Here is a list of all class members with links to the classes they belong to:
- i -
- I()
: haplo::haplo_DP_rectangle
- id
: vg::Node
- id_in_parent
: vg::MinimumDistanceIndex::ChainIndex
, vg::MinimumDistanceIndex::SnarlIndex
, vg::SnarlSeedClusterer::NetgraphNode
- id_interval
: vg::HaplotypeIndexer
- ID_OFFSET
: vg::MIPayload
- id_rank_map
: vg::Viz
- id_sort()
: vg::VG
- id_to_edge_indices
: vg::IndexedVG::CacheEntry
- id_to_name
: vg::Paths
- id_to_node_index
: vg::IndexedVG::CacheEntry
- id_to_prefix()
: vg::StreamIndexBase
- id_to_rank()
: bdsg::ODGI
, handlegraph::RankedHandleGraph
, Vectorizer
, vg::Viz
, xg::XG
- ID_WIDTH
: vg::MIPayload
- 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_chain
: vg::MinimumDistanceIndex::SnarlIndex
- in_from
: vg::ExtraNodeGraph
- in_nontrivial_chain()
: vg::SnarlManager
- include()
: vg::VG
- include_component
: vg::MinimumDistanceIndex
- include_endpoints
: vg::VCFTraversalFinder
- include_full_length_bonuses
: vg::Mapper
- include_maximum
: vg::MinimumDistanceIndex
- include_reversing_traversals
: vg::ExhaustiveTraversalFinder
- inclusive_interval()
: haplo::hDP_gbwt_graph_accessor< GBWTType >
- increment_coverage()
: vg::Packer
- increment_depth()
: vg::DepthMap
- increment_edge_coverage()
: vg::Packer
- increment_node_ids()
: bdsg::HashGraph
, bdsg::ODGI
, bdsg::PackedGraph
, 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
- Index()
: vg::Index
- index
: vg::IndexedVG
, vg::MinimumDistanceIndex::SnarlIndex
, vg::StreamIndex< Message >
- index_edge_by_node_sides()
: vg::VG
- index_node_to_path()
: xg::XG
- index_of
: vg::DozeuInterface::OrderedGraph
- index_to_node()
: vg::Packer
- IndexedVG()
: vg::IndexedVG
- indexes
: vg::GraphSynchronizer
- IndexManager()
: vg::IndexManager
- indexOpenException()
: vg::indexOpenException
- init()
: vg::SpliceMotifs
, vg::VG
, vg::Viz
- init_band_padding_memo()
: vg::MultipathMapper
- init_coverage_bin()
: vg::Packer
- init_edge_coverage_bin()
: vg::Packer
- init_mapper()
: vg::Filter
- init_mapping_quality()
: vg::GSSWAligner
- init_node_quality_bin()
: vg::Packer
- init_state()
: vg::DinucleotideMachine
- init_traceback_indexes()
: vg::BandedGlobalAligner< IntType >::BAMatrix
- initialize_sam_file()
: vg::HTSAlignmentEmitter
- inner_value
: haplo::haplo_DP_rectangle
- input
: vg::io::hFILE_cppstream
- input_in_progress
: vg::Funnel
- input_vcf
: vg::VCFGenotyper
- insert()
: vg::BitStringTree< Item >
, vg::BitStringTree< Item >::TreeNode
, vg::SmallBitset
, vg::SnarlState
- insert_before()
: bdsg::HashGraph::path_t
- insert_col
: vg::BandedGlobalAligner< IntType >::BAMatrix
- insert_distance()
: vg::MinimumDistanceIndex::SnarlIndex
- 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_step()
: bdsg::ODGI
- insert_traceback()
: vg::BandedGlobalAligner< IntType >::AltTracebackStack
- InsertCol
: vg::BandedGlobalAligner< IntType >
- insertion_filter()
: vg::Filter
- insertions
: vg::InsertHaplotypeCommand
, vg::ReplaceLocalHaplotypeCommand
- InsertRow
: vg::BandedGlobalAligner< IntType >
- int_is_inc
: haplo::haplo_DP_rectangle
- IntegratedSnarlFinder()
: vg::IntegratedSnarlFinder
- interchromosomal_filter()
: vg::Filter
- interleaved
: vg::ReadFilter
- internal_score
: vg::GaplessExtension
- intersection()
: haplo::int_itvl_t
- interval_size()
: haplo::haplo_DP_rectangle
- intervals
: vg::SRPE
- into_cutting_snarl()
: vg::MultipathAlignmentGraph
- into_which_snarl()
: vg::MinimumDistanceIndex
, vg::SnarlManager
- introduce()
: vg::Funnel
- invalid
: haplo::linear_haplo_structure
- inverse
: vg::Filter
- inverse_char_assignment
: bdsg::PackedGraph
- inversion_filter()
: vg::Filter
- is_a_duplicate_handle()
: vg::DozeuPinningOverlay
- is_a_duplicate_id()
: vg::DozeuPinningOverlay
- is_acyclic()
: vg::VG
- is_alt
: vg::Paths
- is_ancestor_next()
: vg::VG
- is_ancestor_prev()
: vg::VG
- is_checked_in
: vg::Watchdog::thread_state_t
- is_child()
: vg::NetGraph
- is_circular
: bdsg::HashGraph::path_t
, bdsg::ODGI::path_metadata_t
, vg::Path
, xg::XGPath
- is_compacted
: vg::Packer
- is_consistent()
: vg::MultipathMapper
- is_correct()
: vg::Funnel
- is_dynamic()
: vg::Packer
- is_empty()
: bdsg::ODGI
, handlegraph::PathHandleGraph
, haplo::haplo_DP_column
, vg::MemoizingGraph
- is_end
: vg::CactusSide
, vg::NodeSide
- is_extendable()
: vg::IncrementalSubgraph
- is_finalized()
: vg::FragmentLengthDistribution
- is_fixed
: vg::FragmentLengthDistribution
- is_head_node()
: vg::VG
- is_head_or_tail_node()
: vg::Paths
- is_in_range()
: vg::StreamIndexBase
- is_interval
: gafkluge::GafStep
- is_leaf()
: vg::SnarlManager
- is_left_clipped()
: vg::Filter
- is_looping_chain
: vg::MinimumDistanceIndex::ChainIndex
- is_new()
: haplo::haplo_DP_rectangle
- is_novel_edge()
: vg::AugmentedGraph
- is_novel_node()
: vg::AugmentedGraph
- is_ours()
: vg::ExtraNodeGraph
, vg::SourceSinkOverlay
- is_path_end()
: bdsg::ODGI
- is_path_front_end()
: bdsg::ODGI
- is_phased
: vg::Genotype
- is_rend
: vg::ChainIterator
- is_reverse
: gafkluge::GafStep
, vg::Genotyper::Affinity
, vg::mapping_t
, vg::Position
, vg::position_t
, vg::Transcript
, xg::XGPath
- is_root()
: vg::SnarlManager
- is_secondary
: vg::Alignment
- is_self_looping()
: vg::VG
- is_simple_snarl
: vg::MinimumDistanceIndex::SnarlIndex
- is_snarl_smaller_than_reads()
: vg::Genotyper
- is_snv()
: haplo::linear_haplo_structure
- is_solitary_ref()
: haplo::linear_haplo_structure
- is_split()
: vg::ReadFilter
- is_stable
: gafkluge::GafStep
- is_tail_node()
: vg::VG
- is_top_level_node
: vg::SnarlSeedClusterer::Seed
- is_top_level_snarl
: vg::SnarlSeedClusterer::Seed
- is_traversable()
: vg::LegacyCaller
, vg::MCMCCaller
- is_trivial()
: vg::SnarlManager
- is_trivial_snarl()
: vg::MinimumDistanceIndex::SnarlIndex
- is_unary_snarl
: vg::MinimumDistanceIndex::SnarlIndex
- 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_vo
: vg::io::MessageIterator
- items
: vg::Funnel::Stage
- iteratee
: vg::ShuffledPairs::iterator
- iterator()
: handlegraph::PathForEachSocket::iterator
, vg::PathIndex
, vg::PhasedGenome::iterator
, vg::ShuffledPairs::iterator
- iterator_category
: std::iterator_traits< vg::PhasedGenome::iterator >