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_filename
: vg::IndexManager
- 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
- ff
: vg::SRPE
- file
: vg::VcfBuffer
- file_header
: vg::MinimumDistanceIndex
- filenames
: vg::temp_file::Handler
, vg::VGset
, xg::temp_file::Handler
- fill_buffer()
: vg::VcfBuffer
- fill_depth()
: vg::DepthMap
- fill_matrix()
: vg::BandedGlobalAligner< IntType >::BAMatrix
- fill_node_to_position()
: vg::Filter
- fill_value()
: vg::io::ProtobufIterator< T >
- Filter()
: vg::Filter
- filter()
: vg::ReadFilter
- filter_alignment()
: vg::ReadFilter
- filter_and_process_multimaps()
: vg::Mapper
- filter_hits_to()
: vg::MaximalExactMatch
- filter_local_variants()
: vg::VariantAdder
- filter_matches
: vg::Filter
- filter_on_all
: vg::ReadFilter
- filter_short_mems
: vg::BaseMapper
- filtered
: vg::ReadFilter::Counts
- FilterName
: vg::ReadFilter::Counts
- 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_connecting_paths()
: vg::MinimizerMapper
- find_constriction_edges()
: vg::Surjector
- find_cycle_path_in_cactus()
: vg::IntegratedSnarlFinder::MergedAdjacencyGraph
- find_fanout_mems()
: vg::BaseMapper
- 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_metadata()
: bdsg::ODGI
- find_minimizers()
: vg::MinimizerMapper
- find_named_traversals()
: vg::PathRestrictedTraversalFinder
- find_node_by_name_or_add_new()
: vg::VG
- find_non_ref_tips()
: vg::Homogenizer
- find_optimal_tail_alignments()
: vg::MinimizerMapper
- find_path_traversals()
: vg::PathTraversalFinder
- find_position()
: vg::PathIndex
- 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_tips()
: vg::Homogenizer
- 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::SnarlManager
- finish_current_edit()
: vg::BandedGlobalAligner< IntType >::BABuilder
- finish_current_node()
: vg::BandedGlobalAligner< IntType >::BABuilder
- first
: bdsg::ODGI::path_metadata_t
, vg::FeatureSet::Feature
- first_kmer_key()
: vg::Index
- fix_dozeu_score()
: vg::MinimizerMapper
- fixed_fragment_model
: vg::FragmentLengthStatistics
- flank_range
: vg::VariantAdder
- flat
: vg::Constructor
- flat_node
: haplo::haplo_DP_rectangle
- flatten_common_allele_ends()
: vg::MCMCCaller
, vg::VCFOutputCaller
- flatten_distance_tree()
: vg::OrientedDistanceClusterer
- flip()
: 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::NodeSide
, vg::NullMaskingGraph
, vg::PathSubgraph
, vg::ReverseGraph
, vg::SnarlManager
, vg::SourceSinkOverlay
, vg::StrandSplitGraph
, vg::SubgraphOverlay
, vg::SubHandleGraph
, vg::TreeSubgraph
, vg::VG
, 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
, vg::Index
- 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()
: 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
- for_alignment_in_range()
: vg::Index
- for_alignment_to_node()
: vg::Index
- for_alignment_to_nodes()
: vg::Index
- for_all()
: vg::Index
- for_base_alignments()
: vg::Index
- for_each()
: vg::Paths
, vg::subcommand::Subcommand
, vg::VGset
- for_each_aglomeration_interval()
: vg::MinimizerMapper
- for_each_alignment()
: vg::Index
- for_each_annotation()
: vg::multipath_alignment_t
- for_each_chain()
: vg::SnarlManager
- for_each_chain_parallel()
: vg::SnarlManager
- for_each_connected_node()
: vg::VG
- for_each_edge()
: handlegraph::HandleGraph
, 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()
: 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
- for_each_head()
: vg::IntegratedSnarlFinder::MergedAdjacencyGraph
- for_each_id()
: vg::StreamIndex< Message >
- for_each_kmer_parallel()
: vg::VGset
- for_each_mapping()
: vg::Index
, 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()
: bdsg::HashGraph
, bdsg::ODGI
, bdsg::PackedGraph
, handlegraph::PathHandleGraph
, vg::MemoizingGraph
, vg::PathSubgraphOverlay
, vg::VG
, xg::XG
- 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()
: bdsg::ODGI
, handlegraph::PathHandleGraph
- for_each_step_on_handle()
: handlegraph::PathHandleGraph
- for_each_step_on_handle_impl()
: bdsg::HashGraph
, bdsg::ODGI
, bdsg::PackedGraph
, handlegraph::PathHandleGraph
, 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_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_graph_range()
: vg::Index
- for_kmer_range()
: vg::Index
- for_path_range()
: xg::XG
- for_range()
: vg::Index
- 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
, vg::walk_t
- format()
: Vectorizer
, vg::HTSAlignmentEmitter
- forward()
: bdsg::ODGI
, handlegraph::HandleGraph
, vg::Support
- forward_graph
: vg::ReverseGraph
- forward_multiplier
: vg::GreedyMinDistanceClusterer
- forward_offset()
: vg::MinimizerMapper::Minimizer
- forward_only
: vg::Sampler
- frac_score
: vg::ReadFilter
- frag_stats
: vg::Mapper
- fragl_supports
: vg::BREAKPOINT
- fragment
: vg::Alignment
, vg::MaximalExactMatch
, vg::SnarlSeedClusterer::Cluster
- fragment_best_left
: vg::SnarlSeedClusterer::NodeClusters
- fragment_best_right
: vg::SnarlSeedClusterer::NodeClusters
- fragment_direction()
: vg::FragmentLengthStatistics
- fragment_directions
: vg::FragmentLengthStatistics
- fragment_distance_limit
: vg::SnarlSeedClusterer::TreeState
- 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_sampler
: vg::NGSSimulator
- fragment_score
: vg::Alignment
- fragment_sd
: vg::NGSSimulator
- fragment_sigma
: vg::FragmentLengthStatistics
- fragment_size
: vg::FragmentLengthStatistics
- fragment_union_find
: vg::SnarlSeedClusterer::TreeState
- FragmentLengthDistribution()
: vg::FragmentLengthDistribution
- from
: vg::Edge
, vg::Translation
- from_backing()
: vg::ExtraNodeGraph
, vg::ReverseGraph
, vg::SourceSinkOverlay
- from_big_endian()
: vg::endianness< IntType >
- from_enumerators()
: xg::XG
- from_gfa()
: xg::XG
- from_handle_graph()
: xg::XG
- from_istream()
: vg::VG
- from_length
: vg::Edit
, vg::edit_t
- 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_index
: vg::IncrementalSubgraph
- full()
: vg::GaplessExtension
- full_length_bonus
: vg::GSSWAligner
- full_length_extensions()
: vg::GaplessExtender
- funnel_name
: vg::Funnel