vcfgo

vcfgo is a golang library to read, write and manipulate files in the variant call format.

vcfgo

-- import "github.com/brentp/vcfgo"

Package vcfgo implements a Reader and Writer for variant call format. It eases reading, filtering modifying VCF's even if they are not to spec. Example:

Usage

f, _ := os.Open("examples/test.auto_dom.no_parents.vcf")
rdr, err := vcfgo.NewReader(f, false)
if err != nil {
    panic(err)
}
for {
    variant := rdr.Read()
    if variant == nil {
        break
    }
    fmt.Printf("%s\t%d\t%s\t%v\n", variant.Chromosome, variant.Pos, variant.Ref(), variant.Alt())
    dp, err := variant.Info().Get("DP")
    fmt.Printf("depth: %v\n", dp.(int))
    sample := variant.Samples[0]
    // we can get the PL field as a list (-1 is default in case of missing value)
    PL, err := variant.GetGenotypeField(sample, "PL", -1)
    if err != nil {
        panic(err)
    }
    fmt.Printf("%v\n", PL)
    _ = sample.DP
}
fmt.Fprintln(os.Stderr, rdr.Error())

Status

vcfgo is well-tested, but still in development. It tries to tolerate, but report errors; after every rdr.Read() call, the caller can check rdr.Error() and get feedback on the errors without stopping execution unless it is explicitly requested to do so.

Info and sample fields are pre-parsed and stored as map[string]interface{} so callers will have to cast to the appropriate type upon retrieval.

type Header

type Header struct {
	SampleNames   []string
	Infos         map[string]*Info
	SampleFormats map[string]*SampleFormat
	Filters       map[string]string
	Extras        map[string]string
	FileFormat    string
	// contid id maps to a map of length, URL, etc.
	Contigs map[string]map[string]string
}

Header holds all the type and format information for the variants.

func NewHeader

func NewHeader() *Header

NewHeader returns a Header with the requisite allocations.

type Info

type Info struct {
	Id          string
	Description string
	Number      string // A G R . ''
	Type        string // STRING INTEGER FLOAT FLAG CHARACTER UNKONWN
}

Info holds the Info and Format fields

func (*Info) String

func (i *Info) String() string

String returns a string representation.

type InfoMap

type InfoMap map[string]interface{}

InfoMap holds the parsed Info field which can contain floats, ints and lists thereof.

func (InfoMap) String

func (m InfoMap) String() string

String returns a string that matches the original info field.

type Reader

type Reader struct {
	Header *Header

	LineNumber int64
}

Reader holds information about the current line number (for errors) and The VCF header that indicates the structure of records.

func NewReader

func NewReader(r io.Reader, lazySamples bool) (*Reader, error)

NewReader returns a Reader.

func (*Reader) Clear

func (vr *Reader) Clear()

Clear empties the cache of errors.

func (*Reader) Error

func (vr *Reader) Error() error

Error() aggregates the multiple errors that can occur into a single object.

func (*Reader) Read

func (vr *Reader) Read() *Variant

Read returns a pointer to a Variant. Upon reading the caller is assumed to check Reader.Err()

type SampleFormat

type SampleFormat Info

SampleFormat holds the type info for Format fields.

func (*SampleFormat) String

func (i *SampleFormat) String() string

String returns a string representation.

type SampleGenotype

type SampleGenotype struct {
	Phased bool
	GT     []int
	DP     int
	GL     []float32
	GQ     int
	MQ     int
	Fields map[string]string
}

SampleGenotype holds the information about a sample. Several fields are pre-parsed, but all fields are kept in Fields as well.

func NewSampleGenotype

func NewSampleGenotype() *SampleGenotype

NewSampleGenotype allocates the internals and returns a SampleGenotype

func (*SampleGenotype) String

func (sg *SampleGenotype) String(fields []string) string

String returns the string representation of the sample field.

type VCFError

type VCFError struct {
	Msgs  []string
	Lines []int64
}

VCFError satisfies the error interface and allows multiple errors. This is useful because, for example, on a single line, every sample may have a field that doesn't match the description in the header. We want to keep parsing but also let the caller know about the error.

func NewVCFError

func NewVCFError() *VCFError

NewVCFError allocates the needed ingredients.

func (*VCFError) Add

func (e *VCFError) Add(err error, line int64)

Add adds an error and the line number within the vcf where the error took place.

func (*VCFError) Clear

func (e *VCFError) Clear()

Clear empties the Messages

func (*VCFError) Error

func (e *VCFError) Error() string

Error returns a string with all errors delimited by newlines.

func (*VCFError) IsEmpty

func (e *VCFError) IsEmpty() bool

IsEmpty returns true if there no errors stored.

type Variant

type Variant struct {
	Chromosome      string
	Pos        		uint64
	Id         		string
	Ref        		string
	Alt        		[]string
	Quality    		float32
	Filter     		string
	Info       		InfoMap
	Format     		[]string
	Samples    		[]*SampleGenotype
	Header     		*Header
	LineNumber 		int64
}

Variant holds the information about a single site. It is analagous to a row in a VCF file.

func (*Variant) GetGenotypeField

func (v *Variant) GetGenotypeField(g *SampleGenotype, field string, missing interface{}) (interface{}, error)

GetGenotypeField uses the information from the header to parse the correct time from a genotype field. It returns an interface that can be asserted to the expected type.

func (*Variant) String

func (v *Variant) String() string

String gives a string representation of a variant

type Writer

type Writer struct {
	io.Writer
	Header *Header
}

Writer allows writing VCF files.

func NewWriter

func NewWriter(w io.Writer, h *Header) (*Writer, error)

NewWriter returns a writer after writing the header.

func (*Writer) WriteVariant

func (w *Writer) WriteVariant(v *Variant)

WriteVariant writes a single variant