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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 bgzf
import (
"bytes"
"compress/gzip"
"fmt"
"io"
"sync"
)
// Writer implements BGZF blocked gzip compression.
//
// Because the SAM specification requires that the RFC1952 FLG header field
// be set to 0x04, a Writer's Name and Comment fields should not be set if
// its output is to be read by another BGZF decompressor implementation.
type Writer struct {
gzip.Header
w io.Writer
active *compressor
queue chan *compressor
qwg sync.WaitGroup
waiting chan *compressor
wg sync.WaitGroup
closed bool
m sync.Mutex
err error
}
// NewWriter returns a new Writer. Writes to the returned writer are
// compressed and written to w.
//
// The number of concurrent write compressors is specified by wc.
func NewWriter(w io.Writer, wc int) *Writer {
bg, _ := NewWriterLevel(w, gzip.DefaultCompression, wc)
return bg
}
// NewWriterLevel returns a new Writer using the specified compression level
// instead of gzip.DefaultCompression. Allowable level options are integer
// values between between gzip.BestSpeed and gzip.BestCompression inclusive.
//
// The number of concurrent write compressors is specified by wc.
func NewWriterLevel(w io.Writer, level, wc int) (*Writer, error) {
if level < gzip.DefaultCompression || level > gzip.BestCompression {
return nil, fmt.Errorf("bgzf: invalid compression level: %d", level)
}
wc++ // We count one for the active compressor.
if wc < 2 {
wc = 2
}
bg := &Writer{
w: w,
waiting: make(chan *compressor, wc),
queue: make(chan *compressor, wc),
}
c := make([]compressor, wc)
for i := range c {
c[i].Header = &bg.Header
c[i].level = level
c[i].waiting = bg.waiting
c[i].flush = make(chan *compressor, 1)
c[i].qwg = &bg.qwg
bg.waiting <- &c[i]
}
bg.active = <-bg.waiting
bg.wg.Add(1)
go func() {
defer bg.wg.Done()
for qw := range bg.queue {
if !writeOK(bg, <-qw.flush) {
break
}
}
}()
return bg, nil
}
func writeOK(bg *Writer, c *compressor) bool {
defer func() { bg.waiting <- c }()
if c.err != nil {
bg.setErr(c.err)
return false
}
if c.buf.Len() == 0 {
return true
}
_, err := io.Copy(bg.w, &c.buf)
bg.qwg.Done()
if err != nil {
bg.setErr(err)
return false
}
c.next = 0
return true
}
type compressor struct {
*gzip.Header
gz *gzip.Writer
level int
next int
block [BlockSize]byte
buf bytes.Buffer
flush chan *compressor
qwg *sync.WaitGroup
waiting chan *compressor
err error
}
func (c *compressor) writeBlock() {
defer func() { c.flush <- c }()
if c.gz == nil {
c.gz, c.err = gzip.NewWriterLevel(&c.buf, c.level)
if c.err != nil {
return
}
} else {
c.gz.Reset(&c.buf)
}
c.gz.Header = gzip.Header{
Comment: c.Comment,
Extra: append([]byte(bgzfExtra), c.Extra...),
ModTime: c.ModTime,
Name: c.Name,
OS: c.OS,
}
_, c.err = c.gz.Write(c.block[:c.next])
if c.err != nil {
return
}
c.err = c.gz.Close()
if c.err != nil {
return
}
c.next = 0
b := c.buf.Bytes()
i := bytes.Index(b, bgzfExtraPrefix)
if i < 0 {
c.err = gzip.ErrHeader
return
}
size := len(b) - 1
if size >= MaxBlockSize {
c.err = ErrBlockOverflow
return
}
b[i+4], b[i+5] = byte(size), byte(size>>8)
}
// Next returns the index of the start of the next write within the
// decompressed data block.
func (bg *Writer) Next() (int, error) {
if bg.closed {
return 0, ErrClosed
}
if err := bg.Error(); err != nil {
return 0, err
}
return bg.active.next, nil
}
// Write writes the compressed form of b to the underlying io.Writer.
// Decompressed data blocks are limited to BlockSize, so individual
// byte slices may span block boundaries, however the Writer attempts
// to keep each write within a single data block.
func (bg *Writer) Write(b []byte) (int, error) {
if bg.closed {
return 0, ErrClosed
}
err := bg.Error()
if err != nil {
return 0, err
}
c := bg.active
var n int
for ; len(b) > 0 && err == nil; err = bg.Error() {
var _n int
if c.next == 0 || c.next+len(b) <= len(c.block) {
_n = copy(c.block[c.next:], b)
b = b[_n:]
c.next += _n
n += _n
}
if c.next == len(c.block) || _n == 0 {
bg.queue <- c
bg.qwg.Add(1)
go c.writeBlock()
c = <-bg.waiting
}
}
bg.active = c
return n, bg.Error()
}
// Flush writes unwritten data to the underlying io.Writer. Flush does not block.
func (bg *Writer) Flush() error {
if bg.closed {
return ErrClosed
}
if err := bg.Error(); err != nil {
return err
}
if bg.active.next == 0 {
return nil
}
var c *compressor
c, bg.active = bg.active, <-bg.waiting
bg.queue <- c
bg.qwg.Add(1)
go c.writeBlock()
return bg.Error()
}
// Wait waits for all pending writes to complete and returns the subsequent
// error state of the Writer.
func (bg *Writer) Wait() error {
if err := bg.Error(); err != nil {
return err
}
bg.qwg.Wait()
return bg.Error()
}
// Error returns the error state of the Writer.
func (bg *Writer) Error() error {
bg.m.Lock()
defer bg.m.Unlock()
return bg.err
}
func (bg *Writer) setErr(err error) {
bg.m.Lock()
defer bg.m.Unlock()
if bg.err == nil {
bg.err = err
}
}
// Close closes the Writer, waiting for any pending writes before returning
// the final error of the Writer.
func (bg *Writer) Close() error {
if !bg.closed {
c := bg.active
bg.queue <- c
bg.qwg.Add(1)
<-bg.waiting
c.writeBlock()
bg.closed = true
close(bg.queue)
bg.wg.Wait()
if bg.err == nil {
_, bg.err = bg.w.Write([]byte(magicBlock))
}
}
return bg.err
}