Here is a list of all variables with links to the classes they belong to:
- p -
- p_value_memo : vg::MultipathMapper
- pack_names : vg::Viz
- packer : vg::PackedTraversalSupportFinder
- packs : vg::Viz
- pad_cluster_score_threshold : vg::MinimizerMapper
- pad_suspicious_anchors_to_length : vg::Surjector
- 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
- parent : vg::Snarl, vg::SnarlManager::SnarlRecord, vg::TreeNode< T >, vg::VectorView< Item >::const_iterator, vg::WFANode
- 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::MIPayloadValues
- PARENT_IS_CHAIN_OFFSET : vg::MIPayload
- parent_is_root : vg::MIPayloadValues
- PARENT_IS_ROOT_OFFSET : vg::MIPayload
- parent_len : vg::Deconstructor::NestingInfo
- parent_net_handle : vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem
- parent_path_interval : vg::Deconstructor::NestingInfo
- PARENT_RECORD_MASK : vg::MIPayload
- PARENT_RECORD_OFFSET : vg::MIPayload
- parent_record_offset : vg::MIPayloadValues
- PARENT_RECORD_WIDTH : vg::MIPayload
- parent_ref_len : vg::Deconstructor::NestingInfo
- parent_snarls : vg::SnarlDistanceIndexClusterer::ClusteringProblem
- parse_only : GBWTConfig
- partitioner_parameters : HaplotypesConfig
- 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_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::RecombinatorHaplotype, vg::Subpath, vg::WFAAlignment, vg::WFANode
- path_collapse_type : vg::Transcriptome
- path_component_index : vg::MultipathMapper, vg::PathOrientedDistanceMeasurer
- path_count : xg::XG
- path_cover : GBWTConfig
- path_cover_depth : vg::IndexingParameters
- path_end : gafkluge::GafRecord
- path_finder : vg::VCFTraversalFinder
- path_graph : GraphHandler, vg::MinimizerMapper, vg::PhaseUnfolder
- path_indexes : vg::LegacyCaller
- path_jaccard_window : vg::Deconstructor
- path_length : gafkluge::GafRecord
- path_listeners : vg::algorithms::GFAParser
- path_name : vg::FeatureSet::Feature, vg::GraphSynchronizer::Lock
- path_name_csa_delim : xg::XG
- path_names : vg::VariantAdder
- path_nodes : vg::MultipathAlignmentGraph
- path_offset : vg::GraphSynchronizer::Lock
- path_order_and_length : vg::HTSWriter
- path_position_handle_graph : vg::MCMCCaller
- path_sampler : vg::NGSSimulator, vg::Sampler
- path_start : gafkluge::GafRecord
- path_subset : vg::PathSubgraphOverlay
- path_to_ploidy : vg::VCFGenotyper
- path_to_sample_phase : vg::Deconstructor
- path_to_vcf : vg::HaplotypeIndexer
- path_trav_finder : vg::Deconstructor
- paths : job_type, vg::PathTraversalFinder, vg::SurjectingAlignmentEmitter, vg::VG, xg::XG
- pbSize : vg::io::fdinbuf, vg::io::streaminbuf
- penalties : haplo::linear_haplo_structure
- per_base : vg::WFAExtender::ErrorModel::Event
- perfect_pair_identity_threshold : vg::FragmentLengthStatistics
- peripheral_attachments : vg::GraphSynchronizer::Lock
- periphery : vg::GraphSynchronizer::Lock
- permutation_idx : vg::ShuffledPairs::iterator
- permuted : vg::ShuffledPairs::iterator
- pessimistic_gap_memo : vg::MultipathMapper
- pessimistic_gap_multiplier : vg::MultipathMapper
- pessimistic_tail_gap_memo : vg::MultipathAlignmentGraph
- phase : vg::GFFRecord
- PHASE_BLOCK_MATCH : handlegraph::PathMetadata
- phase_homozygous : vg::HaplotypeIndexer
- phase_visits : vg::VG::Plan
- phred_prob : vg::NGSSimulator
- pi_iv : xg::XG
- pinned_tail_size : vg::VariantAdder
- 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::SmallBitset
- points : vg::algorithms::Anchor
- polyploid_prior_success_logprob : vg::Genotyper
- 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
- 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::RecombinatorHaplotype
- position_file : vg::NGSSimulator
- 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
- prefilter_redundant_hits : vg::BaseMapper
- prefix : vg::BitStringTree< Item >::TreeNode
- prefix_length : vg::MultipathProblem
- prefix_score : vg::MultipathProblem
- prefix_sum : 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
- present : vg::SnarlDistanceIndexClusterer::Cluster
- present_discount : vg::Recombinator::Parameters
- PRESENT_DISCOUNT : vg::Recombinator
- preserve_sinks : vg::DozeuPinningOverlay
- prev : vg::AlignmentChainModelVertex, vg::MEMChainModelVertex, vg::PhasedGenome::HaplotypeNode
- prev_char : vg::kmer_t
- prev_chars : vg::KmerPosition
- prev_cost : vg::AlignmentChainModelVertex, vg::MEMChainModelVertex
- prev_pos : vg::kmer_t
- prev_stage_items : vg::Funnel::Item
- prev_subpath : vg::MultipathProblem
- previous_index : haplo::haplo_DP_rectangle
- 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_updates : vg::VariantAdder
- priority : vg::subcommand::Subcommand
- prng : vg::NGSSimulator::MarkovDistribution< From, To >
- prngs : vg::NGSSimulator
- prob_sampler : vg::NGSSimulator
- problem : vg::AlignmentValidity
- produces_one_gbwt : GBWTConfig
- progress : vg::Progressive
- progress_bars : vg::VGset
- progress_count : vg::Progressive
- progress_message : vg::Progressive
- progress_seen : vg::Progressive
- projected_count : vg::Funnel::Stage
- proto : vg::io::VGAlignmentEmitter
- protobuf_to_tag : vg::io::Registry::Tables
- provided_directly : vg::IndexFile
- prune_subpaths_multiplier : vg::MultipathMapper
- prune_suspicious_anchors : 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
- ptr : json_autoptr