vg
tools for working with variation graphs
- p -
p_value_memo :
vg::MultipathMapper
pack_names :
vg::Viz
packer :
vg::PackedTraversalSupportFinder
packs :
vg::Viz
pad_cluster_score_threshold :
vg::MinimizerMapper
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 >
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_snarl_to_nodes :
vg::SnarlSeedClusterer::TreeState
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::PathNode
,
vg::Subpath
path_component_index :
vg::MultipathMapper
,
vg::PathOrientedDistanceMeasurer
path_count :
xg::XG
path_deleted_steps_iv :
bdsg::PackedGraph
path_end :
gafkluge::GafRecord
path_finder :
vg::VCFTraversalFinder
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_indexes :
vg::LegacyCaller
path_is_circular_iv :
bdsg::PackedGraph
path_is_deleted_iv :
bdsg::PackedGraph
path_length :
gafkluge::GafRecord
,
vg::HTSAlignmentEmitter
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
path_name_length_iv :
bdsg::PackedGraph
path_name_map :
bdsg::ODGI
path_name_start_iv :
bdsg::PackedGraph
path_names :
vg::VariantAdder
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_PREV_OFFSET :
bdsg::PackedGraph
PATH_RECORD_SIZE :
bdsg::PackedGraph
PATH_RESIZE_FACTOR :
bdsg::PackedGraph
path_restricted :
vg::Deconstructor
path_sampler :
vg::NGSSimulator
,
vg::Sampler
path_start :
gafkluge::GafRecord
path_subset :
vg::PathSubgraphOverlay
path_tail_iv :
bdsg::PackedGraph
path_to_sample :
vg::Deconstructor
path_to_vcf :
vg::HaplotypeIndexer
path_trav_finder :
vg::Deconstructor
paths :
bdsg::HashGraph
,
bdsg::PackedGraph
,
vg::PathTraversalFinder
,
vg::VG
,
xg::XG
paths_as_samples :
vg::HaplotypeIndexer
pbSize :
vg::io::fdinbuf
penalties :
haplo::linear_haplo_structure
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_homozygous :
vg::HaplotypeIndexer
phase_visits :
vg::VG::Plan
phred_prob :
vg::NGSSimulator
pi_iv :
xg::XG
pindexes :
vg::SRPE
pinned_tail_size :
vg::VariantAdder
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
polyploid_prior_success_logprob :
vg::Genotyper
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_to_edit_to_depth :
vg::Filter
pos_to_qual :
vg::Filter
pos_to_trans :
vg::Translator
position :
vg::BREAKPOINT
,
vg::KmerMatch
,
vg::Mapping
position_file :
vg::NGSSimulator
positions :
vg::AlignmentChainModel
,
vg::AlignmentChainModelVertex
,
vg::MaximalExactMatch
,
vg::MEMChainModel
posterior :
vg::PoissonSupportSnarlCaller::PoissonCallInfo
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::MinimumDistanceIndex::ChainIndex
prefixes :
vg::PhaseUnfolder
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_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
primary_snarl_assignments :
vg::MinimumDistanceIndex
primary_snarl_ranks :
vg::MinimumDistanceIndex
primitive_root :
vg::ShuffledPairs
print_updates :
vg::VariantAdder
priority :
vg::subcommand::Subcommand
prng :
vg::NGSSimulator::MarkovDistribution< From, To >
,
vg::NGSSimulator
prob_sampler :
vg::NGSSimulator
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
ptr :
json_autoptr
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