Here is a list of all class members with links to the classes they belong to:
- a -
- a()
: vg::uniform_int_distribution< T >
, vg::uniform_real_distribution< T >
- 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_bv()
: Vectorizer
- add_chain_child()
: vg::NetGraph
- add_connection()
: vg::subpath_t
- add_edge()
: vg::MEMClusterer::HitGraph
, vg::VG
- add_edges()
: vg::VG
- add_edit()
: vg::path_mapping_t
- add_exon()
: vg::Transcriptome
- add_group()
: vg::StreamIndex< Message >
, vg::StreamIndexBase
- add_handle()
: vg::SubHandleGraph
- add_haplotype()
: vg::PhasedGenome
- 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::VG
- add_nodes()
: vg::VG
- add_nodes_in_range()
: vg::MinimumDistanceIndex
- add_reachability_edges()
: vg::MultipathAlignmentGraph
- add_snarl()
: vg::SnarlManager
- add_splice_junction_edges()
: vg::Transcriptome
- add_start()
: vg::multipath_alignment_t
- add_start_end_markers()
: vg::VG
- add_subpath()
: vg::multipath_alignment_t
- add_to_number()
: bdsg::ODGI
- add_transcript_splice_junctions()
: vg::Transcriptome
- add_transcripts()
: vg::Transcriptome
- 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
- adjacent()
: vg::VG
- adjacent_positions()
: vg::Mapper
- adjust_alignments_for_base_quality
: vg::AlignerClient
- 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
- 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
- align()
: vg::Aligner
, vg::BandedGlobalAligner< IntType >
, vg::BaseAligner
, 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_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::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_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
- AlignerClient()
: vg::AlignerClient
- alignment
: vg::BandedGlobalAligner< IntType >
, vg::BandedGlobalAligner< IntType >::BABuilder
, vg::BandedGlobalAligner< IntType >::BAMatrix
, vg::Sampler
- alignment_emitter
: vg::FlowCaller
- alignment_end_position()
: vg::Mapper
- alignment_entry_to_string()
: vg::Index
- alignment_pair()
: vg::Sampler
- alignment_qual_score()
: vg::Genotyper
- 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_path_names()
: vg::Paths
- all_seeds
: vg::SnarlSeedClusterer::TreeState
- all_snarls
: vg::Genotyper
- allele()
: haplo::linear_haplo_structure::SNVvector
, vg::Genotype
, vg::Locus
- allele_ambiguity_log_probs()
: vg::Genotyper
- 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_emitters
: vg::MultipathAlignmentEmitter
- aln_to_bseq()
: vg::SRPE
- aln_to_mate
: vg::SRPE
- alphabet
: vg::NGSSimulator
- alt_alignments
: vg::BandedGlobalAligner< IntType >
- alt_anchor_max_length_diff
: vg::MultipathMapper
- alt_paths
: vg::Constructor
- 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
- anchored_filter()
: vg::Filter
- anno_type_t
: vg::multipath_alignment_t
- annotate_mapped_alignment()
: vg::Funnel
- annotation
: vg::Alignment
, vg::MultipathAlignment
- append()
: vg::Paths
, vg::SnarlState
, vg::VG
- append_haplotype()
: vg::GenomeState
- append_left()
: vg::PhasedGenome::Haplotype
- append_mapping()
: vg::Paths
- append_path_name()
: bdsg::PackedGraph
- append_regions
: vg::ReadFilter
- append_right()
: vg::PhasedGenome::Haplotype
- append_step()
: bdsg::HashGraph
, bdsg::ODGI
, bdsg::PackedGraph
, handlegraph::MutablePathHandleGraph
, vg::VG
- append_transcript_paths()
: vg::Transcriptome
- 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_N_mask()
: vg::NGSSimulator
- apply_ordering()
: bdsg::HashGraph
, bdsg::ODGI
, bdsg::PackedGraph
, handlegraph::MutableHandleGraph
, vg::VG
- apply_orientation()
: bdsg::HashGraph
, bdsg::ODGI
, bdsg::PackedGraph
, handlegraph::MutableHandleGraph
, vg::VG
- apply_path_ordering()
: bdsg::ODGI
- 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
- approx_size_of_kmer_matches()
: vg::Index
- approx_sizes_of_kmer_matches()
: vg::Index
- arch_is_big_endian()
: vg::endianness< IntType >
- are_consecutive_nodes_in_path()
: vg::Paths
- are_consistent()
: vg::MultipathMapper
- as_edge_table()
: vg::Packer
- as_quality_table()
: vg::Packer
- as_table()
: vg::Packer
, vg::Packers
- assemble()
: vg::SRPE
- assume_acyclic
: vg::BaseMapper
- at()
: vg::Option< vector< Item >, Parser >
- at_next_deflection()
: vg::BandedGlobalAligner< IntType >::AltTracebackStack
- at_or_after()
: vg::BitString
- at_or_before()
: vg::BitString
- at_position()
: vg::PathIndex
- atomic_header
: vg::HTSAlignmentEmitter
- attempt_rescue()
: vg::MinimizerMapper
, vg::MultipathMapper
- attempt_rescue_for_secondaries()
: 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_splice_graph()
: vg::Transcriptome
- augmented
: vg::NestedTraversalFinder
- 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