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_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::Packer
packer : vg::PackedTraversalSupportFinder
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_rescue() : vg::Mapper
pair_rescue_hang_threshold : vg::Mapper
pair_rescue_retry_threshold : vg::Mapper
paired : vg::MinimizerMapper
paired_distance_stdevs : vg::MinimizerMapper
paired_rescue_score_limit : vg::MinimizerMapper
PairType : vg::MinimizerMapper
ParallelKFFReader() : vg::ParallelKFFReader
param_type : vg::discrete_distribution< T >
Parameters() : vg::Recombinator::Parameters
params : MinimizerConfig
parent : vg::SnarlManager::SnarlRecord, vg::TreeNode< T >, vg::VectorView< Item >::const_iterator, vg::WFANode, vg::WFATree
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
parent_graph : vg::JoinedSpliceGraph
parent_handle : vg::MIPayload
parent_is_chain : vg::MIPayload
parent_is_root : vg::MIPayload
parent_net_handle : vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem
parent_of() : vg::SnarlManager
parent_record_offset : vg::MIPayload
parent_snarls : vg::SnarlDistanceIndexClusterer::ClusteringProblem
parent_type : vg::MIPayload
parse() : vg::algorithms::GFAParser, vg::algorithms::GFATextParser, vg::algorithms::GFAzParser, 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::NegationFlagArgSpec< Receiver >, vg::subcommand::OptionGroup< Receiver >, vg::subcommand::ValueArgSpec< T, Receiver, Holder >
parse_attribute_value() : vg::Transcriptome
parse_attributes() : vg::GFFRecord
parse_base_path() : vg::GrefCover
parse_default() : vg::OptionValueParser< Value >, vg::OptionValueParser< vector< Item > >
parse_gref_index() : vg::GrefCover
parse_h() : vg::algorithms::GFAParser
parse_introns() : vg::Transcriptome
parse_l() : vg::algorithms::GFAParser
parse_matrix() : vg::AlignerClient
parse_only : GBWTConfig
parse_p() : vg::algorithms::GFAParser
parse_s() : vg::algorithms::GFAParser
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 : vg::algorithms::walk_t, vg::CompletedTranscriptPath, vg::EditedTranscriptPath, vg::GaplessExtension, vg::MatchPos, vg::PathNode, vg::Paths, vg::RecombinatorHaplotype, vg::subpath_t, vg::WFAAlignment, vg::WFANode
path_back() : vg::MemoizingGraph, vg::PathSubgraphOverlay, vg::VG
path_begin() : vg::MemoizingGraph, vg::PathSubgraphOverlay, vg::VG
path_chunk_t : vg::Surjector
path_collapse_type : vg::Transcriptome
path_component_index : vg::MultipathMapper, vg::PathOrientedDistanceMeasurer
path_contains_node() : vg::PathIndex
path_contains_node_in_orientation() : vg::PathIndex
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_edge_count() : vg::VG
path_end() : vg::MemoizingGraph, vg::PathSubgraphOverlay, vg::VG
path_end_node_offset() : vg::VG
PATH_FIELD : vg::GAFSorterRecord
path_finder : vg::VCFTraversalFinder
path_front_end() : vg::MemoizingGraph, vg::PathSubgraphOverlay, vg::VG
path_graph : GraphHandler, vg::MinimizerMapper, vg::PhaseUnfolder
path_handle : vg::SequenceDictionaryEntry
path_identity() : vg::VG
path_indexes : vg::LegacyCaller
path_jaccard_window : vg::Deconstructor
path_length : vg::SequenceDictionaryEntry
path_lengths_to_sinks() : vg::BandedGlobalAligner< IntType >
path_listeners : vg::algorithms::GFAParser
path_mapping_t() : vg::path_mapping_t
path_mode : GBWTConfig
path_name : vg::algorithms::GFAzParser::PendingRGFAVisit, vg::FeatureSet::Feature, vg::GraphSynchronizer::Lock, vg::SequenceDictionaryEntry
path_names : GBWTConfig, vg::VariantAdder
path_nodes : vg::MultipathAlignmentGraph
path_offset : vg::GraphSynchronizer::Lock
path_output : GBWTConfig
path_position_handle_graph : vg::MCMCCaller
path_rank : vg::algorithms::GFAzParser::PendingRGFAVisit
path_sampler : vg::NGSSimulator, vg::Sampler
path_score_annotations() : vg::Surjector
path_sequence() : vg::VG
path_subset : vg::PathSubgraphOverlay
path_t() : vg::path_t
path_to_ploidy : vg::VCFGenotyper
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
PathIndex() : vg::PathIndex
PathOrientedDistanceMeasurer() : vg::PathOrientedDistanceMeasurer
PathRestrictedTraversalFinder() : vg::PathRestrictedTraversalFinder
Paths() : vg::Paths
paths : job_type, vg::algorithms::TracedScore, vg::PathTraversalFinder, vg::SnarlDistanceIndexClusterer::Seed, vg::SurjectingAlignmentEmitter, vg::VG
paths_as_alignments() : vg::VG
paths_between() : vg::VG
paths_flags_t : vg::SnarlDistanceIndexClusterer
paths_on_same_component() : vg::PathComponentIndex
PathSubgraph() : vg::PathSubgraph
PathSubgraphOverlay() : vg::PathSubgraphOverlay
PathTraversalFinder() : vg::PathTraversalFinder
payload : vg::SnarlDistanceIndexClusterer::SeedCache
PAYLOAD_KEY : vg::MinimizerIndexParameters
payload_node_length : vg::SnarlDistanceIndexClusterer::SeedCache
PAYLOAD_NONE : vg::MinimizerIndexParameters
payload_prefix_sum : vg::SnarlDistanceIndexClusterer::SeedCache
payload_str() : vg::MinimizerIndexParameters
payload_type : vg::MinimizerMapper, vg::MIPayload, vg::ZipCode
PAYLOAD_ZIPCODES : vg::MinimizerIndexParameters
PAYLOAD_ZIPCODES_WITH_PATHS : vg::MinimizerIndexParameters
PayloadType : vg::MinimizerIndexParameters
peek() : vg::BitString
pending_rgfa_visits : vg::algorithms::GFAzParser
pending_traversals : vg::ZipCodeTree::distance_iterator
per_base : vg::WFAExtender::ErrorModel::Event
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
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
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, vg::ZipCodeTree::distance_iterator
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::VCFOutputCaller::SuppressedRef, vg::WFAPoint, vg::ZipCodeTree::distance_iterator
pos_at() : MappingRun
pos_char() : vg::Sampler
pos_key() : vg::Packer
pos_to_trans : vg::Translator
position : vg::algorithms::GFAFormatError, vg::Funnel, vg::path_mapping_t, vg::RecombinatorHaplotype, vg::Sampler
position_chromosome : vg::Primer
position_file : vg::NGSSimulator
position_in_basis() : vg::Packer
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
predates() : vg::IndexRegistry
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
prepare_decode() : vg::algorithms::GFAzParser
prepend_mapping() : vg::Paths
prepend_step() : vg::VG
present : vg::Recombinator, vg::SnarlDistanceIndexClusterer::Cluster
PRESENT_DISCOUNT : vg::Recombinator
present_discount : vg::Recombinator::Parameters
preserve_sinks : vg::DozeuPinningOverlay
Preset() : vg::subcommand::Preset
preset() : vg::subcommand::ArgSpec< T, Receiver >, vg::subcommand::BaseArgSpec< Receiver >, vg::subcommand::BaseOptionGroup, vg::subcommand::GroupedOptionGroup, vg::subcommand::NegationFlagArgSpec< Receiver >, 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_values : haplo::haplo_DP_column
primary : vg::MaximalExactMatch, vg::subcommand::NegationFlagArgSpec< Receiver >
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::subcommand::NegationFlagArgSpec< Receiver >, vg::WFAAlignment
print_band() : vg::BandedGlobalAligner< IntType >::BAMatrix
print_default() : vg::subcommand::BaseArgSpec< Receiver >, vg::subcommand::FlagArgSpec< Receiver >, vg::subcommand::NegationFlagArgSpec< Receiver >, vg::subcommand::ValueArgSpec< T, Receiver, Holder >
print_edges() : vg::VG
print_flipped_snarl() : vg::VCFOutputCaller
print_full_matrices() : vg::BandedGlobalAligner< IntType >::BAMatrix
print_help() : vg::ConfigurableParser
print_matrix() : vg::BandedGlobalAligner< IntType >::BAMatrix
print_metavar() : vg::subcommand::BaseArgSpec< Receiver >, vg::subcommand::FlagArgSpec< Receiver >, vg::subcommand::NegationFlagArgSpec< 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_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::NegationFlagArgSpec< 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
process_until_threshold_d() : vg::MinimizerMapper
process_until_threshold_e() : vg::MinimizerMapper
processed_input() : vg::Funnel
processing_input() : vg::Funnel
produced_output() : vg::Funnel
produces_one_gbwt : GBWTConfig
producing_output() : vg::Funnel
progress : ChainsConfig, MinimizerConfig, vg::GAFSorterParameters, vg::MinimizerIndexParameters, 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
provide() : vg::IndexFile, vg::IndexRegistry
provided_directly : vg::IndexFile
prune_and_trim_anchors() : vg::Surjector
prune_header_contigs() : vg::VCFOutputCaller
prune_high_shift_edges() : vg::MultipathAlignmentGraph
prune_low_cplx : GiraffeMainOptions
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
purge_unmapped_alignments() : vg::MultipathMapper
push() : vg::MatchPos::PathList, vg::ZipCodeTree::distance_iterator
push_back() : haplo::gbwt_thread_t, vg::IndirectVectorView< Item >
push_edit() : vg::DozeuInterface