// Read a single sequence and return it or an error.
// TODO: Does not read multi-line fastq.
func (self *Reader) Read() (s seq.Sequence, err error) {
var (
buff, line, label []byte
isPrefix bool
seqBuff []alphabet.QLetter
t seqio.SequenceAppender
)
inQual := false
for {
if buff, isPrefix, err = self.r.ReadLine(); err == nil {
if isPrefix {
line = append(line, buff...)
continue
} else {
line = buff
}
line = bytes.TrimSpace(line)
if len(line) == 0 {
continue
}
switch {
case !inQual && line[0] == '@':
t = self.readHeader(line)
label, line = line, nil
case !inQual && line[0] == '+':
if len(label) == 0 {
return nil, bio.NewError("fastq: no header line parsed before +line in fastq format", 0)
}
if len(line) > 1 && bytes.Compare(label[1:], line[1:]) != 0 {
return nil, bio.NewError("fastq: quality header does not match sequence header", 0)
}
inQual = true
case !inQual:
line = bytes.Join(bytes.Fields(line), nil)
seqBuff = make([]alphabet.QLetter, len(line))
for i := range line {
seqBuff[i].L = alphabet.Letter(line[i])
}
case inQual:
line = bytes.Join(bytes.Fields(line), nil)
if len(line) != len(seqBuff) {
return nil, bio.NewError("fastq: sequence/quality length mismatch", 0)
}
for i := range line {
seqBuff[i].Q = alphabet.DecodeToQphred(line[i], self.enc)
}
t.AppendQLetters(seqBuff...)
return t, nil
}
} else {
return
}
}
panic("cannot reach")
}
// Decode a quality letter to a phred score based on the sequence encoding setting.
func (self *QSeq) QDecode(l byte) alphabet.Qphred { return alphabet.DecodeToQphred(l, self.encoding) }