Here is a list of all class members with links to the classes they belong to:
- m -
- m_a
: vg::uniform_int_distribution< T >
, vg::uniform_real_distribution< T >
- m_b
: vg::uniform_int_distribution< T >
, vg::uniform_real_distribution< T >
- m_distU1
: vg::normal_distribution< T >
- m_mean
: vg::normal_distribution< T >
- m_stddev
: vg::normal_distribution< T >
- m_sums
: vg::discrete_distribution< T >
- m_weights
: vg::discrete_distribution< T >
- MAGIC_BYTES
: vg::StreamIndexBase
- main_function
: vg::subcommand::Subcommand
- make_bands()
: vg::Mapper
- make_circular()
: vg::Paths
- make_compact()
: vg::Packer
- make_default_or_null()
: vg::io::VPKG
- make_dynamic()
: vg::Packer
- make_edge()
: vg::PhaseUnfolder
- make_graph()
: vg::MSAConverter
- make_hit_graph()
: vg::ComponentMinDistanceClusterer
, vg::GreedyMinDistanceClusterer
, vg::MEMClusterer
, vg::MinDistanceClusterer
, vg::NullClusterer
, vg::OrientedDistanceClusterer
, vg::TVSClusterer
- make_linear()
: vg::Paths
- make_nontrivial_multipath_alignment()
: vg::MultipathMapper
- make_null_alignment()
: vg::Surjector
- make_subpath_name()
: vg::Paths
- make_subset_graph()
: vg::Genotyper
- manage()
: vg::SnarlManager
- manager
: vg::GenomeState
- map()
: vg::MinimizerMapper
- map_order_to_original
: vg::WindowedVcfBuffer
- map_paired()
: vg::MinimizerMapper
- Mapper()
: vg::Mapper
- mapper_alignment_cutoff
: vg::VariantAdder
- mapping
: vg::Path
, vg::path_t
, vg::PhaseUnfolder
- mapping_edits
: vg::BandedGlobalAligner< IntType >::BABuilder
- mapping_enters_side()
: vg::Genotyper
- mapping_entry_to_string()
: vg::Index
- mapping_exits_side()
: vg::Genotyper
- mapping_is_total_match()
: vg::VG
- mapping_itr
: vg::Paths
- mapping_likelihoods()
: vg::MultipathMapper
- mapping_path_id()
: vg::Paths
- mapping_path_name()
: vg::Paths
- mapping_positions
: vg::PathIndex
- mapping_quality
: vg::Alignment
, vg::multipath_alignment_t
, vg::MultipathAlignment
- mapping_quality_method
: vg::BaseMapper
- mapping_quality_score_diff()
: vg::GSSWAligner
- mapping_size()
: vg::path_t
- mapping_t()
: vg::mapping_t
- mappings_by_rank
: vg::Paths
- mapq
: gafkluge::GafRecord
- mapq_scaling_factor
: vg::MultipathMapper
- mark_dfs()
: vg::FlowSort
- mark_smallVariant_alignments()
: vg::Filter
- mark_sv_alignments()
: vg::Filter
- MarkovDistribution()
: vg::NGSSimulator::MarkovDistribution< From, To >
- match
: vg::BandedGlobalAligner< IntType >::BAMatrix
- Match
: vg::BandedGlobalAligner< IntType >
- match
: vg::GSSWAligner
, vg::SSWAligner
- match_count
: vg::MaximalExactMatch
- match_fanouts_t
: vg::MEMClusterer
, vg::MultipathMapper
- matches
: gafkluge::GafRecord
, vg::DinucleotideMachine
- matching
: vg::BandedGlobalAligner< IntType >::BABuilder
- mate_mapped_to_disjoint_subgraph
: vg::Alignment
- mate_on_reverse_strand
: vg::Alignment
- mate_rescues
: vg::Mapper
- mate_unmapped
: vg::Alignment
- mates
: vg::BREAKPOINT
- matrix_state
: vg::BandedGlobalAligner< IntType >::BABuilder
- matrix_t
: vg::BandedGlobalAligner< IntType >
- max()
: vg::WideningPRNG< PRNG, OutType >
- max_alignment_gap
: vg::MultipathMapper
- max_alignments
: vg::MinimizerMapper
- max_alt_mappings
: vg::MultipathMapper
- max_attempts
: vg::Mapper
- max_band_jump
: vg::Mapper
- max_branch_trim_length
: vg::MultipathMapper
- max_bubble_paths
: vg::LegacyCaller
, vg::RepresentativeTraversalFinder
- max_buf_size
: vg::StreamSorter< Message >
- max_cluster_mapping_quality
: vg::Mapper
- max_context_radius
: vg::VariantAdder
- max_degree
: PruningParameters
- max_deletion_scan_nodes
: vg::VCFTraversalFinder
- max_depth
: vg::RepresentativeTraversalFinder
- max_distance
: vg::IncrementalSubgraph
, vg::MinimumDistanceIndex
- max_distances
: vg::MinimumDistanceIndex
- max_expected_dist_approx_error
: vg::MultipathMapper
, vg::OrientedDistanceClusterer
- max_exponential_rate_intercept
: vg::MultipathMapper
- max_exponential_rate_slope
: vg::MultipathMapper
- max_exponential_shape_intercept
: vg::MultipathMapper
- max_exponential_shape_slope
: vg::MultipathMapper
- max_extensions
: vg::MinimizerMapper
- max_fan_in
: vg::StreamSorter< Message >
- max_fanout_base_quality
: vg::MultipathMapper
- max_fans_out
: vg::MultipathMapper
- max_flow_sort()
: vg::FlowSort
- max_gap
: vg::MEMClusterer
- max_group_size
: vg::io::MessageEmitter
- max_handle
: vg::DozeuPinningOverlay
- max_handle_memo_size
: vg::MemoizingGraph
- max_het_bias
: vg::Genotyper
, vg::RatioSupportSnarlCaller
- max_id
: bdsg::HashGraph
, bdsg::PackedGraph
, vg::ConstructedChunk
, vg::Constructor
, vg::DagifiedGraph
, vg::SubHandleGraph
, xg::XG
- max_indel_het_bias
: vg::RatioSupportSnarlCaller
- MAX_INPUT_VERSION
: vg::StreamIndexBase
- max_intron_length
: vg::MultipathMapper
- max_iterations
: vg::SmallSnarlSimplifier
- max_local_extensions
: vg::MinimizerMapper
- max_ma_bias
: vg::RatioSupportSnarlCaller
- max_mapping_p_value
: vg::MultipathMapper
- max_mapping_quality
: vg::BaseMapper
- MAX_MESSAGE_SIZE
: vg::io::MessageEmitter
, vg::io::MessageIterator
- MAX_MISMATCHES
: vg::GaplessExtender
- max_missing_variant_warnings
: vg::HaplotypeIndexer
- max_multi_alns
: vg::BandedGlobalAligner< IntType >::AltTracebackStack
, vg::BandedGlobalAligner< IntType >
- max_multimaps
: vg::Mapper
, vg::MinimizerMapper
- max_node
: vg::SubgraphOverlay
- max_node_id()
: bdsg::HashGraph
, bdsg::ODGI
, bdsg::PackedGraph
, handlegraph::HandleGraph
, vg::DagifiedGraph
, vg::DozeuPinningOverlay
, vg::ExtraNodeGraph
, vg::IdentityOverlay
, vg::IncrementalSubgraph
, vg::IndexedVG
, vg::JoinedSpliceGraph
, vg::MemoizingGraph
, vg::MinimumDistanceIndex
, vg::NetGraph
, vg::NullMaskingGraph
, vg::PathSubgraph
, vg::ReverseGraph
, vg::SourceSinkOverlay
, vg::StrandSplitGraph
, vg::SubgraphOverlay
, vg::SubHandleGraph
, vg::TreeSubgraph
, vg::VG
, vg::VGset
, xg::XG
- max_node_rank()
: xg::XG
- max_node_size
: vg::Constructor
, vg::VariantAdder
- max_nodes_for_exhaustive
: vg::Deconstructor
- max_overhang
: vg::ReadFilter::Counts
, vg::ReadFilter
- max_p_value_memo_size
: vg::MultipathMapper
- max_path_id
: vg::Paths
- max_path_length
: vg::Filter
- max_path_rank()
: xg::XG
- max_path_search_steps
: vg::Genotyper
, vg::PathRestrictedTraversalFinder
, vg::ReadRestrictedTraversalFinder
- max_possible_mapping_quality()
: vg::GSSWAligner
, vg::Mapper
- max_prune_iterations
: vg::VCFTraversalFinder
- max_reads
: vg::SRPE
- max_ref_het_bias
: vg::RatioSupportSnarlCaller
- max_rescue_attempts
: vg::MinimizerMapper
, vg::MultipathMapper
- max_rescue_p_value
: vg::MultipathMapper
- max_sample_size()
: vg::FragmentLengthDistribution
- max_search_depth
: vg::LegacyCaller
- max_search_width
: vg::LegacyCaller
- max_separation
: vg::GreedyMinDistanceClusterer
- max_single_end_mappings_for_rescue
: vg::MultipathMapper
- max_snarl_cut_size
: vg::MultipathMapper
- max_snarl_edges
: vg::FlowCaller
- max_softclip_iterations
: vg::Mapper
- max_softclip_overlap
: vg::MultipathMapper
- max_splice_overhang
: vg::MultipathMapper
- max_splice_p_value
: vg::MultipathMapper
- max_steps_of_handle_memo_size
: vg::MemoizingGraph
- max_sub_mem_recursion_depth
: vg::BaseMapper
- max_suboptimal_path_score_ratio
: vg::MultipathMapper
- MAX_TAG_LENGTH
: vg::io::Registry
- max_target_factor
: vg::Mapper
- max_trav_size
: vg::PoissonSupportSnarlCaller::PoissonCallInfo
- max_traversal_cutoff
: vg::VCFTraversalFinder
- max_uncalled_alleles
: vg::VCFOutputCaller
- max_vertex()
: vg::AlignmentChainModel
, vg::MEMChainModel
- max_walk
: vg::PathOrientedDistanceMeasurer
- max_width
: vg::MinimumDistanceIndex::ChainIndex
, vg::MinimumDistanceIndex::SnarlIndex
, vg::RepresentativeTraversalFinder
- max_xdrop_gap_length
: vg::Mapper
- MaximalExactMatch()
: vg::MaximalExactMatch
- maximum_mapping_quality_approx()
: vg::GSSWAligner
- maximum_mapping_quality_exact()
: vg::GSSWAligner
- maximum_quality
: vg::Packer
- maximum_sample_size
: vg::FragmentLengthDistribution
- maybe_mq_threshold
: vg::Mapper
- MCMCCaller()
: vg::MCMCCaller
- MCMCGenotyper()
: vg::MCMCGenotyper
- mean()
: vg::FragmentLengthDistribution
, vg::normal_distribution< T >
- mean_node_length()
: vg::Transcriptome
- measurements_begin()
: vg::FragmentLengthDistribution
- measurements_end()
: vg::FragmentLengthDistribution
- median_mem_coverage()
: vg::MEMClusterer::HitGraph
- mem
: vg::MEMChainModelVertex
, vg::MEMClusterer::HitNode
- mem_coverage_min_ratio
: vg::MultipathMapper
- mem_reseed_length
: vg::BaseMapper
- MEMBERSHIP_ID_RECORD_SIZE
: bdsg::PackedGraph
- MEMBERSHIP_NEXT_RECORD_SIZE
: bdsg::PackedGraph
- MEMBERSHIP_OFFSET_RECORD_SIZE
: bdsg::PackedGraph
- MEMChainModel()
: vg::MEMChainModel
- MEMChainModelVertex()
: vg::MEMChainModelVertex
- memcluster_t
: vg::MultipathMapper
- MEMClusterer()
: vg::MEMClusterer
- memo
: haplo::hDP_gbwt_graph_accessor< GBWTType >
- MemoizingGraph()
: vg::MemoizingGraph
- memory_high_water_kb
: vg::Watchdog
- mems_id_clusters_to_alignments()
: vg::Mapper
- merge()
: vg::IntegratedSnarlFinder::MergedAdjacencyGraph
, vg::VG
- merge_from_dynamic()
: vg::Packer
- merge_from_files()
: vg::Packer
- merge_group()
: vg::Funnel
- merge_id_space()
: vg::VGset
- merge_nodes()
: vg::VG
- merge_rescued_mappings()
: vg::MultipathMapper
- merge_state()
: vg::DinucleotideMachine
- merge_union()
: vg::VG
- merged_group
: vg::IndexedVG::CacheEntry
- MergedAdjacencyGraph()
: vg::IntegratedSnarlFinder::MergedAdjacencyGraph
- message
: vg::indexOpenException
, vg::NoAlignmentInBandException
- message_emitter
: vg::io::ProtobufEmitter< T >
- message_handlers
: vg::io::ProtobufEmitter< T >
- message_it
: vg::io::ProtobufIterator< T >
- message_listener_t
: vg::io::ProtobufEmitter< T >
- MessageEmitter()
: vg::io::MessageEmitter
- MessageIterator()
: vg::io::MessageIterator
- metadata_entry_to_string()
: vg::Index
- min()
: vg::WideningPRNG< PRNG, OutType >
- min_ad_log_likelihood_for_filter
: vg::RatioSupportSnarlCaller
- min_alt_path_support
: vg::SupportBasedSnarlCaller
- min_approx_path_distance()
: xg::XG
- min_avg_qual
: vg::Filter
- min_banded_mq
: vg::Mapper
- min_base_qual
: vg::ReadFilter::Counts
- min_base_quality
: vg::ReadFilter
- min_base_quality_fraction
: vg::ReadFilter
- min_cluster_length
: vg::Mapper
- min_clustering_mem_length
: vg::MultipathMapper
- min_count_to_keep
: vg::RareVariantSimplifier
- min_cov
: vg::Filter
- min_cut()
: vg::FlowSort
- min_depth
: vg::Filter
- min_distance()
: vg::MinimumDistanceIndex
- min_distances
: vg::MinimumDistanceIndex
- min_edge_support
: vg::RepresentativeTraversalFinder
, vg::SupportRestrictedTraversalFinder
- min_end_matches
: vg::ReadFilter::Counts
, vg::ReadFilter
- min_extensions
: vg::MinimizerMapper
- min_frequency_to_keep
: vg::RareVariantSimplifier
- min_handle
: vg::DagifiedGraph
, xg::XGPath
- min_id
: bdsg::HashGraph
, bdsg::PackedGraph
, vg::SubHandleGraph
, xg::XG
- min_identity
: vg::Mapper
- min_mad_for_filter
: vg::SupportBasedSnarlCaller
- min_mapq
: vg::ReadFilter::Counts
, vg::ReadFilter
- min_median_mem_coverage_for_split
: vg::MultipathMapper
- min_mem_length
: vg::BaseMapper
- min_multimaps
: vg::Mapper
- min_node
: vg::SubgraphOverlay
- min_node_id()
: bdsg::HashGraph
, bdsg::ODGI
, bdsg::PackedGraph
, handlegraph::HandleGraph
, vg::DagifiedGraph
, vg::DozeuPinningOverlay
, vg::ExtraNodeGraph
, vg::IdentityOverlay
, vg::IncrementalSubgraph
, vg::IndexedVG
, vg::JoinedSpliceGraph
, vg::MemoizingGraph
, vg::MinimumDistanceIndex
, vg::NetGraph
, vg::NullMaskingGraph
, vg::PathSubgraph
, vg::ReverseGraph
, vg::SourceSinkOverlay
, vg::StrandSplitGraph
, vg::SubgraphOverlay
, vg::SubHandleGraph
, vg::TreeSubgraph
, vg::VG
, xg::XG
- min_node_support
: vg::RepresentativeTraversalFinder
, vg::SupportRestrictedTraversalFinder
- min_node_support_cache
: vg::CachedPackedTraversalSupportFinder
- min_pair_fragment_length()
: vg::Mapper
- min_percent_identity
: vg::Filter
- min_pos()
: vg::MinimumDistanceIndex
- min_primary
: vg::ReadFilter
- min_qual
: vg::Filter
- MIN_QUEUE_ITEM_BYTES
: vg::io::StreamMultiplexer
- min_read_separation
: vg::ComponentMinDistanceClusterer
- min_recurrence
: vg::Genotyper
, vg::PathRestrictedTraversalFinder
, vg::ReadRestrictedTraversalFinder
- min_score
: vg::ReadFilter::Counts
- min_score_factor
: vg::VariantAdder
- min_score_per_base
: vg::Genotyper
- min_sec_score
: vg::ReadFilter::Counts
- min_secondary
: vg::ReadFilter
- min_separation
: vg::GreedyMinDistanceClusterer
- min_site_depth
: vg::SupportBasedSnarlCaller
- min_size
: vg::SmallSnarlSimplifier
- min_softclip_length_for_splice
: vg::MultipathMapper
- min_splice_length
: vg::SplicedHTSAlignmentEmitter
, vg::Surjector
- min_support_in_path()
: vg::NestedTraversalFinder
, vg::RepresentativeTraversalFinder
- min_tail_anchor_length
: vg::MultipathMapper
- min_total_support_for_call
: vg::SupportBasedSnarlCaller
- min_unique_per_strand
: vg::Genotyper
- MinDistanceClusterer()
: vg::MinDistanceClusterer
- minimizer
: vg::IndexManager
- minimizer_indexes
: vg::MinimizerMapper
- minimizer_k
: vg::IndexManager
- minimizer_override
: vg::IndexManager
- minimizer_score_fraction
: vg::MinimizerMapper
- minimizer_w
: vg::IndexManager
- MinimizerMapper()
: vg::MinimizerMapper
- MinimumDistanceIndex
: vg::MinimumDistanceIndex::ChainIndex
, vg::MinimumDistanceIndex
, vg::MinimumDistanceIndex::SnarlIndex
- mismatch
: vg::GSSWAligner
, vg::SSWAligner
- mismatch_positions
: vg::GaplessExtension
- mismatches()
: vg::GaplessExtension
- model
: vg::AlignmentChainModel
, vg::MEMChainModel
- motif_matches
: vg::SpliceRegion
- move()
: vg::SmallBitset
- mp_aln_emitters
: vg::MultipathAlignmentEmitter
- mq_overlap
: vg::Mapper
- MSAConverter()
: vg::MSAConverter
- mu
: vg::FragmentLengthDistribution
- multinode_strongly_connected_components()
: vg::VG
- multipath_align()
: vg::MultipathMapper
- multipath_alignment_t()
: vg::multipath_alignment_t
- multipath_map()
: vg::MultipathMapper
- multipath_map_internal()
: vg::MultipathMapper
- multipath_map_paired()
: vg::MultipathMapper
- MultipathAlignmentEmitter()
: vg::MultipathAlignmentEmitter
- MultipathAlignmentGraph()
: vg::MultipathAlignmentGraph
- MultipathMapper()
: vg::MultipathMapper
- MultipathProblem()
: vg::MultipathProblem
- multiplexer
: vg::HTSAlignmentEmitter
, vg::io::GafAlignmentEmitter
, vg::io::TSVAlignmentEmitter
, vg::io::VGAlignmentEmitter
, vg::MultipathAlignmentEmitter
- mut_sampler
: vg::NGSSimulator
- mutable_connection()
: vg::subpath_t
- mutable_edit()
: vg::path_mapping_t
- mutable_mapping()
: vg::path_t
- mutable_next()
: vg::subpath_t
- mutable_path()
: vg::subpath_t
- mutable_position()
: vg::path_mapping_t
- mutable_quality()
: vg::multipath_alignment_t
- mutable_sequence()
: vg::edit_t
, vg::multipath_alignment_t
- mutable_start()
: vg::multipath_alignment_t
- mutable_subpath()
: vg::multipath_alignment_t
- mutate()
: vg::Sampler
- mutate_edit()
: vg::Sampler
- mutation_alphabets
: vg::NGSSimulator
- mutex_splice_graph
: vg::Transcriptome
- mutex_transcript_paths
: vg::Transcriptome
- my_mapper
: vg::Filter
- my_max_distance
: vg::Filter
- my_names
: Vectorizer
- my_path_position_graph
: vg::Filter
- my_vectors
: Vectorizer
- my_vg
: vg::Filter
- my_xg
: Vectorizer