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::algorithms::GFAzParser::PendingRGFAVisit, vg::RecombinatorHaplotype
id_interval : vg::HaplotypeIndexer
id_map() : vg::algorithms::GFAParser
id_rank_map : vg::Viz
id_sort() : vg::VG
id_to_index : vg::subcommand::OptionGroup< Receiver >
id_to_name : vg::algorithms::GFAIDMapInfo, vg::Paths
id_to_prefix() : vg::StreamIndexBase
id_to_rank : Vectorizer, vg::Viz
identifier : vg::IndexFile
identify_aligned_splice_candidates() : vg::MultipathMapper
identify_pinning_points() : vg::GSSWAligner
identify_sources_and_sinks() : vg::MEMClusterer::HitGraph
identify_supplementary_alignments() : vg::MinimizerMapper
identify_unaligned_splice_candidates() : vg::MultipathMapper
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_buffer : vg::zstd_compress_buf, vg::zstd_decompress_buf
in_nontrivial_chain() : vg::SnarlManager
in_offset : vg::zstd_decompress_buf
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() : 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
indel_size : vg::algorithms::transition_info
index : haplo::GBWTScoreProvider< GBWTType >, vg::StreamIndex< Message >, vg::ZipCodeTree::distance_iterator::iteration_position, vg::ZipCodeTree::seed_iterator
index_compressed : vg::GBWTHandler
index_dynamic : vg::GBWTHandler
index_edge_by_node_sides() : vg::VG
index_external : vg::GBWTHandler
index_none : vg::GBWTHandler
index_of : vg::DozeuInterface::OrderedGraph
index_registry : vg::IndexRegistry
index_to_node() : vg::Packer
index_type : vg::GBWTHandler
indexes : vg::GraphSynchronizer, vg::RewindPlanException, vg::VectorView< Item >
IndexFile() : vg::IndexFile
IndexingPlan() : vg::IndexingPlan, vg::IndexRegistry
IndexRecipe() : vg::IndexRecipe
IndexRegistry : vg::IndexingPlan, vg::IndexRegistry
IndirectVectorView() : vg::IndirectVectorView< Item >
info() : vg::Logger
init() : vg::SpliceStats, vg::VG, vg::Viz
init_coverage_bin() : vg::Packer
init_edge_coverage_bin() : vg::Packer
init_node_quality_bin() : vg::Packer
init_snarls() : vg::Masker
init_state() : vg::DinucleotideMachine
init_traceback_indexes() : vg::BandedGlobalAligner< IntType >::BAMatrix
initialize_chain() : vg::ZipCodeTree::distance_iterator
initialize_sam_file() : vg::HTSWriter
initialize_snarl() : vg::ZipCodeTree::distance_iterator
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_file : ChainsConfig
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
insert_col : vg::BandedGlobalAligner< IntType >::BAMatrix
insert_left() : vg::PhasedGenome
insert_mapping() : vg::Paths
insert_path() : vg::PhaseUnfolder
insert_right() : vg::PhasedGenome
insert_row : vg::BandedGlobalAligner< IntType >::BAMatrix
insert_traceback() : vg::BandedGlobalAligner< IntType >::AltTracebackStack
InsertCol : vg::BandedGlobalAligner< IntType >
insertion : vg::WFAAlignment
insertion_bias_large : vg::PoissonSupportSnarlCaller
insertion_bias_small : vg::PoissonSupportSnarlCaller
insertion_threshold : vg::PoissonSupportSnarlCaller
INSERTIONS : vg::WFANode
InsertRow : vg::BandedGlobalAligner< IntType >
InsufficientInputException() : vg::InsufficientInputException
int_is_inc : haplo::haplo_DP_rectangle
IntegratedSnarlFinder() : vg::IntegratedSnarlFinder
interleaved : vg::ReadFilter< Read >
internal_id_map : vg::algorithms::GFAParser
internal_max() : vg::ZipCodeTree::tree_item_t
internal_score : vg::GaplessExtension
intersection() : haplo::int_itvl_t
interval_end : vg::ZipCodeForest::interval_state_t
interval_level : vg::GrefCover
interval_parent : vg::GrefCover
interval_size() : haplo::haplo_DP_rectangle
interval_snarl_bounds : vg::GrefCover
interval_start : vg::ZipCodeForest::interval_state_t
interval_state_t() : vg::ZipCodeForest::interval_state_t
intervals_to_process : vg::ZipCodeForest::forest_growing_state_t
IntervalUnion() : vg::IntervalUnion
into_cutting_snarl() : vg::MultipathAlignmentGraph
into_which_snarl() : vg::SnarlManager
introduce() : vg::Funnel
intron_length_log_likelihood() : vg::SpliceStats
intron_length_score() : vg::SpliceStats
inverse : vg::VectorViewInverse
invert() : vg::Counts
invert_translation() : vg::algorithms::GFAIDMapInfo
invocations : vg::MinimizerMapper::aligner_stats_t
IRREGULAR_SNARL : vg::ZipCode
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
irvl_union : vg::IntervalUnion
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 : vg::ZipCode::decoder_t
is_checked_in : vg::Watchdog::thread_state_t
is_child() : vg::NetGraph
is_compacted : vg::Packer
is_consistent() : vg::MultipathMapper
is_correct() : vg::Funnel
is_correctly_mapped() : vg::ReadFilter< Read >
is_dynamic() : vg::Packer
is_empty() : haplo::haplo_DP_column, vg::MemoizingGraph
is_end : vg::CactusSide, vg::NodeSide
is_equal() : vg::ZipCode
is_extendable() : vg::IncrementalSubgraph
is_externally_end_end_connected() : vg::ZipCode
is_externally_start_end_connected() : vg::ZipCode
is_externally_start_start_connected() : vg::ZipCode
is_farther_than() : vg::ZipCode
is_finalized() : vg::FragmentLengthDistribution
is_finished() : vg::IndexFile
is_fixed : vg::FragmentLengthDistribution
is_gref_derived() : vg::GrefCover
is_gref_name() : vg::GrefCover
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_leaf() : vg::SnarlManager, vg::WFANode
is_looping_chain : vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem
is_mapped() : vg::ReadFilter< Read >
is_new() : haplo::haplo_DP_rectangle
is_novel_edge() : vg::AugmentedGraph
is_novel_node() : vg::AugmentedGraph
is_other_reference_view() : vg::Deconstructor
is_ours() : vg::SourceSinkOverlay
is_proper_pair() : vg::ReadFilter< Read >
is_reference : vg::TranscriptPath
is_rend : vg::ChainIterator
is_repetitive : vg::MinimizerMapper::Minimizer
is_reverse : vg::Genotyper::Affinity, vg::mapping_t, vg::position_t, vg::Transcript
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::oriented_seed_t
is_reversed_in_parent : vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem
is_reversed_or_cyclic : vg::ZipCodeTree::tree_item_t
is_root() : vg::SnarlManager, vg::WFATree
is_secondary() : vg::ReadFilter< Read >
is_seed : vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem::SnarlTreeChild
is_self_looping() : vg::VG
is_skippable() : vg::algorithms::Anchor
is_snarl_smaller_than_reads() : vg::Genotyper
is_split() : vg::ReadFilter< Read >
is_static() : vg::Range< Number >, vg::subcommand::RangeArgSpec< T, Receiver >, vg::subcommand::TickChainLink
is_std_in_out() : vg::GAFSorterFile
is_tail_node() : vg::VG
is_traversable() : vg::LegacyCaller, vg::MCMCCaller
is_trivial() : vg::SnarlManager
is_trivial_chain : vg::MIPayload, vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem
is_valid() : vg::Range< Number >, vg::Sampler, vg::VG
is_vg : vg::LegacyCaller
item_bonus : vg::algorithms::ChainScoringScheme, vg::MinimizerMapper
item_count : vg::MatchPos::PathList
items : vg::Funnel::Stage, vg::IndirectVectorView< Item >, vg::VectorView< Item >
iteratee : vg::ShuffledPairs::iterator
iteration_position() : vg::ZipCodeTree::distance_iterator::iteration_position
iterations : vg::MinimizerIndexParameters
iterator : vg::PathIndex, vg::PhasedGenome::iterator, vg::ShuffledPairs::iterator
iterator_category : std::iterator_traits< vg::PhasedGenome::iterator >, std::iterator_traits< vg::ZipCodeTree::distance_iterator >, std::iterator_traits< vg::ZipCodeTree::seed_iterator >, vg::count_back_inserter< T >, vg::VectorView< Item >::const_iterator