Here is a list of all functions with links to the classes they belong to:
- i -
- I() : haplo::haplo_DP_rectangle
- id_map() : vg::algorithms::GFAParser
- id_sort() : vg::VG
- id_to_prefix() : vg::StreamIndexBase
- id_to_rank() : handlegraph::RankedHandleGraph, vg::Viz, xg::XG
- identify_aligned_splice_candidates() : vg::MultipathMapper
- identify_pinning_points() : vg::GSSWAligner
- identify_sources_and_sinks() : vg::MEMClusterer::HitGraph
- identify_unaligned_splice_candidates() : vg::MultipathMapper
- identity_translation() : vg::VG
- IdentityOverlay() : vg::IdentityOverlay
- immutable_path_from_length() : vg::MinimizerMapper
- in_nontrivial_chain() : vg::SnarlManager
- include() : vg::VG
- inclusive_interval() : haplo::hDP_gbwt_graph_accessor< GBWTType >
- increment_coverage() : vg::Packer
- increment_edge_coverage() : vg::Packer
- increment_node_ids() : handlegraph::MutableHandleGraph, vg::Paths, vg::VG
- increment_node_quality() : vg::Packer
- increment_progress() : vg::Progressive
- incremental_extend() : haplo::GBWTScoreProvider< GBWTType >, haplo::ScoreProvider
- incremental_find() : haplo::GBWTScoreProvider< GBWTType >, haplo::ScoreProvider
- IncrementalSubgraph() : vg::IncrementalSubgraph
- IncrementIter() : vg::IncrementIter
- index() : vg::StreamIndex< Message >
- index_edge_by_node_sides() : vg::VG
- index_node_to_path() : xg::XG
- index_path_names() : xg::XG
- index_to_node() : vg::Packer
- IndexedVG() : vg::IndexedVG
- IndexFile() : vg::IndexFile
- IndexingPlan() : vg::IndexingPlan
- IndexRecipe() : vg::IndexRecipe
- IndexRegistry() : vg::IndexRegistry
- init() : vg::SpliceStats, vg::VG, vg::Viz
- init_coverage_bin() : vg::Packer
- init_edge_coverage_bin() : vg::Packer
- init_mapper() : vg::Filter
- init_node_quality_bin() : vg::Packer
- init_state() : vg::DinucleotideMachine
- init_traceback_indexes() : vg::BandedGlobalAligner< IntType >::BAMatrix
- initialize_sam_file() : vg::HTSWriter
- input_group() : vg::IndexRecipe
- ins_predecessor() : vg::WFATree
- insert() : job_type, vg::BitStringTree< Item >, vg::BitStringTree< Item >::TreeNode, vg::HandleGraphNodeSet, vg::RecombinatorHaplotype, vg::SmallBitset, vg::SnarlState
- insert_handles() : vg::GenomeState
- insert_haplotype() : vg::GenomeState
- insert_left() : vg::PhasedGenome
- insert_mapping() : vg::Paths
- insert_path() : vg::PhaseUnfolder
- insert_right() : vg::PhasedGenome
- insert_size_filter() : vg::Filter
- insert_traceback() : vg::BandedGlobalAligner< IntType >::AltTracebackStack
- insertion_filter() : vg::Filter
- InsufficientInputException() : vg::InsufficientInputException
- IntegratedSnarlFinder() : vg::IntegratedSnarlFinder
- interchromosomal_filter() : vg::Filter
- intersection() : haplo::int_itvl_t
- interval_size() : haplo::haplo_DP_rectangle
- into_cutting_snarl() : vg::MultipathAlignmentGraph
- into_which_snarl() : vg::SnarlManager
- introduce() : vg::Funnel
- intron_length_log_likelihood() : vg::SpliceStats
- intron_length_score() : vg::SpliceStats
- inversion_filter() : vg::Filter
- invert_translation() : vg::algorithms::GFAIDMapInfo
- is_a_duplicate_handle() : vg::DozeuPinningOverlay
- is_a_duplicate_id() : vg::DozeuPinningOverlay
- is_ancestor_next() : vg::VG
- is_ancestor_prev() : vg::VG
- is_any_painted() : vg::Funnel::PaintableSpace
- is_chain() : handlegraph::SnarlDecomposition
- is_child() : vg::NetGraph
- is_consistent() : vg::MultipathMapper
- is_correct() : vg::Funnel
- is_correctly_mapped() : vg::ReadFilter< Read >
- is_dynamic() : vg::Packer
- is_empty() : handlegraph::PathHandleGraph, haplo::haplo_DP_column, vg::MemoizingGraph
- is_extendable() : vg::IncrementalSubgraph
- is_finalized() : vg::FragmentLengthDistribution
- is_finished() : vg::IndexFile
- is_head_node() : vg::VG
- is_head_or_tail_node() : vg::Paths
- is_in_range() : vg::StreamIndexBase
- is_intermediate() : vg::IndexingPlan
- is_leaf() : vg::SnarlManager, vg::WFANode
- is_left_clipped() : vg::Filter
- is_mapped() : vg::ReadFilter< Read >
- is_new() : haplo::haplo_DP_rectangle
- is_node() : handlegraph::SnarlDecomposition
- is_novel_edge() : vg::AugmentedGraph
- is_novel_node() : vg::AugmentedGraph
- is_ours() : vg::ExtraNodeGraph, vg::SourceSinkOverlay
- is_proper_pair() : vg::ReadFilter< Read >
- is_reverse() : vg::mapping_t, vg::position_t, xg::XGPath
- is_reversed() : vg::MIPayload
- is_root() : handlegraph::SnarlDecomposition, vg::SnarlManager, vg::WFATree
- is_secondary() : vg::ReadFilter< Read >
- is_self_looping() : vg::VG
- is_sentinel() : handlegraph::SnarlDecomposition
- is_snarl() : handlegraph::SnarlDecomposition
- is_snarl_smaller_than_reads() : vg::Genotyper
- is_snv() : haplo::linear_haplo_structure
- is_solitary_ref() : haplo::linear_haplo_structure
- is_split() : vg::ReadFilter< Read >
- is_tail_node() : vg::VG
- is_traversable() : vg::LegacyCaller, vg::MCMCCaller
- is_trivial() : vg::SnarlManager
- is_trivial_chain() : vg::MIPayload
- is_valid() : vg::Range< Number >, vg::Sampler, vg::VG
- is_valid_tag() : vg::io::Registry
- IsBGZF() : vg::io::BlockedGzipInputStream
- iterator() : handlegraph::PathForEachSocket::iterator, vg::PhasedGenome::iterator, vg::ShuffledPairs::iterator