Documentation ¶
Index ¶
- Constants
- Variables
- type Annotator
- func (a *Annotator) AnnotateEnds(v interfaces.Relatable, ends string) error
- func (a *Annotator) AnnotateOne(r interfaces.Relatable, strict bool, end ...string) error
- func (a *Annotator) PostAnnotate(info interfaces.Info) error
- func (a *Annotator) Setup(query HeaderUpdater) ([]interfaces.Queryable, error)
- type HeaderTyped
- type HeaderUpdater
- type PostAnnotation
- type Reducer
- type Source
Constants ¶
const BOTH = "both_"
const INTERVAL = ""
const LEFT = "left_"
const RIGHT = "right_"
Variables ¶
Functions ¶
This section is empty.
Types ¶
type Annotator ¶
type Annotator struct { Sources []*Source Strict bool // require a variant to have same ref and share at least 1 alt Ends bool // annotate the ends of the variant in addition to the interval itself. PostAnnos []*PostAnnotation }
Annotator holds the information to annotate a file.
func NewAnnotator ¶
func NewAnnotator(sources []*Source, lua string, ends bool, strict bool, postannos []PostAnnotation) *Annotator
NewAnnotator returns an Annotator with the sources, seeded with some javascript. If ends is true, it will annotate the 1 base ends of the interval as well as the interval itself. If strict is true, when overlapping variants, they must share the ref allele and at least 1 alt allele.
func (*Annotator) AnnotateEnds ¶
func (a *Annotator) AnnotateEnds(v interfaces.Relatable, ends string) error
AnnotatedEnds makes a new 1-base interval for the left and one for the right end so that it can use the same machinery to annotate the ends and the entire interval. Output into the info field is prefixed with "left_" or "right_".
func (*Annotator) AnnotateOne ¶
AnnotateOne annotates a relatable with the Sources in an Annotator. In most cases, no need to specify end (it should always be a single arugment indicting LEFT, RIGHT, or INTERVAL, used from AnnotateEnds
func (*Annotator) PostAnnotate ¶ added in v0.0.9
func (a *Annotator) PostAnnotate(info interfaces.Info) error
func (*Annotator) Setup ¶ added in v0.0.9
func (a *Annotator) Setup(query HeaderUpdater) ([]interfaces.Queryable, error)
type HeaderTyped ¶ added in v0.0.9
type HeaderUpdater ¶ added in v0.0.8
type PostAnnotation ¶ added in v0.0.9
type Source ¶
type Source struct { File string Op string Name string // column number in bed file or ... Column int // info name in VCF. (can also be ID). Field string // 0-based index of the file order this source is from. Index int Vm *goluaez.State // contains filtered or unexported fields }
Source holds the information for a single annotation to be added to a query. Many sources can come from the same file, but each must have their own Source.
func (*Source) AnnotateOne ¶ added in v0.0.6
func (src *Source) AnnotateOne(v interfaces.IVariant, vals []interface{}, prefix string)
func (*Source) IsNumber ¶
IsNumber indicates that we expect the Source to return a number given the op
func (*Source) LuaOp ¶ added in v0.0.9
func (s *Source) LuaOp(v interfaces.IVariant, code string, vals []interface{}) string
LuaOp uses go-lua to run a lua snippet on a list of values and return a single value. It makes the chrom, start, end, and values available to the lua interpreter.
func (*Source) UpdateHeader ¶ added in v0.0.6
func (src *Source) UpdateHeader(r HeaderUpdater, ends bool, htype string)
func (src *Source) UpdateHeader(h HeaderUpdater, ends bool) {