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
- 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
- file : vg::VcfBuffer
- file_i : GafFile
- file_name : vg::algorithms::GFAFormatError
- filename : job_type, vg::GBWTHandler
- filenames : vg::IndexFile, vg::temp_file::Handler, vg::VGset, xg::temp_file::Handler
- fill_buffer() : vg::VcfBuffer
- 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
- first : vg::FeatureSet::Feature
- 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
- 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
- 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_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_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
- 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_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_max : vg::FragmentLengthStatistics
- fragment_mean : vg::NGSSimulator
- fragment_model_str() : vg::FragmentLengthStatistics
- fragment_model_update_interval : vg::FragmentLengthStatistics
- fragment_next : vg::Alignment
- fragment_orientation() : vg::FragmentLengthStatistics
- fragment_orientations : vg::FragmentLengthStatistics
- fragment_prev : vg::Alignment
- fragment_score : vg::Alignment
- fragment_sd : vg::NGSSimulator
- fragment_sigma : vg::FragmentLengthStatistics
- fragment_size : vg::FragmentLengthStatistics
- fragment_union_find : vg::SnarlDistanceIndexClusterer::ClusteringProblem
- FragmentLengthDistribution() : vg::FragmentLengthDistribution
- fragments : vg::Recombinator::Statistics
- frequency : vg::MCMCGenotyper
- frequent : vg::Recombinator
- from : vg::Edge, 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
- 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