// Read a single sequence and return it or an error.
func (self *Reader) Read() (sequence *seq.Seq, err error) {
if self.r == nil {
self.r = bufio.NewReader(self.f)
}
var label, body []byte
for {
read, err := self.r.ReadBytes('>')
if len(read) > 1 {
lines := bytes.Split(read, []byte{'\n'})
if len(lines) > 1 {
label = lines[0]
body = bytes.Join(lines[1:len(lines)-1], []byte{})
}
break
} else if err != nil {
return nil, io.EOF
}
}
if len(label) > 0 && len(body) > 0 {
sequence = seq.New(label, body, nil)
} else {
return nil, errors.New("Invalid fasta entry")
}
return
}
// Read a single sequence and return it or an error.
// TODO: Does not read interleaved fastq.
func (self *Reader) Read() (sequence *seq.Seq, err error) {
if self.r == nil {
self.r = bufio.NewReader(self.f)
}
var line, label, seqBody, qualBody []byte
sequence = &seq.Seq{}
inQual := false
READ:
for {
if line, err = self.r.ReadBytes('\n'); err == nil {
if len(line) > 0 && line[len(line)-1] == '\r' {
line = line[:len(line)-1]
}
line = bytes.TrimSpace(line)
if len(line) == 0 {
continue
}
switch {
case !inQual && line[0] == '@':
label = line[1:]
case !inQual && line[0] == '+':
if len(label) == 0 {
return nil, errors.New("No ID line parsed at +line in fastq format")
}
if len(line) > 1 && bytes.Compare(label, line[1:]) != 0 {
return nil, errors.New("Quality ID does not match sequence ID")
}
inQual = true
case !inQual:
line = bytes.Join(bytes.Fields(line), nil)
seqBody = append(seqBody, line...)
case inQual:
line = bytes.Join(bytes.Fields(line), nil)
qualBody = append(qualBody, line...)
if len(qualBody) >= len(seqBody) {
break READ
}
}
} else {
return
}
}
if len(seqBody) != len(qualBody) {
return nil, errors.New("Quality length does not match sequence length")
}
sequence = seq.New(label, seqBody, qualBody)
return
}
// Read a single sequence and return it or an error.
func (self *Reader) Read() (sequence *seq.Seq, err error) {
var line, label, seqBody []byte
sequence = &seq.Seq{}
for {
if line, err = self.r.ReadBytes('\n'); err == nil {
if len(line) > 0 && line[len(line)-1] == '\r' {
line = line[:len(line)-1]
}
line = bytes.TrimSpace(line)
if len(line) == 0 {
continue
}
//skip header
if line[0] == '@' {
continue
}
seqBody = line
fields := bytes.Split(line, []byte{'\t'})
if len(fields) < 11 {
return nil, errors.New("sam alignment fields less than 11")
}
label = fields[0]
break
} else {
return
}
}
sequence = seq.New(label, seqBody, nil)
return
}