vg
tools for working with variation graphs
- c -
CachedPackedTraversalSupportFinder() :
vg::CachedPackedTraversalSupportFinder
CacheEntry() :
vg::IndexedVG::CacheEntry
CactusSnarlFinder() :
vg::CactusSnarlFinder
calculate_and_save_alignment() :
vg::DozeuInterface
calculate_consistency() :
vg::ConsistencyCalculator
,
vg::SimpleConsistencyCalculator
calculate_I() :
haplo::haplo_DP_rectangle
calculate_log_likelihood() :
vg::GenotypeLikelihoodCalculator
calculate_log_prior() :
vg::FixedGenotypePriorCalculator
,
vg::GenotypePriorCalculator
calculate_max_index() :
vg::MinimumDistanceIndex
calculate_max_position() :
vg::DozeuInterface
calculate_min_index() :
vg::MinimumDistanceIndex
calculate_seed_position() :
vg::DozeuInterface
calculate_supports() :
vg::SimpleTraversalSupportCalculator
,
vg::TraversalSupportCalculator
calibrate_mismapping_detection() :
vg::MultipathMapper
call_snarl() :
vg::FlowCaller
,
vg::GraphCaller
,
vg::LegacyCaller
,
vg::MCMCCaller
,
vg::VCFGenotyper
call_svs() :
vg::SRPE
call_svs_paired_end() :
vg::SRPE
call_svs_split_read() :
vg::SRPE
call_top_level_chains() :
vg::GraphCaller
call_top_level_snarls() :
vg::GraphCaller
,
vg::MCMCCaller
can_get() :
vg::IndexManager
can_get_distance() :
vg::IndexManager
can_get_gbwt() :
vg::IndexManager
can_get_gbwtgraph() :
vg::IndexManager
can_get_graph() :
vg::IndexManager
can_get_minimizer() :
vg::IndexManager
can_get_snarls() :
vg::IndexManager
candidate_splice_sites() :
vg::SpliceRegion
canonicalize_edge() :
bdsg::ODGI
chain() :
vg::Range< Number >
chain_distance() :
vg::MinimumDistanceIndex::ChainIndex
chain_length() :
vg::MinimumDistanceIndex::ChainIndex
chain_of() :
vg::SnarlManager
chain_orientation_of() :
vg::SnarlManager
chain_rank_of() :
vg::SnarlManager
chain_to_json() :
vg::MinimumDistanceIndex::ChainIndex
ChainIndex() :
vg::MinimumDistanceIndex::ChainIndex
chains_of() :
vg::SnarlManager
check_alignment() :
vg::Mapper
check_in() :
vg::Watchdog
check_max_nodes() :
vg::Deconstructor
check_max_trav_cutoff() :
vg::VCFTraversalFinder
check_out() :
vg::Watchdog
check_protobuf_tag() :
vg::io::Registry
children_of() :
vg::SnarlManager
choose_traversals() :
vg::Deconstructor
circularize() :
vg::VG
clear() :
bdsg::HashGraph
,
bdsg::ODGI
,
bdsg::PackedGraph
,
handlegraph::DeletableHandleGraph
,
vg::Annotation< T, Enabled >
,
vg::AugmentedGraph
,
vg::Packer
,
vg::Paths
,
vg::SmallBitset
,
vg::SupportAugmentedGraph
,
vg::VG
clear_annotation() :
vg::multipath_alignment_t
clear_connection() :
vg::subpath_t
clear_edge_indexes() :
vg::VG
clear_edge_indexes_no_resize() :
vg::VG
clear_indexes() :
vg::VG
clear_indexes_no_resize() :
vg::VG
clear_mapping() :
vg::path_t
clear_mapping_ranks() :
vg::Paths
clear_next() :
vg::subpath_t
clear_node_indexes() :
vg::VG
clear_node_indexes_no_resize() :
vg::VG
clear_paths() :
bdsg::ODGI
,
vg::VG
clear_reachability_edges() :
vg::MultipathAlignmentGraph
clear_scores() :
vg::AlignmentChainModel
,
vg::MEMChainModel
clear_start() :
vg::multipath_alignment_t
clear_subpath() :
vg::multipath_alignment_t
close() :
vg::Index
,
vg::Viz
close_edit_tmpfiles() :
vg::Packer
cluster_chain_level() :
vg::SnarlSeedClusterer
cluster_multiplicity() :
vg::MultipathMapper
cluster_one_chain() :
vg::SnarlSeedClusterer
cluster_one_node() :
vg::SnarlSeedClusterer
cluster_one_snarl() :
vg::SnarlSeedClusterer
cluster_only_top_level_chain_seeds() :
vg::SnarlSeedClusterer
cluster_seeds() :
vg::SnarlSeedClusterer
cluster_seeds_internal() :
vg::SnarlSeedClusterer
cluster_simple_snarl() :
vg::SnarlSeedClusterer
cluster_snarl_level() :
vg::SnarlSeedClusterer
clusters() :
vg::MEMClusterer
,
vg::MEMClusterer::HitGraph
clusters_to_drop() :
vg::Mapper
collapse_order_length_runs() :
vg::MultipathAlignmentGraph
collect_coverage() :
vg::Packer
collect_subgraph() :
vg::VG
Colors() :
vg::Colors
combine() :
vg::VG
combine_handles() :
bdsg::ODGI
combine_qualities() :
vg::Packer
common_ancestor_next() :
vg::VG
common_ancestor_prev() :
vg::VG
common_bin() :
vg::StreamIndexBase
common_prefix_length() :
vg::BitString
compact() :
vg::Index
compact_ids() :
bdsg::PackedGraph
,
vg::VG
compact_ordered() :
vg::Transcriptome
compact_ranks() :
vg::Paths
compare_kmers() :
vg::Index
complement_components() :
vg::PhaseUnfolder
complement_encoded_nucleotide() :
bdsg::PackedGraph
CompletedTranscriptPath() :
vg::CompletedTranscriptPath
component_topological_order() :
vg::MEMClusterer::HitGraph
ComponentMinDistanceClusterer() :
vg::ComponentMinDistanceClusterer
compute_borders_and_dimensions() :
vg::Viz
compute_chains() :
vg::SnarlManager
compute_cluster_mapping_quality() :
vg::Mapper
compute_group_mapping_quality() :
vg::GSSWAligner
compute_mapping_qualities() :
vg::Mapper
compute_mapping_quality() :
vg::GSSWAligner
compute_mapq_caps() :
vg::MinimizerMapper
compute_paired_mapping_quality() :
vg::GSSWAligner
compute_path_interval() :
vg::Surjector
compute_quality() :
vg::Packer
compute_raw_mapping_quality_from_scores() :
vg::MultipathMapper
compute_tail_mem_coverage() :
vg::OrientedDistanceClusterer
compute_uniqueness() :
vg::Mapper
concat_mappings_for_node_pair() :
vg::VG
condense_edits() :
vg::Constructor
ConfigurableParser() :
vg::ConfigurableParser
connect_node_to_nodes() :
vg::VG
connect_nodes_to_node() :
vg::VG
connect_to_position_file() :
vg::NGSSimulator
connected_components() :
vg::MEMClusterer::HitGraph
,
vg::Surjector
connection() :
vg::subpath_t
connection_size() :
vg::subpath_t
connection_t() :
vg::connection_t
construct() :
vg::FlowSort::WeightedGraph
construct_chunk() :
vg::Constructor
construct_completed_transcript_paths() :
vg::Transcriptome
construct_edited_transcript_paths() :
vg::Transcriptome
construct_edited_transcript_paths_callback() :
vg::Transcriptome
construct_graph() :
vg::Constructor
contains() :
vg::GaplessExtension
,
vg::SmallBitset
convert() :
vg::VcfRecordConverter
convert_alignment() :
vg::HTSAlignmentEmitter
,
vg::SplicedHTSAlignmentEmitter
convert_multipath_alignment() :
vg::MultipathAlignmentEmitter
convert_paired() :
vg::HTSAlignmentEmitter
convert_unpaired() :
vg::HTSAlignmentEmitter
copy() :
vg::SmallBitset
count() :
vg::SmallBitset
count_haplotypes() :
vg::GenomeState
count_Ns() :
vg::MaximalExactMatch
Counts() :
vg::ReadFilter::Counts
coverage_at_position() :
vg::Packer
coverage_bin_offset() :
vg::Packer
coverage_bin_size() :
vg::Packer
coverage_filter() :
vg::Filter
coverage_size() :
vg::Packer
covered_intervals() :
vg::MultipathMapper
create_edge() :
bdsg::HashGraph
,
bdsg::ODGI
,
bdsg::PackedGraph
,
handlegraph::MutableHandleGraph
,
vg::VG
create_gssw_graph() :
vg::GSSWAligner
create_handle() :
bdsg::HashGraph
,
bdsg::ODGI
,
bdsg::PackedGraph
,
handlegraph::MutableHandleGraph
,
vg::VG
create_hidden_handle() :
bdsg::ODGI
create_identity_projection_trans() :
vg::MultipathAlignmentGraph
create_injection_trans() :
vg::MultipathAlignmentGraph
create_item() :
vg::Funnel
create_match_nodes() :
vg::MultipathAlignmentGraph
create_node() :
vg::VG
create_path() :
vg::Paths
,
vg::VG
create_path_chunk_nodes() :
vg::MultipathAlignmentGraph
create_path_handle() :
bdsg::HashGraph
,
bdsg::ODGI
,
bdsg::PackedGraph
,
handlegraph::MutablePathHandleGraph
,
vg::VG
create_progress() :
vg::Progressive
create_projector() :
vg::MultipathAlignmentGraph
create_state() :
vg::PhaseUnfolder
create_step() :
bdsg::ODGI
create_variant_index() :
vg::VCFTraversalFinder
cross_alignment() :
vg::Index
curr_sample_size() :
vg::FragmentLengthDistribution
current_empty_prefix() :
vg::BandedGlobalAligner< IntType >::AltTracebackStack
current_sum() :
haplo::haplo_DP_column
current_traceback_score() :
vg::BandedGlobalAligner< IntType >::AltTracebackStack
cut_nonref_tips() :
vg::Homogenizer
cut_tips() :
vg::Homogenizer
cycles_in_cactus() :
vg::IntegratedSnarlFinder::MergedAdjacencyGraph
Generated by
1.8.18