Namespaces
	algorithms

	io

	subcommand

	temp_file

Classes
class	AbstractReadSampler

class	AliasGraph

class	Aligner

class	AlignerClient

struct	Alignment

struct	alignment_index_t

class	AlignmentChainModel

class	AlignmentChainModelVertex

struct	AlignmentValidity

struct	Annotation

struct	AppendHaplotypeCommand

struct	AugmentedGraph

class	BackTranslatingAlignmentEmitter

class	BandedGlobalAligner

class	BaseAligner

class	BaseMapper

class	BaseOption

struct	BasePileup

struct	BBEdgeHash

struct	BenchmarkResult

class	BitString

class	BitStringTree

struct	BREAKPOINT

class	CachedPackedTraversalSupportFinder

struct	CactusSide

class	CactusSnarlFinder

struct	ChainIterator

class	Colors

struct	CompletedTranscriptPath

class	ComponentMinDistanceClusterer

class	Configurable

class	ConfigurableParser

struct	Connection
	An edge in a MultipathAlignment between Subpaths that may not be contiguous in the graph. More...

class	connection_t

class	ConsistencyCalculator

struct	ConstructedChunk

class	Constructor

class	ContractingGraph

class	count_back_inserter

struct	Counts

class	DagifiedGraph

class	Deconstructor

struct	DeleteHaplotypeCommand

class	DeletionAligner

class	DiagramExplainer

class	DinucleotideMachine

class	discrete_distribution
	We provide a partial discrete_distribution implementation that is just the parts we need. More...

class	DistanceHeuristic

class	DotDumpExplainer

class	DozeuInterface

class	DozeuPinningOverlay

struct	Edge

struct	EdgePileup
	Keep pileup-like record for reads that span edges. More...

struct	Edit

class	edit_t

struct	EditedTranscriptPath

struct	endianness

class	ExhaustiveTraversalFinder

struct	Exon

class	Explainer

class	ExtraNodeGraph

class	FeatureSet

class	Filter

class	FixedGenotypePriorCalculator

class	FlatFileBackTranslation

class	FlowCaller

class	FlowSort

class	FlowTraversalFinder

class	FragmentLengthDistribution

class	FragmentLengthStatistics

class	Funnel

class	GAFOutputCaller

class	GaplessExtender

struct	GaplessExtension

struct	GBWTHandler

class	GBWTTraversalFinder

class	GBZGraph

class	GenomeState

struct	GenomeStateCommand

struct	Genotype
	Describes a genotype at a particular locus. More...

class	GenotypeLikelihoodCalculator

class	GenotypePriorCalculator

class	Genotyper

class	GFAHandleGraph
	Use to load in GFAs and remember where they came from. More...

class	GFFReader

struct	GFFRecord

struct	Graph

class	GraphCaller

class	GraphSynchronizer

class	GreedyMinDistanceClusterer

class	GSSWAligner

class	HandleGraphNodeSet

class	HandleGraphSnarlFinder

class	HaplotypeIndexer

class	HaplotypePartitioner

class	Haplotypes

class	hash_map

class	hash_map< K *, V >

class	hash_set

class	hash_set< K * >

class	HTSAlignmentEmitter

class	HTSWriter

class	IdentityOverlay

struct	IDScanner

class	IncrementalSubgraph

struct	IncrementIter

class	IndexedVG

class	IndexFile

struct	IndexingParameters

class	IndexingPlan

struct	IndexRecipe

class	IndexRegistry

struct	InsertHaplotypeCommand

class	InsufficientInputException

class	IntegratedSnarlFinder

struct	is_instantiation_of

struct	is_instantiation_of< Predicate< PredicateArgs... >, Predicate >

class	JobSchedule

class	JoinedSpliceGraph

struct	kff_recoding_t
	A mapping of character values from KFF encoding to minimizer index encoding. More...

struct	kmer_t

struct	KmerMatch
	Used to serialize kmer matches. More...

struct	KmerPosition

class	LazyRNG

class	LegacyCaller

struct	LocationSupport
	Support pinned to a location, which can be either a node or an edge. More...

struct	Locus
	Describes a genetic locus with multiple possible alleles, a genotype, and observational support. More...

class	Mapper

struct	Mapping

class	mapping_t

struct	MappingHash

struct	MatchPos

class	MaximalExactMatch

class	MCMCCaller

class	MCMCGenotyper

class	MEMAccelerator

class	MEMChainModel

class	MEMChainModelVertex

class	MEMClusterer

class	MemoizingGraph

class	MinDistanceClusterer

class	MinimizerMapper

struct	MIPayload

struct	MIPayloadValues

class	MSAConverter

class	multipath_alignment_t

struct	MultipathAlignment

class	MultipathAlignmentEmitter

class	MultipathAlignmentGraph

class	MultipathMapper

struct	MultipathProblem

class	NameMapper

class	NestedCachedPackedTraversalSupportFinder

class	NestedFlowCaller

class	NestedTraversalFinder

class	NetGraph

class	NGSSimulator

class	NoAlignmentInBandException

struct	Node
	Nodes store sequence data. More...

struct	NodePileup

class	NodeSide

class	NodeTraversal

class	normal_distribution

class	NullClusterer

class	NullMaskingGraph

class	Option

class	Option< vector< Item >, Parser >

class	OptionInterface

class	OptionValueParser

class	OptionValueParser< vector< Item > >

class	OrientedDistanceClusterer

class	OrientedDistanceMeasurer

class	PackedTraversalSupportFinder

class	Packer

class	Packers

class	pair_hash_map

class	pair_hash_set

class	PairedEndMapper

class	ParallelKFFReader

struct	ParentGenotypeInfo

struct	Path

class	path_mapping_t

class	path_t

class	PathBasedTraversalFinder

struct	PathBranch

class	PathChunker

class	PathComponentIndex

struct	PathIndex

class	PathNode

class	PathOrientedDistanceMeasurer

class	PathRestrictedTraversalFinder

class	Paths

class	PathSubgraph

class	PathSubgraphOverlay

class	PathTraversalFinder

class	PhasedGenome

class	PhaseUnfolder

class	Pictographs

struct	Pileup
	Bundle up Node and Edge pileups. More...

class	PoissonSupportSnarlCaller

struct	Position

class	position_t

struct	PositionIDScanner

class	ProblemDumpExplainer

class	Progressive

class	QualAdjAligner

class	QualAdjXdropAligner

struct	Range

class	RareVariantSimplifier

class	RatioSupportSnarlCaller

struct	read_alignment_index_t
	Type to point to an alignment of a known read. More...

class	ReadFilter

class	ReadMasker

class	ReadRestrictedTraversalFinder

struct	RebuildJob

struct	RebuildParameters
	Parameters for `rebuild_gbwt`. More...

class	Recombinator

struct	RecombinatorHaplotype

struct	Region

class	RegionExpander

struct	ReplaceLocalHaplotypeCommand

struct	ReplaceSnarlHaplotypeCommand

class	RepresentativeTraversalFinder

class	ReverseGraph

class	RewindPlanException

class	Sampler

struct	SeqComplexity

class	ShuffledPairs

class	SimpleConsistencyCalculator

class	SimpleTraversalSupportCalculator

class	SizeLimitExceededException

class	SmallBitset

class	SmallSnarlSimplifier

struct	Snarl
	Describes a subgraph that is connected to the rest of the graph by two nodes. More...

class	SnarlCaller

class	SnarlDistanceIndexClusterer

class	SnarlFinder

class	SnarlGraph

class	SnarlManager

class	SnarlMinDistance

class	SnarlOrientedDistanceMeasurer

class	SnarlState

struct	SnarlTraversal

class	SourceSinkOverlay

class	SparseUnionFind

class	SplicedHTSAlignmentEmitter

class	SpliceRegion

class	SpliceStats

class	SSWAligner

struct	state_hash

class	StrandSplitGraph

class	StreamIndex

class	StreamIndexBase

class	StreamSorter

class	string_hash_map

class	string_hash_set

class	SubgraphOverlay

class	SubHandleGraph

struct	Subpath
	A non-branching path of a MultipathAlignment. More...

class	subpath_t

class	SubpathOverlay

struct	SummaryStatistics

struct	Support
	Aggregates information about the reads supporting an allele. More...

struct	SupportAugmentedGraph
	Augmented Graph that holds some Support annotation data specific to vg call. More...

class	SupportBasedSnarlCaller

class	SupportRestrictedTraversalFinder

class	SurjectingAlignmentEmitter

class	Surjector

struct	SwapHaplotypesCommand

class	TargetValueSearch

class	TipAnchoredMaxDistance

struct	Transcript

class	Transcriptome

struct	TranscriptPath

struct	Translation

class	Translator

class	TraversalFinder

class	TraversalSupportCalculator

class	TraversalSupportFinder

struct	Tree

struct	TreeNode

class	TreeSubgraph

class	TrivialTraversalFinder

class	truncated_normal_distribution

class	TVSClusterer

class	uniform_int_distribution

class	uniform_real_distribution

class	VariantAdder

class	VcfBuffer

class	VCFGenotyper

class	VCFOutputCaller

class	VcfRecordConverter

class	VcfRecordFilter

class	VCFTraversalFinder

struct	VectorView

class	VectorViewInverse

class	Version
	Class for holding vg version and build environment information. More...

class	VG

struct	VGIndexes

class	VGset

struct	Visit
	Describes a step of a walk through a Snarl either on a node or through a child Snarl. More...

class	Viz

struct	wang_hash

struct	wang_hash< handle_t >

struct	wang_hash< handlegraph::net_handle_t >

struct	wang_hash< NodeSide >

struct	wang_hash< NodeTraversal >
	hash function for NodeTraversals More...

struct	wang_hash< path_handle_t >

struct	wang_hash< std::pair< A, B > >

struct	wang_hash< T * >

struct	wang_hash< T, typename std::enable_if< std::is_integral< T >::value >::type >

class	Watchdog

struct	WFAAlignment

class	WFAExtender

struct	WFANode

struct	WFAPoint

class	WFATree

class	WideningPRNG

class	WindowedVcfBuffer

struct	WrappingPositionScanner

class	XdropAligner

Typedefs
using	benchtime = chrono::nanoseconds
	We define a duration type for expressing benchmark times in. More...

typedef unordered_set< handle_t >	HandleSet

typedef unordered_map< handle_t, int >	Handle2Component

typedef std::map< id_t, std::vector< Edge * > >	EdgeMapping

using	handle_t = handlegraph::handle_t

using	nid_t = handlegraph::nid_t

using	offset_t = handlegraph::offset_t

using	subrange_t = handlegraph::subrange_t

using	path_handle_t = handlegraph::path_handle_t

using	PathSense = handlegraph::PathSense

using	step_handle_t = handlegraph::step_handle_t

using	edge_t = handlegraph::edge_t

using	oriented_node_range_t = handlegraph::oriented_node_range_t

using	HandleGraph = handlegraph::HandleGraph

using	RankedHandleGraph = handlegraph::RankedHandleGraph

using	MutableHandleGraph = handlegraph::MutableHandleGraph

using	PathMetadata = handlegraph::PathMetadata

using	PathHandleGraph = handlegraph::PathHandleGraph

using	PathPositionHandleGraph = handlegraph::PathPositionHandleGraph

using	MutablePathHandleGraph = handlegraph::MutablePathHandleGraph

using	MutablePathMutableHandleGraph = handlegraph::MutablePathMutableHandleGraph

using	DeletableHandleGraph = handlegraph::DeletableHandleGraph

using	MutablePathDeletableHandleGraph = handlegraph::MutablePathDeletableHandleGraph

using	SerializableHandleGraph = handlegraph::SerializableHandleGraph

using	VectorizableHandleGraph = handlegraph::VectorizableHandleGraph

using	NamedNodeBackTranslation = handlegraph::NamedNodeBackTranslation

using	thread_t = vector< gbwt::node_type >

using	IndexName = string

using	IndexGroup = set< IndexName >

using	RecipeName = pair< IndexGroup, size_t >

using	RecipeFunc = function< vector< vector< string > >(const vector< const IndexFile * > &, const IndexingPlan *, AliasGraph &, const IndexGroup &)>

typedef std::pair< uint32_t, int32_t >	pareto_point

using	Chain = vector< pair< const Snarl *, bool > >

using	real_t = long double

using	GAMIndex = StreamIndex< Alignment >
	Define a GAM index as a stream index over a stream of Alignments. More...

using	GAMSorter = StreamSorter< Alignment >

typedef vector< gbwt::node_type >	exon_nodes_t

typedef vector< gbwt::size_type >	thread_ids_t

using	Traversal = vector< handle_t >

using	PathInterval = pair< step_handle_t, step_handle_t >

typedef handlegraph::nid_t	id_t

typedef std::tuple< id_t, bool, offset_t >	pos_t

Enumerations
enum	alignment_emitter_flags_t { ALIGNMENT_EMITTER_FLAG_NONE = 0, ALIGNMENT_EMITTER_FLAG_HTS_RAW = 1, ALIGNMENT_EMITTER_FLAG_HTS_SPLICED = 2, ALIGNMENT_EMITTER_FLAG_HTS_PRUNE_SUSPICIOUS_ANCHORS = 4, ALIGNMENT_EMITTER_FLAG_VG_USE_SEGMENT_NAMES = 8 }

enum	MappingQualityMethod { Approx, Exact, Adaptive, None }

enum	SnarlType { UNCLASSIFIED = 0, ULTRABUBBLE = 1, UNARY = 2 }
	Enumeration of the classifications of snarls. More...

Functions
int32_t	score_gap (size_t gap_length, int32_t gap_open, int32_t gap_extension)
	Score a gap with the given open and extension scores. More...

int	hts_for_each (string &filename, function< void(Alignment &)> lambda, const PathPositionHandleGraph *graph)

int	hts_for_each (string &filename, function< void(Alignment &)> lambda)

int	hts_for_each_parallel (string &filename, function< void(Alignment &)> lambda, const PathPositionHandleGraph *graph)

int	hts_for_each_parallel (string &filename, function< void(Alignment &)> lambda)

bam_hdr_t *	hts_file_header (string &filename, string &header)

bam_hdr_t *	hts_string_header (string &header, const map< string, int64_t > &path_length, const map< string, string > &rg_sample)

bam_hdr_t *	hts_string_header (string &header, const vector< pair< string, int64_t >> &path_order_and_length, const map< string, string > &rg_sample)

bool	get_next_alignment_from_fastq (gzFile fp, char *buffer, size_t len, Alignment &alignment)

bool	get_next_interleaved_alignment_pair_from_fastq (gzFile fp, char *buffer, size_t len, Alignment &mate1, Alignment &mate2)

bool	get_next_alignment_pair_from_fastqs (gzFile fp1, gzFile fp2, char *buffer, size_t len, Alignment &mate1, Alignment &mate2)

size_t	fastq_unpaired_for_each_parallel (const string &filename, function< void(Alignment &)> lambda, uint64_t batch_size)

size_t	fastq_paired_interleaved_for_each_parallel (const string &filename, function< void(Alignment &, Alignment &)> lambda, uint64_t batch_size)

size_t	fastq_paired_two_files_for_each_parallel (const string &file1, const string &file2, function< void(Alignment &, Alignment &)> lambda, uint64_t batch_size)

size_t	fastq_paired_interleaved_for_each_parallel_after_wait (const string &filename, function< void(Alignment &, Alignment &)> lambda, function< bool(void)> single_threaded_until_true, uint64_t batch_size)

size_t	fastq_paired_two_files_for_each_parallel_after_wait (const string &file1, const string &file2, function< void(Alignment &, Alignment &)> lambda, function< bool(void)> single_threaded_until_true, uint64_t batch_size)

size_t	fastq_unpaired_for_each (const string &filename, function< void(Alignment &)> lambda)

size_t	fastq_paired_interleaved_for_each (const string &filename, function< void(Alignment &, Alignment &)> lambda)

size_t	fastq_paired_two_files_for_each (const string &file1, const string &file2, function< void(Alignment &, Alignment &)> lambda)

void	parse_rg_sample_map (char *hts_header, map< string, string > &rg_sample)
	Populate a mapping from read group to sample name, given the text BAM header. More...

void	parse_tid_path_handle_map (const bam_hdr_t hts_header, const PathHandleGraph graph, map< int, path_handle_t > &tid_path_handle)

string	alignment_to_sam_internal (const Alignment &alignment, const string &refseq, const int32_t refpos, const bool refrev, const vector< pair< int, char >> &cigar, const string &mateseq, const int32_t matepos, bool materev, const int32_t tlen, bool paired, const int32_t tlen_max)

int32_t	determine_flag (const Alignment &alignment, const string &refseq, const int32_t refpos, const bool refrev, const string &mateseq, const int32_t matepos, bool materev, const int32_t tlen, bool paired, const int32_t tlen_max)
	Returns the SAM bit-coded flag for alignment with. More...

string	alignment_to_sam (const Alignment &alignment, const string &refseq, const int32_t refpos, const bool refrev, const vector< pair< int, char >> &cigar, const string &mateseq, const int32_t matepos, bool materev, const int32_t tlen, const int32_t tlen_max)

string	alignment_to_sam (const Alignment &alignment, const string &refseq, const int32_t refpos, const bool refrev, const vector< pair< int, char >> &cigar)

bam1_t *	alignment_to_bam_internal (bam_hdr_t *header, const Alignment &alignment, const string &refseq, const int32_t refpos, const bool refrev, const vector< pair< int, char >> &cigar, const string &mateseq, const int32_t matepos, bool materev, const int32_t tlen, bool paired, const int32_t tlen_max)

bam1_t *	alignment_to_bam (bam_hdr_t *bam_header, const Alignment &alignment, const string &refseq, const int32_t refpos, const bool refrev, const vector< pair< int, char >> &cigar, const string &mateseq, const int32_t matepos, bool materev, const int32_t tlen, const int32_t tlen_max)

bam1_t *	alignment_to_bam (bam_hdr_t *bam_header, const Alignment &alignment, const string &refseq, const int32_t refpos, const bool refrev, const vector< pair< int, char >> &cigar)

string	cigar_string (const vector< pair< int, char > > &cigar)

string	mapping_string (const string &source, const Mapping &mapping)

void	mapping_cigar (const Mapping &mapping, vector< pair< int, char >> &cigar)

int64_t	cigar_mapping (const bam1_t b, Mapping mapping)

void	mapping_against_path (Alignment &alignment, const bam1_t b, const path_handle_t &path, const PathPositionHandleGraph graph, bool on_reverse_strand)

vector< pair< int, char > >	cigar_against_path (const Alignment &alignment, bool on_reverse_strand, int64_t &pos, size_t path_len, size_t softclip_suppress)

void	simplify_cigar (vector< pair< int, char >> &cigar)

pair< int32_t, int32_t >	compute_template_lengths (const int64_t &pos1, const vector< pair< int, char >> &cigar1, const int64_t &pos2, const vector< pair< int, char >> &cigar2)

int32_t	sam_flag (const Alignment &alignment, bool on_reverse_strand, bool paired)

Alignment	bam_to_alignment (const bam1_t b, const map< string, string > &rg_sample, const map< int, path_handle_t > &tid_path_handle, const bam_hdr_t bh, const PathPositionHandleGraph *graph)

Alignment	bam_to_alignment (const bam1_t *b, const map< string, string > &rg_sample, const map< int, path_handle_t > &tid_path_handle)

int	alignment_to_length (const Alignment &a)

int	alignment_from_length (const Alignment &a)

Alignment	strip_from_start (const Alignment &aln, size_t drop)

Alignment	strip_from_end (const Alignment &aln, size_t drop)

Alignment	trim_alignment (const Alignment &aln, const Position &pos1, const Position &pos2)

vector< Alignment >	alignment_ends (const Alignment &aln, size_t len1, size_t len2)

Alignment	alignment_middle (const Alignment &aln, int len)

vector< Alignment >	reverse_complement_alignments (const vector< Alignment > &alns, const function< int64_t(int64_t)> &node_length)

Alignment	reverse_complement_alignment (const Alignment &aln, const function< int64_t(id_t)> &node_length)

void	reverse_complement_alignment_in_place (Alignment *aln, const function< int64_t(id_t)> &node_length)

Alignment	merge_alignments (const vector< Alignment > &alns)

Alignment &	extend_alignment (Alignment &a1, const Alignment &a2, bool debug)

Alignment	merge_alignments (const Alignment &a1, const Alignment &a2, bool debug)

void	translate_nodes (Alignment &a, const unordered_map< id_t, pair< id_t, bool > > &ids, const std::function< size_t(int64_t)> &node_length)

void	flip_nodes (Alignment &a, const set< int64_t > &ids, const std::function< size_t(int64_t)> &node_length)

int	non_match_start (const Alignment &alignment)

int	non_match_end (const Alignment &alignment)

int	softclip_start (const Alignment &alignment)

int	softclip_end (const Alignment &alignment)

int	softclip_trim (Alignment &alignment)

int	query_overlap (const Alignment &aln1, const Alignment &aln2)

int	edit_count (const Alignment &alignment)

size_t	to_length_after_pos (const Alignment &aln, const Position &pos)

size_t	from_length_after_pos (const Alignment &aln, const Position &pos)

size_t	to_length_before_pos (const Alignment &aln, const Position &pos)

size_t	from_length_before_pos (const Alignment &aln, const Position &pos)

const string	hash_alignment (const Alignment &aln)

Alignment	simplify (const Alignment &a, bool trim_internal_deletions)

void	normalize_alignment (Alignment &alignment)
	Merge adjacent edits of the same type and convert all N matches to mismatches. More...

bool	uses_Us (const Alignment &alignment)

void	convert_alignment_char (Alignment &alignment, char from, char to)

void	convert_Us_to_Ts (Alignment &alignment)
	Replaces any U's in the sequence or the Path with T's. More...

void	convert_Ts_to_Us (Alignment &alignment)
	Replaces any T's in the sequence or the Path with U's. More...

map< id_t, int >	alignment_quality_per_node (const Alignment &aln)

string	middle_signature (const Alignment &aln, int len)

pair< string, string >	middle_signature (const Alignment &aln1, const Alignment &aln2, int len)

string	signature (const Alignment &aln)

pair< string, string >	signature (const Alignment &aln1, const Alignment &aln2)

void	parse_bed_regions (istream &bedstream, const PathPositionHandleGraph graph, vector< Alignment > out_alignments)

void	parse_bed_regions (istream &bedstream, const PathPositionHandleGraph *graph, const std::function< void(Alignment &)> &callback)

void	parse_gff_regions (istream &gffstream, const PathPositionHandleGraph graph, vector< Alignment > out_alignments)

void	parse_gff_regions (istream &gffstream, const PathPositionHandleGraph *graph, const std::function< void(Alignment &)> &callback)

Position	alignment_start (const Alignment &aln)

Position	alignment_end (const Alignment &aln)

map< string,vector< pair< size_t, bool > > >	alignment_refpos_to_path_offsets (const Alignment &aln)
	return the path offsets as cached in the alignment More...

void	alignment_set_distance_to_correct (Alignment &aln, const Alignment &base, const unordered_map< string, string > *translation)

void	alignment_set_distance_to_correct (Alignment &aln, const map< string, vector< pair< size_t, bool > > > &base_offsets, const unordered_map< string, string > *translation)

AlignmentValidity	alignment_is_valid (const Alignment &aln, const HandleGraph *hgraph, bool check_sequence)

Alignment	target_alignment (const PathPositionHandleGraph *graph, const path_handle_t &path, size_t pos1, size_t pos2, const string &feature, bool is_reverse, Mapping &cigar_mapping)

Alignment	target_alignment (const PathPositionHandleGraph *graph, const path_handle_t &path, size_t pos1, size_t pos2, const string &feature, bool is_reverse)

int	fastq_for_each (string &filename, function< void(Alignment &)> lambda)

void	write_alignment_to_file (const Alignment &aln, const string &filename)

void	mapping_cigar (const Mapping &mapping, vector< pair< int, char > > &cigar)

void	cigar_mapping (const bam1_t *b, Mapping &mapping)

void	append_cigar_operation (const int length, const char operation, vector< pair< int, char >> &cigar)

void	alignment_set_distance_to_correct (Alignment &aln, const map< string, vector< pair< size_t, bool >>> &base_offsets, const unordered_map< string, string > *translation=nullptr)

template<typename Annotated >
bool	has_annotation (const Annotated &annotated, const string &name)
	Returns true if the Protobuf object has an annotation with this name. More...

template<typename AnnotationType , typename Annotated >
AnnotationType	get_annotation (const Annotated &annotated, const string &name)

template<typename AnnotationType , typename Annotated >
AnnotationType	get_annotation (Annotated *annotated, const string &name)

template<typename AnnotationType , typename Annotated >
void	set_annotation (Annotated *annotated, const string &name, const AnnotationType &annotation)

template<typename AnnotationType , typename Annotated >
void	set_annotation (Annotated &annotated, const string &name, const AnnotationType &annotation)

template<typename Annotated >
void	clear_annotation (Annotated *annotated, const string &name)
	Clear the annotation with the given name. More...

template<typename Annotated >
void	clear_annotation (Annotated &annotated, const string &name)
	Clear the annotation with the given name. More...

template<typename Annotated >
void	for_each_basic_annotation (const Annotated &annotated, const function< void(const string &)> null_lambda, const function< void(const string &, double)> double_lambda, const function< void(const string &, bool)> bool_lambda, const function< void(const string &, const string &)> string_lambda)

template<typename T >
T	value_cast (const google::protobuf::Value &value)
	Cast a Protobuf generic Value to any type. More...

template<typename T >
google::protobuf::Value	value_cast (const T &wrap)
	Cast any type to a generic Protobuf value. More...

template<>
bool	value_cast< bool > (const google::protobuf::Value &value)

template<>
double	value_cast< double > (const google::protobuf::Value &value)

template<>
string	value_cast< string > (const google::protobuf::Value &value)

template<>
google::protobuf::Value	value_cast< bool > (const bool &wrap)

template<>
google::protobuf::Value	value_cast< double > (const double &wrap)

template<>
google::protobuf::Value	value_cast< string > (const string &wrap)

template<>
google::protobuf::Value	value_cast< size_t > (const size_t &wrap)

template<>
google::protobuf::Value	value_cast< int > (const int &wrap)

template<typename Container >
Container	value_cast (const google::protobuf::Value &value)
	Cast a Protobuf generic Value to any type. More...

template<typename Container >
google::protobuf::Value	value_cast (const Container &wrap)

void	augment (MutablePathMutableHandleGraph graph, const string &gam_path, const string &aln_format, vector< Translation > out_translations, const string &gam_out_path, bool embed_paths, bool break_at_ends, bool remove_softclips, bool filter_out_of_graph_alignments, double min_baseq, double min_mapq, Packer *packer, size_t min_bp_coverage, double max_frac_n, bool edges_only)

void	augment (MutablePathMutableHandleGraph graph, vector< Path > &path_vector, const string &aln_format, vector< Translation > out_translations, const string &gam_out_path, bool embed_paths, bool break_at_ends, bool remove_softclips, bool filter_out_of_graph_alignments, double min_baseq, double min_mapq, Packer *packer, size_t min_bp_coverage, double max_frac_n, bool edges_only)

void	augment_impl (MutablePathMutableHandleGraph graph, function< void(function< void(Alignment &)>, bool, bool)> iterate_gam, const string &aln_format, vector< Translation > out_translation, const string &gam_out_path, bool embed_paths, bool break_at_ends, bool remove_soft_clips, bool filter_out_of_graph_alignments, double min_baseq, double min_mapq, Packer *packer, size_t min_bp_coverage, double max_frac_n, bool edges_only)
	Generic version used to implement the above three methods. More...

double	get_avg_baseq (const Edit &edit, const string &base_quals, size_t position_in_read)

void	find_breakpoints (const Path &path, unordered_map< id_t, set< pos_t >> &breakpoints, bool break_ends, const string &base_quals, double min_baseq, double max_frac_n)

unordered_map< id_t, set< pos_t > >	forwardize_breakpoints (const HandleGraph *graph, const unordered_map< id_t, set< pos_t >> &breakpoints)
	Flips the breakpoints onto the forward strand. More...

void	find_packed_breakpoints (const Path &path, Packer &packed_breakpoints, bool break_ends=true, const string &base_quals="", double min_baseq=0, double max_frac_n=1.)
	Like "find_breakpoints", but store in packed structure (better for large gams and enables coverage filter) More...

unordered_map< id_t, set< pos_t > >	filter_breakpoints_by_coverage (const Packer &packed_breakpoints, size_t min_bp_coverage)

path_handle_t	add_path_to_graph (MutablePathHandleGraph *graph, const Path &path)

map< pos_t, id_t >	ensure_breakpoints (MutableHandleGraph *graph, const unordered_map< id_t, set< pos_t >> &breakpoints)

bool	simplify_filtered_edits (HandleGraph *graph, Alignment &aln, Path &path, const map< pos_t, id_t > &node_translation, const unordered_map< id_t, size_t > &orig_node_sizes, double min_baseq, double max_frac_n)

Path	add_nodes_and_edges (MutableHandleGraph *graph, const Path &path, const map< pos_t, id_t > &node_translation, unordered_map< pair< pos_t, string >, vector< id_t >> &added_seqs, unordered_map< id_t, Path > &added_nodes, const unordered_map< id_t, size_t > &orig_node_sizes, size_t max_node_size=1024)
	This version doesn't require a set of dangling sides to populate More...

Path	add_nodes_and_edges (MutableHandleGraph *graph, const Path &path, const map< pos_t, id_t > &node_translation, unordered_map< pair< pos_t, string >, vector< id_t >> &added_seqs, unordered_map< id_t, Path > &added_nodes, const unordered_map< id_t, size_t > &orig_node_sizes, set< NodeSide > &dangling, size_t max_node_size)

vector< Translation >	make_translation (const HandleGraph *graph, const map< pos_t, id_t > &node_translation, const unordered_map< id_t, Path > &added_nodes, const unordered_map< id_t, size_t > &orig_node_sizes)
	Produce a graph Translation object from information about the editing process. More...

void	add_edges_only (MutableHandleGraph *graph, function< void(function< void(Alignment &)>, bool, bool)> iterate_gam, double min_mapq, size_t min_bp_coverage)

ostream &	operator<< (ostream &out, const BenchmarkResult &result)

void	benchmark_control ()

BenchmarkResult	run_benchmark (const string &name, size_t iterations, const function< void(void)> &under_test)

BenchmarkResult	run_benchmark (const string &name, size_t iterations, const function< void(void)> &setup, const function< void(void)> &under_test)

void	build_gcsa_lcp (const HandleGraph &graph, gcsa::GCSA &gcsa, gcsa::LCPArray &lcp, int kmer_size, size_t doubling_steps, size_t size_limit, const string &base_file_name)

void *	mergeNodeObjects (void a, void b)

void	getReachableBridges2 (stCactusEdgeEnd edgeEnd1, stHash bridgeEndsToBridgeNodes, stList *bridgeEnds)

void	getReachableBridges (stCactusEdgeEnd edgeEnd1, stList bridgeEnds)

void	addArbitraryTelomerePair (vector< stCactusEdgeEnd * > ends, stList *telomeres)

pair< stCactusGraph , stList >	handle_graph_to_cactus (const PathHandleGraph &graph, const unordered_set< string > &hint_paths, bool single_component)

VG	cactus_to_vg (stCactusGraph *cactus_graph)

VG	cactusify (VG &graph)

void	visit_contained_snarls (const PathPositionHandleGraph graph, const vector< Region > &regions, SnarlManager &snarl_manager, bool include_endpoints, function< void(const Snarl , step_handle_t, step_handle_t, int64_t, int64_t, bool, const Region *)> visit_fn)

void	delete_nodes_and_chop_paths (MutablePathMutableHandleGraph graph, const unordered_set< nid_t > &nodes_to_delete, const unordered_set< edge_t > &edges_to_delete, int64_t min_fragment_len, unordered_map< string, size_t > fragments_per_path)

void	clip_contained_snarls (MutablePathMutableHandleGraph graph, PathPositionHandleGraph pp_graph, const vector< Region > &regions, SnarlManager &snarl_manager, bool include_endpoints, int64_t min_fragment_len, size_t max_nodes, size_t max_edges, size_t max_nodes_shallow, size_t max_edges_shallow, double max_avg_degree, double max_reflen_prop, size_t max_reflen, bool out_bed, bool verbose)

void	clip_low_depth_nodes_and_edges_generic (MutablePathMutableHandleGraph graph, function< void(function< void(handle_t, const Region )>)> iterate_handles, function< void(function< void(edge_t, const Region *)>)> iterate_edges, int64_t min_depth, const vector< string > &ref_prefixes, int64_t min_fragment_len, bool verbose)

void	clip_low_depth_nodes_and_edges (MutablePathMutableHandleGraph *graph, int64_t min_depth, const vector< string > &ref_prefixes, int64_t min_fragment_len, bool verbose)

void	clip_contained_low_depth_nodes_and_edges (MutablePathMutableHandleGraph graph, PathPositionHandleGraph pp_graph, const vector< Region > &regions, SnarlManager &snarl_manager, bool include_endpoints, int64_t min_depth, int64_t min_fragment_len, bool verbose)

void	clip_deletion_edges (MutablePathMutableHandleGraph *graph, int64_t max_deletion, int64_t context_steps, const vector< string > &ref_prefixes, int64_t min_fragment_len, bool verbose)

void	clip_stubs_generic (MutablePathMutableHandleGraph graph, function< void(function< void(handle_t, const Region )>)> iterate_handles, function< bool(handle_t)> handle_in_range, const vector< string > &ref_prefixes, int64_t min_fragment_len, bool verbose)

void	clip_stubs (MutablePathMutableHandleGraph *graph, const vector< string > &ref_prefixes, int64_t min_fragment_len, bool verbose)

void	clip_contained_stubs (MutablePathMutableHandleGraph graph, PathPositionHandleGraph pp_graph, const vector< Region > &regions, SnarlManager &snarl_manager, bool include_endpoints, int64_t min_fragment_len, bool verbose)

void	stubbify_ref_paths (MutablePathMutableHandleGraph *graph, const vector< string > &ref_prefixes, int64_t min_fragment_len, bool verbose)

vector< pair< gcsa::node_type, size_t > >	mem_node_start_positions (const HandleGraph &graph, const vg::MaximalExactMatch &mem)
	get the handles that a mem covers More...

bdsg::HashGraph	cluster_subgraph_containing (const HandleGraph &base, const Alignment &aln, const vector< vg::MaximalExactMatch > &cluster, const GSSWAligner *aligner)
	return a containing subgraph connecting the mems More...

bdsg::HashGraph	cluster_subgraph_walk (const HandleGraph &base, const Alignment &aln, const vector< vg::MaximalExactMatch > &mems, double expansion)

template<typename T >
bool	convert (const std::string &s, T &r)

template<typename T >
std::string	convert (const T &r)

void	stacktrace_manually (ostream &out, int signalNumber, void ip, void *bp)

void	emit_stacktrace (int signalNumber, siginfo_t signalInfo, void signalContext)
	Emit a stack trace when something bad happens. Add as a signal handler with sigaction. More...

void	enable_crash_handling ()
	Main should call this to turn on our stack tracing support. More...

void	set_crash_context (const std::string &message)
	User code should call this when it has context for a failure in its thread. More...

void	clear_crash_context ()
	User code should call this when it wants to clear context for a failure in its thread. More...

void	with_exception_handling (const std::function< void(void)> &body)
	User code should call this to get all its exceptions handled. More...

void	report_exception (const std::exception &ex)

void	crash_unless_impl (bool condition, const std::string &condition_string, const std::string &file, int line, const std::string &function)
	crash_unless calls into this function for a real implementation. More...

double	entropy (const string &st)

double	entropy (const char *st, size_t len)

std::ostream &	operator<< (std::ostream &out, const Funnel::State &state)

template<class Element >
void	in_place_subvector (std::vector< Element > &vec, size_t head, size_t tail)

void	set_score (GaplessExtension &extension, const Aligner *aligner)

void	match_initial (GaplessExtension &match, const std::string &seq, gbwtgraph::view_type target)

size_t	match_forward (GaplessExtension &match, const std::string &seq, gbwtgraph::view_type target, uint32_t mismatch_limit)

void	match_backward (GaplessExtension &match, const std::string &seq, gbwtgraph::view_type target, uint32_t mismatch_limit)

void	handle_full_length (const HandleGraph &graph, std::vector< GaplessExtension > &result, double overlap_threshold)

void	remove_duplicates (std::vector< GaplessExtension > &result)

void	find_mismatches (const std::string &seq, const gbwtgraph::CachedGBWTGraph &graph, std::vector< GaplessExtension > &result)

size_t	interval_length (std::pair< size_t, size_t > interval)

std::vector< handle_t >	get_path (const std::vector< handle_t > &first, handle_t second)

std::vector< handle_t >	get_path (handle_t first, const std::vector< handle_t > &second)

std::vector< handle_t >	get_path (const std::vector< handle_t > &first, gbwt::node_type second)

std::vector< handle_t >	get_path (gbwt::node_type reverse_first, const std::vector< handle_t > &second)

bool	trim_mismatches (GaplessExtension &extension, const gbwtgraph::CachedGBWTGraph &graph, const Aligner &aligner)

std::ostream &	operator<< (std::ostream &out, const WFAAlignment::Edit &edit)
	Allow printing an Edit. More...

std::vector< std::string >	parseGenotypes (const std::string &vcf_line, size_t num_samples)

gbwt::vector_type	extract_as_gbwt_path (const PathHandleGraph &graph, const std::string &path_name)
	Extract a path as a GBWT path. If the path does not exist, it is treated as empty. More...

gbwt::vector_type	path_predecessors (const PathHandleGraph &graph, const std::string &path_name)

gbwt::size_type	gbwt_node_width (const HandleGraph &graph)
	Determine the node width in bits for the GBWT nodes based on the given graph. More...

void	load_gbwt (gbwt::GBWT &index, const std::string &filename, bool show_progress=false)
	Load a compressed GBWT from the file. More...

void	load_gbwt (gbwt::DynamicGBWT &index, const std::string &filename, bool show_progress=false)
	Load a dynamic GBWT from the file. More...

void	load_r_index (gbwt::FastLocate &index, const std::string &filename, bool show_progress=false)
	Load an r-index from the file. More...

void	save_gbwt (const gbwt::GBWT &index, const std::string &filename, bool show_progress=false)
	Save a compressed GBWT to the file. More...

void	save_gbwt (const gbwt::DynamicGBWT &index, const std::string &filename, bool show_progress=false)
	Save a dynamic GBWT to the file. More...

void	save_r_index (const gbwt::FastLocate &index, const std::string &filename, bool show_progress=false)
	Save an r-index to the file. More...

std::vector< std::vector< gbwt::size_type > >	partition_gbwt_sequences (const gbwt::GBWT &gbwt_index, const std::unordered_map< nid_t, size_t > &node_to_job, size_t num_jobs)

gbwt::GBWT	rebuild_gbwt_job (const gbwt::GBWT &gbwt_index, const RebuildJob &job, size_t job_id, const std::vector< gbwt::size_type > &sequences, const RebuildParameters &parameters)

void	copy_metadata (const gbwt::GBWT &source, gbwt::GBWT &target, const std::vector< std::vector< gbwt::size_type >> &jobs, const std::vector< size_t > &job_order)

gbwt::GBWT	rebuild_gbwt (const gbwt::GBWT &gbwt_index, const std::vector< RebuildJob > &jobs, const std::unordered_map< nid_t, size_t > &node_to_job, const RebuildParameters &parameters)

gbwt::GBWT	rebuild_gbwt (const gbwt::GBWT &gbwt_index, const std::vector< RebuildJob::mapping_type > &mappings)
	As the general `rebuild_gbwt`, but always using a single job with default parameters. More...

std::vector< gbwt::size_type >	threads_for_sample (const gbwt::GBWT &gbwt_index, const std::string &sample_name)
	Return the list of thread ids / gbwt path ids for the given sample. More...

std::vector< gbwt::size_type >	threads_for_contig (const gbwt::GBWT &gbwt_index, const std::string &contig_name)
	Return the list of thread ids / gbwt path ids for the given contig. More...

std::string	insert_gbwt_path (MutablePathHandleGraph &graph, const gbwt::GBWT &gbwt_index, gbwt::size_type id, std::string path_name)

Path	extract_gbwt_path (const HandleGraph &graph, const gbwt::GBWT &gbwt_index, gbwt::size_type id)

std::string	compose_short_path_name (const gbwt::GBWT &gbwt_index, gbwt::size_type id)

void	copy_reference_samples (const gbwt::GBWT &source, gbwt::GBWT &destination)
	Copies the reference sample tag from the source GBWT index to the destination GBWT index. More...

void	copy_reference_samples (const PathHandleGraph &source, gbwt::GBWT &destination)

gbwt::GBWT	get_gbwt (const std::vector< gbwt::vector_type > &paths)
	Transform the paths into a GBWT index. Primarily for testing. More...

unordered_map< string, vector< nid_t > >	load_translation_map (ifstream &input_stream)

unordered_map< nid_t, pair< string, size_t > >	load_translation_back_map (HandleGraph &graph, ifstream &input_stream)

handle_t	gbwt_to_handle (const HandleGraph &graph, gbwt::node_type node)
	Convert gbwt::node_type to handle_t. More...

pos_t	gbwt_to_pos (gbwt::node_type node, size_t offset)
	Convert gbwt::node_type and an offset as size_t to pos_t. More...

gbwt::node_type	handle_to_gbwt (const HandleGraph &graph, handle_t handle)
	Convert handle_t to gbwt::node_type. More...

gbwt::node_type	pos_to_gbwt (pos_t pos)
	Extract gbwt::node_type from pos_t. More...

gbwt::node_type	mapping_to_gbwt (const Mapping &mapping)
	Convert Mapping to gbwt::node_type. More...

gbwt::vector_type	path_to_gbwt (const Path &path)
	Convert Path to a GBWT path. More...

gbwtgraph::GFAParsingParameters	get_best_gbwtgraph_gfa_parsing_parameters ()

void	load_gbwtgraph (gbwtgraph::GBWTGraph &graph, const std::string &filename, bool show_progress)

void	load_gbz (gbwtgraph::GBZ &gbz, const std::string &filename, bool show_progress=false)
	Load GBZ from the file. More...

void	load_gbz (gbwt::GBWT &index, gbwtgraph::GBWTGraph &graph, const std::string &filename, bool show_progress=false)
	Load GBWT and GBWTGraph from the GBZ file. More...

void	load_gbz (gbwtgraph::GBZ &gbz, const std::string &gbwt_name, const std::string &graph_name, bool show_progress=false)
	Load GBZ from separate GBWT / GBWTGraph files. More...

void	load_minimizer (gbwtgraph::DefaultMinimizerIndex &index, const std::string &filename, bool show_progress=false)
	Load a minimizer index from the file. More...

void	save_gbwtgraph (const gbwtgraph::GBWTGraph &graph, const std::string &filename, bool show_progress=false)
	Save GBWTGraph to the file. More...

void	save_gbz (const gbwtgraph::GBZ &gbz, const std::string &filename, bool show_progress=false)
	Save GBZ to the file. More...

void	save_gbz (const gbwt::GBWT &index, gbwtgraph::GBWTGraph &graph, const std::string &filename, bool show_progress=false)
	Save GBWT and GBWTGraph to the GBZ file. More...

void	save_gbz (const gbwtgraph::GBZ &gbz, const std::string &gbwt_name, const std::string &graph_name, bool show_progress=false)
	Save GBZ to separate GBWT / GBWTGraph files. More...

void	save_minimizer (const gbwtgraph::DefaultMinimizerIndex &index, const std::string &filename, bool show_progress=false)
	Save a minimizer index to the file. More...

unordered_map< string, vector< nid_t > >	load_translation_map (const gbwtgraph::GBWTGraph &graph)
	Return a mapping of the original segment ids to a list of chopped node ids. More...

unordered_map< nid_t, pair< string, size_t > >	load_translation_back_map (const gbwtgraph::GBWTGraph &graph)
	Return a backwards mapping of chopped node to original segment position (id,offset pair) More...

std::string	to_string_gbwtgraph (handle_t handle)
	Returns a string representation of a GBWTGraph handle. More...

std::string	to_string_gbwtgraph (gbwt::node_type node)
	Returns a string representation of a GBWTGraph node. More...

handle_t	empty_gbwtgraph_handle ()
	Returns an empty GBWTGraph handle corresponding to the GBWT endmarker. More...

void	load_gcsa (gcsa::GCSA &index, const std::string &filename, bool show_progress=false)
	Load GCSA from the file. More...

void	load_lcp (gcsa::LCPArray &lcp, const std::string &filename, bool show_progress=false)
	Load LCP array from the file. More...

void	save_gcsa (const gcsa::GCSA &index, const std::string &filename, bool show_progress=false)
	Save GCSA to the file. More...

void	save_lcp (const gcsa::LCPArray &lcp, const std::string &filename, bool show_progress=false)
	Save LCP array to the file. More...

SnarlTraversal	get_traversal_of_snarl (VG &graph, const Snarl *snarl, const SnarlManager &manager, const Path &path)

string	traversal_to_string (VG &graph, const SnarlTraversal &path)

Support	make_support (double forward, double reverse, double quality)

double	total (const Support &support)

Support	support_min (const Support &a, const Support &b)

Support	support_max (const Support &a, const Support &b)

Support	flip (const Support &to_flip)

Support	operator+ (const Support &one, const Support &other)

Support &	operator+= (Support &one, const Support &other)

bool	operator< (const Support &a, const Support &b)

bool	operator> (const Support &a, const Support &b)

ostream &	operator<< (ostream &stream, const Support &support)

string	to_vcf_genotype (const Genotype &gt)

template<typename Scalar >
Support	operator* (const Support &support, const Scalar &scale)

template<typename Scalar >
Support &	operator*= (Support &support, const Scalar &scale)

template<typename Scalar >
Support	operator* (const Scalar &scale, const Support &support)

template<typename Scalar >
Support	operator/ (const Support &support, const Scalar &scale)

template<typename Scalar >
Support &	operator/= (Support &support, const Scalar &scale)

string	allele_to_string (VG &graph, const Path &allele)

template<typename T >
void	set_intersection (const unordered_set< T > &set_1, const unordered_set< T > &set_2, unordered_set< T > *out_intersection)

void	graph_to_gfa (const PathHandleGraph *graph, ostream &out, const set< string > &rgfa_paths, bool rgfa_pline, bool use_w_lines)

void	sort_by_id_dedup_and_clean (Graph &graph)
	remove duplicates and sort by id More...

void	remove_duplicates (Graph &graph)
	remove duplicate nodes and edges More...

void	remove_duplicate_edges (Graph &graph)
	remove duplicate edges More...

void	remove_duplicate_nodes (Graph &graph)
	remove duplicate nodes More...

void	remove_orphan_edges (Graph &graph)
	remove edges that link to a node that is not in the graph More...

void	sort_by_id (Graph &graph)
	order the nodes and edges in the graph by id More...

void	sort_nodes_by_id (Graph &graph)
	order the nodes in the graph by id More...

void	sort_edges_by_id (Graph &graph)
	order the edges in the graph by id pairs More...

bool	is_id_sortable (const Graph &graph)
	returns true if the graph is id-sortable (no reverse links) More...

bool	has_inversion (const Graph &graph)
	returns true if we find an edge that may specify an inversion More...

void	flip_doubly_reversed_edges (Graph &graph)
	clean up doubly-reversed edges More...

void	from_handle_graph (const HandleGraph &from, Graph &to)

void	from_path_handle_graph (const PathHandleGraph &from, Graph &to)

void	trace_haplotypes_and_paths (const PathHandleGraph &source, const gbwt::GBWT &haplotype_database, vg::id_t start_node, int extend_distance, Graph &out_graph, map< string, int > &out_thread_frequencies, bool expand_graph)

void	output_haplotype_counts (ostream &annotation_ostream, vector< pair< thread_t, int >> &haplotype_list)

Graph	output_graph_with_embedded_paths (vector< pair< thread_t, int >> &haplotype_list, const HandleGraph &source)

void	output_graph_with_embedded_paths (ostream &subgraph_ostream, vector< pair< thread_t, int >> &haplotype_list, const HandleGraph &source, bool json)

void	thread_to_graph_spanned (thread_t &t, Graph &g, const HandleGraph &source)

void	add_thread_nodes_to_set (thread_t &t, set< int64_t > &nodes)

void	add_thread_edges_to_set (thread_t &t, set< pair< int, int > > &edges)

void	construct_graph_from_nodes_and_edges (Graph &g, const HandleGraph &source, set< int64_t > &nodes, set< pair< int, int > > &edges)

Path	path_from_thread_t (thread_t &t, const HandleGraph &source)

vector< pair< vector< gbwt::node_type >, gbwt::SearchState > >	list_haplotypes (const HandleGraph &graph, const gbwt::GBWT &gbwt, handle_t start, function< bool(const vector< gbwt::node_type > &)> stop_fn)

unique_ptr< AlignmentEmitter >	get_alignment_emitter (const string &filename, const string &format, const vector< tuple< path_handle_t, size_t, size_t >> &paths, size_t max_threads, const HandleGraph *graph, int flags)

pair< vector< pair< string, int64_t > >, unordered_map< string, int64_t > >	extract_path_metadata (const vector< tuple< path_handle_t, size_t, size_t >> &paths, const PathPositionHandleGraph &graph, bool subpath_support)

vector< tuple< path_handle_t, size_t, size_t > >	get_sequence_dictionary (const string &filename, const vector< string > &path_names, const PathPositionHandleGraph &graph)

void	copy_file (const string &from_fp, const string &to_fp)

int64_t	get_file_size (const string &filename)

bool	is_gzipped (const string &filename)

int64_t	get_num_samples (const string &vcf_filename)

double	approx_num_vars (const string &vcf_filename)

double	format_multiplier ()

int64_t	approx_graph_memory (const vector< string > &fasta_filenames, const vector< string > &vcf_filenames)

vector< int64_t >	each_approx_graph_memory (const vector< string > &fasta_filenames, const vector< string > &vcf_filenames)

int64_t	approx_graph_memory (const string &fasta_filename, const string &vcf_filename)

int64_t	approx_graph_memory (const string &gfa_filename)

int64_t	approx_gbwt_memory (const string &vcf_filename)

int64_t	approx_graph_load_memory (const string &graph_filename)

bool	transcript_file_nonempty (const string &transcripts)

vector< string >	vcf_contigs (const string &filename)

size_t	guess_parallel_gbwt_jobs (size_t node_count, size_t haplotype_count, size_t available_memory, size_t batch_size)

size_t	xg_index_size (const xg::XG &index)

int	execute_in_fork (const function< void(void)> &exec)

bool	kff_is_trivial (const uint8_t *encoding)
	Returns `true` if the encoding is trivial (0, 1, 2, 3). More...

std::string	kff_invert (const uint8_t *encoding)
	Inverts the KFF encoding into a packed -> char table. More...

kff_recoding_t	kff_recoding (const uint8_t *encoding)
	Returns a recoding for the given encoding. More...

uint64_t	kff_parse (const uint8_t *data, size_t bytes)
	Parses a big-endian integer from KFF data. More...

uint8_t	kff_encode (const std::string &kmer, size_t start, size_t limit, const uint8_t *encoding)

std::vector< uint8_t >	kff_encode (const std::string &kmer, const uint8_t *encoding)

void	kff_decode (uint8_t byte, size_t chars, const std::string &decoding, std::string &output)

std::string	kff_decode (const uint8_t *kmer, size_t k, const std::string &decoding)
	Decodes a kmer in KFF format according to the given encoding. More...

uint8_t	kff_recode (gbwtgraph::Key64::value_type kmer, size_t k, size_t chars, const uint8_t *encoding)

std::vector< uint8_t >	kff_recode (gbwtgraph::Key64::value_type kmer, size_t k, const uint8_t *encoding)
	Recodes a kmer from a minimizer index in KFF format according to the given encoding. More...

gbwtgraph::Key64::value_type	kff_recode (const uint8_t *kmer, size_t k, kff_recoding_t recoding)

gbwtgraph::Key64::value_type	kff_recode_trivial (const uint8_t *kmer, size_t k, size_t bytes)

std::vector< gbwtgraph::Key64::value_type >	kff_recode (const uint8_t *kmers, size_t n, size_t k, kff_recoding_t recoding)

uint8_t	kff_get (const uint8_t *kmer, size_t i)

void	kff_set (std::vector< uint8_t > &kmer, size_t i, uint8_t value)

std::vector< uint8_t >	kff_reverse_complement (const uint8_t kmer, size_t k, const uint8_t encoding)
	Returns the reverse complement of a KFF kmer. More...

size_t	kff_bytes (size_t k)
	Returns the number of bytes required for a kmer in KFF format. More...

gbwtgraph::Key64::value_type	minimizer_reverse_complement (gbwtgraph::Key64::value_type kmer, size_t k)
	Returns the reverse complement of a minimizer index kmer. More...

void	for_each_kmer (const HandleGraph &graph, size_t k, const function< void(const kmer_t &)> &lambda, id_t head_id, id_t tail_id, atomic< int > *stop_flag)

ostream &	operator<< (ostream &out, const kmer_t &kmer)
	Print a kmer_t to a stream. More...

void	kmer_to_gcsa_kmers (const kmer_t &kmer, const gcsa::Alphabet &alpha, const function< void(const gcsa::KMer &)> &lambda)
	Convert the kmer_t to a set of gcsa2 binary kmers which are exposed via a callback. More...

gcsa::byte_type	encode_chars (const vector< char > &chars, const gcsa::Alphabet &alpha)
	Encode the chars into the gcsa2 byte. More...

void	write_gcsa_kmers (const HandleGraph &graph, int kmer_size, ostream &out, size_t &size_limit, id_t head_id, id_t tail_id)

string	write_gcsa_kmers_to_tmpfile (const HandleGraph &graph, int kmer_size, size_t &size_limit, id_t head_id, id_t tail_id, const string &base_file_name)

vector< size_t >	make_prefix_suffix_table (const char *pattern, size_t len)

size_t	kmp_search (const char text, size_t text_len, const char pattern, size_t pattern_len, const vector< size_t > &prefix_suffix_table)

int	sub_overlaps_of_first_aln (const vector< Alignment > &alns, float overlap_fraction)

set< pos_t >	gcsa_nodes_to_positions (const vector< gcsa::node_type > &nodes)

const int	balanced_stride (int read_length, int kmer_size, int stride)

const vector< string >	balanced_kmers (const string &seq, const int kmer_size, const int stride)

pair< int64_t, int64_t >	mem_min_oriented_distances (const MaximalExactMatch &m1, const MaximalExactMatch &m2)

bool	operator== (const MaximalExactMatch &m1, const MaximalExactMatch &m2)

bool	operator< (const MaximalExactMatch &m1, const MaximalExactMatch &m2)

ostream &	operator<< (ostream &out, const MaximalExactMatch &mem)

const string	mems_to_json (const vector< MaximalExactMatch > &mems)

vector< string::const_iterator >	cluster_cover (const vector< MaximalExactMatch > &cluster)

int	cluster_coverage (const vector< MaximalExactMatch > &cluster)

bool	mems_overlap (const MaximalExactMatch &mem1, const MaximalExactMatch &mem2)

int	mems_overlap_length (const MaximalExactMatch &mem1, const MaximalExactMatch &mem2)

bool	clusters_overlap_in_read (const vector< MaximalExactMatch > &cluster1, const vector< MaximalExactMatch > &cluster2)

int	clusters_overlap_length (const vector< MaximalExactMatch > &cluster1, const vector< MaximalExactMatch > &cluster2)

vector< pos_t >	cluster_nodes (const vector< MaximalExactMatch > &cluster)

bool	clusters_overlap_in_graph (const vector< MaximalExactMatch > &cluster1, const vector< MaximalExactMatch > &cluster2)

vector< MaximalExactMatch >	translate_mems (const vector< MaximalExactMatch > &mems, const unordered_map< id_t, pair< id_t, bool > > &trans)

string	get_proc_status_value (const string &name)
	Get the string value for a field in /proc/self/status by name, or "" if unsupported or not found. More...

size_t	get_max_rss_kb ()
	Get the max RSS usage ever, in kb, or 0 if unsupported. More...

size_t	get_max_vmem_kb ()
	Get the max virtual memory size ever, in kb, or 0 if unsupported. More...

size_t	get_current_vmem_kb ()
	Get the current virtual memory size, in kb, or 0 if unsupported. More...

vector< size_t >	subpath_topological_order (const multipath_alignment_t &multipath_aln, bool do_index)
	Return either the vector of topological order by index or the vector of indexes within the topological order. More...

void	topologically_order_subpaths (multipath_alignment_t &multipath_aln)
	Put subpaths in topological order (assumed to be true for other algorithms) More...

void	remove_empty_alignment_sections (multipath_alignment_t &multipath_aln)

void	identify_start_subpaths (multipath_alignment_t &multipath_aln)

void	clear_alignment (multipath_alignment_t &multipath_aln)
	Clear all of the field associated with the alignment. More...

tuple< MultipathProblem, int64_t, int32_t >	run_multipath_dp (const multipath_alignment_t &multipath_aln, bool subpath_global=false, bool forward=true)

template<typename TracebackIterator >
void	populate_path_from_traceback (const multipath_alignment_t &multipath_aln, const MultipathProblem &problem, TracebackIterator traceback_start, TracebackIterator traceback_end, Path *output)

int32_t	optimal_alignment_internal (const multipath_alignment_t &multipath_aln, Alignment *aln_out, bool subpath_global)

void	optimal_alignment (const multipath_alignment_t &multipath_aln, Alignment &aln_out, bool subpath_global)

int32_t	optimal_alignment_score (const multipath_alignment_t &multipath_aln, bool subpath_global)

int32_t	worst_alignment_score (const multipath_alignment_t &multipath_aln)

void	remove_low_scoring_sections (multipath_alignment_t &multipath_aln, int32_t max_score_diff)

vector< Alignment >	optimal_alignments (const multipath_alignment_t &multipath_aln, size_t count)

vector< Alignment >	optimal_alignments_with_disjoint_subpaths (const multipath_alignment_t &multipath_aln, size_t count)

vector< Alignment >	haplotype_consistent_alignments (const multipath_alignment_t &multipath_aln, const haplo::ScoreProvider &score_provider, size_t soft_count, size_t hard_count, bool optimal_first)

pair< int64_t, int64_t >	aligned_interval (const multipath_alignment_t &multipath_aln)
	The indexes on the read sequence of the portion of the read that is aligned outside of soft clips. More...

void	rev_comp_subpath (const subpath_t &subpath, const function< int64_t(int64_t)> &node_length, subpath_t &rev_comp_out)

void	rev_comp_multipath_alignment (const multipath_alignment_t &multipath_aln, const function< int64_t(int64_t)> &node_length, multipath_alignment_t &rev_comp_out)

void	rev_comp_multipath_alignment_in_place (multipath_alignment_t *multipath_aln, const function< int64_t(int64_t)> &node_length)

void	convert_multipath_alignment_char (multipath_alignment_t &multipath_aln, char from, char to)

void	convert_Us_to_Ts (multipath_alignment_t &multipath_aln)
	Replaces all U's in the sequence and the aligned Paths with T's. More...

void	convert_Ts_to_Us (multipath_alignment_t &multipath_aln)
	Replaces all T's in the sequence and the aligned Paths with U's. More...

template<class ProtoAlignment >
void	transfer_from_proto_annotation (const ProtoAlignment &from, multipath_alignment_t &to)

template<class ProtoAlignment >
void	transfer_to_proto_annotation (const multipath_alignment_t &from, ProtoAlignment &to)

template<class ProtoAlignment1 , class ProtoAlignment2 >
void	transfer_between_proto_annotation (const ProtoAlignment1 &from, ProtoAlignment2 &to)

template<class Alignment1 , class Alignment2 >
void	transfer_uniform_metadata (const Alignment1 &from, Alignment2 &to)

void	to_proto_multipath_alignment (const multipath_alignment_t &multipath_aln, MultipathAlignment &proto_multipath_aln_out)
	Convert an STL-based multipath_alignment_t to a protobuf MultipathAlignment. More...

void	from_proto_multipath_alignment (const MultipathAlignment &proto_multipath_aln, multipath_alignment_t &multipath_aln_out)
	Convert a protobuf MultipathAlignment to an STL-based multipath_alignment_t. More...

void	to_multipath_alignment (const Alignment &aln, multipath_alignment_t &multipath_aln_out)

void	transfer_read_metadata (const MultipathAlignment &from, multipath_alignment_t &to)

void	transfer_read_metadata (const multipath_alignment_t &from, MultipathAlignment &to)

void	transfer_read_metadata (const multipath_alignment_t &from, multipath_alignment_t &to)

void	transfer_read_metadata (const Alignment &from, multipath_alignment_t &to)

void	transfer_read_metadata (const multipath_alignment_t &from, Alignment &to)

void	transfer_read_metadata (const Alignment &from, Alignment &to)

void	transfer_proto_metadata (const Alignment &from, MultipathAlignment &to)

void	transfer_proto_metadata (const MultipathAlignment &from, Alignment &to)

void	merge_non_branching_subpaths (multipath_alignment_t &multipath_aln, const unordered_set< size_t > *prohibited_merges)

void	connected_comps_do (const multipath_alignment_t &multipath_aln, function< void(void)> &on_new_component, function< void(size_t)> &on_new_node)

size_t	num_connected_components (const multipath_alignment_t &multipath_aln)
	Returns the number of connected components in the multipath alignment. More...

vector< vector< int64_t > >	connected_components (const multipath_alignment_t &multipath_aln)

void	extract_sub_multipath_alignment (const multipath_alignment_t &multipath_aln, const vector< int64_t > &subpath_indexes, multipath_alignment_t &sub_multipath_aln)

void	append_multipath_alignment (multipath_alignment_t &multipath_aln, const multipath_alignment_t &to_append)
	Add the subpaths of one multipath alignment onto another. More...

bool	contains_connection (const multipath_alignment_t &multipath_aln)
	Returns true if any subpath has a connection adjacency. More...

vector< tuple< int64_t, int64_t, int64_t, int64_t > >	search_multipath_alignment (const multipath_alignment_t &multipath_aln, const pos_t &graph_pos, int64_t seq_pos)

pair< tuple< int64_t, int64_t, int64_t >, vector< tuple< int64_t, int64_t, int64_t, int64_t > > >	trace_path (const multipath_alignment_t &multipath_aln, const Path &path, int64_t subpath_idx, int64_t mapping_idx, int64_t edit_idx, int64_t base_idx, bool search_left, int64_t search_limit)

bool	contains_match (const multipath_alignment_t &multipath_aln, const pos_t &pos, int64_t read_pos, int64_t match_length)

vector< pair< int, char > >	cigar_against_path (const multipath_alignment_t &multipath_aln, const string &path_name, bool rev, int64_t path_pos, const PathPositionHandleGraph &graph, int64_t min_splice_length)

bool	validate_multipath_alignment (const multipath_alignment_t &multipath_aln, const HandleGraph &handle_graph)

void	view_multipath_alignment (ostream &out, const multipath_alignment_t &multipath_aln, const HandleGraph &handle_graph)
	Send a formatted string representation of the multipath_alignment_t into the ostream. More...

void	view_multipath_alignment_as_dot (ostream &out, const multipath_alignment_t &multipath_aln, bool show_graph=false)
	Converts a multipath_alignment_t to a GraphViz Dot representation, output to the given ostream. More...

string	debug_string (const connection_t &connection)

string	debug_string (const subpath_t &subpath)

string	debug_string (const multipath_alignment_t &multipath_aln)

string	make_shuffle_seed (const multipath_alignment_t &aln)
	Define seed generation for shuffling multipath alignments. More...

NodeSide	node_start (id_t id)
	Produce the start NodeSide of a Node. More...

NodeSide	node_end (id_t id)
	Produce the end NodeSide of a Node. More...

ostream &	operator<< (ostream &out, const NodeSide &nodeside)
	Print a NodeSide to a stream. More...

ostream &	operator<< (ostream &out, const NodeTraversal &nodetraversal)
	Print the given NodeTraversal. More...

ostream &	operator<< (ostream &out, mapping_t mapping)
	Allow a mapping_t to be printed, for debugging purposes. More...

Path &	append_path (Path &a, const Path &b)

int	path_to_length (const Path &path)

int	path_from_length (const Path &path)

int	mapping_to_length (const Mapping &m)

int	mapping_from_length (const Mapping &m)

int	softclip_start (const Mapping &mapping)

int	softclip_end (const Mapping &mapping)

Position	first_path_position (const Path &path)

Position	last_path_position (const Path &path)

int	to_length (const Mapping &m)

int	from_length (const Mapping &m)

Path &	extend_path (Path &path1, const Path &path2)

Path	concat_paths (const Path &path1, const Path &path2)

Path	simplify (const Path &p, bool trim_internal_deletions)

Mapping	concat_mappings (const Mapping &m, const Mapping &n, bool trim_internal_deletions)

Mapping	simplify (const Mapping &m, bool trim_internal_deletions)

bool	edits_are_compatible (const Edit &e, const Edit &f)
	Return true if two edits could be combined into one (assuming adjacency). More...

void	merge_edits_in_place (Edit &e, const Edit &f)
	Glom the second edit into the first, assuming adjacency. More...

Mapping	merge_adjacent_edits (const Mapping &m)
	Merge adjacent edits of the same type. More...

Path	trim_hanging_ends (const Path &p)

bool	mappings_equivalent (const Mapping &m1, const Mapping &m2)

bool	mapping_ends_in_deletion (const Mapping &m)

bool	mapping_starts_in_deletion (const Mapping &m)

bool	mapping_is_total_deletion (const Mapping &m)

bool	mapping_is_total_insertion (const Mapping &m)

bool	mapping_is_simple_match (const Mapping &m)

bool	path_is_simple_match (const Path &p)

const string	mapping_sequence (const Mapping &mp, const string &node_seq)

const string	mapping_sequence (const Mapping &mp, const Node &n)

string	path_sequence (const HandleGraph &graph, const Path &path)

Mapping	reverse_complement_mapping (const Mapping &m, const function< int64_t(id_t)> &node_length)

void	reverse_complement_mapping_in_place (Mapping *m, const function< int64_t(id_t)> &node_length)

Path	reverse_complement_path (const Path &path, const function< int64_t(id_t)> &node_length)

void	reverse_complement_path_in_place (Path *path, const function< int64_t(id_t)> &node_length)

pair< Mapping, Mapping >	cut_mapping (const Mapping &m, const Position &pos)

pair< mapping_t, mapping_t >	cut_mapping (const mapping_t &m, const Position &pos)

pair< Mapping, Mapping >	cut_mapping_offset (const Mapping &m, size_t offset)

pair< mapping_t, mapping_t >	cut_mapping_offset (const mapping_t &m, size_t offset)

pair< Mapping, Mapping >	cut_mapping (const Mapping &m, size_t offset)

pair< mapping_t, mapping_t >	cut_mapping (const mapping_t &m, size_t offset)

pair< Path, Path >	cut_path (const Path &path, const Position &pos)

pair< Path, Path >	cut_path (const Path &path, size_t offset)

bool	maps_to_node (const Path &p, id_t id)

Position	path_start_position (const Path &path)

string	path_to_string (Path p)

Position	path_end_position (const Path &path)

bool	adjacent_mappings (const Mapping &m1, const Mapping &m2)

bool	mapping_is_match (const Mapping &m)

double	divergence (const Mapping &m)

double	identity (const Path &path)

void	decompose (const Path &path, map< pos_t, int > &ref_positions, map< pos_t, Edit > &edits)

double	overlap (const Path &p1, const Path &p2)

void	translate_node_ids (Path &path, const unordered_map< id_t, id_t > &translator)
	Switches the node ids in the path to the ones indicated by the translator. More...

void	translate_node_ids (Path &path, const unordered_map< id_t, id_t > &translator, id_t cut_node, size_t bases_removed, bool from_right)

void	translate_oriented_node_ids (Path &path, const unordered_map< id_t, pair< id_t, bool >> &translator)
	Switches the node ids and orientations in the path to the ones indicated by the translator. More...

void	translate_oriented_node_ids (Path &path, const function< pair< id_t, bool >(id_t)> &translator)
	Switches node ids and orientations in the path to the ones indicated by the translator. More...

void	translate_node_ids (path_t &path, const unordered_map< id_t, id_t > &translator)

void	translate_oriented_node_ids (path_t &path, const unordered_map< id_t, pair< id_t, bool >> &translator)

void	translate_oriented_node_ids (path_t &path, const function< pair< id_t, bool >(id_t)> &translator)

pos_t	initial_position (const Path &path)

pos_t	final_position (const Path &path)

Path	path_from_node_traversals (const list< NodeTraversal > &traversals)

void	remove_paths (Graph &graph, const function< bool(const string &)> &paths_to_take, std::list< Path > *matching)

Path	path_from_path_handle (const PathHandleGraph &graph, path_handle_t path_handle)

Alignment	alignment_from_path (const HandleGraph &graph, const Path &path)

void	from_proto_edit (const Edit &proto_edit, edit_t &edit)

void	to_proto_edit (const edit_t &edit, Edit &proto_edit)

void	from_proto_mapping (const Mapping &proto_mapping, path_mapping_t &mapping)

void	to_proto_mapping (const path_mapping_t &mapping, Mapping &proto_mapping)

void	from_proto_path (const Path &proto_path, path_t &path)

void	to_proto_path (const path_t &path, Path &proto_path)

int	mapping_from_length (const path_mapping_t &mapping)

int	path_from_length (const path_t &path)

int	mapping_to_length (const path_mapping_t &mapping)

int	path_to_length (const path_t &path)

void	reverse_complement_mapping_in_place (path_mapping_t *m, const function< int64_t(id_t)> &node_length)

path_mapping_t	reverse_complement_mapping (const path_mapping_t &m, const function< int64_t(id_t)> &node_length)

path_t	reverse_complement_path (const path_t &path, const function< int64_t(id_t)> &node_length)

void	reverse_complement_path_in_place (path_t *path, const function< int64_t(id_t)> &node_length)

pos_t	initial_position (const path_t &path)

pos_t	final_position (const path_t &path)

string	debug_string (const path_t &path)

string	debug_string (const path_mapping_t &mapping)

string	debug_string (const edit_t &edit)

int	corresponding_length_internal (const path_t &path, int given_length, bool is_from_length, bool from_end)

int	corresponding_to_length (const path_t &path, int from_length, bool from_end)

int	corresponding_from_length (const path_t &path, int to_length, bool from_end)

Path &	increment_node_mapping_ids (Path &p, id_t inc)

const Paths	paths_from_graph (Graph &g)

Path	merge_adjacent_edits (const Path &m)
	Merge adjacent edits of the same type. More...

vg::id_t	path_node (const vector< pair< vg::id_t, bool >> &path, size_t i)

vg::id_t	path_node (const gbwt::vector_type &path, size_t i)

size_t	path_size (const vector< pair< vg::id_t, bool >> &path)

size_t	path_size (const gbwt::vector_type &path)

bool	path_reverse (const vector< pair< vg::id_t, bool >> &path, size_t i)

bool	path_reverse (const gbwt::vector_type &path, size_t i)

std::ostream &	operator<< (std::ostream &out, PathBranch branch)

template<class PathType >
bool	verify_path (const PathType &path, MutableHandleGraph &unfolded, const hash_map< vg::id_t, std::vector< vg::id_t >> &reverse_mapping)

template<class Decoder >
void	printId (vg::id_t id)

PhaseUnfolder::path_type	canonical_orientation (const PhaseUnfolder::path_type &path, bool &from_border, bool &to_border)

pos_t	make_pos_t (const Position &pos)
	Convert a Position to a (much smaller) pos_t. More...

pos_t	make_pos_t (const position_t &pos)

pos_t	make_pos_t (gcsa::node_type node)
	Create a pos_t from a gcsa node. More...

Position	make_position (const pos_t &pos)
	Convert a pos_t to a Position. More...

Position	make_position (id_t id, bool is_rev, offset_t off)
	Create a Position from a Node ID, an orientation flag, and an offset along that strand of the node. More...

Position	make_position (gcsa::node_type node)
	Make a Position from a gcsa node. More...

Position	reverse (const Position &pos, size_t node_length)

pair< int64_t, int64_t >	min_oriented_distances (const unordered_map< path_handle_t, vector< pair< size_t, bool > > > &path_offsets1, const unordered_map< path_handle_t, vector< pair< size_t, bool > > > &path_offsets2)
	Find the min distance in the path offsets where the path orientation is the same and different. More...

string	debug_string (const position_t &pos)

void	from_proto_position (const Position &from, position_t &to)

void	preflight_check ()

ostream &	operator<< (ostream &os, const Counts &counts)

std::string	to_string (handle_t handle)

hash_map< Haplotypes::Subchain::kmer_type, size_t >::iterator	find_kmer (hash_map< Haplotypes::Subchain::kmer_type, size_t > &counts, Haplotypes::Subchain::kmer_type kmer, size_t k)

void	sa_to_da (std::vector< HaplotypePartitioner::sequence_type > &sequences, const gbwt::FastLocate &r_index)

std::string	generate_haplotype (gbwt::edge_type pos, handle_t end, size_t start_max, size_t end_max, const gbwtgraph::GBWTGraph &graph)

std::vector< HaplotypePartitioner::kmer_type >	take_unique_minimizers (const std::string &sequence, const HaplotypePartitioner::minimizer_index_type &minimizer_index)

void	present_kmers (const std::vector< std::vector< HaplotypePartitioner::kmer_type >> &sequences, std::vector< std::pair< HaplotypePartitioner::kmer_type, size_t >> &all_kmers, sdsl::bit_vector &kmers_present)

void	add_path (const gbwt::GBWT &source, gbwt::size_type path_id, gbwt::GBWTBuilder &builder, gbwtgraph::MetadataBuilder &metadata)

void	recombinator_sanity_checks (const Recombinator::Parameters &parameters)

double	get_or_estimate_coverage (const hash_map< Haplotypes::Subchain::kmer_type, size_t > &counts, const Recombinator::Parameters &parameters, Haplotypes::Verbosity verbosity)

std::vector< std::pair< Recombinator::kmer_presence, double > >	classify_kmers (const Haplotypes::Subchain &subchain, const hash_map< Haplotypes::Subchain::kmer_type, size_t > &kmer_counts, double coverage, Recombinator::Statistics *statistics, const Recombinator::Parameters &parameters)

std::vector< std::pair< size_t, double > >	select_diploid (const Haplotypes::Subchain &subchain, const std::vector< std::pair< size_t, double >> &candidates, const std::vector< std::pair< Recombinator::kmer_presence, double >> &kmer_types)

std::vector< std::pair< size_t, double > >	select_haplotypes (const Haplotypes::Subchain &subchain, const hash_map< Haplotypes::Subchain::kmer_type, size_t > &kmer_counts, double coverage, Recombinator::Statistics statistics, std::vector< Recombinator::LocalHaplotype > local_haplotypes, const Recombinator::Parameters &parameters)

void	parse_region (const string &target, string &name, int64_t &start, int64_t &end)

void	parse_bed_regions (const string &bed_path, vector< Region > &out_regions, vector< string > *out_names)

void	parse_region (string &region, Region &out_region)

pos_t	position_at (PathPositionHandleGraph *graph_ptr, const string &path_name, const size_t &path_offset, bool is_reverse)

string	to_string (const HandleGraph &graph, handle_t handle)

string	to_string (const HandleGraph &graph, edge_t edge)

size_t	minimum_distance (const SnarlDistanceIndex &distance_index, pos_t pos1, pos_t pos2, bool unoriented_distance, const HandleGraph *graph)

size_t	maximum_distance (const SnarlDistanceIndex &distance_index, pos_t pos1, pos_t pos2)

void	fill_in_distance_index (SnarlDistanceIndex distance_index, const HandleGraph graph, const HandleGraphSnarlFinder *snarl_finder, size_t size_limit, bool silence_warnings)

SnarlDistanceIndex::TemporaryDistanceIndex	make_temporary_distance_index (const HandleGraph graph, const HandleGraphSnarlFinder snarl_finder, size_t size_limit)

void	populate_snarl_index (SnarlDistanceIndex::TemporaryDistanceIndex &temp_index, pair< SnarlDistanceIndex::temp_record_t, size_t > snarl_index, size_t size_limit, const HandleGraph *graph)

void	subgraph_in_distance_range (const SnarlDistanceIndex &distance_index, const Path &path, const HandleGraph *super_graph, size_t min_distance, size_t max_distance, std::unordered_set< nid_t > &subgraph, bool look_forward)

void	subgraph_in_distance_range_walk_graph (const HandleGraph *super_graph, size_t min_distance, size_t max_distance, std::unordered_set< nid_t > &subgraph, vector< pair< handle_t, size_t >> &start_nodes, hash_set< pair< nid_t, bool >> &seen_nodes, const pair< nid_t, bool > &traversal_start)

void	subgraph_in_distance_range_walk_across_chain (const SnarlDistanceIndex &distance_index, const HandleGraph *super_graph, std::unordered_set< nid_t > &subgraph, net_handle_t current_node, size_t current_distance, vector< pair< handle_t, size_t >> &search_start_nodes, hash_set< pair< nid_t, bool >> &seen_nodes, const size_t &min_distance, const size_t &max_distance, bool checked_loop)

void	subgraph_containing_path_snarls (const SnarlDistanceIndex &distance_index, const HandleGraph *graph, const Path &path, std::unordered_set< nid_t > &subgraph)

void	add_descendants_to_subgraph (const SnarlDistanceIndex &distance_index, const net_handle_t &parent, std::unordered_set< nid_t > &subgraph)

MIPayloadValues	get_minimizer_distances (const SnarlDistanceIndex &distance_index, pos_t pos)

bool	start_backward (const Chain &chain)

bool	end_backward (const Chain &chain)

Visit	get_start_of (const Chain &chain)

Visit	get_end_of (const Chain &chain)

ChainIterator	chain_begin (const Chain &chain)

ChainIterator	chain_end (const Chain &chain)

ChainIterator	chain_rbegin (const Chain &chain)

ChainIterator	chain_rend (const Chain &chain)

ChainIterator	chain_rcbegin (const Chain &chain)

ChainIterator	chain_rcend (const Chain &chain)

ChainIterator	chain_begin_from (const Chain &chain, const Snarl *start_snarl, bool snarl_orientation)

ChainIterator	chain_end_from (const Chain &chain, const Snarl *start_snarl, bool snarl_orientation)

edge_t	to_edge (const handlegraph::HandleGraph &graph, const Visit &v1, const Visit &v2)
	Make an edge_t from a pair of visits. More...

bool	operator== (const Visit &a, const Visit &b)

bool	operator!= (const Visit &a, const Visit &b)

bool	operator< (const Visit &a, const Visit &b)

ostream &	operator<< (ostream &out, const Visit &visit)

bool	operator== (const SnarlTraversal &a, const SnarlTraversal &b)

bool	operator!= (const SnarlTraversal &a, const SnarlTraversal &b)

bool	operator< (const SnarlTraversal &a, const SnarlTraversal &b)

bool	operator== (const Snarl &a, const Snarl &b)

bool	operator!= (const Snarl &a, const Snarl &b)

bool	operator< (const Snarl &a, const Snarl &b)

ostream &	operator<< (ostream &out, const Snarl &snarl)

NodeTraversal	to_node_traversal (const Visit &visit, const VG &graph)

NodeTraversal	to_rev_node_traversal (const Visit &visit, const VG &graph)

NodeSide	to_left_side (const Visit &visit)
	Converts a Visit to a node or snarl into a NodeSide for its left side. More...

NodeSide	to_right_side (const Visit &visit)
	Converts a Visit to a node or snarl into a NodeSide for its right side. More...

Visit	to_visit (const NodeTraversal &node_traversal)
	Converts a NodeTraversal to a Visit. More...

Visit	to_visit (const Mapping &mapping, bool make_full_node_match=false)

Visit	to_visit (id_t node_id, bool is_reverse)
	Make a Visit from a node ID and an orientation. More...

Visit	to_visit (const Snarl &snarl)
	Make a Visit from a snarl to traverse. More...

Visit	to_visit (const handlegraph::HandleGraph &graph, const handle_t &handle)
	Make a Visit from a handle in a HandleGraph. More...

Visit	reverse (const Visit &visit)
	Get the reversed version of a visit. More...

Visit	to_rev_visit (const NodeTraversal &node_traversal)
	Converts a NodeTraversal to a Visit in the opposite orientation. More...

Mapping	to_mapping (const Visit &visit, std::function< size_t(id_t)> node_length)

Mapping	to_mapping (const Visit &visit, const HandleGraph &vg)

Alignment	to_alignment (const SnarlTraversal &trav, const HandleGraph &graph)
	Convert a snarl traversal into an alignment. More...

void	transfer_boundary_info (const Snarl &from, Snarl &to)
	Copies the boundary Visits from one Snarl into another. More...

NodeTraversal	to_node_traversal (const Visit &visit, VG &graph)

NodeTraversal	to_rev_node_traversal (const Visit &visit, VG &graph)

multipath_alignment_t	from_hit (const Alignment &alignment, const HandleGraph &graph, const pos_t &hit_pos, const MaximalExactMatch &mem, const GSSWAligner &scorer)

tuple< pos_t, int64_t, int32_t >	trimmed_end (const Alignment &aln, int64_t len, bool from_end, const HandleGraph &graph, const GSSWAligner &aligner)

bool	trim_path (path_t *path, bool from_left, int64_t mapping_idx, int64_t edit_idx, int64_t base_idx)

pair< pair< path_t, int32_t >, pair< path_t, int32_t > >	split_splice_segment (const Alignment &splice_segment, const tuple< int64_t, int64_t, int64_t > &left_trace, const tuple< int64_t, int64_t, int64_t > &right_trace, int64_t splice_junction_idx, const GSSWAligner &scorer, const HandleGraph &graph)

multipath_alignment_t &&	fuse_spliced_alignments (const Alignment &alignment, multipath_alignment_t &&left_mp_aln, multipath_alignment_t &&right_mp_aln, int64_t left_bridge_point, const Alignment &splice_segment, int64_t splice_junction_idx, int32_t splice_score, const GSSWAligner &scorer, const HandleGraph &graph)

double	median (std::vector< int > &v)

void	wellford_update (size_t &count, double &mean, double &M2, double new_val)

pair< double, double >	wellford_mean_var (size_t count, double mean, double M2, bool sample_variance)

double	Phi (double x)
	The standard normal cumulative distribution function. More...

double	Phi_inv (double quantile)
	Inverse CDF of a standard normal distribution. Must have 0 < quantile < 1. More...

double	lognormal_pdf (double x, double mu, double sigma)
	Probability density function or log-normal distribution. More...

double	slope (const std::vector< double > &x, const std::vector< double > &y)

double	fit_zipf (const vector< double > &y)

double	fit_fixed_shape_max_exponential (const vector< double > &x, double shape, double tolerance=1e-8)
	Returns the MLE rate parameter for the distribution of (shape) iid exponential RVs. More...

double	fit_fixed_rate_max_exponential (const vector< double > &x, double rate, double tolerance=1e-8)
	Returns the MLE estimate for the number of iid exponential RVs the data are maxima of. More...

pair< double, double >	fit_max_exponential (const vector< double > &x, double tolerance=1e-8)
	Returns the MLE rate and shape parameters of a max exponential. More...

double	max_exponential_log_likelihood (const vector< double > &x, double rate, double shape, double location=0.0)
	The log likelihood of a max exponential with the given parameters on the given data. More...

pair< double, double >	fit_weibull (const vector< double > &x)
	Returns an estimate of the rate and shape parameters of a Weibull distribution. More...

tuple< double, double, double >	fit_offset_weibull (const vector< double > &x, double tolerance=1e-8)
	Returns an estimate of the rate, shape, and location (minimum value) of a 3-parameter Weibull distribution. More...

double	weibull_log_likelihood (const vector< double > &x, double scale, double shape, double location=0.0)
	Returns the log likelihood of some data generated by a Weibull distribution. More...

double	golden_section_search (const function< double(double)> &f, double x_min, double x_max, double tolerance=1e-8)
	Returns a local maximum of a function within an interval. More...

double	phred_to_prob (uint8_t phred)
	Convert 8-bit Phred quality score to probability of wrongness, using a lookup table. More...

double	phred_for_at_least_one (size_t p, size_t n)

double	prob_for_at_least_one (size_t p, size_t n)

vector< vector< double > >	transpose (const vector< vector< double >> &A)
	A shitty set of linear algebra functions. More...

vector< vector< double > >	matrix_multiply (const vector< vector< double >> &A, const vector< vector< double >> &B)

vector< double >	matrix_multiply (const vector< vector< double >> &A, const vector< double > &b)

vector< vector< double > >	matrix_invert (const vector< vector< double >> &A)

vector< double >	regress (const vector< vector< double >> &X, vector< double > &y)
	Returns the coefficients of a regression (does not automatically compute constant) More...

template<typename T >
double	stdev (const T &v)

template<typename Number >
SummaryStatistics	summary_statistics (const std::map< Number, size_t > &values)
	Returns summary statistics for a multiset of numbers. More...

double	add_log (double log_x, double log_y)

double	subtract_log (double log_x, double log_y)

double	ln_to_log10 (double ln)

double	log10_to_ln (double l10)

double	log10_add_one (double x)

double	add_log10 (double i, double j)

template<typename T >
T	normal_pdf (T x, T m=0.0, T s=1.0)

double	prob_to_logprob (double prob)
	Convert a probability to a natural log probability. More...

double	logprob_to_prob (double logprob)
	Convert natural log probability to a probability. More...

double	logprob_add (double logprob1, double logprob2)

double	logprob_invert (double logprob)
	Invert a logprob, and get the probability of its opposite. More...

double	phred_to_prob (double phred)
	Convert floating point Phred quality score to probability of wrongness. More...

double	prob_to_phred (double prob)
	Convert probability of wrongness to integer Phred quality score. More...

double	phred_to_logprob (int phred)
	Convert a Phred quality score directly to a natural log probability of wrongness. More...

double	logprob_to_phred (double logprob)
	Convert a natural log probability of wrongness directly to a Phred quality score. More...

double	logprob_geometric_mean (double lnprob1, double lnprob2)
	Take the geometric mean of two logprobs. More...

double	phred_geometric_mean (double phred1, double phred2)
	Take the geometric mean of two phred-encoded probabilities. More...

double	phred_add (double phred1, double phred2)

template<typename Collection >
Collection::value_type	logprob_sum (const Collection &collection)

template<typename Iterator >
std::iterator_traits< Iterator >::value_type	phred_sum (const Iterator &begin_it, const Iterator &end_it)

template<typename Collection >
Collection::value_type	phred_sum (const Collection &collection)

double	max_exponential_cdf (double x, double rate, double shape, double location=0.0)
	Return the CDF of a max exponential with the given parameters. More...

double	weibull_cdf (double x, double scale, double shape, double location=0.0)
	Return the CDF of a max exponential with the given parameters. More...

real_t	gamma_ln (real_t x)

real_t	factorial_ln (int n)

real_t	pow_ln (real_t m, int n)

real_t	choose_ln (int n, int k)

real_t	multinomial_choose_ln (int n, vector< int > k)

real_t	poisson_prob_ln (int observed, real_t expected)

template<typename ProbIn >
real_t	multinomial_sampling_prob_ln (const vector< ProbIn > &probs, const vector< int > &obs)

template<typename ProbIn >
real_t	binomial_cmf_ln (ProbIn success_logprob, size_t trials, size_t successes)

template<typename ProbIn >
real_t	geometric_sampling_prob_ln (ProbIn success_logprob, size_t trials)

template<typename Iter >
bool	advance_split (Iter start, Iter end)

template<typename ProbIn >
real_t	multinomial_censored_sampling_prob_ln (const vector< ProbIn > &probs, const unordered_map< vector< bool >, int > &obs)

real_t	ewens_af_prob_ln (const vector< int > &a, real_t theta)

auto	operator<< (ostream &out, const BitString &bs)
	Allow BitStrings to be printed for debugging. More...

bool	operator== (const Exon &lhs, const Exon &rhs)

bool	operator!= (const Exon &lhs, const Exon &rhs)

bool	operator< (const Exon &lhs, const Exon &rhs)

bool	operator== (const Transcript &lhs, const Transcript &rhs)

bool	operator!= (const Transcript &lhs, const Transcript &rhs)

bool	operator< (const Transcript &lhs, const Transcript &rhs)

bool	operator== (const Mapping &lhs, const Mapping &rhs)

bool	operator!= (const Mapping &lhs, const Mapping &rhs)

bool	operator== (const Path &lhs, const Path &rhs)

bool	operator!= (const Path &lhs, const Path &rhs)

bool	sort_pair_by_second (const pair< uint32_t, uint32_t > &lhs, const pair< uint32_t, uint32_t > &rhs)

bool	sort_transcript_paths_by_name (const CompletedTranscriptPath &lhs, const CompletedTranscriptPath &rhs)

handle_t	mapping_to_handle (const Mapping &mapping, const HandleGraph &graph)

bool	is_match (const Translation &translation)

double	weighted_jaccard_coefficient (const PathHandleGraph *graph, const multiset< handle_t > &target, const multiset< handle_t > &query)

vector< int >	get_traversal_order (const PathHandleGraph *graph, const vector< Traversal > &traversals, const vector< string > &trav_path_names, const vector< int > &ref_travs, int64_t ref_trav_idx, const vector< bool > &use_traversal)

vector< vector< int > >	cluster_traversals (const PathHandleGraph *graph, const vector< Traversal > &traversals, const vector< int > &traversal_order, const vector< pair< handle_t, handle_t >> &child_snarls, double min_jaccard, vector< pair< double, int64_t >> &out_info, vector< int > &out_child_snarl_to_trav)

vector< vector< int > >	assign_child_snarls_to_traversals (const PathHandleGraph *graph, const vector< Traversal > &traversals, const vector< pair< handle_t, handle_t >> &child_snarls)

void	merge_equivalent_traversals_in_graph (MutablePathHandleGraph *graph, const unordered_set< path_handle_t > &selected_paths, bool use_snarl_manager)

template<typename T , typename U >
double	jaccard_coefficient (const T &target, const U &query)

string	traversal_to_string (const PathHandleGraph *graph, const Traversal &traversal, int64_t max_steps)

string	graph_interval_to_string (const HandleGraph *graph, const handle_t &start_handle, const handle_t &end_handle)

pair< vector< SnarlTraversal >, vector< pair< step_handle_t, step_handle_t > > >	find_path_traversals (const Snarl &site)

pos_t	make_pos_t (id_t id, bool is_rev, offset_t off)
	Create a pos_t from a Node ID, an orientation flag, and an offset along that strand of the node. More...

id_t	id (const pos_t &pos)
	Extract the id of the node a pos_t is on. More...

bool	is_rev (const pos_t &pos)
	Return true if a pos_t is on the reverse strand of its node. More...

offset_t	offset (const pos_t &pos)
	Get the offset along the selected strand of the node from a pos_t. More...

id_t &	get_id (pos_t &pos)
	Get a reference to the Node ID of a pos_t. More...

bool &	get_is_rev (pos_t &pos)
	Get a reference to the reverse flag of a pos_t. More...

offset_t &	get_offset (pos_t &pos)
	Get a reference to the offset field of a pos_t, which counts along the selected strand of the node. More...

bool	is_empty (const pos_t &pos)
	Return true if a pos_t is unset. More...

pos_t	empty_pos_t ()
	Get an unset pos_t. More...

pos_t	reverse (const pos_t &pos, size_t node_length)

pos_t	reverse_base_pos (const pos_t &pos, size_t node_length)
	Reverse a pos_t and get a pos_t at the same base, going the other direction. More...

std::ostream &	operator<< (std::ostream &out, const pos_t &pos)
	Print a pos_t to a stream. More...

char	reverse_complement (const char &c)

string	reverse_complement (const string &seq)

void	reverse_complement_in_place (string &seq)

bool	is_all_n (const string &seq)

double	get_fraction_of_ns (const string &seq)

int	get_thread_count (void)

void	choose_good_thread_count ()

std::vector< std::string > &	split_delims (const std::string &s, const std::string &delims, std::vector< std::string > &elems, size_t max_cuts)

std::vector< std::string >	split_delims (const std::string &s, const std::string &delims, size_t max_cuts)

bool	starts_with (const std::string &value, const std::string &prefix)
	Check if a string starts with another string. More...

const std::string	sha1sum (const std::string &data)

const std::string	sha1head (const std::string &data, size_t head)

string	wrap_text (const string &str, size_t width)

bool	is_number (const std::string &s)

bool	isATGC (const char &b)
	Return true if a character is an uppercase A, C, G, or T, and false otherwise. More...

bool	allATGC (const string &s)

bool	allATGCN (const string &s)

string	nonATGCNtoN (const string &s)

string	allAmbiguousToN (const string &s)

string	toUppercase (const string &s)

void	toUppercaseInPlace (string &s)

void	write_fasta_sequence (const std::string &name, const std::string &sequence, ostream &os, size_t width)

string	get_or_make_variant_id (const vcflib::Variant &variant)

string	make_variant_id (const vcflib::Variant &variant)

vector< size_t >	range_vector (size_t begin, size_t end)
	Vector containing positive integer values in [begin, end) More...

std::vector< size_t >	stack_permutations (const std::vector< size_t > &bottom, const std::vector< size_t > &top)
	Apply one permutation on top of another. Retutn the combined permutation. More...

bool	have_input_file (int &optind, int argc, char **argv)
	Return true if there's a command line argument (i.e. input file name) waiting to be processed. More...

void	get_input_file (int &optind, int argc, char **argv, function< void(istream &)> callback)

string	get_input_file_name (int &optind, int argc, char **argv, bool test_open)

string	get_output_file_name (int &optind, int argc, char **argv)

void	get_input_file (const string &file_name, function< void(istream &)> callback)

pair< string, string >	split_ext (const string &filename)
	Split off the extension from a filename and return both parts. More...

string	file_base_name (const string &filename)
	Get the base name of a filename (without the directory and the extension). More...

bool	file_exists (const string &filename)

void	create_ref_allele (vcflib::Variant &variant, const std::string &allele)

int	add_alt_allele (vcflib::Variant &variant, const std::string &allele)

size_t	integer_power (uint64_t base, uint64_t exponent)
	Computes base^exponent in log(exponent) time. More...

size_t	modular_exponent (uint64_t base, uint64_t exponent, uint64_t modulus)

default_random_engine	random_sequence_gen (102)

string	random_sequence (size_t length)
	Returns a uniformly random DNA sequence of the given length. More...

string	pseudo_random_sequence (size_t length, uint64_t seed)
	Returns a uniformly random DNA sequence sequence deterministically from a seed. More...

string	replace_in_string (string subject, const string &search, const string &replace)

string	percent_url_encode (const string &seq)
	Escape "%" to "%25". More...

bool	deterministic_flip (LazyRNG &rng)
	Flip a coin with 50% probability against the given RNG. More...

unordered_map< id_t, pair< id_t, bool > >	overlay_node_translations (const unordered_map< id_t, pair< id_t, bool >> &over, const unordered_map< id_t, pair< id_t, bool >> &under)
	Compose the translations from two graph operations, both of which involved oriented transformations. More...

unordered_map< id_t, pair< id_t, bool > >	overlay_node_translations (const unordered_map< id_t, id_t > &over, const unordered_map< id_t, pair< id_t, bool >> &under)
	Compose the translations from two graph operations, the first of which involved oriented transformations. More...

unordered_map< id_t, pair< id_t, bool > >	overlay_node_translations (const unordered_map< id_t, pair< id_t, bool >> &over, const unordered_map< id_t, id_t > &under)
	Compose the translations from two graph operations, the second of which involved oriented transformations. More...

unordered_map< id_t, id_t >	overlay_node_translations (const unordered_map< id_t, id_t > &over, const unordered_map< id_t, id_t > &under)
	Compose the translations from two graph operations, neither of which involved oriented transformations. More...

template<>
bool	parse (const string &arg, double &dest)

template<>
bool	parse (const string &arg, std::regex &dest)

template<>
bool	parse (const string &arg, pos_t &dest)

bool	is_number (const string &s)

template<typename T , typename V >
set< T >	map_keys_to_set (const map< T, V > &m)

template<typename T >
vector< T >	pmax (const std::vector< T > &a, const std::vector< T > &b)

template<typename T >
vector< T >	vpmax (const std::vector< std::vector< T >> &vv)

template<typename Collection >
Collection::value_type	sum (const Collection &collection)

template<template< class T, class A=std::allocator< T >> class Container, typename Input , typename Output >
Container< Output >	map_over (const Container< Input > &in, const std::function< Output(const Input &)> &lambda)

template<template< class T, class A=std::allocator< T >> class Container, typename Item >
Container< const Item * >	pointerfy (const Container< Item > &in)

template<typename Item >
VectorView< Item >::const_iterator	operator+ (typename VectorView< Item >::const_iterator::difference_type a, const typename VectorView< Item >::const_iterator &b)
	Allow VectorView iterators to be added to numbers. More...

vector< size_t >	range_vector (size_t end)
	Vector containing positive integer values in [0, end) More...

template<typename Iterator >
std::vector< size_t >	sort_permutation (const Iterator &begin, const Iterator &end, const std::function< bool(const typename Iterator::value_type &, const typename Iterator::value_type &)> &comparator)
	Get the index permutation that sorts the given items with the given comparator instead of <. More...

template<typename Iterator >
std::vector< size_t >	sort_permutation (const Iterator &begin, const Iterator &end)
	Get the index permutation that sorts the given items ascending using <. More...

size_t	integer_power (size_t x, size_t power)

template<class RandomIt >
void	deterministic_shuffle (RandomIt begin, RandomIt end, LazyRNG &rng)

template<typename Number >
bool	deterministic_beats (const Number &a, const Number &b, LazyRNG &rng)
	Return true if a is larger than b, or else equal to b and wins a coin flip. More...

string	make_shuffle_seed (const Alignment &aln)
	Make seeds for Alignments based on their sequences. More...

template<typename T >
string	make_shuffle_seed (const T *ptr)
	Make seeds for pointers to things we can make seeds for. More...

template<typename T1 , typename T2 >
string	make_shuffle_seed (const pair< T1, T2 > &p)
	Make seeds for pairs of things we can make seeds for. More...

template<class RandomIt >
void	deterministic_shuffle (RandomIt begin, RandomIt end)
	Do a deterministic shuffle with automatic seed determination. More...

template<class RandomIt , class Compare >
void	sort_shuffling_ties (RandomIt begin, RandomIt end, Compare comp, LazyRNG &rng)

template<class RandomIt , class Compare >
void	sort_shuffling_ties (RandomIt begin, RandomIt end, Compare comp)

template<typename Result >
Result	parse (const string &arg)

template<typename Result >
Result	parse (const char *arg)

template<typename Result >
bool	parse (const string &arg, Result &dest)

template<typename Result >
bool	parse (const string &arg, typename enable_if< sizeof(Result)<=sizeof(long long) &&is_integral< Result >::value &&is_signed< Result >::value, Result >::type &dest)

void	genotype_svs (VG *graph, string gamfile, string refpath)

void	variant_recall (VG graph, vcflib::VariantCallFile vars, FastaReference ref_genome, vector< FastaReference > insertions, string gamfile)

tuple< double, double, double >	hash_to_rgb (const string &str, double min_sum)

size_t	wang_hash_64 (size_t key)

template<typename Result >
bool	parse (const string &arg, typename enable_if< is_instantiation_of< Result, Range >::value, Result >::type &dest)
	Parse a range as start[:end[:step]]. More...

Variables
const char *const	BAM_DNA_LOOKUP = "=ACMGRSVTWYHKDBN"

const char *	var = "VG_FULL_TRACEBACK"

bool	fullTrace = false

const char *	ISSUE_URL = "https://github.com/vgteam/vg/issues/new/choose"

thread_local std::string	stored_crash_context

const read_alignment_index_t	NO_READ_INDEX = {std::numeric_limits<size_t>::infinity(), std::numeric_limits<size_t>::infinity()}
	Represents an unset index. More...

const alignment_index_t	NO_INDEX {std::numeric_limits<size_t>::max(), std::numeric_limits<size_t>::max(), std::numeric_limits<bool>::max()}
	Represents an unset index. More...

Typedef Documentation

◆ benchtime

using vg::benchtime = typedef chrono::nanoseconds

We define a duration type for expressing benchmark times in.

◆ Chain

using vg::Chain = typedef vector<pair<const Snarl*, bool> >

Snarls are defined at the Protobuf level, but here is how we define chains as real objects.

A chain is a sequence of Snarls, in either normal (false) or reverse (true) orientation.

The SnarlManager is going to have one official copy of each chain stored, and it will give you a pointer to it on demand.

◆ DeletableHandleGraph

using vg::DeletableHandleGraph = typedef handlegraph::DeletableHandleGraph

◆ edge_t

using vg::edge_t = typedef handlegraph::edge_t

◆ EdgeMapping

typedef std::map<id_t, std::vector<Edge*> > vg::EdgeMapping

◆ exon_nodes_t

typedef vector<gbwt::node_type> vg::exon_nodes_t

◆ GAMIndex

using vg::GAMIndex = typedef StreamIndex<Alignment>

Define a GAM index as a stream index over a stream of Alignments.

◆ GAMSorter

using vg::GAMSorter = typedef StreamSorter<Alignment>

◆ Handle2Component

typedef unordered_map<handle_t, int> vg::Handle2Component

◆ handle_t

using vg::handle_t = typedef handlegraph::handle_t

◆ HandleGraph

using vg::HandleGraph = typedef handlegraph::HandleGraph

◆ HandleSet

typedef unordered_set<handle_t> vg::HandleSet

◆ id_t

typedef handlegraph::nid_t vg::id_t

Represents a Node ID. ID type is a 64-bit signed int.

◆ IndexGroup

using vg::IndexGroup = typedef set<IndexName>

A group of indexes that can be made simultaneously

◆ IndexName

using vg::IndexName = typedef string

A unique identifier for an Index

◆ MutableHandleGraph

using vg::MutableHandleGraph = typedef handlegraph::MutableHandleGraph

◆ MutablePathDeletableHandleGraph

using vg::MutablePathDeletableHandleGraph = typedef handlegraph::MutablePathDeletableHandleGraph

◆ MutablePathHandleGraph

using vg::MutablePathHandleGraph = typedef handlegraph::MutablePathHandleGraph

◆ MutablePathMutableHandleGraph

using vg::MutablePathMutableHandleGraph = typedef handlegraph::MutablePathMutableHandleGraph

◆ NamedNodeBackTranslation

using vg::NamedNodeBackTranslation = typedef handlegraph::NamedNodeBackTranslation

◆ nid_t

using vg::nid_t = typedef handlegraph::nid_t

◆ offset_t

typedef size_t vg::offset_t

Represents an offset along the sequence of a Node. Offsets are size_t.

◆ oriented_node_range_t

using vg::oriented_node_range_t = typedef handlegraph::oriented_node_range_t

◆ pareto_point

typedef std::pair<uint32_t, int32_t> vg::pareto_point

◆ path_handle_t

using vg::path_handle_t = typedef handlegraph::path_handle_t

◆ PathHandleGraph

using vg::PathHandleGraph = typedef handlegraph::PathHandleGraph

◆ PathInterval

using vg::PathInterval = typedef pair<step_handle_t, step_handle_t>

◆ PathMetadata

using vg::PathMetadata = typedef handlegraph::PathMetadata

◆ PathPositionHandleGraph

using vg::PathPositionHandleGraph = typedef handlegraph::PathPositionHandleGraph

◆ PathSense

using vg::PathSense = typedef handlegraph::PathSense

◆ pos_t

typedef std::tuple<id_t, bool, offset_t> vg::pos_t

Represents an oriented position on a Node. Position type: id, direction, offset. Offset is counted as for as prorobuf Position, from the node's first base on the forward strand, and from its last base on the reverse strand.

◆ RankedHandleGraph

using vg::RankedHandleGraph = typedef handlegraph::RankedHandleGraph

◆ real_t

using vg::real_t = typedef long double

◆ RecipeFunc

using vg::RecipeFunc = typedef function<vector<vector<string> >(const vector<const IndexFile*>&, const IndexingPlan*, AliasGraph&, const IndexGroup&)>

Is a recipe to create the files (returned by name) associated with some index, from a series of input indexes, given the plan it is being generated for and the index being generated.

◆ RecipeName

using vg::RecipeName = typedef pair<IndexGroup, size_t>

Names a recipe in the collection of registered recipes.

◆ SerializableHandleGraph

using vg::SerializableHandleGraph = typedef handlegraph::SerializableHandleGraph

◆ step_handle_t

using vg::step_handle_t = typedef handlegraph::step_handle_t

◆ subrange_t

using vg::subrange_t = typedef handlegraph::subrange_t

◆ thread_ids_t

typedef vector<gbwt::size_type> vg::thread_ids_t

◆ thread_t

using vg::thread_t = typedef vector<gbwt::node_type>

◆ Traversal

using vg::Traversal = typedef vector<handle_t>

◆ VectorizableHandleGraph

using vg::VectorizableHandleGraph = typedef handlegraph::VectorizableHandleGraph

Enumeration Type Documentation

◆ alignment_emitter_flags_t

enum vg::alignment_emitter_flags_t

Flag enum for controlling the behavior of alignment emitters behind get_alignment_emitter().

Enumerator
ALIGNMENT_EMITTER_FLAG_NONE	Value for no flags set.
ALIGNMENT_EMITTER_FLAG_HTS_RAW	Skip surjection, and expect pre-surjected alignments.
ALIGNMENT_EMITTER_FLAG_HTS_SPLICED	Use splicing-aware conversion to HTSlib formats: alignments are spliced at known splice sites (i.e. edges in the graph), so form spliced CIGAR strings
ALIGNMENT_EMITTER_FLAG_HTS_PRUNE_SUSPICIOUS_ANCHORS	When surjecting, discard low-complexity anchors and realign more freely against the target path.
ALIGNMENT_EMITTER_FLAG_VG_USE_SEGMENT_NAMES	Emit graph alignments in named segment (i.e. GFA space) instead of numerical node ID space.

◆ MappingQualityMethod

enum vg::MappingQualityMethod

Enumerator
Approx
Exact
Adaptive
None

◆ SnarlType

enum vg::SnarlType

Enumeration of the classifications of snarls.

Enumerator
UNCLASSIFIED
ULTRABUBBLE
UNARY

Function Documentation

◆ add_alt_allele()

int vg::add_alt_allele	(	vcflib::Variant &	variant,
		const std::string &	allele
	)

Add a new alt allele to a vcflib Variant, since apaprently there's no method for that already.

If that allele already exists in the variant, does not add it again.

Retuerns the allele number (0, 1, 2, etc.) corresponding to the given allele string in the given variant.

◆ add_descendants_to_subgraph()

void vg::add_descendants_to_subgraph	(	const SnarlDistanceIndex &	distance_index,
		const net_handle_t &	parent,
		std::unordered_set< nid_t > &	subgraph
	)

◆ add_edges_only()

void vg::add_edges_only	(	MutableHandleGraph *	graph,
		function< void(function< void(Alignment &)>, bool, bool)>	iterate_gam,
		double	min_mapq,
		size_t	min_bp_coverage
	)

Add edges between consecutive mappings that aren't already in the graph note: offsets are completely ignored (a simplifying assumption designed to help with SV genotpying with pack/call as edge packing works similarly)

No existing nodes or edges are modified, and no nodes are added, just edges So the output graph will be id-space compatible, and any GAM/GAF will continue to be valid for it.

◆ add_log()

double vg::add_log	(	double	log_x,
		double	log_y
	)

inline

◆ add_log10()

double vg::add_log10	(	double	i,
		double	j
	)

inline

Return the log of the sum of two log10-transformed values without taking them out of log space.

◆ add_nodes_and_edges() [1/2]

Path vg::add_nodes_and_edges	(	MutableHandleGraph *	graph,
		const Path &	path,
		const map< pos_t, id_t > &	node_translation,
		unordered_map< pair< pos_t, string >, vector< id_t >> &	added_seqs,
		unordered_map< id_t, Path > &	added_nodes,
		const unordered_map< id_t, size_t > &	orig_node_sizes,
		set< NodeSide > &	dangling,
		size_t	max_node_size = `1024`
	)

Given a path on nodes that may or may not exist, and a map from start position in the old graph to a node in the current graph, add all the new sequence and edges required by the path. The given path must not contain adjacent perfect match edits in the same mapping, or any deletions on the start or end of mappings (the removal of which can be accomplished with the Path::simplify() function).

Outputs (and caches for subsequent calls) novel node runs in added_seqs, and Paths describing where novel nodes translate back to in the original graph in added_nodes. Also needs a map of the original sizes of nodes deleted from the original graph, for reverse complementing. If dangling is nonempty, left edges of nodes created for initial inserts will connect to the specified sides. At the end, dangling is populated with the side corresponding to the last edit in the path.

Returns a fully embedded version of the path, after all node insertions, divisions, and translations.

◆ add_nodes_and_edges() [2/2]

Path vg::add_nodes_and_edges	(	MutableHandleGraph *	graph,
		const Path &	path,
		const map< pos_t, id_t > &	node_translation,
		unordered_map< pair< pos_t, string >, vector< id_t >> &	added_seqs,
		unordered_map< id_t, Path > &	added_nodes,
		const unordered_map< id_t, size_t > &	orig_node_sizes,
		size_t	max_node_size
	)

This version doesn't require a set of dangling sides to populate

◆ add_path()

void vg::add_path	(	const gbwt::GBWT &	source,
		gbwt::size_type	path_id,
		gbwt::GBWTBuilder &	builder,
		gbwtgraph::MetadataBuilder &	metadata
	)

◆ add_path_to_graph()

path_handle_t vg::add_path_to_graph	(	MutablePathHandleGraph *	graph,
		const Path &	path
	)

Add a path to the graph. This is like VG::extend, and expects a path with no edits, and for all the nodes and edges in the path to exist exactly in the graph

◆ add_thread_edges_to_set()

void vg::add_thread_edges_to_set	(	thread_t &	t,
		set< pair< int, int > > &	edges
	)

◆ add_thread_nodes_to_set()

void vg::add_thread_nodes_to_set	(	thread_t &	t,
		set< int64_t > &	nodes
	)

◆ addArbitraryTelomerePair()

void vg::addArbitraryTelomerePair	(	vector< stCactusEdgeEnd * >	ends,
		stList *	telomeres
	)

Finds an arbitrary pair of telomeres in a Cactus graph, which are either a pair of bridge edge ends or a pair of chain edge ends, oriented such that they form a pair of boundaries.

Mostly copied from the pinchesAndCacti unit tests.

◆ adjacent_mappings()

bool vg::adjacent_mappings	(	const Mapping &	m1,
		const Mapping &	m2
	)

◆ advance_split()

template<typename Iter >

bool vg::advance_split	(	Iter	start,
		Iter	end
	)

Given a split of items across a certain number of categories, as ints between the two given bidirectional iterators, advance to the next split and return true. If there is no next split, leave the collection unchanged and return false.

◆ aligned_interval()

pair< int64_t, int64_t > vg::aligned_interval ( const multipath_alignment_t & multipath_aln )

The indexes on the read sequence of the portion of the read that is aligned outside of soft clips.

◆ alignment_end()

Position vg::alignment_end ( const Alignment & aln )

◆ alignment_ends()

vector< Alignment > vg::alignment_ends	(	const Alignment &	aln,
		size_t	len1,
		size_t	len2
	)

◆ alignment_from_length()

int vg::alignment_from_length ( const Alignment & a )

◆ alignment_from_path()

Alignment vg::alignment_from_path	(	const HandleGraph &	graph,
		const Path &	path
	)

◆ alignment_is_valid()

AlignmentValidity vg::alignment_is_valid	(	const Alignment &	aln,
		const HandleGraph *	hgraph,
		bool	check_sequence = `false`
	)

Check to make sure edits on the alignment's path don't assume incorrect node lengths or ids. Result can be used like a bool or inspected for further details. Does not log anything itself about bad alignments.

◆ alignment_middle()

Alignment vg::alignment_middle	(	const Alignment &	aln,
		int	len
	)

◆ alignment_quality_per_node()

map< id_t, int > vg::alignment_quality_per_node ( const Alignment & aln )

◆ alignment_refpos_to_path_offsets()

map< string,vector< pair< size_t, bool > > > vg::alignment_refpos_to_path_offsets ( const Alignment & aln )

return the path offsets as cached in the alignment

◆ alignment_set_distance_to_correct() [1/3]

void vg::alignment_set_distance_to_correct	(	Alignment &	aln,
		const Alignment &	base,
		const unordered_map< string, string > *	translation = `nullptr`
	)

Annotate the first alignment with its minimum distance to the second in their annotated paths. If translation is set, replace path names in aln using that mapping, if they are found in it.

◆ alignment_set_distance_to_correct() [2/3]

void vg::alignment_set_distance_to_correct	(	Alignment &	aln,
		const map< string, vector< pair< size_t, bool > > > &	base_offsets,
		const unordered_map< string, string > *	translation
	)

◆ alignment_set_distance_to_correct() [3/3]

void vg::alignment_set_distance_to_correct	(	Alignment &	aln,
		const map< string, vector< pair< size_t, bool >>> &	base_offsets,
		const unordered_map< string, string > *	translation = `nullptr`
	)

◆ alignment_start()

Position vg::alignment_start ( const Alignment & aln )

◆ alignment_to_bam() [1/2]

bam1_t * vg::alignment_to_bam	(	bam_hdr_t *	bam_header,
		const Alignment &	alignment,
		const string &	refseq,
		const int32_t	refpos,
		const bool	refrev,
		const vector< pair< int, char >> &	cigar
	)

Convert an unpaired Alignment to a BAM record. If the alignment is unmapped, refpos must be -1. Otherwise, refpos must be the position on the reference sequence to which the alignment is aligned. Similarly, refseq must be the sequence aligned to, or "" if unaligned.

Remember to clean up with bam_destroy1(b);

◆ alignment_to_bam() [2/2]

bam1_t * vg::alignment_to_bam	(	bam_hdr_t *	bam_header,
		const Alignment &	alignment,
		const string &	refseq,
		const int32_t	refpos,
		const bool	refrev,
		const vector< pair< int, char >> &	cigar,
		const string &	mateseq,
		const int32_t	matepos,
		bool	materev,
		const int32_t	tlen,
		const int32_t	tlen_max = `0`
	)

Convert a paired Alignment to a BAM record. If the alignment is unmapped, refpos must be -1. Otherwise, refpos must be the position on the reference sequence to which the alignment is aligned. Similarly, refseq must be the sequence aligned to, or "" if unaligned. The mateseq and matepos fields must be set similarly for the mate. Note that mateseq must not be "=". If tlen_max is given, it is a limit on the magnitude of tlen to consider the read properly paired.

Remember to clean up with bam_destroy1(b);

◆ alignment_to_bam_internal()

bam1_t* vg::alignment_to_bam_internal	(	bam_hdr_t *	header,
		const Alignment &	alignment,
		const string &	refseq,
		const int32_t	refpos,
		const bool	refrev,
		const vector< pair< int, char >> &	cigar,
		const string &	mateseq,
		const int32_t	matepos,
		bool	materev,
		const int32_t	tlen,
		bool	paired,
		const int32_t	tlen_max
	)

◆ alignment_to_length()

int vg::alignment_to_length ( const Alignment & a )

◆ alignment_to_sam() [1/2]

string vg::alignment_to_sam	(	const Alignment &	alignment,
		const string &	refseq,
		const int32_t	refpos,
		const bool	refrev,
		const vector< pair< int, char >> &	cigar
	)

Convert an unpaired Alignment to a SAM record. If the alignment is unmapped, refpos must be -1. Otherwise, refpos must be the position on the reference sequence to which the alignment is aligned. Similarly, refseq must be the sequence aligned to, or "" if unaligned.

◆ alignment_to_sam() [2/2]

string vg::alignment_to_sam	(	const Alignment &	alignment,
		const string &	refseq,
		const int32_t	refpos,
		const bool	refrev,
		const vector< pair< int, char >> &	cigar,
		const string &	mateseq,
		const int32_t	matepos,
		bool	materev,
		const int32_t	tlen,
		const int32_t	tlen_max = `0`
	)

Convert a paired Alignment to a SAM record. If the alignment is unmapped, refpos must be -1. Otherwise, refpos must be the position on the reference sequence to which the alignment is aligned. Similarly, refseq must be the sequence aligned to, or "" if unaligned. The mateseq and matepos fields must be set similarly for the mate. Note that mateseq must not be "=". If tlen_max is given, it is a limit on the magnitude of tlen to consider the read properly paired.

◆ alignment_to_sam_internal()

string vg::alignment_to_sam_internal	(	const Alignment &	alignment,
		const string &	refseq,
		const int32_t	refpos,
		const bool	refrev,
		const vector< pair< int, char >> &	cigar,
		const string &	mateseq,
		const int32_t	matepos,
		bool	materev,
		const int32_t	tlen,
		bool	paired,
		const int32_t	tlen_max
	)

◆ allAmbiguousToN()

string vg::allAmbiguousToN ( const string & s )

Convert known IUPAC ambiguity codes (which we don't support) to N (which we do), while leaving any other garbage to trigger validation checks later.

◆ allATGC()

bool vg::allATGC ( const string & s )

◆ allATGCN()

bool vg::allATGCN ( const string & s )

◆ allele_to_string()

string vg::allele_to_string	(	VG &	graph,
		const Path &	allele
	)

Turn the given path into an allele. Drops the first and last mappings and looks up the sequences for the nodes of the others.

◆ append_cigar_operation()

void vg::append_cigar_operation	(	const int	length,
		const char	operation,
		vector< pair< int, char >> &	cigar
	)

inline

Add a CIGAR operation to a vector representing the parsed CIGAR string.

Coalesces adjacent operations of the same type. Coalesces runs of inserts and deletes into a signle delete followed by a single insert.

◆ append_multipath_alignment()

void vg::append_multipath_alignment	(	multipath_alignment_t &	multipath_aln,
		const multipath_alignment_t &	to_append
	)

Add the subpaths of one multipath alignment onto another.

◆ append_path()

Path & vg::append_path	(	Path &	a,
		const Path &	b
	)

Append the second path onto the end of the first, without combining mappings or simplifying. Modifies and returns a reference to the first path.

◆ approx_gbwt_memory()

int64_t vg::approx_gbwt_memory ( const string & vcf_filename )

◆ approx_graph_load_memory()

int64_t vg::approx_graph_load_memory ( const string & graph_filename )

◆ approx_graph_memory() [1/3]

int64_t vg::approx_graph_memory	(	const string &	fasta_filename,
		const string &	vcf_filename
	)

◆ approx_graph_memory() [2/3]

int64_t vg::approx_graph_memory ( const string & gfa_filename )

◆ approx_graph_memory() [3/3]

int64_t vg::approx_graph_memory	(	const vector< string > &	fasta_filenames,
		const vector< string > &	vcf_filenames
	)

◆ approx_num_vars()

double vg::approx_num_vars ( const string & vcf_filename )

◆ assign_child_snarls_to_traversals()

vector< vector< int > > vg::assign_child_snarls_to_traversals	(	const PathHandleGraph *	graph,
		const vector< Traversal > &	traversals,
		const vector< pair< handle_t, handle_t >> &	child_snarls
	)

assign a list of child snarls to traversals that fully conrtain them the output is a list (for each traversal) of each child snarl that's contained in it so otuput[i] = {x,y,z} means that child_snarls[x],[y],[z] are in traversals[i]

◆ augment() [1/2]

void vg::augment	(	MutablePathMutableHandleGraph *	graph,
		const string &	gam_path,
		const string &	aln_format = `"GAM"`,
		vector< Translation > *	out_translation = `nullptr`,
		const string &	gam_out_path = `""`,
		bool	embed_paths = `false`,
		bool	break_at_ends = `false`,
		bool	remove_soft_clips = `false`,
		bool	filter_out_of_graph_alignments = `false`,
		double	min_baseq = `0`,
		double	min_mapq = `0`,
		Packer *	packer = `nullptr`,
		size_t	min_bp_coverage = `0`,
		double	max_frac_n = `1.`,
		bool	edges_only = `false`
	)

Edit the graph to include all the sequence and edges added by the given paths. Can handle paths that visit nodes in any orientation. Note that this method sorts the graph and rebuilds the path index, so it should not be called in a loop.

if gam_path is "-", then stdin used if gam_out_path is "-", then stdout used If gam_out_path is not empty, the paths will be modified to reflect their embedding in the modified graph and written to the path. aln_format used to toggle between GAM and GAF If out_translation is not null, a list of translations, one per node existing after the edit, describing how each new or conserved node is embedded in the old graph. if embed_paths is true, then the augmented alignemnents will be saved as embededed paths in the graph in order to add it back to the graph. If break_at_ends is true, nodes will be broken at the ends of paths that start/end woth perfect matches, so the paths can be added to the vg graph's paths object. If soft_clip is true, soft clips will be removed from the input paths before processing, and the dangling ends won't end up in the graph If filter_out_of_graph_alignments is true, some extra time will be taken to check if all nodes in the alignment are in the graph. If they aren't, then it will be ignored If an edit sequence's avg base quality is less than min_baseq it will be ignored (considered a match) If an alignment's mapping quality is less than min_mapq it is ignored A packer is required for all non-mapq filters If a breakpoint has less than min_bp_coverage it is not included in the graph Edits with more than max_frac_n N content will be ignored

◆ augment() [2/2]

void vg::augment	(	MutablePathMutableHandleGraph *	graph,
		vector< Path > &	path_vector,
		const string &	aln_format = `"GAM"`,
		vector< Translation > *	out_translation = `nullptr`,
		const string &	gam_out_path = `""`,
		bool	embed_paths = `false`,
		bool	break_at_ends = `false`,
		bool	remove_soft_clips = `false`,
		bool	filter_out_of_graph_alignments = `false`,
		double	min_baseq = `0`,
		double	min_mapq = `0`,
		Packer *	packer = `nullptr`,
		size_t	min_bp_coverage = `0`,
		double	max_frac_n = `1.`,
		bool	edges_only = `false`
	)

Like above, but operates on a vector of Alignments, instead of a file (Note: It is best to use file interface to stream large numbers of alignments to save memory)

◆ augment_impl()

void vg::augment_impl	(	MutablePathMutableHandleGraph *	graph,
		function< void(function< void(Alignment &)>, bool, bool)>	iterate_gam,
		const string &	aln_format,
		vector< Translation > *	out_translations,
		const string &	gam_out_path,
		bool	embed_paths,
		bool	break_at_ends,
		bool	remove_softclips,
		bool	filter_out_of_graph_alignments,
		double	min_baseq,
		double	min_mapq,
		Packer *	packer,
		size_t	min_bp_coverage,
		double	max_frac_n,
		bool	edges_only
	)

Generic version used to implement the above three methods.

◆ balanced_kmers()

const vector< string > vg::balanced_kmers	(	const string &	seq,
		const int	kmer_size,
		const int	stride
	)

◆ balanced_stride()

const int vg::balanced_stride	(	int	read_length,
		int	kmer_size,
		int	stride
	)

◆ bam_to_alignment() [1/2]

Alignment vg::bam_to_alignment	(	const bam1_t *	b,
		const map< string, string > &	rg_sample,
		const map< int, path_handle_t > &	tid_path_handle
	)

◆ bam_to_alignment() [2/2]

Alignment vg::bam_to_alignment	(	const bam1_t *	b,
		const map< string, string > &	rg_sample,
		const map< int, path_handle_t > &	tid_path_handle,
		const bam_hdr_t *	bh,
		const PathPositionHandleGraph *	graph
	)

◆ benchmark_control()

void vg::benchmark_control ( )

The benchmark control function, designed to take some amount of time that might vary with CPU load.

◆ binomial_cmf_ln()

template<typename ProbIn >

real_t vg::binomial_cmf_ln	(	ProbIn	success_logprob,
		size_t	trials,
		size_t	successes
	)

Compute the probability of having the given number of successes or fewer in the given number of trials, with the given success probability. Returns the resulting log probability.

◆ build_gcsa_lcp()

void vg::build_gcsa_lcp	(	const HandleGraph &	graph,
		gcsa::GCSA *&	gcsa,
		gcsa::LCPArray *&	lcp,
		int	kmer_size,
		size_t	doubling_steps,
		size_t	size_limit,
		const string &	base_file_name
	)

◆ cactus_to_vg()

VG vg::cactus_to_vg ( stCactusGraph * cactus_graph )

◆ cactusify()

VG vg::cactusify ( VG & graph )

◆ canonical_orientation()

PhaseUnfolder::path_type vg::canonical_orientation	(	const PhaseUnfolder::path_type &	path,
		bool &	from_border,
		bool &	to_border
	)

◆ chain_begin()

ChainIterator vg::chain_begin ( const Chain & chain )

We define free functions for getting iterators forward and backward through chains.

◆ chain_begin_from()

ChainIterator vg::chain_begin_from	(	const Chain &	chain,
		const Snarl *	start_snarl,
		bool	snarl_orientation
	)

We also define a function for getting the ChainIterator (forward or reverse complement) for a chain starting with a given snarl in the given inward orientation. Only works for bounding snarls of the chain.

◆ chain_end()

ChainIterator vg::chain_end ( const Chain & chain )

◆ chain_end_from()

ChainIterator vg::chain_end_from	(	const Chain &	chain,
		const Snarl *	start_snarl,
		bool	snarl_orientation
	)

And the end iterator for the chain (forward or reverse complement) viewed from a given snarl in the given inward orientation. Only works for bounding snarls of the chain, and should be the same bounding snarl as was used for chain_begin_from.

◆ chain_rbegin()

ChainIterator vg::chain_rbegin ( const Chain & chain )

◆ chain_rcbegin()

ChainIterator vg::chain_rcbegin ( const Chain & chain )

We also define some reverse complement iterators, which go from right to left through the chains, but give us the reverse view. For ecample, if all the snarls are oriented forward in the chain, we will iterate through the snarls in reverse order, with each individual snarl also reversed.

◆ chain_rcend()

ChainIterator vg::chain_rcend ( const Chain & chain )

◆ chain_rend()

ChainIterator vg::chain_rend ( const Chain & chain )

◆ choose_good_thread_count()

void vg::choose_good_thread_count ( )

Decide on and apply a sensible OMP thread count. Pay attention to OMP_NUM_THREADS if set, the "hardware concurrency", and container limit information that may be available in /proc.

◆ choose_ln()

real_t vg::choose_ln	(	int	n,
		int	k
	)

inline

Compute the number of ways to select k items from a collection of n distinguishable items, ignoring order. Returns the natural log of the (integer) result.

◆ cigar_against_path() [1/2]

vector< pair< int, char > > vg::cigar_against_path	(	const Alignment &	alignment,
		bool	on_reverse_strand,
		int64_t &	pos,
		size_t	path_len,
		size_t	softclip_suppress
	)

Create a CIGAR from the given Alignment. If softclip_suppress is nonzero, suppress softclips up to that length. This will necessitate adjusting pos, which is why it is passed by reference.

◆ cigar_against_path() [2/2]

vector< pair< int, char > > vg::cigar_against_path	(	const multipath_alignment_t &	multipath_aln,
		const string &	path_name,
		bool	rev,
		int64_t	path_pos,
		const PathPositionHandleGraph &	graph,
		int64_t	min_splice_length = `numeric_limits< int64_t >::max()`
	)

Convert a surjected multipath alignment into a CIGAR sequence against a path. Splicing will be allowed at connections and at any silent deletions of path sequence. Surjected multipath alignment graph must consist of a single non-branching path

◆ cigar_mapping() [1/2]

void vg::cigar_mapping	(	const bam1_t *	b,
		Mapping &	mapping
	)

◆ cigar_mapping() [2/2]

int64_t vg::cigar_mapping	(	const bam1_t *	b,
		Mapping *	mapping
	)

◆ cigar_string()

string vg::cigar_string ( const vector< pair< int, char > > & cigar )

◆ classify_kmers()

std::vector<std::pair<Recombinator::kmer_presence, double> > vg::classify_kmers	(	const Haplotypes::Subchain &	subchain,
		const hash_map< Haplotypes::Subchain::kmer_type, size_t > &	kmer_counts,
		double	coverage,
		Recombinator::Statistics *	statistics,
		const Recombinator::Parameters &	parameters
	)

◆ clear_alignment()

void vg::clear_alignment ( multipath_alignment_t & multipath_aln )

Clear all of the field associated with the alignment.

◆ clear_annotation() [1/2]

template<typename Annotated >

void vg::clear_annotation	(	Annotated &	annotated,
		const string &	name
	)

inline

Clear the annotation with the given name.

◆ clear_annotation() [2/2]

template<typename Annotated >

void vg::clear_annotation	(	Annotated *	annotated,
		const string &	name
	)

inline

Clear the annotation with the given name.

◆ clear_crash_context()

void vg::clear_crash_context ( )

User code should call this when it wants to clear context for a failure in its thread.

◆ clip_contained_low_depth_nodes_and_edges()

void vg::clip_contained_low_depth_nodes_and_edges	(	MutablePathMutableHandleGraph *	graph,
		PathPositionHandleGraph *	pp_graph,
		const vector< Region > &	regions,
		SnarlManager &	snarl_manager,
		bool	include_endpoints,
		int64_t	min_depth,
		int64_t	min_fragment_len,
		bool	verbose
	)

Or on contained snarls

◆ clip_contained_snarls()

void vg::clip_contained_snarls	(	MutablePathMutableHandleGraph *	graph,
		PathPositionHandleGraph *	pp_graph,
		const vector< Region > &	regions,
		SnarlManager &	snarl_manager,
		bool	include_endpoints,
		int64_t	min_fragment_len,
		size_t	max_nodes,
		size_t	max_edges,
		size_t	max_nodes_shallow,
		size_t	max_edges_shallow,
		double	max_avg_degree,
		double	max_reflen_prop,
		size_t	max_reflen,
		bool	out_bed,
		bool	verbose
	)

If a given bed region spans a snarl (overlaps its end nodes, and forms a traversal) then clip out all other nodes (ie nodes that don't lie on the traversal)

IMPORTANT: for any given snarl, the first region that contains it is used. (but other reference paths now whitelisted via ref_prefixes)

Update: now accepts some snarl complexity thresholds to ignore simple enough snarls

◆ clip_contained_stubs()

void vg::clip_contained_stubs	(	MutablePathMutableHandleGraph *	graph,
		PathPositionHandleGraph *	pp_graph,
		const vector< Region > &	regions,
		SnarlManager &	snarl_manager,
		bool	include_endpoints,
		int64_t	min_fragment_len,
		bool	verbose
	)

◆ clip_deletion_edges()

void vg::clip_deletion_edges	(	MutablePathMutableHandleGraph *	graph,
		int64_t	max_deletion,
		int64_t	context_steps,
		const vector< string > &	ref_prefixes,
		int64_t	min_fragment_len,
		bool	verbose
	)

clip out deletion edges

◆ clip_low_depth_nodes_and_edges()

void vg::clip_low_depth_nodes_and_edges	(	MutablePathMutableHandleGraph *	graph,
		int64_t	min_depth,
		const vector< string > &	ref_prefixes,
		int64_t	min_fragment_len,
		bool	verbose
	)

Run above function on graph

◆ clip_low_depth_nodes_and_edges_generic()

void vg::clip_low_depth_nodes_and_edges_generic	(	MutablePathMutableHandleGraph *	graph,
		function< void(function< void(handle_t, const Region *)>)>	iterate_handles,
		function< void(function< void(edge_t, const Region *)>)>	iterate_edges,
		int64_t	min_depth,
		const vector< string > &	ref_prefixes,
		int64_t	min_fragment_len,
		bool	verbose
	)

Clip out nodes that don't pass depth threshold (depth < min_depth).
"depth" is the number of paths that step on the node. Nodes on path with given prefix ignored (todo: should really switch to regex or something) iterate_handles is a hack to generalize this function to whole graphs or snarls

◆ clip_stubs()

void vg::clip_stubs	(	MutablePathMutableHandleGraph *	graph,
		const vector< string > &	ref_prefixes,
		int64_t	min_fragment_len,
		bool	verbose
	)

clip out stubs

◆ clip_stubs_generic()

void vg::clip_stubs_generic	(	MutablePathMutableHandleGraph *	graph,
		function< void(function< void(handle_t, const Region *)>)>	iterate_handles,
		function< bool(handle_t)>	handle_in_range,
		const vector< string > &	ref_prefixes,
		int64_t	min_fragment_len,
		bool	verbose
	)

◆ cluster_cover()

vector< string::const_iterator > vg::cluster_cover ( const vector< MaximalExactMatch > & cluster )

◆ cluster_coverage()

int vg::cluster_coverage ( const vector< MaximalExactMatch > & cluster )

◆ cluster_nodes()

vector< pos_t > vg::cluster_nodes ( const vector< MaximalExactMatch > & cluster )

◆ cluster_subgraph_containing()

bdsg::HashGraph vg::cluster_subgraph_containing	(	const HandleGraph &	base,
		const Alignment &	aln,
		const vector< vg::MaximalExactMatch > &	cluster,
		const GSSWAligner *	aligner
	)

return a containing subgraph connecting the mems

◆ cluster_subgraph_walk()

bdsg::HashGraph vg::cluster_subgraph_walk	(	const HandleGraph &	base,
		const Alignment &	aln,
		const vector< vg::MaximalExactMatch > &	mems,
		double	expansion
	)

return a subgraph for a cluster of MEMs from the given alignment use walking to get the hits

◆ cluster_traversals()

vector< vector< int > > vg::cluster_traversals	(	const PathHandleGraph *	graph,
		const vector< Traversal > &	traversals,
		const vector< int > &	traversal_order,
		const vector< pair< handle_t, handle_t >> &	child_snarls,
		double	min_jaccard,
		vector< pair< double, int64_t >> &	out_info,
		vector< int > &	out_child_snarl_to_trav
	)

cluster the traversals. The algorithm is:

visit traversals in provided order
- if the traversal is <= min_jaccard away from the reference traversal of cluster, add to cluster
- else start a new cluster, with the given traversal as a reference note that traversal_order can specify a subset of traversals out_info are Simlarity/length-delta pairs comparing the traversal to its cluster reference (if the traversal wasn't in traversal_order, it'll get -1) if child snarls are given, then we make sure that every child snarl is contained in a reference traversal (this guarantees the snarl nesting structure is exactly represented in the vcf alleles!) if child snarls are given, then we also fill in the mapping of each child snarl to its "reference" traversals – ie first traversal in a cluster that contains both its endpoints

◆ clusters_overlap_in_graph()

bool vg::clusters_overlap_in_graph	(	const vector< MaximalExactMatch > &	cluster1,
		const vector< MaximalExactMatch > &	cluster2
	)

◆ clusters_overlap_in_read()

bool vg::clusters_overlap_in_read	(	const vector< MaximalExactMatch > &	cluster1,
		const vector< MaximalExactMatch > &	cluster2
	)

◆ clusters_overlap_length()

int vg::clusters_overlap_length	(	const vector< MaximalExactMatch > &	cluster1,
		const vector< MaximalExactMatch > &	cluster2
	)

◆ compose_short_path_name()

std::string vg::compose_short_path_name	(	const gbwt::GBWT &	gbwt_index,
		gbwt::size_type	id
	)

Get a short version of a string representation of a thread name stored in GBWT metadata, made of just the sample and contig and haplotype. NOTE: id is a gbwt path id, not a gbwt sequence id.

◆ compute_template_lengths()

pair< int32_t, int32_t > vg::compute_template_lengths	(	const int64_t &	pos1,
		const vector< pair< int, char >> &	cigar1,
		const int64_t &	pos2,
		const vector< pair< int, char >> &	cigar2
	)

Work out the TLEN values for two reads. The magnitude is the distance between the outermost aligned bases, and the sign is positive for the leftmost read and negative for the rightmost.

◆ concat_mappings()

Mapping vg::concat_mappings	(	const Mapping &	m,
		const Mapping &	n,
		bool	trim_internal_deletions
	)

◆ concat_paths()

Path vg::concat_paths	(	const Path &	path1,
		const Path &	path2
	)

◆ connected_components()

vector< vector< int64_t > > vg::connected_components ( const multipath_alignment_t & multipath_aln )

Returns a vector whose elements are vectors with the indexes of the subpath_t's in each connected component. An unmapped multipath_alignment_t with no subpaths produces an empty vector.

◆ connected_comps_do()

void vg::connected_comps_do	(	const multipath_alignment_t &	multipath_aln,
		function< void(void)> &	on_new_component,
		function< void(size_t)> &	on_new_node
	)

◆ construct_graph_from_nodes_and_edges()

void vg::construct_graph_from_nodes_and_edges	(	Graph &	g,
		const HandleGraph &	source,
		set< int64_t > &	nodes,
		set< pair< int, int > > &	edges
	)

◆ contains_connection()

bool vg::contains_connection ( const multipath_alignment_t & multipath_aln )

Returns true if any subpath has a connection adjacency.

◆ contains_match()

bool vg::contains_match	(	const multipath_alignment_t &	multipath_aln,
		const pos_t &	pos,
		int64_t	read_pos,
		int64_t	match_length
	)

Returns true if the multipath alignment contains a match of a given length starting at the graph and read position

◆ convert() [1/2]

template<typename T >

bool vg::convert	(	const std::string &	s,
		T &	r
	)

◆ convert() [2/2]

template<typename T >

std::string vg::convert ( const T & r )

◆ convert_alignment_char()

void vg::convert_alignment_char	(	Alignment &	alignment,
		char	from,
		char	to
	)

◆ convert_multipath_alignment_char()

void vg::convert_multipath_alignment_char	(	multipath_alignment_t &	multipath_aln,
		char	from,
		char	to
	)

◆ convert_Ts_to_Us() [1/2]

void vg::convert_Ts_to_Us ( Alignment & alignment )

Replaces any T's in the sequence or the Path with U's.

◆ convert_Ts_to_Us() [2/2]

void vg::convert_Ts_to_Us ( multipath_alignment_t & multipath_aln )

Replaces all T's in the sequence and the aligned Paths with U's.

◆ convert_Us_to_Ts() [1/2]

void vg::convert_Us_to_Ts ( Alignment & alignment )

Replaces any U's in the sequence or the Path with T's.

◆ convert_Us_to_Ts() [2/2]

void vg::convert_Us_to_Ts ( multipath_alignment_t & multipath_aln )

Replaces all U's in the sequence and the aligned Paths with T's.

◆ copy_file()

void vg::copy_file	(	const string &	from_fp,
		const string &	to_fp
	)

◆ copy_metadata()

void vg::copy_metadata	(	const gbwt::GBWT &	source,
		gbwt::GBWT &	target,
		const std::vector< std::vector< gbwt::size_type >> &	jobs,
		const std::vector< size_t > &	job_order
	)

◆ copy_reference_samples() [1/2]

void vg::copy_reference_samples	(	const gbwt::GBWT &	source,
		gbwt::GBWT &	destination
	)

Copies the reference sample tag from the source GBWT index to the destination GBWT index.

◆ copy_reference_samples() [2/2]

void vg::copy_reference_samples	(	const PathHandleGraph &	source,
		gbwt::GBWT &	destination
	)

Copies reference samples from the source graph to the destination GBWT index. Every sample with at least one reference path in the source graph is considered a reference sample.

◆ corresponding_from_length()

int vg::corresponding_from_length	(	const path_t &	path,
		int	to_length,
		bool	from_end
	)

◆ corresponding_length_internal()

int vg::corresponding_length_internal	(	const path_t &	path,
		int	given_length,
		bool	is_from_length,
		bool	from_end
	)

◆ corresponding_to_length()

int vg::corresponding_to_length	(	const path_t &	path,
		int	from_length,
		bool	from_end
	)

◆ crash_unless_impl()

void vg::crash_unless_impl	(	bool	condition,
		const std::string &	condition_string,
		const std::string &	file,
		int	line,
		const std::string &	function
	)

crash_unless calls into this function for a real implementation.

◆ create_ref_allele()

void vg::create_ref_allele	(	vcflib::Variant &	variant,
		const std::string &	allele
	)

Create the reference allele for an empty vcflib Variant, since apaprently there's no method for that already. Must be called before any alt alleles are added.

◆ cut_mapping() [1/4]

pair< Mapping, Mapping > vg::cut_mapping	(	const Mapping &	m,
		const Position &	pos
	)

◆ cut_mapping() [2/4]

pair< Mapping, Mapping > vg::cut_mapping	(	const Mapping &	m,
		size_t	offset
	)

◆ cut_mapping() [3/4]

pair< mapping_t, mapping_t > vg::cut_mapping	(	const mapping_t &	m,
		const Position &	pos
	)

◆ cut_mapping() [4/4]

pair< mapping_t, mapping_t > vg::cut_mapping	(	const mapping_t &	m,
		size_t	offset
	)

◆ cut_mapping_offset() [1/2]

pair< Mapping, Mapping > vg::cut_mapping_offset	(	const Mapping &	m,
		size_t	offset
	)

◆ cut_mapping_offset() [2/2]

pair< mapping_t, mapping_t > vg::cut_mapping_offset	(	const mapping_t &	m,
		size_t	offset
	)

◆ cut_path() [1/2]

pair< Path, Path > vg::cut_path	(	const Path &	path,
		const Position &	pos
	)

◆ cut_path() [2/2]

pair< Path, Path > vg::cut_path	(	const Path &	path,
		size_t	offset
	)

◆ debug_string() [1/7]

string vg::debug_string ( const connection_t & connection )

◆ debug_string() [2/7]

string vg::debug_string ( const edit_t & edit )

◆ debug_string() [3/7]

string vg::debug_string ( const multipath_alignment_t & multipath_aln )

◆ debug_string() [4/7]

string vg::debug_string ( const path_mapping_t & mapping )

◆ debug_string() [5/7]

string vg::debug_string ( const path_t & path )

◆ debug_string() [6/7]

string vg::debug_string ( const position_t & pos )

◆ debug_string() [7/7]

string vg::debug_string ( const subpath_t & subpath )

◆ decompose()

void vg::decompose	(	const Path &	path,
		map< pos_t, int > &	ref_positions,
		map< pos_t, Edit > &	edits
	)

◆ delete_nodes_and_chop_paths()

void vg::delete_nodes_and_chop_paths	(	MutablePathMutableHandleGraph *	graph,
		const unordered_set< nid_t > &	nodes_to_delete,
		const unordered_set< edge_t > &	edges_to_delete,
		int64_t	min_fragment_len,
		unordered_map< string, size_t > *	fragments_per_path
	)

◆ determine_flag()

int32_t vg::determine_flag	(	const Alignment &	alignment,
		const string &	refseq,
		const int32_t	refpos,
		const bool	refrev,
		const string &	mateseq,
		const int32_t	matepos,
		bool	materev,
		const int32_t	tlen,
		bool	paired,
		const int32_t	tlen_max
	)

Returns the SAM bit-coded flag for alignment with.

◆ deterministic_beats()

template<typename Number >

bool vg::deterministic_beats	(	const Number &	a,
		const Number &	b,
		LazyRNG &	rng
	)

Return true if a is larger than b, or else equal to b and wins a coin flip.

◆ deterministic_flip()

bool vg::deterministic_flip ( LazyRNG & rng )

Flip a coin with 50% probability against the given RNG.

◆ deterministic_shuffle() [1/2]

template<class RandomIt >

void vg::deterministic_shuffle	(	RandomIt	begin,
		RandomIt	end
	)

Do a deterministic shuffle with automatic seed determination.

◆ deterministic_shuffle() [2/2]

template<class RandomIt >

void vg::deterministic_shuffle	(	RandomIt	begin,
		RandomIt	end,
		LazyRNG &	rng
	)

Given a pair of random access iterators defining a range, deterministically shuffle the contents of the range based on the given RNG. Allows one RNG from deterministic_start() to be used for multiple shuffles.

◆ divergence()

double vg::divergence ( const Mapping & m )

◆ each_approx_graph_memory()

vector<int64_t> vg::each_approx_graph_memory	(	const vector< string > &	fasta_filenames,
		const vector< string > &	vcf_filenames
	)

◆ edit_count()

int vg::edit_count ( const Alignment & alignment )

◆ edits_are_compatible()

bool vg::edits_are_compatible	(	const Edit &	e,
		const Edit &	f
	)

Return true if two edits could be combined into one (assuming adjacency).

◆ emit_stacktrace()

void vg::emit_stacktrace	(	int	signalNumber,
		siginfo_t *	signalInfo,
		void *	signalContext
	)

Emit a stack trace when something bad happens. Add as a signal handler with sigaction.

◆ empty_gbwtgraph_handle()

handle_t vg::empty_gbwtgraph_handle ( )

inline

Returns an empty GBWTGraph handle corresponding to the GBWT endmarker.

◆ empty_pos_t()

pos_t vg::empty_pos_t ( )

inline

Get an unset pos_t.

◆ enable_crash_handling()

void vg::enable_crash_handling ( )

Main should call this to turn on our stack tracing support.

◆ encode_chars()

gcsa::byte_type vg::encode_chars	(	const vector< char > &	chars,
		const gcsa::Alphabet &	alpha
	)

Encode the chars into the gcsa2 byte.

◆ end_backward()

bool vg::end_backward ( const Chain & chain )

Return true if the last snarl in the given chain is backward relative to the chain.

◆ ensure_breakpoints()

map< pos_t, id_t > vg::ensure_breakpoints	(	MutableHandleGraph *	graph,
		const unordered_map< id_t, set< pos_t >> &	breakpoints
	)

Take a map from node ID to a set of offsets at which new nodes should start (which may include 0 and 1-past-the-end, which should be ignored), break the specified nodes at those positions. Returns a map from old node start position to new node pointer in the graph. Note that the caller will have to crear and rebuild path rank data.

Returns a map from old node start position to new node. This map contains some entries pointing to null, for positions past the ends of original nodes. It also maps from positions on either strand of the old node to the same new node pointer; the new node's forward strand is always the same as the old node's forward strand.

◆ entropy() [1/2]

double vg::entropy	(	const char *	st,
		size_t	len
	)

◆ entropy() [2/2]

double vg::entropy ( const string & st )

◆ ewens_af_prob_ln()

real_t vg::ewens_af_prob_ln	(	const vector< int > &	a,
		real_t	theta
	)

inline

◆ execute_in_fork()

int vg::execute_in_fork ( const function< void(void)> & exec )

◆ extend_alignment()

Alignment & vg::extend_alignment	(	Alignment &	a1,
		const Alignment &	a2,
		bool	debug
	)

◆ extend_path()

Path & vg::extend_path	(	Path &	path1,
		const Path &	path2
	)

◆ extract_as_gbwt_path()

gbwt::vector_type vg::extract_as_gbwt_path	(	const PathHandleGraph &	graph,
		const std::string &	path_name
	)

Extract a path as a GBWT path. If the path does not exist, it is treated as empty.

◆ extract_gbwt_path()

Path vg::extract_gbwt_path	(	const HandleGraph &	graph,
		const gbwt::GBWT &	gbwt_index,
		gbwt::size_type	id
	)

Extract a GBWT thread as a path in the given graph. NOTE: id is a gbwt path id, not a gbwt sequence id.

◆ extract_path_metadata()

pair< vector< pair< string, int64_t > >, unordered_map< string, int64_t > > vg::extract_path_metadata	(	const vector< tuple< path_handle_t, size_t, size_t >> &	paths,
		const PathPositionHandleGraph &	graph,
		bool	subpath_support = `false`
	)

Given a list of path handles and size info (from get_sequence_dictionary), return two things: 1) names and lengths of all of base paths in order. 2) a mapping of path names to length (reflects paths in the graph including subpaths)

If subpath_support is set to false, there won't be a distinction.

◆ extract_sub_multipath_alignment()

void vg::extract_sub_multipath_alignment	(	const multipath_alignment_t &	multipath_aln,
		const vector< int64_t > &	subpath_indexes,
		multipath_alignment_t &	sub_multipath_aln
	)

Extract the multipath_alignment_t consisting of the Subpaths with the given indexes into a new multipath_alignment_t object

◆ factorial_ln()

real_t vg::factorial_ln ( int n )

inline

Calculate the natural log of the factorial of the given integer. TODO: replace with a cache or giant lookup table from Freebayes.

◆ fastq_for_each()

int vg::fastq_for_each	(	string &	filename,
		function< void(Alignment &)>	lambda
	)

◆ fastq_paired_interleaved_for_each()

size_t vg::fastq_paired_interleaved_for_each	(	const string &	filename,
		function< void(Alignment &, Alignment &)>	lambda
	)

◆ fastq_paired_interleaved_for_each_parallel()

size_t vg::fastq_paired_interleaved_for_each_parallel	(	const string &	filename,
		function< void(Alignment &, Alignment &)>	lambda,
		uint64_t	batch_size
	)

◆ fastq_paired_interleaved_for_each_parallel_after_wait()

size_t vg::fastq_paired_interleaved_for_each_parallel_after_wait	(	const string &	filename,
		function< void(Alignment &, Alignment &)>	lambda,
		function< bool(void)>	single_threaded_until_true,
		uint64_t	batch_size
	)

◆ fastq_paired_two_files_for_each()

size_t vg::fastq_paired_two_files_for_each	(	const string &	file1,
		const string &	file2,
		function< void(Alignment &, Alignment &)>	lambda
	)

◆ fastq_paired_two_files_for_each_parallel()

size_t vg::fastq_paired_two_files_for_each_parallel	(	const string &	file1,
		const string &	file2,
		function< void(Alignment &, Alignment &)>	lambda,
		uint64_t	batch_size
	)

◆ fastq_paired_two_files_for_each_parallel_after_wait()

size_t vg::fastq_paired_two_files_for_each_parallel_after_wait	(	const string &	file1,
		const string &	file2,
		function< void(Alignment &, Alignment &)>	lambda,
		function< bool(void)>	single_threaded_until_true,
		uint64_t	batch_size
	)

◆ fastq_unpaired_for_each()

size_t vg::fastq_unpaired_for_each	(	const string &	filename,
		function< void(Alignment &)>	lambda
	)

◆ fastq_unpaired_for_each_parallel()

size_t vg::fastq_unpaired_for_each_parallel	(	const string &	filename,
		function< void(Alignment &)>	lambda,
		uint64_t	batch_size
	)

◆ file_base_name()

string vg::file_base_name ( const string & filename )

Get the base name of a filename (without the directory and the extension).

◆ file_exists()

bool vg::file_exists ( const string & filename )

Determine if a file exists. Only works for files readable by the current user.

◆ fill_in_distance_index()

void vg::fill_in_distance_index	(	SnarlDistanceIndex *	distance_index,
		const HandleGraph *	graph,
		const HandleGraphSnarlFinder *	snarl_finder,
		size_t	size_limit,
		bool	silence_warnings
	)

◆ filter_breakpoints_by_coverage()

unordered_map< id_t, set< pos_t > > vg::filter_breakpoints_by_coverage	(	const Packer &	packed_breakpoints,
		size_t	min_bp_coverage
	)

Filters the breakpoints by coverage, and converts them back from the Packer to the STL map expected by following methods

◆ final_position() [1/2]

pos_t vg::final_position ( const Path & path )

◆ final_position() [2/2]

pos_t vg::final_position ( const path_t & path )

◆ find_breakpoints()

void vg::find_breakpoints	(	const Path &	path,
		unordered_map< id_t, set< pos_t >> &	breakpoints,
		bool	break_ends = `true`,
		const string &	base_quals = `""`,
		double	min_baseq = `0`,
		double	max_frac_n = `1.`
	)

Find all the points at which a Path enters or leaves nodes in the graph. Adds them to the given map by node ID of sets of bases in the node that will need to become the starts of new nodes.

If break_ends is true, emits breakpoints at the ends of the path, even if it starts/ends with perfect matches. Find all the points at which a Path enters or leaves nodes in the graph. Adds them to the given map by node ID of sets of bases in the node that will need to become the starts of new nodes.

If break_ends is true, emits breakpoints at the ends of the path, even if it starts/ends with perfect matches.

◆ find_kmer()

hash_map<Haplotypes::Subchain::kmer_type, size_t>::iterator vg::find_kmer	(	hash_map< Haplotypes::Subchain::kmer_type, size_t > &	counts,
		Haplotypes::Subchain::kmer_type	kmer,
		size_t	k
	)

◆ find_mismatches()

void vg::find_mismatches	(	const std::string &	seq,
		const gbwtgraph::CachedGBWTGraph &	graph,
		std::vector< GaplessExtension > &	result
	)

◆ find_packed_breakpoints()

void vg::find_packed_breakpoints	(	const Path &	path,
		Packer &	packed_breakpoints,
		bool	break_ends,
		const string &	base_quals,
		double	min_baseq,
		double	max_frac_n
	)

Like "find_breakpoints", but store in packed structure (better for large gams and enables coverage filter)

◆ find_path_traversals()

pair<vector<SnarlTraversal>, vector<pair<step_handle_t, step_handle_t> > > vg::find_path_traversals ( const Snarl & site )

◆ first_path_position()

Position vg::first_path_position ( const Path & path )

◆ fit_fixed_rate_max_exponential()

double vg::fit_fixed_rate_max_exponential	(	const vector< double > &	x,
		double	rate,
		double	tolerance
	)

Returns the MLE estimate for the number of iid exponential RVs the data are maxima of.

◆ fit_fixed_shape_max_exponential()

double vg::fit_fixed_shape_max_exponential	(	const vector< double > &	x,
		double	shape,
		double	tolerance
	)

Returns the MLE rate parameter for the distribution of (shape) iid exponential RVs.

◆ fit_max_exponential()

pair< double, double > vg::fit_max_exponential	(	const vector< double > &	x,
		double	tolerance
	)

Returns the MLE rate and shape parameters of a max exponential.

◆ fit_offset_weibull()

tuple< double, double, double > vg::fit_offset_weibull	(	const vector< double > &	x,
		double	tolerance
	)

Returns an estimate of the rate, shape, and location (minimum value) of a 3-parameter Weibull distribution.

◆ fit_weibull()

pair< double, double > vg::fit_weibull ( const vector< double > & x )

Returns an estimate of the rate and shape parameters of a Weibull distribution.

◆ fit_zipf()

double vg::fit_zipf ( const vector< double > & y )

◆ flip()

Support vg::flip ( const Support & to_flip )

Flip the orientations of a Support.

◆ flip_doubly_reversed_edges()

void vg::flip_doubly_reversed_edges ( Graph & graph )

clean up doubly-reversed edges

◆ flip_nodes()

void vg::flip_nodes	(	Alignment &	a,
		const set< int64_t > &	ids,
		const std::function< size_t(int64_t)> &	node_length
	)

◆ for_each_basic_annotation()

template<typename Annotated >

void vg::for_each_basic_annotation	(	const Annotated &	annotated,
		const function< void(const string &)>	null_lambda,
		const function< void(const string &, double)>	double_lambda,
		const function< void(const string &, bool)>	bool_lambda,
		const function< void(const string &, const string &)>	string_lambda
	)

Apply a lambda to all annotations, except for Struct and ListValue annotations (which cannot be easily typed without exposing ugly Protobuf internals

◆ for_each_kmer()

void vg::for_each_kmer	(	const HandleGraph &	graph,
		size_t	k,
		const function< void(const kmer_t &)> &	lambda,
		id_t	head_id = `0`,
		id_t	tail_id = `0`,
		atomic< int > *	stop_flag = `nullptr`
	)

Iterate over all the kmers in the graph, running lambda on each If the stop flag is included, stop execution if it ever evaluates to true

◆ format_multiplier()

double vg::format_multiplier ( )

◆ forwardize_breakpoints()

unordered_map< id_t, set< pos_t > > vg::forwardize_breakpoints	(	const HandleGraph *	graph,
		const unordered_map< id_t, set< pos_t >> &	breakpoints
	)

Flips the breakpoints onto the forward strand.

◆ from_handle_graph()

void vg::from_handle_graph	(	const HandleGraph &	from,
		Graph &	to
	)

◆ from_hit()

multipath_alignment_t vg::from_hit	(	const Alignment &	alignment,
		const HandleGraph &	graph,
		const pos_t &	hit_pos,
		const MaximalExactMatch &	mem,
		const GSSWAligner &	scorer
	)

◆ from_length()

int vg::from_length ( const Mapping & m )

◆ from_length_after_pos()

size_t vg::from_length_after_pos	(	const Alignment &	aln,
		const Position &	pos
	)

◆ from_length_before_pos()

size_t vg::from_length_before_pos	(	const Alignment &	aln,
		const Position &	pos
	)

◆ from_path_handle_graph()

void vg::from_path_handle_graph	(	const PathHandleGraph &	from,
		Graph &	to
	)

◆ from_proto_edit()

void vg::from_proto_edit	(	const Edit &	proto_edit,
		edit_t &	edit
	)

◆ from_proto_mapping()

void vg::from_proto_mapping	(	const Mapping &	proto_mapping,
		path_mapping_t &	mapping
	)

◆ from_proto_multipath_alignment()

void vg::from_proto_multipath_alignment	(	const MultipathAlignment &	proto_multipath_aln,
		multipath_alignment_t &	multipath_aln_out
	)

Convert a protobuf MultipathAlignment to an STL-based multipath_alignment_t.

◆ from_proto_path()

void vg::from_proto_path	(	const Path &	proto_path,
		path_t &	path
	)

◆ from_proto_position()

void vg::from_proto_position	(	const Position &	from,
		position_t &	to
	)

◆ fuse_spliced_alignments()

multipath_alignment_t && vg::fuse_spliced_alignments	(	const Alignment &	alignment,
		multipath_alignment_t &&	left_mp_aln,
		multipath_alignment_t &&	right_mp_aln,
		int64_t	left_bridge_point,
		const Alignment &	splice_segment,
		int64_t	splice_junction_idx,
		int32_t	splice_score,
		const GSSWAligner &	scorer,
		const HandleGraph &	graph
	)

◆ gamma_ln()

real_t vg::gamma_ln ( real_t x )

inline

Calculate the natural log of the gamma function of the given argument.

◆ gbwt_node_width()

gbwt::size_type vg::gbwt_node_width ( const HandleGraph & graph )

Determine the node width in bits for the GBWT nodes based on the given graph.

◆ gbwt_to_handle()

handle_t vg::gbwt_to_handle	(	const HandleGraph &	graph,
		gbwt::node_type	node
	)

inline

Convert gbwt::node_type to handle_t.

◆ gbwt_to_pos()

pos_t vg::gbwt_to_pos	(	gbwt::node_type	node,
		size_t	offset
	)

inline

Convert gbwt::node_type and an offset as size_t to pos_t.

◆ gcsa_nodes_to_positions()

set< pos_t > vg::gcsa_nodes_to_positions ( const vector< gcsa::node_type > & nodes )

◆ generate_haplotype()

std::string vg::generate_haplotype	(	gbwt::edge_type	pos,
		handle_t	end,
		size_t	start_max,
		size_t	end_max,
		const gbwtgraph::GBWTGraph &	graph
	)

◆ genotype_svs()

void vg::genotype_svs	(	VG *	graph,
		string	gamfile,
		string	refpath
	)

Takes a graph and two GAMs, one tumor and one normal Locates existing variation supported by the tumor and annotate it with a path Then overlay the normal sample Use a depthmap of snarltraversal transforms, one for tumor, one for normal which we can use to count the normal and tumor alleles void somatic_genotyper(VG* graph, string tumorgam, string normalgam);

Do smart augment, maintaining a depth map for tumor/normal perfect matches and then editing in all of the SV reads (after normalization) with a T/N_ prefix Then, get our Snarls count reads supporting each and genotype void somatic_caller_genotyper(VG* graph, string tumorgam, string normalgam);

◆ geometric_sampling_prob_ln()

template<typename ProbIn >

real_t vg::geometric_sampling_prob_ln	(	ProbIn	success_logprob,
		size_t	trials
	)

Get the log probability for sampling the given value from a geometric distribution with the given success log probability. The geometric distribution is the distribution of the number of trials, with a given success probability, required to observe a single success.

◆ get_alignment_emitter()

unique_ptr< AlignmentEmitter > vg::get_alignment_emitter	(	const string &	filename,
		const string &	format,
		const vector< tuple< path_handle_t, size_t, size_t >> &	paths,
		size_t	max_threads,
		const HandleGraph *	graph = `nullptr`,
		int	flags = `ALIGNMENT_EMITTER_FLAG_NONE`
	)

Get an AlignmentEmitter that can emit to the given file (or "-") in the given format. When writing HTSlib formats (SAM, BAM, CRAM), paths should contain the paths in the linear reference in sequence dictionary order (see get_sequence_dictionary), and a PathPositionHandleGraph must be provided. When writing GAF, a HandleGraph must be provided for obtaining node lengths and sequences. Other formats do not need a graph.

flags is an ORed together set of flags from alignment_emitter_flags_t.

Automatically applies per-thread buffering, but needs to know how many OMP threads will be in use.

◆ get_annotation() [1/2]

template<typename AnnotationType , typename Annotated >

AnnotationType vg::get_annotation	(	Annotated *	annotated,
		const string &	name
	)

inline

Get the annotation with the given name and return it. If not present, returns the Protobuf default value for the annotation type. The value may be a primitive type or an entire Protobuf object. It is undefined behavior to read a value out into a different type than it was stored with.

◆ get_annotation() [2/2]

template<typename AnnotationType , typename Annotated >

AnnotationType vg::get_annotation	(	const Annotated &	annotated,
		const string &	name
	)

inline

Get the annotation with the given name and return it. If not present, returns the Protobuf default value for the annotation type. The value may be a primitive type or an entire Protobuf object. It is undefined behavior to read a value out into a different type than it was stored with.

◆ get_avg_baseq()

double vg::get_avg_baseq	(	const Edit &	edit,
		const string &	base_quals,
		size_t	position_in_read
	)

Compute the average base quality of an edit. If the edit has no sequence or there are no base_quals given, then double_max is returned.

◆ get_best_gbwtgraph_gfa_parsing_parameters()

gbwtgraph::GFAParsingParameters vg::get_best_gbwtgraph_gfa_parsing_parameters ( )

Get the best configuration to use for the GBWTGraph library GFA parser, to best matcch the behavior of vg's GFA parser.

◆ get_current_vmem_kb()

size_t vg::get_current_vmem_kb ( )

Get the current virtual memory size, in kb, or 0 if unsupported.

◆ get_end_of()

Visit vg::get_end_of ( const Chain & chain )

Get the outward-facing end Visit for a chain.

◆ get_file_size()

int64_t vg::get_file_size ( const string & filename )

◆ get_fraction_of_ns()

double vg::get_fraction_of_ns ( const string & seq )

Return the number of Ns as a fraction of the total sequence length (or 0 if the sequence is empty)

◆ get_gbwt()

gbwt::GBWT vg::get_gbwt ( const std::vector< gbwt::vector_type > & paths )

Transform the paths into a GBWT index. Primarily for testing.

◆ get_id()

id_t& vg::get_id ( pos_t & pos )

inline

Get a reference to the Node ID of a pos_t.

◆ get_input_file() [1/2]

void vg::get_input_file	(	const string &	file_name,
		function< void(istream &)>	callback
	)

Get a callback with an istream& to an open file. Handles "-" as a filename as indicating standard input. The reference passed is guaranteed to be valid only until the callback returns.

◆ get_input_file() [2/2]

void vg::get_input_file	(	int &	optind,
		int	argc,
		char **	argv,
		function< void(istream &)>	callback
	)

Get a callback with an istream& to an open file if a file name argument is present after the parsed options, or print an error message and exit if one is not. Handles "-" as a filename as indicating standard input. The reference passed is guaranteed to be valid only until the callback returns. Bumps up optind to the next argument if a filename is found.

Warning: If you're reading a HandleGraph via VPKG::load_one (as is the pattern in vg) it is best to use get_input_file_name() below instead, and run load_one on that. This allows better GFA support because it allows memmapping the file directly

◆ get_input_file_name()

string vg::get_input_file_name	(	int &	optind,
		int	argc,
		char **	argv,
		bool	test_open = `true`
	)

Parse out the name of an input file (i.e. the next positional argument), or throw an error. File name must be nonempty, but may be "-" or may not exist.

◆ get_is_rev()

bool& vg::get_is_rev ( pos_t & pos )

inline

Get a reference to the reverse flag of a pos_t.

◆ get_max_rss_kb()

size_t vg::get_max_rss_kb ( )

Get the max RSS usage ever, in kb, or 0 if unsupported.

◆ get_max_vmem_kb()

size_t vg::get_max_vmem_kb ( )

Get the max virtual memory size ever, in kb, or 0 if unsupported.

◆ get_minimizer_distances()

MIPayloadValues vg::get_minimizer_distances	(	const SnarlDistanceIndex &	distance_index,
		pos_t	pos
	)

◆ get_next_alignment_from_fastq()

bool vg::get_next_alignment_from_fastq	(	gzFile	fp,
		char *	buffer,
		size_t	len,
		Alignment &	alignment
	)

◆ get_next_alignment_pair_from_fastqs()

bool vg::get_next_alignment_pair_from_fastqs	(	gzFile	fp1,
		gzFile	fp2,
		char *	buffer,
		size_t	len,
		Alignment &	mate1,
		Alignment &	mate2
	)

◆ get_next_interleaved_alignment_pair_from_fastq()

bool vg::get_next_interleaved_alignment_pair_from_fastq	(	gzFile	fp,
		char *	buffer,
		size_t	len,
		Alignment &	mate1,
		Alignment &	mate2
	)

◆ get_num_samples()

int64_t vg::get_num_samples ( const string & vcf_filename )

◆ get_offset()

offset_t& vg::get_offset ( pos_t & pos )

inline

Get a reference to the offset field of a pos_t, which counts along the selected strand of the node.

◆ get_or_estimate_coverage()

double vg::get_or_estimate_coverage	(	const hash_map< Haplotypes::Subchain::kmer_type, size_t > &	counts,
		const Recombinator::Parameters &	parameters,
		Haplotypes::Verbosity	verbosity
	)

◆ get_or_make_variant_id()

string vg::get_or_make_variant_id ( const vcflib::Variant & variant )

◆ get_output_file_name()

string vg::get_output_file_name	(	int &	optind,
		int	argc,
		char **	argv
	)

Parse out the name of an output file (i.e. the next positional argument), or throw an error. File name must be nonempty.

◆ get_path() [1/4]

std::vector<handle_t> vg::get_path	(	const std::vector< handle_t > &	first,
		gbwt::node_type	second
	)

◆ get_path() [2/4]

std::vector<handle_t> vg::get_path	(	const std::vector< handle_t > &	first,
		handle_t	second
	)

◆ get_path() [3/4]

std::vector<handle_t> vg::get_path	(	gbwt::node_type	reverse_first,
		const std::vector< handle_t > &	second
	)

◆ get_path() [4/4]

std::vector<handle_t> vg::get_path	(	handle_t	first,
		const std::vector< handle_t > &	second
	)

◆ get_proc_status_value()

string vg::get_proc_status_value ( const string & name )

Get the string value for a field in /proc/self/status by name, or "" if unsupported or not found.

◆ get_sequence_dictionary()

vector< tuple< path_handle_t, size_t, size_t > > vg::get_sequence_dictionary	(	const string &	filename,
		const vector< string > &	path_names,
		const PathPositionHandleGraph &	graph
	)

Produce a list of path handles in a fixed order, suitable for use with get_alignment_emitter_with_surjection(), by parsing a file. The file may be an HTSlib-style "sequence dictionary" (consisting of SAM @SQ header lines), or a plain list of sequence names (which do not start with "@SQ"). If the file is not openable or contains no entries, reports an error and quits.

If path_names has entries, they are treated as path names that supplement those in the file, if any.

If the filename is itself an empty string, and no path names are passed, then all reference-sense paths from the graph will be collected in arbitrary order. If there are none, all non-alt-allele generic sense paths from the graph will be collected in arbitrary order.

TODO: Be able to generate the autosomes human-sort, X, Y, MT order typical of references.

The tuple is <path, path length in graph, base path length> For a subpath (ie chr1[1000-10000]) the base path length would be that of chr1 This information needs to come from the user in order to be correct, but if it's not specified, it'll be guessed from the graph

◆ get_start_of()

Visit vg::get_start_of ( const Chain & chain )

Get the inward-facing start Visit for a chain.

◆ get_thread_count()

int vg::get_thread_count ( void )

Return the number of threads that OMP will produce for a parallel section. TODO: Assumes that this is the same for every parallel section.

◆ get_traversal_of_snarl()

SnarlTraversal vg::get_traversal_of_snarl	(	VG &	graph,
		const Snarl *	snarl,
		const SnarlManager &	manager,
		const Path &	path
	)

Given a path (which may run either direction through a snarl, or not touch the ends at all), collect a list of NodeTraversals in order for the part of the path that is inside the snarl, in the same orientation as the path.

◆ get_traversal_order()

vector< int > vg::get_traversal_order	(	const PathHandleGraph *	graph,
		const vector< Traversal > &	traversals,
		const vector< string > &	trav_path_names,
		const vector< int > &	ref_travs,
		int64_t	ref_trav_idx,
		const vector< bool > &	use_traversal
	)

sort the traversals, putting the reference first then using names traversals masked out by use_traversal will be filrtered out entirely (so the output vector may be smaller than the input...)

◆ getReachableBridges()

void vg::getReachableBridges	(	stCactusEdgeEnd *	edgeEnd1,
		stList *	bridgeEnds
	)

Get the bridge ends that form boundary pairs with edgeEnd1. Duplicated from the pinchesAndCacti tests.

◆ getReachableBridges2()

void vg::getReachableBridges2	(	stCactusEdgeEnd *	edgeEnd1,
		stHash *	bridgeEndsToBridgeNodes,
		stList *	bridgeEnds
	)

Get the bridge ends that form boundary pairs with edgeEnd1, using the given getBridgeEdgeEndsToBridgeNodes hash map. Duplicated from the pinchesAndCacti tests.

◆ golden_section_search()

double vg::golden_section_search	(	const function< double(double)> &	f,
		double	x_min,
		double	x_max,
		double	tolerance
	)

Returns a local maximum of a function within an interval.

◆ graph_interval_to_string()

string vg::graph_interval_to_string	(	const HandleGraph *	graph,
		const handle_t &	start_handle,
		const handle_t &	end_handle
	)

◆ graph_to_gfa()

void vg::graph_to_gfa	(	const PathHandleGraph *	graph,
		ostream &	out,
		const set< string > &	rgfa_paths = `{}`,
		bool	rgfa_pline = `false`,
		bool	use_w_lines = `true`
	)

Export the given VG graph to the given GFA file. Express paths mentioned in rgfa_paths as rGFA. If rgfa_pline is set, also express them as dedicated lines. If use_w_lines is set, reference and haplotype paths will use W lines instead of P lines.

◆ guess_parallel_gbwt_jobs()

size_t vg::guess_parallel_gbwt_jobs	(	size_t	node_count,
		size_t	haplotype_count,
		size_t	available_memory,
		size_t	batch_size
	)

◆ handle_full_length()

void vg::handle_full_length	(	const HandleGraph &	graph,
		std::vector< GaplessExtension > &	result,
		double	overlap_threshold
	)

◆ handle_graph_to_cactus()

pair< stCactusGraph , stList > vg::handle_graph_to_cactus	(	const PathHandleGraph &	graph,
		const unordered_set< string > &	hint_paths,
		bool	single_component
	)

◆ handle_to_gbwt()

gbwt::node_type vg::handle_to_gbwt	(	const HandleGraph &	graph,
		handle_t	handle
	)

inline

Convert handle_t to gbwt::node_type.

◆ haplotype_consistent_alignments()

vector< Alignment > vg::haplotype_consistent_alignments	(	const multipath_alignment_t &	multipath_aln,
		const haplo::ScoreProvider &	score_provider,
		size_t	soft_count,
		size_t	hard_count,
		bool	optimal_first = `false`
	)

Finds all alignments consistent with haplotypes available by incremental search with the given haplotype score provider. Pads to a certain count with haplotype-inconsistent alignments that are population-scorable (i.e. use only edges used by some haplotype in the index), and then with unscorable alignments if scorable ones are unavailable. This may result in an empty vector.

Output Alignments may not be unique. The input multipath_alignment_t may have exponentially many ways to spell the same Alignment, and we will look at all of them. We also may have duplicates of the optimal alignment if we are asked to produce it unconsitionally.

Note: Assumes that each subpath's Path object uses one Mapping per node and that start subpaths have been identified

Args: multipath_aln multipath alignment to find optimal paths through score_provider a haplo::ScoreProvider that supports incremental search over its haplotype database (such as a GBWTScoreProvider) soft_count maximum number of haplotype-inconsistent alignments to pad to hard_count maximum number of alignments, including haplotype-consistent (0 if no limit) optimal_first always compute and return first the optimal alignment, even if not haplotype-consistent

◆ has_annotation()

template<typename Annotated >

bool vg::has_annotation	(	const Annotated &	annotated,
		const string &	name
	)

inline

Returns true if the Protobuf object has an annotation with this name.

◆ has_inversion()

bool vg::has_inversion ( const Graph & graph )

returns true if we find an edge that may specify an inversion

◆ hash_alignment()

const string vg::hash_alignment ( const Alignment & aln )

◆ hash_to_rgb()

tuple< double, double, double > vg::hash_to_rgb	(	const string &	str,
		double	min_sum
	)

◆ have_input_file()

bool vg::have_input_file	(	int &	optind,
		int	argc,
		char **	argv
	)

Return true if there's a command line argument (i.e. input file name) waiting to be processed.

◆ hts_file_header()

bam_hdr_t * vg::hts_file_header	(	string &	filename,
		string &	header
	)

◆ hts_for_each() [1/2]

int vg::hts_for_each	(	string &	filename,
		function< void(Alignment &)>	lambda
	)

◆ hts_for_each() [2/2]

int vg::hts_for_each	(	string &	filename,
		function< void(Alignment &)>	lambda,
		const PathPositionHandleGraph *	graph
	)

◆ hts_for_each_parallel() [1/2]

int vg::hts_for_each_parallel	(	string &	filename,
		function< void(Alignment &)>	lambda
	)

◆ hts_for_each_parallel() [2/2]

int vg::hts_for_each_parallel	(	string &	filename,
		function< void(Alignment &)>	lambda,
		const PathPositionHandleGraph *	graph
	)

◆ hts_string_header() [1/2]

bam_hdr_t * vg::hts_string_header	(	string &	header,
		const map< string, int64_t > &	path_length,
		const map< string, string > &	rg_sample
	)

◆ hts_string_header() [2/2]

bam_hdr_t * vg::hts_string_header	(	string &	header,
		const vector< pair< string, int64_t >> &	path_order_and_length,
		const map< string, string > &	rg_sample
	)

◆ id()

id_t vg::id ( const pos_t & pos )

inline

Extract the id of the node a pos_t is on.

◆ identify_start_subpaths()

void vg::identify_start_subpaths ( multipath_alignment_t & multipath_aln )

Finds the start subpaths (i.e. the source nodes of the multipath DAG) and stores them in the 'start' field of the multipath_alignment_t

◆ identity()

double vg::identity ( const Path & path )

◆ in_place_subvector()

template<class Element >

void vg::in_place_subvector	(	std::vector< Element > &	vec,
		size_t	head,
		size_t	tail
	)

◆ increment_node_mapping_ids()

Path& vg::increment_node_mapping_ids	(	Path &	p,
		id_t	inc
	)

◆ initial_position() [1/2]

pos_t vg::initial_position ( const Path & path )

◆ initial_position() [2/2]

pos_t vg::initial_position ( const path_t & path )

◆ insert_gbwt_path()

std::string vg::insert_gbwt_path	(	MutablePathHandleGraph &	graph,
		const gbwt::GBWT &	gbwt_index,
		gbwt::size_type	id,
		std::string	path_name = `""`
	)

Insert a GBWT thread into the graph and return its name. Returns an empty string on failure. If a path name is specified and not empty, that name will be used for the inserted path. NOTE: id is a gbwt path id, not a gbwt sequence id.

◆ integer_power() [1/2]

size_t vg::integer_power	(	size_t	x,
		size_t	power
	)

◆ integer_power() [2/2]

size_t vg::integer_power	(	uint64_t	base,
		uint64_t	exponent
	)

Computes base^exponent in log(exponent) time.

◆ interval_length()

size_t vg::interval_length ( std::pair< size_t, size_t > interval )

◆ is_all_n()

bool vg::is_all_n ( const string & seq )

Return True if the given string is entirely Ns of either case, and false otherwise.

◆ is_empty()

bool vg::is_empty ( const pos_t & pos )

inline

Return true if a pos_t is unset.

◆ is_gzipped()

bool vg::is_gzipped ( const string & filename )

◆ is_id_sortable()

bool vg::is_id_sortable ( const Graph & graph )

returns true if the graph is id-sortable (no reverse links)

◆ is_match()

bool vg::is_match ( const Translation & translation )

◆ is_number() [1/2]

bool vg::is_number ( const std::string & s )

◆ is_number() [2/2]

bool vg::is_number ( const string & s )

◆ is_rev()

bool vg::is_rev ( const pos_t & pos )

inline

Return true if a pos_t is on the reverse strand of its node.

◆ isATGC()

bool vg::isATGC ( const char & b )

Return true if a character is an uppercase A, C, G, or T, and false otherwise.

◆ jaccard_coefficient()

template<typename T , typename U >

double vg::jaccard_coefficient	(	const T &	target,
		const U &	query
	)

inline

◆ kff_bytes()

size_t vg::kff_bytes ( size_t k )

inline

Returns the number of bytes required for a kmer in KFF format.

◆ kff_decode() [1/2]

std::string vg::kff_decode	(	const uint8_t *	kmer,
		size_t	k,
		const std::string &	decoding
	)

Decodes a kmer in KFF format according to the given encoding.

◆ kff_decode() [2/2]

void vg::kff_decode	(	uint8_t	byte,
		size_t	chars,
		const std::string &	decoding,
		std::string &	output
	)

◆ kff_encode() [1/2]

std::vector< uint8_t > vg::kff_encode	(	const std::string &	kmer,
		const uint8_t *	encoding
	)

Encodes a kmer in KFF format according to the given encoding. Non-ACGT characters are encoded as 0s.

◆ kff_encode() [2/2]

uint8_t vg::kff_encode	(	const std::string &	kmer,
		size_t	start,
		size_t	limit,
		const uint8_t *	encoding
	)

◆ kff_get()

uint8_t vg::kff_get	(	const uint8_t *	kmer,
		size_t	i
	)

◆ kff_invert()

std::string vg::kff_invert ( const uint8_t * encoding )

Inverts the KFF encoding into a packed -> char table.

◆ kff_is_trivial()

bool vg::kff_is_trivial ( const uint8_t * encoding )

Returns true if the encoding is trivial (0, 1, 2, 3).

◆ kff_parse()

uint64_t vg::kff_parse	(	const uint8_t *	data,
		size_t	bytes
	)

Parses a big-endian integer from KFF data.

◆ kff_recode() [1/4]

gbwtgraph::Key64::value_type vg::kff_recode	(	const uint8_t *	kmer,
		size_t	k,
		kff_recoding_t	recoding
	)

Recodes a KFF kmer in the minimizer index format according to the given encoding. Will fail silently if k is too large or recoding is not from kff_recoding().

◆ kff_recode() [2/4]

std::vector< gbwtgraph::Key64::value_type > vg::kff_recode	(	const uint8_t *	kmers,
		size_t	n,
		size_t	k,
		kff_recoding_t	recoding
	)

Recodes n KFF kmers in the minimizer index format according to the given encoding. Will fail silently if k is too large or recoding is not from kff_recoding().

◆ kff_recode() [3/4]

std::vector< uint8_t > vg::kff_recode	(	gbwtgraph::Key64::value_type	kmer,
		size_t	k,
		const uint8_t *	encoding
	)

Recodes a kmer from a minimizer index in KFF format according to the given encoding.

◆ kff_recode() [4/4]

uint8_t vg::kff_recode	(	gbwtgraph::Key64::value_type	kmer,
		size_t	k,
		size_t	chars,
		const uint8_t *	encoding
	)

◆ kff_recode_trivial()

gbwtgraph::Key64::value_type vg::kff_recode_trivial	(	const uint8_t *	kmer,
		size_t	k,
		size_t	bytes
	)

Recodes a KFF kmer in the minimizer index format, assuming that the encoding is the same. Will fail silently if k or bytes is too large.

◆ kff_recoding()

kff_recoding_t vg::kff_recoding ( const uint8_t * encoding )

Returns a recoding for the given encoding.

◆ kff_reverse_complement()

std::vector< uint8_t > vg::kff_reverse_complement	(	const uint8_t *	kmer,
		size_t	k,
		const uint8_t *	encoding
	)

Returns the reverse complement of a KFF kmer.

◆ kff_set()

void vg::kff_set	(	std::vector< uint8_t > &	kmer,
		size_t	i,
		uint8_t	value
	)

◆ kmer_to_gcsa_kmers()

void vg::kmer_to_gcsa_kmers	(	const kmer_t &	kmer,
		const gcsa::Alphabet &	alpha,
		const function< void(const gcsa::KMer &)> &	lambda
	)

Convert the kmer_t to a set of gcsa2 binary kmers which are exposed via a callback.

◆ kmp_search()

size_t vg::kmp_search	(	const char *	text,
		size_t	text_len,
		const char *	pattern,
		size_t	pattern_len,
		const vector< size_t > &	prefix_suffix_table
	)

◆ last_path_position()

Position vg::last_path_position ( const Path & path )

◆ list_haplotypes()

vector< pair< vector< gbwt::node_type >, gbwt::SearchState > > vg::list_haplotypes	(	const HandleGraph &	graph,
		const gbwt::GBWT &	gbwt,
		handle_t	start,
		function< bool(const vector< gbwt::node_type > &)>	stop_fn
	)

◆ ln_to_log10()

double vg::ln_to_log10 ( double ln )

inline

Convert a number ln to the same number log 10.

◆ load_gbwt() [1/2]

void vg::load_gbwt	(	gbwt::DynamicGBWT &	index,
		const std::string &	filename,
		bool	show_progress
	)

Load a dynamic GBWT from the file.

◆ load_gbwt() [2/2]

void vg::load_gbwt	(	gbwt::GBWT &	index,
		const std::string &	filename,
		bool	show_progress
	)

Load a compressed GBWT from the file.

◆ load_gbwtgraph()

void vg::load_gbwtgraph	(	gbwtgraph::GBWTGraph &	graph,
		const std::string &	filename,
		bool	show_progress = `false`
	)

Load GBWTGraph from the file. NOTE: Call graph.set_gbwt() afterwards with the appropriate GBWT index.

◆ load_gbz() [1/3]

void vg::load_gbz	(	gbwt::GBWT &	index,
		gbwtgraph::GBWTGraph &	graph,
		const std::string &	filename,
		bool	show_progress
	)

Load GBWT and GBWTGraph from the GBZ file.

◆ load_gbz() [2/3]

void vg::load_gbz	(	gbwtgraph::GBZ &	gbz,
		const std::string &	filename,
		bool	show_progress
	)

Load GBZ from the file.

◆ load_gbz() [3/3]

void vg::load_gbz	(	gbwtgraph::GBZ &	gbz,
		const std::string &	gbwt_name,
		const std::string &	graph_name,
		bool	show_progress
	)

Load GBZ from separate GBWT / GBWTGraph files.

◆ load_gcsa()

void vg::load_gcsa	(	gcsa::GCSA &	index,
		const std::string &	filename,
		bool	show_progress
	)

Load GCSA from the file.

◆ load_lcp()

void vg::load_lcp	(	gcsa::LCPArray &	lcp,
		const std::string &	filename,
		bool	show_progress
	)

Load LCP array from the file.

◆ load_minimizer()

void vg::load_minimizer	(	gbwtgraph::DefaultMinimizerIndex &	index,
		const std::string &	filename,
		bool	show_progress
	)

Load a minimizer index from the file.

◆ load_r_index()

void vg::load_r_index	(	gbwt::FastLocate &	index,
		const std::string &	filename,
		bool	show_progress
	)

Load an r-index from the file.

◆ load_translation_back_map() [1/2]

std::unordered_map< nid_t, std::pair< std::string, size_t > > vg::load_translation_back_map ( const gbwtgraph::GBWTGraph & graph )

Return a backwards mapping of chopped node to original segment position (id,offset pair)

Return a backwards mapping of chopped node to original segment position (id,offset pair) (mimicking logic and interface from function of same name in gbwt_helper.cpp)

◆ load_translation_back_map() [2/2]

unordered_map< nid_t, pair< string, size_t > > vg::load_translation_back_map	(	HandleGraph &	graph,
		ifstream &	input_stream
	)

Load a translation file (created with vg gbwt –translation) and return a backwards mapping of chopped node to original segment position (id,offset pair) NOTE: hopefully this is just a short-term hack, and we get a general interface baked into the handlegraphs themselves

◆ load_translation_map() [1/2]

std::unordered_map< std::string, std::vector< nid_t > > vg::load_translation_map ( const gbwtgraph::GBWTGraph & graph )

Return a mapping of the original segment ids to a list of chopped node ids.

Return a mapping of the original segment ids to a list of chopped node ids (mimicking logic and interface from function of same name in gbwt_helper.cpp)

◆ load_translation_map() [2/2]

unordered_map< string, vector< nid_t > > vg::load_translation_map ( ifstream & input_stream )

Load a translation file (created with vg gbwt –translation) and return a mapping original segment ids to a list of chopped node ids

◆ log10_add_one()

double vg::log10_add_one ( double x )

inline

Given the log10 of a value, retunr the log10 of (that value plus one).

◆ log10_to_ln()

double vg::log10_to_ln ( double l10 )

inline

Convert a number log 10 to the same number ln.

◆ lognormal_pdf()

double vg::lognormal_pdf	(	double	x,
		double	mu,
		double	sigma
	)

Probability density function or log-normal distribution.

◆ logprob_add()

double vg::logprob_add	(	double	logprob1,
		double	logprob2
	)

inline

Add two probabilities (expressed as logprobs) together and return the result as a logprob.

◆ logprob_geometric_mean()

double vg::logprob_geometric_mean	(	double	lnprob1,
		double	lnprob2
	)

inline

Take the geometric mean of two logprobs.

◆ logprob_invert()

double vg::logprob_invert ( double logprob )

inline

Invert a logprob, and get the probability of its opposite.

◆ logprob_sum()

template<typename Collection >

Collection::value_type vg::logprob_sum ( const Collection & collection )

Compute the sum of the values in a collection, where the values are log probabilities and the result is the log of the total probability. Items must be convertible to/from doubles for math.

◆ logprob_to_phred()

double vg::logprob_to_phred ( double logprob )

inline

Convert a natural log probability of wrongness directly to a Phred quality score.

◆ logprob_to_prob()

double vg::logprob_to_prob ( double logprob )

inline

Convert natural log probability to a probability.

◆ make_pos_t() [1/4]

pos_t vg::make_pos_t ( const Position & pos )

Convert a Position to a (much smaller) pos_t.

◆ make_pos_t() [2/4]

pos_t vg::make_pos_t ( const position_t & pos )

◆ make_pos_t() [3/4]

pos_t vg::make_pos_t ( gcsa::node_type node )

Create a pos_t from a gcsa node.

◆ make_pos_t() [4/4]

pos_t vg::make_pos_t	(	id_t	id,
		bool	is_rev,
		offset_t	off
	)

inline

Create a pos_t from a Node ID, an orientation flag, and an offset along that strand of the node.

◆ make_position() [1/3]

Position vg::make_position ( const pos_t & pos )

Convert a pos_t to a Position.

◆ make_position() [2/3]

Position vg::make_position ( gcsa::node_type node )

Make a Position from a gcsa node.

◆ make_position() [3/3]

Position vg::make_position	(	id_t	id,
		bool	is_rev,
		offset_t	off
	)

Create a Position from a Node ID, an orientation flag, and an offset along that strand of the node.

◆ make_prefix_suffix_table()

vector< size_t > vg::make_prefix_suffix_table	(	const char *	pattern,
		size_t	len
	)

◆ make_shuffle_seed() [1/4]

string vg::make_shuffle_seed ( const Alignment & aln )

inline

Make seeds for Alignments based on their sequences.

◆ make_shuffle_seed() [2/4]

string vg::make_shuffle_seed ( const multipath_alignment_t & aln )

inline

Define seed generation for shuffling multipath alignments.

◆ make_shuffle_seed() [3/4]

template<typename T1 , typename T2 >

string vg::make_shuffle_seed ( const pair< T1, T2 > & p )

inline

Make seeds for pairs of things we can make seeds for.

◆ make_shuffle_seed() [4/4]

template<typename T >

string vg::make_shuffle_seed ( const T * ptr )

inline

Make seeds for pointers to things we can make seeds for.

◆ make_support()

Support vg::make_support	(	double	forward,
		double	reverse,
		double	quality
	)

TBD Create a Support for the given forward and reverse coverage and quality.

◆ make_temporary_distance_index()

SnarlDistanceIndex::TemporaryDistanceIndex vg::make_temporary_distance_index	(	const HandleGraph *	graph,
		const HandleGraphSnarlFinder *	snarl_finder,
		size_t	size_limit
	)

◆ make_translation()

vector< Translation > vg::make_translation	(	const HandleGraph *	graph,
		const map< pos_t, id_t > &	node_translation,
		const unordered_map< id_t, Path > &	added_nodes,
		const unordered_map< id_t, size_t > &	orig_node_sizes
	)

Produce a graph Translation object from information about the editing process.

◆ make_variant_id()

string vg::make_variant_id ( const vcflib::Variant & variant )

◆ map_keys_to_set()

template<typename T , typename V >

set<T> vg::map_keys_to_set ( const map< T, V > & m )

◆ map_over()

template<template< class T, class A=std::allocator< T >> class Container, typename Input , typename Output >

Container<Output> vg::map_over	(	const Container< Input > &	in,
		const std::function< Output(const Input &)> &	lambda
	)

We have a transforming map function that we can chain.

◆ mapping_against_path()

void vg::mapping_against_path	(	Alignment &	alignment,
		const bam1_t *	b,
		const path_handle_t &	path,
		const PathPositionHandleGraph *	graph,
		bool	on_reverse_strand
	)

Translate the CIGAR in the given BAM record into mappings in the given Alignment against the given path in the given graph.

◆ mapping_cigar() [1/2]

void vg::mapping_cigar	(	const Mapping &	mapping,
		vector< pair< int, char > > &	cigar
	)

◆ mapping_cigar() [2/2]

void vg::mapping_cigar	(	const Mapping &	mapping,
		vector< pair< int, char >> &	cigar
	)

◆ mapping_ends_in_deletion()

bool vg::mapping_ends_in_deletion ( const Mapping & m )

◆ mapping_from_length() [1/2]

int vg::mapping_from_length ( const Mapping & m )

◆ mapping_from_length() [2/2]

int vg::mapping_from_length ( const path_mapping_t & mapping )

◆ mapping_is_match()

bool vg::mapping_is_match ( const Mapping & m )

◆ mapping_is_simple_match()

bool vg::mapping_is_simple_match ( const Mapping & m )

◆ mapping_is_total_deletion()

bool vg::mapping_is_total_deletion ( const Mapping & m )

◆ mapping_is_total_insertion()

bool vg::mapping_is_total_insertion ( const Mapping & m )

◆ mapping_sequence() [1/2]

const string vg::mapping_sequence	(	const Mapping &	mp,
		const Node &	n
	)

◆ mapping_sequence() [2/2]

const string vg::mapping_sequence	(	const Mapping &	mp,
		const string &	node_seq
	)

◆ mapping_starts_in_deletion()

bool vg::mapping_starts_in_deletion ( const Mapping & m )

◆ mapping_string()

string vg::mapping_string	(	const string &	source,
		const Mapping &	mapping
	)

◆ mapping_to_gbwt()

gbwt::node_type vg::mapping_to_gbwt ( const Mapping & mapping )

inline

Convert Mapping to gbwt::node_type.

◆ mapping_to_handle()

handle_t vg::mapping_to_handle	(	const Mapping &	mapping,
		const HandleGraph &	graph
	)

◆ mapping_to_length() [1/2]

int vg::mapping_to_length ( const Mapping & m )

◆ mapping_to_length() [2/2]

int vg::mapping_to_length ( const path_mapping_t & mapping )

◆ mappings_equivalent()

bool vg::mappings_equivalent	(	const Mapping &	m1,
		const Mapping &	m2
	)

◆ maps_to_node()

bool vg::maps_to_node	(	const Path &	p,
		id_t	id
	)

◆ match_backward()

void vg::match_backward	(	GaplessExtension &	match,
		const std::string &	seq,
		gbwtgraph::view_type	target,
		uint32_t	mismatch_limit
	)

◆ match_forward()

size_t vg::match_forward	(	GaplessExtension &	match,
		const std::string &	seq,
		gbwtgraph::view_type	target,
		uint32_t	mismatch_limit
	)

◆ match_initial()

void vg::match_initial	(	GaplessExtension &	match,
		const std::string &	seq,
		gbwtgraph::view_type	target
	)

◆ matrix_invert()

vector< vector< double > > vg::matrix_invert ( const vector< vector< double >> & A )

◆ matrix_multiply() [1/2]

vector< double > vg::matrix_multiply	(	const vector< vector< double >> &	A,
		const vector< double > &	b
	)

◆ matrix_multiply() [2/2]

vector< vector< double > > vg::matrix_multiply	(	const vector< vector< double >> &	A,
		const vector< vector< double >> &	B
	)

◆ max_exponential_cdf()

double vg::max_exponential_cdf	(	double	x,
		double	rate,
		double	shape,
		double	location = `0.0`
	)

inline

Return the CDF of a max exponential with the given parameters.

◆ max_exponential_log_likelihood()

double vg::max_exponential_log_likelihood	(	const vector< double > &	x,
		double	rate,
		double	shape,
		double	location
	)

The log likelihood of a max exponential with the given parameters on the given data.

◆ maximum_distance()

size_t vg::maximum_distance	(	const SnarlDistanceIndex &	distance_index,
		pos_t	pos1,
		pos_t	pos2
	)

◆ median()

double vg::median ( std::vector< int > & v )

◆ mem_min_oriented_distances()

pair< int64_t, int64_t > vg::mem_min_oriented_distances	(	const MaximalExactMatch &	m1,
		const MaximalExactMatch &	m2
	)

◆ mem_node_start_positions()

vector< pair< gcsa::node_type, size_t > > vg::mem_node_start_positions	(	const HandleGraph &	graph,
		const vg::MaximalExactMatch &	mem
	)

get the handles that a mem covers

◆ mems_overlap()

bool vg::mems_overlap	(	const MaximalExactMatch &	mem1,
		const MaximalExactMatch &	mem2
	)

◆ mems_overlap_length()

int vg::mems_overlap_length	(	const MaximalExactMatch &	mem1,
		const MaximalExactMatch &	mem2
	)

◆ mems_to_json()

const string vg::mems_to_json ( const vector< MaximalExactMatch > & mems )

◆ merge_adjacent_edits() [1/2]

Mapping vg::merge_adjacent_edits ( const Mapping & m )

Merge adjacent edits of the same type.

◆ merge_adjacent_edits() [2/2]

Path vg::merge_adjacent_edits ( const Path & m )

Merge adjacent edits of the same type.

◆ merge_alignments() [1/2]

Alignment vg::merge_alignments	(	const Alignment &	a1,
		const Alignment &	a2,
		bool	debug
	)

◆ merge_alignments() [2/2]

Alignment vg::merge_alignments ( const vector< Alignment > & alns )

◆ merge_edits_in_place()

void vg::merge_edits_in_place	(	Edit &	e,
		const Edit &	f
	)

Glom the second edit into the first, assuming adjacency.

◆ merge_equivalent_traversals_in_graph()

void vg::merge_equivalent_traversals_in_graph	(	MutablePathHandleGraph *	graph,
		const unordered_set< path_handle_t > &	selected_paths,
		bool	use_snarl_manager = `false`
	)

For every top-level snarl in the graph, compute the traversal strings of every embedded path that spans it If two or more traversals share an allele string, then a "canoncial" path is chosen and all remaining paths are edited so that they share the exact same interval through the snarl as the canonical path's traversal. A path is considered "canoncial" if it's in the "selected_paths" and the other paths are not (otherwise the lowest name is used as a fallback)

Note: this doesn't modify the graph toplogy, so uncovered nodes and edges as a result of path editing would usually need removale with vg clip afterwards

the use_snarl_manager toggles between distnace index and snarl manager for computing snarls (adding this option to (hopefully) temporarily revert to the snarl manager for performance reasons)

◆ merge_non_branching_subpaths()

void vg::merge_non_branching_subpaths	(	multipath_alignment_t &	multipath_aln,
		const unordered_set< size_t > *	prohibited_merges = `nullptr`
	)

Merges non-branching paths in a multipath alignment in place Does not assume topological order among subpaths

◆ mergeNodeObjects()

void* vg::mergeNodeObjects	(	void *	a,
		void *	b
	)

◆ middle_signature() [1/2]

string vg::middle_signature	(	const Alignment &	aln,
		int	len
	)

◆ middle_signature() [2/2]

pair< string, string > vg::middle_signature	(	const Alignment &	aln1,
		const Alignment &	aln2,
		int	len
	)

◆ min_oriented_distances()

pair< int64_t, int64_t > vg::min_oriented_distances	(	const unordered_map< path_handle_t, vector< pair< size_t, bool > > > &	path_offsets1,
		const unordered_map< path_handle_t, vector< pair< size_t, bool > > > &	path_offsets2
	)

Find the min distance in the path offsets where the path orientation is the same and different.

◆ minimizer_reverse_complement()

gbwtgraph::Key64::value_type vg::minimizer_reverse_complement	(	gbwtgraph::Key64::value_type	kmer,
		size_t	k
	)

inline

Returns the reverse complement of a minimizer index kmer.

◆ minimum_distance()

size_t vg::minimum_distance	(	const SnarlDistanceIndex &	distance_index,
		pos_t	pos1,
		pos_t	pos2,
		bool	unoriented_distance,
		const HandleGraph *	graph
	)

◆ modular_exponent()

size_t vg::modular_exponent	(	uint64_t	base,
		uint64_t	exponent,
		uint64_t	modulus
	)

Computes base^exponent mod modulus in log(exponent) time without requiring more than 64 bits to represent exponentiated number

◆ multinomial_censored_sampling_prob_ln()

template<typename ProbIn >

real_t vg::multinomial_censored_sampling_prob_ln	(	const vector< ProbIn > &	probs,
		const unordered_map< vector< bool >, int > &	obs
	)

Get the log probability for sampling any actual set of category counts that is consistent with the constraints specified by obs, using the per-category probabilities defined in probs.

Obs maps from a vector of per-category flags (called a "class") to a number of items that might be in any of the flagged categories.

For example, if there are two equally likely categories, and one item flagged as potentially from either category, the probability of sampling a set of category counts consistent with that constraint is 1. If instead there are three equally likely categories, and one item flagged as potentially from two of the three but not the third, the probability of sampling a set of category counts consistent with that constraint is 2/3.

◆ multinomial_choose_ln()

real_t vg::multinomial_choose_ln	(	int	n,
		vector< int >	k
	)

inline

Compute the number of ways to select k_1, k_2, ... k_i items into i buckets from a collection of n distinguishable items, ignoring order. All of the items have to go into the buckets, so all k_i must sum to n. To compute choose you have to call this function with a 2-element vector, to represent the chosen and not-chosen buckets. Returns the natural log of the (integer) result.

TODO: Turns out we don't actually need this for the ambiguous multinomial after all.

◆ multinomial_sampling_prob_ln()

template<typename ProbIn >

real_t vg::multinomial_sampling_prob_ln	(	const vector< ProbIn > &	probs,
		const vector< int > &	obs
	)

Get the probability for sampling the counts in obs from a set of categories weighted by the probabilities in probs. Works for both double and real_t probabilities. Also works for binomials.

◆ node_end()

NodeSide vg::node_end ( id_t id )

inline

Produce the end NodeSide of a Node.

◆ node_start()

NodeSide vg::node_start ( id_t id )

inline

Produce the start NodeSide of a Node.

◆ non_match_end()

int vg::non_match_end ( const Alignment & alignment )

◆ non_match_start()

int vg::non_match_start ( const Alignment & alignment )

◆ nonATGCNtoN()

string vg::nonATGCNtoN ( const string & s )

◆ normal_pdf()

template<typename T >

T vg::normal_pdf	(	T	x,
		T	m = `0.0`,
		T	s = `1.0`
	)

◆ normalize_alignment()

void vg::normalize_alignment ( Alignment & alignment )

Merge adjacent edits of the same type and convert all N matches to mismatches.

◆ num_connected_components()

size_t vg::num_connected_components ( const multipath_alignment_t & multipath_aln )

Returns the number of connected components in the multipath alignment.

◆ offset()

offset_t vg::offset ( const pos_t & pos )

inline

Get the offset along the selected strand of the node from a pos_t.

◆ operator!=() [1/7]

bool vg::operator!=	(	const Exon &	lhs,
		const Exon &	rhs
	)

◆ operator!=() [2/7]

bool vg::operator!=	(	const Mapping &	lhs,
		const Mapping &	rhs
	)

◆ operator!=() [3/7]

bool vg::operator!=	(	const Path &	lhs,
		const Path &	rhs
	)

◆ operator!=() [4/7]

bool vg::operator!=	(	const Snarl &	a,
		const Snarl &	b
	)

Two Snarls are unequal if they are not equal.

◆ operator!=() [5/7]

bool vg::operator!=	(	const SnarlTraversal &	a,
		const SnarlTraversal &	b
	)

Two SnarlTraversals are unequal if they are not equal.

◆ operator!=() [6/7]

bool vg::operator!=	(	const Transcript &	lhs,
		const Transcript &	rhs
	)

◆ operator!=() [7/7]

bool vg::operator!=	(	const Visit &	a,
		const Visit &	b
	)

Two Visits are unequal if they are not equal.

◆ operator*() [1/2]

template<typename Scalar >

Support vg::operator*	(	const Scalar &	scale,
		const Support &	support
	)

Scale a Support by a factor, the other way

◆ operator*() [2/2]

template<typename Scalar >

Support vg::operator*	(	const Support &	support,
		const Scalar &	scale
	)

Scale a Support by a factor.

◆ operator*=()

template<typename Scalar >

Support& vg::operator*=	(	Support &	support,
		const Scalar &	scale
	)

Scale a Support by a factor, in place.

◆ operator+() [1/2]

Support vg::operator+	(	const Support &	one,
		const Support &	other
	)

Add two Support values together, accounting for strand.

◆ operator+() [2/2]

template<typename Item >

VectorView<Item>::const_iterator vg::operator+	(	typename VectorView< Item >::const_iterator::difference_type	a,
		const typename VectorView< Item >::const_iterator &	b
	)

Allow VectorView iterators to be added to numbers.

◆ operator+=()

Support & vg::operator+=	(	Support &	one,
		const Support &	other
	)

Add in a Support to another.

◆ operator/()

template<typename Scalar >

Support vg::operator/	(	const Support &	support,
		const Scalar &	scale
	)

Divide a Support by a factor.

◆ operator/=()

template<typename Scalar >

Support& vg::operator/=	(	Support &	support,
		const Scalar &	scale
	)

Divide a Support by a factor, in place.

◆ operator<() [1/7]

bool vg::operator<	(	const Exon &	lhs,
		const Exon &	rhs
	)

◆ operator<() [2/7]

bool vg::operator<	(	const MaximalExactMatch &	m1,
		const MaximalExactMatch &	m2
	)

◆ operator<() [3/7]

bool vg::operator<	(	const Snarl &	a,
		const Snarl &	b
	)

A Snarl is less than another Snarl if its type is smaller, or its start Visit is smaller, or its end Visit is smaller, or its parent is smaller.

◆ operator<() [4/7]

bool vg::operator<	(	const SnarlTraversal &	a,
		const SnarlTraversal &	b
	)

A SnalTraversal is less than another if it is a traversal of a smaller Snarl, or if its list of Visits has a smaller Visit first, or if its list of Visits is shorter.

◆ operator<() [5/7]

bool vg::operator<	(	const Support &	a,
		const Support &	b
	)

Support less-than, based on total coverage.

◆ operator<() [6/7]

bool vg::operator<	(	const Transcript &	lhs,
		const Transcript &	rhs
	)

◆ operator<() [7/7]

bool vg::operator<	(	const Visit &	a,
		const Visit &	b
	)

A Visit is less than another Visit if it represents a traversal of a smaller node, or it represents a traversal of a smaller snarl, or it represents a traversal of the same node or snarl forward instead of backward.

◆ operator<<() [1/15]

ostream & vg::operator<<	(	ostream &	os,
		const Counts &	counts
	)

◆ operator<<() [2/15]

ostream & vg::operator<<	(	ostream &	out,
		const BenchmarkResult &	result
	)

Benchmark results can be output to streams

◆ operator<<() [3/15]

ostream & vg::operator<<	(	ostream &	out,
		const BitString &	bs
	)		-> ostream &

Allow BitStrings to be printed for debugging.

◆ operator<<() [4/15]

ostream & vg::operator<<	(	ostream &	out,
		const kmer_t &	kmer
	)

Print a kmer_t to a stream.

◆ operator<<() [5/15]

ostream& vg::operator<<	(	ostream &	out,
		const MaximalExactMatch &	mem
	)

◆ operator<<() [6/15]

ostream& vg::operator<<	(	ostream &	out,
		const NodeSide &	nodeside
	)

inline

Print a NodeSide to a stream.

◆ operator<<() [7/15]

ostream& vg::operator<<	(	ostream &	out,
		const NodeTraversal &	nodetraversal
	)

inline

Print the given NodeTraversal.

◆ operator<<() [8/15]

ostream & vg::operator<<	(	ostream &	out,
		const Snarl &	snarl
	)

A Snarl can be printed.

◆ operator<<() [9/15]

ostream & vg::operator<<	(	ostream &	out,
		const Visit &	visit
	)

A Visit can be printed.

◆ operator<<() [10/15]

ostream & vg::operator<<	(	ostream &	out,
		mapping_t	mapping
	)

Allow a mapping_t to be printed, for debugging purposes.

◆ operator<<() [11/15]

ostream & vg::operator<<	(	ostream &	stream,
		const Support &	support
	)

Allow printing a Support.

◆ operator<<() [12/15]

std::ostream& vg::operator<<	(	std::ostream &	out,
		const Funnel::State &	state
	)

inline

◆ operator<<() [13/15]

std::ostream& vg::operator<<	(	std::ostream &	out,
		const pos_t &	pos
	)

inline

Print a pos_t to a stream.

◆ operator<<() [14/15]

std::ostream & vg::operator<<	(	std::ostream &	out,
		const WFAAlignment::Edit &	edit
	)

Allow printing an Edit.

◆ operator<<() [15/15]

std::ostream& vg::operator<<	(	std::ostream &	out,
		PathBranch	branch
	)

◆ operator==() [1/8]

bool vg::operator==	(	const Exon &	lhs,
		const Exon &	rhs
	)

◆ operator==() [2/8]

bool vg::operator==	(	const Mapping &	lhs,
		const Mapping &	rhs
	)

◆ operator==() [3/8]

bool vg::operator==	(	const MaximalExactMatch &	m1,
		const MaximalExactMatch &	m2
	)

◆ operator==() [4/8]

bool vg::operator==	(	const Path &	lhs,
		const Path &	rhs
	)

◆ operator==() [5/8]

bool vg::operator==	(	const Snarl &	a,
		const Snarl &	b
	)

Two Snarls are equal if their types are equal and their bounding Visits are equal and their parents are equal.

◆ operator==() [6/8]

bool vg::operator==	(	const SnarlTraversal &	a,
		const SnarlTraversal &	b
	)

Two SnarlTraversals are equal if their snarls are equal and they have the same number of visits and all their visits are equal.

◆ operator==() [7/8]

bool vg::operator==	(	const Transcript &	lhs,
		const Transcript &	rhs
	)

◆ operator==() [8/8]

bool vg::operator==	(	const Visit &	a,
		const Visit &	b
	)

Two Visits are equal if they represent the same traversal of the same Node or Snarl.

◆ operator>()

bool vg::operator>	(	const Support &	a,
		const Support &	b
	)

Support greater-than, based on total coverage.

◆ optimal_alignment()

void vg::optimal_alignment	(	const multipath_alignment_t &	multipath_aln,
		Alignment &	aln_out,
		bool	subpath_global = `false`
	)

Stores the highest scoring alignment contained in the multipath_alignment_t in an Alignment

Note: Assumes that each subpath's Path object uses one Mapping per node and that start subpaths have been identified

Args: multipath_aln multipath alignment to find optimal path through aln_out empty alignment to store optimal alignment in (data will be overwritten if not empty) subpath_global if true, only allows alignments that source subpath to sink subpath in the multipath DAG, else allows any start and end subpath

◆ optimal_alignment_internal()

int32_t vg::optimal_alignment_internal	(	const multipath_alignment_t &	multipath_aln,
		Alignment *	aln_out,
		bool	subpath_global
	)

◆ optimal_alignment_score()

int32_t vg::optimal_alignment_score	(	const multipath_alignment_t &	multipath_aln,
		bool	subpath_global = `false`
	)

Returns the score of the highest scoring alignment contained in the multipath_alignment_t

Note: Assumes that each subpath's Path object uses one Mapping per node and that start subpaths have been identified

Args: multipath_aln multipath alignment to find optimal score in subpath_global if true, only allows alignments that source subpath to sink subpath in the multipath DAG, else allows any start and end subpath

◆ optimal_alignments()

vector< Alignment > vg::optimal_alignments	(	const multipath_alignment_t &	multipath_aln,
		size_t	count
	)

Returns the top k highest-scoring alignments contained in the multipath_alignment_t. Note that some or all of these may be duplicate Alignments, which were spelled out by tracebacks through different sequences of subpaths that shared alignment material.

If the best alignment is no alignment (i.e. the read is unmapped), returns an empty vector.

Note: Assumes that each subpath's Path object uses one Mapping per node and that start subpaths have been identified

Args: multipath_aln multipath alignment to find optimal paths through count maximum number of top alignments to return

◆ optimal_alignments_with_disjoint_subpaths()

vector< Alignment > vg::optimal_alignments_with_disjoint_subpaths	(	const multipath_alignment_t &	multipath_aln,
		size_t	count
	)

Finds k or fewer top-scoring alignments using only distinct subpaths. Asymmetrical: the optimal alignment for each end subpath is found, greedily, subject to the constraint, but the other subpaths are first-come first-serve. Also, distinct subpaths may not guarantee distinct actual alignments, so alignments may need deduplication.

If the best alignment is no alignment (i.e. the read is unmapped), returns an empty vector.

Note: Assumes that each subpath's Path object uses one Mapping per node and that start subpaths have been identified

Args: multipath_aln multipath alignment to find optimal paths through count maximum number of top alignments to return

◆ output_graph_with_embedded_paths() [1/2]

void vg::output_graph_with_embedded_paths	(	ostream &	subgraph_ostream,
		vector< pair< thread_t, int >> &	haplotype_list,
		const HandleGraph &	source,
		bool	json
	)

◆ output_graph_with_embedded_paths() [2/2]

Graph vg::output_graph_with_embedded_paths	(	vector< pair< thread_t, int >> &	haplotype_list,
		const HandleGraph &	source
	)

◆ output_haplotype_counts()

void vg::output_haplotype_counts	(	ostream &	annotation_ostream,
		vector< pair< thread_t, int >> &	haplotype_list
	)

◆ overlap()

double vg::overlap	(	const Path &	p1,
		const Path &	p2
	)

◆ overlay_node_translations() [1/4]

unordered_map< id_t, id_t > vg::overlay_node_translations	(	const unordered_map< id_t, id_t > &	over,
		const unordered_map< id_t, id_t > &	under
	)

Compose the translations from two graph operations, neither of which involved oriented transformations.

◆ overlay_node_translations() [2/4]

unordered_map< id_t, pair< id_t, bool > > vg::overlay_node_translations	(	const unordered_map< id_t, id_t > &	over,
		const unordered_map< id_t, pair< id_t, bool >> &	under
	)

Compose the translations from two graph operations, the first of which involved oriented transformations.

◆ overlay_node_translations() [3/4]

unordered_map< id_t, pair< id_t, bool > > vg::overlay_node_translations	(	const unordered_map< id_t, pair< id_t, bool >> &	over,
		const unordered_map< id_t, id_t > &	under
	)

Compose the translations from two graph operations, the second of which involved oriented transformations.

◆ overlay_node_translations() [4/4]

unordered_map< id_t, pair< id_t, bool > > vg::overlay_node_translations	(	const unordered_map< id_t, pair< id_t, bool >> &	over,
		const unordered_map< id_t, pair< id_t, bool >> &	under
	)

Compose the translations from two graph operations, both of which involved oriented transformations.

◆ parse() [1/8]

template<typename Result >

Result vg::parse ( const char * arg )

Parse a command-line argument C string. Exits with an error if the string does not contain exactly an item of the appropriate type.

◆ parse() [2/8]

template<typename Result >

Result vg::parse ( const string & arg )

Parse a command-line argument string. Exits with an error if the string does not contain exactly an item of the appropriate type.

◆ parse() [3/8]

template<>

bool vg::parse	(	const string &	arg,
		double &	dest
	)

◆ parse() [4/8]

template<>

bool vg::parse	(	const string &	arg,
		pos_t &	dest
	)

◆ parse() [5/8]

template<typename Result >

bool vg::parse	(	const string &	arg,
		Result &	dest
	)

Parse the appropriate type from the string to the destination value. Return true if parsing is successful and false (or throw something) otherwise.

◆ parse() [6/8]

template<>

bool vg::parse	(	const string &	arg,
		std::regex &	dest
	)

◆ parse() [7/8]

template<typename Result >

bool vg::parse	(	const string &	arg,
		typename enable_if< is_instantiation_of< Result, Range >::value, Result >::type &	dest
	)

inline

Parse a range as start[:end[:step]].

◆ parse() [8/8]

template<typename Result >

bool vg::parse ( const string & arg )

◆ parse_bed_regions() [1/3]

void vg::parse_bed_regions	(	const string &	bed_path,
		vector< Region > &	out_regions,
		vector< string > *	out_names
	)

◆ parse_bed_regions() [2/3]

void vg::parse_bed_regions	(	istream &	bedstream,
		const PathPositionHandleGraph *	graph,
		const std::function< void(Alignment &)> &	callback
	)

Parse regions from the given BED file and call the given callback with each. Does not write them to standard output. Reads the optional name, is_reverse, and score fields if present, and populates the relevant Alignment fields. Skips and warns about malformed or illegal BED records.

◆ parse_bed_regions() [3/3]

void vg::parse_bed_regions	(	istream &	bedstream,
		const PathPositionHandleGraph *	graph,
		vector< Alignment > *	out_alignments
	)

Parse regions from the given BED file into the given vector. Does not write them to standard output.

◆ parse_gff_regions() [1/2]

void vg::parse_gff_regions	(	istream &	gtfstream,
		const PathPositionHandleGraph *	graph,
		const std::function< void(Alignment &)> &	callback
	)

Parse regions from the given GFF file and call the given callback with each. Does not write them to standard output.

◆ parse_gff_regions() [2/2]

void vg::parse_gff_regions	(	istream &	gtfstream,
		const PathPositionHandleGraph *	graph,
		vector< Alignment > *	out_alignments
	)

Parse regions from the given GFF file into the given vector. Does not write them to standard output.

◆ parse_region() [1/2]

void vg::parse_region	(	const string &	target,
		string &	name,
		int64_t &	start,
		int64_t &	end
	)

◆ parse_region() [2/2]

void vg::parse_region	(	string &	region,
		Region &	out_region
	)

inline

◆ parse_rg_sample_map()

void vg::parse_rg_sample_map	(	char *	hts_header,
		map< string, string > &	rg_sample
	)

Populate a mapping from read group to sample name, given the text BAM header.

◆ parse_tid_path_handle_map()

void vg::parse_tid_path_handle_map	(	const bam_hdr_t *	hts_header,
		const PathHandleGraph *	graph,
		map< int, path_handle_t > &	tid_path_handle
	)

Populate a mapping from target ID number to path handle in the given graph, given a parsed BAM header. The graph may be null. Missing target paths in the graph produce no warning or error and no map entry.

◆ parseGenotypes()

std::vector< std::string > vg::parseGenotypes	(	const std::string &	vcf_line,
		size_t	num_samples
	)

◆ partition_gbwt_sequences()

std::vector<std::vector<gbwt::size_type> > vg::partition_gbwt_sequences	(	const gbwt::GBWT &	gbwt_index,
		const std::unordered_map< nid_t, size_t > &	node_to_job,
		size_t	num_jobs
	)

◆ path_end_position()

Position vg::path_end_position ( const Path & path )

◆ path_from_length() [1/2]

int vg::path_from_length ( const Path & path )

◆ path_from_length() [2/2]

int vg::path_from_length ( const path_t & path )

◆ path_from_node_traversals()

Path vg::path_from_node_traversals ( const list< NodeTraversal > & traversals )

◆ path_from_path_handle()

Path vg::path_from_path_handle	(	const PathHandleGraph &	graph,
		path_handle_t	path_handle
	)

◆ path_from_thread_t()

Path vg::path_from_thread_t	(	thread_t &	t,
		const HandleGraph &	source
	)

◆ path_is_simple_match()

bool vg::path_is_simple_match ( const Path & p )

◆ path_node() [1/2]

vg::id_t vg::path_node	(	const gbwt::vector_type &	path,
		size_t	i
	)

◆ path_node() [2/2]

vg::id_t vg::path_node	(	const vector< pair< vg::id_t, bool >> &	path,
		size_t	i
	)

◆ path_predecessors()

gbwt::vector_type vg::path_predecessors	(	const PathHandleGraph &	graph,
		const std::string &	path_name
	)

Find all predecessor nodes of the path, ignoring self-loops. If the path does not exist, it is treated as empty.

◆ path_reverse() [1/2]

bool vg::path_reverse	(	const gbwt::vector_type &	path,
		size_t	i
	)

◆ path_reverse() [2/2]

bool vg::path_reverse	(	const vector< pair< vg::id_t, bool >> &	path,
		size_t	i
	)

◆ path_sequence()

string vg::path_sequence	(	const HandleGraph &	graph,
		const Path &	path
	)

◆ path_size() [1/2]

size_t vg::path_size ( const gbwt::vector_type & path )

◆ path_size() [2/2]

size_t vg::path_size ( const vector< pair< vg::id_t, bool >> & path )

◆ path_start_position()

Position vg::path_start_position ( const Path & path )

◆ path_to_gbwt()

gbwt::vector_type vg::path_to_gbwt ( const Path & path )

inline

Convert Path to a GBWT path.

◆ path_to_length() [1/2]

int vg::path_to_length ( const Path & path )

◆ path_to_length() [2/2]

int vg::path_to_length ( const path_t & path )

◆ path_to_string()

string vg::path_to_string ( Path p )

◆ paths_from_graph()

const Paths vg::paths_from_graph ( Graph & g )

◆ percent_url_encode()

string vg::percent_url_encode ( const string & seq )

Escape "%" to "%25".

◆ Phi()

double vg::Phi ( double x )

The standard normal cumulative distribution function.

◆ Phi_inv()

double vg::Phi_inv ( double p )

Inverse CDF of a standard normal distribution. Must have 0 < quantile < 1.

◆ phred_add()

double vg::phred_add	(	double	phred1,
		double	phred2
	)

inline

Add two probabilities (expressed as phred scores) together and return the result as a phred score.

◆ phred_for_at_least_one()

double vg::phred_for_at_least_one	(	size_t	p,
		size_t	n
	)

Assume that we have n independent random events that occur with probability p each (p is interpreted as a real number between 0 at 0 and 1 at its maximum value). Return an approximate probability for at least one event occurring as a phred score.

n must be <= MAX_AT_LEAST_ONE_EVENTS.

Assume that we have n <= MAX_AT_LEAST_ONE_EVENTS independent events with probability p each. Let x be the AT_LEAST_ONE_PRECISION most significant bits of p. Then

phred_at_least_one[(n << AT_LEAST_ONE_PRECISION) + x]

is an approximate phred score of at least one event occurring.

We exploit the magical thread-safety of static local initialization to fill this in exactly once when needed.

◆ phred_geometric_mean()

double vg::phred_geometric_mean	(	double	phred1,
		double	phred2
	)

inline

Take the geometric mean of two phred-encoded probabilities.

◆ phred_sum() [1/2]

template<typename Collection >

Collection::value_type vg::phred_sum ( const Collection & collection )

Compute the sum of the values in a collection, where the values are Phred scores and the result is the Phred score of the total probability. Items must be convertible to/from doubles for math.

◆ phred_sum() [2/2]

template<typename Iterator >

std::iterator_traits<Iterator>::value_type vg::phred_sum	(	const Iterator &	begin_it,
		const Iterator &	end_it
	)

Compute the sum of the values in a collection, represented by an iterator range, where the values are Phred scores and the result is the Phred score of the total probability. Items must be convertible to/from doubles for math.

◆ phred_to_logprob()

double vg::phred_to_logprob ( int phred )

inline

Convert a Phred quality score directly to a natural log probability of wrongness.

◆ phred_to_prob() [1/2]

double vg::phred_to_prob ( double phred )

inline

Convert floating point Phred quality score to probability of wrongness.

◆ phred_to_prob() [2/2]

double vg::phred_to_prob ( uint8_t phred )

Convert 8-bit Phred quality score to probability of wrongness, using a lookup table.

◆ pmax()

template<typename T >

vector<T> vg::pmax	(	const std::vector< T > &	a,
		const std::vector< T > &	b
	)

◆ pointerfy()

template<template< class T, class A=std::allocator< T >> class Container, typename Item >

Container<const Item*> vg::pointerfy ( const Container< Item > & in )

We have a wrapper of that to turn a container reference into a container of pointers.

◆ poisson_prob_ln()

real_t vg::poisson_prob_ln	(	int	observed,
		real_t	expected
	)

inline

Compute the log probability of a Poisson-distributed process: observed events in an interval where expected events happen on average.

◆ populate_path_from_traceback()

template<typename TracebackIterator >

void vg::populate_path_from_traceback	(	const multipath_alignment_t &	multipath_aln,
		const MultipathProblem &	problem,
		TracebackIterator	traceback_start,
		TracebackIterator	traceback_end,
		Path *	output
	)

We define this helper to turn tracebacks through a DP problem into Paths that we can put in an Alignment. We use iterators to the start and past-the-end of the traceback (in some kind of list of int64_t subpath indexes) to define it.

◆ populate_snarl_index()

void vg::populate_snarl_index	(	SnarlDistanceIndex::TemporaryDistanceIndex &	temp_index,
		pair< SnarlDistanceIndex::temp_record_t, size_t >	snarl_index,
		size_t	size_limit,
		const HandleGraph *	graph
	)

Record the distance

Add the next node to the priority queue

Check the minimum length of the snarl passing through this node

◆ pos_to_gbwt()

gbwt::node_type vg::pos_to_gbwt ( pos_t pos )

inline

Extract gbwt::node_type from pos_t.

◆ position_at()

pos_t vg::position_at	(	PathPositionHandleGraph *	graph_ptr,
		const string &	path_name,
		const size_t &	path_offset,
		bool	is_reverse
	)

We have a helper function to convert path positions and orientations to pos_t values.

We have a utility function for turning positions along paths, with orientations, into pos_ts. Remember that pos_t counts offset from the start of the reoriented node, while here we count offset from the beginning of the forward version of the path.

◆ pow_ln()

real_t vg::pow_ln	(	real_t	m,
		int	n
	)

inline

Raise a log probability to a power

◆ preflight_check()

void vg::preflight_check ( )

Run a preflight check to make sure that the system is usable for this build of vg. Aborts with a helpful message if this is not the case. We make sure to build it for a lowest-common-denominator architecture.

◆ present_kmers()

void vg::present_kmers	(	const std::vector< std::vector< HaplotypePartitioner::kmer_type >> &	sequences,
		std::vector< std::pair< HaplotypePartitioner::kmer_type, size_t >> &	all_kmers,
		sdsl::bit_vector &	kmers_present
	)

◆ printId()

template<class Decoder >

void vg::printId ( vg::id_t id )

◆ prob_for_at_least_one()

double vg::prob_for_at_least_one	(	size_t	p,
		size_t	n
	)

Assume that we have n independent random events that occur with probability p each (p is interpreted as a real number between 0 at 0 and 1 at its maximum value). Return an approximate probability for at least one event occurring as a raw probability.

n must be <= MAX_AT_LEAST_ONE_EVENTS.

Assume that we have n <= MAX_AT_LEAST_ONE_EVENTS independent events with probability p each. Let x be the AT_LEAST_ONE_PRECISION most significant bits of p. Then

prob_at_least_one[(n << AT_LEAST_ONE_PRECISION) + x]

is an approximate probability of at least one event occurring.

We exploit the magical thread-safety of static local initialization to fill this in exactly once when needed.

◆ prob_to_logprob()

double vg::prob_to_logprob ( double prob )

inline

Convert a probability to a natural log probability.

◆ prob_to_phred()

double vg::prob_to_phred ( double prob )

inline

Convert probability of wrongness to integer Phred quality score.

◆ pseudo_random_sequence()

string vg::pseudo_random_sequence	(	size_t	length,
		uint64_t	seed
	)

Returns a uniformly random DNA sequence sequence deterministically from a seed.

◆ query_overlap()

int vg::query_overlap	(	const Alignment &	aln1,
		const Alignment &	aln2
	)

◆ random_sequence()

string vg::random_sequence ( size_t length )

Returns a uniformly random DNA sequence of the given length.

◆ random_sequence_gen()

default_random_engine vg::random_sequence_gen ( 102 )

◆ range_vector() [1/2]

vector< size_t > vg::range_vector	(	size_t	begin,
		size_t	end
	)

Vector containing positive integer values in [begin, end)

◆ range_vector() [2/2]

vector<size_t> vg::range_vector ( size_t end )

inline

Vector containing positive integer values in [0, end)

◆ rebuild_gbwt() [1/2]

gbwt::GBWT vg::rebuild_gbwt	(	const gbwt::GBWT &	gbwt_index,
		const std::vector< RebuildJob > &	jobs,
		const std::unordered_map< nid_t, size_t > &	node_to_job,
		const RebuildParameters &	parameters
	)

Rebuild the GBWT by applying all provided mappings. Each mapping is a pair (original subpath, new subpath). If the original subpath is empty, the mapping is ignored. If there are multiple applicable mappings, the first one will be used.

The mappings will be applied in both orientations. The reverse mapping replaces the reverse of the original subpath with the reverse of the new subpath.

The first and the last node can be used as context. For example (aXb, aYb) can be interpreted as "replace X with Y in context a b". If both subpaths end with the same node, the cursor will point at that node after the mapping. Otherwise the cursor will be set past the original subpath.

NOTE: To avoid infinite loops, the cursor will proceed after a mapping of the type (a, Xa).

The process can be partitioned into multiple non-overlapping jobs, each of them corresponding to one or more weakly connected components in the graph. Multiple jobs can be run in parallel using 2 threads each, and the jobs will be started from the largest to the smallest.

node_to_job maps each node identifier to the corresponding job identifier. Empty paths go to the first job, but this can be overridden by including gbwt::ENDMARKER in node_to_job.

NOTE: Paths may be reordered if there are multiple jobs. Old path ids are no longer valid after rebuilding the GBWT.

NOTE: This could use the ConstructionJob / MetadataBuilder scheme for parallelization, but it would change the interface.

◆ rebuild_gbwt() [2/2]

gbwt::GBWT vg::rebuild_gbwt	(	const gbwt::GBWT &	gbwt_index,
		const std::vector< RebuildJob::mapping_type > &	mappings
	)

As the general rebuild_gbwt, but always using a single job with default parameters.

◆ rebuild_gbwt_job()

gbwt::GBWT vg::rebuild_gbwt_job	(	const gbwt::GBWT &	gbwt_index,
		const RebuildJob &	job,
		size_t	job_id,
		const std::vector< gbwt::size_type > &	sequences,
		const RebuildParameters &	parameters
	)

◆ recombinator_sanity_checks()

void vg::recombinator_sanity_checks ( const Recombinator::Parameters & parameters )

◆ regress()

vector< double > vg::regress	(	const vector< vector< double >> &	X,
		vector< double > &	y
	)

Returns the coefficients of a regression (does not automatically compute constant)

◆ remove_duplicate_edges()

void vg::remove_duplicate_edges ( Graph & graph )

remove duplicate edges

◆ remove_duplicate_nodes()

void vg::remove_duplicate_nodes ( Graph & graph )

remove duplicate nodes

◆ remove_duplicates() [1/2]

void vg::remove_duplicates ( Graph & graph )

remove duplicate nodes and edges

◆ remove_duplicates() [2/2]

void vg::remove_duplicates ( std::vector< GaplessExtension > & result )

◆ remove_empty_alignment_sections()

void vg::remove_empty_alignment_sections ( multipath_alignment_t & multipath_aln )

Removes all edit, mappings, and subpaths that have no aligned bases, and introduces transitive edges to preserve connectivity through any completely removed subpaths

◆ remove_low_scoring_sections()

void vg::remove_low_scoring_sections	(	multipath_alignment_t &	multipath_aln,
		int32_t	max_score_diff
	)

Removes all subpaths and edges whose optimal full length alignment is less than the given difference from the highest-scoring full length alignment

◆ remove_orphan_edges()

void vg::remove_orphan_edges ( Graph & graph )

remove edges that link to a node that is not in the graph

◆ remove_paths()

void vg::remove_paths	(	Graph &	graph,
		const function< bool(const string &)> &	paths_to_take,
		std::list< Path > *	matching
	)

◆ replace_in_string()

string vg::replace_in_string	(	string	subject,
		const string &	search,
		const string &	replace
	)

◆ report_exception()

void vg::report_exception ( const std::exception & ex )

User code should call this if it catches an exception it doesn't know what to do with.

◆ rev_comp_multipath_alignment()

void vg::rev_comp_multipath_alignment	(	const multipath_alignment_t &	multipath_aln,
		const function< int64_t(int64_t)> &	node_length,
		multipath_alignment_t &	rev_comp_out
	)

Stores the reverse complement of a multipath_alignment_t in another multipath_alignment_t

Args: multipath_aln multipath alignment to reverse complement node_length a function that returns the length of a node sequence from its node ID rev_comp_out empty multipath alignment to store reverse complement in (some data may be overwritten if not empty)

◆ rev_comp_multipath_alignment_in_place()

void vg::rev_comp_multipath_alignment_in_place	(	multipath_alignment_t *	multipath_aln,
		const function< int64_t(int64_t)> &	node_length
	)

Stores the reverse complement of a multipath_alignment_t in another multipath_alignment_t

Args: multipath_aln multipath alignment to reverse complement in place node_length a function that returns the length of a node sequence from its node ID

◆ rev_comp_subpath()

void vg::rev_comp_subpath	(	const subpath_t &	subpath,
		const function< int64_t(int64_t)> &	node_length,
		subpath_t &	rev_comp_out
	)

inline

Stores the reverse complement of a Subpath in another Subpath

note: this is not included in the header because reversing a subpath without going through the multipath alignment can break invariants related to the edge lists

Args: subpath subpath to reverse complement node_length a function that returns the length of a node sequence from its node ID rev_comp_out empty subpath to store reverse complement in (data will be overwritten if not empty)

◆ reverse() [1/3]

pos_t vg::reverse	(	const pos_t &	pos,
		size_t	node_length
	)

inline

Reverse a pos_t and get a pos_t at the same point between bases, going the other direction. To get a pos_t to the same base, subtract 1 from the resulting offset or call reverse_base_pos().

◆ reverse() [2/3]

Position vg::reverse	(	const Position &	pos,
		size_t	node_length
	)

Reverse a Position and get a Position at the same point between bases, going the other direction. To get a Position to the same base, subtract 1 from the resulting offset.

◆ reverse() [3/3]

Visit vg::reverse ( const Visit & visit )

inline

Get the reversed version of a visit.

◆ reverse_base_pos()

pos_t vg::reverse_base_pos	(	const pos_t &	pos,
		size_t	node_length
	)

inline

Reverse a pos_t and get a pos_t at the same base, going the other direction.

◆ reverse_complement() [1/2]

char vg::reverse_complement ( const char & c )

◆ reverse_complement() [2/2]

string vg::reverse_complement ( const string & seq )

◆ reverse_complement_alignment()

Alignment vg::reverse_complement_alignment	(	const Alignment &	aln,
		const function< int64_t(id_t)> &	node_length
	)

◆ reverse_complement_alignment_in_place()

void vg::reverse_complement_alignment_in_place	(	Alignment *	aln,
		const function< int64_t(id_t)> &	node_length
	)

◆ reverse_complement_alignments()

vector< Alignment > vg::reverse_complement_alignments	(	const vector< Alignment > &	alns,
		const function< int64_t(int64_t)> &	node_length
	)

◆ reverse_complement_in_place()

void vg::reverse_complement_in_place ( string & seq )

◆ reverse_complement_mapping() [1/2]

Mapping vg::reverse_complement_mapping	(	const Mapping &	m,
		const function< int64_t(id_t)> &	node_length
	)

◆ reverse_complement_mapping() [2/2]

path_mapping_t vg::reverse_complement_mapping	(	const path_mapping_t &	m,
		const function< int64_t(id_t)> &	node_length
	)

◆ reverse_complement_mapping_in_place() [1/2]

void vg::reverse_complement_mapping_in_place	(	Mapping *	m,
		const function< int64_t(id_t)> &	node_length
	)

◆ reverse_complement_mapping_in_place() [2/2]

void vg::reverse_complement_mapping_in_place	(	path_mapping_t *	m,
		const function< int64_t(id_t)> &	node_length
	)

◆ reverse_complement_path() [1/2]

Path vg::reverse_complement_path	(	const Path &	path,
		const function< int64_t(id_t)> &	node_length
	)

◆ reverse_complement_path() [2/2]

path_t vg::reverse_complement_path	(	const path_t &	path,
		const function< int64_t(id_t)> &	node_length
	)

◆ reverse_complement_path_in_place() [1/2]

void vg::reverse_complement_path_in_place	(	Path *	path,
		const function< int64_t(id_t)> &	node_length
	)

◆ reverse_complement_path_in_place() [2/2]

void vg::reverse_complement_path_in_place	(	path_t *	path,
		const function< int64_t(id_t)> &	node_length
	)

◆ run_benchmark() [1/2]

BenchmarkResult vg::run_benchmark	(	const string &	name,
		size_t	iterations,
		const function< void(void)> &	setup,
		const function< void(void)> &	under_test
	)

Run a benchmark with a setup function.

◆ run_benchmark() [2/2]

BenchmarkResult vg::run_benchmark	(	const string &	name,
		size_t	iterations,
		const function< void(void)> &	under_test
	)

Run the given function the given number of times, interleaved with runs of the control function, and return a BenchmarkResult describing its performance.

◆ run_multipath_dp()

tuple<MultipathProblem, int64_t, int32_t> vg::run_multipath_dp	(	const multipath_alignment_t &	multipath_aln,
		bool	subpath_global = `false`,
		bool	forward = `true`
	)

Internal helper function for running the dynamic programming problem represented by a multipath alignment. Returns the filled DP problem, the optimal ending subpath, or -1 if no subpath is optimal, and the optimal score, or 0 if no score is optimal. An option toggles whether the traceback should be global (a source to a sink in the multipath DAG) or local (starting and ending at any subpath)

◆ sa_to_da()

void vg::sa_to_da	(	std::vector< HaplotypePartitioner::sequence_type > &	sequences,
		const gbwt::FastLocate &	r_index
	)

◆ sam_flag()

int32_t vg::sam_flag	(	const Alignment &	alignment,
		bool	on_reverse_strand,
		bool	paired
	)

◆ save_gbwt() [1/2]

void vg::save_gbwt	(	const gbwt::DynamicGBWT &	index,
		const std::string &	filename,
		bool	show_progress
	)

Save a dynamic GBWT to the file.

◆ save_gbwt() [2/2]

void vg::save_gbwt	(	const gbwt::GBWT &	index,
		const std::string &	filename,
		bool	show_progress
	)

Save a compressed GBWT to the file.

◆ save_gbwtgraph()

void vg::save_gbwtgraph	(	const gbwtgraph::GBWTGraph &	graph,
		const std::string &	filename,
		bool	show_progress
	)

Save GBWTGraph to the file.

◆ save_gbz() [1/3]

void vg::save_gbz	(	const gbwt::GBWT &	index,
		gbwtgraph::GBWTGraph &	graph,
		const std::string &	filename,
		bool	show_progress
	)

Save GBWT and GBWTGraph to the GBZ file.

◆ save_gbz() [2/3]

void vg::save_gbz	(	const gbwtgraph::GBZ &	gbz,
		const std::string &	filename,
		bool	show_progress
	)

Save GBZ to the file.

◆ save_gbz() [3/3]

void vg::save_gbz	(	const gbwtgraph::GBZ &	gbz,
		const std::string &	gbwt_name,
		const std::string &	graph_name,
		bool	show_progress
	)

Save GBZ to separate GBWT / GBWTGraph files.

◆ save_gcsa()

void vg::save_gcsa	(	const gcsa::GCSA &	index,
		const std::string &	filename,
		bool	show_progress
	)

Save GCSA to the file.

◆ save_lcp()

void vg::save_lcp	(	const gcsa::LCPArray &	lcp,
		const std::string &	filename,
		bool	show_progress
	)

Save LCP array to the file.

◆ save_minimizer()

void vg::save_minimizer	(	const gbwtgraph::DefaultMinimizerIndex &	index,
		const std::string &	filename,
		bool	show_progress
	)

Save a minimizer index to the file.

◆ save_r_index()

void vg::save_r_index	(	const gbwt::FastLocate &	index,
		const std::string &	filename,
		bool	show_progress
	)

Save an r-index to the file.

◆ score_gap()

int32_t vg::score_gap	(	size_t	gap_length,
		int32_t	gap_open,
		int32_t	gap_extension
	)

Score a gap with the given open and extension scores.

◆ search_multipath_alignment()

vector< tuple< int64_t, int64_t, int64_t, int64_t > > vg::search_multipath_alignment	(	const multipath_alignment_t &	multipath_aln,
		const pos_t &	graph_pos,
		int64_t	seq_pos
	)

Returns all of the positions where a given sequence index occurs at a given graph graph position (if any), where positions are represented as tuples of (subpath index, mapping index, edit index, index within edit)

◆ select_diploid()

std::vector<std::pair<size_t, double> > vg::select_diploid	(	const Haplotypes::Subchain &	subchain,
		const std::vector< std::pair< size_t, double >> &	candidates,
		const std::vector< std::pair< Recombinator::kmer_presence, double >> &	kmer_types
	)

◆ select_haplotypes()

std::vector<std::pair<size_t, double> > vg::select_haplotypes	(	const Haplotypes::Subchain &	subchain,
		const hash_map< Haplotypes::Subchain::kmer_type, size_t > &	kmer_counts,
		double	coverage,
		Recombinator::Statistics *	statistics,
		std::vector< Recombinator::LocalHaplotype > *	local_haplotypes,
		const Recombinator::Parameters &	parameters
	)

◆ set_annotation() [1/2]

template<typename AnnotationType , typename Annotated >

void vg::set_annotation	(	Annotated &	annotated,
		const string &	name,
		const AnnotationType &	annotation
	)

inline

Set the annotation with the given name to the given value. The value may be a primitive type or a vector of a primitive type.

◆ set_annotation() [2/2]

template<typename AnnotationType , typename Annotated >

void vg::set_annotation	(	Annotated *	annotated,
		const string &	name,
		const AnnotationType &	annotation
	)

inline

Set the annotation with the given name to the given value. The value may be a primitive type or a vector of a primitive type.

◆ set_crash_context()

void vg::set_crash_context ( const std::string & message )

User code should call this when it has context for a failure in its thread.

◆ set_intersection()

template<typename T >

void vg::set_intersection	(	const unordered_set< T > &	set_1,
		const unordered_set< T > &	set_2,
		unordered_set< T > *	out_intersection
	)

inline

◆ set_score()

void vg::set_score	(	GaplessExtension &	extension,
		const Aligner *	aligner
	)

◆ sha1head()

const std::string vg::sha1head	(	const std::string &	data,
		size_t	head
	)

◆ sha1sum()

const std::string vg::sha1sum ( const std::string & data )

◆ signature() [1/2]

string vg::signature ( const Alignment & aln )

◆ signature() [2/2]

pair< string, string > vg::signature	(	const Alignment &	aln1,
		const Alignment &	aln2
	)

◆ simplify() [1/3]

Alignment vg::simplify	(	const Alignment &	a,
		bool	trim_internal_deletions = `true`
	)

Simplifies the Path in the Alignment. Note that this removes deletions at the start and end of Mappings, so code that handles simplified Alignments needs to handle offsets on internal Mappings.

◆ simplify() [2/3]

Mapping vg::simplify	(	const Mapping &	m,
		bool	trim_internal_deletions = `true`
	)

Merge adjacent edits of the same type, strip leading and trailing deletion edits (while updating positions if necessary), and makes sure position is actually set.

◆ simplify() [3/3]

Path vg::simplify	(	const Path &	p,
		bool	trim_internal_deletions = `true`
	)

Simplify the path for addition as new material in the graph. Remove any mappings that are merely single deletions, merge adjacent edits of the same type, strip leading and trailing deletion edits on mappings, and make sure no mappings have missing positions.

◆ simplify_cigar()

void vg::simplify_cigar ( vector< pair< int, char >> & cigar )

Merge runs of successive I/D operations into a single I and D, remove 0-length operations, and merge adjacent operations of the same type

◆ simplify_filtered_edits()

bool vg::simplify_filtered_edits	(	HandleGraph *	graph,
		Alignment &	aln,
		Path &	path,
		const map< pos_t, id_t > &	node_translation,
		const unordered_map< id_t, size_t > &	orig_node_sizes,
		double	min_baseq = `0`,
		double	max_frac_n = `1.`
	)

Remove edits in our graph that don't correspond to breakpoints (ie were effectively filtered out due to insufficient coverage. This way, subsequent logic in add_nodes_and_edges can be run correctly. Returns true if at least one edit survived the filter.

◆ slope()

double vg::slope	(	const std::vector< double > &	x,
		const std::vector< double > &	y
	)

◆ softclip_end() [1/2]

int vg::softclip_end ( const Alignment & alignment )

◆ softclip_end() [2/2]

int vg::softclip_end ( const Mapping & mapping )

◆ softclip_start() [1/2]

int vg::softclip_start ( const Alignment & alignment )

◆ softclip_start() [2/2]

int vg::softclip_start ( const Mapping & mapping )

◆ softclip_trim()

int vg::softclip_trim ( Alignment & alignment )

◆ sort_by_id()

void vg::sort_by_id ( Graph & graph )

order the nodes and edges in the graph by id

◆ sort_by_id_dedup_and_clean()

void vg::sort_by_id_dedup_and_clean ( Graph & graph )

remove duplicates and sort by id

◆ sort_edges_by_id()

void vg::sort_edges_by_id ( Graph & graph )

order the edges in the graph by id pairs

◆ sort_nodes_by_id()

void vg::sort_nodes_by_id ( Graph & graph )

order the nodes in the graph by id

◆ sort_pair_by_second()

bool vg::sort_pair_by_second	(	const pair< uint32_t, uint32_t > &	lhs,
		const pair< uint32_t, uint32_t > &	rhs
	)

◆ sort_permutation() [1/2]

template<typename Iterator >

std::vector<size_t> vg::sort_permutation	(	const Iterator &	begin,
		const Iterator &	end
	)

Get the index permutation that sorts the given items ascending using <.

◆ sort_permutation() [2/2]

template<typename Iterator >

std::vector<size_t> vg::sort_permutation	(	const Iterator &	begin,
		const Iterator &	end,
		const std::function< bool(const typename Iterator::value_type &, const typename Iterator::value_type &)> &	comparator
	)

Get the index permutation that sorts the given items with the given comparator instead of <.

◆ sort_shuffling_ties() [1/2]

template<class RandomIt , class Compare >

void vg::sort_shuffling_ties	(	RandomIt	begin,
		RandomIt	end,
		Compare	comp
	)

Sort the items between the two given random-access iterators, as with std::sort. Deterministically shuffle the ties, if any, at the top end, using automatic seed determination as defined by a make_shuffle_seed() overload for the collection's item type.

◆ sort_shuffling_ties() [2/2]

template<class RandomIt , class Compare >

void vg::sort_shuffling_ties	(	RandomIt	begin,
		RandomIt	end,
		Compare	comp,
		LazyRNG &	rng
	)

Sort the items between the two given random-access iterators, as with std::sort. Deterministically shuffle the ties, if any, at the top end.

◆ sort_transcript_paths_by_name()

bool vg::sort_transcript_paths_by_name	(	const CompletedTranscriptPath &	lhs,
		const CompletedTranscriptPath &	rhs
	)

◆ split_delims() [1/2]

std::vector< std::string > vg::split_delims	(	const std::string &	s,
		const std::string &	delims,
		size_t	max_cuts
	)

◆ split_delims() [2/2]

std::vector< std::string > & vg::split_delims	(	const std::string &	s,
		const std::string &	delims,
		std::vector< std::string > &	elems,
		size_t	max_cuts
	)

◆ split_ext()

pair< string, string > vg::split_ext ( const string & filename )

Split off the extension from a filename and return both parts.

◆ split_splice_segment()

pair<pair<path_t, int32_t>, pair<path_t, int32_t> > vg::split_splice_segment	(	const Alignment &	splice_segment,
		const tuple< int64_t, int64_t, int64_t > &	left_trace,
		const tuple< int64_t, int64_t, int64_t > &	right_trace,
		int64_t	splice_junction_idx,
		const GSSWAligner &	scorer,
		const HandleGraph &	graph
	)

◆ stack_permutations()

std::vector< size_t > vg::stack_permutations	(	const std::vector< size_t > &	bottom,
		const std::vector< size_t > &	top
	)

Apply one permutation on top of another. Retutn the combined permutation.

◆ stacktrace_manually()

void vg::stacktrace_manually	(	ostream &	out,
		int	signalNumber,
		void *	ip,
		void **	bp
	)

◆ start_backward()

bool vg::start_backward ( const Chain & chain )

Return true if the first snarl in the given chain is backward relative to the chain.

◆ starts_with()

bool vg::starts_with	(	const std::string &	value,
		const std::string &	prefix
	)

Check if a string starts with another string.

◆ stdev()

template<typename T >

double vg::stdev ( const T & v )

◆ strip_from_end()

Alignment vg::strip_from_end	(	const Alignment &	aln,
		size_t	drop
	)

◆ strip_from_start()

Alignment vg::strip_from_start	(	const Alignment &	aln,
		size_t	drop
	)

◆ stubbify_ref_paths()

void vg::stubbify_ref_paths	(	MutablePathMutableHandleGraph *	graph,
		const vector< string > &	ref_prefixes,
		int64_t	min_fragment_len,
		bool	verbose
	)

stubbify reference

◆ sub_overlaps_of_first_aln()

int vg::sub_overlaps_of_first_aln	(	const vector< Alignment > &	alns,
		float	overlap_fraction
	)

◆ subgraph_containing_path_snarls()

void vg::subgraph_containing_path_snarls	(	const SnarlDistanceIndex &	distance_index,
		const HandleGraph *	graph,
		const Path &	path,
		std::unordered_set< nid_t > &	subgraph
	)

◆ subgraph_in_distance_range()

void vg::subgraph_in_distance_range	(	const SnarlDistanceIndex &	distance_index,
		const Path &	path,
		const HandleGraph *	super_graph,
		size_t	min_distance,
		size_t	max_distance,
		std::unordered_set< nid_t > &	subgraph,
		bool	look_forward
	)

◆ subgraph_in_distance_range_walk_across_chain()

void vg::subgraph_in_distance_range_walk_across_chain	(	const SnarlDistanceIndex &	distance_index,
		const HandleGraph *	super_graph,
		std::unordered_set< nid_t > &	subgraph,
		net_handle_t	current_node,
		size_t	current_distance,
		vector< pair< handle_t, size_t >> &	search_start_nodes,
		hash_set< pair< nid_t, bool >> &	seen_nodes,
		const size_t &	min_distance,
		const size_t &	max_distance,
		bool	checked_loop
	)

◆ subgraph_in_distance_range_walk_graph()

void vg::subgraph_in_distance_range_walk_graph	(	const HandleGraph *	super_graph,
		size_t	min_distance,
		size_t	max_distance,
		std::unordered_set< nid_t > &	subgraph,
		vector< pair< handle_t, size_t >> &	start_nodes,
		hash_set< pair< nid_t, bool >> &	seen_nodes,
		const pair< nid_t, bool > &	traversal_start
	)

Helper for subgraph_in_distance_range Given starting handles in the super graph and the distances to each handle (including the start position and

◆ subpath_topological_order()

vector<size_t> vg::subpath_topological_order	(	const multipath_alignment_t &	multipath_aln,
		bool	do_index
	)

Return either the vector of topological order by index or the vector of indexes within the topological order.

◆ subtract_log()

double vg::subtract_log	(	double	log_x,
		double	log_y
	)

inline

◆ sum()

template<typename Collection >

Collection::value_type vg::sum ( const Collection & collection )

Compute the sum of the values in a collection. Values must be default- constructable (like numbers are).

◆ summary_statistics()

template<typename Number >

SummaryStatistics vg::summary_statistics ( const std::map< Number, size_t > & values )

Returns summary statistics for a multiset of numbers.

◆ support_max()

Support vg::support_max	(	const Support &	a,
		const Support &	b
	)

Get the maximum support of a pair of Supports, by taking the max in each orientation.

◆ support_min()

Support vg::support_min	(	const Support &	a,
		const Support &	b
	)

Get the minimum support of a pair of Supports, by taking the min in each orientation.

◆ take_unique_minimizers()

std::vector<HaplotypePartitioner::kmer_type> vg::take_unique_minimizers	(	const std::string &	sequence,
		const HaplotypePartitioner::minimizer_index_type &	minimizer_index
	)

◆ target_alignment() [1/2]

Alignment vg::target_alignment	(	const PathPositionHandleGraph *	graph,
		const path_handle_t &	path,
		size_t	pos1,
		size_t	pos2,
		const string &	feature,
		bool	is_reverse
	)

Make an Alignment corresponding to a subregion of a stored path. Positions are 0-based, and pos2 is excluded. Respects path circularity, so pos2 < pos1 is not a problem. If pos1 == pos2, returns an empty alignment.

◆ target_alignment() [2/2]

Alignment vg::target_alignment	(	const PathPositionHandleGraph *	graph,
		const path_handle_t &	path,
		size_t	pos1,
		size_t	pos2,
		const string &	feature,
		bool	is_reverse,
		Mapping &	cigar_mapping
	)

Same as above, but uses the given Mapping, translated directly form a CIGAR string, as a source of edits. The edits are inserted into the generated Alignment, cut as necessary to fit into the Alignment's Mappings.

◆ thread_to_graph_spanned()

void vg::thread_to_graph_spanned	(	thread_t &	t,
		Graph &	g,
		const HandleGraph &	source
	)

◆ threads_for_contig()

std::vector< gbwt::size_type > vg::threads_for_contig	(	const gbwt::GBWT &	gbwt_index,
		const std::string &	contig_name
	)

Return the list of thread ids / gbwt path ids for the given contig.

◆ threads_for_sample()

std::vector< gbwt::size_type > vg::threads_for_sample	(	const gbwt::GBWT &	gbwt_index,
		const std::string &	sample_name
	)

Return the list of thread ids / gbwt path ids for the given sample.

◆ to_alignment()

Alignment vg::to_alignment	(	const SnarlTraversal &	trav,
		const HandleGraph &	graph
	)

inline

Convert a snarl traversal into an alignment.

◆ to_edge()

edge_t vg::to_edge	(	const HandleGraph &	graph,
		const Visit &	v1,
		const Visit &	v2
	)

Make an edge_t from a pair of visits.

◆ to_left_side()

NodeSide vg::to_left_side ( const Visit & visit )

inline

Converts a Visit to a node or snarl into a NodeSide for its left side.

◆ to_length()

int vg::to_length ( const Mapping & m )

◆ to_length_after_pos()

size_t vg::to_length_after_pos	(	const Alignment &	aln,
		const Position &	pos
	)

◆ to_length_before_pos()

size_t vg::to_length_before_pos	(	const Alignment &	aln,
		const Position &	pos
	)

◆ to_mapping() [1/2]

Mapping vg::to_mapping	(	const Visit &	visit,
		const HandleGraph &	vg
	)

inline

Converts a Visit to a Mapping. Throws an exception if the Visit is of a Snarl instead of a Node. Uses a graph to get node length.

◆ to_mapping() [2/2]

Mapping vg::to_mapping	(	const Visit &	visit,
		std::function< size_t(id_t)>	node_length
	)

inline

Converts a Visit to a Mapping. Throws an exception if the Visit is of a Snarl instead of a Node. Uses a function to get node length.

◆ to_multipath_alignment()

void vg::to_multipath_alignment	(	const Alignment &	aln,
		multipath_alignment_t &	multipath_aln_out
	)

Converts a Alignment into a multipath_alignment_t with one subpath and stores it in an object

Args: aln alignment to convert multipath_aln empty multipath alignment to store converted alignment in (data may be be overwritten if not empty)

◆ to_node_traversal() [1/2]

NodeTraversal vg::to_node_traversal	(	const Visit &	visit,
		const VG &	graph
	)

inline

Converts a Visit to a NodeTraversal. Throws an exception if the Visit is of a Snarl instead of a Node

◆ to_node_traversal() [2/2]

NodeTraversal vg::to_node_traversal	(	const Visit &	visit,
		VG &	graph
	)

inline

◆ to_proto_edit()

void vg::to_proto_edit	(	const edit_t &	edit,
		Edit &	proto_edit
	)

◆ to_proto_mapping()

void vg::to_proto_mapping	(	const path_mapping_t &	mapping,
		Mapping &	proto_mapping
	)

◆ to_proto_multipath_alignment()

void vg::to_proto_multipath_alignment	(	const multipath_alignment_t &	multipath_aln,
		MultipathAlignment &	proto_multipath_aln_out
	)

Convert an STL-based multipath_alignment_t to a protobuf MultipathAlignment.

◆ to_proto_path()

void vg::to_proto_path	(	const path_t &	path,
		Path &	proto_path
	)

◆ to_rev_node_traversal() [1/2]

NodeTraversal vg::to_rev_node_traversal	(	const Visit &	visit,
		const VG &	graph
	)

inline

Converts a Visit to a NodeTraversal in the opposite orientation. Throws an exception if the Visit is of a Snarl instead of a Node

◆ to_rev_node_traversal() [2/2]

NodeTraversal vg::to_rev_node_traversal	(	const Visit &	visit,
		VG &	graph
	)

inline

◆ to_rev_visit()

Visit vg::to_rev_visit ( const NodeTraversal & node_traversal )

inline

Converts a NodeTraversal to a Visit in the opposite orientation.

◆ to_right_side()

NodeSide vg::to_right_side ( const Visit & visit )

inline

Converts a Visit to a node or snarl into a NodeSide for its right side.

◆ to_string() [1/3]

string vg::to_string	(	const HandleGraph &	graph,
		edge_t	edge
	)

inline

◆ to_string() [2/3]

string vg::to_string	(	const HandleGraph &	graph,
		handle_t	handle
	)

inline

◆ to_string() [3/3]

std::string vg::to_string ( handle_t handle )

◆ to_string_gbwtgraph() [1/2]

std::string vg::to_string_gbwtgraph ( gbwt::node_type node )

Returns a string representation of a GBWTGraph node.

◆ to_string_gbwtgraph() [2/2]

std::string vg::to_string_gbwtgraph ( handle_t handle )

Returns a string representation of a GBWTGraph handle.

◆ to_vcf_genotype()

string vg::to_vcf_genotype ( const Genotype & gt )

Get a VCF-style 1/2, 1|2|3, etc. string from a Genotype.

◆ to_visit() [1/5]

Visit vg::to_visit	(	const handlegraph::HandleGraph &	graph,
		const handle_t &	handle
	)

inline

Make a Visit from a handle in a HandleGraph.

◆ to_visit() [2/5]

Visit vg::to_visit	(	const Mapping &	mapping,
		bool	make_full_node_match = `false`
	)

inline

Converts a Mapping to a Visit. The mapping must represent a full node match. If make_full_node_match is true, the mapping will automatically be made a full node match during the conversion process.

◆ to_visit() [3/5]

Visit vg::to_visit ( const NodeTraversal & node_traversal )

inline

Converts a NodeTraversal to a Visit.

◆ to_visit() [4/5]

Visit vg::to_visit ( const Snarl & snarl )

inline

Make a Visit from a snarl to traverse.

◆ to_visit() [5/5]

Visit vg::to_visit	(	id_t	node_id,
		bool	is_reverse
	)

inline

Make a Visit from a node ID and an orientation.

◆ topologically_order_subpaths()

void vg::topologically_order_subpaths ( multipath_alignment_t & multipath_aln )

Put subpaths in topological order (assumed to be true for other algorithms)

◆ total()

double vg::total ( const Support & support )

Get the total read support in a Support.

◆ toUppercase()

string vg::toUppercase ( const string & s )

◆ toUppercaseInPlace()

void vg::toUppercaseInPlace ( string & s )

◆ trace_haplotypes_and_paths()

void vg::trace_haplotypes_and_paths	(	const PathHandleGraph &	source,
		const gbwt::GBWT &	haplotype_database,
		vg::id_t	start_node,
		int	extend_distance,
		Graph &	out_graph,
		map< string, int > &	out_thread_frequencies,
		bool	expand_graph
	)

◆ trace_path()

pair< tuple< int64_t, int64_t, int64_t >, vector< tuple< int64_t, int64_t, int64_t, int64_t > > > vg::trace_path	(	const multipath_alignment_t &	multipath_aln,
		const Path &	path,
		int64_t	subpath_idx,
		int64_t	mapping_idx,
		int64_t	edit_idx,
		int64_t	base_idx,
		bool	search_left,
		int64_t	search_limit
	)

Returns a pair of (mapping, edit, base) and possibly multiple (subpath, mapping, edit, base),of the furthest position that can be traced through the multipath alignment along the pathstarting the indicated position in the multipath alignment. The path can be traced rightward starting at the beginning, or leftward starting. Search is limited to not passing a given mapping on the path.

◆ transcript_file_nonempty()

bool vg::transcript_file_nonempty ( const string & transcripts )

◆ transfer_between_proto_annotation()

template<class ProtoAlignment1 , class ProtoAlignment2 >

void vg::transfer_between_proto_annotation	(	const ProtoAlignment1 &	from,
		ProtoAlignment2 &	to
	)

◆ transfer_boundary_info()

void vg::transfer_boundary_info	(	const Snarl &	from,
		Snarl &	to
	)

inline

Copies the boundary Visits from one Snarl into another.

◆ transfer_from_proto_annotation()

template<class ProtoAlignment >

void vg::transfer_from_proto_annotation	(	const ProtoAlignment &	from,
		multipath_alignment_t &	to
	)

◆ transfer_proto_metadata() [1/2]

void vg::transfer_proto_metadata	(	const Alignment &	from,
		MultipathAlignment &	to
	)

Transfer the annotations that are carried with the Protobuf formats but not the internal multipath_alignment_t (and which therefore get lost when using it as an intermediate format).

◆ transfer_proto_metadata() [2/2]

void vg::transfer_proto_metadata	(	const MultipathAlignment &	from,
		Alignment &	to
	)

◆ transfer_read_metadata() [1/6]

void vg::transfer_read_metadata	(	const Alignment &	from,
		Alignment &	to
	)

◆ transfer_read_metadata() [2/6]

void vg::transfer_read_metadata	(	const Alignment &	from,
		multipath_alignment_t &	to
	)

All functions of this form transfer:

sequence
base quality
mapping quality
read annotations (including multiple encodings of secondary)

◆ transfer_read_metadata() [3/6]

void vg::transfer_read_metadata	(	const multipath_alignment_t &	from,
		Alignment &	to
	)

◆ transfer_read_metadata() [4/6]

void vg::transfer_read_metadata	(	const multipath_alignment_t &	from,
		multipath_alignment_t &	to
	)

◆ transfer_read_metadata() [5/6]

void vg::transfer_read_metadata	(	const multipath_alignment_t &	from,
		MultipathAlignment &	to
	)

◆ transfer_read_metadata() [6/6]

void vg::transfer_read_metadata	(	const MultipathAlignment &	from,
		multipath_alignment_t &	to
	)

◆ transfer_to_proto_annotation()

template<class ProtoAlignment >

void vg::transfer_to_proto_annotation	(	const multipath_alignment_t &	from,
		ProtoAlignment &	to
	)

◆ transfer_uniform_metadata()

template<class Alignment1 , class Alignment2 >

void vg::transfer_uniform_metadata	(	const Alignment1 &	from,
		Alignment2 &	to
	)

◆ translate_mems()

vector< MaximalExactMatch > vg::translate_mems	(	const vector< MaximalExactMatch > &	mems,
		const unordered_map< id_t, pair< id_t, bool > > &	trans
	)

◆ translate_node_ids() [1/3]

void vg::translate_node_ids	(	Path &	path,
		const unordered_map< id_t, id_t > &	translator
	)

Switches the node ids in the path to the ones indicated by the translator.

◆ translate_node_ids() [2/3]

void vg::translate_node_ids	(	Path &	path,
		const unordered_map< id_t, id_t > &	translator,
		id_t	cut_node,
		size_t	bases_removed,
		bool	from_right
	)

Replaces the node IDs in the path with the ones indicated by the translator. Supports a single cut node in the source graph, where the given number of bases of the given node were removed from its left or right side when making the source graph from the destination graph.

◆ translate_node_ids() [3/3]

void vg::translate_node_ids	(	path_t &	path,
		const unordered_map< id_t, id_t > &	translator
	)

◆ translate_nodes()

void vg::translate_nodes	(	Alignment &	a,
		const unordered_map< id_t, pair< id_t, bool > > &	ids,
		const std::function< size_t(int64_t)> &	node_length
	)

◆ translate_oriented_node_ids() [1/4]

void vg::translate_oriented_node_ids	(	Path &	path,
		const function< pair< id_t, bool >(id_t)> &	translator
	)

Switches node ids and orientations in the path to the ones indicated by the translator.

◆ translate_oriented_node_ids() [2/4]

void vg::translate_oriented_node_ids	(	Path &	path,
		const unordered_map< id_t, pair< id_t, bool >> &	translator
	)

Switches the node ids and orientations in the path to the ones indicated by the translator.

◆ translate_oriented_node_ids() [3/4]

void vg::translate_oriented_node_ids	(	path_t &	path,
		const function< pair< id_t, bool >(id_t)> &	translator
	)

◆ translate_oriented_node_ids() [4/4]

void vg::translate_oriented_node_ids	(	path_t &	path,
		const unordered_map< id_t, pair< id_t, bool >> &	translator
	)

◆ transpose()

vector< vector< double > > vg::transpose ( const vector< vector< double >> & A )

A shitty set of linear algebra functions.

◆ traversal_to_string() [1/2]

string vg::traversal_to_string	(	const PathHandleGraph *	graph,
		const Traversal &	traversal,
		int64_t	max_steps
	)

◆ traversal_to_string() [2/2]

string vg::traversal_to_string	(	VG &	graph,
		const SnarlTraversal &	path
	)

Make a SnarlTraversal into the string it represents, including notes for nested child snarls.

◆ trim_alignment()

Alignment vg::trim_alignment	(	const Alignment &	aln,
		const Position &	pos1,
		const Position &	pos2
	)

◆ trim_hanging_ends()

Path vg::trim_hanging_ends ( const Path & p )

◆ trim_mismatches()

bool vg::trim_mismatches	(	GaplessExtension &	extension,
		const gbwtgraph::CachedGBWTGraph &	graph,
		const Aligner &	aligner
	)

◆ trim_path()

bool vg::trim_path	(	path_t *	path,
		bool	from_left,
		int64_t	mapping_idx,
		int64_t	edit_idx,
		int64_t	base_idx
	)

◆ trimmed_end()

tuple< pos_t, int64_t, int32_t > vg::trimmed_end	(	const Alignment &	aln,
		int64_t	len,
		bool	from_end,
		const HandleGraph &	graph,
		const GSSWAligner &	aligner
	)

◆ uses_Us()

bool vg::uses_Us ( const Alignment & alignment )

Returns true if the alignment sequence contains any U's and false if the alignment sequence contains and T's. In the case that both T's and U's are included, responds according to whichever comes first. If the sequence contains neither U's nor T's, returns false.

◆ validate_multipath_alignment()

bool vg::validate_multipath_alignment	(	const multipath_alignment_t &	multipath_aln,
		const HandleGraph &	handle_graph
	)

Debugging function to check that multipath alignment meets the formalism's basic invariants. Returns true if multipath alignment is valid, else false. Does not validate alignment score.

◆ value_cast() [1/4]

template<typename Container >

google::protobuf::Value vg::value_cast ( const Container & wrap )

inline

◆ value_cast() [2/4]

template<typename T >

T vg::value_cast ( const google::protobuf::Value & value )

inline

Cast a Protobuf generic Value to any type.

◆ value_cast() [3/4]

template<typename Container >

Container vg::value_cast ( const google::protobuf::Value & value )

inline

Cast a Protobuf generic Value to any type.

◆ value_cast() [4/4]

template<typename T >

google::protobuf::Value vg::value_cast ( const T & wrap )

inline

Cast any type to a generic Protobuf value.

◆ value_cast< bool >() [1/2]

template<>

google::protobuf::Value vg::value_cast< bool > ( const bool & wrap )

inline

◆ value_cast< bool >() [2/2]

template<>

bool vg::value_cast< bool > ( const google::protobuf::Value & value )

inline

◆ value_cast< double >() [1/2]

template<>

google::protobuf::Value vg::value_cast< double > ( const double & wrap )

inline

◆ value_cast< double >() [2/2]

template<>

double vg::value_cast< double > ( const google::protobuf::Value & value )

inline

◆ value_cast< int >()

template<>

google::protobuf::Value vg::value_cast< int > ( const int & wrap )

inline

◆ value_cast< size_t >()

template<>

google::protobuf::Value vg::value_cast< size_t > ( const size_t & wrap )

inline

◆ value_cast< string >() [1/2]

template<>

string vg::value_cast< string > ( const google::protobuf::Value & value )

inline

◆ value_cast< string >() [2/2]

template<>

google::protobuf::Value vg::value_cast< string > ( const string & wrap )

inline

◆ variant_recall()

void vg::variant_recall	(	VG *	graph,
		vcflib::VariantCallFile *	vars,
		FastaReference *	ref_genome,
		vector< FastaReference * >	insertions,
		string	gamfile
	)

run with : vg genotype -L -V v.vcf -I i.fa -R ref.fa

◆ vcf_contigs()

vector<string> vg::vcf_contigs ( const string & filename )

◆ verify_path()

template<class PathType >

bool vg::verify_path	(	const PathType &	path,
		MutableHandleGraph &	unfolded,
		const hash_map< vg::id_t, std::vector< vg::id_t >> &	reverse_mapping
	)

◆ view_multipath_alignment()

void vg::view_multipath_alignment	(	ostream &	out,
		const multipath_alignment_t &	multipath_aln,
		const HandleGraph &	handle_graph
	)

Send a formatted string representation of the multipath_alignment_t into the ostream.

◆ view_multipath_alignment_as_dot()

void vg::view_multipath_alignment_as_dot	(	ostream &	out,
		const multipath_alignment_t &	multipath_aln,
		bool	show_graph
	)

Converts a multipath_alignment_t to a GraphViz Dot representation, output to the given ostream.

◆ visit_contained_snarls()

void vg::visit_contained_snarls	(	const PathPositionHandleGraph *	graph,
		const vector< Region > &	regions,
		SnarlManager &	snarl_manager,
		bool	include_endpoints,
		function< void(const Snarl , step_handle_t, step_handle_t, int64_t, int64_t, bool, const Region )>	visit_fn
	)

Visit each snarl if it is fully contained in at least one region from the input set. Only the top-most snarl is visited. The parameters to visit_fn are: <the snarl, start_step, end_step, steps_reversed, the containing input region>

◆ vpmax()

template<typename T >

vector<T> vg::vpmax ( const std::vector< std::vector< T >> & vv )

◆ wang_hash_64()

size_t vg::wang_hash_64 ( size_t key )

inline

Thomas Wang's integer hash function. In many implementations, std::hash is identity function for integers, which leads to performance issues.

◆ weibull_cdf()

double vg::weibull_cdf	(	double	x,
		double	scale,
		double	shape,
		double	location = `0.0`
	)

inline

Return the CDF of a max exponential with the given parameters.

◆ weibull_log_likelihood()

double vg::weibull_log_likelihood	(	const vector< double > &	x,
		double	scale,
		double	shape,
		double	location
	)

Returns the log likelihood of some data generated by a Weibull distribution.

◆ weighted_jaccard_coefficient()

double vg::weighted_jaccard_coefficient	(	const PathHandleGraph *	graph,
		const multiset< handle_t > &	target,
		const multiset< handle_t > &	query
	)

◆ wellford_mean_var()

pair< double, double > vg::wellford_mean_var	(	size_t	count,
		double	mean,
		double	M2,
		bool	sample_variance
	)

◆ wellford_update()

void vg::wellford_update	(	size_t &	count,
		double &	mean,
		double &	M2,
		double	new_val
	)

◆ with_exception_handling()

void vg::with_exception_handling ( const std::function< void(void)> & body )

User code should call this to get all its exceptions handled.

◆ worst_alignment_score()

int32_t vg::worst_alignment_score ( const multipath_alignment_t & multipath_aln )

Returns the score of the lowest-scoring source-to-sink alignment in the multipath_alignment_t. Assumes that subpaths are topologically ordered and starts have been identified.

◆ wrap_text()

string vg::wrap_text	(	const string &	str,
		size_t	width
	)

◆ write_alignment_to_file()

void vg::write_alignment_to_file	(	const Alignment &	aln,
		const string &	filename
	)

◆ write_fasta_sequence()

void vg::write_fasta_sequence	(	const std::string &	name,
		const std::string &	sequence,
		ostream &	os,
		size_t	width
	)

◆ write_gcsa_kmers()

void vg::write_gcsa_kmers	(	const HandleGraph &	graph,
		int	kmer_size,
		ostream &	out,
		size_t &	size_limit,
		id_t	head_id,
		id_t	tail_id
	)

Write GCSA2 formatted binary KMers to the given ostream. size_limit is the maximum size of the kmer file in bytes. When the function returns, size_limit is the size of the kmer file in bytes.

◆ write_gcsa_kmers_to_tmpfile()

string vg::write_gcsa_kmers_to_tmpfile	(	const HandleGraph &	graph,
		int	kmer_size,
		size_t &	size_limit,
		id_t	head_id,
		id_t	tail_id,
		const string &	base_file_name = `"vg-kmers-tmp-"`
	)

Open a tempfile and write the kmers to it. The calling context should remove it with temp_file::remove(). In the case that the size limit is exceeded, throws a SizeLimitExceededException and deletes the temp file.

◆ xg_index_size()

size_t vg::xg_index_size ( const xg::XG & index )

Variable Documentation

◆ BAM_DNA_LOOKUP

const char* const vg::BAM_DNA_LOOKUP = "=ACMGRSVTWYHKDBN"

◆ fullTrace

bool vg::fullTrace = false

◆ ISSUE_URL

const char* vg::ISSUE_URL = "https://github.com/vgteam/vg/issues/new/choose"

◆ NO_INDEX

const alignment_index_t vg::NO_INDEX {std::numeric_limits<size_t>::max(), std::numeric_limits<size_t>::max(), std::numeric_limits<bool>::max()}

Represents an unset index.

◆ NO_READ_INDEX

const read_alignment_index_t vg::NO_READ_INDEX = {std::numeric_limits<size_t>::infinity(), std::numeric_limits<size_t>::infinity()}

Represents an unset index.

◆ stored_crash_context

thread_local std::string vg::stored_crash_context

◆ var

const char* vg::var = "VG_FULL_TRACEBACK"

Namespaces

Classes

Typedefs

Enumerations

Functions

Variables

Typedef Documentation

◆ benchtime

◆ Chain

◆ DeletableHandleGraph

◆ edge_t

◆ EdgeMapping

◆ exon_nodes_t

◆ GAMIndex

◆ GAMSorter

◆ Handle2Component

◆ handle_t

◆ HandleGraph

◆ HandleSet

◆ id_t

◆ IndexGroup

◆ IndexName

◆ MutableHandleGraph

◆ MutablePathDeletableHandleGraph

◆ MutablePathHandleGraph

◆ MutablePathMutableHandleGraph

◆ NamedNodeBackTranslation

◆ nid_t

◆ offset_t

◆ oriented_node_range_t

◆ pareto_point

◆ path_handle_t

◆ PathHandleGraph

◆ PathInterval

◆ PathMetadata

◆ PathPositionHandleGraph

◆ PathSense

◆ pos_t

◆ RankedHandleGraph

◆ real_t

◆ RecipeFunc

◆ RecipeName

◆ SerializableHandleGraph

◆ step_handle_t

◆ subrange_t

◆ thread_ids_t

◆ thread_t

◆ Traversal

◆ VectorizableHandleGraph

Enumeration Type Documentation

◆ alignment_emitter_flags_t

◆ MappingQualityMethod

◆ SnarlType

Function Documentation

◆ add_alt_allele()

◆ add_descendants_to_subgraph()

◆ add_edges_only()

◆ add_log()

◆ add_log10()

◆ add_nodes_and_edges() [1/2]

◆ add_nodes_and_edges() [2/2]

◆ add_path()

◆ add_path_to_graph()

◆ add_thread_edges_to_set()

◆ add_thread_nodes_to_set()

◆ addArbitraryTelomerePair()

◆ adjacent_mappings()

◆ advance_split()

◆ aligned_interval()

◆ alignment_end()

◆ alignment_ends()

◆ alignment_from_length()

◆ alignment_from_path()

◆ alignment_is_valid()

◆ alignment_middle()

◆ alignment_quality_per_node()

◆ alignment_refpos_to_path_offsets()

◆ alignment_set_distance_to_correct() [1/3]

◆ alignment_set_distance_to_correct() [2/3]

◆ alignment_set_distance_to_correct() [3/3]