- 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 , vg::ZipCodeCollection
• main_function : vg::subcommand::Subcommand
• manager : vg::GenomeState
• MANDATORY_FIELDS : vg::GAFSorterRecord
• MANY_LIMIT : vg::MinimizerMapper
• map_order_to_original : vg::WindowedVcfBuffer
• mapped_nodes_ids : vg::Primer
• mapper_alignment_cutoff : vg::VariantAdder
• mapping : vg::Path , vg::PhaseUnfolder
• mapping_edits : vg::BandedGlobalAligner< IntType >::BABuilder
• mapping_itr : vg::Paths
• mapping_positions : vg::PathIndex
• mapping_quality : vg::Alignment , vg::MultipathAlignment
• mapping_quality_method : vg::BaseMapper
• mappings : vg::RebuildJob
• mappings_by_rank : vg::Paths
• mapq : gafkluge::GafRecord
• mapq_scaling_factor : vg::MultipathMapper
• mapq_score_scale : vg::MinimizerMapper
• mapq_score_window : vg::MinimizerMapper
• margin_after : vg::algorithms::Anchor
• margin_before : vg::algorithms::Anchor
• mask : vg::GaplessExtender , vg::ReadMasker , vg::WFAExtender
• match : ScoringOptions , vg::BandedGlobalAligner< IntType >::BAMatrix , vg::GSSWAligner , vg::SSWAligner
• match_count : vg::MaximalExactMatch
• matches : gafkluge::GafRecord , vg::SeqComplexity< MaxOrder >
• MATCHES : vg::WFANode
• 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
• max : vg::WFAExtender::ErrorModel::Event
• max_alignment_gap : vg::MultipathMapper
• max_alignments : vg::MinimizerMapper
• max_alt_mappings : vg::MultipathMapper
• max_anchors : vg::Surjector
• max_attempts : vg::Mapper
• max_band_cells : vg::Surjector
• 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_chaining_problems : vg::MinimizerMapper
• max_chains_per_tree : vg::MinimizerMapper
• max_cluster_mapping_quality : vg::Mapper
• 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_direct_to_chain : vg::MinimizerMapper
• MAX_DISPLAYED_SUGGESTIONS_PER_CATEGORY : vg::DiagramExplainer
• max_distance : vg::IncrementalSubgraph , vg::WFATree
• max_dozeu_cells : vg::MinimizerMapper
• max_dp_cells : 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_extension_mismatches : vg::MinimizerMapper
• max_extensions : vg::MinimizerMapper
• max_fan_in : vg::StreamSorter< Message >
• max_fanout_base_quality : vg::MultipathMapper
• max_fans_out : vg::MultipathMapper
• max_fragment_length : vg::MinimizerMapper
• max_fragments : vg::MinimizerMapper
• max_gap : vg::MEMClusterer
• max_graph_lookback_bases : vg::MinimizerMapper
• max_graph_lookback_bases_per_base : vg::MinimizerMapper
• 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_indel_bases : vg::MinimizerMapper
• max_indel_bases_per_base : 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_length : vg::ReadFilter< Read >
• max_local_extensions : vg::MinimizerMapper
• max_low_complexity_anchor_prune : vg::Surjector
• max_low_complexity_anchor_trim : 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_middle_dp_length : vg::MinimizerMapper
• max_middle_gap : vg::MinimizerMapper
• max_min_chain_score : vg::MinimizerMapper
• 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_size : vg::Constructor , vg::IndexingParameters , vg::VariantAdder
• max_num_nodes : vg::IncrementalSubgraph
• max_overhang : 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_search_steps : vg::Genotyper , vg::PathRestrictedTraversalFinder , vg::ReadRestrictedTraversalFinder
• max_product_size : vg::PrimerPair
• max_prune_iterations : vg::VCFTraversalFinder
• max_read_lookback_bases : vg::MinimizerMapper
• max_read_lookback_bases_per_base : vg::MinimizerMapper
• max_reads : vg::ReadFilter< Read >
• max_reads_used : vg::ReadFilter< Read >
• 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_search_depth : vg::LegacyCaller
• max_search_width : vg::LegacyCaller
• max_separation : vg::GreedyMinDistanceClusterer
• max_single_end_mappings_for_rescue : vg::MultipathMapper
• max_skipped_bases : vg::MinimizerMapper
• max_slide : vg::Surjector
• 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_per_read_base : vg::Surjector
• max_suboptimal_path_score_ratio : vg::MultipathMapper
• MAX_TAG_LENGTH : vg::io::Registry
• max_tail_anchor_prune : vg::Surjector
• max_tail_dp_length : vg::MinimizerMapper
• max_tail_gap : vg::MinimizerMapper
• max_tail_length : vg::MinimizerMapper , vg::Surjector
• max_tail_merge_supress_length : vg::MultipathMapper
• max_target_factor : vg::Mapper
• max_to_fragment : vg::MinimizerMapper
• 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_VALUE : vg::varint_vector_t
• max_vcf_line_length : vg::VCFOutputCaller
• max_walk : vg::PathOrientedDistanceMeasurer
• max_width : vg::RepresentativeTraversalFinder
• max_xdrop_gap_length : vg::Mapper
• maximum_quality : vg::Packer
• maximum_sample_size : vg::FragmentLengthDistribution
• maybe_mq_threshold : vg::Mapper
• mean : vg::SummaryStatistics
• median : vg::SummaryStatistics
• mem : vg::MEMChainModelVertex , vg::MEMClusterer::HitNode
• mem_coverage_min_ratio : vg::MultipathMapper
• mem_reseed_length : vg::BaseMapper
• memo : haplo::hDP_gbwt_graph_accessor< GBWTType >
• memory_high_water_kb : vg::Watchdog
• merge : GBWTConfig
• merge_parameters : GBWTConfig
• merged_group : vg::IndexedVG::CacheEntry
• 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 >
• metadata : GBWTConfig , vg::RecombinatorHaplotype
• metadata_mode : GBWTConfig
• min : vg::WFAExtender::ErrorModel::Event
• min_ad_log_likelihood_for_filter : vg::RatioSupportSnarlCaller
• min_alt_path_support : vg::SupportBasedSnarlCaller
• min_avg_qual : vg::Filter
• min_banded_mq : vg::Mapper
• min_base_quality : vg::ReadFilter< Read >
• min_base_quality_fraction : vg::ReadFilter< Read >
• min_bp_edge_override : vg::TraversalSupportFinder
• min_chain_score_per_base : vg::MinimizerMapper
• min_chaining_problems : vg::MinimizerMapper
• min_chains : vg::MinimizerMapper
• min_cluster_length : vg::Mapper
• min_clustering_mem_length : vg::MultipathMapper
• min_count_to_keep : vg::RareVariantSimplifier
• min_cov : vg::Filter
• min_depth : vg::Filter
• min_diagonal : vg::WFATree::ScoreProperties
• min_distance : vg::WFATree
• min_edge_support : vg::RepresentativeTraversalFinder , vg::SupportRestrictedTraversalFinder
• min_end_matches : 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_handle : vg::DagifiedGraph , xg::XGPath
• min_id : handlegraph::algorithms::SubHandleGraph , vg::SubHandleGraph , xg::XG
• min_identity : vg::Mapper
• min_mad_for_filter : vg::SupportBasedSnarlCaller
• min_mapq : 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_support : vg::RepresentativeTraversalFinder , vg::SupportRestrictedTraversalFinder
• min_node_support_cache : vg::CachedPackedTraversalSupportFinder
• min_percent_identity : vg::Filter
• min_primary : vg::ReadFilter< Read >
• min_product_size : vg::PrimerPair
• 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_factor : vg::VariantAdder
• min_score_per_base : vg::Genotyper
• 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_tail_anchor_length : vg::MultipathMapper
• min_to_fragment : vg::MinimizerMapper
• min_total_support_for_call : vg::SupportBasedSnarlCaller
• min_unique_node_fraction : vg::MinimizerMapper
• min_unique_per_strand : vg::Genotyper
• MIN_VERSION : vg::Haplotypes::Header
• minimizer_coverage_flank : vg::MinimizerMapper
• minimizer_downsampling_max_window_length : vg::MinimizerMapper
• minimizer_downsampling_window_count : vg::MinimizerMapper
• minimizer_downweight_threshold : vg::IndexingParameters
• minimizer_index : vg::HaplotypePartitioner , vg::MinimizerMapper
• minimizer_s : vg::IndexingParameters
• minimizer_score_fraction : vg::MinimizerMapper
• mismatch : ScoringOptions , vg::GSSWAligner , vg::SSWAligner , vg::WFATree
• mismatch_positions : vg::GaplessExtension
• mismatches : vg::WFAExtender::ErrorModel
• MISSING_KEY : vg::GAFSorterRecord
• mixture_weights : vg::SpliceStats
• mode : HaplotypesConfig , vg::SummaryStatistics
• mode_log_likelihood : vg::SpliceStats
• model : vg::AlignmentChainModel , vg::MEMChainModel
• motif_data : vg::SpliceStats
• motif_matches : vg::SpliceRegion
• mp_aln_emitter : vg::ReadFilter< Read >
• mp_aln_emitters : vg::MultipathAlignmentEmitter
• mq_overlap : vg::Mapper
• msg : vg::InsufficientInputException , vg::RewindPlanException , vg::SizeLimitExceededException
• mtx : vg::ParallelKFFReader
• mu : vg::FragmentLengthDistribution
• multi_position_annotations : vg::AbstractReadSampler
• multiallelic_sv_warned : vg::Constructor
• multiplexer : vg::HTSWriter , vg::io::GafAlignmentEmitter , vg::io::TSVAlignmentEmitter , vg::io::VGAlignmentEmitter
• mut_graph_impl : vg::IndexingParameters
• mut_sampler : vg::NGSSimulator
• 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