vg
tools for working with variation graphs
- s -
same_context() :
vg::VG
sample_path() :
vg::NGSSimulator
sample_read() :
vg::NGSSimulator
,
vg::ReadFilter
sample_read_internal() :
vg::NGSSimulator
sample_read_pair() :
vg::NGSSimulator
sample_read_quality() :
vg::NGSSimulator
sample_read_quality_internal() :
vg::NGSSimulator
sample_read_quality_pair() :
vg::NGSSimulator
sample_start_graph_pos() :
vg::NGSSimulator
sample_start_path_pos() :
vg::NGSSimulator
sample_start_pos() :
vg::NGSSimulator
sample_transition() :
vg::NGSSimulator::MarkovDistribution< From, To >
Sampler() :
vg::Sampler
save() :
vg::io::VPKG
,
vg::StreamIndexBase
save_bed() :
vg::FeatureSet
save_frag_lens_to_alns() :
vg::FragmentLengthStatistics
save_records() :
vg::HTSAlignmentEmitter
save_to_file() :
vg::Packer
scan() :
vg::DozeuInterface
,
vg::IDScanner< Message >
,
vg::PositionIDScanner< Message >
,
vg::QualAdjXdropAligner
,
vg::WrappingPositionScanner< Message >
,
vg::XdropAligner
scan_backward() :
vg::StreamIndexBase
scan_contig_lengths() :
vg::VCFGenotyper
scan_for_deletion() :
vg::VCFTraversalFinder
scan_path() :
handlegraph::PathHandleGraph
scan_seed_position() :
vg::DozeuInterface
scc_copy_of_handle() :
vg::DagifiedGraph
scc_copy_of_node_id() :
vg::DagifiedGraph
score() :
haplo::GBWTScoreProvider< GBWTType >
,
haplo::haplo_DP
,
haplo::linear_haplo_structure
,
haplo::LinearScoreProvider
,
haplo::ScoreProvider
,
vg::AlignmentChainModel
,
vg::BenchmarkResult
,
vg::connection_t
,
vg::Funnel
,
vg::MEMChainModel
,
vg::SpliceMotifs
,
vg::subpath_t
score_alignment() :
vg::Mapper
score_cluster() :
vg::MinimizerMapper
score_contiguous_alignment() :
vg::GSSWAligner
score_discontiguous_alignment() :
vg::GSSWAligner
score_error() :
vg::BenchmarkResult
score_exact_match() :
vg::Aligner
,
vg::GSSWAligner
,
vg::QualAdjAligner
score_extension_group() :
vg::MinimizerMapper
score_extensions() :
vg::MinimizerMapper
score_gap() :
vg::GSSWAligner
score_mismatch() :
vg::Aligner
,
vg::GSSWAligner
,
vg::QualAdjAligner
score_partial_alignment() :
vg::Aligner
,
vg::GSSWAligner
,
vg::QualAdjAligner
score_sort_and_deduplicate_alignments() :
vg::Mapper
score_to_unnormalized_likelihood_ln() :
vg::GSSWAligner
search_left() :
vg::NestedTraversalFinder
search_right() :
vg::NestedTraversalFinder
seeds_in_subgraph() :
vg::MinimizerMapper
Seek() :
vg::io::BlockedGzipInputStream
seek_group() :
vg::io::MessageIterator
,
vg::io::ProtobufIterator< T >
sequence() :
vg::edit_t
,
vg::MaximalExactMatch
,
vg::multipath_alignment_t
,
vg::Sampler
sequence_positions() :
vg::BaseMapper
serialize() :
bdsg::HashGraph::node_t
,
bdsg::HashGraph::path_t
,
handlegraph::SerializableHandleGraph
,
vg::MinimumDistanceIndex::ChainIndex
,
vg::MinimumDistanceIndex
,
vg::MinimumDistanceIndex::SnarlIndex
,
vg::Packer
,
vg::SnarlManager
,
vg::VG
,
xg::XGPath
serialize_and_measure() :
bdsg::ODGI
,
xg::XG
serialize_members() :
bdsg::HashGraph
,
bdsg::ODGI
,
bdsg::PackedGraph
,
handlegraph::SerializableHandleGraph
,
xg::XG
serialize_members_and_measure() :
xg::XG
serialize_to_emitter() :
vg::VG
serialize_to_file() :
vg::VG
serialize_to_function() :
vg::VG
serialize_to_ostream() :
vg::VG
set_alignment_scores() :
vg::AlignerClient
,
vg::BaseMapper
,
vg::MultipathMapper
set_allele() :
vg::PhasedGenome
set_annotation() :
vg::multipath_alignment_t
set_automatic_min_clustering_length() :
vg::MultipathMapper
set_avg() :
vg::Filter
set_baseline_error() :
vg::PoissonSupportSnarlCaller
set_cache_size() :
vg::BaseMapper
set_circularity() :
bdsg::HashGraph
,
bdsg::ODGI
,
bdsg::PackedGraph
,
handlegraph::MutablePathHandleGraph
,
vg::VG
set_connection() :
vg::subpath_t
set_depth() :
vg::DepthMap
set_distance_override() :
vg::IndexManager
set_edge() :
vg::VG
set_edge_target() :
bdsg::PackedGraph
set_fasta_filename() :
vg::IndexManager
set_filter_matches() :
vg::Filter
set_fragment_length_distr_params() :
vg::PairedEndMapper
set_from_length() :
vg::edit_t
set_gbwt_override() :
vg::IndexManager
set_gbwtgraph_override() :
vg::IndexManager
set_graph_override() :
vg::IndexManager
set_handle_of_step() :
bdsg::ODGI
set_handle_sequence() :
bdsg::ODGI
set_hash_color() :
vg::Viz
set_het_bias() :
vg::RatioSupportSnarlCaller
set_id() :
bdsg::HashGraph
set_id_increment() :
bdsg::HashGraph
,
bdsg::ODGI
,
bdsg::PackedGraph
,
handlegraph::MutableHandleGraph
,
vg::VG
set_inverse() :
vg::Filter
set_is_reverse() :
vg::mapping_t
,
vg::position_t
set_mapping_quality() :
vg::multipath_alignment_t
set_membership_path() :
bdsg::PackedGraph
set_membership_step() :
bdsg::PackedGraph
set_min_depth() :
vg::Filter
set_min_percent_identity() :
vg::Filter
set_min_qual() :
vg::Filter
set_min_supports() :
vg::SupportBasedSnarlCaller
set_minimizer_override() :
vg::IndexManager
set_my_path_position_graph() :
vg::Filter
set_my_vg() :
vg::Filter
set_next() :
vg::connection_t
,
vg::subpath_t
set_next_membership() :
bdsg::PackedGraph
set_node_id() :
vg::mapping_t
,
vg::position_t
set_offset() :
haplo::haplo_DP_rectangle
,
vg::position_t
set_paired_all() :
vg::ReadFilter::Counts
set_paired_any() :
vg::ReadFilter::Counts
set_path_position() :
vg::Surjector
set_path_position_inexact() :
vg::Surjector
set_prev_idx() :
haplo::haplo_DP_rectangle
set_quality() :
vg::multipath_alignment_t
set_read_group() :
vg::MultipathAlignmentEmitter
set_region() :
vg::VcfBuffer
,
vg::WindowedVcfBuffer
set_remove_failing_edits() :
vg::Filter
set_sample_name() :
vg::MultipathAlignmentEmitter
set_score() :
vg::connection_t
,
vg::subpath_t
set_sequence() :
vg::edit_t
,
vg::multipath_alignment_t
set_snarls_override() :
vg::IndexManager
set_soft_clip_limit() :
vg::Filter
set_source_paths() :
vg::Sampler
set_split_read_limit() :
vg::Filter
set_start() :
vg::multipath_alignment_t
set_step() :
bdsg::ODGI
set_step_next() :
bdsg::PackedGraph
set_step_prev() :
bdsg::PackedGraph
set_step_trav() :
bdsg::PackedGraph
set_support_switch_threshold() :
vg::TraversalSupportFinder
set_to_length() :
vg::edit_t
set_vcf_filename() :
vg::IndexManager
set_window_length() :
vg::Filter
setK() :
vg::FlowTraversalFinder
shallow_contents() :
vg::SnarlManager
share_terminal_positions() :
vg::MultipathMapper
shortest_seq_paths() :
vg::BandedGlobalAligner< IntType >
show_structure() :
vg::Packer
ShuffledPairs() :
vg::ShuffledPairs
sides_context() :
vg::VG
sides_from() :
vg::VG
sides_of() :
vg::VG
sides_to() :
vg::VG
simplify() :
vg::RareVariantSimplifier
,
vg::SmallSnarlSimplifier
simplify_once() :
vg::SmallSnarlSimplifier
size() :
haplo::gbwt_thread_t
,
haplo::int_itvl_t
,
haplo::linear_haplo_structure::SNVvector
,
vg::DozeuInterface::OrderedGraph
,
vg::Option< vector< Item >, Parser >
,
vg::Paths
,
vg::SmallBitset
,
vg::SnarlState
,
vg::SpliceMotifs
,
vg::Transcriptome
,
vg::VG
Skip() :
vg::io::BlockedGzipInputStream
small() :
vg::SmallBitset
SmallBitset() :
vg::SmallBitset
SmallSnarlSimplifier() :
vg::SmallSnarlSimplifier
smart_align() :
vg::VariantAdder
SmellsLikeGzip() :
vg::io::BlockedGzipInputStream
sn_deletion_between_ref() :
haplo::linear_haplo_structure
snarl_boundary_index() :
vg::SnarlManager
snarl_distance() :
vg::MinimumDistanceIndex::SnarlIndex
snarl_end_index() :
vg::SnarlManager
snarl_length() :
vg::MinimumDistanceIndex::SnarlIndex
snarl_sharing_end() :
vg::SnarlManager
snarl_sharing_start() :
vg::SnarlManager
snarl_start_index() :
vg::SnarlManager
snarl_to_json() :
vg::MinimumDistanceIndex::SnarlIndex
SnarlIndex() :
vg::MinimumDistanceIndex::SnarlIndex
SnarlManager() :
vg::SnarlManager
SnarlMinDistance() :
vg::SnarlMinDistance
SnarlOrientedDistanceMeasurer() :
vg::SnarlOrientedDistanceMeasurer
SnarlSeedClusterer() :
vg::SnarlSeedClusterer
SnarlState() :
vg::SnarlState
sniff_magic() :
vg::io::VPKG
sniff_tag() :
vg::io::MessageIterator
SNVs() :
haplo::linear_haplo_structure
soft_clip_filter() :
vg::Filter
sort() :
vg::StreamSorter< Message >
,
vg::VG
sort_and_compute_mapping_quality() :
vg::MultipathMapper
sort_by_mapping_rank() :
vg::Paths
SourceSinkOverlay() :
vg::SourceSinkOverlay
splice_graph() :
vg::Transcriptome
splice_graph_node_updated() :
vg::Transcriptome
spliced_cigar_against_path() :
vg::SplicedHTSAlignmentEmitter
spliced_surject() :
vg::Surjector
SplicedHTSAlignmentEmitter() :
vg::SplicedHTSAlignmentEmitter
SpliceMotifs() :
vg::SpliceMotifs
SpliceRegion() :
vg::SpliceRegion
split() :
vg::BitString
split_multicomponent_alignments() :
vg::MultipathMapper
split_read_filter() :
vg::Filter
ssw_to_vg() :
vg::SSWAligner
SSWAligner() :
vg::SSWAligner
stack_up_valid_walks() :
vg::ExhaustiveTraversalFinder
stage() :
vg::Funnel
stage_stop() :
vg::Funnel
standard_extend() :
haplo::haplo_DP_column
start() :
vg::Funnel
,
vg::multipath_alignment_t
start_degree() :
vg::VG
start_size() :
vg::multipath_alignment_t
start_vcf() :
vg::Genotyper
StartFile() :
vg::io::BlockedGzipOutputStream
starting_position() :
vg::GaplessExtension
std_dev() :
vg::FragmentLengthDistribution
stddev() :
vg::normal_distribution< T >
step_in_path() :
vg::VCFTraversalFinder
step_rank_at_position() :
xg::XGPath
steps_of_handle() :
bdsg::ODGI
,
handlegraph::PathHandleGraph
,
vg::MemoizingGraph
stop() :
vg::Funnel
store_batch() :
vg::Index
store_in_index() :
vg::VGset
store_path() :
vg::Index
store_paths() :
vg::Index
store_paths_in_index() :
vg::VGset
stored_kmer_sizes() :
vg::Index
StrandSplitGraph() :
vg::StrandSplitGraph
stream_sort() :
vg::StreamSorter< Message >
StreamIndex() :
vg::StreamIndex< Message >
StreamIndexBase() :
vg::StreamIndexBase
streaming_merge() :
vg::StreamSorter< Message >
StreamMultiplexer() :
vg::io::StreamMultiplexer
StreamSorter() :
vg::StreamSorter< Message >
strip_full_length_bonuses() :
vg::MultipathMapper
strongly_connected_components() :
vg::VG
Subcommand() :
vg::subcommand::Subcommand
subgraph_in_range() :
vg::MinimumDistanceIndex
SubgraphOverlay() :
vg::SubgraphOverlay
SubHandleGraph() :
vg::SubHandleGraph
subpath() :
vg::multipath_alignment_t
subpath_size() :
vg::multipath_alignment_t
subpath_t() :
vg::subpath_t
substage() :
vg::Funnel
substage_stop() :
vg::Funnel
support_val() :
vg::SupportBasedSnarlCaller
,
vg::TraversalSupportFinder
SupportBasedSnarlCaller() :
vg::SupportBasedSnarlCaller
SupportRestrictedTraversalFinder() :
vg::SupportRestrictedTraversalFinder
surject() :
vg::Surjector
Surjector() :
vg::Surjector
swap() :
vg::SnarlState
swap_alleles() :
vg::PhasedGenome
swap_endianness() :
vg::endianness< IntType >
swap_handles() :
bdsg::ODGI
,
vg::VG
swap_haplotypes() :
vg::GenomeState
swap_label() :
vg::PhasedGenome
swap_node_id() :
vg::VG
swap_node_ids() :
vg::Paths
swap_nodes() :
vg::VG
sync_offsets() :
xg::XGPath
sync_paths() :
vg::VG
synthesize_tail_anchors() :
vg::MultipathAlignmentGraph
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