// Read returns the next sam.Record in the BAM stream.
func (br *Reader) Read() (*sam.Record, error) {
if br.c != nil && vOffset(br.r.LastChunk().End) >= vOffset(br.c.End) {
return nil, io.EOF
}
r := errReader{r: br.r}
bin := binaryReader{r: &r}
// Read record header data.
blockSize := int(bin.readInt32())
r.n = 0 // The blocksize field is not included in the blocksize.
// br.r.Chunk() is only valid after the call the Read(), so this
// must come after the first read in the record.
tx := br.r.Begin()
defer func() {
br.lastChunk = tx.End()
}()
var rec sam.Record
refID := bin.readInt32()
rec.Pos = int(bin.readInt32())
nLen := bin.readUint8()
rec.MapQ = bin.readUint8()
_ = bin.readUint16()
nCigar := bin.readUint16()
rec.Flags = sam.Flags(bin.readUint16())
lSeq := bin.readInt32()
nextRefID := bin.readInt32()
rec.MatePos = int(bin.readInt32())
rec.TempLen = int(bin.readInt32())
if r.err != nil {
return nil, r.err
}
// Read variable length data.
name := make([]byte, nLen)
if nf, _ := r.Read(name); nf != int(nLen) {
return nil, errors.New("bam: truncated record name")
}
rec.Name = string(name[:len(name)-1]) // The BAM spec indicates name is null terminated.
rec.Cigar = readCigarOps(&bin, nCigar)
if r.err != nil {
return nil, r.err
}
seq := make(doublets, (lSeq+1)>>1)
if nf, _ := r.Read(seq.Bytes()); nf != int((lSeq+1)>>1) {
return nil, errors.New("bam: truncated sequence")
}
rec.Seq = sam.Seq{Length: int(lSeq), Seq: seq}
rec.Qual = make([]byte, lSeq)
if nf, _ := r.Read(rec.Qual); nf != int(lSeq) {
return nil, errors.New("bam: truncated quality")
}
auxTags := make([]byte, blockSize-r.n)
r.Read(auxTags)
if r.n != blockSize {
return nil, errors.New("bam: truncated auxilliary data")
}
rec.AuxFields = parseAux(auxTags)
if r.err != nil {
return nil, r.err
}
refs := int32(len(br.h.Refs()))
if refID != -1 {
if refID < -1 || refID >= refs {
return nil, errors.New("bam: reference id out of range")
}
rec.Ref = br.h.Refs()[refID]
}
if nextRefID != -1 {
if nextRefID < -1 || nextRefID >= refs {
return nil, errors.New("bam: mate reference id out of range")
}
rec.MateRef = br.h.Refs()[nextRefID]
}
return &rec, nil
}
