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https://github.com/brentp/vcfgo
a golang library to read, write and manipulate files in the variant call format.
https://github.com/brentp/vcfgo
Last synced: 2 days ago
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a golang library to read, write and manipulate files in the variant call format.
- Host: GitHub
- URL: https://github.com/brentp/vcfgo
- Owner: brentp
- License: mit
- Created: 2015-04-15T15:25:28.000Z (over 9 years ago)
- Default Branch: master
- Last Pushed: 2024-09-30T17:16:03.000Z (3 months ago)
- Last Synced: 2024-10-13T02:21:14.919Z (3 months ago)
- Language: Go
- Size: 545 KB
- Stars: 67
- Watchers: 8
- Forks: 19
- Open Issues: 7
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
- awesome-bio-go - vcfgo
README
[](https://godoc.org/github.com/brentp/vcfgo)
[](https://github.com/brentp/vcfgo/actions/workflows/tests.yml)
[](https://coveralls.io/r/brentp/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
```go
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
```go
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
```go
func NewHeader() *Header
```
NewHeader returns a Header with the requisite allocations.
#### type Info
```go
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
```go
func (i *Info) String() string
```
String returns a string representation.
#### type InfoMap
```go
type InfoMap map[string]interface{}
```
InfoMap holds the parsed Info field which can contain floats, ints and lists
thereof.
#### func (InfoMap) String
```go
func (m InfoMap) String() string
```
String returns a string that matches the original info field.
#### type Reader
```go
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
```go
func NewReader(r io.Reader, lazySamples bool) (*Reader, error)
```
NewReader returns a Reader.
#### func (*Reader) Clear
```go
func (vr *Reader) Clear()
```
Clear empties the cache of errors.
#### func (*Reader) Error
```go
func (vr *Reader) Error() error
```
Error() aggregates the multiple errors that can occur into a single object.
#### func (*Reader) Read
```go
func (vr *Reader) Read() *Variant
```
Read returns a pointer to a Variant. Upon reading the caller is assumed to check
Reader.Err()
#### type SampleFormat
```go
type SampleFormat Info
```
SampleFormat holds the type info for Format fields.
#### func (*SampleFormat) String
```go
func (i *SampleFormat) String() string
```
String returns a string representation.
#### type SampleGenotype
```go
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
```go
func NewSampleGenotype() *SampleGenotype
```
NewSampleGenotype allocates the internals and returns a SampleGenotype
#### func (*SampleGenotype) String
```go
func (sg *SampleGenotype) String(fields []string) string
```
String returns the string representation of the sample field.
#### type VCFError
```go
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
```go
func NewVCFError() *VCFError
```
NewVCFError allocates the needed ingredients.
#### func (*VCFError) Add
```go
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
```go
func (e *VCFError) Clear()
```
Clear empties the Messages
#### func (*VCFError) Error
```go
func (e *VCFError) Error() string
```
Error returns a string with all errors delimited by newlines.
#### func (*VCFError) IsEmpty
```go
func (e *VCFError) IsEmpty() bool
```
IsEmpty returns true if there no errors stored.
#### type Variant
```go
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
```go
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
```go
func (v *Variant) String() string
```
String gives a string representation of a variant
#### type Writer
```go
type Writer struct {
io.Writer
Header *Header
}
```
Writer allows writing VCF files.
#### func NewWriter
```go
func NewWriter(w io.Writer, h *Header) (*Writer, error)
```
NewWriter returns a writer after writing the header.
#### func (*Writer) WriteVariant
```go
func (w *Writer) WriteVariant(v *Variant)
```
WriteVariant writes a single variant