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

-- 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:

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())

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 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() *Header

NewHeader returns a Header with the requisite allocations.

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 (i *Info) String() string

String returns a string representation.

type InfoMap map[string]interface{}

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

func (m InfoMap) String() string

String returns a string that matches the original info field.

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

NewReader returns a Reader.

func (vr *Reader) Clear()

Clear empties the cache of errors.

func (vr *Reader) Error() error

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

func (vr *Reader) Read() *Variant

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

type SampleFormat Info

SampleFormat holds the type info for Format fields.

func (i *SampleFormat) String() string

String returns a string representation.

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() *SampleGenotype

NewSampleGenotype allocates the internals and returns a SampleGenotype

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

String returns the string representation of the sample field.

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() *VCFError

NewVCFError allocates the needed ingredients.

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 (e *VCFError) Clear()

Clear empties the Messages

func (e *VCFError) Error() string

Error returns a string with all errors delimited by newlines.

func (e *VCFError) IsEmpty() bool

IsEmpty returns true if there no errors stored.

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 (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 (v *Variant) String() string

String gives a string representation of a variant

type Writer struct {	io.Writer Header *Header }

Writer allows writing VCF files.

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

NewWriter returns a writer after writing the header.

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

WriteVariant writes a single variant