- i -

• id : ReferenceInterval , vg::Node , vg::RecombinatorHaplotype
• id_interval : vg::HaplotypeIndexer
• id_rank_map : vg::Viz
• 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_rank : Vectorizer
• identifier : vg::IndexFile
• identity : vg::Alignment
• identity_weight : vg::Mapper
• ignore_missing_contigs : vg::VariantAdder
• image_height : vg::Viz
• image_width : vg::Viz
• imperfect_pairs_to_retry : vg::Mapper
• in : vg::GFFReader
• in_buffer : vg::zstd_compress_buf , vg::zstd_decompress_buf
• in_from : vg::ExtraNodeGraph
• in_offset : vg::zstd_decompress_buf
• in_use : GraphHandler , vg::GBWTHandler
• 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
• indel_error_prop : vg::NGSSimulator
• indel_poly_rate : vg::NGSSimulator
• index : haplo::GBWTScoreProvider< GBWTType > , haplo::linear_haplo_structure , haplo::LinearScoreProvider , vg::IndexedVG
• index_of : vg::DozeuInterface::OrderedGraph
• index_registry : vg::IndexRegistry
• indexes : vg::GraphSynchronizer , vg::RewindPlanException , vg::VectorView< Item >
• inline_items : vg::MatchPos::PathList
• inner : vg::zstd_compress_buf , vg::zstd_decompress_buf , vg::zstd_ifstream , vg::zstd_ofstream
• inner_value : haplo::haplo_DP_rectangle
• input : vg::io::hFILE_cppstream
• input_filenames : GBWTConfig
• input_in_progress : vg::Funnel
• input_vcf : vg::VCFGenotyper
• inputs : vg::IndexRecipe , vg::InsufficientInputException
• inputs_as_jobs : GBWTConfig
• insert_col : vg::BandedGlobalAligner< IntType >::BAMatrix
• insert_mean : vg::Filter
• insert_row : vg::BandedGlobalAligner< IntType >::BAMatrix
• insert_sd : vg::Filter
• insertion_bias_large : vg::PoissonSupportSnarlCaller
• insertion_bias_small : vg::PoissonSupportSnarlCaller
• insertion_threshold : vg::PoissonSupportSnarlCaller
• insertions : vg::InsertHaplotypeCommand , vg::ReplaceLocalHaplotypeCommand
• INSERTIONS : vg::WFANode
• int_is_inc : haplo::haplo_DP_rectangle
• interleaved : vg::ReadFilter< Read >
• internal_id_map : vg::algorithms::GFAParser
• internal_score : vg::GaplessExtension
• interval_end : vg::ZipCodeForest::interval_state_t
• interval_start : vg::ZipCodeForest::interval_state_t
• intervals_to_process : vg::ZipCodeForest::forest_growing_state_t
• inverse : vg::Filter , vg::VectorViewInverse
• invocations : vg::MinimizerMapper::aligner_stats_t
• IRREGULAR_SNARL_DISTANCE_LEFT_END_OFFSET : vg::ZipCode
• IRREGULAR_SNARL_DISTANCE_LEFT_START_OFFSET : vg::ZipCode
• IRREGULAR_SNARL_DISTANCE_RIGHT_END_OFFSET : vg::ZipCode
• IRREGULAR_SNARL_DISTANCE_RIGHT_START_OFFSET : vg::ZipCode
• IRREGULAR_SNARL_RECORD_OFFSET : vg::ZipCode
• IRREGULAR_SNARL_SIZE : vg::ZipCode
• is_alt : vg::Paths
• is_chain : vg::ZipCode::decoder_t
• is_checked_in : vg::Watchdog::thread_state_t
• is_circular : vg::Path , xg::XGPath
• is_compacted : vg::Packer
• is_end : vg::CactusSide , vg::NodeSide
• is_fixed : vg::FragmentLengthDistribution
• is_haplotype : vg::TranscriptPath
• is_interval : gafkluge::GafStep
• is_looping_chain : vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem
• is_ordered : vg::ZipCodeForest::interval_state_t
• is_phased : vg::Genotype
• is_reference : vg::TranscriptPath
• is_rend : vg::ChainIterator
• is_repetitive : vg::MinimizerMapper::Minimizer
• is_reverse : gafkluge::GafStep , vg::Genotyper::Affinity , vg::Position , vg::Transcript , vg::ZipCodeTree::oriented_seed_t
• is_reverse_ordered : vg::ZipCodeForest::interval_state_t
• is_reversed : vg::MIPayload , vg::ZipCode::node_code_t , vg::ZipCode::snarl_code_t , vg::ZipCodeForest::child_info_t , vg::ZipCodeForest::interval_state_t , vg::ZipCodeTree::tree_item_t
• is_reversed_in_parent : vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem
• is_secondary : vg::Alignment
• is_seed : vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem::SnarlTreeChild
• is_stable : gafkluge::GafStep
• is_trivial_chain : vg::MIPayload , vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem
• is_vg : vg::LegacyCaller
• isForward : vg::BREAKPOINT
• it : vg::ZipCodeTree::iterator , vg::ZipCodeTree::reverse_iterator
• item_bonus : vg::MinimizerMapper
• item_count : vg::MatchPos::PathList
• item_scale : vg::MinimizerMapper
• item_vo : vg::io::MessageIterator
• items : vg::Funnel::Stage , vg::VectorView< Item >
• iteratee : vg::ShuffledPairs::iterator