Here is a list of all class members with links to the classes they belong to:

- h -

half_coverage_chains : vg::Recombinator::Parameters
half_coverage_contigs : HaplotypesConfig
half_coverage_num_haplotypes : vg::Recombinator::Parameters
half_coverage_scoring : vg::Recombinator::Parameters
halt() : vg::ZipCodeTree::distance_iterator
handle_at_order() : vg::IncrementalSubgraph
handle_base_option : vg::ConfigurableParser
handle_buffer() : vg::VcfBuffer
handle_duplicate_paths() : vg::algorithms::GFAzParser
handle_graph : vg::MinDistanceClusterer, vg::TargetValueSearch
handle_idxs : vg::JoinedSpliceGraph
handle_val_range : vg::DagifiedGraph, vg::DozeuPinningOverlay
HandleGraphNodeSet() : vg::HandleGraphNodeSet
HandleGraphSnarlFinder() : vg::HandleGraphSnarlFinder
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::PhasedGenome::Haplotype, vg::PhasedGenome::iterator
haplotype_consistency_exponent : vg::BaseMapper
haplotype_gbwt_ids : vg::TranscriptPath
haplotype_id : vg::RecombinatorFragment
haplotype_indexer : GBWTConfig
haplotype_input : HaplotypesConfig
haplotype_number : vg::PhasedGenome::iterator
haplotype_output : HaplotypesConfig
haplotype_positions : vg::MinimizerMapper
haplotype_sampling_diploid : vg::IndexingParameters
haplotype_sampling_minimizer_k : vg::IndexingParameters
haplotype_sampling_minimizer_w : vg::IndexingParameters
haplotype_sampling_num_haplotypes : vg::IndexingParameters
haplotype_sampling_reference_samples : vg::IndexingParameters
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
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_edge() : 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_incorrect_order_exons() : vg::Transcriptome
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_magic() : vg::algorithms::GFAzParser
has_mapping() : vg::Paths
has_next() : vg::BandedGlobalAligner< IntType >::AltTracebackStack, vg::subpath_t
has_next_step() : vg::MemoizingGraph, vg::PathSubgraphOverlay, vg::VG
has_node() : vg::DagifiedGraph, vg::DozeuPinningOverlay, vg::IdentityOverlay, vg::IncrementalSubgraph, 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
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() : vg::MemoizingGraph, vg::Paths, vg::PathSubgraphOverlay, vg::subpath_t, vg::VG
has_position : vg::algorithms::GFAFormatError
has_previous_step() : vg::MemoizingGraph, vg::PathSubgraphOverlay, vg::VG
has_qualities() : vg::Packer
has_reachability_edges : vg::MultipathAlignmentGraph
has_recipe() : vg::IndexRegistry
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
HASH_TABLE_MAX_WIDTH : vg::MinimizerIndexParameters
HASH_TABLE_MIN_WIDTH : vg::MinimizerIndexParameters
hash_table_width : vg::MinimizerIndexParameters
hashed() : vg::Colors, vg::Pictographs
hashed_char() : vg::Pictographs
hasher : vg::GAFSorterRecord
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_lines : vg::GAFSorterFile
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
high_coverage_chains : vg::Recombinator::Parameters
high_coverage_contigs : HaplotypesConfig
high_coverage_num_haplotypes : vg::Recombinator::Parameters
high_coverage_scoring : vg::Recombinator::Parameters
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
HTSLIB_CRAM_THREADS : vg::HTSWriter
HTSLIB_HEADERS : vg::Version
HTSLIB_LIBRARY : vg::Version
HTSWriter() : vg::HTSWriter