg::GFFRecord
• aug : vg::ReadRestrictedTraversalFinder , vg::SupportRestrictedTraversalFinder
• augment_from_alignment_edits() : vg::AugmentedGraph
• augment_graph() : vg::Transcriptome
• augmented : vg::NestedTraversalFinder
• available() : vg::IndexRegistry
• available_short_options : vg::ConfigurableParser
• average_node_quality() : vg::Packer
• average_node_support_switch_threshold : vg::TraversalSupportFinder
• average_traversal_support_switch_threshold : vg::TraversalSupportFinder
• avg_node_length : vg::BaseMapper
• avg_node_mapq_cache : vg::CachedPackedTraversalSupportFinder
• avg_node_support_cache : vg::CachedPackedTraversalSupportFinder
• avg_qual_filter() : vg::Filter