// Write writes r to the BAM stream.
func (bw *Writer) Write(r *sam.Record) error {
if len(r.Name) == 0 || len(r.Name) > 254 {
return errors.New("bam: name absent or too long")
}
if r.Qual != nil && len(r.Qual) != r.Seq.Length {
return errors.New("bam: sequence/quality length mismatch")
}
tags := buildAux(r.AuxFields)
recLen := bamFixedRemainder +
len(r.Name) + 1 + // Null terminated.
len(r.Cigar)<<2 + // CigarOps are 4 bytes.
len(r.Seq.Seq) +
len(r.Qual) +
len(tags)
bw.buf.Reset()
wb := errWriter{w: &bw.buf}
bin := binaryWriter{w: &wb}
// Write record header data.
bin.writeInt32(int32(recLen))
bin.writeInt32(int32(r.Ref.ID()))
bin.writeInt32(int32(r.Pos))
bin.writeUint8(byte(len(r.Name) + 1))
bin.writeUint8(r.MapQ)
bin.writeUint16(uint16(r.Bin())) //r.bin
bin.writeUint16(uint16(len(r.Cigar)))
bin.writeUint16(uint16(r.Flags))
bin.writeInt32(int32(r.Seq.Length))
bin.writeInt32(int32(r.MateRef.ID()))
bin.writeInt32(int32(r.MatePos))
bin.writeInt32(int32(r.TempLen))
// Write variable length data.
wb.Write(append([]byte(r.Name), 0))
writeCigarOps(&bin, r.Cigar)
wb.Write(doublets(r.Seq.Seq).Bytes())
if r.Qual != nil {
wb.Write(r.Qual)
} else {
for i := 0; i < r.Seq.Length; i++ {
wb.WriteByte(0xff)
}
}
wb.Write(tags)
if wb.err != nil {
return wb.err
}
_, err := bw.bg.Write(bw.buf.Bytes())
return err
}
// Add records the SAM record as having being located at the given chunk.
func (i *Index) Add(r *sam.Record, c bgzf.Chunk) error {
return i.idx.Add(r, uint32(r.Bin()), c, isPlaced(r), isMapped(r))
}