Here is a list of all functions with links to the classes they belong to:
- g -
- GafAlignmentEmitter() : vg::io::GafAlignmentEmitter
- GAFOutputCaller() : vg::GAFOutputCaller
- GafRecord() : gafkluge::GafRecord
- gap_extend_penalty() : vg::WFATree
- gap_penalty() : vg::WFATree
- GaplessExtender() : vg::GaplessExtender
- gbwt_thread_t() : haplo::gbwt_thread_t
- GBWTConfig() : GBWTConfig
- GBWTScoreProvider() : haplo::GBWTScoreProvider< GBWTType >
- GBWTTraversalFinder() : vg::GBWTTraversalFinder
- 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
- GenomeState() : vg::GenomeState
- genotype() : vg::PoissonSupportSnarlCaller, vg::RatioSupportSnarlCaller, vg::SnarlCaller
- genotype_likelihood() : vg::PoissonSupportSnarlCaller
- genotype_snarl() : vg::Genotyper
- 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_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_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_codename() : vg::Version
- get_connected_components() : vg::MultipathAlignmentGraph
- get_contained_orientations() : vg::PathIndex
- get_context() : vg::Deconstructor
- 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_default_giraffe_indexes() : vg::VGIndexes
- get_default_map_indexes() : vg::VGIndexes
- get_default_mpmap_indexes() : vg::VGIndexes
- get_default_rpvg_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_limit() : vg::MinimizerMapper
- get_distance_measurer() : vg::MultipathMapper
- 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::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_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_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_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
- get_index() : vg::IndexRegistry
- get_indexes() : vg::RewindPlanException
- get_inward_backing_handle() : vg::NetGraph
- get_is_circular() : handlegraph::PathHandleGraph, vg::MemoizingGraph, vg::PathSubgraphOverlay, vg::VG, xg::XG
- 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_item() : vg::Funnel
- get_iterator() : vg::subcommand::TickChainLink
- 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::ReverseGraph, vg::SnarlGraph, vg::SourceSinkOverlay, vg::StrandSplitGraph, vg::SubgraphOverlay, vg::SubHandleGraph, vg::SubpathOverlay, vg::TreeSubgraph, vg::VG, 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, xg::XG
- 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_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_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_nodes() : vg::ContractingGraph, vg::SnarlDistanceIndexClusterer
- get_nonoverlapping() : vg::WindowedVcfBuffer
- 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_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_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_prefix() : vg::IndexRegistry, vg::PhaseUnfolder
- get_previous_step() : handlegraph::PathHandleGraph, vg::MemoizingGraph, vg::PathSubgraphOverlay, vg::VG, xg::XG
- 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_read_fn() : vg::io::JSONStreamHelper< T >
- get_read_name() : vg::NGSSimulator
- get_read_offset() : vg::GaplessExtender
- get_recipe() : vg::IndexRegistry
- 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_traversal() : vg::LegacyCaller
- get_registry() : vg::subcommand::Subcommand
- get_regular_aligner() : vg::AlignerClient
- get_release() : vg::Version
- 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_pos() : vg::SpliceRegion
- get_sense() : handlegraph::PathMetadata
- get_sequence() : 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_sequence_visits() : vg::HaplotypePartitioner
- 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_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_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_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_type() : haplo::linear_haplo_structure
- 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 >
- 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
- GFADuplicatePathError() : vg::algorithms::GFADuplicatePathError
- GFAFormatError() : vg::algorithms::GFAFormatError
- GFAHandleGraph() : vg::GFAHandleGraph
- GFFReader() : vg::GFFReader
- GFFRecord() : vg::GFFRecord
- graph() : vg::Transcriptome
- graph_cigar() : vg::GSSWAligner
- graph_end() : vg::algorithms::Anchor
- graph_mixed_distance_estimate() : vg::Mapper
- graph_pos_at_path_position() : xg::XG
- graph_start() : vg::algorithms::Anchor
- GraphCaller() : vg::GraphCaller
- GraphSynchronizer() : vg::GraphSynchronizer
- GreedyMinDistanceClusterer() : vg::GreedyMinDistanceClusterer
- groom_components() : vg::FlowSort
- group() : vg::SparseUnionFind
- group_mapping_quality_exact() : vg::GSSWAligner
- group_size() : vg::SparseUnionFind
- GroupedOptionGroup() : vg::subcommand::GroupedOptionGroup
- Growth() : vg::FlowSort::Growth
- gssw_mapping_to_alignment() : vg::GSSWAligner
- GSSWAligner() : vg::GSSWAligner