api

README

api

-- import "github.com/brentp/vcfanno/api"

Usage

const BOTH = "both_"

const INTERVAL = ""

const LEFT = "left_"

const RIGHT = "right_"

var Reducers = map[string]Reducer{
	"mean":   Reducer(mean),
	"max":    Reducer(max),
	"min":    Reducer(min),
	"concat": Reducer(concat),
	"count":  Reducer(count),
	"uniq":   Reducer(uniq),
	"first":  Reducer(first),
	"flag":   Reducer(vflag),
}

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.
}

Annotator holds the information to annotate a file.

func NewAnnotator

func NewAnnotator(sources []*Source, js string, ends bool, strict bool) *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) Annotate

func (a *Annotator) Annotate(streams ...irelate.RelatableChannel) irelate.RelatableChannel

Annotate annotates a file with the sources in the Annotator. It accepts RelatableChannels, and returns a RelatableChannel on which it will send annotated variants.

func (*Annotator) AnnotateEnds

func (a *Annotator) AnnotateEnds(r irelate.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

func (a *Annotator) AnnotateOne(r irelate.Relatable, strict bool, end ...string) error

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) JsOp

func (a *Annotator) JsOp(v *vcfgo.Variant, js *otto.Script, vals []interface{}) interface{}

JsOp uses Otto to run a javascript snippet on a list of values and return a single value. It makes the chrom, start, end, and values available to the js interpreter.

func (*Annotator) SetupStreams

func (a *Annotator) SetupStreams(queryFile string) ([]irelate.RelatableChannel, *vcfgo.Header)

SetupStreams takes the query file and sets everything up for annotation. If the input was a vcf, it returns the header with the new annotation fields added.

func (*Annotator) UpdateHeader

func (a *Annotator) UpdateHeader(h *vcfgo.Header)

UpdateHeader adds to the Infos in the vcf Header so that the annotations will be reported in the header.

type Reducer

type Reducer func([]interface{}) interface{}

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
	Js    *otto.Script
}

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) IsNumber

func (s *Source) IsNumber() bool

IsNumber indicates that we expect the Source to return a number given the op

Documentation

Index

• Constants
• Variables
• type Annotator
  • func NewAnnotator(sources []*Source, js string, ends bool, strict bool, natsort bool) *Annotator
  • func (a *Annotator) Annotate(streams ...irelate.RelatableChannel) irelate.RelatableChannel
  • func (a *Annotator) AnnotateEnds(r irelate.Relatable, ends string) error
  • func (a *Annotator) AnnotateOne(r irelate.Relatable, strict bool, end ...string) error
  • func (a *Annotator) SetupStreams(queryFile string) ([]irelate.RelatableChannel, *vcfgo.Reader)
  • func (a *Annotator) UpdateHeader(h *vcfgo.Header)
• type Reducer
• type Source
  • func (src *Source) AnnotateOne(v *irelate.Variant, vals []interface{}, prefix string)
  • func (s *Source) IsNumber() bool
  • func (s *Source) JsOp(v *vcfgo.Variant, js *otto.Script, vals []interface{}) interface{}
  • func (src *Source) UpdateHeader(h *vcfgo.Header, ends bool)

Constants

const BOTH = "both_"

const INTERVAL = ""

const LEFT = "left_"

const RIGHT = "right_"

Variables

var Reducers = map[string]Reducer{
	"mean":   Reducer(mean),
	"max":    Reducer(max),
	"min":    Reducer(min),
	"concat": Reducer(concat),
	"count":  Reducer(count),
	"uniq":   Reducer(uniq),
	"first":  Reducer(first),
	"flag":   Reducer(vflag),
}

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.
	Less    func(a, b irelate.Relatable) bool
}

Annotator holds the information to annotate a file.

func NewAnnotator

func NewAnnotator(sources []*Source, js string, ends bool, strict bool, natsort bool) *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) Annotate

func (a *Annotator) Annotate(streams ...irelate.RelatableChannel) irelate.RelatableChannel

Annotate annotates a file with the sources in the Annotator. It accepts RelatableChannels, and returns a RelatableChannel on which it will send annotated variants.

func (*Annotator) AnnotateEnds

func (a *Annotator) AnnotateEnds(r irelate.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

func (a *Annotator) AnnotateOne(r irelate.Relatable, strict bool, end ...string) error

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) SetupStreams

func (a *Annotator) SetupStreams(queryFile string) ([]irelate.RelatableChannel, *vcfgo.Reader)

SetupStreams takes the query file and sets everything up for annotation. If the input was a vcf, it returns the header with the new annotation fields added.

func (*Annotator) UpdateHeader

func (a *Annotator) UpdateHeader(h *vcfgo.Header)

UpdateHeader adds to the Infos in the vcf Header so that the annotations will be reported in the header.

type Reducer

type Reducer func([]interface{}) interface{}

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
	Js    *otto.Script
	Vm    *otto.Otto
}

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

func (src *Source) AnnotateOne(v *irelate.Variant, vals []interface{}, prefix string)

func (*Source) IsNumber

func (s *Source) IsNumber() bool

IsNumber indicates that we expect the Source to return a number given the op

func (*Source) JsOp

func (s *Source) JsOp(v *vcfgo.Variant, js *otto.Script, vals []interface{}) interface{}

JsOp uses Otto to run a javascript snippet on a list of values and return a single value. It makes the chrom, start, end, and values available to the js interpreter.

func (*Source) UpdateHeader

func (src *Source) UpdateHeader(h *vcfgo.Header, ends bool)