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

- p -

• p_value() : vg::SeqComplexity< MaxOrder >
• p_value_memo : vg::MultipathMapper
• pack() : handlegraph::number_bool_packing
• pack_names : vg::Viz
• pack_query_forward() : vg::DozeuInterface , vg::QualAdjXdropAligner , vg::XdropAligner
• pack_query_reverse() : vg::DozeuInterface , vg::QualAdjXdropAligner , vg::XdropAligner
• PackedGraph : vg::IndexingParameters
• PackedTraversalSupportFinder() : vg::PackedTraversalSupportFinder
• packer : vg::PackedTraversalSupportFinder
• Packer() : vg::Packer
• packs : vg::Viz
• pad_cluster_score_threshold : vg::MinimizerMapper
• pad_suspicious_anchors_to_length : vg::Surjector
• pad_traversal() : vg::GAFOutputCaller
• pad_zipcode_tree_score_threshold : vg::MinimizerMapper
• paint() : vg::Funnel::PaintableSpace
• pair_all() : vg::MinimizerMapper
• pair_cluster_multiplicity() : vg::MultipathMapper
• pair_clusters() : vg::MEMClusterer , vg::MinDistanceClusterer , vg::NullClusterer , vg::OrientedDistanceClusterer , vg::TVSClusterer
• pair_consistent() : vg::Mapper
• pair_from_edge() : vg::NodeSide
• pair_from_end_edge() : vg::NodeSide
• pair_from_start_edge() : vg::NodeSide
• pair_mapping_likelihoods() : vg::MultipathMapper
• pair_orientation_filter() : vg::Filter
• pair_rescue() : vg::Mapper
• pair_rescue_hang_threshold : vg::Mapper
• pair_rescue_retry_threshold : vg::Mapper
• paired_distance_stdevs : vg::MinimizerMapper
• paired_read_name : vg::MultipathAlignment
• paired_rescue_score_limit : vg::MinimizerMapper
• ParallelKFFReader() : vg::ParallelKFFReader
• param_type : vg::discrete_distribution< T >
• Parameters() : vg::Recombinator::Parameters
• parent : vg::Snarl , vg::SnarlManager::SnarlRecord , vg::TreeNode< T > , vg::VectorView< Item >::const_iterator , vg::WFANode , vg::WFATree
• parent_allele : vg::Deconstructor::NestingInfo
• parent_chain : vg::SnarlManager::SnarlRecord
• parent_chain_index : vg::SnarlManager::SnarlRecord
• parent_chains : vg::SnarlDistanceIndexClusterer::ClusteringProblem
• parent_depth : vg::MIPayload
• parent_directory : vg::temp_file::Handler , xg::temp_file::Handler
• parent_graph : vg::JoinedSpliceGraph
• parent_handle : vg::MIPayload
• parent_is_chain : vg::MIPayload
• parent_is_root : vg::MIPayload
• parent_len : vg::Deconstructor::NestingInfo
• parent_net_handle : vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem
• parent_of() : vg::SnarlManager
• parent_path_interval : vg::Deconstructor::NestingInfo
• parent_record_offset : vg::MIPayload
• parent_ref_len : vg::Deconstructor::NestingInfo
• parent_snarls : vg::SnarlDistanceIndexClusterer::ClusteringProblem
• parent_type : vg::MIPayload
• parse() : vg::algorithms::GFAParser , vg::BaseOption< Value, Parser > , vg::ConfigurableParser , vg::OptionInterface , vg::OptionValueParser< Value > , vg::OptionValueParser< vector< Item > > , vg::subcommand::BaseArgSpec< Receiver > , vg::subcommand::BaseOptionGroup , vg::subcommand::FlagArgSpec< Receiver > , vg::subcommand::GroupedOptionGroup , vg::subcommand::OptionGroup< Receiver > , vg::subcommand::ValueArgSpec< T, Receiver, Holder >
• parse_attribute_value() : vg::Transcriptome
• parse_attributes() : vg::GFFRecord
• parse_default() : vg::OptionValueParser< Value > , vg::OptionValueParser< vector< Item > >
• parse_from_string() : vg::io::ProtobufIterator< T >
• parse_h() : vg::algorithms::GFAParser
• parse_haplotype() : handlegraph::PathMetadata
• parse_introns() : vg::Transcriptome
• parse_l() : vg::algorithms::GFAParser
• parse_locus_name() : handlegraph::PathMetadata
• parse_matrix() : vg::AlignerClient
• parse_only : GBWTConfig
• parse_p() : vg::algorithms::GFAParser
• parse_path_name() : handlegraph::PathMetadata
• parse_phase_block() : handlegraph::PathMetadata
• parse_s() : vg::algorithms::GFAParser
• parse_sample_name() : handlegraph::PathMetadata
• parse_sense() : handlegraph::PathMetadata
• parse_subrange() : handlegraph::PathMetadata
• parse_tags() : vg::algorithms::GFAParser
• parse_transcripts() : vg::Transcriptome
• parse_translation() : vg::PathIndex
• parse_vcf() : vg::HaplotypeIndexer
• parse_w() : vg::algorithms::GFAParser
• partition_haplotypes() : vg::HaplotypePartitioner
• partitioner_parameters : HaplotypesConfig
• pass() : vg::Funnel
• pass_number : vg::algorithms::GFAFormatError
• passed_filters : vg::Funnel::Item
• passed_statistics : vg::Funnel::Item
• passing : vg::Funnel::FilterPerformance
• passing_correct : vg::Funnel::FilterPerformance
• past_end : vg::GraphSynchronizer::Lock
• patch_alignment() : vg::Mapper
• patch_alignments : vg::Mapper
• path : gafkluge::GafRecord , handlegraph::PathForEachSocket , vg::algorithms::walk_t , vg::Alignment , vg::CompletedTranscriptPath , vg::EditedTranscriptPath , vg::GaplessExtension , vg::Graph , vg::MatchPos , vg::PathNode , vg::Paths , vg::RecombinatorHaplotype , vg::Subpath , vg::subpath_t , vg::WFAAlignment , vg::WFANode
• path_back() : handlegraph::PathHandleGraph , vg::MemoizingGraph , vg::PathSubgraphOverlay , vg::VG , xg::XG
• path_begin() : handlegraph::PathHandleGraph , vg::MemoizingGraph , vg::PathSubgraphOverlay , vg::VG , xg::XG
• path_chunk_t : vg::Surjector
• path_collapse_type : vg::Transcriptome
• path_component_index : vg::MultipathMapper , vg::PathOrientedDistanceMeasurer
• path_contains_handle() : xg::XG
• path_contains_node() : vg::PathIndex
• path_contains_node_in_orientation() : vg::PathIndex
• path_count : xg::XG
• path_cover : GBWTConfig
• path_cover_augment : GBWTConfig
• path_cover_depth : vg::IndexingParameters
• path_cover_greedy : GBWTConfig
• path_cover_local : GBWTConfig
• path_cover_mode : GBWTConfig
• path_cover_none : GBWTConfig
• path_cover_parameters() : GBWTConfig
• path_divergence_filter() : vg::Filter
• path_edge_count() : vg::VG
• path_end : gafkluge::GafRecord , handlegraph::PathHandleGraph , vg::MemoizingGraph , vg::PathSubgraphOverlay , vg::VG , xg::XG
• path_end_node_offset() : vg::VG
• PATH_FIELD : vg::GAFSorterRecord
• path_finder : vg::VCFTraversalFinder
• path_front_end() : handlegraph::PathHandleGraph , vg::MemoizingGraph , vg::PathSubgraphOverlay , vg::VG , xg::XG
• path_graph : GraphHandler , vg::MinimizerMapper , vg::PhaseUnfolder
• path_identity() : vg::VG
• path_indexes : vg::LegacyCaller
• path_jaccard_window : vg::Deconstructor
• path_length : gafkluge::GafRecord
• path_length_filter() : vg::Filter
• path_lengths_to_sinks() : vg::BandedGlobalAligner< IntType >
• path_listeners : vg::algorithms::GFAParser
• path_mapping_node_id() : haplo::linear_haplo_structure
• path_mapping_offset() : haplo::linear_haplo_structure
• path_mapping_t() : vg::path_mapping_t
• path_mode : GBWTConfig
• path_name : vg::FeatureSet::Feature , vg::GraphSynchronizer::Lock , xg::XG
• path_name_csa_delim : xg::XG
• path_names : GBWTConfig , vg::VariantAdder
• path_names_by_prefix() : xg::XG
• path_nodes : vg::MultipathAlignmentGraph
• path_offset : vg::GraphSynchronizer::Lock
• path_order_and_length : vg::HTSWriter
• path_output : GBWTConfig
• path_position_handle_graph : vg::MCMCCaller
• path_ranks_by_prefix() : xg::XG
• path_sampler : vg::NGSSimulator , vg::Sampler
• path_score_annotations() : vg::Surjector
• path_sequence() : vg::VG
• path_start : gafkluge::GafRecord
• path_subset : vg::PathSubgraphOverlay
• path_t() : vg::path_t
• path_to_input_haplotype() : haplo::linear_haplo_structure
• path_to_ploidy : vg::VCFGenotyper
• path_to_sample_phase : vg::Deconstructor
• path_to_vcf : vg::HaplotypeIndexer
• path_trav_finder : vg::Deconstructor
• path_type : job_type , vg::PhaseUnfolder
• PathBasedTraversalFinder() : vg::PathBasedTraversalFinder
• PathChunker() : vg::PathChunker
• PathComponentIndex() : vg::PathComponentIndex
• PathForEachSocket : handlegraph::PathForEachSocket::iterator , handlegraph::PathForEachSocket
• PathHandleGraph : handlegraph::PathForEachSocket
• PathIndex() : vg::PathIndex
• PathOrientedDistanceMeasurer() : vg::PathOrientedDistanceMeasurer
• PathRestrictedTraversalFinder() : vg::PathRestrictedTraversalFinder
• paths : job_type
• Paths() : vg::Paths
• paths : vg::PathTraversalFinder , vg::SurjectingAlignmentEmitter , vg::VG , xg::XG
• paths_as_alignments() : vg::VG
• paths_between() : vg::VG
• paths_of_handle() : xg::XG
• paths_on_same_component() : vg::PathComponentIndex
• PathSubgraph() : vg::PathSubgraph
• PathSubgraphOverlay() : vg::PathSubgraphOverlay
• PathTraversalFinder() : vg::PathTraversalFinder
• payload : vg::SnarlDistanceIndexClusterer::SeedCache
• payload_node_length : vg::SnarlDistanceIndexClusterer::SeedCache
• payload_prefix_sum : vg::SnarlDistanceIndexClusterer::SeedCache
• pbSize : vg::io::fdinbuf , vg::io::streaminbuf
• peek() : vg::BitString
• penalties : haplo::linear_haplo_structure
• per_base : vg::WFAExtender::ErrorModel::Event
• percent_identity_filter() : vg::Filter
• perfect_filter() : vg::Filter
• perfect_pair_identity_threshold : vg::FragmentLengthStatistics
• perform_dp() : vg::MEMClusterer::HitGraph
• performed_duplications() : vg::DozeuPinningOverlay
• peripheral_attachments : vg::GraphSynchronizer::Lock
• periphery : vg::GraphSynchronizer::Lock
• permutation_idx : vg::ShuffledPairs::iterator
• permuted : vg::ShuffledPairs::iterator
• pessimistic_gap() : vg::MultipathMapper
• pessimistic_gap_memo : vg::MultipathMapper
• pessimistic_gap_multiplier : vg::MultipathMapper
• pessimistic_tail_gap() : vg::MultipathAlignmentGraph
• pessimistic_tail_gap_memo : vg::MultipathAlignmentGraph
• phase : vg::GFFRecord
• PHASE_BLOCK_MATCH : handlegraph::PathMetadata
• phase_homozygous : vg::HaplotypeIndexer
• phase_visits : vg::VG::Plan
• PhasedGenome : vg::PhasedGenome::Haplotype , vg::PhasedGenome::iterator , vg::PhasedGenome
• PhaseUnfolder() : vg::PhaseUnfolder
• phred_prob : vg::NGSSimulator
• pi_iv : xg::XG
• pick_mappings_from_alignments() : vg::MinimizerMapper
• Pictographs() : vg::Pictographs
• pin_offset() : vg::MinimizerMapper::Minimizer
• pinned_tail_size : vg::VariantAdder
• Plan() : vg::VG::Plan
• plausible_rescue_cluster_coverage_diff : vg::MultipathMapper
• pn_bv : xg::XG
• pn_bv_rank : xg::XG
• pn_bv_select : xg::XG
• pn_csa : xg::XG
• pn_iv : xg::XG
• pointer : vg::count_back_inserter< T > , vg::SmallBitset , vg::VectorView< Item >::const_iterator
• points : vg::algorithms::Anchor
• points_per_possible_match : vg::MinimizerMapper
• PoissonSupportSnarlCaller() : vg::PoissonSupportSnarlCaller
• polyploid_prior_success_logprob : vg::Genotyper
• pop() : vg::MatchPos::PathList , vg::MatchPos , vg::ZipCodeTree::reverse_iterator
• pop_back_step() : handlegraph::MutablePathHandleGraph
• pop_front_step() : handlegraph::MutablePathHandleGraph
• population_max_paths : vg::MultipathMapper
• population_paths_hard_cap : vg::MultipathMapper
• population_size : haplo::haploMath::RRMemo
• pos : vg::ChainIterator , vg::KmerPosition , vg::SnarlDistanceIndexClusterer::Seed , vg::WFAPoint
• pos_at() : MappingRun
• pos_char() : vg::Sampler , xg::XG
• pos_key() : vg::Packer
• pos_substr() : xg::XG
• pos_to_edit_to_depth : vg::Filter
• pos_to_qual : vg::Filter
• pos_to_trans : vg::Translator
• position : vg::algorithms::GFAFormatError , vg::BREAKPOINT , vg::Funnel , vg::KmerMatch , vg::Mapping , vg::path_mapping_t , vg::RecombinatorHaplotype , vg::Sampler
• position_assuming_acyclic() : haplo::linear_haplo_structure
• position_chromosome : vg::Primer
• position_file : vg::NGSSimulator
• position_in_basis() : vg::Packer
• position_in_path() : xg::XG
• position_in_paths() : xg::XG
• position_t() : vg::position_t
• position_template : vg::Primer
• positions : vg::AlignmentChainModel , vg::AlignmentChainModelVertex , vg::MaximalExactMatch , vg::MEMChainModel
• possible_scores : vg::WFATree
• posterior : vg::PoissonSupportSnarlCaller::PoissonCallInfo
• precollapse_order_length_hits : vg::BaseMapper
• precollapse_order_length_runs() : vg::BaseMapper
• predecessor_offset() : vg::WFATree
• prefilter_redundant_hits : vg::BaseMapper
• prefilter_redundant_sub_mems() : vg::BaseMapper
• prefix : vg::BitStringTree< Item >::TreeNode , vg::GaplessExtension , vg::Haplotypes::Subchain , vg::RecombinatorHaplotype , vg::WFAExtender
• prefix_length : vg::MultipathProblem
• prefix_score : vg::MultipathProblem
• prefix_sum : vg::MIPayload , vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem::SnarlTreeChild
• prefix_sum_or_identifier : vg::ZipCode::node_code_t , vg::ZipCode::snarl_code_t
• prefix_sum_value : vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem
• prefixes : vg::PhaseUnfolder
• preload_progress() : vg::Progressive
• prepend_mapping() : vg::Paths
• prepend_step() : handlegraph::MutablePathHandleGraph , vg::VG
• present : vg::Recombinator , vg::SnarlDistanceIndexClusterer::Cluster
• present_discount : vg::Recombinator::Parameters
• PRESENT_DISCOUNT : vg::Recombinator
• preserve_sinks : vg::DozeuPinningOverlay
• preset() : vg::subcommand::ArgSpec< T, Receiver > , vg::subcommand::BaseArgSpec< Receiver > , vg::subcommand::BaseOptionGroup , vg::subcommand::GroupedOptionGroup , vg::subcommand::OptionGroup< Receiver >
• preset_default : vg::Recombinator::Parameters
• preset_diploid : vg::Recombinator::Parameters
• preset_haploid : vg::Recombinator::Parameters
• preset_t : vg::Recombinator::Parameters
• prev : vg::AlignmentChainModelVertex , vg::MEMChainModelVertex , vg::PhasedGenome::HaplotypeNode
• prev_char : vg::kmer_t
• prev_chars : vg::KmerPosition
• prev_cost : vg::AlignmentChainModelVertex , vg::MEMChainModelVertex
• prev_idx() : haplo::haplo_DP_rectangle
• prev_pos : vg::kmer_t
• prev_snarl() : vg::SnarlManager
• prev_stage_items : vg::Funnel::Item
• prev_subpath : vg::MultipathProblem
• previous_index : haplo::haplo_DP_rectangle
• previous_R() : haplo::haplo_DP_column
• previous_sizes : haplo::haplo_DP_column
• previous_sum : haplo::haplo_DP_column
• previous_tag : vg::io::MessageIterator
• previous_values : haplo::haplo_DP_column
• primary : vg::MaximalExactMatch
• PrimerFinder() : vg::PrimerFinder
• primitive_root : vg::ShuffledPairs
• print() : haplo::haplo_DP_column , haplo::hDP_gbwt_graph_accessor< GBWTType > , vg::HaplotypePartitioner::Parameters , vg::Recombinator::Parameters , vg::Recombinator::Statistics , vg::subcommand::BaseArgSpec< Receiver > , vg::subcommand::FlagArgSpec< Receiver > , vg::WFAAlignment
• print_band() : vg::BandedGlobalAligner< IntType >::BAMatrix
• print_default() : vg::subcommand::BaseArgSpec< Receiver > , vg::subcommand::FlagArgSpec< Receiver > , vg::subcommand::ValueArgSpec< T, Receiver, Holder >
• print_edges() : vg::VG
• print_full_matrices() : vg::BandedGlobalAligner< IntType >::BAMatrix
• print_graph() : xg::XG
• print_help() : vg::ConfigurableParser
• print_matrix() : vg::BandedGlobalAligner< IntType >::BAMatrix
• print_metavar() : vg::subcommand::BaseArgSpec< Receiver > , vg::subcommand::FlagArgSpec< Receiver > , vg::subcommand::ValueArgSpec< T, Receiver, Holder >
• print_options() : vg::subcommand::BaseOptionGroup , vg::subcommand::GroupedOptionGroup , vg::subcommand::OptionGroup< Receiver >
• print_phased_genome() : vg::PhasedGenome
• print_rectangularized_bands() : vg::BandedGlobalAligner< IntType >::BAMatrix
• print_report() : vg::IndexedVG
• print_self() : vg::varint_vector_t , vg::ZipCodeForest , vg::ZipCodeTree
• print_snarl() : vg::VCFOutputCaller
• print_statistics() : vg::Genotyper
• print_updates : vg::VariantAdder
• print_value() : vg::subcommand::BaseArgSpec< Receiver > , vg::subcommand::FlagArgSpec< Receiver > , vg::subcommand::ValueArgSpec< T, Receiver, Holder >
• PrintAlignment() : vg::SSWAligner
• priority : vg::subcommand::Subcommand
• prng : vg::NGSSimulator::MarkovDistribution< From, To > , vg::NGSSimulator
• prngs : vg::NGSSimulator
• prob_sampler : vg::NGSSimulator
• Problem : vg::AlignmentValidity
• problem : vg::AlignmentValidity
• ProblemDumpExplainer() : vg::ProblemDumpExplainer
• process_in_out_growth() : vg::FlowSort
• process_until_threshold_a() : vg::MinimizerMapper
• process_until_threshold_b() : vg::MinimizerMapper
• process_until_threshold_c() : vg::MinimizerMapper
• processed_input() : vg::Funnel
• processing_input() : vg::Funnel
• produced_output() : vg::Funnel
• produces_one_gbwt : GBWTConfig
• producing_output() : vg::Funnel
• progress : vg::GAFSorterParameters , vg::Progressive
• progress_bars : vg::VGset
• progress_count : vg::Progressive
• progress_message : vg::Progressive
• progress_seen : vg::Progressive
• project() : vg::Funnel
• project_group() : vg::Funnel
• project_haplotype_transcripts() : vg::Transcriptome
• project_haplotype_transcripts_callback() : vg::Transcriptome
• project_transcript_embedded() : vg::Transcriptome
• project_transcript_gbwt() : vg::Transcriptome
• projected_count : vg::Funnel::Stage
• proper_pair : vg::Counts
• proposal_sample() : vg::MCMCGenotyper
• propose_deflection() : vg::BandedGlobalAligner< IntType >::AltTracebackStack
• proto : vg::io::VGAlignmentEmitter
• protobuf_to_tag : vg::io::Registry::Tables
• ProtobufEmitter() : vg::io::ProtobufEmitter< T >
• ProtobufIterator() : vg::io::ProtobufIterator< T >
• provide() : vg::IndexFile , vg::IndexRegistry
• provided_directly : vg::IndexFile
• prune_and_trim_anchors() : vg::Surjector
• prune_high_shift_edges() : vg::MultipathAlignmentGraph
• prune_low_scoring_edges() : vg::MEMClusterer::HitGraph
• prune_subpaths_multiplier : vg::MultipathMapper
• prune_suspicious_anchors : vg::Surjector
• prune_to_high_scoring_paths() : vg::MultipathAlignmentGraph
• prune_unconnectable() : vg::Surjector
• pruning_max_edge_count : vg::IndexingParameters
• pruning_max_node_degree : vg::IndexingParameters
• pruning_max_node_degree_decrease_factor : vg::IndexingParameters
• pruning_min_component_size : vg::IndexingParameters
• pruning_walk_length : vg::IndexingParameters
• pruning_walk_length_increase_factor : vg::IndexingParameters
• pseudo_length() : vg::MultipathMapper
• ptr : json_autoptr
• purge_unmapped_alignments() : vg::MultipathMapper
• push() : vg::MatchPos::PathList , vg::ZipCodeTree::reverse_iterator
• push_back() : haplo::gbwt_thread_t , haplo::linear_haplo_structure::SNVvector
• push_edit() : vg::DozeuInterface