vcfgo

package module
v0.0.0-...-56aaf2e Latest Latest
Warning

This package is not in the latest version of its module.

 Go to latest Published: Apr 11, 2022 License: MIT Imports: 16 Imported by: 2

README

GoDoc Build Status Coverage Status

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

Documentation

Overview

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)
if err != nil {
	panic(err)
}
for {
	variant := rdr.Read()
	if variant == nil {
		break
	}
	fmt.Printf("%s\t%d\t%s\t%s\n", variant.Chromosome, variant.Pos, variant.Ref, variant.Alt)
	fmt.Printf("%s", variant.Info["DP"].(int) > 10)
	sample := variant.Samples[0]
	// we can get the PL field as a list (-1 is default in case of missing value)
	fmt.Println("%s", variant.GetGenotypeField(sample, "PL", -1))
	_ = sample.DP
}
fmt.Fprintln(os.Stderr, rdr.Error())
Example 
package main

import (
	"fmt"
	"os"

	"github.com/brentp/vcfgo"
)

func main() {
	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%s\n", variant.Chromosome, variant.Pos, variant.Ref(), variant.Alt())
		dp, _ := variant.Info().Get("DP")
		fmt.Printf("%v", dp.(int) > 10)
		

Output:

Index

Examples

Constants

View Source 
const MISSING_VAL = 256

used for the quality score which is 0 to 255, but allows "."

Variables

This section is empty.

Functions

func ItoS 

func ItoS(k string, v interface{}) string

Types 

type Header struct {
	sync.RWMutex

	SampleNames   []string
	Infos         map[string]*Info
	SampleFormats map[string]*SampleFormat
	Filters       map[string]string
	Extras        []string
	FileFormat    string
	// Contigs is a list of maps of length, URL, etc.
	Contigs []map[string]string
	// ##SAMPLE
	Samples   map[string]string
	Pedigrees []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.

func (*Header) ParseSamples 

func (h *Header) ParseSamples(v *Variant) error

Force parsing of the sample fields.

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 InfoByte 

type InfoByte struct {
	Info []byte
	// contains filtered or unexported fields
}

func NewInfoByte 

func NewInfoByte(info []byte, h *Header) *InfoByte

func (*InfoByte) Add 

func (i *InfoByte) Add(key string, value interface{})

func (InfoByte) Bytes 

func (i InfoByte) Bytes() []byte

func (InfoByte) Contains 

func (i InfoByte) Contains(key string) bool

func (*InfoByte) Delete 

func (i *InfoByte) Delete(key string)

func (InfoByte) Get 

func (i InfoByte) Get(key string) (interface{}, error)

Get a value from the bytes typed according to the header.

func (InfoByte) Keys 

func (i InfoByte) Keys() []string

func (InfoByte) SGet 

func (i InfoByte) SGet(key string) []byte

func (*InfoByte) Set 

func (i *InfoByte) Set(key string, value interface{}) error

func (InfoByte) String 

func (i InfoByte) String() string

func (*InfoByte) UpdateHeader 

func (i *InfoByte) UpdateHeader(key string, value interface{})

type Reader 

type Reader struct {
	Header *Header

	LineNumber int64
	// contains filtered or unexported fields
}

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. If lazySamples is true, then the user will have to call Reader.ParseSamples() in order to access simple info.

func NewWithHeader 

func NewWithHeader(r io.Reader, h *Header, lazySamples bool) (*Reader, error)

func (*Reader) AddFormatToHeader 

func (vr *Reader) AddFormatToHeader(id string, num string, stype string, desc string)

AddFormatToHeader adds a FORMAT field to the header.

func (*Reader) AddInfoToHeader 

func (vr *Reader) AddInfoToHeader(id string, num string, stype string, desc string)

AddInfoToHeader adds a INFO field to the header.

func (*Reader) Clear 

func (vr *Reader) Clear()

Clear empties the cache of errors.

func (*Reader) Close 

func (vr *Reader) Close() error

func (*Reader) Error 

func (vr *Reader) Error() error

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

func (*Reader) GetHeaderType 

func (vr *Reader) GetHeaderType(field string) string

func (*Reader) Parse 

func (vr *Reader) Parse(fields [][]byte) *Variant

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     []float64
	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) AltDepths 

func (s *SampleGenotype) AltDepths() ([]int, error)

AltDepths returns the depths of the alternates for this sample

func (*SampleGenotype) RefDepth 

func (s *SampleGenotype) RefDepth() (int, error)

RefDepth returns the depths of the alternates for this sample

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
	Reference  string
	Alternate  []string
	Quality    float32
	Filter     string
	Info_      interfaces.Info
	Format     []string
	Samples    []*SampleGenotype

	Header     *Header
	LineNumber int64
	// contains filtered or unexported fields
}

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

func SplitAlts 

func SplitAlts(v *Variant) []*Variant

func (*Variant) Alt 

func (v *Variant) Alt() []string

func (*Variant) CIEnd 

func (v *Variant) CIEnd() (uint32, uint32, bool)

CIEnd reports the Left and Right end of an SV using the CIEND tag. It is in bed format so the end is +1'ed. E.g. If there is no CIEND, the return value is v.End() - 1, v.End()

func (*Variant) CIPos 

func (v *Variant) CIPos() (uint32, uint32, bool)

CIPos reports the Left and Right end of an SV using the CIPOS tag. It is in bed format so the end is +1'ed. E.g. If there is not CIPOS, the return value is v.Start(), v.Start() + 1

func (*Variant) Chrom 

func (v *Variant) Chrom() string

Chrom returns the chromosome name.

func (*Variant) End 

func (v *Variant) End() uint32

End returns the 0-based start + the length of the reference allele.

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) Id 

func (v *Variant) Id() string

func (*Variant) Info 

func (v *Variant) Info() interfaces.Info

func (*Variant) Ref 

func (v *Variant) Ref() string

func (*Variant) Start 

func (v *Variant) Start() uint32

Start returns the 0-based start

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

Source Files

View all Source files

Directories

Path Synopsis

Jump to

Keyboard shortcuts

? : This menu
/ : Search site
f or F : Jump to
y or Y : Canonical URL
go.dev uses cookies from Google to deliver and enhance the quality of its services and to analyze traffic. Learn more.