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package parsers
import (
"io"
"github.com/brentp/irelate/interfaces"
"github.com/brentp/vcfgo"
)
type Variant struct {
interfaces.IVariant
source uint32
related []interfaces.Relatable
}
func (v *Variant) String() string {
return v.IVariant.String()
}
func NewVariant(v interfaces.IVariant, source uint32, related []interfaces.Relatable) *Variant {
return &Variant{v, source, related}
}
func (v *Variant) AddRelated(r interfaces.Relatable) {
if len(v.related) == 0 {
v.related = make([]interfaces.Relatable, 0, 2)
}
v.related = append(v.related, r)
}
func (v *Variant) Related() []interfaces.Relatable {
return v.related
}
func (v *Variant) SetSource(src uint32) { v.source = src }
func (v *Variant) Source() uint32 { return v.source }
func Vopen(rdr io.Reader, hdr *vcfgo.Header) (*vcfgo.Reader, error) {
if hdr == nil {
return vcfgo.NewReader(rdr, true)
}
return vcfgo.NewWithHeader(rdr, hdr, true)
}
func StreamVCF(vcf *vcfgo.Reader) interfaces.RelatableChannel {
ch := make(interfaces.RelatableChannel, 256)
go func() {
j := 0
for {
v := vcf.Read()
if v == nil {
break
}
ch <- &Variant{v, 0, nil}
j++
if j < 1000 {
vcf.Clear()
j = 0
}
}
close(ch)
}()
return ch
}
type vWrapper struct {
*vcfgo.Reader
}
func (v vWrapper) Next() (interfaces.Relatable, error) {
r := v.Read()
if r == nil {
return nil, io.EOF
}
return &Variant{r, 0, nil}, nil
}
func (v vWrapper) AddInfoToHeader(id, itype, number, description string) {
v.Reader.AddInfoToHeader(id, itype, number, description)
}
func VCFIterator(buf io.Reader) (interfaces.RelatableIterator, *vcfgo.Reader, error) {
v, err := Vopen(buf, nil)
if err != nil {
return nil, v, err
}
return vWrapper{v}, v, nil
}
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