vg
tools for working with variation graphs
- 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
manager :
vg::GenomeState
map_order_to_original :
vg::WindowedVcfBuffer
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_by_rank :
vg::Paths
mapq :
gafkluge::GafRecord
mapq_scaling_factor :
vg::MultipathMapper
match :
vg::BandedGlobalAligner< IntType >::BAMatrix
,
vg::GSSWAligner
,
vg::SSWAligner
match_count :
vg::MaximalExactMatch
matches :
gafkluge::GafRecord
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_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
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_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 :
vg::MinimumDistanceIndex
max_node_size :
vg::Constructor
,
vg::VariantAdder
max_nodes_for_exhaustive :
vg::Deconstructor
max_overhang :
vg::ReadFilter
max_p_value_memo_size :
vg::MultipathMapper
max_path_id :
vg::Paths
max_path_length :
vg::Filter
max_path_search_steps :
vg::Genotyper
,
vg::PathRestrictedTraversalFinder
,
vg::ReadRestrictedTraversalFinder
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_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_walk :
vg::PathOrientedDistanceMeasurer
max_width :
vg::MinimumDistanceIndex::ChainIndex
,
vg::MinimumDistanceIndex::SnarlIndex
,
vg::RepresentativeTraversalFinder
max_xdrop_gap_length :
vg::Mapper
maximum_quality :
vg::Packer
maximum_sample_size :
vg::FragmentLengthDistribution
maybe_mq_threshold :
vg::Mapper
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
memo :
haplo::hDP_gbwt_graph_accessor< GBWTType >
memory_high_water_kb :
vg::Watchdog
merged_group :
vg::IndexedVG::CacheEntry
message :
vg::indexOpenException
,
vg::NoAlignmentInBandException
message_emitter :
vg::io::ProtobufEmitter< T >
message_handlers :
vg::io::ProtobufEmitter< T >
message_it :
vg::io::ProtobufIterator< T >
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
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_depth :
vg::Filter
min_distances :
vg::MinimumDistanceIndex
min_edge_support :
vg::RepresentativeTraversalFinder
,
vg::SupportRestrictedTraversalFinder
min_end_matches :
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
min_median_mem_coverage_for_split :
vg::MultipathMapper
min_mem_length :
vg::BaseMapper
min_multimaps :
vg::Mapper
min_node :
vg::SubgraphOverlay
min_node_id :
vg::MinimumDistanceIndex
min_node_support :
vg::RepresentativeTraversalFinder
,
vg::SupportRestrictedTraversalFinder
min_node_support_cache :
vg::CachedPackedTraversalSupportFinder
min_percent_identity :
vg::Filter
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_factor :
vg::VariantAdder
min_score_per_base :
vg::Genotyper
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_tail_anchor_length :
vg::MultipathMapper
min_total_support_for_call :
vg::SupportBasedSnarlCaller
min_unique_per_strand :
vg::Genotyper
minimizer :
vg::IndexManager
minimizer_indexes :
vg::MinimizerMapper
minimizer_k :
vg::IndexManager
minimizer_override :
vg::IndexManager
minimizer_score_fraction :
vg::MinimizerMapper
minimizer_w :
vg::IndexManager
mismatch :
vg::GSSWAligner
,
vg::SSWAligner
mismatch_positions :
vg::GaplessExtension
model :
vg::AlignmentChainModel
,
vg::MEMChainModel
motif_matches :
vg::SpliceRegion
mp_aln_emitters :
vg::MultipathAlignmentEmitter
mq_overlap :
vg::Mapper
mu :
vg::FragmentLengthDistribution
multiplexer :
vg::HTSAlignmentEmitter
,
vg::io::GafAlignmentEmitter
,
vg::io::TSVAlignmentEmitter
,
vg::io::VGAlignmentEmitter
,
vg::MultipathAlignmentEmitter
mut_sampler :
vg::NGSSimulator
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
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