Here is a list of all class members with links to the classes they belong to:
- o -
- object_end() : vg::ProblemDumpExplainer
- object_start() : vg::ProblemDumpExplainer
- occs : vg::MinimizerMapper::Minimizer
- of_node() : vg::Paths
- off_ref_paths : vg::Deconstructor
- offset : vg::GaplessExtension, vg::Haplotypes::TopLevelChain, vg::PathBranch, vg::Position, vg::position_t, vg::VectorView< Item >::const_iterator
- offsets : xg::XGPath
- offsets_in_paths() : xg::XG
- offsets_rank : xg::XGPath
- offsets_select : xg::XGPath
- OK : vg::AlignmentValidity
- ok : vg::WFAAlignment
- OLD_EDGE_TYPE_END_END : xg::XG
- OLD_EDGE_TYPE_END_START : xg::XG
- OLD_EDGE_TYPE_MAX : xg::XG
- OLD_EDGE_TYPE_MIN : xg::XG
- OLD_EDGE_TYPE_START_END : xg::XG
- OLD_EDGE_TYPE_START_START : xg::XG
- OLD_G_EDGE_LENGTH : xg::XG
- OLD_G_EDGE_OFFSET_OFFSET : xg::XG
- OLD_G_EDGE_TYPE_OFFSET : xg::XG
- OLD_G_NODE_FROM_COUNT_OFFSET : xg::XG
- OLD_G_NODE_TO_COUNT_OFFSET : xg::XG
- old_node : haplo::hDP_gbwt_graph_accessor< GBWTType >
- old_score : vg::GaplessExtension
- old_version_path_name_end : xg::XG
- old_version_path_name_start : xg::XG
- on_group() : vg::io::MessageEmitter, vg::io::ProtobufEmitter< T >
- on_message() : vg::io::ProtobufEmitter< T >
- on_path_edit() : vg::FeatureSet
- one_end_anchored_filter() : vg::Filter
- oneof_location : vg::LocationSupport
- only_correctly_mapped : vg::ReadFilter< Read >
- only_mapped : vg::ReadFilter< Read >
- only_proper_pairs : vg::ReadFilter< Read >
- open_all() : vg::StreamSorter< Message >
- open_fd() : handlegraph::TriviallySerializable
- OperatingMode : HaplotypesConfig
- operator bool() : vg::AlignmentValidity, vg::WFAAlignment
- operator Number() : vg::Range< Number >
- operator Value &() : vg::BaseOption< Value, Parser >
- operator!=() : handlegraph::PathForEachSocket::iterator, vg::algorithms::TracedScore, vg::alignment_index_t, vg::BitString, vg::ChainIterator, vg::edit_t, vg::GaplessExtension, vg::IncrementIter, vg::io::MessageIterator, vg::io::ProtobufIterator< T >, vg::NodeSide, vg::NodeTraversal, vg::path_mapping_t, vg::path_t, vg::PhasedGenome::iterator, vg::position_t, vg::read_alignment_index_t, vg::ShuffledPairs::iterator, vg::VectorView< Item >::const_iterator
- operator&=() : vg::SmallBitset
- operator()() : compare_gaf, greater_gaffile, std::hash< const vg::Snarl >, std::hash< handlegraph::edge_t >, std::hash< handlegraph::handle_t >, std::hash< handlegraph::net_handle_t >, std::hash< handlegraph::path_handle_t >, std::hash< handlegraph::step_handle_t >, std::hash< pair< A, B > >, std::hash< std::tuple< TT... > >, std::hash< vg::NodeSide >, std::hash< vg::NodeTraversal >, vg::BBEdgeHash, vg::discrete_distribution< T >, vg::DistanceHeuristic, vg::Genotyper::hash_ambiguous_allele_set, vg::Genotyper::hash_node_traversal, vg::Genotyper::hash_oriented_edge, vg::IncrementalSubgraph::FCmp, vg::IncrementalSubgraph::IterFCmp, vg::LazyRNG, vg::MappingHash, vg::MEMClusterer::DPScoreComparator, vg::NestedCachedPackedTraversalSupportFinder::snarl_less, vg::normal_distribution< T >, vg::ReadMasker, vg::SnarlMinDistance, vg::state_hash, vg::subcommand::Subcommand, vg::TipAnchoredMaxDistance, vg::truncated_normal_distribution< T >, vg::uniform_int_distribution< T >, vg::uniform_real_distribution< T >, vg::wang_hash< handle_t >, vg::wang_hash< handlegraph::net_handle_t >, vg::wang_hash< NodeSide >, vg::wang_hash< NodeTraversal >, vg::wang_hash< path_handle_t >, vg::wang_hash< std::pair< A, B > >, vg::wang_hash< T * >, vg::wang_hash< T, typename std::enable_if< std::is_integral< T >::value >::type >, vg::WideningPRNG< PRNG, OutType >
- operator*() : handlegraph::PathForEachSocket::iterator, vg::ChainIterator, vg::count_back_inserter< T >, vg::IncrementIter, vg::io::MessageIterator, vg::io::ProtobufIterator< T >, vg::PhasedGenome::iterator, vg::ShuffledPairs::iterator, vg::VectorView< Item >::const_iterator
- operator+() : vg::VectorView< Item >::const_iterator
- operator++() : handlegraph::PathForEachSocket::iterator, vg::ChainIterator, vg::count_back_inserter< T >, vg::IncrementIter, vg::io::MessageIterator, vg::io::ProtobufIterator< T >, vg::PhasedGenome::iterator, vg::ShuffledPairs::iterator, vg::VectorView< Item >::const_iterator
- operator+=() : vg::Counts, vg::VectorView< Item >::const_iterator
- operator-() : vg::VectorView< Item >::const_iterator
- operator--() : vg::VectorView< Item >::const_iterator
- operator-=() : vg::VectorView< Item >::const_iterator
- operator->() : vg::ChainIterator, vg::VectorView< Item >::const_iterator
- operator<() : job_type, vg::algorithms::TracedScore, vg::GaplessExtension, vg::MatchPos, vg::MaximalExactMatch, vg::MinimizerMapper::Minimizer, vg::NodeSide, vg::NodeTraversal, vg::WFAPoint
- operator<< : vg::MaximalExactMatch
- operator=() : handlegraph::PathForEachSocket::iterator, vg::algorithms::Anchor, vg::AlignmentChainModelVertex, vg::BaseOption< Value, Parser >, vg::BitString, vg::connection_t, vg::count_back_inserter< T >, vg::edit_t, vg::HTSAlignmentEmitter, vg::HTSWriter, vg::IncrementIter, vg::IndexedVG::CacheEntry, vg::IndexRegistry, vg::io::BlockedGzipInputStream, vg::io::BlockedGzipOutputStream, vg::io::MessageEmitter, vg::io::ProtobufEmitter< T >, vg::io::StreamMultiplexer, vg::MaximalExactMatch, vg::MEMChainModelVertex, vg::multipath_alignment_t, vg::ParallelKFFReader, vg::path_mapping_t, vg::path_t, vg::Paths, vg::PhasedGenome::iterator, vg::PhasedGenome, vg::position_t, vg::QualAdjXdropAligner, vg::Range< Number >, vg::SmallBitset, vg::SnarlManager, vg::SnarlManager::SnarlRecord, vg::StreamIndexBase, vg::subcommand::GroupedOptionGroup, vg::subpath_t, vg::VcfBuffer, vg::VectorView< Item >, vg::VG, vg::Watchdog, vg::WindowedVcfBuffer, vg::XdropAligner, xg::XG, xg::XGPath
- operator==() : handlegraph::PathForEachSocket::iterator, vg::algorithms::TracedScore, vg::alignment_index_t, vg::BitString, vg::ChainIterator, vg::edit_t, vg::GaplessExtension, vg::IncrementIter, vg::io::MessageIterator, vg::io::ProtobufIterator< T >, vg::MaximalExactMatch, vg::NodeSide, vg::NodeTraversal, vg::path_mapping_t, vg::path_t, vg::PhasedGenome::iterator, vg::position_t, vg::read_alignment_index_t, vg::ShuffledPairs::iterator, vg::VectorView< Item >::const_iterator
- operator>() : vg::algorithms::TracedScore
- operator[]() : haplo::gbwt_thread_t, vg::VectorView< Item >, vg::VectorViewInverse
- operator|=() : vg::SmallBitset
- opt_fields : gafkluge::GafRecord
- optimal_score_on_genome() : vg::PhasedGenome
- optimize() : handlegraph::MutableHandleGraph, vg::VG
- Option() : vg::Option< Value, Parser >, vg::Option< vector< Item >, Parser >
- option : vg::subcommand::BaseArgSpec< Receiver >, vg::subcommand::BaseValuation
- option_id : vg::subcommand::BaseArgSpec< Receiver >
- option_offsets : vg::Configurable
- option_to_index : vg::subcommand::OptionGroup< Receiver >
- OptionGroup() : vg::subcommand::OptionGroup< Receiver >
- options_by_code : vg::ConfigurableParser
- order : ReferenceInterval, vg::DozeuInterface::OrderedGraph
- order_length_repeat_hit_max : vg::MultipathMapper
- order_of() : vg::IncrementalSubgraph
- OrderedGraph() : vg::DozeuInterface::OrderedGraph
- orientation_from_old_edge_type() : xg::XG
- oriented_distance() : vg::OrientedDistanceMeasurer, vg::PathOrientedDistanceMeasurer, vg::SnarlOrientedDistanceMeasurer
- oriented_motif() : vg::SpliceStats
- OrientedDistanceClusterer() : vg::OrientedDistanceClusterer
- OS : vg::Version
- other : vg::algorithms::Edge, vg::io::streaminbuf
- other_orientation_timeout : vg::RepresentativeTraversalFinder
- other_supports : vg::BREAKPOINT
- out : vg::ProblemDumpExplainer
- out_file : vg::HTSWriter, vg::io::GafAlignmentEmitter, vg::io::TSVAlignmentEmitter, vg::io::VGAlignmentEmitter
- out_mutex : vg::io::ProtobufEmitter< T >
- out_stream : vg::MCMCCaller
- out_to : vg::ExtraNodeGraph
- outfile : vg::Viz
- output : vg::io::hFILE_cppstream
- output_fields : vg::ReadFilter< Read >
- output_filepath() : vg::IndexingPlan
- output_format_t : vg::MultipathAlignmentEmitter
- output_in_progress : vg::Funnel
- output_is_bgzf : vg::HTSWriter
- output_names : Vectorizer
- output_png : vg::Viz
- output_prefix : vg::IndexRegistry
- output_svg : vg::Viz
- output_tabbed : Vectorizer
- output_variants : vg::VCFOutputCaller
- output_vcf : vg::VCFOutputCaller
- OUTPUT_VERSION : vg::StreamIndexBase
- output_wabbit_map() : Vectorizer
- over_directed_edge() : vg::Paths
- over_edge() : vg::Paths
- overall_support : vg::Locus
- overflow() : vg::io::fdoutbuf
- overlap : ReferenceInterval, vg::BREAKPOINT, vg::Edge, vg::GaplessExtension
- OVERLAP_THRESHOLD : vg::GaplessExtender
- overlay() : vg::Translator
- overlay_node_translations() : vg::VG