- s -

• same_chain() : vg::FragmentedHaplotypeVisit
• same_context() : vg::VG
• sample_path() : vg::NGSSimulator
• 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_transition() : vg::NGSSimulator::MarkovDistribution< From, To >
• Sampler() : vg::Sampler
• sanitize_sequence_in_place() : vg::Constructor
• save() : vg::io::VPKG , vg::StreamIndexBase
• save_bed() : vg::FeatureSet
• save_frag_lens_to_alns() : vg::FragmentLengthStatistics
• 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_path() : handlegraph::PathHandleGraph
• scan_seed_position() : vg::DozeuInterface
• scan_snarl() : vg::VCFOutputCaller
• scan_visits() : vg::algorithms::GFAParser
• scan_w_visits() : vg::algorithms::GFAParser
• scc_copy_of_handle() : vg::DagifiedGraph
• scc_copy_of_node_id() : vg::DagifiedGraph
• score() : haplo::GBWTScoreProvider< GBWTType > , haplo::haplo_DP , haplo::linear_haplo_structure , haplo::LinearScoreProvider , haplo::ScoreProvider , vg::algorithms::Anchor , vg::AlignmentChainModel , vg::BenchmarkResult , vg::connection_t , vg::Funnel , vg::MEMChainModel , vg::subpath_t
• score_alignment() : vg::Mapper
• score_alignment_pair() : vg::MinimizerMapper
• score_cluster() : vg::MinimizerMapper
• score_contiguous_alignment() : vg::GSSWAligner
• score_discontiguous_alignment() : vg::GSSWAligner
• score_error() : vg::BenchmarkResult
• score_exact_match() : vg::Aligner , vg::GSSWAligner , vg::QualAdjAligner
• score_extension_group() : vg::MinimizerMapper
• score_extensions() : vg::MinimizerMapper
• score_from() : vg::algorithms::TracedScore
• score_full_length_bonus() : vg::Aligner , vg::GSSWAligner , vg::QualAdjAligner
• score_gap() : vg::GSSWAligner
• score_mismatch() : vg::Aligner , vg::GSSWAligner , vg::QualAdjAligner
• score_partial_alignment() : vg::Aligner , vg::GSSWAligner , vg::QualAdjAligner
• score_sort_and_deduplicate_alignments() : vg::Mapper
• score_to_unnormalized_likelihood_ln() : vg::GSSWAligner
• score_tree() : vg::MinimizerMapper
• search_left() : vg::NestedTraversalFinder
• search_right() : vg::NestedTraversalFinder
• Seed() : vg::SnarlDistanceIndexClusterer::Seed
• seed_end() : vg::algorithms::Anchor
• seed_is_reversed_at_depth() : vg::ZipCodeTree
• seed_start() : vg::algorithms::Anchor
• seeds_in_subgraph() : vg::MinimizerMapper
• Seek() : vg::io::BlockedGzipInputStream
• seek_group() : vg::io::MessageIterator , vg::io::ProtobufIterator< T >
• SeqComplexity() : vg::SeqComplexity< MaxOrder >
• sequence() : vg::edit_t , vg::MaximalExactMatch , vg::multipath_alignment_t , vg::Sampler
• sequence_positions() : vg::BaseMapper
• serialize() : handlegraph::Serializable , handlegraph::TriviallySerializable , vg::GAFSorterRecord , vg::GBWTHandler , vg::Packer , vg::SnarlManager , vg::VG , vg::ZipCodeCollection , xg::XGPath
• serialize_and_measure() : xg::XG
• serialize_members() : handlegraph::Serializable , xg::XG
• serialize_members_and_measure() : xg::XG
• 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::OptionGroup< Receiver >
• set_alignment_scores() : vg::AlignerClient , vg::BaseMapper , vg::MinimizerMapper , vg::MultipathMapper
• set_allele() : vg::PhasedGenome
• set_annotation() : vg::multipath_alignment_t
• set_automatic_min_clustering_length() : vg::MultipathMapper
• set_avg() : vg::Filter
• 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() : handlegraph::MutablePathHandleGraph , 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_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_edge() : vg::VG
• set_filter_matches() : vg::Filter
• set_fragment_length_distr_params() : vg::PairedEndMapper
• set_from_length() : vg::edit_t
• set_hash_color() : vg::Viz
• set_het_bias() : vg::RatioSupportSnarlCaller
• set_id_increment() : handlegraph::MutableHandleGraph , vg::VG
• set_insertion_bias() : vg::PoissonSupportSnarlCaller
• set_intermediate_file_keeping() : vg::IndexRegistry
• set_intron_length_distribution() : vg::MultipathMapper
• set_inverse() : vg::Filter
• set_is_reverse() : vg::mapping_t , vg::position_t
• set_is_reversed() : vg::ZipCode::node_code_t , vg::ZipCode::snarl_code_t
• 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_depth() : vg::Filter
• set_min_percent_identity() : vg::Filter
• set_min_qual() : vg::Filter
• set_min_softclip_length_for_splice() : vg::MultipathMapper
• set_min_splice_length() : vg::MultipathAlignmentEmitter
• set_min_supports() : vg::SupportBasedSnarlCaller
• set_my_path_position_graph() : vg::Filter
• set_my_vg() : vg::Filter
• 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_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_region() : vg::VcfBuffer , vg::WindowedVcfBuffer
• set_remove_failing_edits() : vg::Filter
• set_sample_name() : vg::MultipathAlignmentEmitter
• set_score() : vg::connection_t , vg::subpath_t
• set_sequence() : vg::edit_t , vg::multipath_alignment_t
• set_show_progress() : vg::GraphCaller
• set_snarl_rank_or_identifier() : vg::ZipCode::chain_code_t
• set_snarl_values() : vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem
• set_soft_clip_limit() : vg::Filter
• set_sort_value() : vg::ZipCodeForest::sort_value_t
• set_source_paths() : vg::Sampler
• set_split_read_limit() : vg::Filter
• 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 >
• set_window_length() : vg::Filter
• setK() : vg::FlowTraversalFinder
• shallow_contents() : vg::SnarlManager
• share_terminal_positions() : vg::MultipathMapper
• shortest_seq_paths() : vg::BandedGlobalAligner< IntType >
• show_structure() : vg::Packer
• ShuffledPairs() : vg::ShuffledPairs
• sides_context() : vg::VG
• sides_from() : vg::VG
• sides_of() : vg::VG
• sides_to() : vg::VG
• 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
• size() : haplo::gbwt_thread_t , haplo::int_itvl_t , haplo::linear_haplo_structure::SNVvector , vg::DozeuInterface::OrderedGraph , vg::HandleGraphNodeSet , vg::MatchPos::PathList , vg::MultipathAlignmentGraph , vg::Option< vector< Item >, Parser > , vg::Paths , vg::SmallBitset , vg::SnarlState , vg::SparseUnionFind , vg::VectorView< Item > , vg::VG , vg::WFATree , vg::ZipCodeCollection
• SizeLimitExceededException() : vg::SizeLimitExceededException
• Skip() : vg::io::BlockedGzipInputStream
• small() : vg::SmallBitset
• SmallBitset() : vg::SmallBitset
• SmallSnarlSimplifier() : vg::SmallSnarlSimplifier
• smart_align() : vg::VariantAdder
• SmellsLikeGzip() : vg::io::BlockedGzipInputStream
• sn_deletion_between_ref() : haplo::linear_haplo_structure
• snarl_boundary_index() : vg::SnarlManager
• snarl_end_index() : vg::SnarlManager
• snarl_number() : vg::SnarlManager
• snarl_sharing_end() : vg::SnarlManager
• snarl_sharing_start() : vg::SnarlManager
• snarl_start_index() : vg::SnarlManager
• SnarlDistanceIndexClusterer() : vg::SnarlDistanceIndexClusterer
• SnarlGraph() : vg::SnarlGraph
• SnarlManager() : vg::SnarlManager
• SnarlMinDistance() : vg::SnarlMinDistance
• SnarlOrientedDistanceMeasurer() : vg::SnarlOrientedDistanceMeasurer
• SnarlState() : vg::SnarlState
• SnarlTreeNodeProblem() : vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem
• sniff_magic() : vg::io::Registry
• sniff_tag() : vg::io::MessageIterator
• SNVs() : haplo::linear_haplo_structure
• soft_clip_filter() : vg::Filter
• sort() : vg::StreamSorter< Message > , vg::VG
• sort_and_compute_mapping_quality() : vg::MultipathMapper
• 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_t() : vg::ZipCodeForest::sort_value_t
• SourceSinkOverlay() : vg::SourceSinkOverlay
• SparseUnionFind() : vg::SparseUnionFind
• spliced_cigar_against_path() : vg::SplicedHTSAlignmentEmitter
• spliced_surject() : vg::Surjector
• SplicedHTSAlignmentEmitter() : vg::SplicedHTSAlignmentEmitter
• SpliceRegion() : vg::SpliceRegion
• SpliceStats() : vg::SpliceStats
• split() : vg::BitString , vg::PrimerFinder
• split_multicomponent_alignments() : vg::MultipathMapper
• split_read_filter() : vg::Filter
• ssw_to_vg() : vg::SSWAligner
• SSWAligner() : vg::SSWAligner
• stack() : vg::ZipCodeTree::reverse_iterator
• stack_up_valid_walks() : vg::ExhaustiveTraversalFinder
• stage() : vg::Funnel
• stage_stop() : vg::Funnel
• standard_extend() : haplo::haplo_DP_column
• start() : vg::Funnel , vg::multipath_alignment_t
• start_degree() : vg::VG
• start_handle() : vg::Haplotypes::Subchain
• start_hint() : vg::algorithms::Anchor
• start_hint_offset() : vg::algorithms::Anchor
• start_size() : vg::multipath_alignment_t
• start_vcf() : vg::Genotyper
• StartFile() : vg::io::BlockedGzipOutputStream
• starting_position() : vg::GaplessExtension
• starts_at() : handlegraph::SnarlDecomposition
• starts_at_end() : handlegraph::SnarlDecomposition
• starts_at_start() : handlegraph::SnarlDecomposition
• starts_at_tip() : handlegraph::SnarlDecomposition
• startswith() : vg::PrimerFinder
• state() : vg::ZipCodeTree::reverse_iterator
• std_dev() : vg::FragmentLengthDistribution
• stddev() : vg::normal_distribution< T > , vg::truncated_normal_distribution< T >
• step_in_path() : vg::VCFTraversalFinder
• step_rank_at_position() : xg::XGPath
• steps_of_handle() : handlegraph::PathHandleGraph , vg::MemoizingGraph
• stop() : vg::Funnel
• str_view() : vg::str_view
• StrandSplitGraph() : vg::StrandSplitGraph
• stream_sort() : vg::StreamSorter< Message >
• streaminbuf() : vg::io::streaminbuf
• StreamIndex() : vg::StreamIndex< Message >
• StreamIndexBase() : vg::StreamIndexBase
• streaming_merge() : vg::StreamSorter< Message >
• streamistream() : vg::io::streamistream
• StreamMultiplexer() : vg::io::StreamMultiplexer
• StreamSorter() : vg::StreamSorter< Message >
• strip() : vg::PrimerFinder
• strip_full_length_bonuses() : vg::MultipathMapper
• strip_subrange() : vg::Paths
• Subcommand() : vg::subcommand::Subcommand
• subgraph() : vg::SubgraphExplainer
• SubgraphExplainer() : vg::SubgraphExplainer
• SubgraphOverlay() : vg::SubgraphOverlay
• SubHandleGraph() : handlegraph::algorithms::SubHandleGraph , vg::SubHandleGraph
• subpath() : vg::multipath_alignment_t
• subpath_size() : vg::multipath_alignment_t
• subpath_t() : vg::subpath_t
• SubpathOverlay() : vg::SubpathOverlay
• substage() : vg::Funnel
• substage_stop() : vg::Funnel
• substr() : vg::str_view
• successor_offset() : vg::WFATree
• suffix() : vg::RecombinatorHaplotype , vg::WFAExtender
• suggest_edge() : vg::DiagramExplainer
• support_val() : vg::SupportBasedSnarlCaller , vg::TraversalSupportFinder
• SupportBasedSnarlCaller() : vg::SupportBasedSnarlCaller
• SupportRestrictedTraversalFinder() : vg::SupportRestrictedTraversalFinder
• surject() : vg::Surjector
• surject_alignments_in_place() : vg::SurjectingAlignmentEmitter
• surject_internal() : vg::Surjector
• SurjectingAlignmentEmitter() : vg::SurjectingAlignmentEmitter
• Surjector() : vg::Surjector
• swap() : vg::SnarlState , vg::ZipCodeTree::reverse_iterator
• swap_alleles() : vg::PhasedGenome
• swap_endianness() : vg::endianness< IntType >
• swap_handles() : vg::VG
• swap_haplotypes() : vg::GenomeState
• swap_label() : vg::PhasedGenome
• swap_node_id() : vg::VG
• swap_node_ids() : vg::Paths
• swap_nodes() : vg::VG
• sync() : vg::zstd_compress_buf
• sync_offsets() : xg::XGPath
• sync_paths() : vg::VG
• synthesize_tail_anchors() : vg::MultipathAlignmentGraph