Here is a list of all class members with links to the classes they belong to:
- p -
- p_value_memo
: vg::MultipathMapper
- pack()
: bdsg::ODGI::edge_helper
, 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()
: bdsg::PackedGraph
- PackedPath()
: bdsg::PackedGraph::PackedPath
- PackedTraversalSupportFinder()
: vg::PackedTraversalSupportFinder
- packer
: vg::PackedTraversalSupportFinder
- Packer()
: vg::Packer
- packs
: vg::Viz
- pad_cluster_score_threshold
: vg::MinimizerMapper
- pad_traversal()
: vg::GAFOutputCaller
- 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
- param_type
: vg::discrete_distribution< T >
- parent
: vg::Snarl
, vg::SnarlManager::SnarlRecord
, vg::TreeNode< T >
- parent_chain
: vg::SnarlManager::SnarlRecord
- parent_chain_index
: vg::SnarlManager::SnarlRecord
- parent_directory
: vg::temp_file::Handler
, xg::temp_file::Handler
- parent_graph
: vg::JoinedSpliceGraph
- parent_id
: vg::MinimumDistanceIndex::ChainIndex
, vg::MinimumDistanceIndex::SnarlIndex
- parent_of()
: vg::SnarlManager
- parent_snarl_to_nodes
: vg::SnarlSeedClusterer::TreeState
- parse()
: vg::BaseOption< Value, Parser >
, vg::ConfigurableParser
, vg::OptionInterface
, vg::OptionValueParser< Value >
, vg::OptionValueParser< vector< Item > >
- parse_alignment()
: vg::Index
- parse_attributes()
: vg::GFFRecord
- parse_base()
: vg::Index
- parse_default()
: vg::OptionValueParser< Value >
, vg::OptionValueParser< vector< Item > >
- parse_edge()
: vg::Index
- parse_from_string()
: vg::io::ProtobufIterator< T >
- parse_introns()
: vg::Transcriptome
- parse_kmer()
: vg::Index
- parse_mapping()
: vg::Index
- parse_matrix()
: vg::AlignerClient
- parse_node()
: vg::Index
- parse_node_path()
: vg::Index
- parse_path_position()
: vg::Index
- parse_subpath_name()
: vg::Paths
- parse_transcripts()
: vg::Transcriptome
- parse_translation()
: vg::PathIndex
- parse_traversal()
: vg::Index
- parse_vcf()
: vg::HaplotypeIndexer
- pass()
: vg::Funnel
- 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::PathNode
, vg::Paths
, vg::Subpath
, vg::subpath_t
- path_back()
: bdsg::HashGraph
, bdsg::ODGI
, bdsg::PackedGraph
, handlegraph::PathHandleGraph
, vg::MemoizingGraph
, vg::PathSubgraphOverlay
, vg::VG
, xg::XG
- path_begin()
: bdsg::HashGraph
, bdsg::ODGI
, bdsg::PackedGraph
, handlegraph::PathHandleGraph
, vg::MemoizingGraph
, vg::PathSubgraphOverlay
, vg::VG
, xg::XG
- path_chunk_t
: vg::Surjector
- 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_deleted_steps_iv
: bdsg::PackedGraph
- path_divergence_filter()
: vg::Filter
- path_edge_count()
: vg::VG
- path_end()
: bdsg::HashGraph
, bdsg::ODGI
, bdsg::PackedGraph
, gafkluge::GafRecord
, handlegraph::PathHandleGraph
, vg::MemoizingGraph
, vg::PathSubgraphOverlay
, vg::VG
, xg::XG
- path_end_node_offset()
: vg::VG
- path_finder
: vg::VCFTraversalFinder
- path_first_node()
: vg::Index
- path_front_end()
: bdsg::HashGraph
, bdsg::ODGI
, bdsg::PackedGraph
, handlegraph::PathHandleGraph
, vg::MemoizingGraph
, vg::PathSubgraphOverlay
, vg::VG
, xg::XG
- path_graph
: vg::MinimizerMapper
, vg::PhaseUnfolder
- path_head_iv
: bdsg::PackedGraph
- path_id
: bdsg::HashGraph
, bdsg::HashGraph::path_mapping_t
, bdsg::HashGraph::path_t
, bdsg::PackedGraph
- path_id_prefix()
: vg::Index
- path_identity()
: vg::VG
- path_indexes
: vg::LegacyCaller
- path_is_circular_iv
: bdsg::PackedGraph
- path_is_deleted_iv
: bdsg::PackedGraph
- path_last_node()
: vg::Index
- path_layout()
: vg::Index
- path_length
: gafkluge::GafRecord
, vg::HTSAlignmentEmitter
- path_length_filter()
: vg::Filter
- path_lengths_to_sinks()
: vg::BandedGlobalAligner< IntType >
- path_mapping_node_id()
: haplo::linear_haplo_structure
- path_mapping_offset()
: haplo::linear_haplo_structure
- path_mapping_t()
: bdsg::HashGraph::path_mapping_t
, vg::path_mapping_t
- path_membership_id_iv
: bdsg::PackedGraph
- path_membership_next_iv
: bdsg::PackedGraph
- path_membership_node_iv
: bdsg::PackedGraph
- path_membership_offset_iv
: bdsg::PackedGraph
- path_metadata_v
: bdsg::ODGI
- path_name
: vg::FeatureSet::Feature
, vg::GraphSynchronizer::Lock
, xg::XG
- path_name_length_iv
: bdsg::PackedGraph
- path_name_map
: bdsg::ODGI
- path_name_prefix()
: vg::Index
- path_name_start_iv
: bdsg::PackedGraph
- path_names
: vg::VariantAdder
- path_names_by_prefix()
: xg::XG
- path_names_iv
: bdsg::PackedGraph
- PATH_NEXT_OFFSET
: bdsg::PackedGraph
- path_nodes
: vg::MultipathAlignmentGraph
- path_offset
: vg::GraphSynchronizer::Lock
- path_origin_names
: vg::TranscriptPath
- path_position_handle_graph
: vg::MCMCCaller
- path_position_to_string()
: vg::Index
- PATH_PREV_OFFSET
: bdsg::PackedGraph
- path_ranks_by_prefix()
: xg::XG
- PATH_RECORD_SIZE
: bdsg::PackedGraph
- path_relative_mapping()
: vg::Index
- PATH_RESIZE_FACTOR
: bdsg::PackedGraph
- path_restricted
: vg::Deconstructor
- path_sampler
: vg::NGSSimulator
, vg::Sampler
- path_sequence()
: vg::VG
- path_start
: gafkluge::GafRecord
- path_string()
: vg::VG
- path_subset
: vg::PathSubgraphOverlay
- path_t()
: bdsg::HashGraph::path_t
, vg::path_t
- path_tail_iv
: bdsg::PackedGraph
- path_to_handles()
: vg::Transcriptome
- path_to_input_haplotype()
: haplo::linear_haplo_structure
- path_to_rank()
: bdsg::ODGI
- path_to_sample
: vg::Deconstructor
- path_to_vcf
: vg::HaplotypeIndexer
- path_trav_finder
: vg::Deconstructor
- path_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
: bdsg::HashGraph
, bdsg::PackedGraph
- Paths()
: vg::Paths
- paths
: vg::PathTraversalFinder
, vg::VG
, xg::XG
- paths_as_alignments()
: vg::VG
- paths_as_samples
: vg::HaplotypeIndexer
- paths_between()
: vg::VG
- paths_by_id()
: vg::Index
- paths_of_handle()
: xg::XG
- paths_on_same_component()
: vg::PathComponentIndex
- PathSubgraph()
: vg::PathSubgraph
- PathSubgraphOverlay()
: vg::PathSubgraphOverlay
- PathTraversalFinder()
: vg::PathTraversalFinder
- pbSize
: vg::io::fdinbuf
- peek()
: vg::BitString
- penalties
: haplo::linear_haplo_structure
- 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_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
- pindexes
: vg::SRPE
- pinned_tail_size
: vg::VariantAdder
- Plan()
: vg::VG::Plan
- plausible_rescue_cluster_coverage_diff
: vg::MultipathMapper
- ploidy
: vg::Deconstructor
- 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
- PoissonSupportSnarlCaller()
: vg::PoissonSupportSnarlCaller
- polyploid_prior_success_logprob
: vg::Genotyper
- populate_snarl_index()
: vg::MinimumDistanceIndex
- population_max_paths
: vg::MultipathMapper
- population_paths_hard_cap
: vg::MultipathMapper
- population_size
: haplo::haploMath::RRMemo
- pos
: vg::ChainIterator
, vg::KmerPosition
, vg::SnarlSeedClusterer::Seed
- 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::BREAKPOINT
, vg::KmerMatch
, vg::Mapping
, vg::path_mapping_t
, vg::Sampler
- position_assuming_acyclic()
: haplo::linear_haplo_structure
- position_entry_to_string()
: vg::Index
- 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
- posterior
: vg::PoissonSupportSnarlCaller::PoissonCallInfo
- precollapse_order_length_hits
: vg::BaseMapper
- precollapse_order_length_runs()
: vg::BaseMapper
- prefilter_redundant_hits
: vg::BaseMapper
- prefilter_redundant_sub_mems()
: vg::BaseMapper
- prefix
: vg::BitStringTree< Item >::TreeNode
- prefix_length
: vg::MultipathProblem
- prefix_score
: vg::MultipathProblem
- prefix_sum
: vg::MinimumDistanceIndex::ChainIndex
- prefixes
: vg::PhaseUnfolder
- preload_progress()
: vg::Progressive
- prepend_mapping()
: vg::Paths
- prepend_step()
: bdsg::HashGraph
, bdsg::ODGI
, bdsg::PackedGraph
, handlegraph::MutablePathHandleGraph
, vg::VG
- present
: vg::SnarlSeedClusterer::Cluster
- preserve_sinks
: vg::DozeuPinningOverlay
- prev
: bdsg::HashGraph::path_mapping_t
, 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
- primary_snarl_assignments
: vg::MinimumDistanceIndex
- primary_snarl_ranks
: vg::MinimumDistanceIndex
- primitive_root
: vg::ShuffledPairs
- print()
: haplo::haplo_DP_column
, haplo::hDP_gbwt_graph_accessor< GBWTType >
- print_band()
: vg::BandedGlobalAligner< IntType >::BAMatrix
- 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_phased_genome()
: vg::PhasedGenome
- print_rectangularized_bands()
: vg::BandedGlobalAligner< IntType >::BAMatrix
- print_report()
: vg::IndexedVG
- print_self()
: vg::MinimumDistanceIndex::ChainIndex
, vg::MinimumDistanceIndex
, vg::MinimumDistanceIndex::SnarlIndex
- print_snarl_stats()
: vg::MinimumDistanceIndex
- print_statistics()
: vg::Genotyper
- print_updates
: vg::VariantAdder
- PrintAlignment()
: vg::SSWAligner
- priority
: vg::subcommand::Subcommand
- prng
: vg::NGSSimulator::MarkovDistribution< From, To >
, vg::NGSSimulator
- prob_sampler
: vg::NGSSimulator
- 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
- 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_and_add_transcripts()
: vg::Transcriptome
- project_and_add_transcripts_callback()
: vg::Transcriptome
- project_group()
: vg::Funnel
- project_transcript_embedded()
: vg::Transcriptome
- project_transcript_gbwt()
: vg::Transcriptome
- projected_count
: vg::Funnel::Stage
- 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 >
- prune_complex()
: vg::VG
- prune_complex_paths()
: vg::VG
- prune_complex_with_head_tail()
: vg::VG
- prune_kmers()
: vg::Index
- prune_low_scoring_edges()
: vg::MEMClusterer::HitGraph
- prune_short_subgraphs()
: vg::VG
- prune_to_high_scoring_paths()
: vg::MultipathAlignmentGraph
- pseudo_length()
: vg::MultipathMapper
- ptr
: json_autoptr
- push_back()
: bdsg::HashGraph::path_t
, haplo::gbwt_thread_t
, haplo::linear_haplo_structure::SNVvector
- push_edit()
: vg::DozeuInterface
- push_front()
: bdsg::HashGraph::path_t
- put_alignment()
: vg::Index
- put_base()
: vg::Index
- put_edge()
: vg::Index
- put_kmer()
: vg::Index
- put_mapping()
: vg::Index
- put_max_path_id()
: vg::Index
- put_metadata()
: vg::Index
- put_node()
: vg::Index
- put_node_path()
: vg::Index
- put_path_id_to_name()
: vg::Index
- put_path_name_to_id()
: vg::Index
- put_path_position()
: vg::Index
- put_traversal()
: vg::Index