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

- g -

• g_bv : xg::XG
• g_bv_rank : xg::XG
• g_bv_select : xg::XG
• g_iv : xg::XG
• G_NODE_HEADER_LENGTH : xg::XG
• G_NODE_ID_OFFSET : xg::XG
• G_NODE_LEFT_COUNT_OFFSET : xg::XG
• G_NODE_LENGTH_OFFSET : xg::XG
• G_NODE_RIGHT_COUNT_OFFSET : xg::XG
• G_NODE_SEQ_START_OFFSET : xg::XG
• GAF : vg::MultipathAlignmentEmitter
• gaf_output : vg::FlowCaller , vg::NestedFlowCaller , vg::VCFGenotyper
• gaf_sample_name : vg::GAFOutputCaller
• GafAlignmentEmitter() : vg::io::GafAlignmentEmitter
• GAFOutputCaller() : vg::GAFOutputCaller
• GafRecord() : gafkluge::GafRecord
• GAFSorterFile() : vg::GAFSorterFile
• GAFSorterRecord() : vg::GAFSorterRecord
• GAM : vg::MultipathAlignmentEmitter
• gam_format : GBWTConfig
• GAMP : vg::MultipathAlignmentEmitter
• gap_distance_limit : vg::ZipCodeForest::forest_growing_state_t
• gap_extend : ScoringOptions , vg::WFATree
• gap_extend_penalty() : vg::WFATree
• gap_extension : vg::DeletionAligner , vg::GSSWAligner , vg::SSWAligner
• gap_length : vg::WFAExtender::ErrorModel
• gap_memo_max_size : vg::MultipathMapper
• gap_open : ScoringOptions , vg::DeletionAligner , vg::GSSWAligner , vg::SSWAligner , vg::WFATree
• gap_penalty() : vg::WFATree
• gap_scale : vg::MinimizerMapper
• gapless_extension_limit : vg::MinimizerMapper
• GaplessExtender() : vg::GaplessExtender
• gaps : vg::WFAExtender::ErrorModel
• gbwt : vg::Deconstructor , vg::GBWTTraversalFinder
• gbwt_buffer_size : vg::HaplotypeIndexer
• gbwt_graph : GraphHandler , vg::MinimizerMapper , vg::PrimerFinder
• gbwt_index : vg::PhaseUnfolder , vg::PrimerFinder
• gbwt_insert_batch_size : vg::IndexingParameters
• gbwt_insert_batch_size_increase_factor : vg::IndexingParameters
• gbwt_name : GBWTConfig
• gbwt_node_offset : vg::FragmentedHaplotypeVisit
• GBWT_OFFSET_TAG : vg::GAFSorterRecord
• gbwt_output : GBWTConfig
• gbwt_reference_samples : vg::Deconstructor
• gbwt_sample_to_phase_range : vg::Deconstructor
• gbwt_sampling_interval : vg::IndexingParameters
• gbwt_thread_t() : haplo::gbwt_thread_t
• gbwt_trav_finder : vg::Deconstructor
• GBWTConfig() : GBWTConfig
• gbwtgraph_name : GBWTConfig
• GBWTScoreProvider() : haplo::GBWTScoreProvider< GBWTType >
• GBWTTraversalFinder() : vg::GBWTTraversalFinder
• gbz : vg::GBZGraph , vg::HaplotypePartitioner , vg::Recombinator
• gbz_format : GBWTConfig
• gbz_output : HaplotypesConfig
• gc_content_estimate : vg::AlignerClient
• gcsa : vg::BaseMapper
• gcsa_doubling_steps : vg::IndexingParameters
• gcsa_ind : vg::Filter
• gcsa_initial_kmer_length : vg::IndexingParameters
• gcsa_size_limit : vg::IndexingParameters
• gen_flat_node : haplo::haplo_DP_rectangle
• gen_range_t : haplo::haplo_DP_rectangle
• generalizations : vg::IndexRegistry
• generate() : vg::RecombinatorFragment
• generate_continuous_uniform() : vg::MCMCGenotyper
• generate_discrete_uniform() : vg::MCMCGenotyper
• generate_from_wide_generator() : vg::uniform_int_distribution< T >
• generate_haplotypes() : vg::Recombinator
• generate_initial_guess() : vg::MCMCGenotyper
• generate_paths() : vg::PhaseUnfolder
• generate_threads() : vg::PhaseUnfolder
• genome : vg::MCMCCaller
• GenomeState() : vg::GenomeState
• genotype : vg::Locus , vg::PoissonSupportSnarlCaller , vg::RatioSupportSnarlCaller , vg::SnarlCaller
• genotype_by_ploidy : vg::NestedFlowCaller::CallRecord
• genotype_likelihood() : vg::PoissonSupportSnarlCaller
• genotype_snarl() : vg::Genotyper
• genotype_snarls : vg::FlowCaller , vg::NestedFlowCaller
• get() : vg::Annotation< T, Enabled > , vg::GBZGraph , vg::subcommand::Subcommand , vg::VcfBuffer , vg::WindowedVcfBuffer
• get_adaptive_min_reseed_length() : vg::BaseMapper
• get_affinities() : vg::Genotyper
• get_affinities_fast() : vg::Genotyper
• get_aligner() : vg::AlignerClient
• get_alignment_start() : vg::BandedGlobalAligner< IntType >::AltTracebackStack
• get_alignments() : vg::AugmentedGraph
• get_allele() : vg::PhasedGenome
• get_alleles() : vg::Deconstructor
• get_alt_path() : vg::VCFTraversalFinder
• get_alt_traversal() : vg::VCFTraversalFinder
• get_annotation() : vg::multipath_alignment_t
• get_any_graph() : GraphHandler
• get_average_traversal_support_switch_threshold() : vg::TraversalSupportFinder
• get_avg_node_mapq() : vg::CachedPackedTraversalSupportFinder , vg::PackedTraversalSupportFinder , vg::TraversalSupportFinder
• get_avg_node_support() : vg::CachedPackedTraversalSupportFinder , vg::PackedTraversalSupportFinder , vg::TraversalSupportFinder
• get_back_graph_node_name() : handlegraph::NamedNodeBackTranslation , vg::algorithms::GFAIDMapInfo , vg::FlatFileBackTranslation
• get_base() : handlegraph::HandleGraph , vg::IncrementalSubgraph , vg::JoinedSpliceGraph , vg::VG , xg::XG
• get_base_gbwt_path_name() : vg::Transcriptome
• get_best_alignment_against_any_tree() : vg::MinimizerMapper
• get_best_chain_stats() : vg::MinimizerMapper
• get_best_support() : vg::SupportBasedSnarlCaller
• get_bias() : vg::RatioSupportSnarlCaller
• get_bin_size() : vg::Packer
• get_bound() : handlegraph::SnarlDecomposition
• get_bounds() : vg::Constructor
• get_buckets() : vg::OrientedDistanceMeasurer , vg::PathOrientedDistanceMeasurer , vg::SnarlOrientedDistanceMeasurer
• get_category() : vg::subcommand::Subcommand
• get_cc_in_wg() : vg::FlowSort
• get_center() : vg::VariantAdder
• get_center_and_radius() : vg::VariantAdder
• get_chain_code() : vg::ZipCode
• get_chain_component() : vg::ZipCode , vg::ZipCode::node_code_t , vg::ZipCode::snarl_code_t , vg::ZipCodeForest::sort_value_t
• get_child_count() : vg::ZipCode::snarl_code_t
• get_child_support() : vg::NestedCachedPackedTraversalSupportFinder , vg::TraversalSupportFinder
• get_clipped_position() : vg::Filter
• get_clipped_ref_position() : vg::Filter
• get_clipped_seq() : vg::Filter
• get_cluster_pairs() : vg::MultipathMapper
• get_clusters() : vg::MultipathMapper
• get_code_type() : vg::ZipCode , vg::ZipCode::snarl_code_t , vg::ZipCodeForest::sort_value_t
• get_codename() : vg::Version
• get_connected_components() : vg::MultipathAlignmentGraph
• get_connectivity() : vg::ZipCode::chain_code_t
• get_contained_orientations() : vg::PathIndex
• get_context() : vg::Deconstructor
• get_correlation() : vg::ZipCodeForest
• get_count() : vg::NoAlignmentInBandException
• get_create_path() : vg::Paths
• get_created_handle() : vg::ExtraNodeGraph
• get_current_column() : haplo::haplo_DP
• get_cut_segments() : vg::MultipathAlignmentGraph
• get_cyclic_snarl_intervals() : vg::ZipCodeForest
• get_default_long_giraffe_indexes() : vg::VGIndexes
• get_default_map_indexes() : vg::VGIndexes
• get_default_mpmap_indexes() : vg::VGIndexes
• get_default_rpvg_indexes() : vg::VGIndexes
• get_default_short_giraffe_indexes() : vg::VGIndexes
• get_default_value() : vg::BaseOption< Value, Parser > , vg::OptionInterface
• get_degree() : handlegraph::HandleGraph , vg::ExtraNodeGraph , vg::IncrementalSubgraph , vg::SourceSinkOverlay , vg::VG
• get_description() : vg::BaseOption< Value, Parser > , vg::OptionInterface , vg::subcommand::Subcommand
• get_diagonals() : vg::WFATree
• get_disjoint_sets() : vg::ContractingGraph
• get_distance() : vg::HaplotypePartitioner
• get_distance_end_left() : vg::ZipCode::snarl_code_t
• get_distance_end_right() : vg::ZipCode::snarl_code_t
• get_distance_index_address() : vg::ZipCode
• get_distance_limit() : vg::MinimizerMapper
• get_distance_measurer() : vg::MultipathMapper
• get_distance_start_left() : vg::ZipCode::snarl_code_t
• get_distance_start_right() : vg::ZipCode::snarl_code_t
• get_distance_to_snarl_bound() : vg::ZipCode
• get_distance_value() : vg::ZipCodeForest::sort_value_t
• get_duplicate_handle() : vg::DozeuPinningOverlay
• get_edge() : vg::VG
• get_edge_count() : handlegraph::HandleGraph , vg::IncrementalSubgraph , vg::VG , xg::XG
• get_edge_length() : vg::TraversalSupportFinder
• get_edge_support() : vg::CachedPackedTraversalSupportFinder , vg::PackedTraversalSupportFinder , vg::RepresentativeTraversalFinder , vg::TraversalSupportFinder
• get_edges() : vg::ContractingGraph
• get_end() : vg::NetGraph
• get_end_bound() : handlegraph::SnarlDecomposition
• get_end_matches() : vg::ReadFilter< Read >
• get_endpoints() : vg::GraphSynchronizer::Lock
• get_exon_haplotypes() : vg::Transcriptome
• get_features() : vg::FeatureSet
• get_field() : vg::GAFSorterRecord
• get_filenames() : vg::IndexFile
• get_first_node_handle() : vg::CompletedTranscriptPath , vg::EditedTranscriptPath
• get_fragment_length_mean() : vg::MinimizerMapper
• get_fragment_length_sample_size() : vg::MinimizerMapper
• get_fragment_length_stdev() : vg::MinimizerMapper
• get_g_iv_size() : xg::XG
• get_gbwt() : vg::GBWTTraversalFinder
• get_genotype_log_likelihood() : vg::Genotyper
• get_genotype_log_prior() : vg::Genotyper
• get_genotypes() : vg::Deconstructor
• get_graph() : GraphHandler , vg::Packer , vg::VariantAdder
• get_graph_coordinates_from_sequence() : vg::PrimerFinder
• get_handle() : handlegraph::algorithms::SubHandleGraph , handlegraph::HandleGraph , handlegraph::SnarlDecomposition , vg::DagifiedGraph , vg::DozeuPinningOverlay , vg::ExtraNodeGraph , vg::GaplessExtender , vg::IdentityOverlay , vg::IncrementalSubgraph , vg::IndexedVG , vg::JoinedSpliceGraph , vg::MemoizingGraph , vg::NetGraph , vg::NullMaskingGraph , vg::PathSubgraph , vg::ReverseGraph , vg::SnarlGraph , vg::SourceSinkOverlay , vg::StrandSplitGraph , vg::SubgraphOverlay , vg::SubHandleGraph , vg::SubpathOverlay , vg::TreeSubgraph , vg::VG , xg::XG
• get_handle_from_inward_backing_handle() : vg::NetGraph
• get_handle_memo : vg::MemoizingGraph
• get_handle_of_step() : handlegraph::PathHandleGraph , vg::MemoizingGraph , vg::PathSubgraphOverlay , vg::VG , xg::XG
• get_haplotype() : handlegraph::PathMetadata
• get_haplotype_alt_contents() : vg::VCFTraversalFinder
• get_haplotype_count() : haplo::GBWTScoreProvider< GBWTType > , haplo::ScoreProvider
• get_haplotypes_with_snarl() : vg::PhasedGenome
• get_help() : vg::subcommand::BaseOptionGroup , vg::subcommand::GroupedOptionGroup , vg::subcommand::OptionGroup< Receiver >
• get_id() : handlegraph::algorithms::SubHandleGraph , handlegraph::HandleGraph , vg::DagifiedGraph , vg::DozeuPinningOverlay , vg::ExtraNodeGraph , vg::IdentityOverlay , vg::IncrementalSubgraph , vg::IndexedVG , vg::JoinedSpliceGraph , vg::MemoizingGraph , vg::NetGraph , vg::NullMaskingGraph , vg::PathSubgraph , vg::ReverseGraph , vg::SnarlGraph , vg::SourceSinkOverlay , vg::StrandSplitGraph , vg::SubgraphOverlay , vg::SubHandleGraph , vg::SubpathOverlay , vg::TreeSubgraph , vg::VG , xg::XG
• get_identifier() : vg::IndexFile , vg::ZipCode
• get_index() : vg::IndexRegistry , vg::RepresentativeTraversalFinder
• get_indexes() : vg::RewindPlanException
• get_inward_backing_handle() : vg::NetGraph
• get_irregular_snarl_code() : vg::ZipCode
• get_is_circular() : handlegraph::PathHandleGraph , vg::MemoizingGraph , vg::PathSubgraphOverlay , vg::VG , xg::XG
• get_is_looping_chain() : vg::ZipCode::chain_code_t , vg::ZipCode
• get_is_paired() : vg::ReadFilter< Read >
• get_is_reverse() : handlegraph::algorithms::SubHandleGraph , handlegraph::HandleGraph , vg::DagifiedGraph , vg::DozeuPinningOverlay , vg::ExtraNodeGraph , vg::IdentityOverlay , vg::IncrementalSubgraph , vg::IndexedVG , vg::JoinedSpliceGraph , vg::MemoizingGraph , vg::NetGraph , vg::NullMaskingGraph , vg::PathSubgraph , vg::ReverseGraph , vg::SnarlGraph , vg::SourceSinkOverlay , vg::StrandSplitGraph , vg::SubgraphOverlay , vg::SubHandleGraph , vg::SubpathOverlay , vg::TreeSubgraph , vg::VG , xg::XG
• get_is_reversed() : vg::ZipCode::node_code_t , vg::ZipCode::snarl_code_t , vg::ZipCodeTree::tree_item_t
• get_is_reversed_in_parent() : vg::ZipCode
• get_item() : vg::Funnel
• get_item_at_index() : vg::ZipCodeTree
• get_iterator() : vg::subcommand::TickChainLink
• get_last_chain_component() : vg::ZipCode
• get_last_component() : vg::ZipCode::chain_code_t
• get_leaves() : vg::WFATree
• get_length() : handlegraph::algorithms::SubHandleGraph , handlegraph::HandleGraph , vg::DagifiedGraph , vg::DozeuPinningOverlay , vg::ExtraNodeGraph , vg::IdentityOverlay , vg::IncrementalSubgraph , vg::IndexedVG , vg::JoinedSpliceGraph , vg::MemoizingGraph , vg::NetGraph , vg::NullMaskingGraph , vg::PathSubgraph , vg::ReadFilter< Read > , vg::ReverseGraph , vg::SnarlGraph , vg::SourceSinkOverlay , vg::StrandSplitGraph , vg::SubgraphOverlay , vg::SubHandleGraph , vg::SubpathOverlay , vg::TreeSubgraph , vg::VG , vg::ZipCode::chain_code_t , vg::ZipCode , vg::ZipCode::node_code_t , vg::ZipCode::snarl_code_t , xg::XG
• get_locus_name() : handlegraph::PathMetadata
• get_log10_prob_of_disruption_in_interval() : vg::MinimizerMapper
• get_long() : vg::Version
• get_long_option() : vg::BaseOption< Value, Parser > , vg::OptionInterface
• get_magic_number() : handlegraph::Serializable , vg::ZipCodeCollection , xg::XG
• get_magic_number_as_string() : vg::ZipCodeCollection
• get_main() : vg::subcommand::Subcommand
• get_mapping() : vg::PhaseUnfolder
• get_mapq() : vg::ReadFilter< Read >
• get_min_base_qual_fraction() : vg::ReadFilter< Read >
• get_min_node_support() : vg::CachedPackedTraversalSupportFinder , vg::PackedTraversalSupportFinder , vg::TraversalSupportFinder
• get_min_position() : vg::StreamSorter< Message >
• get_min_total_support_for_call() : vg::SupportBasedSnarlCaller
• get_mutable() : vg::Annotation< T, Enabled >
• get_n_bins() : vg::Packer
• get_name() : vg::Configurable , vg::subcommand::Subcommand , vg::TranscriptPath
• get_net() : handlegraph::SnarlDecomposition
• get_net_graph() : vg::GenomeState
• get_net_handle() : vg::ZipCode
• get_net_handle_slow() : vg::ZipCode
• get_next_intervals() : vg::ZipCodeForest
• get_next_node_recalc_degrees() : vg::FlowSort
• get_next_rank() : vg::Paths
• get_next_step() : handlegraph::PathHandleGraph , vg::MemoizingGraph , vg::PathSubgraphOverlay , vg::VG , xg::XG
• get_node() : vg::VG
• get_node_at_nucleotide() : vg::VG
• get_node_by_id() : vg::algorithms::Graph
• get_node_code() : vg::ZipCode
• get_node_count() : handlegraph::algorithms::SubHandleGraph , handlegraph::HandleGraph , vg::DagifiedGraph , vg::DozeuPinningOverlay , vg::ExtraNodeGraph , vg::IdentityOverlay , vg::IncrementalSubgraph , vg::IndexedVG , vg::JoinedSpliceGraph , vg::MemoizingGraph , vg::NetGraph , vg::NullMaskingGraph , vg::PathSubgraph , vg::ReverseGraph , vg::SnarlGraph , vg::SourceSinkOverlay , vg::StrandSplitGraph , vg::SubgraphOverlay , vg::SubHandleGraph , vg::SubpathOverlay , vg::TreeSubgraph , vg::VG , xg::XG
• get_node_degree() : vg::FlowSort
• get_node_ids() : vg::algorithms::Graph
• get_node_length() : vg::Mapper
• get_node_mapping() : vg::Paths
• get_node_mapping_by_path_name() : vg::Paths
• get_node_mapping_copies_by_rank() : vg::Paths
• get_node_mappings_by_rank() : vg::Paths
• get_node_nid_to_variant() : vg::VG
• get_node_offset() : vg::GaplessExtender
• get_node_support : vg::RepresentativeTraversalFinder
• get_nodes() : vg::ContractingGraph , vg::SnarlDistanceIndexClusterer
• get_nonoverlapping() : vg::WindowedVcfBuffer
• get_offset_in_chain() : vg::ZipCode
• get_on_strand_distance_tree() : vg::OrientedDistanceClusterer
• get_option_struct() : vg::subcommand::BaseArgSpec< Receiver > , vg::subcommand::FlagArgSpec< Receiver > , vg::subcommand::ValueArgSpec< T, Receiver, Holder >
• get_option_value() : vg::subcommand::BaseOptionGroup
• get_options() : vg::Configurable
• get_overhang() : vg::ReadFilter< Read >
• get_overlay_handle() : vg::StrandSplitGraph
• get_parent() : handlegraph::SnarlDecomposition
• get_parent_identifier() : vg::ZipCode
• get_parent_traversal() : handlegraph::SnarlDecomposition
• get_parsed_genotypes() : vg::WindowedVcfBuffer
• get_path() : vg::Paths , xg::XG
• get_path_count() : handlegraph::PathHandleGraph , vg::MemoizingGraph , vg::PathSubgraphOverlay , vg::VG , xg::XG
• get_path_edge_index() : vg::PathChunker
• get_path_edges() : vg::VG
• get_path_handle() : handlegraph::PathHandleGraph , vg::MemoizingGraph , vg::PathSubgraphOverlay , vg::VG , xg::XG
• get_path_handle_of_step() : handlegraph::PathHandleGraph , handlegraph::PathMetadata , vg::MemoizingGraph , vg::PathSubgraphOverlay , vg::VG , xg::XG
• get_path_id() : vg::Paths
• get_path_index() : vg::GraphSynchronizer
• get_path_length() : handlegraph::PathPositionHandleGraph , vg::MemoizingGraph , xg::XG
• get_path_name() : handlegraph::PathHandleGraph , handlegraph::PathMetadata , vg::MemoizingGraph , vg::Paths , vg::PathSubgraphOverlay , vg::VG , xg::XG
• get_path_sequence() : vg::GraphSynchronizer
• get_payload_from_zip() : vg::ZipCode
• get_payload_from_zipcode() : vg::ZipCode
• get_peripheral_attachments() : vg::GraphSynchronizer::Lock
• get_phase_block() : handlegraph::PathMetadata
• get_pos() : vg::GaplessExtender
• get_position_of_step() : handlegraph::PathPositionHandleGraph , vg::MemoizingGraph , xg::XG
• get_positions() : vg::Funnel
• get_possible_filenames() : vg::IndexRegistry
• get_prefix() : vg::IndexRegistry , vg::PhaseUnfolder
• get_prefix_sum_or_identifier() : vg::ZipCode::node_code_t , vg::ZipCode::snarl_code_t
• get_previous_step() : handlegraph::PathHandleGraph , vg::MemoizingGraph , vg::PathSubgraphOverlay , vg::VG , xg::XG
• get_primer_pairs_of_chrom() : vg::PrimerFinder
• get_priority() : vg::subcommand::Subcommand
• get_prob_of_disruption_in_column() : vg::MinimizerMapper
• get_protobuf_tag() : vg::io::Registry
• get_pruned_alt_alleles() : vg::VCFTraversalFinder
• get_qual_adj_aligner() : vg::AlignerClient
• get_qualities_in_snarl() : vg::Genotyper
• get_radius() : vg::VariantAdder
• get_rank_in_snarl() : vg::ZipCode
• get_raw_chain_component() : vg::ZipCode::node_code_t , vg::ZipCode::snarl_code_t
• get_raw_child_count() : vg::ZipCode::snarl_code_t
• get_raw_code_type() : vg::ZipCode::snarl_code_t
• get_raw_connectivity() : vg::ZipCode::chain_code_t
• get_raw_distance_end_left() : vg::ZipCode::snarl_code_t
• get_raw_distance_end_right() : vg::ZipCode::snarl_code_t
• get_raw_distance_start_left() : vg::ZipCode::snarl_code_t
• get_raw_distance_start_right() : vg::ZipCode::snarl_code_t
• get_raw_is_reversed() : vg::ZipCode::node_code_t , vg::ZipCode::snarl_code_t
• get_raw_last_component() : vg::ZipCode::chain_code_t
• get_raw_length() : vg::ZipCode::chain_code_t , vg::ZipCode::node_code_t , vg::ZipCode::snarl_code_t
• get_raw_prefix_sum_or_identifier() : vg::ZipCode::node_code_t , vg::ZipCode::snarl_code_t
• get_raw_record_offset() : vg::ZipCode::snarl_code_t
• get_raw_snarl_rank_or_identifier() : vg::ZipCode::chain_code_t
• get_read_coverage() : vg::MinimizerMapper
• get_read_fn() : vg::io::JSONStreamHelper< T >
• get_read_name() : vg::NGSSimulator
• get_read_offset() : vg::GaplessExtender
• get_recipe() : vg::IndexRegistry
• get_record_offset() : vg::ZipCode::snarl_code_t
• get_ref_following() : haplo::linear_haplo_structure
• get_ref_interval() : vg::VCFOutputCaller
• get_ref_offsets() : vg::RatioSupportSnarlCaller , vg::TraversalSupportFinder
• get_ref_position() : vg::MCMCCaller , vg::VCFOutputCaller
• get_ref_positions() : vg::VCFGenotyper
• get_reference_paths() : vg::PrimerFinder
• get_reference_traversal() : vg::LegacyCaller
• get_registry() : vg::subcommand::Subcommand
• get_regular_aligner() : vg::AlignerClient
• get_regular_snarl_code() : vg::ZipCode
• get_release() : vg::Version
• get_rescue_graph_from_paths : vg::MultipathMapper
• get_resolver() : vg::io::Registry
• get_root() : handlegraph::SnarlDecomposition , vg::TreeSubgraph
• get_rr_memo() : vg::MultipathMapper
• get_sample_name() : handlegraph::PathMetadata
• get_score() : vg::ReadFilter< Read > , vg::Surjector
• get_scores() : haplo::haplo_DP_column
• get_seed : vg::LazyRNG
• get_seed_pos() : vg::SpliceRegion
• get_sense() : handlegraph::PathMetadata
• get_sequence() : handlegraph::algorithms::SubHandleGraph , handlegraph::HandleGraph , vg::DagifiedGraph , vg::DozeuPinningOverlay , vg::ExtraNodeGraph , vg::Haplotypes::Subchain , vg::IdentityOverlay , vg::IncrementalSubgraph , vg::IndexedVG , vg::JoinedSpliceGraph , vg::MemoizingGraph , vg::NetGraph , vg::NullMaskingGraph , vg::PathSubgraph , vg::ReverseGraph , vg::SnarlGraph , vg::SourceSinkOverlay , vg::StrandSplitGraph , vg::SubgraphOverlay , vg::SubHandleGraph , vg::SubpathOverlay , vg::TreeSubgraph , vg::VG , xg::XG
• get_sequences() : vg::HaplotypePartitioner
• get_short() : vg::Version
• get_short_options() : vg::BaseOption< Value, Parser > , vg::OptionInterface
• get_sink_handle() : vg::SourceSinkOverlay
• get_size() : vg::algorithms::Graph
• get_sizes() : haplo::haplo_DP_column
• get_skip_allele_fn() : vg::SnarlCaller , vg::SupportBasedSnarlCaller
• get_snarl_child_count() : vg::ZipCode
• get_snarl_rank_or_identifier() : vg::ZipCode::chain_code_t
• get_snarl_reference_bounds() : vg::Genotyper
• get_snarl_traversals() : vg::Genotyper
• get_SNP_ref_position() : haplo::linear_haplo_structure
• get_SNV_allele() : haplo::linear_haplo_structure
• get_sort_value() : vg::ZipCodeForest::sort_value_t
• get_source_handle() : vg::SourceSinkOverlay
• get_spanning_haplotypes() : vg::GBWTTraversalFinder
• get_start() : vg::NetGraph
• get_start_bound() : handlegraph::SnarlDecomposition
• get_step_at_position() : handlegraph::PathPositionHandleGraph , vg::MemoizingGraph , xg::XG
• get_step_count() : handlegraph::PathHandleGraph , vg::MemoizingGraph , vg::PathSubgraphOverlay , vg::VG , xg::XG
• get_steps() : vg::IndexingPlan
• get_subchains() : vg::HaplotypePartitioner
• get_subgraph() : vg::GraphSynchronizer::Lock , vg::SpliceRegion
• get_subrange() : handlegraph::PathMetadata
• get_subsequence() : handlegraph::HandleGraph , vg::IncrementalSubgraph , vg::JoinedSpliceGraph , vg::VG , xg::XG
• get_suffix() : vg::IndexFile , vg::PhaseUnfolder
• get_support() : vg::AugmentedGraph , vg::SupportAugmentedGraph
• get_support_finder() : vg::SupportBasedSnarlCaller
• get_symbolic_bounds() : vg::Constructor
• get_system_memory() : vg::IndexRegistry
• get_tables() : vg::io::Registry
• get_tail_forest() : vg::MinimizerMapper
• get_target_memory_usage() : vg::IndexRegistry
• get_thread_stream() : vg::io::StreamMultiplexer
• get_top_level_chain_offset() : vg::ZipCode
• get_topological_order() : vg::PathSubgraph , vg::TreeSubgraph
• get_total_length() : handlegraph::HandleGraph , xg::XG
• get_translation() : vg::Translator
• get_traversal_genotype_support() : vg::TraversalSupportFinder
• get_traversal_mapqs() : vg::TraversalSupportFinder
• get_traversal_set_support() : vg::TraversalSupportFinder
• get_traversal_sizes() : vg::TraversalSupportFinder
• get_traversal_support() : vg::TraversalSupportFinder
• get_traversals() : vg::Deconstructor
• get_tree_size() : vg::ZipCodeTree
• get_type() : haplo::linear_haplo_structure , vg::ZipCodeTree::tree_item_t
• get_underlying_handle() : handlegraph::algorithms::SubHandleGraph , handlegraph::ExpandingOverlayGraph , vg::DagifiedGraph , vg::DozeuPinningOverlay , vg::IdentityOverlay , vg::IncrementalSubgraph , vg::NullMaskingGraph , vg::PathSubgraph , vg::ReverseGraph , vg::SourceSinkOverlay , vg::StrandSplitGraph , vg::SubHandleGraph , vg::SubpathOverlay , vg::TreeSubgraph
• get_underlying_id() : vg::DagifiedGraph , vg::DozeuPinningOverlay
• get_unique_haplotypes() : vg::VariantAdder
• get_value() : vg::subcommand::ArgSpec< T, Receiver > , vg::subcommand::ValueArgSpec< T, Receiver, Holder > , vg::ZipCodeTree::tree_item_t
• get_value_and_next_index() : vg::varint_vector_t
• get_variants_in_site() : vg::VCFTraversalFinder
• get_vcf_header() : vg::Deconstructor
• get_version() : vg::Version
• get_vg_index_registry() : vg::VGIndexes
• get_weight_using_other() : vg::algorithms::Graph
• get_work_dir() : vg::IndexRegistry
• gfa_has_haplotypes() : vg::IndexRegistry
• gfa_id_space : vg::GFAHandleGraph
• gfa_parameters : GBWTConfig
• GFADuplicatePathError() : vg::algorithms::GFADuplicatePathError
• GFAFormatError() : vg::algorithms::GFAFormatError
• GFAHandleGraph() : vg::GFAHandleGraph
• gff_feature_name : vg::IndexingParameters
• gff_transcript_tag : vg::IndexingParameters
• GFFReader() : vg::GFFReader
• GFFRecord() : vg::GFFRecord
• giraffe_gbwt_downsample : vg::IndexingParameters
• giraffe_mapper : vg::PrimerFinder
• globals : vg::DiagramExplainer
• go_left : vg::ChainIterator
• gq : vg::PoissonSupportSnarlCaller::PoissonCallInfo
• grandparent_net_handle : vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem
• graph : handlegraph::PathForEachSocket , handlegraph::PathForEachSocket::iterator , haplo::hDP_gbwt_graph_accessor< GBWTType > , haplo::linear_haplo_structure , vg::AbstractReadSampler , vg::AliasGraph , vg::AugmentedGraph , vg::BandedGlobalAligner< IntType >::AltTracebackStack , vg::BandedGlobalAligner< IntType > , vg::CactusSnarlFinder , vg::ConstructedChunk , vg::ContractingGraph , vg::DagifiedGraph , vg::Deconstructor , vg::DozeuInterface::OrderedGraph , vg::DozeuPinningOverlay , vg::ExhaustiveTraversalFinder , vg::FlowCaller , vg::FlowTraversalFinder , vg::GaplessExtender , vg::GBWTTraversalFinder , vg::GraphSynchronizer , vg::HandleGraphNodeSet , vg::HandleGraphSnarlFinder , vg::IdentityOverlay , vg::IncrementalSubgraph , vg::IntegratedSnarlFinder::MergedAdjacencyGraph , vg::io::GafAlignmentEmitter , vg::LegacyCaller , vg::Masker , vg::MCMCGenotyper , vg::MemoizingGraph , vg::MultipathAlignmentEmitter , vg::NestedFlowCaller , vg::NetGraph , vg::NullMaskingGraph , vg::Packer , vg::PathBasedTraversalFinder , vg::PathChunker , vg::PathOrientedDistanceMeasurer , vg::PathRestrictedTraversalFinder , vg::PathTraversalFinder , vg::PrimerFinder , vg::RareVariantSimplifier , vg::ReadFilter< Read > , vg::RegionExpander , vg::RepresentativeTraversalFinder , vg::SmallSnarlSimplifier , vg::SnarlDistanceIndexClusterer , vg::SnarlState , vg::SplicedHTSAlignmentEmitter , vg::StrandSplitGraph , vg::SupportBasedSnarlCaller , vg::Surjector , vg::Transcriptome , vg::TraversalSupportFinder , vg::TrivialTraversalFinder , vg::VariantAdder , vg::VCFGenotyper , vg::VCFTraversalFinder , vg::VG , vg::VG::Plan , vg::WFAExtender , vg::WFATree
• graph_cigar() : vg::GSSWAligner
• graph_end() : vg::algorithms::Anchor
• graph_gbwtgraph : GraphHandler
• graph_gbz : GraphHandler
• graph_mixed_distance_estimate() : vg::Mapper
• graph_name : GBWTConfig , HaplotypesConfig
• graph_none : GraphHandler
• graph_output : GBWTConfig
• graph_path : GraphHandler
• graph_pos_at_path_position() : xg::XG
• graph_source : GraphHandler
• graph_start() : vg::algorithms::Anchor
• graph_type : GraphHandler
• GraphCaller() : vg::GraphCaller
• GraphSynchronizer() : vg::GraphSynchronizer
• greedy_min_dist : vg::MultipathMapper
• greedy_pieces : vg::Constructor
• greedy_restart_assume_substitution : vg::BaseMapper
• greedy_restart_max_count : vg::BaseMapper
• greedy_restart_max_lcp : vg::BaseMapper
• greedy_restart_min_length : vg::BaseMapper
• GreedyMinDistanceClusterer() : vg::GreedyMinDistanceClusterer
• groom_components() : vg::FlowSort
• group : vg::io::MessageEmitter , vg::SparseUnionFind
• group_cache : vg::IndexedVG
• group_count : vg::io::MessageIterator
• group_handlers : vg::io::MessageEmitter , vg::io::ProtobufEmitter< T >
• group_idx : vg::io::MessageIterator
• group_listener_t : vg::io::MessageEmitter , vg::io::ProtobufEmitter< T >
• group_mapping_quality_exact() : vg::GSSWAligner
• group_size : vg::Funnel::Item , vg::SparseUnionFind
• group_tag : vg::io::MessageEmitter
• group_vo : vg::io::MessageIterator
• GroupedOptionGroup() : vg::subcommand::GroupedOptionGroup
• Growth() : vg::FlowSort::Growth
• gssw_mapping_to_alignment() : vg::GSSWAligner
• GSSWAligner() : vg::GSSWAligner