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
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
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_in_zipcode_from_pos() : vg::ZipCode
fill_matrix() : vg::BandedGlobalAligner< IntType >::BAMatrix
fill_uncovered_nodes() : vg::GrefCover
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_on_all : vg::ReadFilter< Read >
filter_redundant_path_chunks() : vg::Surjector
filter_short_intervals() : vg::GrefCover
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::IntegratedSnarlFinder::MergedAdjacencyGraph, vg::StreamIndex< Message >, vg::StreamIndexBase
find_allele_traversals() : vg::VCFTraversalFinder
find_backbone() : vg::RepresentativeTraversalFinder
find_banded_paths() : vg::BandedGlobalAligner< IntType >
find_bubble() : vg::RepresentativeTraversalFinder
find_chain_alignment() : vg::MinimizerMapper
find_child_traversal_set() : vg::FlowCaller
find_constriction_bicliques() : vg::Surjector
find_cycle_path_in_cactus() : vg::IntegratedSnarlFinder::MergedAdjacencyGraph
find_distances() : vg::ZipCodeTree
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_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_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_supplementaries : vg::MinimizerMapper
find_traversals() : vg::ExhaustiveTraversalFinder, vg::FlowTraversalFinder, vg::GBWTTraversalFinder, 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
finish_decode() : vg::algorithms::GFAzParser
finished_decoding : vg::ZipCode
first : vg::FeatureSet::Feature
first_alignment : vg::Counts
first_mapping_quality_approx() : vg::MappingQualityCalculator
first_mapping_quality_exact() : vg::MappingQualityCalculator
fix_dozeu_end_deletions() : vg::MinimizerMapper
fix_dozeu_score() : vg::MinimizerMapper
fixed_fragment_model : vg::FragmentLengthStatistics
flag_repetitive_minimizers() : vg::MinimizerMapper
flank_offset : vg::ZipCodeForest::seed_info_t
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() : vg::DagifiedGraph, vg::DozeuPinningOverlay, vg::IdentityOverlay, vg::IncrementalSubgraph, 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
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, vg::QualAdjXdropAligner, vg::XdropAligner
follow_edges_impl() : vg::DagifiedGraph, vg::DozeuPinningOverlay, vg::IdentityOverlay, vg::IncrementalSubgraph, 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
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_connected_node() : vg::VG
for_each_edge() : 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_impl() : vg::DagifiedGraph, vg::DozeuPinningOverlay, vg::IdentityOverlay, vg::IncrementalSubgraph, 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
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_impl() : vg::MemoizingGraph, vg::PathSubgraphOverlay, vg::VG
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_on_handle_impl() : vg::MemoizingGraph, vg::PathSubgraphOverlay, vg::VG
for_each_step_position_on_handle() : 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
force_fragment_length_distr() : vg::MinimizerMapper, vg::PairedEndMapper
force_haplotype_count : vg::MultipathMapper
force_parameters() : vg::FragmentLengthDistribution
force_phasing : vg::HaplotypeIndexer
forest_growing_state_t() : vg::ZipCodeForest::forest_growing_state_t
forks : vg::algorithms::kmer_t, vg::algorithms::walk_t
Format : ChainsConfig
format() : Vectorizer, vg::HTSWriter, vg::MultipathAlignmentEmitter
Forward : vg::MultipathMapper
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
fragment : vg::MaximalExactMatch, vg::MinimizerMapper::alignment_index_t, vg::MinimizerMapper::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_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_mean : vg::NGSSimulator
fragment_model_str() : vg::FragmentLengthStatistics
fragment_model_update_interval : vg::FragmentLengthStatistics
fragment_orientation() : vg::FragmentLengthStatistics
fragment_orientations : vg::FragmentLengthStatistics
fragment_sd : vg::NGSSimulator
fragment_sigma : vg::FragmentLengthStatistics
fragment_size : vg::FragmentLengthStatistics
fragment_union_find : vg::SnarlDistanceIndexClusterer::ClusteringProblem
FragmentedHaplotypeVisit() : vg::FragmentedHaplotypeVisit
FragmentLengthDistribution() : vg::FragmentLengthDistribution
fragments : vg::GrefCover::TopLevelSnarlStats, vg::Recombinator::Statistics
fragments_in_one_snarl : vg::GrefCover::TopLevelSnarlStats
fragments_on_one_spine_node : vg::GrefCover::TopLevelSnarlStats
fragments_spanning_snarls : vg::GrefCover::TopLevelSnarlStats
fragments_spanning_units : vg::GrefCover::TopLevelSnarlStats
fragments_touching_spine : vg::GrefCover::TopLevelSnarlStats
fragments_with_unmapped_nodes : vg::GrefCover::TopLevelSnarlStats
frequency : vg::MCMCGenotyper
frequent : vg::Recombinator
from : vg::RecombinatorFragment, vg::WFATree
from_anchor : vg::algorithms::transition_info
from_backing() : vg::ReverseGraph, vg::SourceSinkOverlay
from_extension() : vg::WFAAlignment
from_istream() : vg::VG
from_key_value() : vg::WFAPoint
from_length() : vg::edit_t
from_map_entry() : vg::WFAPoint
from_node_id : vg::BandedGlobalAligner< IntType >::AltTracebackStack::Deflection
from_simple_reverse() : vg::FlowSort
from_simple_reverse_orientation() : vg::FlowSort
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::EditAlignmentScorer
full_length_extensions() : vg::GaplessExtender
funnel_name : vg::Funnel