graph

Documentation

Overview

Package graph is used to process graphs. It converts, writes, aligns reads and processes GROOT graphs.

Index

• func LoadGFA(fileName string) (*gfa.GFA, error)
• type GrootGraph
  • func CreateGrootGraph(gfaInstance *gfa.GFA, id int) (*GrootGraph, error)
  • func (GrootGraph *GrootGraph) AlignRead(read *seqio.FASTQread, mapping *lshe.Key, references []*sam.Reference) ([]*sam.Record, error)
  • func (GrootGraph *GrootGraph) GetEMpaths() ([]string, []float64)
  • func (GrootGraph *GrootGraph) GetNode(nodeID uint64) (*GrootGraphNode, error)
  • func (GrootGraph *GrootGraph) GetPaths() error
  • func (GrootGraph *GrootGraph) GetRefIDs() ([]string, error)
  • func (GrootGraph *GrootGraph) GetSketchStats() (int, int, int, error)
  • func (GrootGraph *GrootGraph) Graph2Seqs() (map[uint32][]byte, error)
  • func (GrootGraph *GrootGraph) IncrementKmerCount(increment uint64)
  • func (GrootGraph *GrootGraph) IncrementSubPath(ContainedNodes map[uint64]float64, numKmers float64) error
  • func (GrootGraph *GrootGraph) ProcessEMpaths(cutoff float64, totalKmers int) error
  • func (GrootGraph *GrootGraph) Prune(minKmerCoverage float64) bool
  • func (GrootGraph *GrootGraph) RemoveDeadPaths() error
  • func (GrootGraph *GrootGraph) RunEM(minIterations, numIterations int) error
  • func (GrootGraph *GrootGraph) SaveGraphAsGFA(fileName string, totalKmers int) (int, error)
  • func (GrootGraph *GrootGraph) WindowGraph(windowSize, kmerSize, sketchSize int) (map[string]lshe.Keys, error)
• type GrootGraphNode
  • func (GrootGraphNode *GrootGraphNode) IncrementKmerFreq(increment float64) error
• type Nodes
  • func (Nodes Nodes) Len() int
  • func (Nodes Nodes) Less(i, j int) bool
  • func (Nodes Nodes) Swap(i, j int)
• type Store
  • func (graphStore Store) GetSAMrefs() (map[int][]*sam.Reference, error)

Functions

func LoadGFA

func LoadGFA(fileName string) (*gfa.GFA, error)

LoadGFA reads a GFA file into a GFA struct

Types

type GrootGraph

type GrootGraph struct {
	GrootVersion string
	GraphID      uint32
	SortedNodes  []*GrootGraphNode // essentially, this is the graph - a topologically sorted array of nodes
	Paths        map[uint32][]byte // lookup to relate PathIDs in each node to a path name
	Lengths      map[uint32]int    // lengths of sequences held in graph (lookup key corresponds to key in Paths)
	NodeLookup   map[uint64]int    // this map returns a the position of a node in the SortedNodes array, using the node segmentID as the locator
	Masked       bool              // a flag to prevent the graph being used by GROOT
	KmerTotal    uint64            // the total number of k-mers projected onto the graph
	EMiterations int               // the number of EM iterations ran
	// contains filtered or unexported fields
}

GrootGraph is the variation graph implementation used by GROOT

func CreateGrootGraph

func CreateGrootGraph(gfaInstance *gfa.GFA, id int) (*GrootGraph, error)

CreateGrootGraph is a GrootGraph constructor that takes a GFA instance and stores the info as a graph and then runs a topological sort

func (*GrootGraph) AlignRead

func (GrootGraph *GrootGraph) AlignRead(read *seqio.FASTQread, mapping *lshe.Key, references []*sam.Reference) ([]*sam.Record, error)

AlignRead is a method to run a read to graph hierarchical alignment

func (*GrootGraph) GetEMpaths

func (GrootGraph *GrootGraph) GetEMpaths() ([]string, []float64)

GetEMpaths is a method to print the paths and abundance values

func (*GrootGraph) GetNode

func (GrootGraph *GrootGraph) GetNode(nodeID uint64) (*GrootGraphNode, error)

GetNode takes a nodeID and returns a pointer to the corresponding node struct in the graph Note: this is method does not allow concurrent map access

func (*GrootGraph) GetPaths

func (GrootGraph *GrootGraph) GetPaths() error

GetPaths is a method to get the paths from a graph

func (*GrootGraph) GetRefIDs

func (GrootGraph *GrootGraph) GetRefIDs() ([]string, error)

GetRefIDs is a method to return all the reference IDs that are encoded as sequences in the graph

func (*GrootGraph) GetSketchStats

func (GrootGraph *GrootGraph) GetSketchStats() (int, int, int, error)

GetSketchStats returns the number of windows processed from the graph, the number of distinct sketches, the max span for merged sketches and any error

func (*GrootGraph) Graph2Seqs

func (GrootGraph *GrootGraph) Graph2Seqs() (map[uint32][]byte, error)

Graph2Seqs is a method to convert a variation graph to linear reference sequences

func (*GrootGraph) IncrementKmerCount

func (GrootGraph *GrootGraph) IncrementKmerCount(increment uint64)

IncrementKmerCount is a method to increment the counter for the number of kmers projected onto the graph

func (*GrootGraph) IncrementSubPath

func (GrootGraph *GrootGraph) IncrementSubPath(ContainedNodes map[uint64]float64, numKmers float64) error

IncrementSubPath is a method to adjust the weight of segments that are contained within a given sketch

• given a ContainedNodes through a graph, the offset in the first segment, and the number of k-mers in this ContainedNodes
• increment the weight of each segment contained in that ContainedNodes by their share of the k-mer coverage for the sketch

func (*GrootGraph) ProcessEMpaths

func (GrootGraph *GrootGraph) ProcessEMpaths(cutoff float64, totalKmers int) error

ProcessEMpaths is a method to process the paths after EM has been run

func (*GrootGraph) Prune

func (GrootGraph *GrootGraph) Prune(minKmerCoverage float64) bool

Prune is a method to remove paths and segments from the graph if they have insufficient coverage returns false if pruning results in no paths through the graph remaining

func (*GrootGraph) RemoveDeadPaths

func (GrootGraph *GrootGraph) RemoveDeadPaths() error

RemoveDeadPaths is a method to remove pathIDs from nodes if the path is no longer present in the graph

func (*GrootGraph) RunEM

func (GrootGraph *GrootGraph) RunEM(minIterations, numIterations int) error

RunEM is a method to run EM on an approximately weighted variation graph

func (*GrootGraph) SaveGraphAsGFA

func (GrootGraph *GrootGraph) SaveGraphAsGFA(fileName string, totalKmers int) (int, error)

SaveGraphAsGFA is a method to convert and save a GrootGraph in GFA format

func (*GrootGraph) WindowGraph

func (GrootGraph *GrootGraph) WindowGraph(windowSize, kmerSize, sketchSize int) (map[string]lshe.Keys, error)

WindowGraph is a method to slide a window over each path through the graph, sketching the paths and getting window information

type GrootGraphNode

type GrootGraphNode struct {
	SegmentID     uint64
	SegmentLength float64
	Sequence      []byte
	OutEdges      Nodes
	PathIDs       []uint32    // PathIDs are the lookup IDs to the linear reference sequences that use this segment (value corresponds to key in GrootGraph.Paths)
	Position      map[int]int // the start position of this segment in each reference sequence, using 1-based indexing (lookup key corresponds to PathID)
	KmerFreq      float64
	Marked        bool // TODO: tmp idea to mark nodes during pruning, rather than deleting
}

GrootGraphNode is a GFA segment (plus the extra info from path, links etc.) Note: GrootGraphNodes are not set up for concurrent access

func (*GrootGraphNode) IncrementKmerFreq

func (GrootGraphNode *GrootGraphNode) IncrementKmerFreq(increment float64) error

IncrementKmerFreq is a method to increment a node's k-mer count

type Nodes

type Nodes []uint64

Nodes is a slice of GrootGraphNodes

func (Nodes) Len

func (Nodes Nodes) Len() int

methods for Nodes to satisfy the sort interface

func (Nodes) Less

func (Nodes Nodes) Less(i, j int) bool

func (Nodes) Swap

func (Nodes Nodes) Swap(i, j int)

type Store

type Store map[uint32]*GrootGraph

Store stores the GROOT graphs, using the graphID as the lookup key

func (Store) GetSAMrefs

func (graphStore Store) GetSAMrefs() (map[int][]*sam.Reference, error)

GetSAMrefs is a method to convert all paths held in graphStore to sam.References