Here is a list of all functions with links to the classes they belong to:
- 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_is_chain() : vg::MIPayload
- parent_is_root() : vg::MIPayload
- parent_of() : vg::SnarlManager
- parent_record_offset() : vg::MIPayload
- 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
- Pictographs() : vg::Pictographs
- Plan() : vg::VG::Plan
- PoissonSupportSnarlCaller() : vg::PoissonSupportSnarlCaller
- pop() : vg::MatchPos::PathList, vg::MatchPos
- 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::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
- prefix_sum() : vg::MIPayload
- 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
- 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_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
- push_back() : haplo::gbwt_thread_t, haplo::linear_haplo_structure::SNVvector
- push_edit() : vg::DozeuInterface