Here is a list of all class members with links to the classes they belong to:
- h -
- handle : vg::io::BlockedGzipInputStream, vg::io::BlockedGzipOutputStream, vg::io::MessageIterator, vg::io::ProtobufEmitter< T >, xg::XGPath
- handle_at_order() : vg::IncrementalSubgraph
- handle_at_path_position() : xg::XG
- handle_at_position() : xg::XGPath
- handle_base_option : vg::ConfigurableParser
- handle_buffer() : vg::VcfBuffer
- handle_graph : vg::MinDistanceClusterer, vg::TargetValueSearch
- handle_idxs : vg::JoinedSpliceGraph
- handle_rank() : xg::XG
- handle_start() : xg::XGPath
- handle_to_rank() : handlegraph::RankedHandleGraph
- handle_val_range : vg::DagifiedGraph, vg::DozeuPinningOverlay
- HandleGraphNodeSet() : vg::HandleGraphNodeSet
- HandleGraphSnarlFinder() : vg::HandleGraphSnarlFinder
- handles : xg::XGPath
- haplo_DP() : haplo::haplo_DP
- haplo_DP_column() : haplo::haplo_DP_column
- haplo_DP_rectangle() : haplo::haplo_DP_rectangle
- haplo_node : vg::PhasedGenome::iterator
- haplo_score_provider : vg::BaseMapper
- haploid_prior_logprob : vg::Genotyper
- haploid_scoring : vg::Recombinator::Parameters
- haplotype : vg::AppendHaplotypeCommand
- Haplotype() : vg::PhasedGenome::Haplotype, vg::PhasedGenome::iterator
- haplotype : vg::ReplaceSnarlHaplotypeCommand
- haplotype_consistency_exponent : vg::BaseMapper
- haplotype_gbwt_ids : vg::TranscriptPath
- haplotype_indexer : GBWTConfig
- haplotype_input : HaplotypesConfig
- HAPLOTYPE_MATCH : handlegraph::PathMetadata
- haplotype_number : vg::PhasedGenome::iterator
- haplotype_output : HaplotypesConfig
- haplotype_to_string() : vg::VariantAdder
- haplotype_transcript_paths() : vg::Transcriptome
- HaplotypeIndexer() : vg::HaplotypeIndexer
- HaplotypeNode : vg::PhasedGenome::Haplotype, vg::PhasedGenome::HaplotypeNode
- HaplotypePartitioner() : vg::HaplotypePartitioner
- haplotypes : GBWTConfig, vg::PhasedGenome, vg::Recombinator, vg::Recombinator::Statistics, vg::SnarlState
- HaplotypesConfig() : HaplotypesConfig
- hard_hit_cap : vg::MinimizerMapper
- hard_hit_max : vg::BaseMapper
- has_annotation() : vg::multipath_alignment_t
- has_argument() : vg::BaseOption< Value, Parser >, vg::OptionInterface, vg::OptionValueParser< Value >, vg::OptionValueParser< vector< Item > >
- has_base_graph() : vg::AugmentedGraph
- has_buffer : vg::VcfBuffer
- has_chain_values : vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem::SnarlTreeChild
- has_connection() : vg::subpath_t
- has_content : vg::BitStringTree< Item >::TreeNode
- has_current() : vg::io::MessageIterator, vg::io::ProtobufIterator< T >
- has_edge() : handlegraph::HandleGraph, haplo::hDP_gbwt_graph_accessor< GBWTType >, vg::VG
- has_end() : vg::HaplotypePartitioner::Subchain, vg::Haplotypes::Subchain
- has_excluded_refpos() : vg::ReadFilter< Read >
- has_excuded_feature() : vg::ReadFilter< Read >
- has_fixed_fragment_length_distr() : vg::PairedEndMapper
- has_grandparent_handle : vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem
- has_incremental_search() : haplo::GBWTScoreProvider< GBWTType >, haplo::ScoreProvider
- has_inverting_edge() : vg::VG
- has_inverting_edge_from() : vg::VG
- has_inverting_edge_to() : vg::VG
- has_inverting_edges() : vg::VG
- has_mapping() : vg::Paths
- has_next() : vg::BandedGlobalAligner< IntType >::AltTracebackStack, vg::subpath_t
- has_next_step() : handlegraph::PathHandleGraph, vg::MemoizingGraph, vg::PathSubgraphOverlay, vg::VG, xg::XG
- has_node() : handlegraph::algorithms::SubHandleGraph, handlegraph::HandleGraph, vg::DagifiedGraph, vg::DozeuPinningOverlay, vg::ExtraNodeGraph, vg::IdentityOverlay, vg::IncrementalSubgraph, vg::IndexedVG, vg::JoinedSpliceGraph, vg::MemoizingGraph, vg::NetGraph, vg::NullMaskingGraph, vg::PathSubgraph, vg::ReverseGraph, vg::SnarlGraph, vg::SourceSinkOverlay, vg::StrandSplitGraph, vg::SubgraphOverlay, vg::SubHandleGraph, vg::SubpathOverlay, vg::TreeSubgraph, vg::VG, xg::XG
- has_node_mapping() : vg::Paths
- has_novel_exon_boundaries() : vg::Transcriptome
- has_overlapping_exons() : vg::Transcriptome
- has_overlay_node_for() : vg::StrandSplitGraph
- has_parent_handle : vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem
- has_path() : handlegraph::PathHandleGraph, vg::MemoizingGraph, vg::Paths, vg::PathSubgraphOverlay, vg::subpath_t, vg::VG, xg::XG
- has_position : vg::algorithms::GFAFormatError
- has_previous_step() : handlegraph::PathHandleGraph, vg::MemoizingGraph, vg::PathSubgraphOverlay, vg::VG, xg::XG
- has_qualities() : vg::Packer
- has_reachability_edges : vg::MultipathAlignmentGraph
- has_ref : vg::Deconstructor::NestingInfo
- has_repeat() : vg::ReadFilter< Read >
- has_start() : vg::HaplotypePartitioner::Subchain, vg::Haplotypes::Subchain, vg::multipath_alignment_t
- has_supports() : vg::AugmentedGraph, vg::RepresentativeTraversalFinder, vg::SupportAugmentedGraph
- has_tabix() : vg::VcfBuffer, vg::WindowedVcfBuffer
- has_translation() : vg::Translator
- hash() : vg::VG
- hashed() : vg::Colors, vg::Pictographs
- hashed_char() : vg::Pictographs
- HashGraph : vg::IndexingParameters
- hDP_gbwt_graph_accessor() : haplo::hDP_gbwt_graph_accessor< GBWTType >
- head_nodes() : vg::VG
- head_tail_nodes : vg::Paths
- header : vg::Haplotypes
- header_listeners : vg::algorithms::GFAParser
- header_mutex : vg::HTSWriter
- heading : vg::subcommand::OptionGroup< Receiver >
- help : vg::subcommand::BaseArgSpec< Receiver >
- here : vg::Range< Number >
- HET_ADJUSTMENT : vg::Recombinator
- het_adjustment : vg::Recombinator::Parameters
- het_prior_logprob : vg::Genotyper
- heterozygous : vg::Recombinator
- heterozygous_prior_ln : vg::FixedGenotypePriorCalculator
- hint_paths : vg::CactusSnarlFinder
- hit_cap : vg::MinimizerMapper
- hit_max : vg::BaseMapper
- hit_t : vg::MEMClusterer
- HitEdge() : vg::MEMClusterer::HitEdge
- HitGraph() : vg::MEMClusterer::HitGraph
- HitNode() : vg::MEMClusterer::HitNode
- hits : vg::MinimizerMapper::Minimizer
- Holder : vg::subcommand::FlagArgSpec< Receiver >, vg::subcommand::RangeArgSpec< T, Receiver >
- homozygous_prior_ln : vg::FixedGenotypePriorCalculator
- hts_mode : vg::HTSWriter
- HTSAlignmentEmitter() : vg::HTSAlignmentEmitter
- HTSWriter() : vg::HTSWriter