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fq2fa.go
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fq2fa.go
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package fq2fa
import (
"bytes"
"github.com/MG-RAST/Shock/shock-server/node/file"
"github.com/MG-RAST/Shock/shock-server/node/file/format/fasta"
"github.com/MG-RAST/Shock/shock-server/node/file/format/fastq"
"github.com/MG-RAST/Shock/shock-server/node/file/format/seq"
"io"
)
type Reader struct {
f file.SectionReader
r seq.Reader
overflow []byte
}
func NewReader(f file.SectionReader) io.Reader {
return &Reader{
f: f,
r: fastq.NewReader(f),
overflow: nil,
}
}
func (r *Reader) Read(p []byte) (n int, err error) {
n = 0
buf := bytes.NewBuffer(nil)
if r.overflow != nil {
ln, _ := buf.Write(r.overflow)
n += ln
}
for {
seq, er := r.r.Read()
if er != nil {
if er == io.EOF {
copy(p[0:n], buf.Bytes()[0:n])
}
err = er
break
}
ln, _ := fasta.Format(seq, buf)
if n+ln > cap(p) {
copy(p[0:n], buf.Bytes()[0:n])
r.overflow = buf.Bytes()[n:]
break
} else {
n += ln
}
}
return
}
func (r *Reader) Close() error {
r.Close()
return nil
}