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
- 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_directory : vg::temp_file::Handler, xg::temp_file::Handler
- parent_graph : vg::JoinedSpliceGraph
- parent_is_chain() : vg::MIPayload, vg::MIPayloadValues
- PARENT_IS_CHAIN_OFFSET : vg::MIPayload
- parent_is_root() : vg::MIPayload, vg::MIPayloadValues
- PARENT_IS_ROOT_OFFSET : 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_MASK : vg::MIPayload
- PARENT_RECORD_OFFSET : vg::MIPayload
- parent_record_offset() : vg::MIPayload, vg::MIPayloadValues
- PARENT_RECORD_WIDTH : vg::MIPayload
- parent_ref_len : vg::Deconstructor::NestingInfo
- parent_snarls : vg::SnarlDistanceIndexClusterer::ClusteringProblem
- 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_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_name : vg::FeatureSet::Feature, vg::GraphSynchronizer::Lock, xg::XG
- path_name_csa_delim : xg::XG
- path_names : vg::VariantAdder
- path_names_by_prefix() : xg::XG
- path_nodes : vg::MultipathAlignmentGraph
- path_offset : vg::GraphSynchronizer::Lock
- path_order_and_length : vg::HTSWriter
- 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
- 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
- Pictographs() : vg::Pictographs
- 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
- PoissonSupportSnarlCaller() : vg::PoissonSupportSnarlCaller
- polyploid_prior_success_logprob : vg::Genotyper
- pop() : vg::MatchPos::PathList, vg::MatchPos
- 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::algorithms::Anchor, vg::ChainIterator, vg::KmerPosition, vg::SnarlDistanceIndexClusterer::Seed, vg::SnarlDistanceIndexClusterer::SeedCache, 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::KmerMatch, vg::Mapping, vg::path_mapping_t, vg::RecombinatorHaplotype, vg::Sampler
- position_assuming_acyclic() : haplo::linear_haplo_structure
- position_file : vg::NGSSimulator
- position_in_basis() : vg::Packer
- position_in_path() : xg::XG
- position_in_paths() : xg::XG
- position_t() : vg::position_t
- positions : vg::AlignmentChainModel, vg::AlignmentChainModelVertex, vg::MaximalExactMatch, vg::MEMChainModel
- possible_scores : vg::WFATree
- posterior : vg::PoissonSupportSnarlCaller::PoissonCallInfo
- precluster_connection_coverage_threshold : vg::MinimizerMapper
- 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::MIPayloadValues, vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem::SnarlTreeChild
- PREFIX_SUM_MASK : vg::MIPayload
- PREFIX_SUM_OFFSET : vg::MIPayload
- prefix_sum_value : vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem
- PREFIX_SUM_WIDTH : vg::MIPayload
- 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
- 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_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::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
- push_back() : haplo::gbwt_thread_t, haplo::linear_haplo_structure::SNVvector
- push_edit() : vg::DozeuInterface