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::IntervalUnion, 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_close_bound() : vg::ZipCodeTree
add_connection() : vg::subpath_t
add_contigs_to_vcf_header() : vg::Deconstructor
add_decomposed_tail_alignments() : vg::MultipathAlignmentGraph
add_distance_matrix() : vg::ZipCodeForest
add_edge() : vg::DiagramExplainer, vg::MEMClusterer::HitGraph, vg::VG
add_edges() : vg::VG
add_edges_for_chains() : vg::ZipCodeForest
add_edges_to_end() : vg::ZipCodeForest
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() : vg::SubHandleGraph
add_haplotype() : vg::PhasedGenome
add_haplotype_transcripts() : vg::Transcriptome
add_interval() : vg::GrefCover
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::Graph, vg::VG
add_nodes() : vg::VG
add_one_byte() : vg::varint_vector_t
add_option() : vg::subcommand::OptionGroup< Receiver >
add_path() : vg::algorithms::Anchor
add_paths() : vg::algorithms::Anchor
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_SA_tag() : vg::Surjector
add_SA_tag_internal() : vg::Surjector
add_scope() : vg::IndexFile, vg::IndexingPlan
add_seed_to_chain_problem() : vg::SnarlDistanceIndexClusterer
add_snarl() : vg::SnarlManager
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
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::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::BandedGlobalAligner< IntType >, vg::BandedGlobalAligner< IntType >::BABuilder, vg::BandedGlobalAligner< IntType >::BAMatrix, vg::MinimizerMapper::alignment_index_t, vg::MinimizerMapper::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::AlignmentScorer
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::MappingQualityCalculator
all_node_problems : vg::SnarlDistanceIndexClusterer::ClusteringProblem
all_path_names() : vg::Paths
all_seeds : vg::SnarlDistanceIndexClusterer::ClusteringProblem
all_snarls : vg::Genotyper
allele_core_length() : vg::VCFOutputCaller
allele_length_range : vg::FlowCaller
allele_merge_min_len : vg::VCFOutputCaller
allele_merge_threshold : vg::VCFOutputCaller
alleles : vg::VG::Plan
allow_duplicates : vg::PathRestrictedTraversalFinder
allowed_vcf_names : vg::Constructor
allowed_vcf_regions : vg::Constructor
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
anchor_end_paths() : vg::algorithms::Anchor
anchor_paths() : vg::algorithms::Anchor
anchor_start_paths() : vg::algorithms::Anchor
anno_type_t : vg::multipath_alignment_t
anno_type_tag() : vg::multipath_alignment_t
annotate_graph_cigar() : vg::Surjector
annotate_mapped_alignment() : vg::Funnel
annotate_off_reference_pos : vg::Surjector
annotate_with_all_path_scores : vg::Surjector
annotate_with_graph_alignment : vg::Surjector
annotate_with_minimizer_statistics() : vg::MinimizerMapper
annotate_with_path_positions() : vg::AbstractReadSampler
annotation : vg::Counts
annotation_path_filter : vg::AbstractReadSampler
annotation_t : vg::DiagramExplainer
annotation_to_match : vg::ReadFilter< Read >
append() : vg::Paths, vg::VG, vg::WFAAlignment
append_left() : vg::PhasedGenome::Haplotype
append_mapping() : vg::Paths
append_node() : vg::WFANode
append_right() : vg::PhasedGenome::Haplotype
append_step() : vg::VG
apply() : vg::GrefCover, vg::subcommand::BaseArgSpec< Receiver >, vg::subcommand::GroupedOptionGroup, vg::subcommand::NegationFlagArgSpec< Receiver >, 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() : vg::VG
apply_orientation() : 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
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_chars() : vg::algorithms::GFAParser
as_edge_table() : vg::Packer
as_gbwt_path() : vg::GAFSorterRecord
as_quality_table() : vg::Packer
as_table() : vg::Packer, vg::Packers
assign_constructed() : vg::IndexFile
assign_nesting() : vg::GrefCover
assign_new_sequence_id() : vg::algorithms::GFAParser
assign_reference_paths() : vg::Haplotypes
assign_top_level_snarls() : vg::GrefCover
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
attach_option() : vg::subcommand::OptionGroup< Receiver >
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
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