Here is a list of all class members 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::HTSAlignmentEmitter
- sam_header
: vg::HTSAlignmentEmitter
- same_context()
: vg::VG
- sample_counter
: vg::NGSSimulator
- sample_name
: vg::Alignment
, vg::MCMCCaller
, vg::MinimizerMapper
, vg::MultipathAlignment
, vg::MultipathAlignmentEmitter
, vg::VCFOutputCaller
- sample_names
: vg::Deconstructor
- sample_path()
: vg::NGSSimulator
- sample_range
: vg::HaplotypeIndexer
- sample_read()
: vg::NGSSimulator
, vg::ReadFilter
- sample_read_internal()
: vg::NGSSimulator
- sample_read_pair()
: vg::NGSSimulator
- 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 >
- sample_unsheared_paths
: vg::NGSSimulator
- Sampler()
: vg::Sampler
- samplers
: vg::NGSSimulator::MarkovDistribution< From, To >
- samples_in_batch
: vg::HaplotypeIndexer
- save()
: vg::io::VPKG
, vg::StreamIndexBase
- save_bed()
: vg::FeatureSet
- save_frag_lens_to_alns()
: vg::FragmentLengthStatistics
- save_records()
: vg::HTSAlignmentEmitter
- 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_path()
: handlegraph::PathHandleGraph
- scan_seed_position()
: vg::DozeuInterface
- scc_copy_count
: vg::DagifiedGraph
- scc_copy_of_handle()
: vg::DagifiedGraph
- scc_copy_of_node_id()
: vg::DagifiedGraph
- scc_of_handle
: vg::DagifiedGraph
- score()
: haplo::GBWTScoreProvider< GBWTType >
, haplo::haplo_DP
, haplo::linear_haplo_structure
, haplo::LinearScoreProvider
, haplo::ScoreProvider
, vg::Alignment
, vg::AlignmentChainModel
, vg::AlignmentChainModelVertex
, vg::BenchmarkResult
, vg::Connection
, 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::SnarlSeedClusterer::Cluster
, vg::SpliceMotifs
, vg::Subpath
, vg::subpath_t
- score_alignment()
: vg::Mapper
- 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_gap()
: vg::GSSWAligner
- score_matrix
: 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
- scratch
: vg::ChainIterator
- search_left()
: vg::NestedTraversalFinder
- search_right()
: vg::NestedTraversalFinder
- search_type
: vg::PhaseUnfolder
- 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
- Seed
: vg::MinimizerMapper
- seed
: vg::NGSSimulator
, vg::SpliceRegion
- seed_type
: vg::GaplessExtender
, vg::GaplessExtension
- seeds
: vg::BandedGlobalAligner< IntType >::BAMatrix
, vg::SnarlSeedClusterer::Cluster
- seeds_in_subgraph()
: vg::MinimizerMapper
- seek
: hFILE_backend
- Seek()
: vg::io::BlockedGzipInputStream
- seek_group()
: vg::io::MessageIterator
, vg::io::ProtobufIterator< T >
- 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::edit_t
, vg::ExtraNodeGraph
, vg::KmerMatch
, vg::MaximalExactMatch
, vg::multipath_alignment_t
, vg::MultipathAlignment
, vg::Node
, vg::PathIndex
, vg::Sampler
- sequence_id
: vg::GFFRecord
- sequence_positions()
: vg::BaseMapper
- serialize()
: bdsg::HashGraph::node_t
, bdsg::HashGraph::path_t
, handlegraph::SerializableHandleGraph
, vg::MinimumDistanceIndex::ChainIndex
, vg::MinimumDistanceIndex
, vg::MinimumDistanceIndex::SnarlIndex
, vg::Packer
, vg::SnarlManager
, vg::VG
, xg::XGPath
- serialize_and_measure()
: bdsg::ODGI
, xg::XG
- serialize_members()
: bdsg::HashGraph
, bdsg::ODGI
, bdsg::PackedGraph
, handlegraph::SerializableHandleGraph
, xg::XG
- serialize_members_and_measure()
: xg::XG
- serialize_to_emitter()
: vg::VG
- serialize_to_file()
: vg::VG
- serialize_to_function()
: vg::VG
- serialize_to_ostream()
: vg::VG
- set_alignment_scores()
: vg::AlignerClient
, vg::BaseMapper
, 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_cache_size()
: vg::BaseMapper
- set_circularity()
: bdsg::HashGraph
, bdsg::ODGI
, bdsg::PackedGraph
, handlegraph::MutablePathHandleGraph
, vg::VG
- set_connection()
: vg::subpath_t
- set_depth()
: vg::DepthMap
- set_distance_override()
: vg::IndexManager
- set_edge()
: vg::VG
- set_edge_target()
: bdsg::PackedGraph
- set_fasta_filename()
: vg::IndexManager
- set_filter_matches()
: vg::Filter
- set_fragment_length_distr_params()
: vg::PairedEndMapper
- set_from_length()
: vg::edit_t
- set_gbwt_override()
: vg::IndexManager
- set_gbwtgraph_override()
: vg::IndexManager
- set_graph_override()
: vg::IndexManager
- set_handle_of_step()
: bdsg::ODGI
- set_handle_sequence()
: bdsg::ODGI
- set_hash_color()
: vg::Viz
- set_het_bias()
: vg::RatioSupportSnarlCaller
- set_id()
: bdsg::HashGraph
- set_id_increment()
: bdsg::HashGraph
, bdsg::ODGI
, bdsg::PackedGraph
, handlegraph::MutableHandleGraph
, vg::VG
- set_inverse()
: vg::Filter
- set_is_reverse()
: vg::mapping_t
, vg::position_t
- set_mapping_quality()
: vg::multipath_alignment_t
- set_membership_path()
: bdsg::PackedGraph
- set_membership_step()
: bdsg::PackedGraph
- set_min_depth()
: vg::Filter
- set_min_percent_identity()
: vg::Filter
- set_min_qual()
: vg::Filter
- set_min_supports()
: vg::SupportBasedSnarlCaller
- set_minimizer_override()
: vg::IndexManager
- set_my_path_position_graph()
: vg::Filter
- set_my_vg()
: vg::Filter
- set_next()
: vg::connection_t
, vg::subpath_t
- set_next_membership()
: bdsg::PackedGraph
- set_node_id()
: vg::mapping_t
, vg::position_t
- set_offset()
: haplo::haplo_DP_rectangle
, vg::position_t
- set_paired_all()
: vg::ReadFilter::Counts
- set_paired_any()
: vg::ReadFilter::Counts
- set_path_position()
: vg::Surjector
- set_path_position_inexact()
: vg::Surjector
- set_prev_idx()
: haplo::haplo_DP_rectangle
- set_quality()
: vg::multipath_alignment_t
- set_read_group()
: vg::MultipathAlignmentEmitter
- 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_snarls_override()
: vg::IndexManager
- set_soft_clip_limit()
: vg::Filter
- set_source_paths()
: vg::Sampler
- set_split_read_limit()
: vg::Filter
- set_start()
: vg::multipath_alignment_t
- set_step()
: bdsg::ODGI
- set_step_next()
: bdsg::PackedGraph
- set_step_prev()
: bdsg::PackedGraph
- set_step_trav()
: bdsg::PackedGraph
- set_support_switch_threshold()
: vg::TraversalSupportFinder
- set_to_length()
: vg::edit_t
- set_vcf_filename()
: vg::IndexManager
- set_window_length()
: vg::Filter
- setK()
: vg::FlowTraversalFinder
- shallow_contents()
: vg::SnarlManager
- share_terminal_positions()
: vg::MultipathMapper
- short_mem_filter_factor
: vg::BaseMapper
- short_options
: vg::ConfigurableParser
- short_opts
: vg::BaseOption< Value, Parser >
- shortest_seq_paths()
: vg::BandedGlobalAligner< IntType >
- show_cnv
: vg::Viz
- show_dna
: vg::Viz
- show_paths
: vg::Viz
- show_progress
: vg::Genotyper
, vg::Progressive
, vg::VGset
- show_structure()
: vg::Packer
- ShuffledPairs
: vg::ShuffledPairs::iterator
, vg::ShuffledPairs
- sides_context()
: vg::VG
- sides_from()
: vg::VG
- sides_of()
: vg::VG
- sides_to()
: vg::VG
- sigma
: vg::FragmentLengthDistribution
- simple_snarl_to_nodes_by_component
: vg::SnarlSeedClusterer::TreeState
- simplify()
: vg::RareVariantSimplifier
, vg::SmallSnarlSimplifier
- 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
, haplo::linear_haplo_structure::SNVvector
, vg::DepthMap
, vg::DozeuInterface::OrderedGraph
, vg::Option< vector< Item >, Parser >
, vg::Paths
, vg::SmallBitset
, vg::SnarlState
, vg::SpliceMotifs
, vg::Transcriptome
, vg::VG
- Skip()
: vg::io::BlockedGzipInputStream
- skip_alt
: vg::VCFTraversalFinder
- skip_structural_duplications
: vg::VariantAdder
- 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
: vg::ReplaceSnarlHaplotypeCommand
, vg::SnarlManager::SnarlRecord
- SNARL
: vg::SnarlSeedClusterer
- snarl
: vg::Visit
- snarl_boundary_index()
: vg::SnarlManager
- snarl_caller
: vg::GraphCaller
- snarl_distance()
: vg::MinimumDistanceIndex::SnarlIndex
- snarl_end_index()
: vg::SnarlManager
- snarl_indexes
: vg::MinimumDistanceIndex
- snarl_into
: vg::SnarlManager
- snarl_length()
: vg::MinimumDistanceIndex::SnarlIndex
- 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_sharing_end()
: vg::SnarlManager
- snarl_sharing_start()
: vg::SnarlManager
- snarl_start_index()
: vg::SnarlManager
- snarl_to_json()
: vg::MinimumDistanceIndex::SnarlIndex
- snarl_to_nodes
: vg::SnarlSeedClusterer::TreeState
- snarl_traversals
: vg::Genotyper
- SnarlIndex
: vg::MinimumDistanceIndex
, vg::MinimumDistanceIndex::SnarlIndex
- snarlmanager
: vg::PathBasedTraversalFinder
- SnarlManager()
: vg::SnarlManager
- SnarlMinDistance()
: vg::SnarlMinDistance
- SnarlOrientedDistanceMeasurer()
: vg::SnarlOrientedDistanceMeasurer
- snarls
: vg::IndexManager
, vg::MCMCGenotyper
, vg::SnarlManager
- snarls_override
: vg::IndexManager
- SnarlSeedClusterer
: vg::MinimumDistanceIndex::ChainIndex
, vg::MinimumDistanceIndex::SnarlIndex
, vg::MinimumDistanceIndex
, vg::SnarlSeedClusterer
- SnarlState()
: vg::SnarlState
- sniff_magic()
: vg::io::VPKG
- sniff_tag()
: vg::io::MessageIterator
- snv
: haplo::linear_haplo_structure
- SNVs()
: haplo::linear_haplo_structure
- soft_clip_filter()
: vg::Filter
- soft_clip_limit
: vg::Filter
- soft_clipped
: vg::Alignment
- softclip_threshold
: vg::Mapper
- sort()
: vg::StreamSorter< Message >
, vg::VG
- sort_and_compute_mapping_quality()
: vg::MultipathMapper
- sort_by_mapping_rank()
: vg::Paths
- 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
- SourceSinkOverlay()
: vg::SourceSinkOverlay
- splice_graph()
: vg::Transcriptome
- splice_graph_node_updated()
: vg::Transcriptome
- splice_motifs
: vg::MultipathMapper
- spliced_cigar_against_path()
: vg::SplicedHTSAlignmentEmitter
- spliced_surject()
: vg::Surjector
- SplicedHTSAlignmentEmitter()
: vg::SplicedHTSAlignmentEmitter
- SpliceMotifs()
: vg::SpliceMotifs
- SpliceRegion()
: vg::SpliceRegion
- split()
: vg::BitString
, vg::ReadFilter::Counts
- split_multicomponent_alignments()
: vg::MultipathMapper
- split_read_filter()
: vg::Filter
- split_read_limit
: vg::Filter
- split_supports
: vg::BREAKPOINT
- ssw_to_vg()
: vg::SSWAligner
- SSWAligner()
: vg::SSWAligner
- stack_up_valid_walks()
: vg::ExhaustiveTraversalFinder
- stage()
: vg::Funnel
- stage_name
: vg::Funnel
- stage_stop()
: vg::Funnel
- stages
: vg::Funnel
- standard_extend()
: haplo::haplo_DP_column
- STANDARD_LIBRARY
: vg::Version
- start
: gafkluge::GafStep
, vg::BREAKPOINT
, vg::Funnel
, vg::GFFRecord
, vg::GraphSynchronizer::Lock
, vg::multipath_alignment_t
, vg::MultipathAlignment
, vg::NetGraph
, vg::Range< Number >
, vg::Region
, vg::Snarl
- start_degree()
: vg::VG
- 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
- start_size()
: vg::multipath_alignment_t
- start_vcf()
: vg::Genotyper
- StartFile()
: vg::io::BlockedGzipOutputStream
- starting_position()
: vg::GaplessExtension
- state
: haplo::haplo_DP_rectangle
, vg::GaplessExtension
, vg::GenomeState
, vg::Watchdog
- state_type
: vg::PhaseUnfolder
- states
: vg::PhaseUnfolder
- std_dev()
: vg::FragmentLengthDistribution
- stddev()
: vg::normal_distribution< T >
- step
: handlegraph::PathForEachSocket::iterator
, vg::Range< Number >
- step_in_path()
: vg::VCFTraversalFinder
- step_rank_at_position()
: xg::XGPath
- STEP_RECORD_SIZE
: bdsg::PackedGraph
- steps_iv
: bdsg::PackedGraph::PackedPath
- steps_of_handle()
: bdsg::ODGI
, handlegraph::PathHandleGraph
, vg::MemoizingGraph
- steps_of_handle_memo
: vg::MemoizingGraph
- stop()
: vg::Funnel
- stop_watcher
: vg::Watchdog
- store_batch()
: vg::Index
- store_in_index()
: vg::VGset
- store_path()
: vg::Index
- store_paths()
: vg::Index
- store_paths_in_index()
: vg::VGset
- stored_kmer_sizes()
: vg::Index
- strand
: gafkluge::GafRecord
- 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 >
- StreamMultiplexer()
: vg::io::StreamMultiplexer
- StreamSorter()
: vg::StreamSorter< Message >
- String
: vg::multipath_alignment_t
- strip_bonuses
: vg::BaseMapper
- strip_full_length_bonuses()
: vg::MultipathMapper
- stripped_match_alg_max_length
: vg::MultipathMapper
- stripped_match_alg_strip_length
: vg::MultipathMapper
- stripped_match_alg_target_count
: vg::MultipathMapper
- strongly_connected_components()
: vg::VG
- sub_mem_count_thinning
: vg::BaseMapper
- sub_mem_thinning_burn_in
: vg::BaseMapper
- sub_poly_rate
: vg::NGSSimulator
- sub_score
: vg::ReadFilter
- Subcommand()
: vg::subcommand::Subcommand
- subgraph
: vg::GraphSynchronizer::Lock
, vg::SpliceRegion
- subgraph_in_range()
: vg::MinimumDistanceIndex
- subgraph_min
: PruningParameters
- subgraph_prune
: vg::VariantAdder
- SubgraphOverlay()
: vg::SubgraphOverlay
- SubHandleGraph()
: vg::SubHandleGraph
- subpath()
: vg::multipath_alignment_t
, vg::MultipathAlignment
- subpath_size()
: vg::multipath_alignment_t
- subpath_t()
: vg::subpath_t
- substage()
: vg::Funnel
- substage_name
: vg::Funnel
- substage_stop()
: 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
- support_val()
: vg::SupportBasedSnarlCaller
, vg::TraversalSupportFinder
- SupportBasedSnarlCaller()
: vg::SupportBasedSnarlCaller
- 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
- surface
: vg::Viz
- surject()
: vg::Surjector
- Surjector()
: vg::Surjector
- SV_TYPE
: vg::BREAKPOINT
- swap()
: vg::SnarlState
- swap_alleles()
: vg::PhasedGenome
- swap_endianness()
: vg::endianness< IntType >
- swap_handles()
: bdsg::ODGI
, vg::VG
- swap_haplotypes()
: vg::GenomeState
- 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
- sync_offsets()
: xg::XGPath
- sync_paths()
: vg::VG
- synchronizer
: vg::GraphSynchronizer::Lock
- synthesize_tail_anchors()
: vg::MultipathAlignmentGraph