Here is a list of all variables with links to the classes they belong to:
- a -
- ABSENT_SCORE : vg::Recombinator
- absent_score : vg::Recombinator::Parameters
- accelerator : vg::BaseMapper
- access_mutex : vg::Watchdog::thread_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