vg
tools for working with variation graphs
- 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
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
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_kmer_key() :
vg::Index
fix_dozeu_score() :
vg::MinimizerMapper
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() :
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_parameters() :
vg::FragmentLengthDistribution
format() :
Vectorizer
forward() :
bdsg::ODGI
,
handlegraph::HandleGraph
forward_offset() :
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
FragmentLengthDistribution() :
vg::FragmentLengthDistribution
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_t
from_path_handle_graph() :
xg::XG
from_simple_reverse() :
vg::FlowSort
from_simple_reverse_orientation() :
vg::FlowSort
from_turtle() :
vg::VG
full() :
vg::GaplessExtension
full_length_extensions() :
vg::GaplessExtender
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