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_graph
: vg::DepthMap
- 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_output
: vg::FlowCaller
, vg::VCFGenotyper
- gaf_sample_name
: vg::GAFOutputCaller
- GafAlignmentEmitter()
: vg::io::GafAlignmentEmitter
- GAFOutputCaller()
: vg::GAFOutputCaller
- GafRecord()
: gafkluge::GafRecord
- gap_extension
: vg::GSSWAligner
, vg::SSWAligner
- gap_memo_max_size
: vg::MultipathMapper
- gap_open
: vg::GSSWAligner
, vg::SSWAligner
- GaplessExtender()
: vg::GaplessExtender
- gbwt
: vg::GBWTTraversalFinder
, vg::IndexManager
- gbwt_buffer_size
: vg::HaplotypeIndexer
- gbwt_graph
: vg::MinimizerMapper
- gbwt_index
: vg::PhaseUnfolder
- gbwt_override
: vg::IndexManager
- gbwt_thread_t()
: haplo::gbwt_thread_t
- gbwtgraph
: vg::IndexManager
- gbwtgraph_override
: vg::IndexManager
- GBWTScoreProvider()
: haplo::GBWTScoreProvider< GBWTType >
- GBWTTraversalFinder()
: vg::GBWTTraversalFinder
- gc_content_estimate
: vg::AlignerClient
- gcsa
: vg::BaseMapper
- gcsa_ind
: vg::Filter
- gen_flat_node
: haplo::haplo_DP_rectangle
- gen_range_t
: haplo::haplo_DP_rectangle
- generate_continuous_uniform()
: vg::MCMCGenotyper
- generate_discrete_uniform()
: vg::MCMCGenotyper
- generate_from_wide_generator()
: vg::uniform_int_distribution< T >
- 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_likelihood()
: vg::PoissonSupportSnarlCaller
- genotype_snarl()
: vg::Genotyper
- genotype_snarls
: vg::FlowCaller
- get()
: vg::Annotation< T, Enabled >
, 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
, vg::Index
- 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_assignment()
: bdsg::PackedGraph
- 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_base()
: bdsg::HashGraph
, bdsg::PackedGraph
, handlegraph::HandleGraph
, vg::IncrementalSubgraph
, vg::JoinedSpliceGraph
, vg::VG
, xg::XG
- get_best_alignment_against_any_tree()
: 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_assignment()
: vg::MinimumDistanceIndex
- get_chain_rank()
: vg::MinimumDistanceIndex
- get_char()
: bdsg::PackedGraph
- get_child_support()
: 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_codename()
: vg::Version
- get_connected_component()
: vg::MinimumDistanceIndex
- get_connected_components()
: vg::MultipathAlignmentGraph
- get_connected_nodes()
: vg::Index
- get_contained_orientations()
: vg::PathIndex
- get_context()
: vg::Index
- get_count()
: vg::NoAlignmentInBandException
- get_create_path()
: vg::Paths
- get_created_handle()
: vg::ExtraNodeGraph
- get_current_column()
: haplo::haplo_DP
- get_default_value()
: vg::BaseOption< Value, Parser >
, vg::OptionInterface
- get_degree()
: bdsg::HashGraph
, bdsg::ODGI
, handlegraph::HandleGraph
, vg::ExtraNodeGraph
, vg::IncrementalSubgraph
, vg::SourceSinkOverlay
, vg::VG
- get_depth()
: vg::DepthMap
- get_description()
: vg::BaseOption< Value, Parser >
, vg::OptionInterface
, vg::subcommand::Subcommand
- get_distance()
: vg::IndexManager
- get_distance_limit()
: vg::MinimizerMapper
- get_duplicate_handle()
: vg::DozeuPinningOverlay
- get_edge()
: vg::Index
, vg::VG
- get_edge_count()
: bdsg::PackedGraph
, 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_edge_target()
: bdsg::PackedGraph
- get_edges_of()
: vg::Index
- get_edges_on_end()
: vg::Index
- get_edges_on_start()
: vg::Index
- get_end()
: vg::NetGraph
- get_endpoints()
: vg::GraphSynchronizer::Lock
- get_exon_haplotypes()
: vg::Transcriptome
- get_features()
: vg::FeatureSet
- get_filename()
: vg::IndexManager
- 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::IndexManager
- get_gbwtgraph()
: vg::IndexManager
- get_genotype_log_likelihood()
: vg::Genotyper
- get_genotype_log_prior()
: vg::Genotyper
- get_genotypes()
: vg::Deconstructor
- get_graph()
: vg::IndexManager
, vg::Packer
- get_handle()
: bdsg::HashGraph
, bdsg::ODGI
, bdsg::PackedGraph
, handlegraph::HandleGraph
, 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::SourceSinkOverlay
, vg::StrandSplitGraph
, vg::SubgraphOverlay
, vg::SubHandleGraph
, vg::TreeSubgraph
, vg::VG
, xg::XG
- get_handle_from_inward_backing_handle()
: vg::NetGraph
- get_handle_memo
: vg::MemoizingGraph
- get_handle_of_step()
: bdsg::HashGraph
, bdsg::ODGI
, bdsg::PackedGraph
, handlegraph::PathHandleGraph
, vg::MemoizingGraph
, vg::PathSubgraphOverlay
, vg::VG
, xg::XG
- get_haplotype_alt_contents()
: vg::VCFTraversalFinder
- get_haplotype_count()
: haplo::GBWTScoreProvider< GBWTType >
, haplo::ScoreProvider
- get_haplotypes_with_snarl()
: vg::PhasedGenome
- get_id()
: bdsg::HashGraph
, bdsg::ODGI
, bdsg::PackedGraph
, 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::SourceSinkOverlay
, vg::StrandSplitGraph
, vg::SubgraphOverlay
, vg::SubHandleGraph
, vg::TreeSubgraph
, vg::VG
, xg::XG
- get_index
: vg::RepresentativeTraversalFinder
- get_inward_backing_handle()
: vg::NetGraph
- get_is_circular()
: bdsg::HashGraph
, bdsg::ODGI
, bdsg::PackedGraph
, handlegraph::PathHandleGraph
, vg::MemoizingGraph
, vg::PathSubgraphOverlay
, vg::VG
, xg::XG
- get_is_reverse()
: bdsg::HashGraph
, bdsg::ODGI
, bdsg::PackedGraph
, 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::SourceSinkOverlay
, vg::StrandSplitGraph
, vg::SubgraphOverlay
, vg::SubHandleGraph
, vg::TreeSubgraph
, vg::VG
, xg::XG
- get_item()
: vg::Funnel
- get_iterator()
: vg::Range< Number >
- get_kmer_positions()
: vg::Index
- get_kmer_subgraph()
: vg::Index
- get_length()
: bdsg::HashGraph
, bdsg::ODGI
, bdsg::PackedGraph
, 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::SourceSinkOverlay
, vg::StrandSplitGraph
, vg::SubgraphOverlay
, vg::SubHandleGraph
, vg::TreeSubgraph
, vg::VG
, xg::XG
- 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()
: bdsg::HashGraph
, bdsg::ODGI
, bdsg::PackedGraph
, handlegraph::SerializableHandleGraph
, xg::XG
- get_main()
: vg::subcommand::Subcommand
- get_mapping()
: vg::PhaseUnfolder
- get_mappings()
: vg::Index
- get_max_path_id()
: vg::Index
- get_membership_path()
: bdsg::PackedGraph
- get_membership_step()
: bdsg::PackedGraph
- get_metadata()
: vg::Index
- 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_minimizer()
: vg::IndexManager
- get_minimizer_distances()
: vg::MinimumDistanceIndex
- get_mutable()
: vg::Annotation< T, Enabled >
- get_n_bins()
: vg::Packer
- get_name()
: vg::Configurable
, vg::subcommand::Subcommand
- get_nearest_node_next_path_member()
: vg::Index
- get_nearest_node_prev_path_member()
: vg::Index
- get_net_graph()
: vg::GenomeState
- get_next_edge_index()
: bdsg::PackedGraph
- get_next_membership()
: bdsg::PackedGraph
- get_next_node_recalc_degrees()
: vg::FlowSort
- get_next_rank()
: vg::Paths
- get_next_step()
: bdsg::HashGraph
, bdsg::ODGI
, bdsg::PackedGraph
, handlegraph::PathHandleGraph
, vg::MemoizingGraph
, vg::PathSubgraphOverlay
, vg::VG
, xg::XG
- get_node()
: vg::Index
, vg::VG
- get_node_at_nucleotide()
: vg::VG
- get_node_count()
: bdsg::HashGraph
, bdsg::ODGI
, bdsg::PackedGraph
, 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::SourceSinkOverlay
, vg::StrandSplitGraph
, vg::SubgraphOverlay
, vg::SubHandleGraph
, vg::TreeSubgraph
, vg::VG
, xg::XG
- get_node_degree()
: vg::FlowSort
- 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_path()
: vg::Index
- get_node_path_relative_position()
: vg::Index
- get_node_support
: vg::RepresentativeTraversalFinder
- get_nodes()
: vg::SnarlSeedClusterer
- get_nodes_next()
: vg::Index
- get_nodes_prev()
: vg::Index
- get_nonoverlapping()
: vg::WindowedVcfBuffer
- get_on_strand_distance_tree()
: vg::OrientedDistanceClusterer
- get_options()
: vg::Configurable
- get_or_make_assignment()
: bdsg::PackedGraph
- get_parsed_genotypes()
: vg::WindowedVcfBuffer
- get_path()
: vg::Index
, vg::Paths
, xg::XG
- get_path_count()
: bdsg::HashGraph
, bdsg::ODGI
, bdsg::PackedGraph
, handlegraph::PathHandleGraph
, vg::MemoizingGraph
, vg::PathSubgraphOverlay
, vg::VG
, xg::XG
- get_path_edge_index()
: vg::PathChunker
- get_path_edges()
: vg::VG
- get_path_handle()
: bdsg::HashGraph
, bdsg::ODGI
, bdsg::PackedGraph
, handlegraph::PathHandleGraph
, vg::MemoizingGraph
, vg::PathSubgraphOverlay
, vg::VG
, xg::XG
- get_path_handle_of_step()
: bdsg::HashGraph
, bdsg::ODGI
, bdsg::PackedGraph
, handlegraph::PathHandleGraph
, vg::MemoizingGraph
, vg::PathSubgraphOverlay
, vg::VG
, xg::XG
- get_path_id()
: vg::Index
, vg::Paths
- get_path_index()
: vg::GraphSynchronizer
- get_path_length()
: handlegraph::PathPositionHandleGraph
, vg::MemoizingGraph
, xg::XG
- get_path_name()
: bdsg::HashGraph
, bdsg::ODGI
, bdsg::PackedGraph
, handlegraph::PathHandleGraph
, vg::Index
, vg::MemoizingGraph
, vg::Paths
, vg::PathSubgraphOverlay
, vg::VG
, xg::XG
- get_path_sequence()
: vg::GraphSynchronizer
- get_peripheral_attachments()
: vg::GraphSynchronizer::Lock
- get_pos()
: vg::GaplessExtender
- get_position_of_step()
: handlegraph::PathPositionHandleGraph
, vg::MemoizingGraph
, xg::XG
- get_prefix()
: vg::PhaseUnfolder
- get_previous_step()
: bdsg::HashGraph
, bdsg::ODGI
, bdsg::PackedGraph
, handlegraph::PathHandleGraph
, vg::MemoizingGraph
, vg::PathSubgraphOverlay
, vg::VG
, xg::XG
- get_primary_assignment()
: vg::MinimumDistanceIndex
- get_primary_rank()
: vg::MinimumDistanceIndex
- 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_range()
: vg::Index
- get_read_fn()
: vg::io::JSONStreamHelper< T >
- get_read_name()
: vg::NGSSimulator
- get_read_offset()
: vg::GaplessExtender
- get_ref_following()
: haplo::linear_haplo_structure
- get_ref_interval()
: vg::VCFOutputCaller
- get_ref_offsets()
: vg::RatioSupportSnarlCaller
, vg::TraversalSupportFinder
- get_ref_position()
: vg::MCMCCaller
- get_ref_positions()
: vg::VCFGenotyper
- get_reference_traversal()
: vg::LegacyCaller
- get_registry()
: vg::subcommand::Subcommand
- get_regular_aligner()
: vg::AlignerClient
- get_release()
: vg::Version
- get_rescue_graph_from_paths
: vg::MultipathMapper
- get_resolver()
: vg::io::Registry
- get_root()
: vg::TreeSubgraph
- get_rr_memo()
: vg::MultipathMapper
- get_scores()
: haplo::haplo_DP_column
- get_secondary_assignment()
: vg::MinimumDistanceIndex
- get_secondary_rank()
: vg::MinimumDistanceIndex
- get_seed_pos()
: vg::SpliceRegion
- get_sequence()
: bdsg::HashGraph
, bdsg::ODGI
, bdsg::PackedGraph
, 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::SourceSinkOverlay
, vg::StrandSplitGraph
, vg::SubgraphOverlay
, vg::SubHandleGraph
, vg::TreeSubgraph
, vg::VG
, xg::XG
- get_short()
: vg::Version
- get_short_options()
: vg::BaseOption< Value, Parser >
, vg::OptionInterface
- get_sink_handle()
: vg::SourceSinkOverlay
- get_sizes()
: haplo::haplo_DP_column
- get_skip_allele_fn()
: vg::SnarlCaller
, vg::SupportBasedSnarlCaller
- get_snarl_reference_bounds()
: vg::Genotyper
- get_snarl_traversals()
: vg::Genotyper
- get_snarls()
: vg::IndexManager
- get_SNP_ref_position()
: haplo::linear_haplo_structure
- get_SNV_allele()
: haplo::linear_haplo_structure
- get_source_handle()
: vg::SourceSinkOverlay
- get_spanning_haplotypes()
: vg::GBWTTraversalFinder
- get_start()
: vg::NetGraph
- get_step_at_position()
: handlegraph::PathPositionHandleGraph
, vg::MemoizingGraph
, xg::XG
- get_step_count()
: bdsg::HashGraph
, bdsg::ODGI
, bdsg::PackedGraph
, handlegraph::PathHandleGraph
, vg::MemoizingGraph
, vg::PathSubgraphOverlay
, vg::VG
, xg::XG
- get_step_next()
: bdsg::PackedGraph
- get_step_prev()
: bdsg::PackedGraph
- get_step_trav()
: bdsg::PackedGraph
- get_subgraph()
: vg::GraphSynchronizer::Lock
, vg::SpliceRegion
- get_subsequence()
: bdsg::HashGraph
, bdsg::PackedGraph
, handlegraph::HandleGraph
, vg::IncrementalSubgraph
, vg::JoinedSpliceGraph
, vg::VG
, xg::XG
- get_suffix()
: vg::PhaseUnfolder
- get_support()
: vg::AugmentedGraph
, vg::SupportAugmentedGraph
- get_support_finder()
: vg::SupportBasedSnarlCaller
- get_symbolic_bounds()
: vg::Constructor
- get_tables()
: vg::io::Registry
- get_tail_forest()
: vg::MinimizerMapper
- get_thread_stream()
: vg::io::StreamMultiplexer
- get_topological_order()
: vg::PathSubgraph
, vg::TreeSubgraph
- get_total_length()
: bdsg::PackedGraph
, 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_type()
: haplo::linear_haplo_structure
- get_underlying_handle()
: handlegraph::ExpandingOverlayGraph
, vg::DagifiedGraph
, vg::DozeuPinningOverlay
, vg::IdentityOverlay
, vg::IncrementalSubgraph
, vg::NullMaskingGraph
, vg::PathSubgraph
, vg::ReverseGraph
, vg::StrandSplitGraph
, vg::SubHandleGraph
, vg::TreeSubgraph
- get_underlying_id()
: vg::DagifiedGraph
, vg::DozeuPinningOverlay
- get_unique_haplotypes()
: vg::VariantAdder
- get_variants_in_site()
: vg::VCFTraversalFinder
- get_version()
: vg::Version
- GetOptions()
: vg::Index
- GFFReader()
: vg::GFFReader
- GFFRecord()
: vg::GFFRecord
- go_left
: vg::ChainIterator
- gq
: vg::PoissonSupportSnarlCaller::PoissonCallInfo
- graph
: bdsg::HashGraph
, handlegraph::PathForEachSocket
, handlegraph::PathForEachSocket::iterator
, haplo::hDP_gbwt_graph_accessor< GBWTType >
, haplo::linear_haplo_structure
, vg::AugmentedGraph
, vg::BandedGlobalAligner< IntType >::AltTracebackStack
, vg::BandedGlobalAligner< IntType >
, vg::CactusSnarlFinder
, vg::ConstructedChunk
, vg::DagifiedGraph
, vg::Deconstructor
, vg::DozeuInterface::OrderedGraph
, vg::DozeuPinningOverlay
, vg::ExhaustiveTraversalFinder
, vg::FlowCaller
, vg::FlowTraversalFinder
, vg::GaplessExtender
, vg::GBWTTraversalFinder
, vg::GraphSynchronizer
, vg::HandleGraphSnarlFinder
, vg::IdentityOverlay
, vg::IncrementalSubgraph
, vg::IndexManager
, vg::IntegratedSnarlFinder::MergedAdjacencyGraph
, vg::io::GafAlignmentEmitter
, vg::LegacyCaller
, vg::MCMCGenotyper
, vg::MemoizingGraph
, vg::MultipathAlignmentEmitter
, vg::NetGraph
, vg::NGSSimulator
, vg::NullMaskingGraph
, vg::Packer
, vg::PathBasedTraversalFinder
, vg::PathChunker
, vg::PathOrientedDistanceMeasurer
, vg::PathRestrictedTraversalFinder
, vg::PathTraversalFinder
, vg::RareVariantSimplifier
, vg::ReadFilter
, vg::RegionExpander
, vg::RepresentativeTraversalFinder
, vg::SmallSnarlSimplifier
, vg::SnarlState
, vg::SplicedHTSAlignmentEmitter
, vg::SRPE
, vg::StrandSplitGraph
, vg::SupportBasedSnarlCaller
, vg::Surjector
, vg::TraversalSupportFinder
, vg::TrivialTraversalFinder
, vg::VariantAdder
, vg::VCFGenotyper
, vg::VCFTraversalFinder
, vg::VG
, vg::VG::Plan
- graph_cigar()
: vg::GSSWAligner
- GRAPH_END_EDGES_OFFSET
: bdsg::PackedGraph
- graph_entry_to_string()
: vg::Index
- graph_id_hidden_set
: bdsg::ODGI
- graph_index_to_node_member_index()
: bdsg::PackedGraph
- graph_index_to_seq_len_index()
: bdsg::PackedGraph
- graph_index_to_seq_start_index()
: bdsg::PackedGraph
- graph_iv
: bdsg::PackedGraph
- graph_iv_index()
: bdsg::PackedGraph
- graph_key_type()
: vg::Index
- graph_mixed_distance_estimate()
: vg::Mapper
- graph_override
: vg::IndexManager
- graph_pos_at_path_position()
: xg::XG
- GRAPH_RECORD_SIZE
: bdsg::PackedGraph
- GRAPH_START_EDGES_OFFSET
: bdsg::PackedGraph
- 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
- 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
- group_tag
: vg::io::MessageEmitter
- group_vo
: vg::io::MessageIterator
- Growth()
: vg::FlowSort::Growth
- gssw_mapping_to_alignment()
: vg::GSSWAligner
- GSSWAligner()
: vg::GSSWAligner