// 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
}
func (d *DiversityFilter) Diff(r *sam.Record, genome []byte) (diff, length int) {
start := r.Start()
end := r.End()
if start < 0 || end > len(genome) {
if *debug {
text, err := r.MarshalSAM(sam.FlagDecimal)
raiseError(err)
log.Printf("acc: %s, genome length %d, read starts at %d and ends at %d: %s\n", r.Ref.Name(), len(genome), start, end, text)
}
length = 0
return
}
refSeq := genome[start:end]
diff = 0
read := map2Ref(r)
length = len(read)
for i := 0; i < length; i++ {
if read[i] != refSeq[i] {
diff++
}
}
return
}
func (d *DiversityFilter) filter(buf []*sam.Record, acc string, genome []byte) (out []*sam.Record, acc1 string, genome1 []byte) {
fn := func(txn *lmdb.Txn) error {
dbi, err := txn.OpenDBI("read", 0)
if err != nil {
return err
}
for _, r := range buf {
key := []byte(r.Name)
val, err := txn.Get(dbi, key)
if err != nil {
if lmdb.IsNotFound(err) {
val, err = r.MarshalText()
if err != nil {
return err
}
err = txn.Put(dbi, key, val, 0)
if err != nil {
return err
}
} else {
return err
}
} else {
var mate *sam.Record = &sam.Record{}
err := mate.UnmarshalText(val)
raiseError(err)
if r.Ref.Name() == mate.Ref.Name() {
if acc != r.Ref.Name() {
genome, err = d.findGenome(r, d.featureDB, "fna")
raiseError(err)
acc = r.Ref.Name()
if *debug {
log.Println(acc)
}
}
diff1, len1 := d.Diff(r, genome)
diff2, len2 := d.Diff(mate, genome)
if len1 > 0 && len2 > 0 && float64(diff1+diff2)/float64(len1+len2) <= d.Cutoff {
out = append(out, r)
out = append(out, mate)
} else {
if *debug {
log.Printf("%d, %d, %d, %d\n", diff1, diff2, len1, len2)
}
}
}
txn.Del(dbi, key, val)
}
}
return nil
}
retry:
err := d.db.Update(fn)
if lmdb.IsMapFull(err) {
d.sizeDB *= 2
err = d.db.SetMapSize(d.sizeDB)
raiseError(err)
goto retry
}
raiseError(err)
genome1 = genome
acc1 = acc
return
}
// 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
}
// 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))
}
