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

- g -

GAF : vg::MultipathAlignmentEmitter
gaf_output : vg::FlowCaller, vg::NestedFlowCaller, vg::VCFGenotyper
gaf_sample_name : vg::GAFOutputCaller
GAFOutputCaller() : vg::GAFOutputCaller
GAFSorterFile() : vg::GAFSorterFile
GAFSorterRecord() : vg::GAFSorterRecord
GAM : vg::MultipathAlignmentEmitter
gam_format : GBWTConfig
GAMP : vg::MultipathAlignmentEmitter
gap_extend : ScoringOptions, vg::WFATree
gap_extend_penalty() : vg::WFATree
gap_extension : vg::DeletionAligner, vg::EditAlignmentScorer, vg::SSWAligner
gap_length : vg::WFAExtender::ErrorModel
gap_lengths : vg::LoggedGapAlignmentScorer
gap_memo_max_size : vg::MultipathMapper
gap_open : ScoringOptions, vg::DeletionAligner, vg::EditAlignmentScorer, vg::SSWAligner, vg::WFATree
gap_penalty() : vg::WFATree
gap_scale : vg::algorithms::ChainScoringScheme, 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_file : vg::GAFSorterFile, vg::GAFSorterParameters
gbwt_graph : 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_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_graph : GraphHandler
gbz_output : HaplotypesConfig
gbz_version : GBWTConfig
gc_content_estimate : vg::AlignerClient
gcsa : vg::BaseMapper
gcsa_doubling_steps : vg::IndexingParameters
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_hard_clipped_alignments() : vg::Surjector
generate_initial_guess() : vg::MCMCGenotyper
generate_paths() : vg::PhaseUnfolder
generate_threads() : vg::PhaseUnfolder
genome : vg::MCMCCaller
genotype() : 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_all_seeds() : vg::ZipCodeTree
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() : vg::algorithms::GFAIDMapInfo, vg::FlatFileBackTranslation
get_base() : vg::IncrementalSubgraph, vg::JoinedSpliceGraph, vg::VG
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_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_child_sort_info() : vg::ZipCodeForest
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_chain_numbers() : vg::ZipCodeTree::seed_iterator
get_child_count() : vg::ZipCode::snarl_code_t
get_child_support() : vg::NestedCachedPackedTraversalSupportFinder, vg::TraversalSupportFinder
get_cigar() : vg::Surjector
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_compressed() : vg::GBWTHandler
get_connected_components() : vg::MultipathAlignmentGraph
get_connectivity() : vg::ZipCode::chain_code_t
get_contained_orientations() : vg::PathIndex
get_context() : vg::Deconstructor
get_count() : vg::NoAlignmentInBandException
get_create_path() : vg::Paths
get_current_column() : haplo::haplo_DP
get_cut_segments() : vg::MultipathAlignmentGraph
get_cyclic_snarl_bound_distance() : vg::ZipCodeTree::distance_iterator
get_default_haplotype_sampling_indexes() : vg::VGIndexes
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() : 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() : vg::IncrementalSubgraph, vg::VG
get_edge_length() : vg::TraversalSupportFinder
get_edge_seeds() : vg::ZipCodeForest
get_edge_support() : vg::CachedPackedTraversalSupportFinder, vg::PackedTraversalSupportFinder, vg::RepresentativeTraversalFinder, vg::TraversalSupportFinder
get_edges() : vg::ContractingGraph
get_end() : vg::NetGraph
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_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() : vg::DagifiedGraph, vg::DozeuPinningOverlay, vg::GaplessExtender, vg::IdentityOverlay, vg::IncrementalSubgraph, 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
get_handle_from_inward_backing_handle() : vg::NetGraph
get_handle_memo : vg::MemoizingGraph
get_handle_of_step() : vg::MemoizingGraph, vg::PathSubgraphOverlay, vg::VG
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() : vg::DagifiedGraph, vg::DozeuPinningOverlay, vg::IdentityOverlay, vg::IncrementalSubgraph, 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
get_identifier() : vg::IndexFile, vg::ZipCode
get_index() : vg::IndexRegistry, vg::RepresentativeTraversalFinder, vg::ZipCodeTree::seed_iterator
get_indexes() : vg::RewindPlanException
get_inward_backing_handle() : vg::NetGraph
get_irregular_snarl_code() : vg::ZipCode
get_is_circular() : vg::MemoizingGraph, vg::PathSubgraphOverlay, vg::VG
get_is_cyclic() : vg::ZipCodeTree::tree_item_t
get_is_looping_chain() : vg::ZipCode::chain_code_t, vg::ZipCode
get_is_paired() : vg::ReadFilter< Read >
get_is_reverse() : vg::DagifiedGraph, vg::DozeuPinningOverlay, vg::IdentityOverlay, vg::IncrementalSubgraph, 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
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_is_secondary() : vg::Surjector
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() : vg::DagifiedGraph, vg::DozeuPinningOverlay, vg::IdentityOverlay, vg::IncrementalSubgraph, 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
get_log10_prob_of_disruption_in_interval() : vg::MinimizerMapper
get_log_base() : vg::AlignmentScorer, vg::LoggedGapAlignmentScorer, vg::MatrixAlignmentScorer
get_long() : vg::Version
get_long_option() : vg::BaseOption< Value, Parser >, vg::OptionInterface
get_magic_number() : vg::ZipCodeCollection
get_magic_number_as_string() : vg::ZipCodeCollection
get_main() : vg::subcommand::Subcommand
get_mapping() : vg::PhaseUnfolder
get_mapq() : vg::ReadFilter< Read >
get_matrix_value() : vg::ZipCodeTree::distance_iterator
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_handle() : vg::ZipCode
get_net_handle_slow() : vg::ZipCode
get_new_explanation_number() : vg::Explainer
get_next_intervals() : vg::ZipCodeForest
get_next_node_recalc_degrees() : vg::FlowSort
get_next_rank() : vg::Paths
get_next_step() : vg::MemoizingGraph, vg::PathSubgraphOverlay, vg::VG
get_node() : vg::VG
get_node_at_nucleotide() : vg::VG
get_node_by_id() : vg::algorithms::Graph, vg::Graph
get_node_code() : vg::ZipCode
get_node_count() : vg::DagifiedGraph, vg::DozeuPinningOverlay, vg::IdentityOverlay, vg::IncrementalSubgraph, 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
get_node_degree() : vg::FlowSort
get_node_ids() : vg::algorithms::Graph, vg::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_offset_to_seed() : vg::ZipCodeTree
get_on_strand_distance_tree() : vg::OrientedDistanceClusterer
get_option_struct() : vg::subcommand::BaseArgSpec< Receiver >, vg::subcommand::FlagArgSpec< Receiver >, vg::subcommand::NegationFlagArgSpec< Receiver >, vg::subcommand::ValueArgSpec< T, Receiver, Holder >
get_option_value() : vg::subcommand::BaseOptionGroup
get_options() : vg::Configurable
get_other_bound_offset() : vg::ZipCodeTree::tree_item_t
get_output_contigs() : vg::VCFOutputCaller
get_overhang() : vg::ReadFilter< Read >
get_overlay_handle() : vg::StrandSplitGraph
get_parent_identifier() : vg::ZipCode
get_parsed_genotypes() : vg::WindowedVcfBuffer
get_path() : vg::Paths
get_path_count() : vg::MemoizingGraph, vg::PathSubgraphOverlay, vg::VG
get_path_edge_index() : vg::PathChunker
get_path_edges() : vg::VG
get_path_handle() : vg::MemoizingGraph, vg::PathSubgraphOverlay, vg::VG
get_path_handle_of_step() : vg::MemoizingGraph, vg::PathSubgraphOverlay, vg::VG
get_path_id() : vg::Paths
get_path_index() : vg::GraphSynchronizer
get_path_length() : vg::MemoizingGraph
get_path_name() : vg::MemoizingGraph, vg::Paths, vg::PathSubgraphOverlay, vg::VG
get_path_sequence() : vg::GraphSynchronizer
get_payload_from_zip() : vg::ZipCode
get_payload_from_zipcode() : vg::ZipCode
get_peripheral_attachments() : vg::GraphSynchronizer::Lock
get_pos() : vg::GaplessExtender
get_position_of_step() : vg::MemoizingGraph
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() : vg::MemoizingGraph, vg::PathSubgraphOverlay, vg::VG
get_primer_pairs_of_chrom() : vg::PrimerFinder
get_priority() : vg::subcommand::Subcommand
get_prob_of_disruption_in_column() : vg::MinimizerMapper
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_interval() : vg::VCFOutputCaller
get_ref_offsets() : vg::RatioSupportSnarlCaller, vg::TraversalSupportFinder
get_ref_position() : vg::MCMCCaller, vg::VCFOutputCaller
get_ref_positions() : vg::VCFGenotyper
get_ref_trav_size() : vg::PoissonSupportSnarlCaller
get_reference_nodes() : vg::GrefCover
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_right_to_left() : vg::ZipCodeTree::seed_iterator
get_root() : vg::TreeSubgraph
get_rr_memo() : vg::MultipathMapper
get_scopes() : vg::IndexFile, vg::IndexingPlan
get_score() : vg::ReadFilter< Read >, vg::Surjector
get_scores() : haplo::haplo_DP_column
get_section_length() : vg::ZipCodeTree::tree_item_t
get_seed : vg::LazyRNG
get_seed_pos() : vg::SpliceRegion
get_sequence() : vg::DagifiedGraph, vg::DozeuPinningOverlay, vg::Haplotypes::Subchain, vg::IdentityOverlay, vg::IncrementalSubgraph, 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
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, vg::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_sort_value() : vg::ZipCodeForest::sort_value_t
get_source_handle() : vg::SourceSinkOverlay
get_spanning_haplotypes() : vg::GBWTTraversalFinder
get_start() : vg::NetGraph
get_step_at_position() : vg::MemoizingGraph
get_step_count() : vg::MemoizingGraph, vg::PathSubgraphOverlay, vg::VG
get_steps() : vg::IndexingPlan
get_subchains() : vg::HaplotypePartitioner
get_subgraph() : vg::GraphSynchronizer::Lock, vg::SpliceRegion
get_subsequence() : vg::IncrementalSubgraph, vg::JoinedSpliceGraph, vg::VG
get_suffix() : vg::PhaseUnfolder
get_suffixes() : vg::IndexFile
get_support() : vg::AugmentedGraph, vg::SupportAugmentedGraph
get_support_finder() : vg::SupportBasedSnarlCaller
get_symbolic_bounds() : vg::Constructor
get_system_memory() : vg::IndexRegistry
get_tail_forest() : vg::MinimizerMapper
get_target_memory_usage() : vg::IndexRegistry
get_top_level_chain_offset() : vg::ZipCode
get_topological_order() : vg::PathSubgraph, vg::TreeSubgraph
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() : vg::ZipCodeTree::tree_item_t
get_underlying_handle() : 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_union() : vg::IntervalUnion
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, vg::Graph
get_weighted_length() : vg::IntegratedSnarlFinder::MergedAdjacencyGraph
get_wildcards() : vg::IndexRegistry
get_work_dir() : vg::IndexRegistry
GFA : ChainsConfig
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 : haplo::hDP_gbwt_graph_accessor< GBWTType >, 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::GrefCover, vg::HandleGraphNodeSet, vg::HandleGraphSnarlFinder, vg::IdentityOverlay, vg::IncrementalSubgraph, vg::IntegratedSnarlFinder::MergedAdjacencyGraph, 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::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_file : ChainsConfig
graph_gbz : GraphHandler
graph_mixed_distance_estimate() : vg::Mapper
graph_naive : GraphHandler
graph_name : GBWTConfig, HaplotypesConfig, MinimizerConfig, vg::GBZGraph, vg::Haplotypes
graph_none : GraphHandler
graph_output : GBWTConfig
graph_path : 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
gref_intervals : vg::GrefCover
gref_prefix : vg::GrefCover
gref_suffix : vg::GrefCover
groom_components() : vg::FlowSort
group() : vg::SparseUnionFind
group_mapping_quality_exact() : vg::MappingQualityCalculator
group_size : vg::Funnel::Item, vg::SparseUnionFind
GroupedOptionGroup() : vg::subcommand::GroupedOptionGroup
Growth() : vg::FlowSort::Growth
gssw_mapping_to_alignment() : vg::GSSWAligner
GSSWAligner() : vg::GSSWAligner