vg
tools for working with variation graphs
- m -
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
map() :
vg::MinimizerMapper
map_paired() :
vg::MinimizerMapper
Mapper() :
vg::Mapper
mapping() :
vg::path_t
mapping_enters_side() :
vg::Genotyper
mapping_entry_to_string() :
vg::Index
mapping_exits_side() :
vg::Genotyper
mapping_is_total_match() :
vg::VG
mapping_likelihoods() :
vg::MultipathMapper
mapping_path_id() :
vg::Paths
mapping_path_name() :
vg::Paths
mapping_quality() :
vg::multipath_alignment_t
mapping_quality_score_diff() :
vg::GSSWAligner
mapping_size() :
vg::path_t
mapping_t() :
vg::mapping_t
mark_dfs() :
vg::FlowSort
mark_smallVariant_alignments() :
vg::Filter
mark_sv_alignments() :
vg::Filter
MarkovDistribution() :
vg::NGSSimulator::MarkovDistribution< From, To >
matches() :
vg::DinucleotideMachine
max() :
vg::WideningPRNG< PRNG, OutType >
max_distance() :
vg::MinimumDistanceIndex
max_flow_sort() :
vg::FlowSort
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::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_path_rank() :
xg::XG
max_possible_mapping_quality() :
vg::GSSWAligner
,
vg::Mapper
max_sample_size() :
vg::FragmentLengthDistribution
max_vertex() :
vg::AlignmentChainModel
,
vg::MEMChainModel
MaximalExactMatch() :
vg::MaximalExactMatch
maximum_mapping_quality_approx() :
vg::GSSWAligner
maximum_mapping_quality_exact() :
vg::GSSWAligner
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
MEMChainModel() :
vg::MEMChainModel
MEMChainModelVertex() :
vg::MEMChainModelVertex
MEMClusterer() :
vg::MEMClusterer
MemoizingGraph() :
vg::MemoizingGraph
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
MergedAdjacencyGraph() :
vg::IntegratedSnarlFinder::MergedAdjacencyGraph
MessageEmitter() :
vg::io::MessageEmitter
MessageIterator() :
vg::io::MessageIterator
metadata_entry_to_string() :
vg::Index
min() :
vg::WideningPRNG< PRNG, OutType >
min_approx_path_distance() :
xg::XG
min_cut() :
vg::FlowSort
min_distance() :
vg::MinimumDistanceIndex
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::NetGraph
,
vg::NullMaskingGraph
,
vg::PathSubgraph
,
vg::ReverseGraph
,
vg::SourceSinkOverlay
,
vg::StrandSplitGraph
,
vg::SubgraphOverlay
,
vg::SubHandleGraph
,
vg::TreeSubgraph
,
vg::VG
,
xg::XG
min_pair_fragment_length() :
vg::Mapper
min_pos() :
vg::MinimumDistanceIndex
min_support_in_path() :
vg::NestedTraversalFinder
,
vg::RepresentativeTraversalFinder
MinDistanceClusterer() :
vg::MinDistanceClusterer
MinimizerMapper() :
vg::MinimizerMapper
MinimumDistanceIndex() :
vg::MinimumDistanceIndex
mismatches() :
vg::GaplessExtension
move() :
vg::SmallBitset
MSAConverter() :
vg::MSAConverter
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
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
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