vg
tools for working with variation graphs
- i -
I() :
haplo::haplo_DP_rectangle
id_in_parent() :
vg::SnarlSeedClusterer::NetgraphNode
id_sort() :
vg::VG
id_to_prefix() :
vg::StreamIndexBase
id_to_rank() :
bdsg::ODGI
,
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_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
Index() :
vg::Index
index() :
vg::MinimumDistanceIndex::SnarlIndex
,
vg::StreamIndex< Message >
index_edge_by_node_sides() :
vg::VG
index_node_to_path() :
xg::XG
index_to_node() :
vg::Packer
IndexedVG() :
vg::IndexedVG
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
insert() :
vg::BitStringTree< Item >
,
vg::BitStringTree< Item >::TreeNode
,
vg::SmallBitset
,
vg::SnarlState
insert_before() :
bdsg::HashGraph::path_t
insert_distance() :
vg::MinimumDistanceIndex::SnarlIndex
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_step() :
bdsg::ODGI
insert_traceback() :
vg::BandedGlobalAligner< IntType >::AltTracebackStack
insertion_filter() :
vg::Filter
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::MinimumDistanceIndex
,
vg::SnarlManager
introduce() :
vg::Funnel
inversion_filter() :
vg::Filter
is_a_duplicate_handle() :
vg::DozeuPinningOverlay
is_a_duplicate_id() :
vg::DozeuPinningOverlay
is_acyclic() :
vg::VG
is_ancestor_next() :
vg::VG
is_ancestor_prev() :
vg::VG
is_child() :
vg::NetGraph
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_extendable() :
vg::IncrementalSubgraph
is_finalized() :
vg::FragmentLengthDistribution
is_head_node() :
vg::VG
is_head_or_tail_node() :
vg::Paths
is_in_range() :
vg::StreamIndexBase
is_leaf() :
vg::SnarlManager
is_left_clipped() :
vg::Filter
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_reverse() :
vg::mapping_t
,
vg::position_t
,
xg::XGPath
is_root() :
vg::SnarlManager
is_self_looping() :
vg::VG
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_tail_node() :
vg::VG
is_traversable() :
vg::LegacyCaller
,
vg::MCMCCaller
is_trivial() :
vg::SnarlManager
is_trivial_snarl() :
vg::MinimumDistanceIndex::SnarlIndex
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
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