Here is a list of all class members with links to the classes they belong to:

- s -

S_SCAN_CHAIN : vg::ZipCodeTree::distance_iterator
S_SCAN_CYCLIC_SNARL : vg::ZipCodeTree::distance_iterator
S_SCAN_DAG_SNARL : vg::ZipCodeTree::distance_iterator
S_START : vg::ZipCodeTree::distance_iterator
safe_to_get : vg::VcfBuffer
SAM : vg::MultipathAlignmentEmitter
sam_files : vg::HTSWriter
sam_header : vg::HTSWriter
same_chain() : vg::FragmentedHaplotypeVisit
same_context() : vg::VG
sample_counter : vg::NGSSimulator
sample_interval : vg::RebuildParameters
sample_name : vg::MCMCCaller, vg::MinimizerMapper, vg::MultipathAlignmentEmitter, vg::VCFOutputCaller
sample_names : vg::Deconstructor
sample_path() : vg::NGSSimulator
sample_ploidys : vg::Deconstructor
sample_range : vg::HaplotypeIndexer
sample_read() : vg::NGSSimulator, vg::ReadFilter< Read >, vg::Sampler
sample_read_internal() : vg::NGSSimulator
sample_read_pair() : vg::NGSSimulator, vg::Sampler
sample_read_quality() : vg::NGSSimulator
sample_read_quality_internal() : vg::NGSSimulator
sample_read_quality_pair() : vg::NGSSimulator
sample_start_graph_pos() : vg::NGSSimulator
sample_start_path_pos() : vg::NGSSimulator
sample_start_pos() : vg::NGSSimulator
sample_to_haplotypes : vg::Deconstructor::ChildContext
sample_to_ploidy : vg::ParentGenotypeInfo
sample_transition() : vg::NGSSimulator::MarkovDistribution< From, To >
sample_unsheared_paths : vg::NGSSimulator
Sampler() : vg::Sampler
samplers : vg::NGSSimulator::MarkovDistribution< From, To >
samples : GBWTConfig
samples_in_batch : vg::HaplotypeIndexer
sanitize_sequence_in_place() : vg::Constructor
save() : vg::StreamIndexBase
save_bed() : vg::FeatureSet
save_explanations : vg::Explainer
save_frag_lens_to_alns() : vg::FragmentLengthStatistics
save_opposite_cyclic_snarl_exit() : vg::ZipCodeTree::distance_iterator
save_records() : vg::HTSWriter
save_to_file() : vg::Packer
scan() : vg::DozeuInterface, vg::IDScanner< Message >, vg::PositionIDScanner< Message >, vg::QualAdjXdropAligner, vg::WrappingPositionScanner< Message >, vg::XdropAligner
scan_backward() : vg::StreamIndexBase
scan_contig_lengths() : vg::VCFGenotyper
scan_for_deletion() : vg::VCFTraversalFinder
scan_p_visits() : vg::algorithms::GFAParser
scan_seed_position() : vg::DozeuInterface
scan_snarl() : vg::VCFOutputCaller
scan_visits() : vg::algorithms::GFAParser
scan_w_visits() : vg::algorithms::GFAParser
scc_copy_count : vg::DagifiedGraph
scc_copy_of_handle() : vg::DagifiedGraph
scc_copy_of_node_id() : vg::DagifiedGraph
scc_of_handle : vg::DagifiedGraph
scopes : vg::IndexFile, vg::IndexingPlan
score() : haplo::GBWTScoreProvider< GBWTType >, haplo::haplo_DP, haplo::ScoreProvider, vg::algorithms::Anchor, vg::algorithms::TracedScore, vg::AlignmentChainModel, vg::AlignmentChainModelVertex, vg::BenchmarkResult, vg::connection_t, vg::Funnel::Item, vg::Funnel, vg::GaplessExtension, vg::Genotyper::Affinity, vg::GFFRecord, vg::MEMChainModel, vg::MEMChainModelVertex, vg::MEMClusterer::HitNode, vg::MinimizerMapper::Minimizer, vg::Recombinator::Statistics, vg::SnarlDistanceIndexClusterer::Cluster, vg::subpath_t, vg::WFAAlignment, vg::WFAPoint
score_alignment() : vg::AlignmentScorer, vg::EditAlignmentScorer, vg::LoggedGapAlignmentScorer, vg::Mapper
score_alignment_pair() : vg::MinimizerMapper
score_bound : vg::WFATree
score_cluster() : vg::MinimizerMapper
score_contiguous_alignment() : vg::EditAlignmentScorer
score_discontiguous_alignment() : vg::EditAlignmentScorer
score_error() : vg::BenchmarkResult
score_exact_match() : vg::EditAlignmentScorer, vg::MatrixAlignmentScorer, vg::QualAdjAlignmentScorer
score_extension_group() : vg::MinimizerMapper
score_extensions() : vg::MinimizerMapper
score_from() : vg::algorithms::TracedScore
score_from_counts() : vg::LoggedGapAlignmentScorer
score_full_length_bonus() : vg::EditAlignmentScorer, vg::MatrixAlignmentScorer, vg::QualAdjAlignmentScorer
score_gap() : vg::EditAlignmentScorer
score_matrix : vg::MatrixAlignmentScorer
score_mismatch() : vg::EditAlignmentScorer, vg::MatrixAlignmentScorer, vg::QualAdjAlignmentScorer
score_partial_alignment() : vg::EditAlignmentScorer, vg::MatrixAlignmentScorer, vg::QualAdjAlignmentScorer
score_sort_and_deduplicate_alignments() : vg::Mapper
score_to_unnormalized_likelihood_ln() : vg::MappingQualityCalculator
score_tree() : vg::MinimizerMapper
scored_chain : vg::algorithms::ChainWithRec
scorer : vg::GSSWAligner
scores : vg::Recombinator::LocalHaplotype
scoring_model : vg::Recombinator::Parameters
scoring_model_t : vg::Recombinator::Parameters
scratch : vg::ChainIterator
search_threads : GBWTConfig
search_type : vg::PhaseUnfolder
secondary_rescue_attempts : vg::MultipathMapper
secondary_rescue_score_diff : vg::MultipathMapper
secondary_rescue_subopt_diff : vg::MultipathMapper
section_length : vg::ZipCodeTree::tree_item_t
SEED : vg::ZipCodeTree
Seed : vg::MinimizerMapper, vg::SnarlDistanceIndexClusterer::Seed, vg::ZipCodeForest, vg::ZipCodeTree
seed : vg::MCMCGenotyper, vg::NGSSimulator, vg::SnarlDistanceIndexClusterer::SeedCache, vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem, vg::SpliceRegion, vg::StreamSorter< Message >, vg::ZipCodeTree::oriented_seed_t
seed_count_prefix_sum : vg::SnarlDistanceIndexClusterer::ClusteringProblem
seed_end() : vg::algorithms::Anchor
seed_indices : vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem::SnarlTreeChild
seed_info_t() : vg::ZipCodeForest::seed_info_t
seed_is_reversed_at_depth() : vg::ZipCodeTree
seed_iterator() : vg::ZipCodeTree::seed_iterator
seed_length : vg::algorithms::Anchor
seed_pos : vg::ZipCodeForest::seed_info_t
seed_result_t() : vg::ZipCodeTree::seed_result_t
seed_sort_order : vg::ZipCodeForest::forest_growing_state_t
seed_start() : vg::algorithms::Anchor
seed_type : vg::GaplessExtender, vg::GaplessExtension
seeds : vg::BandedGlobalAligner< IntType >::BAMatrix, vg::SnarlDistanceIndexClusterer::Cluster, vg::ZipCodeForest::forest_growing_state_t
seeds_in_subgraph() : vg::MinimizerMapper
seen_read_names : vg::ReadFilter< Read >
segment_to_name : vg::FlatFileBackTranslation
segment_translation : GBWTConfig
seq : vg::algorithms::kmer_t, vg::algorithms::walk_t, vg::kmer_t, vg::Region, vg::VG::Plan
SEQ_DOES_NOT_MATCH : vg::AlignmentValidity
seq_length : vg::Viz
seq_offset : vg::MatchPos, vg::WFAAlignment, vg::WFAPoint
SeqComplexity() : vg::SeqComplexity< MaxOrder >
sequence() : vg::edit_t, vg::MaximalExactMatch, vg::multipath_alignment_t, vg::PathIndex, vg::Primer, vg::Recombinator::LocalHaplotype, vg::Sampler, vg::WFATree
sequence_dictionary : vg::HTSWriter
sequence_id : vg::FragmentedHaplotypeVisit, vg::GFFRecord, vg::RecombinatorFragment, vg::RecombinatorHaplotype
sequence_positions() : vg::BaseMapper
sequence_type : vg::HaplotypePartitioner, vg::Haplotypes, vg::Recombinator, vg::RecombinatorHaplotype
sequence_visits : vg::PrimerPair
sequences : vg::Haplotypes::Subchain
serialize() : vg::GAFSorterRecord, vg::GBWTHandler, vg::Packer, vg::SnarlManager, vg::VG, vg::ZipCodeCollection
serialize_segment_translation() : GraphHandler
serialize_to() : vg::Haplotypes
serialize_to_emitter() : vg::VG
serialize_to_file() : vg::VG
serialize_to_function() : vg::VG
serialize_to_ostream() : vg::VG
set() : vg::subcommand::ArgSpec< T, Receiver >, vg::subcommand::BaseArgSpec< Receiver >, vg::subcommand::BaseOptionGroup, vg::subcommand::GroupedOptionGroup, vg::subcommand::NegationFlagArgSpec< Receiver >, vg::subcommand::OptionGroup< Receiver >
set_alignment_scores() : vg::AlignerClient, vg::BaseMapper, vg::MinimizerMapper, vg::MultipathMapper, vg::Surjector
set_allele() : vg::PhasedGenome
set_allele_merge() : vg::VCFOutputCaller
set_annotation() : vg::multipath_alignment_t
set_automatic_min_clustering_length() : vg::MultipathMapper
set_baseline_error() : vg::PoissonSupportSnarlCaller
set_chain_component() : vg::ZipCode::node_code_t, vg::ZipCode::snarl_code_t, vg::ZipCodeForest::sort_value_t
set_chain_order() : vg::ZipCodeForest::sort_value_t
set_chain_values() : vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem
set_child_count() : vg::ZipCode::snarl_code_t
set_circularity() : vg::VG
set_code_type() : vg::ZipCode::snarl_code_t, vg::ZipCodeForest::sort_value_t
set_connection() : vg::subpath_t
set_connectivity() : vg::ZipCode::chain_code_t
set_context() : vg::Explainer
set_distance_end_left() : vg::ZipCode::snarl_code_t
set_distance_end_right() : vg::ZipCode::snarl_code_t
set_distance_start_left() : vg::ZipCode::snarl_code_t
set_distance_start_right() : vg::ZipCode::snarl_code_t
set_dp_alignment_scores() : vg::Surjector
set_edge() : vg::VG
set_fragment_length_distr_params() : vg::PairedEndMapper
set_from_length() : vg::edit_t
set_graph_name() : vg::Haplotypes
set_hash_color() : vg::Viz
set_het_bias() : vg::RatioSupportSnarlCaller
set_id_increment() : vg::VG
set_insertion_bias() : vg::PoissonSupportSnarlCaller
set_intermediate_file_keeping() : vg::IndexRegistry
set_intron_length_distribution() : vg::MultipathMapper
set_is_cyclic() : vg::ZipCodeTree::tree_item_t
set_is_reverse() : vg::mapping_t, vg::position_t
set_is_reversed() : vg::ZipCode::node_code_t, vg::ZipCode::snarl_code_t
set_is_secondary() : vg::Surjector
set_key() : vg::GAFSorterRecord
set_last_component() : vg::ZipCode::chain_code_t
set_length() : vg::ZipCode::chain_code_t, vg::ZipCode::node_code_t, vg::ZipCode::snarl_code_t
set_log_odds_against_splice() : vg::MultipathMapper
set_mapping_quality() : vg::multipath_alignment_t
set_max_merge_supression_length() : vg::MultipathMapper
set_min_bp_edge_override() : vg::TraversalSupportFinder
set_min_softclip_length_for_splice() : vg::MultipathMapper
set_min_splice_length() : vg::MultipathAlignmentEmitter
set_min_supports() : vg::SupportBasedSnarlCaller
set_nested() : vg::VCFOutputCaller
set_next() : vg::connection_t, vg::subpath_t
set_node_id() : vg::mapping_t, vg::position_t
set_offset() : haplo::haplo_DP_rectangle, vg::position_t
set_option_value() : vg::subcommand::BaseOptionGroup
set_paired_all() : vg::Counts
set_paired_any() : vg::Counts
set_path_position() : vg::Surjector
set_paths() : vg::algorithms::Anchor
set_pggname : GBWTConfig
set_prefix() : vg::IndexRegistry
set_prefix_sum_or_identifier() : vg::ZipCode::node_code_t, vg::ZipCode::snarl_code_t
set_prev_idx() : haplo::haplo_DP_rectangle
set_quality() : vg::multipath_alignment_t
set_raw_chain_component() : vg::ZipCode::node_code_t, vg::ZipCode::snarl_code_t
set_raw_child_count() : vg::ZipCode::snarl_code_t
set_raw_code_type() : vg::ZipCode::snarl_code_t
set_raw_connectivity() : vg::ZipCode::chain_code_t
set_raw_distance_end_left() : vg::ZipCode::snarl_code_t
set_raw_distance_end_right() : vg::ZipCode::snarl_code_t
set_raw_distance_start_left() : vg::ZipCode::snarl_code_t
set_raw_distance_start_right() : vg::ZipCode::snarl_code_t
set_raw_is_reversed() : vg::ZipCode::node_code_t, vg::ZipCode::snarl_code_t
set_raw_last_component() : vg::ZipCode::chain_code_t
set_raw_length() : vg::ZipCode::chain_code_t, vg::ZipCode::node_code_t, vg::ZipCode::snarl_code_t
set_raw_prefix_sum_or_identifier() : vg::ZipCode::node_code_t, vg::ZipCode::snarl_code_t
set_raw_record_offset() : vg::ZipCode::snarl_code_t
set_raw_snarl_rank_or_identifier() : vg::ZipCode::chain_code_t
set_read_1_adapter() : vg::MultipathMapper
set_read_2_adapter() : vg::MultipathMapper
set_read_coverage() : vg::MultipathMapper
set_read_group() : vg::MultipathAlignmentEmitter
set_record_offset() : vg::ZipCode::snarl_code_t
set_refpos : vg::MinimizerMapper, vg::Surjector
set_region() : vg::VcfBuffer, vg::WindowedVcfBuffer
set_sample_name() : vg::MultipathAlignmentEmitter
set_score() : vg::connection_t, vg::ReadFilter< Read >, vg::subpath_t
set_section_length() : vg::ZipCodeTree::tree_item_t
set_sequence() : vg::edit_t, vg::multipath_alignment_t
set_shared_paths() : vg::algorithms::TracedScore
set_show_progress() : vg::GraphCaller
set_snarl_rank_or_identifier() : vg::ZipCode::chain_code_t
set_snarl_values() : vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem
set_sort_value() : vg::ZipCodeForest::sort_value_t
set_source_paths() : vg::Sampler
set_start() : vg::multipath_alignment_t
set_support_switch_threshold() : vg::TraversalSupportFinder
set_target_memory_usage() : vg::IndexRegistry
set_to_length() : vg::edit_t
set_translation() : vg::VCFOutputCaller
set_value() : vg::subcommand::ArgSpec< T, Receiver >, vg::subcommand::ValueArgSpec< T, Receiver, Holder >, vg::ZipCodeTree::tree_item_t
set_verbose() : vg::GrefCover
setK() : vg::FlowTraversalFinder
sha1_variant_name : vg::Constructor
shallow_contents() : vg::SnarlManager
share_terminal_positions() : vg::MultipathMapper
shift_index_by() : vg::ZipCodeTree::distance_iterator
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 >
short_read_minimizer_k : vg::IndexingParameters
short_read_minimizer_W : vg::IndexingParameters
short_read_minimizer_w : vg::IndexingParameters
shortest_seq_paths() : vg::BandedGlobalAligner< IntType >
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_structure() : vg::Packer
show_work : vg::MinimizerMapper
ShuffledPairs : vg::ShuffledPairs::iterator, vg::ShuffledPairs
sibling_indices_at_depth : vg::ZipCodeForest::forest_growing_state_t
sides_context() : vg::VG
sides_from() : vg::VG
sides_of() : vg::VG
sides_to() : vg::VG
sigma : vg::FragmentLengthDistribution
simple_sds_load() : vg::Haplotypes, vg::Haplotypes::Subchain, vg::Haplotypes::TopLevelChain
simple_sds_serialize() : vg::Haplotypes, vg::Haplotypes::Subchain, vg::Haplotypes::TopLevelChain
simple_sds_size() : vg::Haplotypes, vg::Haplotypes::Subchain, vg::Haplotypes::TopLevelChain
simplify() : vg::RareVariantSimplifier, vg::SmallSnarlSimplifier
simplify_complicated_multipath_alignment() : vg::MultipathMapper
simplify_once() : vg::SmallSnarlSimplifier
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() : haplo::gbwt_thread_t, haplo::int_itvl_t, job_type, vg::algorithms::Anchor, vg::DozeuInterface::OrderedGraph, vg::HandleGraphNodeSet, vg::IndirectVectorView< Item >, vg::MatchPos::PathList, vg::MultipathAlignmentGraph, vg::Option< vector< Item >, Parser >, vg::Paths, vg::SmallBitset, vg::SparseUnionFind, vg::VectorView< Item >, vg::VG, vg::WFATree, vg::ZipCodeCollection
SizeLimitExceededException() : vg::SizeLimitExceededException
skip_alt : vg::VCFTraversalFinder
skip_chain() : vg::ZipCodeTree::distance_iterator
skip_structural_duplications : vg::VariantAdder
skippable : vg::algorithms::Anchor
small() : vg::SmallBitset
SmallBitset() : vg::SmallBitset
SmallSnarlSimplifier() : vg::SmallSnarlSimplifier
smart_align() : vg::VariantAdder
snarl : vg::SnarlManager::SnarlRecord
snarl_boundary_index() : vg::SnarlManager
snarl_caller : vg::GraphCaller
SNARL_CHAIN_COMPONENT_OFFSET : vg::ZipCode
SNARL_CHILD_COUNT_OFFSET : vg::ZipCode
SNARL_END : vg::ZipCodeTree
snarl_end_index() : vg::SnarlManager
snarl_into : vg::SnarlManager
SNARL_IS_REGULAR_OFFSET : vg::ZipCode
SNARL_LENGTH_OFFSET : vg::ZipCode
snarl_manager : vg::ExhaustiveTraversalFinder, vg::FlowTraversalFinder, vg::GraphCaller, vg::Masker, vg::MCMCCaller, vg::MultipathMapper, vg::PathRestrictedTraversalFinder, vg::PhasedGenome, vg::ReadRestrictedTraversalFinder, vg::RegionExpander, vg::RepresentativeTraversalFinder, vg::SnarlGraph, vg::SupportBasedSnarlCaller, vg::TraversalSupportFinder, vg::VCFTraversalFinder
snarl_number() : vg::SnarlManager, vg::SnarlManager::SnarlRecord
SNARL_OFFSET_IN_CHAIN_OFFSET : vg::ZipCode
snarl_rank_or_identifier : vg::ZipCode::chain_code_t
snarl_reference_length_histogram : vg::Genotyper
snarl_sharing_end() : vg::SnarlManager
snarl_sharing_start() : vg::SnarlManager
SNARL_START : vg::ZipCodeTree
snarl_start_index() : vg::SnarlManager
snarl_traversal_to_handles() : vg::VCFOutputCaller
snarl_traversals : vg::Genotyper
SnarlDistanceIndexClusterer() : vg::SnarlDistanceIndexClusterer
SnarlGraph() : vg::SnarlGraph
SnarlManager() : vg::SnarlManager
snarlmanager : vg::PathBasedTraversalFinder
SnarlMinDistance() : vg::SnarlMinDistance
SnarlOrientedDistanceMeasurer() : vg::SnarlOrientedDistanceMeasurer
snarls : vg::MCMCGenotyper, vg::SnarlGraph, vg::SnarlManager
SnarlTreeNodeProblem() : vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem
softclip_penalty : vg::MinimizerMapper
softclip_threshold : vg::Mapper
sort() : vg::StreamSorter< Message >, vg::VG
sort_and_compute_mapping_quality() : vg::MultipathMapper
sort_by_chain_score : vg::MinimizerMapper
sort_by_mapping_rank() : vg::Paths
sort_compact_nodes() : vg::Transcriptome
sort_minimizers_by_score() : vg::MinimizerMapper
sort_one_interval() : vg::ZipCodeForest
sort_transcript_paths_update_copy_id() : vg::Transcriptome
sort_value : vg::ZipCodeForest::sort_value_t
sort_value_t() : vg::ZipCodeForest::sort_value_t
sort_values_by_seed : vg::ZipCodeForest::forest_growing_state_t
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
SourceSinkOverlay() : vg::SourceSinkOverlay
space_efficient_counting : vg::IndexingParameters, vg::MinimizerIndexParameters
sparse_to_dense : vg::SparseUnionFind
SparseUnionFind() : vg::SparseUnionFind
spine_nodes : vg::GrefCover::TopLevelSnarlStats
splice_rescue_graph_std_devs : vg::MultipathMapper
splice_stats : vg::MultipathMapper
SPLICED_DEFAULT_SUBGRAPH_LIMIT : vg::Surjector
spliced_surject() : vg::Surjector
SplicedHTSAlignmentEmitter() : vg::SplicedHTSAlignmentEmitter
SpliceRegion() : vg::SpliceRegion
SpliceStats() : vg::SpliceStats
SpliceStrand : vg::MultipathMapper
split() : vg::BitString, vg::Counts, vg::PrimerFinder
split_multicomponent_alignments() : vg::MultipathMapper
ssw_to_vg() : vg::SSWAligner
SSWAligner() : vg::SSWAligner
stable : vg::GAFSorterParameters
stack_below_top() : vg::ZipCodeTree::distance_iterator
stack_data : vg::ZipCodeTree::distance_iterator::iteration_position
stack_matrix_value() : vg::ZipCodeTree::distance_iterator
stack_snarl_distances() : vg::ZipCodeTree::distance_iterator
stack_up_valid_walks() : vg::ExhaustiveTraversalFinder
stage() : vg::Funnel
stage_name : vg::Funnel
stage_start_time : vg::Funnel
stage_stop() : vg::Funnel
stages : vg::Funnel
standard_address : vg::LoggedGapAlignmentScorer
standard_extend() : haplo::haplo_DP_column
STANDARD_LIBRARY : vg::Version
standard_scoring : vg::Recombinator::Parameters
star_allele : vg::Deconstructor, vg::FlowCaller
start : MappingRun, ReferenceInterval, vg::algorithms::Anchor, vg::Funnel, vg::GFFRecord, vg::GraphSynchronizer::Lock, vg::HaplotypePartitioner::Subchain, vg::Haplotypes::Subchain, vg::multipath_alignment_t, vg::NetGraph, vg::PathPiece, vg::Range< Number >, vg::Region
start_degree() : vg::VG
start_handle() : vg::Haplotypes::Subchain
start_hint() : vg::algorithms::Anchor
start_hint_offset() : vg::algorithms::Anchor
start_offset : vg::algorithms::Anchor
start_paths : vg::algorithms::Anchor
start_pos : vg::algorithms::Anchor, vg::MEMClusterer::HitNode
start_pos_samplers : vg::NGSSimulator
start_seed : vg::algorithms::Anchor
start_size() : vg::multipath_alignment_t
start_time : vg::Funnel
start_vcf() : vg::Genotyper
start_zip : vg::algorithms::Anchor
starting_position() : vg::GaplessExtension
startswith() : vg::PrimerFinder
State : vg::Funnel, vg::ZipCodeTree::distance_iterator
state : haplo::haplo_DP_rectangle, vg::GaplessExtension, vg::Watchdog, vg::WFANode, vg::ZipCodeTree::distance_iterator::iteration_position
state_type : vg::PhaseUnfolder
states : vg::PhaseUnfolder
std_dev() : vg::FragmentLengthDistribution
stddev() : vg::normal_distribution< T >, vg::truncated_normal_distribution< T >
stdev : vg::SummaryStatistics
step : vg::Range< Number >
step_in_path() : vg::VCFTraversalFinder
steps : vg::IndexingPlan
steps_of_handle() : vg::MemoizingGraph
steps_of_handle_memo : vg::MemoizingGraph
stop() : vg::Funnel
stop_on_duplicate_paths : vg::algorithms::GFAParser
stop_time : vg::Funnel
stop_watcher : vg::Watchdog
stored_edge_t : vg::DiagramExplainer
STRAND_FIELD : vg::GAFSorterRecord
strand_is_rev : vg::GFFRecord
strand_sampler : vg::NGSSimulator
StrandSplitGraph() : vg::StrandSplitGraph
stream_sort() : vg::StreamSorter< Message >
StreamIndex() : vg::StreamIndex< Message >
StreamIndexBase() : vg::StreamIndexBase
streaming_merge() : vg::StreamSorter< Message >
StreamSorter() : vg::StreamSorter< Message >
strict_conflict_checking : vg::Deconstructor
String : vg::multipath_alignment_t
strip() : vg::PrimerFinder
strip_bonuses : vg::BaseMapper
strip_full_length_bonuses() : vg::MultipathMapper
strip_subrange() : vg::Paths
stripped_match_alg_max_length : vg::MultipathMapper
stripped_match_alg_strip_length : vg::MultipathMapper
stripped_match_alg_target_count : vg::MultipathMapper
sub_durations : vg::Funnel::Stage
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 : vg::RecombinatorFragment
SUBCHAIN_LENGTH : vg::HaplotypePartitioner
subchain_length : vg::HaplotypePartitioner::Parameters
subchain_t : vg::Haplotypes::Subchain
subchains : vg::Haplotypes::TopLevelChain, vg::Recombinator::Statistics
Subcommand() : vg::subcommand::Subcommand
subgraph : vg::GraphSynchronizer::Lock, vg::SpliceRegion, vg::SubgraphExplainer
subgraph_min : PruningParameters
subgraph_prune : vg::VariantAdder
SubgraphExplainer() : vg::SubgraphExplainer
SubgraphOverlay() : vg::SubgraphOverlay
subgroups : vg::subcommand::GroupedOptionGroup
SubHandleGraph() : vg::SubHandleGraph
subpath() : vg::multipath_alignment_t
subpath_handles : vg::SubpathOverlay
subpath_size() : vg::multipath_alignment_t
subpath_t() : vg::subpath_t
subpath_to_index : vg::HTSWriter
SubpathOverlay() : vg::SubpathOverlay
subsequence : vg::Counts
subsequences : vg::ReadFilter< Read >
substage() : vg::Funnel
substage_name : vg::Funnel
substage_start_time : vg::Funnel
substage_stop() : vg::Funnel
substitute_wildcards() : vg::IndexRegistry
successor_offset() : vg::WFATree
suffix : vg::Haplotypes::Subchain, vg::RecombinatorHaplotype, vg::WFAExtender
suffixes : vg::IndexFile, vg::PhaseUnfolder
suggest_edge() : vg::DiagramExplainer
suggested_edge_t : vg::DiagramExplainer
suggested_edges : vg::DiagramExplainer
sum : haplo::haplo_DP_column
super : vg::PathSubgraph, vg::SubHandleGraph, vg::TreeSubgraph
supergraph_filename : GBWTConfig
supplementary_cover() : vg::Surjector
support_finder : vg::SupportBasedSnarlCaller
support_val() : vg::SupportBasedSnarlCaller, vg::TraversalSupportFinder
SupportBasedSnarlCaller() : vg::SupportBasedSnarlCaller
SupportMap : vg::NestedCachedPackedTraversalSupportFinder
SupportRestrictedTraversalFinder() : vg::SupportRestrictedTraversalFinder
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
suppressed_ref_info : vg::VCFOutputCaller
surface : vg::Viz
surject() : vg::Surjector
surject_in_place() : vg::Surjector
surject_internal() : vg::Surjector
surject_paired_in_place() : vg::Surjector
surject_subpath_global : vg::SurjectingAlignmentEmitter
SurjectingAlignmentEmitter() : vg::SurjectingAlignmentEmitter
Surjector() : vg::Surjector
surjector : vg::SurjectingAlignmentEmitter
swap() : vg::ZipCodeTree::distance_iterator
swap_alleles() : vg::PhasedGenome
swap_handles() : vg::VG
swap_label() : vg::PhasedGenome
swap_node_id() : vg::VG
swap_node_ids() : vg::Paths
swap_nodes() : vg::VG
symbol_count : vg::Pictographs
symbolic_allele_warnings : vg::Constructor
symbols : vg::Pictographs
sync : vg::VariantAdder, vg::zstd_compress_buf
sync_paths() : vg::VG
synchronizer : vg::GraphSynchronizer::Lock
syncmers() : vg::MinimizerIndexParameters
synthesize_tail_anchors() : vg::MultipathAlignmentGraph