README
¶
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)
Index ¶
- Constants
- func ItoS(k string, v interface{}) string
- func ParseHeaderContig(contig string) (map[string]string, error)
- func ParseHeaderExtraKV(kv string) ([]string, error)
- func ParseHeaderFileVersion(format string) (string, error)
- func ParseHeaderFilter(info string) ([]string, error)
- func ParseHeaderSample(line string) (string, error)
- func ParseOne(key, val, itype string) (interface{}, error)
- func ParseSampleLine(line string) ([]string, error)
- type Header
- type Info
- type InfoByte
- func (i *InfoByte) Add(key string, value interface{})
- func (i InfoByte) Bytes() []byte
- func (i InfoByte) Contains(key string) bool
- func (i *InfoByte) Delete(key string)
- func (i InfoByte) Get(key string) (interface{}, error)
- func (i InfoByte) Keys() []string
- func (i InfoByte) SGet(key string) []byte
- func (i *InfoByte) Set(key string, value interface{}) error
- func (i InfoByte) String() string
- func (i *InfoByte) UpdateHeader(key string, value interface{})
- type Reader
- func (vr *Reader) AddFormatToHeader(id string, num string, stype string, desc string)
- func (vr *Reader) AddInfoToHeader(id string, num string, stype string, desc string)
- func (vr *Reader) Clear()
- func (vr *Reader) Close() error
- func (vr *Reader) Error() error
- func (vr *Reader) GetHeaderType(field string) string
- func (vr *Reader) Parse(fields [][]byte) *Variant
- func (vr *Reader) Read() *Variant
- type SampleFormat
- type SampleGenotype
- type VCFError
- type Variant
- func (v *Variant) Alt() []string
- func (v *Variant) CIEnd() (uint32, uint32, bool)
- func (v *Variant) CIPos() (uint32, uint32, bool)
- func (v *Variant) Chrom() string
- func (v *Variant) End() uint32
- func (v *Variant) GetGenotypeField(g *SampleGenotype, field string, missing interface{}) (interface{}, error)
- func (v *Variant) Id() string
- func (v *Variant) Info() interfaces.Info
- func (v *Variant) Ref() string
- func (v *Variant) Start() uint32
- func (v *Variant) String() string
- type Writer
Examples ¶
Constants ¶
const MISSING_VAL = 256
used for the quality score which is 0 to 255, but allows "."
Variables ¶
This section is empty.
Functions ¶
func ParseHeaderExtraKV ¶
func ParseHeaderFileVersion ¶
func ParseHeaderFilter ¶
func ParseHeaderSample ¶
return just the sample id.
func ParseSampleLine ¶
Types ¶
type Header ¶
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) ParseSample ¶
func (h *Header) ParseSample(format []string, s string) (*SampleGenotype, []error)
func (*Header) ParseSamples ¶
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 ParseHeaderInfo ¶
type InfoByte ¶
type InfoByte struct {
Info []byte
// contains filtered or unexported fields
}
func NewInfoByte ¶
func (*InfoByte) UpdateHeader ¶
type Reader ¶
Reader holds information about the current line number (for errors) and The VCF header that indicates the structure of records.
func NewReader ¶
NewReader returns a Reader. If lazySamples is true, then the user will have to call Reader.ParseSamples() in order to access simple info.
func (*Reader) AddFormatToHeader ¶
AddFormatToHeader adds a FORMAT field to the header.
func (*Reader) AddInfoToHeader ¶
AddInfoToHeader adds a INFO field to the header.
func (*Reader) GetHeaderType ¶
type SampleFormat ¶
type SampleFormat Info
SampleFormat holds the type info for Format fields.
func ParseHeaderFormat ¶
func ParseHeaderFormat(info string) (*SampleFormat, error)
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 ¶
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 (*VCFError) Add ¶
Add adds an error and the line number within the vcf where the error took place.
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 NewVariant ¶
func (*Variant) CIEnd ¶
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 ¶
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) 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) Info ¶
func (v *Variant) Info() interfaces.Info
Source Files
Directories