vg
tools for working with variation graphs
- r -
R :
haplo::haplo_DP_rectangle
r_iv :
xg::XG
random_engine :
vg::MCMCGenotyper
range :
vg::MaximalExactMatch
rank :
vg::Mapping
,
vg::mapping_t
,
vg::PhasedGenome::iterator
RANK_MASK :
vg::MIPayload
RANK_OFFSET :
vg::MIPayload
RANK_WIDTH :
vg::MIPayload
read :
hFILE_backend
read_best_left :
vg::SnarlSeedClusterer::NodeClusters
read_best_right :
vg::SnarlSeedClusterer::NodeClusters
read_cluster_dists :
vg::SnarlSeedClusterer::TreeState
read_cluster_heads :
vg::SnarlSeedClusterer::NodeClusters
read_distance_limit :
vg::SnarlSeedClusterer::TreeState
read_group :
vg::Alignment
,
vg::MinimizerMapper
,
vg::MultipathAlignment
,
vg::MultipathAlignmentEmitter
read_index_offsets :
vg::SnarlSeedClusterer::TreeState
read_interval :
vg::GaplessExtension
read_mapped :
vg::Alignment
read_on_reverse_strand :
vg::Alignment
read_paired :
vg::Alignment
read_union_find :
vg::SnarlSeedClusterer::TreeState
reader :
vg::WindowedVcfBuffer
reads_by_name :
vg::PathRestrictedTraversalFinder
realign_indels :
vg::Genotyper
recombination_penalty :
vg::BaseMapper
,
vg::MultipathMapper
record_bases :
vg::Packer
record_edges :
vg::Packer
record_edits :
vg::Packer
record_qualities :
vg::Packer
redundant_vertexes :
vg::AlignmentChainModel
,
vg::MEMChainModel
reestimation_frequency :
vg::FragmentLengthDistribution
ref_base :
vg::BasePileup
ref_names :
vg::SRPE
ref_offset :
vg::DozeuInterface::graph_pos_s
ref_offsets :
vg::FlowCaller
,
vg::LegacyCaller
,
vg::MCMCCaller
ref_path :
vg::FlowSort::Growth
ref_path_handle :
haplo::linear_haplo_structure
ref_path_lengths :
vg::MCMCCaller
ref_path_offsets :
vg::MCMCCaller
ref_path_set :
vg::FlowCaller
ref_paths :
vg::Deconstructor
,
vg::FlowCaller
,
vg::GAFOutputCaller
,
vg::LegacyCaller
,
vg::MCMCCaller
ref_positions :
haplo::linear_haplo_structure::SNVvector
reference_origin :
vg::TranscriptPath
reference_paths :
vg::PhaseUnfolder
reflect :
vg::GraphSynchronizer::Lock
refpos :
vg::Alignment
regions :
vg::HaplotypeIndexer
regular_aligner :
vg::AlignerClient
remove_failing_edits :
vg::Filter
rename_variants :
vg::HaplotypeIndexer
repeat_size :
vg::ReadFilter
report_group_mapq :
vg::MultipathMapper
rescore :
vg::ReadFilter
rescue_algorithm :
vg::MinimizerMapper
rescue_graph_std_devs :
vg::MultipathMapper
rescue_only_anchor_max :
vg::MultipathMapper
rescue_only_min :
vg::MultipathMapper
rescue_subgraph_stdevs :
vg::MinimizerMapper
reserved :
vg::Alignment
reset_chain_parent :
vg::Range< Number >
restrained_graph_extraction :
vg::MultipathMapper
retry_on_Ns :
vg::NGSSimulator
rev_in_chain :
vg::SnarlSeedClusterer::Seed
rev_in_parent :
vg::MinimumDistanceIndex::ChainIndex
,
vg::MinimumDistanceIndex::SnarlIndex
REV_OFFSET :
vg::MIPayload
reverse :
vg::Support
reversing_self_edge_records :
bdsg::PackedGraph
reversing_walk_length :
vg::MultipathMapper
rho :
haplo::haploMath::RRMemo
right :
vg::Support
right_edges :
bdsg::HashGraph::node_t
right_ends :
vg::ConstructedChunk
right_full :
vg::GaplessExtension
right_handle_trans :
vg::JoinedSpliceGraph
right_maximal :
vg::GaplessExtension
right_splice_offset :
vg::JoinedSpliceGraph
right_subgraph :
vg::JoinedSpliceGraph
right_telomere_node :
vg::PhasedGenome::Haplotype
RING_BUFFER_SIZE :
vg::io::StreamMultiplexer
rng :
vg::Colors
,
vg::Pictographs
,
vg::Sampler
robust_estimation_fraction :
vg::FragmentLengthDistribution
root :
vg::BitStringTree< Item >
,
vg::Tree< T >
root_chains :
vg::SnarlManager
root_trim :
vg::TreeSubgraph
roots :
vg::SnarlManager
row_idx :
vg::BandedGlobalAligner< IntType >::AltTracebackStack::Deflection
rr_memos :
vg::MultipathMapper
running :
vg::Range< Number >
runs :
vg::BenchmarkResult
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