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

- f -

• fail() : vg::Funnel
• failed_filter : vg::Funnel::Item
• failed_statistic : vg::Funnel::Item
• failing : vg::Funnel::FilterPerformance
• failing_correct : vg::Funnel::FilterPerformance
• fallbacks : vg::MinimizerMapper::aligner_stats_t
• false_extend() : haplo::haplo_DP_rectangle
• fanout_length_threshold : vg::BaseMapper
• fast_linear_sort() : vg::FlowSort
• fast_reseed : vg::BaseMapper
• fast_reseed_length_diff : vg::BaseMapper
• fasta_to_vcf() : vg::NameMapper
• fasta_to_vcf_renames : vg::NameMapper
• faster_cap() : vg::MinimizerMapper
• fd : vg::io::fdinbuf , vg::io::fdoutbuf
• fdinbuf() : vg::io::fdinbuf
• fdistream() : vg::io::fdistream
• fdostream() : vg::io::fdostream
• fdoutbuf() : vg::io::fdoutbuf
• feature_name : vg::FeatureSet::Feature
• feature_type : vg::Transcriptome
• features : vg::FeatureSet , vg::SmallSnarlSimplifier
• field() : vg::TSVExplainer
• file : vg::VcfBuffer
• file_name : vg::algorithms::GFAFormatError
• filename : job_type , vg::GBWTHandler
• filenames : vg::IndexFile , vg::temp_file::Handler , vg::VGset , xg::temp_file::Handler
• FILES_PER_MERGE : vg::GAFSorterParameters
• files_per_merge : vg::GAFSorterParameters
• 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_matches : vg::Filter
• filter_on_all : vg::ReadFilter< Read >
• filter_redundant_path_chunks() : vg::Surjector
• filter_short_mems : vg::BaseMapper
• filtered : vg::Counts
• FilterName : vg::Counts
• 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
• finished_decoding : vg::ZipCode
• first : vg::FeatureSet::Feature
• first_alignment : vg::Counts
• first_mapping_quality_approx() : vg::GSSWAligner
• first_mapping_quality_exact() : vg::GSSWAligner
• fix_dozeu_end_deletions() : vg::MinimizerMapper
• fix_dozeu_score() : vg::MinimizerMapper
• fixed_fragment_model : vg::FragmentLengthStatistics
• flag_repetitive_minimizers() : vg::MinimizerMapper
• flank_range : vg::VariantAdder
• flat : vg::Constructor
• flat_node : haplo::haplo_DP_rectangle
• 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 : hFILE_backend , 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_haplotype_count : vg::MultipathMapper
• force_parameters() : vg::FragmentLengthDistribution
• force_phasing : vg::HaplotypeIndexer
• force_unequal : handlegraph::PathForEachSocket::iterator
• forest_growing_state_t() : vg::ZipCodeForest::forest_growing_state_t
• forks : vg::algorithms::kmer_t , vg::algorithms::walk_t
• FORMAT : handlegraph::PathMetadata
• format() : Vectorizer , vg::HTSWriter , vg::MultipathAlignmentEmitter
• forward() : handlegraph::HandleGraph
• Forward : vg::MultipathMapper
• forward : vg::Support
• forward_graph : vg::ReverseGraph
• forward_multiplier : vg::GreedyMinDistanceClusterer
• forward_offset() : vg::MinimizerMapper::Minimizer
• forward_only : vg::Sampler
• forward_sequence() : vg::MinimizerMapper::Minimizer
• frac_score : vg::ReadFilter< Read >
• frag_stats : vg::Mapper
• fragl_supports : vg::BREAKPOINT
• fragment : vg::Alignment , vg::alignment_index_t , vg::MaximalExactMatch , vg::read_alignment_index_t , vg::RecombinatorHaplotype , vg::SnarlDistanceIndexClusterer::Cluster
• fragment_best_left : vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem
• fragment_best_right : vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem
• fragment_direction() : vg::FragmentLengthStatistics
• fragment_directions : vg::FragmentLengthStatistics
• fragment_distance_limit : vg::SnarlDistanceIndexClusterer::ClusteringProblem
• fragment_distr_is_finalized() : vg::MinimizerMapper
• fragment_gap_scale : vg::MinimizerMapper
• fragment_length_cache_size : vg::FragmentLengthStatistics
• fragment_length_distr : vg::MinimizerMapper , vg::PairedEndMapper
• fragment_length_distribution : vg::Alignment
• 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_length_warning_factor : vg::MultipathMapper
• fragment_lengths : vg::FragmentLengthStatistics
• fragment_map : vg::HaplotypePartitioner , vg::Recombinator
• fragment_max : vg::FragmentLengthStatistics
• fragment_max_graph_lookback_bases : vg::MinimizerMapper
• fragment_max_graph_lookback_bases_per_base : vg::MinimizerMapper
• fragment_max_indel_bases : vg::MinimizerMapper
• fragment_max_indel_bases_per_base : vg::MinimizerMapper
• fragment_max_min_score : vg::MinimizerMapper
• fragment_max_read_lookback_bases : vg::MinimizerMapper
• fragment_max_read_lookback_bases_per_base : vg::MinimizerMapper
• fragment_mean : vg::NGSSimulator
• fragment_min_score : vg::MinimizerMapper
• fragment_model_str() : vg::FragmentLengthStatistics
• fragment_model_update_interval : vg::FragmentLengthStatistics
• fragment_next : vg::Alignment
• fragment_orientation() : vg::FragmentLengthStatistics
• fragment_orientations : vg::FragmentLengthStatistics
• fragment_points_per_possible_match : vg::MinimizerMapper
• fragment_prev : vg::Alignment
• fragment_score : vg::Alignment
• fragment_score_fraction : vg::MinimizerMapper
• fragment_sd : vg::NGSSimulator
• fragment_set_score_threshold : vg::MinimizerMapper
• fragment_sigma : vg::FragmentLengthStatistics
• fragment_size : vg::FragmentLengthStatistics
• fragment_union_find : vg::SnarlDistanceIndexClusterer::ClusteringProblem
• FragmentedHaplotypeVisit() : vg::FragmentedHaplotypeVisit
• FragmentLengthDistribution() : vg::FragmentLengthDistribution
• fragments : vg::Recombinator::Statistics
• frequency : vg::MCMCGenotyper
• frequent : vg::Recombinator
• from : vg::Edge , vg::RecombinatorFragment , vg::Translation , vg::WFATree
• 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 , vg::edit_t
• from_map_entry() : vg::WFAPoint
• from_node_id : vg::BandedGlobalAligner< IntType >::AltTracebackStack::Deflection
• from_path_handle_graph() : xg::XG
• from_simple_reverse() : vg::FlowSort
• from_simple_reverse_orientation() : vg::FlowSort
• from_start : vg::Edge
• from_turtle() : vg::VG
• from_vector() : vg::varint_vector_t , vg::ZipCode
• frontier : vg::IncrementalSubgraph
• frontier_copy_limit : vg::IncrementalSubgraph
• frontier_count : vg::IncrementalSubgraph
• frontier_index : vg::IncrementalSubgraph
• full() : vg::GaplessExtension
• full_haplotype : vg::Haplotypes::Subchain
• full_haplotypes : vg::Recombinator::Statistics
• full_length_bonus : ScoringOptions , vg::GSSWAligner
• full_length_extensions() : vg::GaplessExtender
• funnel_name : vg::Funnel