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writer.go
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writer.go
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// Copyright ©2012 The bíogo Authors. All rights reserved.
// Use of this source code is governed by a BSD-style
// license that can be found in the LICENSE file.
package bam
import (
"bytes"
"compress/gzip"
"encoding/binary"
"errors"
"io"
"github.com/biogo/hts/bgzf"
"github.com/biogo/hts/sam"
)
// Writer implements BAM data writing.
type Writer struct {
h *sam.Header
bg *bgzf.Writer
buf bytes.Buffer
}
// NewWriter returns a new Writer using the given SAM header. Write
// concurrency is set to wc.
func NewWriter(w io.Writer, h *sam.Header, wc int) (*Writer, error) {
return NewWriterLevel(w, h, gzip.DefaultCompression, wc)
}
func makeWriter(w io.Writer, level, wc int) (*bgzf.Writer, error) {
if bw, ok := w.(*bgzf.Writer); ok {
return bw, nil
}
return bgzf.NewWriterLevel(w, level, wc)
}
// NewWriterLevel returns a new Writer using the given SAM header. Write
// concurrency is set to wc and compression level is set to level. Valid
// values for level are described in the compress/gzip documentation.
func NewWriterLevel(w io.Writer, h *sam.Header, level, wc int) (*Writer, error) {
bg, err := makeWriter(w, level, wc)
if err != nil {
return nil, err
}
bw := &Writer{
bg: bg,
h: h,
}
err = bw.writeHeader(h)
if err != nil {
return nil, err
}
bw.bg.Flush()
err = bw.bg.Wait()
if err != nil {
return nil, err
}
return bw, nil
}
func (bw *Writer) writeHeader(h *sam.Header) error {
bw.buf.Reset()
err := h.EncodeBinary(&bw.buf)
if err != nil {
return err
}
_, err = bw.bg.Write(bw.buf.Bytes())
return err
}
// 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 writeCigarOps(bin *binaryWriter, co []sam.CigarOp) {
for _, o := range co {
bin.writeUint32(uint32(o))
if bin.w.err != nil {
return
}
}
return
}
// Close closes the writer.
func (bw *Writer) Close() error {
return bw.bg.Close()
}
type errWriter struct {
w *bytes.Buffer
err error
}
func (w *errWriter) Write(p []byte) (int, error) {
if w.err != nil {
return 0, w.err
}
var n int
n, w.err = w.w.Write(p)
return n, w.err
}
func (w *errWriter) WriteByte(b byte) error {
if w.err != nil {
return w.err
}
w.err = w.w.WriteByte(b)
return w.err
}
type binaryWriter struct {
w *errWriter
buf [4]byte
}
func (w *binaryWriter) writeUint8(v uint8) {
w.buf[0] = v
w.w.Write(w.buf[:1])
}
func (w *binaryWriter) writeUint16(v uint16) {
binary.LittleEndian.PutUint16(w.buf[:2], v)
w.w.Write(w.buf[:2])
}
func (w *binaryWriter) writeInt32(v int32) {
binary.LittleEndian.PutUint32(w.buf[:4], uint32(v))
w.w.Write(w.buf[:4])
}
func (w *binaryWriter) writeUint32(v uint32) {
binary.LittleEndian.PutUint32(w.buf[:4], v)
w.w.Write(w.buf[:4])
}