Here is a list of all class members with links to the classes they belong to:
- o -
- occs
: vg::MinimizerMapper::Minimizer
- occurrences
: bdsg::HashGraph::node_t
- ODGI()
: bdsg::ODGI
- of_node()
: vg::Paths
- offset
: vg::GaplessExtension
, vg::PathBranch
, vg::Position
, vg::position_t
, vg::SnarlSeedClusterer::Seed
- OFFSET_MASK
: vg::MIPayload
- OFFSET_WIDTH
: vg::MIPayload
- offsets
: xg::XGPath
- offsets_in_paths()
: xg::XG
- offsets_rank
: xg::XGPath
- offsets_select
: xg::XGPath
- 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
- 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
- open()
: vg::Index
- open_all()
: vg::StreamSorter< Message >
- open_for_bulk_load()
: vg::Index
- open_for_write()
: vg::Index
- open_read_only()
: vg::Index
- operator Number()
: vg::Range< Number >
- operator Value &()
: vg::BaseOption< Value, Parser >
- operator!=()
: handlegraph::PathForEachSocket::iterator
, vg::BitString
, vg::ChainIterator
, vg::GaplessExtension
, vg::IncrementIter
, vg::io::MessageIterator
, vg::io::ProtobufIterator< T >
, vg::NodeSide
, vg::NodeTraversal
, vg::PhasedGenome::iterator
, vg::ShuffledPairs::iterator
- operator&=()
: vg::SmallBitset
- operator()()
: std::hash< const vg::Snarl >
, std::hash< handlegraph::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::discrete_distribution< T >
, vg::DistanceHeuristic
, vg::Genotyper::hash_ambiguous_allele_set
, vg::Genotyper::hash_node_traversal
, vg::Genotyper::hash_oriented_edge
, vg::MEMClusterer::DPScoreComparator
, vg::normal_distribution< T >
, vg::SnarlMinDistance
, vg::state_hash
, vg::subcommand::Subcommand
, vg::TipAnchoredMaxDistance
, vg::uniform_int_distribution< T >
, vg::uniform_real_distribution< T >
, vg::wang_hash< 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::IncrementIter
, vg::io::MessageIterator
, vg::io::ProtobufIterator< T >
, vg::PhasedGenome::iterator
, vg::ShuffledPairs::iterator
- operator++()
: handlegraph::PathForEachSocket::iterator
, vg::ChainIterator
, vg::IncrementIter
, vg::io::MessageIterator
, vg::io::ProtobufIterator< T >
, vg::PhasedGenome::iterator
, vg::ShuffledPairs::iterator
- operator+=()
: vg::ReadFilter::Counts
- operator->()
: vg::ChainIterator
- operator<()
: vg::GaplessExtension
, vg::MaximalExactMatch
, vg::MinimizerMapper::Minimizer
, vg::NodeSide
, vg::NodeTraversal
- operator<<
: vg::MaximalExactMatch
- operator=()
: bdsg::HashGraph::path_t
, handlegraph::PathForEachSocket::iterator
, vg::AlignmentChainModelVertex
, vg::BaseOption< Value, Parser >
, vg::BitString
, vg::connection_t
, vg::edit_t
, vg::HTSAlignmentEmitter
, vg::IncrementIter
, vg::IndexedVG::CacheEntry
, 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::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::subpath_t
, vg::VcfBuffer
, vg::VG
, vg::Watchdog
, vg::WindowedVcfBuffer
, vg::XdropAligner
, xg::XG
, xg::XGPath
- operator==()
: handlegraph::PathForEachSocket::iterator
, vg::BitString
, vg::ChainIterator
, vg::GaplessExtension
, vg::IncrementIter
, vg::io::MessageIterator
, vg::io::ProtobufIterator< T >
, vg::MaximalExactMatch
, vg::NodeSide
, vg::NodeTraversal
, vg::PhasedGenome::iterator
, vg::ShuffledPairs::iterator
- operator[]()
: haplo::gbwt_thread_t
- operator|=()
: vg::SmallBitset
- opt_fields
: gafkluge::GafRecord
- optimal_score_on_genome()
: vg::PhasedGenome
- optimize()
: bdsg::HashGraph
, bdsg::ODGI
, bdsg::PackedGraph
, handlegraph::MutableHandleGraph
, vg::VG
- Option()
: vg::Option< Value, Parser >
, vg::Option< vector< Item >, Parser >
- option_offsets
: vg::Configurable
- options_by_code
: vg::ConfigurableParser
- order
: 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::SpliceMotifs
- OrientedDistanceClusterer()
: vg::OrientedDistanceClusterer
- OS
: vg::Version
- other_orientation_timeout
: vg::RepresentativeTraversalFinder
- other_supports
: vg::BREAKPOINT
- out
: vg::MultipathAlignmentEmitter
- out_file
: vg::HTSAlignmentEmitter
, 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_in_progress
: vg::Funnel
- output_is_bgzf
: vg::HTSAlignmentEmitter
- output_names
: Vectorizer
- output_png
: vg::Viz
- output_svg
: vg::Viz
- output_tabbed
: Vectorizer
- output_variants
: vg::VCFOutputCaller
- output_vcf
: vg::VCFOutputCaller
- OUTPUT_VERSION
: vg::StreamIndexBase
- output_wabbit_map()
: Vectorizer
- outvcf
: vg::Deconstructor
- over_directed_edge()
: vg::Paths
- over_edge()
: vg::Paths
- overall_support
: vg::Locus
- overflow()
: vg::io::fdoutbuf
- overlap()
: vg::BREAKPOINT
, vg::Edge
, vg::GaplessExtension
- OVERLAP_THRESHOLD
: vg::GaplessExtender
- overlapping_refs
: vg::SRPE
- overlay()
: vg::Translator
- overlay_node_translations()
: vg::VG