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_alpha : vg::truncated_normal_distribution< T >
- m_b : vg::uniform_int_distribution< T >, vg::uniform_real_distribution< T >
- m_beta : vg::truncated_normal_distribution< T >
- m_distU1 : vg::normal_distribution< T >, vg::truncated_normal_distribution< T >
- m_mean : vg::normal_distribution< T >
- m_mu : vg::truncated_normal_distribution< T >
- m_sigma : vg::truncated_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
- MAGIC_NUMBER : vg::Haplotypes::Header
- magic_number : vg::Haplotypes::Header
- main_function : vg::subcommand::Subcommand
- make_bands() : vg::Mapper
- make_circular() : vg::Paths
- make_compact() : vg::Packer
- make_dynamic() : vg::Packer
- make_edge() : vg::PhaseUnfolder
- make_empty() : vg::WFAAlignment
- make_graph() : vg::MSAConverter
- make_hit_graph() : vg::ComponentMinDistanceClusterer, vg::GreedyMinDistanceClusterer, vg::MEMClusterer, vg::MinDistanceClusterer, vg::NullClusterer, vg::OrientedDistanceClusterer, vg::TVSClusterer
- make_indexes() : vg::IndexRegistry
- make_linear() : vg::Paths
- make_long_options() : vg::subcommand::BaseOptionGroup, vg::subcommand::GroupedOptionGroup, vg::subcommand::OptionGroup< Receiver >
- make_nontrivial_multipath_alignment() : vg::MultipathMapper
- make_null_alignment() : vg::Surjector
- make_null_mp_alignment() : vg::Surjector
- make_plan() : vg::IndexRegistry
- make_short_options() : vg::subcommand::BaseOptionGroup, vg::subcommand::GroupedOptionGroup, vg::subcommand::OptionGroup< Receiver >
- make_snarl_graph() : vg::MCMCGenotyper
- make_snarl_map() : vg::MCMCGenotyper
- make_subset_graph() : vg::Genotyper
- make_unlocalized_insertion() : vg::WFAAlignment
- manage() : vg::SnarlManager
- manager : vg::GenomeState
- MANY_LIMIT : vg::MinimizerMapper
- map() : vg::MinimizerMapper
- map_entry_type : vg::WFAPoint
- map_from_chains() : vg::MinimizerMapper
- map_from_extensions() : 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_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
- mapping_type : vg::RebuildJob
- mappings : vg::RebuildJob
- 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 >
- mask : vg::GaplessExtender, vg::ReadMasker, vg::WFAExtender
- match : ScoringOptions, vg::BandedGlobalAligner< IntType >::BAMatrix
- Match : vg::BandedGlobalAligner< IntType >
- match : vg::GSSWAligner, vg::SSWAligner, vg::WFAAlignment
- match_count : vg::MaximalExactMatch
- match_fanouts_t : vg::MEMClusterer, vg::MultipathMapper
- match_forward() : vg::WFANode
- match_predecessor() : vg::WFATree
- matches : gafkluge::GafRecord, vg::DinucleotideMachine, vg::SeqComplexity< MaxOrder >
- MATCHES : vg::WFANode
- matches_annotation() : vg::ReadFilter< Read >
- matches_name() : vg::ReadFilter< Read >
- matching : vg::BandedGlobalAligner< IntType >::BABuilder
- MatchPos() : vg::MatchPos
- 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::WFAExtender::ErrorModel::Event, vg::WideningPRNG< PRNG, OutType >
- max_alignment_gap : vg::MultipathMapper
- max_alignments : vg::MinimizerMapper
- max_alt_mappings : vg::MultipathMapper
- max_anchors : vg::Surjector
- 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_chain_connection : vg::MinimizerMapper
- max_cluster_mapping_quality : vg::Mapper
- max_clusters_to_chain : vg::MinimizerMapper
- max_context_radius : vg::VariantAdder
- max_dagify_duplications : vg::MultipathMapper
- max_degree : PruningParameters
- max_deletion_scan_nodes : vg::VCFTraversalFinder
- max_depth : vg::RepresentativeTraversalFinder
- max_diagonal : vg::WFATree::ScoreProperties
- MAX_DISPLAYED_SUGGESTIONS_PER_CATEGORY : vg::DiagramExplainer
- max_distance : vg::IncrementalSubgraph, vg::WFATree
- max_distance_from_start() : vg::IncrementalSubgraph
- max_dozeu_cells : vg::MinimizerMapper
- max_dp_cells : vg::MinimizerMapper
- MAX_DP_LENGTH : vg::MinimizerMapper
- 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_fragment_length : vg::MinimizerMapper
- 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 : handlegraph::algorithms::SubHandleGraph, vg::algorithms::GFAIDMapInfo, vg::ConstructedChunk, vg::Constructor, vg::DagifiedGraph, vg::SubHandleGraph, xg::XG
- max_in() : vg::algorithms::TracedScore
- max_indel_bases : vg::MinimizerMapper
- max_indel_het_bias : vg::RatioSupportSnarlCaller
- MAX_INPUT_VERSION : vg::StreamIndexBase
- max_intron_length : vg::MultipathMapper
- max_iterations : vg::SmallSnarlSimplifier
- max_kmers_per_block : vg::ParallelKFFReader
- max_link_length() : vg::JoinedSpliceGraph
- max_local_extensions : vg::MinimizerMapper
- max_lookback_bases : vg::MinimizerMapper
- max_low_complexity_anchor_prune : vg::Surjector
- max_ma_bias : vg::RatioSupportSnarlCaller
- max_mapping_p_value : vg::MultipathMapper
- max_mapping_quality : vg::BaseMapper
- max_memory_proportion : vg::IndexingParameters
- MAX_MESSAGE_SIZE : vg::io::MessageEmitter, vg::io::MessageIterator
- MAX_MISMATCHES : vg::GaplessExtender
- max_missing_variant_warnings : vg::HaplotypeIndexer
- max_motif_pairs : vg::MultipathMapper
- max_multi_alns : vg::BandedGlobalAligner< IntType >::AltTracebackStack, vg::BandedGlobalAligner< IntType >
- max_multimaps : vg::Mapper, vg::MinimizerMapper
- max_node : vg::SubgraphOverlay
- max_node_id() : handlegraph::algorithms::SubHandleGraph, handlegraph::HandleGraph, vg::DagifiedGraph, vg::DozeuPinningOverlay, vg::ExtraNodeGraph, vg::IdentityOverlay, vg::IncrementalSubgraph, vg::IndexedVG, vg::JoinedSpliceGraph, vg::MemoizingGraph, vg::NetGraph, vg::NullMaskingGraph, vg::PathSubgraph, vg::ReverseGraph, vg::SnarlGraph, vg::SourceSinkOverlay, vg::StrandSplitGraph, vg::SubgraphOverlay, vg::SubHandleGraph, vg::SubpathOverlay, vg::TreeSubgraph, vg::VG, vg::VGset, xg::XG
- max_node_rank() : xg::XG
- max_node_size : vg::Constructor, vg::IndexingParameters, vg::VariantAdder
- max_num_nodes : vg::IncrementalSubgraph
- max_overhang : vg::Counts, vg::ReadFilter< Read >
- max_p_value_memo_size : vg::MultipathMapper
- max_parsed_variant_size : vg::Constructor
- 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_precluster_connections : vg::MinimizerMapper
- max_prune_iterations : vg::VCFTraversalFinder
- max_ref_het_bias : vg::RatioSupportSnarlCaller
- max_rescue_attempts : vg::MinimizerMapper, vg::MultipathMapper
- max_rescue_p_value : vg::MultipathMapper
- max_rgfa_rank : vg::algorithms::GFAParser
- max_sample_size() : vg::FragmentLengthDistribution
- max_search_depth : vg::LegacyCaller
- max_search_width : vg::LegacyCaller
- max_separation : vg::GreedyMinDistanceClusterer
- max_shift() : vg::MultipathAlignmentGraph
- max_single_end_mappings_for_rescue : vg::MultipathMapper
- max_snarl_cut_size : vg::MultipathMapper
- max_snarl_edges : vg::FlowCaller
- max_snarl_shallow_size : vg::NestedFlowCaller
- max_softclip_iterations : vg::Mapper
- max_softclip_overlap : vg::MultipathMapper
- max_splice_overhang : vg::MultipathMapper
- max_splice_ref_search_length : vg::MultipathMapper
- max_steps_of_handle_memo_size : vg::MemoizingGraph
- max_sub_mem_recursion_depth : vg::BaseMapper
- max_subgraph_bases : vg::Surjector
- max_suboptimal_path_score_ratio : vg::MultipathMapper
- MAX_TAG_LENGTH : vg::io::Registry
- max_tail_anchor_prune : vg::Surjector
- max_tail_length : vg::MinimizerMapper, vg::Surjector
- max_tail_merge_supress_length : vg::MultipathMapper
- max_target_factor : vg::Mapper
- max_trav_size : vg::PoissonSupportSnarlCaller::PoissonCallInfo
- max_traversal_cutoff : vg::VCFTraversalFinder
- max_traversal_length : vg::FlowTraversalFinder
- max_tries : vg::AbstractReadSampler
- max_uncalled_alleles : vg::VCFOutputCaller
- max_unique_min : vg::MinimizerMapper
- max_value : vg::SummaryStatistics
- max_vcf_line_length : vg::VCFOutputCaller
- max_vertex() : vg::AlignmentChainModel, vg::MEMChainModel
- max_walk : vg::PathOrientedDistanceMeasurer
- max_width : 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 >, vg::SummaryStatistics, vg::truncated_normal_distribution< T >
- mean_node_length() : vg::Transcriptome
- measurements_begin() : vg::FragmentLengthDistribution
- measurements_end() : vg::FragmentLengthDistribution
- median : vg::SummaryStatistics
- median_mem_coverage() : vg::MEMClusterer::HitGraph
- mem : vg::MEMChainModelVertex, vg::MEMClusterer::HitNode
- mem_coverage_min_ratio : vg::MultipathMapper
- mem_reseed_length : vg::BaseMapper
- MEMAccelerator() : vg::MEMAccelerator
- MEMChainModel() : vg::MEMChainModel
- MEMChainModelVertex() : vg::MEMChainModelVertex
- memcluster_t : vg::MultipathMapper
- MEMClusterer() : vg::MEMClusterer
- memo : haplo::hDP_gbwt_graph_accessor< GBWTType >
- memoized_LF() : vg::MEMAccelerator
- MemoizingGraph() : vg::MemoizingGraph
- memory_high_water_kb : vg::Watchdog
- mems_id_clusters_to_alignments() : vg::Mapper
- merge : GBWTConfig, vg::Funnel, vg::IntegratedSnarlFinder::MergedAdjacencyGraph, vg::VG
- merge_fast : GBWTConfig
- merge_from_dynamic() : vg::Packer
- merge_from_files() : vg::Packer
- merge_group() : vg::Funnel
- merge_groups() : vg::Funnel
- merge_id_space() : vg::VGset
- merge_insert : GBWTConfig
- merge_mode : GBWTConfig
- merge_nodes() : vg::VG
- merge_none : GBWTConfig
- merge_parallel : GBWTConfig
- merge_parameters : GBWTConfig
- merge_partially_redundant_match_nodes() : vg::MultipathAlignmentGraph
- merge_rescued_mappings() : vg::MultipathMapper
- merge_state() : vg::DinucleotideMachine
- merge_union() : vg::VG
- merged_group : vg::IndexedVG::CacheEntry
- MergedAdjacencyGraph() : vg::IntegratedSnarlFinder::MergedAdjacencyGraph
- message : vg::AlignmentValidity, vg::NoAlignmentInBandException
- message_buffer : vg::algorithms::GFAFormatError
- 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 : GBWTConfig
- metadata_mode : GBWTConfig
- min : vg::WFAExtender::ErrorModel::Event, 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::Counts
- min_base_quality : vg::ReadFilter< Read >
- min_base_quality_fraction : vg::ReadFilter< Read >
- min_bp_edge_override : vg::TraversalSupportFinder
- min_chains : vg::MinimizerMapper
- min_cluster_length : vg::Mapper
- min_clustering_mem_length : vg::MultipathMapper
- min_clusters_to_chain : vg::MinimizerMapper
- min_count_to_keep : vg::RareVariantSimplifier
- min_cov : vg::Filter
- min_cut() : vg::FlowSort
- min_depth : vg::Filter
- min_diagonal : vg::WFATree::ScoreProperties
- min_distance : vg::WFATree
- min_distance_from_start() : vg::IncrementalSubgraph
- min_dists() : vg::DeletionAligner
- min_edge_support : vg::RepresentativeTraversalFinder, vg::SupportRestrictedTraversalFinder
- min_end_matches : vg::Counts, vg::ReadFilter< Read >
- min_extension_sets : vg::MinimizerMapper
- min_extensions : vg::MinimizerMapper
- min_fold_coverage_for_downsample : vg::Surjector
- min_frequency_to_keep : vg::RareVariantSimplifier
- min_good_transition_score_per_base : vg::MinimizerMapper
- min_handle : vg::DagifiedGraph, xg::XGPath
- min_id : handlegraph::algorithms::SubHandleGraph, vg::SubHandleGraph, xg::XG
- min_identity : vg::Mapper
- min_link_length() : vg::JoinedSpliceGraph
- min_lookback_items : vg::MinimizerMapper
- min_mad_for_filter : vg::SupportBasedSnarlCaller
- min_mapq : vg::Counts, vg::ReadFilter< Read >
- min_median_mem_coverage_for_split : vg::MultipathMapper
- min_mem_length : vg::BaseMapper
- min_multimaps : vg::Mapper
- min_node : vg::SubgraphOverlay
- min_node_id() : handlegraph::algorithms::SubHandleGraph, handlegraph::HandleGraph, vg::DagifiedGraph, vg::DozeuPinningOverlay, vg::ExtraNodeGraph, vg::IdentityOverlay, vg::IncrementalSubgraph, vg::IndexedVG, vg::JoinedSpliceGraph, vg::MemoizingGraph, vg::NetGraph, vg::NullMaskingGraph, vg::PathSubgraph, vg::ReverseGraph, vg::SnarlGraph, vg::SourceSinkOverlay, vg::StrandSplitGraph, vg::SubgraphOverlay, vg::SubHandleGraph, vg::SubpathOverlay, 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_precluster_connections : vg::MinimizerMapper
- min_primary : vg::ReadFilter< Read >
- 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::Counts
- min_score_factor : vg::VariantAdder
- min_score_per_base : vg::Genotyper
- min_sec_score : vg::Counts
- min_secondary : vg::ReadFilter< Read >
- min_separation : vg::GreedyMinDistanceClusterer
- min_shift_for_prune : vg::Surjector
- min_site_depth : vg::SupportBasedSnarlCaller
- min_size : vg::SmallSnarlSimplifier
- min_softclip_length_for_splice : vg::MultipathMapper
- min_softclipped_score_for_splice : vg::MultipathMapper
- min_splice_length : vg::MultipathAlignmentEmitter, vg::SplicedHTSAlignmentEmitter, vg::Surjector
- min_splice_repair_length : vg::Surjector
- min_splice_rescue_matches : vg::MultipathMapper
- 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
- MIN_VERSION : vg::Haplotypes::Header
- MinDistanceClusterer() : vg::MinDistanceClusterer
- minimizer_cache : vg::SnarlDistanceIndexClusterer::Seed, vg::SnarlDistanceIndexClusterer::SeedCache
- minimizer_index : vg::HaplotypePartitioner, vg::MinimizerMapper
- minimizer_index_type : vg::HaplotypePartitioner
- minimizer_k : vg::IndexingParameters
- minimizer_s : vg::IndexingParameters
- minimizer_score_fraction : vg::MinimizerMapper
- minimizer_w : vg::IndexingParameters
- MinimizerMapper() : vg::MinimizerMapper
- mismatch : ScoringOptions, vg::GSSWAligner, vg::SSWAligner, vg::WFAAlignment, vg::WFATree
- mismatch_positions : vg::GaplessExtension
- mismatches() : vg::GaplessExtension, vg::WFAExtender::ErrorModel
- mixture_weights : vg::SpliceStats
- mode : HaplotypesConfig, vg::SummaryStatistics
- mode_classify : HaplotypesConfig
- mode_extract : HaplotypesConfig
- mode_invalid : HaplotypesConfig
- mode_log_likelihood : vg::SpliceStats
- mode_map_variants : HaplotypesConfig
- mode_preprocess : HaplotypesConfig
- mode_sample_graph : HaplotypesConfig
- mode_sample_haplotypes : HaplotypesConfig
- model : vg::AlignmentChainModel, vg::MEMChainModel
- motif_data : vg::SpliceStats
- motif_frequency() : vg::SpliceStats
- motif_is_reverse() : vg::SpliceStats
- motif_matches : vg::SpliceRegion
- motif_score() : vg::SpliceStats
- motif_size() : vg::SpliceStats
- move() : vg::SmallBitset
- mp_aln_emitter : vg::ReadFilter< Read >
- mp_aln_emitters : vg::MultipathAlignmentEmitter
- mq_overlap : vg::Mapper
- MSAConverter() : vg::MSAConverter
- msg : vg::InsufficientInputException, vg::RewindPlanException, vg::SizeLimitExceededException
- mtx : vg::ParallelKFFReader
- mu : vg::FragmentLengthDistribution
- multi_position_annotations : vg::AbstractReadSampler
- multi_surject() : vg::Surjector
- multiallelic_sv_warned : vg::Constructor
- multipath_align() : vg::MultipathMapper
- multipath_alignment_t() : vg::multipath_alignment_t
- multipath_map() : vg::MultipathMapper
- multipath_map_paired() : vg::MultipathMapper
- MultipathAlignmentEmitter() : vg::MultipathAlignmentEmitter
- MultipathAlignmentGraph() : vg::MultipathAlignmentGraph
- MultipathMapper() : vg::MultipathMapper
- MultipathProblem() : vg::MultipathProblem
- multiplexer : vg::HTSWriter, vg::io::GafAlignmentEmitter, vg::io::TSVAlignmentEmitter, vg::io::VGAlignmentEmitter
- mut_graph_impl : vg::IndexingParameters
- 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
- MutableGraphImplementation : vg::IndexingParameters
- mutate() : vg::Sampler
- mutate_edit() : vg::Sampler
- mutation_alphabets : vg::NGSSimulator
- mutex_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