vg
tools for working with variation graphs
- s -
s_bv :
xg::XG
s_bv_rank :
xg::XG
s_bv_select :
xg::XG
s_iv :
xg::XG
safe_to_get :
vg::VcfBuffer
sam_files :
vg::HTSAlignmentEmitter
sam_header :
vg::HTSAlignmentEmitter
sample_counter :
vg::NGSSimulator
sample_name :
vg::Alignment
,
vg::MCMCCaller
,
vg::MinimizerMapper
,
vg::MultipathAlignment
,
vg::MultipathAlignmentEmitter
,
vg::VCFOutputCaller
sample_names :
vg::Deconstructor
sample_range :
vg::HaplotypeIndexer
sample_unsheared_paths :
vg::NGSSimulator
samplers :
vg::NGSSimulator::MarkovDistribution< From, To >
samples_in_batch :
vg::HaplotypeIndexer
scc_copy_count :
vg::DagifiedGraph
scc_of_handle :
vg::DagifiedGraph
score :
vg::Alignment
,
vg::AlignmentChainModelVertex
,
vg::Connection
,
vg::Funnel::Item
,
vg::GaplessExtension
,
vg::Genotyper::Affinity
,
vg::GFFRecord
,
vg::MEMChainModelVertex
,
vg::MEMClusterer::HitNode
,
vg::MinimizerMapper::Minimizer
,
vg::SnarlSeedClusterer::Cluster
,
vg::Subpath
score_matrix :
vg::GSSWAligner
scratch :
vg::ChainIterator
secondary_rescue_attempts :
vg::MultipathMapper
secondary_rescue_score_diff :
vg::MultipathMapper
secondary_rescue_subopt_diff :
vg::MultipathMapper
secondary_score :
vg::Alignment
secondary_snarl_assignments :
vg::MinimumDistanceIndex
secondary_snarl_ranks :
vg::MinimumDistanceIndex
seed :
vg::MCMCGenotyper
,
vg::NGSSimulator
,
vg::SpliceRegion
seeds :
vg::BandedGlobalAligner< IntType >::BAMatrix
,
vg::SnarlSeedClusterer::Cluster
seek :
hFILE_backend
seq :
vg::algorithms::kmer_t
,
vg::algorithms::walk_t
,
vg::kmer_t
,
vg::Region
,
vg::VG::Plan
seq_iv :
bdsg::PackedGraph
seq_length :
vg::Viz
,
xg::XG
seq_length_iv :
bdsg::PackedGraph
SEQ_LENGTH_RECORD_SIZE :
bdsg::PackedGraph
seq_start_iv :
bdsg::PackedGraph
SEQ_START_RECORD_SIZE :
bdsg::PackedGraph
sequence :
bdsg::HashGraph::node_t
,
vg::Alignment
,
vg::Edit
,
vg::ExtraNodeGraph
,
vg::KmerMatch
,
vg::MultipathAlignment
,
vg::Node
,
vg::PathIndex
sequence_id :
vg::GFFRecord
short_mem_filter_factor :
vg::BaseMapper
short_options :
vg::ConfigurableParser
short_opts :
vg::BaseOption< Value, Parser >
show_cnv :
vg::Viz
show_dna :
vg::Viz
show_paths :
vg::Viz
show_progress :
vg::Genotyper
,
vg::Progressive
,
vg::VGset
sigma :
vg::FragmentLengthDistribution
simple_snarl_to_nodes_by_component :
vg::SnarlSeedClusterer::TreeState
simplify_topologies :
vg::MultipathMapper
simultaneous_pair_alignment :
vg::Mapper
since_last_fragment_length_estimate :
vg::FragmentLengthStatistics
sink_fwd :
vg::SourceSinkOverlay
sink_id :
vg::SourceSinkOverlay
sink_nodes :
vg::BandedGlobalAligner< IntType >
sink_rev :
vg::SourceSinkOverlay
site_ends :
vg::PhasedGenome
site_manager :
vg::SmallSnarlSimplifier
site_starts :
vg::PhasedGenome
sites :
vg::PhasedGenome::Haplotype
size :
vg::DepthMap
skip_alt :
vg::VCFTraversalFinder
skip_structural_duplications :
vg::VariantAdder
snarl :
vg::ReplaceSnarlHaplotypeCommand
,
vg::SnarlManager::SnarlRecord
,
vg::Visit
snarl_caller :
vg::GraphCaller
snarl_indexes :
vg::MinimumDistanceIndex
snarl_into :
vg::SnarlManager
snarl_manager :
vg::Deconstructor
,
vg::ExhaustiveTraversalFinder
,
vg::FlowTraversalFinder
,
vg::GraphCaller
,
vg::MCMCCaller
,
vg::MultipathMapper
,
vg::NestedTraversalFinder
,
vg::PathRestrictedTraversalFinder
,
vg::PathTraversalFinder
,
vg::PhasedGenome
,
vg::ReadRestrictedTraversalFinder
,
vg::RegionExpander
,
vg::RepresentativeTraversalFinder
,
vg::SupportBasedSnarlCaller
,
vg::TraversalSupportFinder
,
vg::VCFTraversalFinder
snarl_rank :
vg::SnarlSeedClusterer::Seed
snarl_reference_length_histogram :
vg::Genotyper
snarl_to_nodes :
vg::SnarlSeedClusterer::TreeState
snarl_traversals :
vg::Genotyper
snarlmanager :
vg::PathBasedTraversalFinder
snarls :
vg::IndexManager
,
vg::MCMCGenotyper
,
vg::SnarlManager
snarls_override :
vg::IndexManager
soft_clip_limit :
vg::Filter
soft_clipped :
vg::Alignment
softclip_threshold :
vg::Mapper
source :
vg::GFFRecord
,
vg::SnarlSeedClusterer::Seed
source_fwd :
vg::SourceSinkOverlay
source_id :
vg::SourceSinkOverlay
source_nodes :
vg::BandedGlobalAligner< IntType >
source_paths :
vg::NGSSimulator
,
vg::Sampler
source_rev :
vg::SourceSinkOverlay
splice_motifs :
vg::MultipathMapper
split_read_limit :
vg::Filter
split_supports :
vg::BREAKPOINT
stage_name :
vg::Funnel
stages :
vg::Funnel
STANDARD_LIBRARY :
vg::Version
start :
gafkluge::GafStep
,
vg::BREAKPOINT
,
vg::GFFRecord
,
vg::GraphSynchronizer::Lock
,
vg::MultipathAlignment
,
vg::NetGraph
,
vg::Range< Number >
,
vg::Region
,
vg::Snarl
start_end_reachable :
vg::Snarl
START_LEN_OFFSET :
vg::MIPayload
start_length :
vg::SnarlSeedClusterer::Seed
start_marker :
xg::XG
start_pos :
vg::MEMClusterer::HitNode
start_pos_samplers :
vg::NGSSimulator
start_self_reachable :
vg::Snarl
start_sep :
vg::Index
state :
haplo::haplo_DP_rectangle
,
vg::GaplessExtension
,
vg::GenomeState
,
vg::Watchdog
states :
vg::PhaseUnfolder
step :
handlegraph::PathForEachSocket::iterator
,
vg::Range< Number >
STEP_RECORD_SIZE :
bdsg::PackedGraph
steps_iv :
bdsg::PackedGraph::PackedPath
steps_of_handle_memo :
vg::MemoizingGraph
stop_watcher :
vg::Watchdog
strand :
gafkluge::GafRecord
strand_is_rev :
vg::GFFRecord
strand_sampler :
vg::NGSSimulator
strip_bonuses :
vg::BaseMapper
stripped_match_alg_max_length :
vg::MultipathMapper
stripped_match_alg_strip_length :
vg::MultipathMapper
stripped_match_alg_target_count :
vg::MultipathMapper
sub_mem_count_thinning :
vg::BaseMapper
sub_mem_thinning_burn_in :
vg::BaseMapper
sub_poly_rate :
vg::NGSSimulator
sub_score :
vg::ReadFilter
subgraph :
vg::GraphSynchronizer::Lock
,
vg::SpliceRegion
subgraph_min :
PruningParameters
subgraph_prune :
vg::VariantAdder
subpath :
vg::MultipathAlignment
substage_name :
vg::Funnel
suffixes :
vg::PhaseUnfolder
sum :
haplo::haplo_DP_column
super :
vg::PathSubgraph
,
vg::SubHandleGraph
,
vg::TreeSubgraph
support :
vg::LocationSupport
,
vg::Locus
support_finder :
vg::SupportBasedSnarlCaller
suppress_cluster_merging :
vg::MultipathMapper
suppress_mismapping_detection :
vg::MultipathMapper
suppress_multicomponent_splitting :
vg::MultipathMapper
suppress_p_value_memoization :
vg::MultipathMapper
suppress_tail_anchors :
vg::MultipathMapper
surface :
vg::Viz
SV_TYPE :
vg::BREAKPOINT
symbol_count :
vg::Pictographs
symbolic_allele_warnings :
vg::Constructor
symbols :
vg::Pictographs
sync :
vg::VariantAdder
synchronizer :
vg::GraphSynchronizer::Lock
Generated by
1.8.18