- a -

• ABSENT_SCORE : vg::Recombinator
• absent_score : vg::Recombinator::Parameters
• accelerator : vg::BaseMapper
• access_mutex : vg::Watchdog::thread_state_t
• active_tree_index : vg::ZipCodeForest::forest_growing_state_t
• adaptive_diff_exponent : vg::BaseMapper
• adaptive_reseed_diff : vg::BaseMapper
• adaptive_reseed_length_memo : vg::BaseMapper
• added_fwd : vg::ExtraNodeGraph
• added_id : vg::ExtraNodeGraph
• added_rev : vg::ExtraNodeGraph
• additional_items : vg::MatchPos::PathList
• adjust_alignments_for_base_quality : vg::AlignerClient
• adjust_for_base_quality : vg::BandedGlobalAligner< IntType >
• affinity : vg::Genotyper::Affinity
• agglomerate_multipath_alns : vg::MultipathMapper
• agglomeration_length : vg::MinimizerMapper::Minimizer
• agglomeration_start : vg::MinimizerMapper::Minimizer
• alg2name : vg::Genotyper
• align_from_chains : vg::MinimizerMapper
• aligner : vg::GaplessExtender , vg::VariantAdder , vg::WFAExtender
• alignment : vg::alignment_index_t , vg::BandedGlobalAligner< IntType > , vg::BandedGlobalAligner< IntType >::BABuilder , vg::BandedGlobalAligner< IntType >::BAMatrix , vg::read_alignment_index_t
• alignment_emitter : vg::FlowCaller , vg::NestedFlowCaller
• alignments : vg::MSAConverter
• alignments_by_edge : vg::AugmentedGraph
• alignments_by_node : vg::AugmentedGraph
• all_node_problems : vg::SnarlDistanceIndexClusterer::ClusteringProblem
• all_seeds : vg::SnarlDistanceIndexClusterer::ClusteringProblem
• all_snarls : vg::Genotyper
• allele : vg::Genotype , vg::Locus
• 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
• aln : vg::AlignmentChainModelVertex
• aln_emitter : vg::ReadFilter< Read >
• aln_emitters : vg::MultipathAlignmentEmitter
• 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
• always_check_population : vg::MultipathMapper
• always_rescue : vg::Mapper
• ambiguous_warned_sequences : vg::Constructor
• annotate_with_all_path_scores : vg::Surjector
• annotation : vg::Alignment , vg::MultipathAlignment
• annotation_path_filter : vg::AbstractReadSampler
• annotation_to_match : vg::ReadFilter< Read >
• APPROXIMATE_JOBS : vg::HaplotypePartitioner
• approximate_jobs : vg::HaplotypePartitioner::Parameters
• args : vg::subcommand::OptionGroup< Receiver >
• ASSEMBLY_OR_NAME_MATCH : handlegraph::PathMetadata
• assume_acyclic : vg::BaseMapper
• atomic_header : vg::HTSWriter
• attributes : vg::GFFRecord
• aug : vg::ReadRestrictedTraversalFinder , vg::SupportRestrictedTraversalFinder
• augmented : vg::NestedTraversalFinder
• available_short_options : vg::ConfigurableParser
• 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