vg
tools for working with variation graphs
- g -
GafAlignmentEmitter() :
vg::io::GafAlignmentEmitter
GAFOutputCaller() :
vg::GAFOutputCaller
GafRecord() :
gafkluge::GafRecord
GaplessExtender() :
vg::GaplessExtender
gbwt_thread_t() :
haplo::gbwt_thread_t
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_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::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::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_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_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_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_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
graph_cigar() :
vg::GSSWAligner
graph_entry_to_string() :
vg::Index
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_index() :
bdsg::PackedGraph
graph_key_type() :
vg::Index
graph_mixed_distance_estimate() :
vg::Mapper
graph_pos_at_path_position() :
xg::XG
GraphCaller() :
vg::GraphCaller
GraphSynchronizer() :
vg::GraphSynchronizer
GreedyMinDistanceClusterer() :
vg::GreedyMinDistanceClusterer
groom_components() :
vg::FlowSort
group_mapping_quality_exact() :
vg::GSSWAligner
Growth() :
vg::FlowSort::Growth
gssw_mapping_to_alignment() :
vg::GSSWAligner
GSSWAligner() :
vg::GSSWAligner
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