Here is a list of all variables with links to the classes they belong to:
- 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::HTSWriter
- sam_header : vg::HTSWriter
- sample_counter : vg::NGSSimulator
- sample_interval : vg::RebuildParameters
- sample_name : vg::Alignment, vg::MCMCCaller, vg::MinimizerMapper, vg::MultipathAlignment, vg::MultipathAlignmentEmitter, vg::VCFOutputCaller
- sample_names : vg::Deconstructor
- sample_ploidys : vg::Deconstructor
- sample_range : vg::HaplotypeIndexer
- sample_to_haplotypes : vg::Deconstructor::NestingInfo
- sample_to_ploidy : vg::ParentGenotypeInfo
- sample_unsheared_paths : vg::NGSSimulator
- samplers : vg::NGSSimulator::MarkovDistribution< From, To >
- samples : GBWTConfig
- samples_in_batch : vg::HaplotypeIndexer
- save_explanations : vg::Explainer
- scc_copy_count : vg::DagifiedGraph
- scc_of_handle : vg::DagifiedGraph
- score : vg::algorithms::TracedScore, 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::Recombinator::Statistics, vg::SnarlDistanceIndexClusterer::Cluster, vg::Subpath, vg::WFAAlignment, vg::WFAPoint
- score_bound : vg::WFATree
- score_matrix : vg::GSSWAligner
- score_output : HaplotypesConfig
- scores : vg::Recombinator::LocalHaplotype
- scratch : vg::ChainIterator
- search_threads : GBWTConfig
- secondary_rescue_attempts : vg::MultipathMapper
- secondary_rescue_score_diff : vg::MultipathMapper
- secondary_rescue_subopt_diff : vg::MultipathMapper
- secondary_score : vg::Alignment
- seed : vg::MCMCGenotyper, vg::NGSSimulator, vg::SpliceRegion
- seed_count_prefix_sum : vg::SnarlDistanceIndexClusterer::ClusteringProblem
- seed_indices : vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem::SnarlTreeChild
- seeds : vg::BandedGlobalAligner< IntType >::BAMatrix, vg::SnarlDistanceIndexClusterer::Cluster
- seek : hFILE_backend
- segment_to_name : vg::FlatFileBackTranslation
- segment_translation : GBWTConfig
- SEPARATOR : handlegraph::PathMetadata
- seq : vg::algorithms::kmer_t, vg::algorithms::walk_t, vg::kmer_t, vg::Region, vg::VG::Plan
- seq_length : vg::Viz, xg::XG
- seq_offset : vg::MatchPos, vg::WFAAlignment, vg::WFAPoint
- sequence : vg::Alignment, vg::Edit, vg::ExtraNodeGraph, vg::KmerMatch, vg::MultipathAlignment, vg::Node, vg::PathIndex, vg::Recombinator::LocalHaplotype, vg::WFATree
- sequence_id : vg::GFFRecord, vg::RecombinatorHaplotype
- sequence_source : GraphHandler
- sequences : vg::Haplotypes::Subchain
- sha1_variant_name : vg::Constructor
- shift_prune_diff : vg::Surjector
- short_mem_filter_factor : vg::BaseMapper
- short_option : vg::subcommand::BaseArgSpec< Receiver >
- short_options : vg::ConfigurableParser
- short_opts : vg::BaseOption< Value, Parser >
- show_cnv : vg::Viz
- show_dna : vg::Viz
- show_path_info : vg::Deconstructor
- show_paths : vg::Viz
- show_progress : GBWTConfig, vg::GBWTHandler, vg::Genotyper, vg::GraphCaller, vg::Progressive, vg::RebuildParameters, vg::Transcriptome, vg::VGset
- show_work : vg::MinimizerMapper
- sigma : vg::FragmentLengthDistribution
- 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 : job_type, vg::algorithms::Anchor
- skip_alt : vg::VCFTraversalFinder
- skip_structural_duplications : vg::VariantAdder
- snarl : vg::ReplaceSnarlHaplotypeCommand, vg::SnarlManager::SnarlRecord, vg::Visit
- snarl_caller : vg::GraphCaller
- snarl_into : vg::SnarlManager
- snarl_manager : vg::ExhaustiveTraversalFinder, vg::FlowTraversalFinder, vg::GraphCaller, vg::MCMCCaller, vg::MultipathMapper, vg::NestedTraversalFinder, vg::PathRestrictedTraversalFinder, vg::PhasedGenome, vg::ReadRestrictedTraversalFinder, vg::RegionExpander, vg::RepresentativeTraversalFinder, vg::SnarlGraph, vg::SupportBasedSnarlCaller, vg::TraversalSupportFinder, vg::VCFTraversalFinder
- snarl_number : vg::SnarlManager::SnarlRecord
- snarl_reference_length_histogram : vg::Genotyper
- snarl_traversals : vg::Genotyper
- snarlmanager : vg::PathBasedTraversalFinder
- snarls : vg::MCMCGenotyper, vg::SnarlGraph, vg::SnarlManager
- soft_clip_limit : vg::Filter
- soft_clipped : vg::Alignment
- softclip_threshold : vg::Mapper
- source : vg::algorithms::TracedScore, vg::GFFRecord, vg::SnarlDistanceIndexClusterer::Seed
- source_fwd : vg::SourceSinkOverlay
- source_id : vg::SourceSinkOverlay
- source_nodes : vg::BandedGlobalAligner< IntType >
- source_paths : vg::NGSSimulator, vg::Sampler
- source_rev : vg::SourceSinkOverlay
- sparse_to_dense : vg::SparseUnionFind
- splice_rescue_graph_std_devs : vg::MultipathMapper
- splice_stats : vg::MultipathMapper
- split_read_limit : vg::Filter
- split_supports : vg::BREAKPOINT
- stage_name : vg::Funnel
- stage_start_time : vg::Funnel
- stages : vg::Funnel
- STANDARD_LIBRARY : vg::Version
- star_allele : vg::Deconstructor
- start : gafkluge::GafStep, MappingRun, ReferenceInterval, vg::algorithms::Anchor, vg::BREAKPOINT, vg::GFFRecord, vg::GraphSynchronizer::Lock, vg::HaplotypePartitioner::Subchain, vg::Haplotypes::Subchain, vg::MultipathAlignment, vg::NetGraph, vg::Range< Number >, vg::Region, vg::Snarl
- start_end_reachable : vg::Snarl
- start_pos : vg::MEMClusterer::HitNode
- start_pos_samplers : vg::NGSSimulator
- start_self_reachable : vg::Snarl
- start_time : vg::Funnel
- state : haplo::haplo_DP_rectangle, vg::GaplessExtension, vg::GenomeState, vg::Watchdog, vg::WFANode
- states : vg::PhaseUnfolder
- stdev : vg::SummaryStatistics
- step : handlegraph::PathForEachSocket::iterator, vg::Range< Number >
- steps : vg::IndexingPlan
- steps_of_handle_memo : vg::MemoizingGraph
- stop_on_duplicate_paths : vg::algorithms::GFAParser
- stop_time : vg::Funnel
- stop_watcher : vg::Watchdog
- strand : gafkluge::GafRecord
- strand_is_rev : vg::GFFRecord
- strand_sampler : vg::NGSSimulator
- strict_conflict_checking : vg::Deconstructor
- 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< Read >
- subchain_id : HaplotypesConfig
- subchain_length : vg::HaplotypePartitioner::Parameters
- SUBCHAIN_LENGTH : vg::HaplotypePartitioner
- subchains : vg::Haplotypes::TopLevelChain, vg::Recombinator::Statistics
- subgraph : vg::GraphSynchronizer::Lock, vg::SpliceRegion
- subgraph_min : PruningParameters
- subgraph_prune : vg::VariantAdder
- subgroups : vg::subcommand::GroupedOptionGroup
- subpath : vg::MultipathAlignment
- subpath_handles : vg::SubpathOverlay
- subpath_to_length : vg::HTSWriter
- subsequences : vg::ReadFilter< Read >
- substage_name : vg::Funnel
- suffix : vg::IndexFile
- suffixes : vg::PhaseUnfolder
- suggested_edges : vg::DiagramExplainer
- sum : haplo::haplo_DP_column
- super : handlegraph::algorithms::SubHandleGraph, 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
- surject_subpath_global : vg::SurjectingAlignmentEmitter
- surjector : vg::SurjectingAlignmentEmitter
- SV_TYPE : vg::BREAKPOINT
- symbol_count : vg::Pictographs
- symbolic_allele_warnings : vg::Constructor
- symbols : vg::Pictographs
- sync : vg::VariantAdder
- synchronizer : vg::GraphSynchronizer::Lock