- f -

• fail() : vg::Funnel
• false_extend() : haplo::haplo_DP_rectangle
• fast_linear_sort() : vg::FlowSort
• fasta_to_vcf() : vg::NameMapper
• faster_cap() : vg::MinimizerMapper
• fdinbuf() : vg::io::fdinbuf
• fdistream() : vg::io::fdistream
• fdostream() : vg::io::fdostream
• fdoutbuf() : vg::io::fdoutbuf
• field() : vg::TSVExplainer
• fill_buffer() : vg::VcfBuffer
• fill_in_forest() : vg::ZipCodeForest
• fill_in_full_decoder() : vg::ZipCode
• fill_in_next_decoder() : vg::ZipCode
• fill_in_zipcode() : vg::ZipCode
• fill_in_zipcode_from_payload() : vg::ZipCode
• fill_matrix() : vg::BandedGlobalAligner< IntType >::BAMatrix
• fill_node_to_position() : vg::Filter
• fill_value() : vg::io::ProtobufIterator< T >
• Filter() : vg::Filter
• filter() : vg::ReadFilter< Read >
• filter_alignment() : vg::ReadFilter< Read >
• filter_and_process_multimaps() : vg::Mapper
• filter_hits_to() : vg::MaximalExactMatch
• filter_internal() : vg::ReadFilter< Read >
• filter_local_variants() : vg::VariantAdder
• filter_redundant_path_chunks() : vg::Surjector
• final_offset() : vg::WFAAlignment
• finalize() : vg::NGSSimulator , vg::NGSSimulator::MarkovDistribution< From, To >
• finalize_alignment() : vg::BandedGlobalAligner< IntType >::BABuilder
• finalize_fragment_length_distr() : vg::MinimizerMapper
• find() : vg::IndexedVG , vg::IntegratedSnarlFinder::MergedAdjacencyGraph , vg::StreamIndex< Message > , vg::StreamIndexBase
• find_allele_traversals() : vg::VCFTraversalFinder
• find_backbone() : vg::RepresentativeTraversalFinder
• find_banded_paths() : vg::BandedGlobalAligner< IntType >
• find_bare_loaders() : vg::io::Registry
• find_bubble() : vg::NestedTraversalFinder , vg::RepresentativeTraversalFinder
• find_chain_alignment() : vg::MinimizerMapper
• find_constriction_bicliques() : vg::Surjector
• find_cycle_path_in_cactus() : vg::IntegratedSnarlFinder::MergedAdjacencyGraph
• find_existing_sequence_id() : vg::algorithms::GFAParser
• find_fanout_mems() : vg::BaseMapper
• find_gbwt_traversals() : vg::GBWTTraversalFinder
• find_group() : vg::SparseUnionFind
• find_in_orientation() : vg::PathIndex
• find_in_out_web() : vg::FlowSort
• find_index() : vg::LegacyCaller
• find_loader() : vg::io::Registry
• find_mapping() : vg::Paths
• find_max_node() : vg::FlowSort
• find_mems() : vg::MultipathMapper
• find_mems_deep() : vg::BaseMapper
• find_mems_simple() : vg::BaseMapper
• find_minimizers() : vg::MinimizerMapper
• find_named_traversals() : vg::PathRestrictedTraversalFinder
• find_node_by_name_or_add_new() : vg::VG
• find_optimal_tail_alignments() : vg::MinimizerMapper
• find_path_traversals() : vg::GBWTTraversalFinder , vg::PathTraversalFinder
• find_pos() : vg::WFANode , vg::WFATree
• find_position() : vg::PathIndex
• find_rescuable_spliced_alignments() : vg::MultipathMapper
• find_saver() : vg::io::Registry
• find_seeds() : vg::MinimizerMapper
• find_snarls() : vg::CactusSnarlFinder , vg::HandleGraphSnarlFinder , vg::SnarlFinder
• find_snarls_impl() : vg::CactusSnarlFinder
• find_snarls_parallel() : vg::CactusSnarlFinder , vg::IntegratedSnarlFinder , vg::SnarlFinder
• find_snarls_unindexed() : vg::HandleGraphSnarlFinder
• find_spliced_alignments() : vg::MultipathMapper
• find_stripped_matches() : vg::BaseMapper
• find_sub_mems() : vg::BaseMapper
• find_sub_mems_fast() : vg::BaseMapper
• find_traversals() : vg::ExhaustiveTraversalFinder , vg::FlowTraversalFinder , vg::GBWTTraversalFinder , vg::NestedTraversalFinder , vg::PathBasedTraversalFinder , vg::PathRestrictedTraversalFinder , vg::PathTraversalFinder , vg::ReadRestrictedTraversalFinder , vg::RepresentativeTraversalFinder , vg::TraversalFinder , vg::TrivialTraversalFinder , vg::VCFTraversalFinder
• find_weighted_traversals() : vg::FlowTraversalFinder
• finish() : vg::RecombinatorHaplotype , vg::SnarlManager
• finish_current_edit() : vg::BandedGlobalAligner< IntType >::BABuilder
• finish_current_node() : vg::BandedGlobalAligner< IntType >::BABuilder
• first_mapping_quality_approx() : vg::GSSWAligner
• first_mapping_quality_exact() : vg::GSSWAligner
• fix_dozeu_end_deletions() : vg::MinimizerMapper
• fix_dozeu_score() : vg::MinimizerMapper
• flag_repetitive_minimizers() : vg::MinimizerMapper
• FlatFileBackTranslation() : vg::FlatFileBackTranslation
• flatten_alt_allele() : vg::NestedFlowCaller
• flatten_common_allele_ends() : vg::MCMCCaller , vg::VCFOutputCaller
• flatten_distance_tree() : vg::OrientedDistanceClusterer
• flatten_reference_allele() : vg::NestedFlowCaller
• flip() : handlegraph::algorithms::SubHandleGraph , handlegraph::HandleGraph , handlegraph::SnarlDecomposition , vg::DagifiedGraph , vg::DozeuPinningOverlay , vg::ExtraNodeGraph , vg::IdentityOverlay , vg::IncrementalSubgraph , vg::IndexedVG , vg::JoinedSpliceGraph , vg::MemoizingGraph , vg::NetGraph , vg::NodeSide , vg::NullMaskingGraph , vg::PathSubgraph , vg::ReverseGraph , vg::SnarlGraph , vg::SnarlManager , vg::SourceSinkOverlay , vg::StrandSplitGraph , vg::SubgraphOverlay , vg::SubHandleGraph , vg::SubpathOverlay , vg::TreeSubgraph , vg::VG , vg::WFAAlignment , xg::XG
• flip_doubly_reversed_edges() : vg::VG
• flip_key() : vg::GAFSorterRecord
• flow_sort_nodes() : vg::FlowSort
• FlowCaller() : vg::FlowCaller
• FlowSort() : vg::FlowSort
• FlowTraversalFinder() : vg::FlowTraversalFinder
• flush() : vg::DozeuInterface
• Flush() : vg::io::BlockedGzipOutputStream
• flush() : vg::io::MessageEmitter , vg::io::ProtobufEmitter< T > , vg::QualAdjXdropAligner , vg::XdropAligner
• flush_self() : vg::io::BlockedGzipOutputStream
• follow_edges() : handlegraph::HandleGraph
• follow_edges_impl() : 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
• follow_net_edges() : handlegraph::SnarlDecomposition
• follow_net_edges_impl() : handlegraph::SnarlDecomposition
• for_each() : vg::Paths , vg::subcommand::Subcommand , vg::VGset
• for_each_agglomeration_interval() : vg::MinimizerMapper
• for_each_annotation() : vg::multipath_alignment_t
• for_each_chain() : vg::SnarlManager
• for_each_chain_parallel() : vg::SnarlManager
• for_each_child() : handlegraph::SnarlDecomposition
• for_each_child_impl() : handlegraph::SnarlDecomposition
• for_each_connected_node() : vg::VG
• for_each_edge() : handlegraph::HandleGraph , vg::DiagramExplainer , vg::VG
• for_each_edge_parallel() : vg::VG
• for_each_field() : vg::GAFSorterRecord
• for_each_filter() : vg::Funnel
• for_each_gff_record() : vg::GFFReader
• for_each_handle() : handlegraph::HandleGraph
• for_each_handle_impl() : 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
• for_each_head() : vg::IntegratedSnarlFinder::MergedAdjacencyGraph
• for_each_id() : vg::StreamIndex< Message >
• for_each_kmer_parallel() : vg::VGset
• for_each_mapping() : vg::Paths
• for_each_member() : vg::IntegratedSnarlFinder::MergedAdjacencyGraph
• for_each_membership() : vg::IntegratedSnarlFinder::MergedAdjacencyGraph
• for_each_name() : vg::Paths
• for_each_name_stoppable() : vg::Paths
• for_each_neighbor() : vg::DozeuInterface::OrderedGraph
• for_each_node() : vg::VG
• for_each_node_parallel() : vg::VG
• for_each_other_member() : vg::IntegratedSnarlFinder::MergedAdjacencyGraph
• for_each_path_handle() : handlegraph::PathHandleGraph
• for_each_path_handle_impl() : handlegraph::PathHandleGraph , handlegraph::PathMetadata , vg::MemoizingGraph , vg::PathSubgraphOverlay , vg::VG , xg::XG
• for_each_path_matching() : handlegraph::PathMetadata
• for_each_path_matching_impl() : handlegraph::PathMetadata
• for_each_path_of_sample() : handlegraph::PathMetadata
• for_each_path_of_sense() : handlegraph::PathMetadata
• for_each_postorder() : vg::Tree< T > , vg::TreeNode< T >
• for_each_preorder() : vg::Tree< T > , vg::TreeNode< T >
• for_each_read_interval() : vg::GaplessExtension
• for_each_snarl_parallel() : vg::SnarlManager
• for_each_snarl_preorder() : vg::SnarlManager
• for_each_snarl_unindexed() : vg::SnarlManager
• for_each_stage() : vg::Funnel
• for_each_step_in_path() : handlegraph::PathHandleGraph
• for_each_step_of_sense() : handlegraph::PathMetadata
• for_each_step_of_sense_impl() : handlegraph::PathMetadata
• for_each_step_on_handle() : handlegraph::PathHandleGraph
• for_each_step_on_handle_impl() : handlegraph::PathHandleGraph , handlegraph::PathMetadata , vg::MemoizingGraph , vg::PathSubgraphOverlay , vg::VG , xg::XG
• for_each_step_position_on_handle() : handlegraph::PathPositionHandleGraph , vg::MemoizingGraph
• for_each_stream() : vg::Paths
• for_each_tippy_child() : handlegraph::SnarlDecomposition
• for_each_tippy_child_impl() : handlegraph::SnarlDecomposition
• for_each_top_level_chain() : vg::SnarlManager
• for_each_top_level_chain_parallel() : vg::SnarlManager
• for_each_top_level_snarl() : vg::SnarlManager
• for_each_top_level_snarl_parallel() : vg::SnarlManager
• for_each_traversal() : handlegraph::SnarlDecomposition
• for_each_traversal_end() : handlegraph::SnarlDecomposition
• for_each_traversal_end_impl() : handlegraph::SnarlDecomposition
• for_each_traversal_impl() : handlegraph::SnarlDecomposition
• for_each_traversal_start() : handlegraph::SnarlDecomposition
• for_each_traversal_start_impl() : handlegraph::SnarlDecomposition
• for_path_range() : xg::XG
• force_close() : vg::io::BlockedGzipOutputStream
• force_fragment_length_distr() : vg::MinimizerMapper , vg::PairedEndMapper
• force_parameters() : vg::FragmentLengthDistribution
• forest_growing_state_t() : vg::ZipCodeForest::forest_growing_state_t
• format() : Vectorizer
• forward() : handlegraph::HandleGraph
• forward_offset() : vg::MinimizerMapper::Minimizer
• forward_sequence() : vg::MinimizerMapper::Minimizer
• fragment_direction() : vg::FragmentLengthStatistics
• fragment_distr_is_finalized() : vg::MinimizerMapper
• fragment_length_log_likelihood() : vg::MultipathMapper
• fragment_length_mean() : vg::FragmentLengthStatistics
• fragment_length_pdf() : vg::FragmentLengthStatistics
• fragment_length_pval() : vg::FragmentLengthStatistics
• fragment_length_stdev() : vg::FragmentLengthStatistics
• fragment_model_str() : vg::FragmentLengthStatistics
• fragment_orientation() : vg::FragmentLengthStatistics
• FragmentedHaplotypeVisit() : vg::FragmentedHaplotypeVisit
• FragmentLengthDistribution() : vg::FragmentLengthDistribution
• from_backing() : vg::ExtraNodeGraph , vg::ReverseGraph , vg::SourceSinkOverlay
• from_big_endian() : vg::endianness< IntType >
• from_enumerators() : xg::XG
• from_extension() : vg::WFAAlignment
• from_gfa() : xg::XG
• from_handle_graph() : xg::XG
• from_istream() : vg::VG
• from_key_value() : vg::WFAPoint
• from_length() : vg::edit_t
• from_map_entry() : vg::WFAPoint
• from_path_handle_graph() : xg::XG
• from_simple_reverse() : vg::FlowSort
• from_simple_reverse_orientation() : vg::FlowSort
• from_turtle() : vg::VG
• from_vector() : vg::varint_vector_t , vg::ZipCode
• full() : vg::GaplessExtension
• full_length_extensions() : vg::GaplessExtender