Here is a list of all class members with links to the classes they belong to:
- a -
- A() : vg::truncated_normal_distribution< T >
- a() : vg::uniform_int_distribution< T >, vg::uniform_real_distribution< T >
- absent : vg::Recombinator
- ABSENT_SCORE : vg::Recombinator
- absent_score : vg::Recombinator::Parameters
- AbstractReadSampler() : vg::AbstractReadSampler
- accelerate_mem_query() : vg::BaseMapper
- accelerator : vg::BaseMapper
- accept_record() : vg::VcfRecordFilter
- access_mutex : vg::Watchdog::thread_state_t
- Adaptive : vg::Genotyper
- adaptive_diff_exponent : vg::BaseMapper
- adaptive_reseed_diff : vg::BaseMapper
- adaptive_reseed_length_memo : vg::BaseMapper
- add() : vg::Packer
- add_allele_path_to_info() : vg::VCFOutputCaller
- add_annotations() : vg::MultipathAlignmentEmitter
- add_bv() : Vectorizer
- add_chain_child() : vg::NetGraph
- add_connection() : vg::subpath_t
- add_contigs_to_vcf_header() : vg::Deconstructor
- add_decomposed_tail_alignments() : vg::MultipathAlignmentGraph
- add_edge() : vg::DiagramExplainer, vg::MEMClusterer::HitGraph, vg::VG
- add_edges() : vg::VG
- add_edit() : vg::path_mapping_t
- add_edited_transcript_paths() : vg::Transcriptome
- add_entry() : vg::subcommand::Preset
- add_exon() : vg::Transcriptome
- add_flag() : vg::subcommand::OptionGroup< Receiver >
- add_globals() : vg::DiagramExplainer
- add_group() : vg::StreamIndex< Message >, vg::StreamIndexBase, vg::subcommand::GroupedOptionGroup
- add_handle() : handlegraph::algorithms::SubHandleGraph, vg::SubHandleGraph
- add_haplotype() : vg::PhasedGenome
- add_haplotype_transcripts() : vg::Transcriptome
- add_intron_splice_junctions() : vg::Transcriptome
- add_mapping() : vg::path_t
- add_name() : Vectorizer
- add_name_mapping() : vg::NameMapper
- add_next() : vg::subpath_t
- add_node() : vg::algorithms::Graph, vg::DiagramExplainer, vg::VG
- add_nodes() : vg::VG
- add_option() : vg::subcommand::OptionGroup< Receiver >
- add_points() : vg::algorithms::TracedScore
- add_range() : vg::subcommand::OptionGroup< Receiver >
- add_reachability_edges() : vg::MultipathAlignmentGraph
- add_reference_transcripts() : vg::Transcriptome
- add_seed_to_chain_problem() : vg::SnarlDistanceIndexClusterer
- add_snarl() : vg::SnarlManager
- add_snarl_to_chain_problem() : vg::SnarlDistanceIndexClusterer
- add_splice_junction_edges() : vg::Transcriptome
- add_star_traversals() : vg::Deconstructor
- add_start() : vg::multipath_alignment_t
- add_start_end_markers() : vg::VG
- add_subpath() : vg::multipath_alignment_t
- add_transcripts_to_gbwt() : vg::Transcriptome
- add_traversals() : vg::ExhaustiveTraversalFinder
- add_unary_child() : vg::NetGraph
- add_variant() : vg::VCFOutputCaller
- add_variants() : vg::VariantAdder
- added_fwd : vg::ExtraNodeGraph
- added_id : vg::ExtraNodeGraph
- added_rev : vg::ExtraNodeGraph
- additional_items : vg::MatchPos::PathList
- adjacent() : vg::VG
- adjacent_positions() : vg::Mapper
- adjust_alignments_for_base_quality : vg::AlignerClient
- adjust_diagonal_range() : vg::WFATree
- adjust_for_base_quality : vg::BandedGlobalAligner< IntType >
- advance() : vg::io::MessageIterator, vg::io::ProtobufIterator< T >, vg::NGSSimulator, vg::PathBranch
- advance_by_distance() : vg::NGSSimulator
- advance_on_graph() : vg::NGSSimulator
- advance_on_graph_by_distance() : vg::NGSSimulator
- advance_on_path() : vg::NGSSimulator
- advance_on_path_by_distance() : vg::NGSSimulator
- Affinity() : vg::Genotyper::Affinity
- affinity : vg::Genotyper::Affinity
- after : ReferenceInterval
- agglomerate() : vg::MultipathMapper
- agglomerate_alignment_pairs() : vg::MultipathMapper
- agglomerate_alignments() : vg::MultipathMapper
- agglomerate_multipath_alns : vg::MultipathMapper
- agglomeration_length : vg::MinimizerMapper::Minimizer
- agglomeration_start : vg::MinimizerMapper::Minimizer
- agglomeration_window_count() : vg::MinimizerMapper::Minimizer
- alg2name : vg::Genotyper
- AliasGraph() : vg::AliasGraph
- align() : vg::Aligner, vg::BandedGlobalAligner< IntType >, vg::BaseAligner, vg::DeletionAligner, vg::DozeuInterface, vg::Mapper, vg::MultipathAlignmentGraph, vg::QualAdjAligner, vg::SSWAligner, vg::VG
- align_banded() : vg::Mapper
- align_cluster() : vg::Mapper
- align_downward() : vg::DozeuInterface
- align_from_chains : vg::MinimizerMapper
- align_global_banded() : vg::Aligner, vg::GSSWAligner, vg::QualAdjAligner
- align_global_banded_multi() : vg::Aligner, vg::GSSWAligner, vg::QualAdjAligner
- align_internal() : vg::Aligner, vg::QualAdjAligner
- align_maybe_flip() : vg::Mapper
- align_mem_multi() : vg::Mapper
- align_multi() : vg::DeletionAligner, vg::Mapper
- align_multi_internal() : vg::Mapper
- align_ns() : vg::VariantAdder
- align_paired_multi() : vg::Mapper
- align_pinned() : vg::Aligner, vg::DozeuInterface, vg::GSSWAligner, vg::QualAdjAligner
- align_pinned_multi() : vg::Aligner, vg::GSSWAligner, vg::QualAdjAligner
- align_qual_adjusted() : vg::VG
- align_sequence_between() : vg::MinimizerMapper
- align_tails() : vg::MultipathAlignmentGraph
- align_to_cluster_graph_pairs() : vg::MultipathMapper
- align_to_cluster_graphs() : vg::MultipathMapper
- align_to_cluster_graphs_with_rescue() : vg::MultipathMapper
- align_to_graph() : vg::Mapper
- align_to_splice_candidates() : vg::MultipathMapper
- align_xdrop() : vg::Aligner, vg::GSSWAligner, vg::QualAdjAligner
- Aligner() : vg::Aligner
- aligner : vg::GaplessExtender, vg::VariantAdder, vg::WFAExtender
- AlignerClient() : vg::AlignerClient
- alignment : vg::alignment_index_t, vg::BandedGlobalAligner< IntType >, vg::BandedGlobalAligner< IntType >::BABuilder, vg::BandedGlobalAligner< IntType >::BAMatrix, vg::read_alignment_index_t, vg::Sampler
- alignment_emitter : vg::FlowCaller, vg::NestedFlowCaller
- alignment_end_matches() : vg::ReadFilter< Read >
- alignment_end_position() : vg::Mapper
- alignment_overhang() : vg::ReadFilter< Read >
- alignment_pair() : vg::Sampler
- alignment_qual_score() : vg::Genotyper
- alignment_score() : vg::WFAPoint
- alignment_score_partition_function() : vg::GSSWAligner
- alignment_seq() : vg::Sampler
- alignment_to_a_hot() : Vectorizer
- alignment_to_custom_score() : Vectorizer
- alignment_to_graph() : vg::Sampler
- alignment_to_identity_hot() : Vectorizer
- alignment_to_onehot() : Vectorizer
- alignment_to_path() : vg::Sampler
- alignment_with_error() : vg::Sampler
- AlignmentChainModel() : vg::AlignmentChainModel
- AlignmentChainModelVertex() : vg::AlignmentChainModelVertex
- alignments : vg::MSAConverter
- alignments_by_edge : vg::AugmentedGraph
- alignments_by_node : vg::AugmentedGraph
- alignments_consistent() : vg::Mapper
- all_children_trivial() : vg::SnarlManager
- all_finished() : vg::IndexRegistry
- all_groups() : vg::SparseUnionFind
- all_mapping_qualities_exact() : vg::GSSWAligner
- all_node_problems : vg::SnarlDistanceIndexClusterer::ClusteringProblem
- all_path_names() : vg::Paths
- all_seeds : vg::SnarlDistanceIndexClusterer::ClusteringProblem
- all_snarls : vg::Genotyper
- allele() : haplo::linear_haplo_structure::SNVvector, vg::Genotype, vg::Locus
- allele_ambiguity_log_probs() : vg::Genotyper
- allele_length_range : vg::FlowCaller
- allele_log_likelihood : vg::Locus
- alleles : haplo::linear_haplo_structure::SNVvector, vg::VG::Plan
- allow_duplicates : vg::PathRestrictedTraversalFinder
- allowed_vcf_names : vg::Constructor
- allowed_vcf_regions : vg::Constructor
- AllowsAliasing() : vg::io::BlockedGzipOutputStream
- aln : vg::AlignmentChainModelVertex
- aln_emitter : vg::ReadFilter< Read >
- aln_emitters : vg::MultipathAlignmentEmitter
- alphabet : vg::NGSSimulator
- also_merge_group() : vg::Funnel
- also_relevant() : vg::Funnel
- alt_alignments : vg::BandedGlobalAligner< IntType >
- alt_anchor_max_length_diff : vg::MultipathMapper
- alt_paths : vg::Constructor
- alt_proposal_sample() : vg::MCMCGenotyper
- alt_tracebacks : vg::BandedGlobalAligner< IntType >::AltTracebackStack
- alts_as_loci : vg::Constructor
- AltTracebackStack() : vg::BandedGlobalAligner< IntType >::AltTracebackStack, vg::BandedGlobalAligner< IntType >::BAMatrix
- always_check_population : vg::MultipathMapper
- always_rescue : vg::Mapper
- ambiguous_warned_sequences : vg::Constructor
- Anchor() : vg::algorithms::Anchor
- anchored_filter() : vg::Filter
- anno_type_t : vg::multipath_alignment_t
- annotate_mapped_alignment() : vg::Funnel
- annotate_with_all_path_scores : vg::Surjector
- annotate_with_minimizer_statistics() : vg::MinimizerMapper
- annotate_with_path_positions() : vg::AbstractReadSampler
- annotation : vg::Alignment, vg::Counts, vg::MultipathAlignment
- annotation_path_filter : vg::AbstractReadSampler
- annotation_t : vg::DiagramExplainer
- annotation_to_match : vg::ReadFilter< Read >
- append() : vg::Paths, vg::SnarlState, vg::VG, vg::WFAAlignment
- append_haplotype() : vg::GenomeState
- append_left() : vg::PhasedGenome::Haplotype
- append_mapping() : vg::Paths
- append_node() : vg::WFANode
- append_right() : vg::PhasedGenome::Haplotype
- append_step() : handlegraph::MutablePathHandleGraph, vg::VG
- apply() : vg::subcommand::BaseArgSpec< Receiver >, vg::subcommand::GroupedOptionGroup, vg::subcommand::OptionGroup< Receiver >, vg::subcommand::Preset, vg::subcommand::ValueArgSpec< T, Receiver, Holder >
- apply_aligned_base() : vg::NGSSimulator
- apply_deletion() : vg::NGSSimulator
- apply_edit() : vg::GraphSynchronizer::Lock
- apply_full_length_edit() : vg::GraphSynchronizer::Lock
- apply_haplotype_consistency_scores() : vg::BaseMapper
- apply_insertion() : vg::NGSSimulator
- apply_min_bp_edge_override() : vg::TraversalSupportFinder
- apply_N_mask() : vg::NGSSimulator
- apply_ordering() : handlegraph::MutableHandleGraph, vg::VG
- apply_orientation() : handlegraph::MutableHandleGraph, vg::VG
- apply_translation() : vg::PathIndex
- apply_translations() : vg::PathIndex
- approx_alignment_position() : vg::Mapper
- approx_distance() : vg::Mapper
- approx_fragment_length() : vg::Mapper
- approx_position() : vg::Mapper
- APPROXIMATE_JOBS : vg::HaplotypePartitioner
- approximate_jobs : vg::HaplotypePartitioner::Parameters
- arch_is_big_endian() : vg::endianness< IntType >
- are_consecutive_nodes_in_path() : vg::Paths
- are_consistent() : vg::MultipathMapper
- args : vg::subcommand::OptionGroup< Receiver >
- ArgSpec() : vg::subcommand::ArgSpec< T, Receiver >
- array_end() : vg::ProblemDumpExplainer
- array_start() : vg::ProblemDumpExplainer
- as_edge_table() : vg::Packer
- as_quality_table() : vg::Packer
- as_table() : vg::Packer, vg::Packers
- ASSEMBLY_OR_NAME_MATCH : handlegraph::PathMetadata
- assign_constructed() : vg::IndexFile
- assign_new_sequence_id() : vg::algorithms::GFAParser
- assume_acyclic : vg::BaseMapper
- at() : vg::Option< vector< Item >, Parser >
- at_dead_end() : vg::WFATree
- at_last_node() : vg::MatchPos
- at_next_deflection() : vg::BandedGlobalAligner< IntType >::AltTracebackStack
- at_or_after() : vg::BitString
- at_or_before() : vg::BitString
- at_position() : vg::PathIndex
- atomic_header : vg::HTSWriter
- attempt_rescue() : vg::MinimizerMapper, vg::MultipathMapper
- attempt_rescue_for_secondaries() : vg::MultipathMapper
- attempt_rescue_for_splice_segment() : vg::MultipathMapper
- attempt_unpaired_multipath_map_of_pair() : vg::MultipathMapper
- attributes : vg::GFFRecord
- aug : vg::ReadRestrictedTraversalFinder, vg::SupportRestrictedTraversalFinder
- augment_from_alignment_edits() : vg::AugmentedGraph
- augment_graph() : vg::Transcriptome
- augmented : vg::NestedTraversalFinder
- available() : vg::IndexRegistry
- available_short_options : vg::ConfigurableParser
- average_node_quality() : vg::Packer
- average_node_support_switch_threshold : vg::TraversalSupportFinder
- average_traversal_support_switch_threshold : vg::TraversalSupportFinder
- avg_node_length : vg::BaseMapper
- avg_node_mapq_cache : vg::CachedPackedTraversalSupportFinder
- avg_node_support_cache : vg::CachedPackedTraversalSupportFinder
- avg_qual_filter() : vg::Filter