Here is a list of all functions with links to the classes they belong to:
- s -
- 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_merged_cluster() : vg::MinimizerMapper
- 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
- search_left() : vg::NestedTraversalFinder
- search_right() : vg::NestedTraversalFinder
- 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::GBWTHandler, vg::Packer, vg::SnarlManager, vg::VG, 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_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::MIPayload
- set_chain_values() : vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem
- set_circularity() : handlegraph::MutablePathHandleGraph, vg::VG
- set_connection() : vg::subpath_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::MIPayload
- set_is_trivial_chain() : vg::MIPayload
- 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_node_length() : vg::MIPayload
- set_node_record_offset() : vg::MIPayload
- 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_parent_is_chain() : vg::MIPayload
- set_parent_is_root() : vg::MIPayload
- set_parent_record_offset() : vg::MIPayload
- set_path_position() : vg::Surjector
- set_prefix() : vg::IndexRegistry
- set_prefix_sum() : vg::MIPayload
- set_prev_idx() : haplo::haplo_DP_rectangle
- set_quality() : vg::multipath_alignment_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::MIPayload
- 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_values() : vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem
- set_soft_clip_limit() : vg::Filter
- 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
- 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_transcript_paths_update_copy_id() : vg::Transcriptome
- 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
- split_multicomponent_alignments() : vg::MultipathMapper
- split_read_filter() : vg::Filter
- ssw_to_vg() : vg::SSWAligner
- SSWAligner() : vg::SSWAligner
- 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_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
- 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
- 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_full_length_bonuses() : vg::MultipathMapper
- strip_subrange() : vg::Paths
- Subcommand() : vg::subcommand::Subcommand
- 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
- 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
- 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_offsets() : xg::XGPath
- sync_paths() : vg::VG
- synthesize_tail_anchors() : vg::MultipathAlignmentGraph