Method List
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#<< Bio::AssemblyGraphAlgorithms::BubblyAssembler::MetaPath
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#== Bio::Velvet::Graph::OrientedNodeTrail::OrientedNode
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#== Bio::Velvet::Graph::OrientedNodeTrail
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#[] Bio::AssemblyGraphAlgorithms::BubblyAssembler::Bubble
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#[] Bio::AssemblyGraphAlgorithms::BubblyAssembler::MetaPath
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#[] Bio::FinishM::ReadToNode
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#[] Bio::KmerMultipleAbundanceHash
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#[] Bio::Velvet::Graph::OrientedNodeTrail
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#[] Bio::FinishM::HybridGraph::NodeArray
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#[]= Bio::FinishM::HybridGraph::NodeArray
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#add_metapath Bio::FinishM::BadFormatWriter
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#add_node Bio::AssemblyGraphAlgorithms::GraphExplorer::ExplorationPath
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#add_node Bio::Velvet::Graph::OrientedNodeTrail
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#add_options Bio::FinishM::PathCounter
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#add_options Bio::FinishM::GraphGenerator
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#add_options Bio::FinishM::GapFiller
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#add_options Bio::FinishM::Finisher
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#add_options Bio::FinishM::Visualise
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#add_options Bio::FinishM::Fluff
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#add_options Bio::FinishM::ORFsFinder
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#add_options Bio::FinishM::Primers
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#add_options Bio::FinishM::Explorer
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#add_options Bio::FinishM::Assembler
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#add_options Bio::FinishM::Sequence
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#add_options Bio::FinishM::Wanderer
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#add_options Bio::FinishM::Primers::Checker
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#add_options Bio::FinishM::RoundUp
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#add_options Bio::FinishM::ReadInput
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#add_oriented_node Bio::Velvet::Graph::OrientedNodeTrail
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#add_oriented_node_and_copy Bio::AssemblyGraphAlgorithms::SingleCoherentWanderer::DistancedOrientedNodeSet
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#add_probe_options Bio::FinishM::Visualise
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#add_scaffold_options Bio::FinishM::Visualise
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#add_setabled_nodes Bio::Velvet::Graph::OrientedNodeTrail
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#add_visualisation_options Bio::FinishM::Visualise
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#adjusted_leash_length Bio::FinishM::ProbedGraph
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#adjusted_position Bio::Velvet::Graph::NodedRead
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#array_trail_to_settable Bio::AssemblyGraphAlgorithms::SingleCoherentPathsBetweenNodesFinder
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#assemble Bio::AssemblyGraphAlgorithms::SingleEndedAssembler
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#assemble_from Bio::AssemblyGraphAlgorithms::PairedEndAssembler
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#assemble_from Bio::AssemblyGraphAlgorithms::BubblyAssembler
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#assemble_from Bio::AssemblyGraphAlgorithms::SingleEndedAssembler
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#assembly_options Bio::AssemblyGraphAlgorithms::SingleEndedAssembler
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#base_number Bio::AssemblyGraphAlgorithms::ContigPrinter::Variant
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#binary_string KmerAbundancePattern
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#bio_velvet_underground_graph Bio::FinishM::HybridGraph
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#break_scaffolds Bio::FinishM::ScaffoldBreaker
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#calibrate_distance_accounting_for_probes Bio::AssemblyGraphAlgorithms::AcyclicConnectionFinder
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#check_contig_universe Bio::FinishM::Primers::Checker
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#check_primer_compatibilities Bio::FinishM::Primers::Checker
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#check_probe_sequences Bio::FinishM::GraphGenerator
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#circuitous? Bio::AssemblyGraphAlgorithms::BubblyAssembler::Bubble
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#circular Bio::FinishM::ConnectionInterpreter::Scaffold
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#circular Bio::FinishM::ConnectionInterpreter::PossiblyCircularArray
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#circular? Bio::FinishM::ConnectionInterpreter::Scaffold
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#circular_path_detected Bio::AssemblyGraphAlgorithms::BubblyAssembler::DynamicProgrammingProblem
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#circular_paths_detected Bio::AssemblyGraphAlgorithms::TrailSet
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#circular_sequences Bio::FinishM::ConnectionInterpreter
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#closed Bio::AssemblyGraphAlgorithms::HeightFinder::CyclicTraversalNode::CyclePath
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#closed? Bio::AssemblyGraphAlgorithms::HeightFinder::CyclicTraversalNode::CyclePath
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#collapse_paths_to_maximal_coverage_path! Bio::AssemblyGraphAlgorithms::ContigPrinter::AnchoredConnection
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#companion Bio::FinishM::ConnectionInterpreter::Probe
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#completely_probed? Bio::FinishM::ProbedGraph
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#confirm_connection_backwards Bio::AssemblyGraphAlgorithms::PairedEndAssembler
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#connection_type Bio::FinishM::PairedEndNeighbourFinder::Neighbour
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#connections Bio::FinishM::ConnectionInterpreter
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#consistent_with? KmerAbundancePattern
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#contig NumberedProbe
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#contig_name Bio::FinishM::Primers::PrimerList
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#contig_name Bio::FinishM::Explorer::InterestingPlace
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#contig_number Bio::FinishM::ScaffoldBreaker::Scaffold
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#contig_side Bio::FinishM::Primers::PrimerList
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#contigs Bio::FinishM::ScaffoldBreaker::Scaffold
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#contigs Bio::FinishM::ConnectionInterpreter::Scaffold
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#converge_on Bio::AssemblyGraphAlgorithms::BubblyAssembler::Bubble
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#converged? Bio::AssemblyGraphAlgorithms::BubblyAssembler::Bubble
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#convergent_on? Bio::AssemblyGraphAlgorithms::BubblyAssembler::Bubble
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#converging_oriented_node Bio::AssemblyGraphAlgorithms::BubblyAssembler::Bubble
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#converging_oriented_node_settable Bio::AssemblyGraphAlgorithms::BubblyAssembler::Bubble
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#coords Bio::FinishM::ScaffoldBreaker::Gap
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#copy Bio::Velvet::Graph::OrientedNodeTrail::OrientedNode
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#copy Bio::AssemblyGraphAlgorithms::SequenceHasher::DistancedOrientedNodeTrail
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#copy Bio::Velvet::Graph::OrientedNodeTrail
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#copy Bio::AssemblyGraphAlgorithms::GraphExplorer::ExplorationPath
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#copy Bio::AssemblyGraphAlgorithms::HeightFinder::CyclicTraversalNode::CyclePath
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#copy Bio::AssemblyGraphAlgorithms::AllOrfsFinder::Marker
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#count_paths_through_graph Bio::FinishM::PathCounter
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#coverage Bio::AssemblyGraphAlgorithms::BubblyAssembler::MetaPath
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#coverage Bio::AssemblyGraphAlgorithms::BubblyAssembler::Bubble
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#coverage Bio::Velvet::Graph::OrientedNodeTrail
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create_from_shorthand Bio::Velvet::Graph::OrientedNodeTrail
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create_from_super_shorthand Bio::Velvet::Graph::OrientedNodeTrail
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create_from_velvet_graph Bio::Assembly::ABVisualiser::SimplifiedGraph
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#create_graphviz_output Bio::FinishM::Visualise
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#cycles Bio::AssemblyGraphAlgorithms::HeightFinder::CyclicTraversalNode
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#delete Bio::FinishM::HybridGraph::NodeArray
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#delete_at Bio::Velvet::Graph::OrientedNodeTrail
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#delete_at Bio::AssemblyGraphAlgorithms::BubblyAssembler::MetaPath
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#deletion_length Bio::AssemblyGraphAlgorithms::ContigPrinter::Variant
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#depth_first_search Bio::Velvet::Graph
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#dequeue Bio::AssemblyGraphAlgorithms::SingleCoherentPathsBetweenNodesFinder::ProblemTrailFinder
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#describe Bio::AssemblyGraphAlgorithms::HeightFinder::TraversalNode
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#direction Bio::FinishM::ConnectionInterpreter::UnscaffoldedContig
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#distance Bio::AssemblyGraphAlgorithms::SequenceHasher::DistancedOrientedNodeTrail
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#distance Bio::FinishM::PairedEndNeighbourFinder::Neighbour
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#distance Bio::AssemblyGraphAlgorithms::BubblyAssembler::DynamicProgrammingProblem
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#distance Bio::AssemblyGraphAlgorithms::Dijkstra::DistancedOrientedNode
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#distance Bio::FinishM::ConnectionInterpreter::Connection
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#distance Bio::AssemblyGraphAlgorithms::SingleCoherentWanderer::DistancedOrientedNodeSet
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#distance OligoDesigner::Oligo
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#distance Bio::AssemblyGraphAlgorithms::SingleEndedAssembler::MaxDistancedOrientedNode
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#doubly_single_contig_connections Bio::FinishM::ConnectionInterpreter
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#each DS::AnyPriorityQueue
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#each Bio::FinishM::HybridGraph::NodeArray
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#each Bio::AssemblyGraphAlgorithms::AllOrfsFinder::ORFsTracingTrail
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#each Bio::Velvet::Graph::OrientedNodeTrail
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#each Bio::AssemblyGraphAlgorithms::TrailSet
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#each Bio::AssemblyGraphAlgorithms::BubblyAssembler::MetaPath
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#each_gap_probe_pair Bio::FinishM::InputGenome
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#each_numbered_probe Bio::FinishM::InputGenome
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#each_oriented_node Bio::AssemblyGraphAlgorithms::BubblyAssembler::MetaPath
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#each_path Bio::AssemblyGraphAlgorithms::BubblyAssembler::Bubble
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#each_scaffold_end_numbered_probe Bio::FinishM::InputGenome
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#empty? Bio::AssemblyGraphAlgorithms::BubblyAssembler::MetaPath
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#end_probe_contig_offset Bio::AssemblyGraphAlgorithms::ContigPrinter::AnchoredConnection
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#end_probe_noded_read Bio::AssemblyGraphAlgorithms::ContigPrinter::AnchoredConnection
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#end_probe_read_length Bio::AssemblyGraphAlgorithms::ContigPrinter::AnchoredConnection
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#enqueue Bio::AssemblyGraphAlgorithms::BubblyAssembler::Bubble
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#estimate_distance_between_nodes Bio::FinishM::PairedEndNeighbourFinder
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#explore_from_node Bio::AssemblyGraphAlgorithms::GraphExplorer
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#extend_overlap Bio::AssemblyGraphAlgorithms::SequenceHasher
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#fate Bio::AssemblyGraphAlgorithms::BubblyAssembler::MetaPath
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#fates Bio::AssemblyGraphAlgorithms::Fluffer::FlufferPathSet
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#filename Bio::FinishM::InputGenome
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#filter Bio::AssemblyGraphAlgorithms::KmerCoverageBasedPathFilter
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#final_start_markers Bio::AssemblyGraphAlgorithms::AllOrfsFinder::ORFsResult
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#find_all_connections_between_two_nodes Bio::AssemblyGraphAlgorithms::SingleCoherentPathsBetweenNodesFinder
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#find_all_problems Bio::AssemblyGraphAlgorithms::AllOrfsFinder
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#find_all_problems Bio::AssemblyGraphAlgorithms::SingleCoherentPathsBetweenNodesFinder
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#find_beginning_trail_from_node Bio::AssemblyGraphAlgorithms::SingleEndedAssembler
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#find_nodes_with_kmers Bio::AssemblyGraphAlgorithms::NodeFinder
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#find_orfs_from_problems Bio::AssemblyGraphAlgorithms::AllOrfsFinder
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#find_orfs_in_graph Bio::AssemblyGraphAlgorithms::AllOrfsFinder
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#find_orfs_in_graph Bio::FinishM::ORFsFinder
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#find_oriented_edge_of_range Bio::AssemblyGraphAlgorithms::HeightFinder
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#find_paired_end_linkages Bio::FinishM::Visualise
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#find_paths_from_problems Bio::AssemblyGraphAlgorithms::SingleCoherentPathsBetweenNodesFinder
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#find_probe_nodes Bio::FinishM::CProbeNodeFinder
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#find_probe_read_alignment_from_contig_end Bio::AssemblyGraphAlgorithms::BamProbeReadSelector
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#find_probes Bio::FinishM::CProbeNodeFinder
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#find_probes Bio::AssemblyGraphAlgorithms::BamProbeReadSelector
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#find_probes_from_read_to_node Bio::AssemblyGraphAlgorithms::NodeFinder
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#find_tip_distance Bio::AssemblyGraphAlgorithms::SingleEndedAssembler
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#find_trails_between_nodes Bio::AssemblyGraphAlgorithms::AcyclicConnectionFinder
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#find_unique_node_with_kmers Bio::AssemblyGraphAlgorithms::NodeFinder
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#find_unique_nodes_with_sequence_ids Bio::AssemblyGraphAlgorithms::NodeFinder
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#first_probe Bio::FinishM::InputGenome
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#first_side Bio::AssemblyGraphAlgorithms::Dijkstra::DistancedOrientedNode
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#first_side Bio::FinishM::Sequence::PathSteppingStone
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#first_side Bio::FinishM::PairedEndNeighbourFinder::Neighbour
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#first_side Bio::Velvet::Graph::OrientedNodeTrail::OrientedNode
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#fluff Bio::AssemblyGraphAlgorithms::Fluffer
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#fluff_part1 Bio::AssemblyGraphAlgorithms::Fluffer
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#fluff_part2 Bio::AssemblyGraphAlgorithms::Fluffer
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#fwd_orfs_result Bio::AssemblyGraphAlgorithms::AllOrfsFinder::ORFsTracingTrail
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#gap_length Bio::FinishM::InputGenome
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#gap_lengths Bio::FinishM::ConnectionInterpreter::Scaffold
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#gapfill Bio::FinishM::GapFiller
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#gapfill_a_scaffold Bio::FinishM::RoundUp
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#gaps Bio::FinishM::ScaffoldBreaker::Scaffold
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#gather_starting_nodes Bio::AssemblyGraphAlgorithms::SingleEndedAssembler
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#generate_graph Bio::FinishM::GraphGenerator
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#generate_graph_from_assembly Bio::FinishM::Visualise
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#generate_graph_from_nodes Bio::FinishM::Visualise
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#generate_graph_from_probes Bio::FinishM::Visualise
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#generate_numbered_probes Bio::FinishM::InputGenome
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#get_leash_start_nodes Bio::FinishM::PathCounter
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#get_nodes_within_leash Bio::FinishM::Visualise
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#get_overlap_sequences Bio::AssemblyGraphAlgorithms::AllOrfsFinder
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#get_sequences Bio::AssemblyGraphAlgorithms::AllOrfsFinder
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#golden_path_fates Bio::AssemblyGraphAlgorithms::Fluffer::FlufferHalfResult
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#golden_path_fragments Bio::AssemblyGraphAlgorithms::Fluffer::FlufferHalfResult
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#golden_paths Bio::AssemblyGraphAlgorithms::Fluffer::FlufferHalfResult
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#graph Bio::FinishM::ProbedGraph
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#graph Bio::AssemblyGraphAlgorithms::SingleEndedAssembler
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#graphviz Bio::Assembly::ABVisualiser
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#hash Bio::Velvet::Graph::OrientedNodeTrail::OrientedNode
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#height Bio::AssemblyGraphAlgorithms::HeightFinder::TraversalNode
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#human_scaffold_end_name Bio::FinishM::InputGenome
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#include? Bio::AssemblyGraphAlgorithms::GraphExplorer::ExplorationPath
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#include_oriented_node? Bio::Velvet::Graph::OrientedNodeTrail
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#includes_kmers? Bio::Velvet::Graph::Node
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#index NumberedProbe
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#initial_path_from_probe Bio::FinishM::ProbedGraph
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#initial_start_markers Bio::AssemblyGraphAlgorithms::AllOrfsFinder::ORFsResult
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#initial_stop_markers Bio::AssemblyGraphAlgorithms::AllOrfsFinder::ORFsResult
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#initialize Bio::FinishM::ReadToNode
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#initialize Bio::AssemblyGraphAlgorithms::SingleCoherentPathsBetweenNodesFinder::CycleCounter
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#initialize Bio::AssemblyGraphAlgorithms::BubblyAssembler::MetaPath
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#initialize Bio::FinishM::InputGenome
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#initialize Bio::AssemblyGraphAlgorithms::SingleCoherentPathsBetweenNodesFinder::DualStack
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#initialize Bio::FinishM::HybridGraph::LazyShortReadArray
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#initialize Bio::FinishM::ConnectionInterpreter
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#initialize Bio::FinishM::ConnectionInterpreter::Scaffold
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#initialize Bio::AssemblyGraphAlgorithms::SingleCoherentPathsBetweenNodesFinder::ProblemTrailFinder
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#initialize Bio::AssemblyGraphAlgorithms::AllOrfsFinder::ORFsResult
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#initialize Bio::AssemblyGraphAlgorithms::AllOrfsFinder::AllProblemTrailsFinder
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#initialize Bio::AssemblyGraphAlgorithms::AllOrfsFinder::SearchResult
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#initialize Bio::FinishM::ConnectionInterpreter::Probe
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#initialize Bio::AssemblyGraphAlgorithms::BubblyAssembler::Bubble
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#initialize Bio::FinishM::HybridGraph::NodeArray
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#initialize Bio::FinishM::BadFormatWriter
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#initialize Bio::Velvet::Graph::OrientedNodeTrail::OrientedNode
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#initialize Bio::AssemblyGraphAlgorithms::BubblyAssembler
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#initialize Bio::AssemblyGraphAlgorithms::Fluffer::FlufferPathSet
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#initialize Bio::AssemblyGraphAlgorithms::SingleEndedAssembler
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#initialize Bio::AssemblyGraphAlgorithms::Fluffer::FlufferHalfResult
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#initialize Bio::AssemblyGraphAlgorithms::TrailSet
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#initialize Bio::FinishM::ConnectionInterpreter::PossiblyCircularArray
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#initialize Bio::AssemblyGraphAlgorithms::SingleCoherentPathsBetweenNodesFinder::DynamicProgrammingProblem
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#initialize Bio::FinishM::PairedEndNeighbourFinder
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#initialize Bio::AssemblyGraphAlgorithms::BubblyAssembler::DynamicProgrammingProblem
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#initialize Bio::AssemblyGraphAlgorithms::ContigPrinter::Variant
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#initialize Bio::FinishM::HybridGraph
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#initialize DS::AnyPriorityQueue
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#initialize Bio::AssemblyGraphAlgorithms::GraphExplorer::ExplorationPath
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#initialize Bio::Velvet::Graph::OrientedNodeTrail
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#initiate_cycle Bio::AssemblyGraphAlgorithms::HeightFinder::CyclicTraversalNode
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#inspect Bio::AssemblyGraphAlgorithms::Dijkstra::DistancedOrientedNode
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#inspect Bio::FinishM::PairedEndNeighbourFinder::Neighbour
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#inspect Bio::Velvet::Graph::OrientedNodeTrail
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#is_reverse Bio::AssemblyGraphAlgorithms::BubblyAssembler::Bubble
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#is_short_tip? Bio::AssemblyGraphAlgorithms::SingleEndedAssembler
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#just_below OligoDesigner
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#kmer_length Bio::KmerMultipleAbundanceHash
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#known_paths Bio::AssemblyGraphAlgorithms::SingleCoherentPathsBetweenNodesFinder::DynamicProgrammingProblem
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#last Bio::Velvet::Graph::OrientedNodeTrail
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#last_node_recoherent? Bio::AssemblyGraphAlgorithms::SingleCoherentWanderer::DistancedOrientedNodeSet
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#last_oriented_node Bio::AssemblyGraphAlgorithms::BubblyAssembler::MetaPath
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#last_probe Bio::FinishM::InputGenome
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#length Bio::Velvet::Graph::OrientedNodeTrail
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#length Bio::AssemblyGraphAlgorithms::SingleCoherentPathsBetweenNodesFinder::ProblemTrailFinder
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#length Bio::AssemblyGraphAlgorithms::BubblyAssembler::MetaPath
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#length Bio::FinishM::HybridGraph::NodeArray
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#length Bio::FinishM::ScaffoldBreaker::Gap
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#length Bio::FinishM::ScaffoldBreaker::UnscaffoldedContig
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#length_in_bp Bio::AssemblyGraphAlgorithms::BubblyAssembler::MetaPath
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#length_in_bp Bio::Velvet::Graph::OrientedNodeTrail
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#length_in_bp_within_path Bio::Velvet::Graph::OrientedNodeTrail
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#log Bio::FinishM::Logging
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#max_adjoining_node_coverage Bio::FinishM::PairedEndNeighbourFinder
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#max_path_limit_exceeded Bio::AssemblyGraphAlgorithms::TrailSet
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#max_paths_through Bio::AssemblyGraphAlgorithms::HeightFinder
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#melting_temperature OligoDesigner
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#merge_unclosed_cycle Bio::AssemblyGraphAlgorithms::HeightFinder::CyclicTraversalNode
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#method_missing Bio::FinishM::HybridGraph::LazyShortReadArray
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#min_adjoining_reads Bio::FinishM::PairedEndNeighbourFinder
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#min_distance Bio::AssemblyGraphAlgorithms::SingleCoherentPathsBetweenNodesFinder::DynamicProgrammingProblem
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#min_distances Bio::AssemblyGraphAlgorithms::Dijkstra
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#min_distances_from_many_nodes_in_both_directions Bio::AssemblyGraphAlgorithms::Dijkstra
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#min_distances_in_both_directions Bio::AssemblyGraphAlgorithms::Dijkstra
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#min_paths_through Bio::AssemblyGraphAlgorithms::HeightFinder
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#missing_probe_indices Bio::FinishM::ProbedGraph
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#name Bio::FinishM::ScaffoldBreaker::Scaffold
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#name Bio::FinishM::ScaffoldBreaker::UnscaffoldedContig
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#neighbours Bio::FinishM::PairedEndNeighbourFinder
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#neighbours_of Bio::Velvet::Graph
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#neighbours_of_last_node Bio::Velvet::Graph::OrientedNodeTrail
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#neighbours_of_node_id Bio::Velvet::Graph
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#next_neighbours Bio::AssemblyGraphAlgorithms::Dijkstra::DistancedOrientedNode
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#next_neighbours Bio::Velvet::Graph::OrientedNodeTrail::OrientedNode
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#node Bio::AssemblyGraphAlgorithms::Dijkstra::DistancedOrientedNode
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#node Bio::AssemblyGraphAlgorithms::AllOrfsFinder::Marker
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#node Bio::FinishM::PairedEndNeighbourFinder::Neighbour
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#node Bio::Velvet::Graph::OrientedNodeTrail::OrientedNode
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#node_id Bio::Velvet::Graph::OrientedNodeTrail::OrientedNode
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#node_id Bio::FinishM::Sequence::PathSteppingStone
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#node_id Bio::AssemblyGraphAlgorithms::HeightFinder::TraversalNode
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#nodes_in Bio::AssemblyGraphAlgorithms::HeightFinder::TraversalNode
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#nodes_out Bio::AssemblyGraphAlgorithms::HeightFinder::TraversalNode
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#num_adjoining_reads Bio::FinishM::PairedEndNeighbourFinder::Neighbour
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#num_known_problems Bio::AssemblyGraphAlgorithms::BubblyAssembler::Bubble
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#num_legit_forks Bio::AssemblyGraphAlgorithms::BubblyAssembler::Bubble
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#number NumberedProbe
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#number Bio::FinishM::ScaffoldBreaker::Gap
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#number_of_abundances Bio::KmerMultipleAbundanceHash
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#number_of_probes Bio::FinishM::InputGenome
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#numbered_probes Bio::FinishM::InputGenome
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#one_connection_between_two_contigs Bio::AssemblyGraphAlgorithms::ContigPrinter
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#onode Bio::AssemblyGraphAlgorithms::SingleEndedAssembler::MaxDistancedOrientedNode
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#onode Bio::AssemblyGraphAlgorithms::HeightFinder::TraversalNode
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#onodes Bio::AssemblyGraphAlgorithms::HeightFinder::CyclicTraversalNode::CyclePath
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#orf_sequences_from_trails Bio::AssemblyGraphAlgorithms::AllOrfsFinder
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#orf_to_settable Bio::FinishM::ORFsFinder
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#orfs_from_start_stop_markers Bio::AssemblyGraphAlgorithms::AllOrfsFinder
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#oriented_nodes Bio::AssemblyGraphAlgorithms::BubblyAssembler::Bubble
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#oriented_trail Bio::AssemblyGraphAlgorithms::SingleCoherentWanderer::DistancedOrientedNodeSet
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#otrail Bio::AssemblyGraphAlgorithms::AllOrfsFinder::ORFsTracingTrail
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#paired_neighbour_distances Bio::FinishM::PairedEndNeighbourFinder
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#paired_nodes Bio::FinishM::ProbedGraph
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parse_from_file Bio::KmerMultipleAbundanceHash
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#parse_from_human KmerAbundancePattern
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#parse_from_kmer_abundance KmerAbundancePattern
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parse_genome_fasta_files Bio::FinishM::InputGenome
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#parse_options Bio::FinishM::ReadInput
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#parse_velvet_binary_reads Bio::FinishM::GraphGenerator
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#path Bio::AssemblyGraphAlgorithms::GraphExplorer::ExplorationPath
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#path Bio::AssemblyGraphAlgorithms::BubblyAssembler::DynamicProgrammingProblem
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#path_cycle_count Bio::AssemblyGraphAlgorithms::SingleCoherentPathsBetweenNodesFinder::CycleCounter
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#path_cycle_count_for_node Bio::AssemblyGraphAlgorithms::SingleCoherentPathsBetweenNodesFinder::CycleCounter
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#path_to_settable Bio::AssemblyGraphAlgorithms::SingleCoherentPathsBetweenNodesFinder
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#path_to_settable Bio::AssemblyGraphAlgorithms::AllOrfsFinder
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#paths Bio::AssemblyGraphAlgorithms::ContigPrinter::AnchoredConnection
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#paths Bio::AssemblyGraphAlgorithms::BubblyAssembler::Bubble
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#pick_best_node_for_read_id Bio::AssemblyGraphAlgorithms::NodeFinder
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#piece_together_gapfill Bio::FinishM::RoundUp
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#pop Bio::AssemblyGraphAlgorithms::AllOrfsFinder::AllProblemTrailsFinder
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#pop Bio::AssemblyGraphAlgorithms::SingleCoherentPathsBetweenNodesFinder::DualStack
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#position Bio::AssemblyGraphAlgorithms::ContigPrinter::Variant
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#position_in_node Bio::AssemblyGraphAlgorithms::AllOrfsFinder::Marker
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#position_in_trail Bio::AssemblyGraphAlgorithms::AllOrfsFinder::Marker
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#possible_oligos_ordered_by_temperature_difference OligoDesigner
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#primers Bio::FinishM::Primers::PrimerList
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#probe1 Bio::FinishM::ConnectionInterpreter::Connection
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#probe2 Bio::FinishM::ConnectionInterpreter::Connection
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#probe_at_start_of_scaffold? Bio::FinishM::InputGenome
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#probe_node_directions Bio::FinishM::ProbedGraph
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#probe_node_reads Bio::FinishM::ProbedGraph
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#probe_nodes Bio::FinishM::ProbedGraph
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#probe_sequences Bio::FinishM::InputGenome
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#probed_graph_to_connections Bio::FinishM::Wanderer
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#probes_on_single_node_ok? Bio::AssemblyGraphAlgorithms::SingleCoherentWanderer
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#push Bio::AssemblyGraphAlgorithms::SingleCoherentPathsBetweenNodesFinder::DualStack
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#push_next_neighbours Bio::AssemblyGraphAlgorithms::SingleCoherentPathsBetweenNodesFinder::ProblemTrailFinder
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#push_next_neighbours Bio::AssemblyGraphAlgorithms::AllOrfsFinder::AllProblemTrailsFinder
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#read_short_reads Bio::FinishM::HybridGraph::LazyShortReadArray
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#read_to_nodes Bio::FinishM::ProbedGraph
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#ready_two_contigs_and_connections Bio::AssemblyGraphAlgorithms::ContigPrinter
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#reference_name Bio::AssemblyGraphAlgorithms::ContigPrinter::Variant
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#reference_path Bio::AssemblyGraphAlgorithms::ContigPrinter::PrintableConnection
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#reference_trail Bio::AssemblyGraphAlgorithms::BubblyAssembler::Bubble
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#reference_trail Bio::AssemblyGraphAlgorithms::BubblyAssembler::MetaPath
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#remove_last_node Bio::Velvet::Graph::OrientedNodeTrail
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#remove_low_coverage_nodes Bio::AssemblyGraphAlgorithms::CoverageBasedGraphFilter
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#remove_overly_short_contigs! Bio::FinishM::InputGenome
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#remove_seen_nodes_from_end_of_path Bio::AssemblyGraphAlgorithms::BubblyAssembler
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#remove_seen_nodes_from_end_of_path Bio::AssemblyGraphAlgorithms::SingleEndedAssembler
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#remove_tips Bio::AssemblyGraphAlgorithms::SingleEndedAssembler
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#remove_unconnected_nodes Bio::AssemblyGraphAlgorithms::ConnectivityBasedGraphFilter
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#revcom Bio::FinishM::RoundUp
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#reverse Bio::Velvet::Graph::OrientedNodeTrail
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#reverse Bio::Velvet::Graph::OrientedNodeTrail::OrientedNode
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#reverse! Bio::Velvet::Graph::OrientedNodeTrail
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#reverse! Bio::AssemblyGraphAlgorithms::ContigPrinter::Variant
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#reverse! Bio::AssemblyGraphAlgorithms::BubblyAssembler::Bubble
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#reverse! Bio::AssemblyGraphAlgorithms::BubblyAssembler::MetaPath
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#reverse! Bio::Velvet::Graph::OrientedNodeTrail::OrientedNode
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#root Bio::AssemblyGraphAlgorithms::BubblyAssembler::Bubble
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#run Bio::FinishM::Primers::Checker
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#run Bio::FinishM::PathCounter
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#run Bio::FinishM::Visualise
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#run Bio::FinishM::ORFsFinder
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#run Bio::FinishM::Sequence
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#run Bio::FinishM::Finisher
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#run Bio::FinishM::Assembler
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#run Bio::FinishM::RoundUp
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#run Bio::FinishM::Primers
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#run Bio::FinishM::Explorer
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#run Bio::FinishM::GapFiller
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#run Bio::FinishM::Wanderer
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#run Bio::FinishM::Fluff
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#same_as? KmerAbundancePattern
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#scaffold Bio::FinishM::ScaffoldBreaker::Gap
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#scaffold Bio::FinishM::ScaffoldBreaker::UnscaffoldedContig
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#scaffold_position_end Bio::FinishM::ScaffoldBreaker::UnscaffoldedContig
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#scaffold_position_start Bio::FinishM::ScaffoldBreaker::UnscaffoldedContig
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#scaffolds Bio::FinishM::InputGenome
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#scaffolds Bio::FinishM::ConnectionInterpreter
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#search_for_codons Bio::AssemblyGraphAlgorithms::AllOrfsFinder
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#second_side Bio::AssemblyGraphAlgorithms::Dijkstra::DistancedOrientedNode
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#seen_last_in_path? Bio::AssemblyGraphAlgorithms::BubblyAssembler
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#seen_last_in_path? Bio::AssemblyGraphAlgorithms::SingleEndedAssembler
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#sequence Bio::Velvet::Graph::OrientedNodeTrail
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#sequence Bio::FinishM::ScaffoldBreaker::Scaffold
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#sequence Bio::FinishM::ScaffoldBreaker::UnscaffoldedContig
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#sequence NumberedProbe
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#sequence Bio::AssemblyGraphAlgorithms::ContigPrinter::Variant
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#sequence OligoDesigner::Oligo
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#sequence Bio::FinishM::ConnectionInterpreter::Scaffold
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#sequence Bio::AssemblyGraphAlgorithms::BubblyAssembler::MetaPath
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#sequence2AA Bio::AssemblyGraphAlgorithms::AllOrfsFinder
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#sequence_index Bio::FinishM::ConnectionInterpreter::Probe
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#sequence_index Bio::FinishM::ConnectionInterpreter::UnscaffoldedContig
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#sequences_within_path Bio::Velvet::Graph::OrientedNodeTrail
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#set_of_nodes Bio::AssemblyGraphAlgorithms::GraphExplorer::ExplorationPath
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#setup_output_directory Bio::FinishM::RoundUp
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#setup_progressbar Bio::AssemblyGraphAlgorithms::SingleEndedAssembler
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#shift Bio::AssemblyGraphAlgorithms::BubblyAssembler::Bubble
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#shortest_problem_distance Bio::AssemblyGraphAlgorithms::BubblyAssembler::Bubble
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#side NumberedProbe
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#side Bio::FinishM::ConnectionInterpreter::Probe
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#size Bio::AssemblyGraphAlgorithms::AllOrfsFinder::AllProblemTrailsFinder
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#sizes Bio::AssemblyGraphAlgorithms::SingleCoherentPathsBetweenNodesFinder::DualStack
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#start Bio::FinishM::ScaffoldBreaker::Gap
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#start_markers Bio::AssemblyGraphAlgorithms::AllOrfsFinder::SearchResult
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#start_or_end Bio::FinishM::Explorer::InterestingPlace
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#start_probe_contig_offset Bio::AssemblyGraphAlgorithms::ContigPrinter::AnchoredConnection
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#start_probe_noded_read Bio::AssemblyGraphAlgorithms::ContigPrinter::AnchoredConnection
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#start_probe_read_length Bio::AssemblyGraphAlgorithms::ContigPrinter::AnchoredConnection
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#start_stop_pairs Bio::AssemblyGraphAlgorithms::AllOrfsFinder::ORFsResult
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#starts_at_end? Bio::Velvet::Graph::OrientedNodeTrail::OrientedNode
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#starts_at_start? Bio::Velvet::Graph::OrientedNodeTrail::OrientedNode
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#stop Bio::FinishM::ScaffoldBreaker::Gap
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#stop_markers Bio::AssemblyGraphAlgorithms::AllOrfsFinder::SearchResult
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#sub_kmer_sequence_overlap? Bio::AssemblyGraphAlgorithms::SingleCoherentPathsBetweenNodesFinder
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#subgraph Bio::FinishM::ProbedGraph
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#terminal_node_keys Bio::AssemblyGraphAlgorithms::SingleCoherentPathsBetweenNodesFinder::ProblemSet
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#termination_type Bio::AssemblyGraphAlgorithms::GraphExplorer::ExplorationPath
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#tm OligoDesigner::Oligo
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#to_s Bio::Velvet::Graph::OrientedNodeTrail
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#to_s Bio::AssemblyGraphAlgorithms::SequenceHasher::DistancedOrientedNodeTrail
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#to_s Bio::AssemblyGraphAlgorithms::GraphExplorer::ExplorationPath
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#to_s Bio::AssemblyGraphAlgorithms::BubblyAssembler::DynamicProgrammingProblem
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#to_s Bio::FinishM::Explorer::InterestingPlace
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#to_s Bio::AssemblyGraphAlgorithms::SingleCoherentWanderer::DistancedOrientedNodeSet
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#to_s Bio::FinishM::ConnectionInterpreter::Probe
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#to_s Bio::FinishM::ConnectionInterpreter::Connection
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#to_s Bio::Velvet::Graph::OrientedNodeTrail::OrientedNode
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#to_settable Bio::AssemblyGraphAlgorithms::HeightFinder::CyclicTraversalNode::CyclePath
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#to_settable Bio::AssemblyGraphAlgorithms::Dijkstra::DistancedOrientedNode
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#to_settable Bio::AssemblyGraphAlgorithms::BubblyAssembler::DynamicProgrammingProblem
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#to_settable Bio::FinishM::PairedEndNeighbourFinder::Neighbour
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#to_settable Bio::AssemblyGraphAlgorithms::SingleCoherentWanderer::DistancedOrientedNodeSet
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#to_settable Bio::FinishM::ConnectionInterpreter::Probe
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#to_settable Bio::FinishM::ConnectionInterpreter::Connection
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#to_settable Bio::Velvet::Graph::OrientedNodeTrail::OrientedNode
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#to_short_s Bio::Velvet::Graph::OrientedNodeTrail
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#to_shorthand Bio::Velvet::Graph::OrientedNodeTrail
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#to_shorthand Bio::AssemblyGraphAlgorithms::BubblyAssembler::MetaPath
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#to_shorthand Bio::AssemblyGraphAlgorithms::BubblyAssembler::Bubble
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#to_shorthand Bio::AssemblyGraphAlgorithms::ContigPrinter::Variant
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#to_shorthand Bio::AssemblyGraphAlgorithms::BubblyAssembler::DynamicProgrammingProblem
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#to_shorthand Bio::Velvet::Graph::OrientedNodeTrail::OrientedNode
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#trail Bio::Velvet::Graph::OrientedNodeTrail
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#trail_sequence Bio::AssemblyGraphAlgorithms::LazyGraphWalker
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#trails Bio::AssemblyGraphAlgorithms::TrailSet
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#traverse Bio::AssemblyGraphAlgorithms::HeightFinder
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#twin_orfs_result Bio::AssemblyGraphAlgorithms::AllOrfsFinder::ORFsTracingTrail
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#type Bio::AssemblyGraphAlgorithms::ContigPrinter::Variant
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#ubiquitous_oriented_nodes Bio::AssemblyGraphAlgorithms::BubblyAssembler::DynamicProgrammingProblem
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#ubiquitous_oriented_nodes Bio::AssemblyGraphAlgorithms::BubblyAssembler::Bubble
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#unconnected_probes Bio::FinishM::ConnectionInterpreter
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#unconnected_sequences Bio::FinishM::ConnectionInterpreter
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#validate_argv_length Bio::FinishM::Visualise
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#validate_assembly_options Bio::FinishM::Visualise
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#validate_last_node_of_path_by_recoherence Bio::AssemblyGraphAlgorithms::SingleCoherentPathsBetweenNodesFinder
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#validate_options Bio::FinishM::ReadInput
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#validate_options Bio::FinishM::ORFsFinder
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#validate_options Bio::FinishM::PathCounter
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#validate_options Bio::FinishM::Primers::Checker
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#validate_options Bio::FinishM::Visualise
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#validate_options Bio::FinishM::Finisher
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#validate_options Bio::FinishM::Assembler
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#validate_options Bio::FinishM::Sequence
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#validate_options Bio::FinishM::RoundUp
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#validate_options Bio::FinishM::Explorer
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#validate_options Bio::FinishM::GapFiller
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#validate_options Bio::FinishM::Wanderer
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#validate_options Bio::FinishM::Fluff
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#validate_options Bio::FinishM::Primers
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#validate_probe_options Bio::FinishM::Visualise
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#validate_scaffold_options Bio::FinishM::Visualise
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#validate_visualisation_options Bio::FinishM::Visualise
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#variants Bio::AssemblyGraphAlgorithms::ContigPrinter::PrintableConnection
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#vcf Bio::AssemblyGraphAlgorithms::ContigPrinter::Variant
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#vcf_array Bio::AssemblyGraphAlgorithms::ContigPrinter::Variant
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#velvet_oriented_node Bio::FinishM::ProbedGraph
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#velvet_read_arguments Bio::FinishM::ReadInput
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#velvet_result_directory Bio::FinishM::ProbedGraph
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#velvet_sequences Bio::FinishM::ProbedGraph
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#visited_oriented_nodes Bio::AssemblyGraphAlgorithms::BubblyAssembler::DynamicProgrammingProblem
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#visited_oriented_nodes Bio::AssemblyGraphAlgorithms::BubblyAssembler::Bubble
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#wander Bio::AssemblyGraphAlgorithms::SingleCoherentWanderer
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#wander_a_genome Bio::FinishM::RoundUp
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#word_search Bio::AssemblyGraphAlgorithms::AllOrfsFinder
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#write Bio::FinishM::BadFormatWriter
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#write_depths Bio::AssemblyGraphAlgorithms::KmerCoverageBasedPathFilter
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#write_orfs_to_file Bio::FinishM::ORFsFinder
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#write_probe_to_node_map Bio::FinishM::Visualise
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#yaml Bio::FinishM::BadFormatWriter