Here is a list of all class members with links to the classes they belong to:
- i -
- I() : haplo::haplo_DP_rectangle
- id : ReferenceInterval, vg::Node, vg::RecombinatorHaplotype
- id_interval : vg::HaplotypeIndexer
- id_map() : vg::algorithms::GFAParser
- id_rank_map : vg::Viz
- id_sort() : vg::VG
- id_to_edge_indices : vg::IndexedVG::CacheEntry
- id_to_index : vg::subcommand::OptionGroup< Receiver >
- id_to_name : vg::algorithms::GFAIDMapInfo, vg::Paths
- id_to_node_index : vg::IndexedVG::CacheEntry
- id_to_prefix() : vg::StreamIndexBase
- id_to_rank() : handlegraph::RankedHandleGraph, Vectorizer, vg::Viz, xg::XG
- identifier : vg::IndexFile
- 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 : vg::Alignment
- identity_translation() : vg::VG
- identity_weight : vg::Mapper
- IdentityOverlay() : vg::IdentityOverlay
- ignore_missing_contigs : vg::VariantAdder
- image_height : vg::Viz
- image_width : vg::Viz
- immutable_path_from_length() : vg::MinimizerMapper
- ImmutablePath : vg::MinimizerMapper
- imperfect_pairs_to_retry : vg::Mapper
- in : vg::GFFReader
- in_from : vg::ExtraNodeGraph
- in_nontrivial_chain() : vg::SnarlManager
- in_use : GraphHandler, vg::GBWTHandler
- include() : vg::VG
- include_children : vg::SparseUnionFind
- include_endpoints : vg::VCFTraversalFinder
- include_full_length_bonuses : vg::Mapper
- include_named_paths : GBWTConfig
- include_nested : vg::VCFOutputCaller
- include_reference : vg::Recombinator::Parameters
- include_reversing_traversals : vg::ExhaustiveTraversalFinder
- inclusive_interval() : haplo::hDP_gbwt_graph_accessor< GBWTType >
- incorrectly_mapped : vg::Counts
- 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
- indel_error_prop : vg::NGSSimulator
- indel_poly_rate : vg::NGSSimulator
- index : haplo::GBWTScoreProvider< GBWTType >, haplo::linear_haplo_structure, haplo::LinearScoreProvider, vg::IndexedVG, vg::StreamIndex< Message >
- index_compressed : vg::GBWTHandler
- index_dynamic : vg::GBWTHandler
- index_edge_by_node_sides() : vg::VG
- index_node_to_path() : xg::XG
- index_none : vg::GBWTHandler
- index_of : vg::DozeuInterface::OrderedGraph
- index_path_names() : xg::XG
- index_registry : vg::IndexRegistry
- index_to_node() : vg::Packer
- index_type : vg::GBWTHandler
- IndexedVG() : vg::IndexedVG
- indexes : vg::GraphSynchronizer, vg::RewindPlanException, vg::VectorView< Item >
- IndexFile() : vg::IndexFile
- IndexingPlan() : vg::IndexingPlan, vg::IndexRegistry
- IndexRecipe() : vg::IndexRecipe
- IndexRegistry : vg::IndexingPlan, 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
- initial_lookback_threshold : vg::MinimizerMapper
- initialize_sam_file() : vg::HTSWriter
- inline_items : vg::MatchPos::PathList
- inner_value : haplo::haplo_DP_rectangle
- input : vg::io::hFILE_cppstream
- input_filenames : GBWTConfig
- input_group() : vg::IndexRecipe
- input_in_progress : vg::Funnel
- input_vcf : vg::VCFGenotyper
- inputs : vg::IndexRecipe, vg::InsufficientInputException
- inputs_as_jobs : GBWTConfig
- ins_predecessor() : vg::WFATree
- insert() : job_type, vg::BitStringTree< Item >, vg::BitStringTree< Item >::TreeNode, vg::HandleGraphNodeSet, vg::RecombinatorHaplotype, vg::SmallBitset, vg::SnarlState
- insert_col : vg::BandedGlobalAligner< IntType >::BAMatrix
- insert_handles() : vg::GenomeState
- insert_haplotype() : vg::GenomeState
- insert_left() : vg::PhasedGenome
- insert_mapping() : vg::Paths
- insert_mean : vg::Filter
- insert_path() : vg::PhaseUnfolder
- insert_right() : vg::PhasedGenome
- insert_row : vg::BandedGlobalAligner< IntType >::BAMatrix
- insert_sd : vg::Filter
- insert_size_filter() : vg::Filter
- insert_traceback() : vg::BandedGlobalAligner< IntType >::AltTracebackStack
- InsertCol : vg::BandedGlobalAligner< IntType >
- insertion : vg::WFAAlignment
- insertion_bias_large : vg::PoissonSupportSnarlCaller
- insertion_bias_small : vg::PoissonSupportSnarlCaller
- insertion_filter() : vg::Filter
- insertion_threshold : vg::PoissonSupportSnarlCaller
- insertions : vg::InsertHaplotypeCommand, vg::ReplaceLocalHaplotypeCommand
- INSERTIONS : vg::WFANode
- InsertRow : vg::BandedGlobalAligner< IntType >
- InsufficientInputException() : vg::InsufficientInputException
- int_is_inc : haplo::haplo_DP_rectangle
- IntegratedSnarlFinder() : vg::IntegratedSnarlFinder
- interchromosomal_filter() : vg::Filter
- interleaved : vg::ReadFilter< Read >
- internal_id_map : vg::algorithms::GFAParser
- internal_score : vg::GaplessExtension
- 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
- invalid : haplo::linear_haplo_structure
- inverse : vg::Filter, vg::VectorViewInverse
- inversion_filter() : vg::Filter
- invert_translation() : vg::algorithms::GFAIDMapInfo
- is_a_duplicate_handle() : vg::DozeuPinningOverlay
- is_a_duplicate_id() : vg::DozeuPinningOverlay
- is_alt : vg::Paths
- is_ancestor_next() : vg::VG
- is_ancestor_prev() : vg::VG
- is_any_painted() : vg::Funnel::PaintableSpace
- is_chain() : handlegraph::SnarlDecomposition
- is_checked_in : vg::Watchdog::thread_state_t
- is_child() : vg::NetGraph
- is_circular : vg::Path, xg::XGPath
- is_compacted : vg::Packer
- 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_end : vg::CactusSide, vg::NodeSide
- is_extendable() : vg::IncrementalSubgraph
- is_finalized() : vg::FragmentLengthDistribution
- is_finished() : vg::IndexFile
- is_fixed : vg::FragmentLengthDistribution
- is_haplotype : vg::TranscriptPath
- is_head_node() : vg::VG
- is_head_or_tail_node() : vg::Paths
- is_in_range() : vg::StreamIndexBase
- is_intermediate() : vg::IndexingPlan
- is_interval : gafkluge::GafStep
- is_leaf() : vg::SnarlManager, vg::WFANode
- is_left_clipped() : vg::Filter
- is_looping_chain : vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem
- 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_phased : vg::Genotype
- is_proper_pair() : vg::ReadFilter< Read >
- is_reference : vg::TranscriptPath
- is_rend : vg::ChainIterator
- is_reverse : gafkluge::GafStep, vg::Genotyper::Affinity, vg::mapping_t, vg::Position, vg::position_t, vg::Transcript, xg::XGPath
- is_reversed() : vg::MIPayload, vg::MIPayloadValues
- is_reversed_in_parent : vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem
- IS_REVERSED_OFFSET : vg::MIPayload
- is_root() : handlegraph::SnarlDecomposition, vg::SnarlManager, vg::WFATree
- is_secondary : vg::Alignment, vg::ReadFilter< Read >
- is_seed : vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem::SnarlTreeChild
- 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_stable : gafkluge::GafStep
- is_tail_node() : vg::VG
- is_traversable() : vg::LegacyCaller, vg::MCMCCaller
- is_trivial() : vg::SnarlManager
- is_trivial_chain() : vg::MIPayload, vg::MIPayloadValues, vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem
- IS_TRIVIAL_CHAIN_OFFSET : vg::MIPayload
- is_valid() : vg::Range< Number >, vg::Sampler, vg::VG
- is_valid_tag() : vg::io::Registry
- is_vg : vg::LegacyCaller
- IsBGZF() : vg::io::BlockedGzipInputStream
- isForward : vg::BREAKPOINT
- item_bonus : vg::MinimizerMapper
- item_count : vg::MatchPos::PathList
- item_vo : vg::io::MessageIterator
- items : vg::Funnel::Stage, vg::VectorView< Item >
- iteratee : vg::ShuffledPairs::iterator
- iterator() : handlegraph::PathForEachSocket::iterator, vg::PathIndex, vg::PhasedGenome::iterator, vg::ShuffledPairs::iterator
- iterator_category : std::iterator_traits< vg::PhasedGenome::iterator >, vg::count_back_inserter< T >, vg::VectorView< Item >::const_iterator