vg
tools for working with variation graphs
- p -
pack() :
bdsg::ODGI::edge_helper
,
handlegraph::number_bool_packing
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::Packer
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
parent_of() :
vg::SnarlManager
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
patch_alignment() :
vg::Mapper
path() :
vg::Paths
,
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_contains_handle() :
xg::XG
path_contains_node() :
vg::PathIndex
path_contains_node_in_orientation() :
vg::PathIndex
path_divergence_filter() :
vg::Filter
path_edge_count() :
vg::VG
path_end() :
bdsg::HashGraph
,
bdsg::ODGI
,
bdsg::PackedGraph
,
handlegraph::PathHandleGraph
,
vg::MemoizingGraph
,
vg::PathSubgraphOverlay
,
vg::VG
,
xg::XG
path_end_node_offset() :
vg::VG
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_id_prefix() :
vg::Index
path_identity() :
vg::VG
path_last_node() :
vg::Index
path_layout() :
vg::Index
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_name() :
xg::XG
path_name_prefix() :
vg::Index
path_names_by_prefix() :
xg::XG
path_position_to_string() :
vg::Index
path_ranks_by_prefix() :
xg::XG
path_relative_mapping() :
vg::Index
path_sequence() :
vg::VG
path_string() :
vg::VG
path_t() :
bdsg::HashGraph::path_t
,
vg::path_t
path_to_handles() :
vg::Transcriptome
path_to_input_haplotype() :
haplo::linear_haplo_structure
path_to_rank() :
bdsg::ODGI
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_by_id() :
vg::Index
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
populate_snarl_index() :
vg::MinimumDistanceIndex
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_entry_to_string() :
vg::Index
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
prefilter_redundant_sub_mems() :
vg::BaseMapper
preload_progress() :
vg::Progressive
prepend_mapping() :
vg::Paths
prepend_step() :
bdsg::HashGraph
,
bdsg::ODGI
,
bdsg::PackedGraph
,
handlegraph::MutablePathHandleGraph
,
vg::VG
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 >
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
PrintAlignment() :
vg::SSWAligner
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_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
proposal_sample() :
vg::MCMCGenotyper
propose_deflection() :
vg::BandedGlobalAligner< IntType >::AltTracebackStack
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
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
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