- p -

• p_value() : vg::SeqComplexity< MaxOrder >
• pack() : handlegraph::number_bool_packing
• pack_query_forward() : vg::DozeuInterface , vg::QualAdjXdropAligner , vg::XdropAligner
• pack_query_reverse() : vg::DozeuInterface , vg::QualAdjXdropAligner , vg::XdropAligner
• PackedTraversalSupportFinder() : vg::PackedTraversalSupportFinder
• Packer() : vg::Packer
• 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
• ParallelKFFReader() : vg::ParallelKFFReader
• Parameters() : vg::Recombinator::Parameters
• parent() : vg::WFATree
• parent_of() : vg::SnarlManager
• 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_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
• pass() : vg::Funnel
• patch_alignment() : vg::Mapper
• path() : vg::Paths , vg::subpath_t
• 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_contains_handle() : xg::XG
• path_contains_node() : vg::PathIndex
• path_contains_node_in_orientation() : vg::PathIndex
• path_cover_parameters() : GBWTConfig
• path_divergence_filter() : vg::Filter
• path_edge_count() : vg::VG
• path_end() : handlegraph::PathHandleGraph , vg::MemoizingGraph , vg::PathSubgraphOverlay , vg::VG , xg::XG
• path_end_node_offset() : vg::VG
• path_front_end() : handlegraph::PathHandleGraph , vg::MemoizingGraph , vg::PathSubgraphOverlay , vg::VG , xg::XG
• path_identity() : vg::VG
• 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() : vg::path_mapping_t
• path_name() : xg::XG
• path_names_by_prefix() : xg::XG
• path_ranks_by_prefix() : xg::XG
• path_score_annotations() : vg::Surjector
• path_sequence() : vg::VG
• path_t() : vg::path_t
• path_to_input_haplotype() : haplo::linear_haplo_structure
• PathBasedTraversalFinder() : vg::PathBasedTraversalFinder
• PathChunker() : vg::PathChunker
• PathComponentIndex() : vg::PathComponentIndex
• PathForEachSocket() : handlegraph::PathForEachSocket
• PathIndex() : vg::PathIndex
• PathOrientedDistanceMeasurer() : vg::PathOrientedDistanceMeasurer
• PathRestrictedTraversalFinder() : vg::PathRestrictedTraversalFinder
• Paths() : vg::Paths
• 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
• peek() : vg::BitString
• percent_identity_filter() : vg::Filter
• perfect_filter() : vg::Filter
• perform_dp() : vg::MEMClusterer::HitGraph
• performed_duplications() : vg::DozeuPinningOverlay
• pessimistic_gap() : vg::MultipathMapper
• pessimistic_tail_gap() : vg::MultipathAlignmentGraph
• PhasedGenome() : vg::PhasedGenome
• PhaseUnfolder() : vg::PhaseUnfolder
• pick_mappings_from_alignments() : vg::MinimizerMapper
• Pictographs() : vg::Pictographs
• pin_offset() : vg::MinimizerMapper::Minimizer
• Plan() : vg::VG::Plan
• PoissonSupportSnarlCaller() : vg::PoissonSupportSnarlCaller
• pop() : vg::MatchPos::PathList , vg::MatchPos , vg::ZipCodeTree::reverse_iterator
• pop_back_step() : handlegraph::MutablePathHandleGraph
• pop_front_step() : handlegraph::MutablePathHandleGraph
• pos() : vg::WFAPoint
• pos_at() : MappingRun
• pos_char() : vg::Sampler , xg::XG
• pos_key() : vg::Packer
• pos_substr() : xg::XG
• position() : vg::Funnel , vg::path_mapping_t , vg::Sampler
• position_assuming_acyclic() : haplo::linear_haplo_structure
• position_in_basis() : vg::Packer
• position_in_path() : xg::XG
• position_in_paths() : xg::XG
• position_t() : vg::position_t
• precollapse_order_length_runs() : vg::BaseMapper
• predecessor_offset() : vg::WFATree
• prefilter_redundant_sub_mems() : vg::BaseMapper
• prefix() : vg::GaplessExtension , vg::RecombinatorHaplotype , vg::WFAExtender
• preload_progress() : vg::Progressive
• prepend_mapping() : vg::Paths
• prepend_step() : handlegraph::MutablePathHandleGraph , vg::VG
• preset() : vg::subcommand::ArgSpec< T, Receiver > , vg::subcommand::BaseArgSpec< Receiver > , vg::subcommand::BaseOptionGroup , vg::subcommand::GroupedOptionGroup , vg::subcommand::OptionGroup< Receiver >
• prev_idx() : haplo::haplo_DP_rectangle
• prev_snarl() : vg::SnarlManager
• previous_R() : haplo::haplo_DP_column
• PrimerFinder() : vg::PrimerFinder
• 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_value() : vg::subcommand::BaseArgSpec< Receiver > , vg::subcommand::FlagArgSpec< Receiver > , vg::subcommand::ValueArgSpec< T, Receiver, Holder >
• PrintAlignment() : vg::SSWAligner
• prng() : vg::NGSSimulator
• 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
• producing_output() : vg::Funnel
• 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
• proposal_sample() : vg::MCMCGenotyper
• propose_deflection() : vg::BandedGlobalAligner< IntType >::AltTracebackStack
• ProtobufEmitter() : vg::io::ProtobufEmitter< T >
• ProtobufIterator() : vg::io::ProtobufIterator< T >
• provide() : vg::IndexFile , vg::IndexRegistry
• prune_and_trim_anchors() : vg::Surjector
• prune_high_shift_edges() : vg::MultipathAlignmentGraph
• prune_low_scoring_edges() : vg::MEMClusterer::HitGraph
• prune_to_high_scoring_paths() : vg::MultipathAlignmentGraph
• prune_unconnectable() : vg::Surjector
• pseudo_length() : vg::MultipathMapper
• 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