/
reader.go
703 lines (614 loc) · 15.9 KB
/
reader.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 (
"bufio"
"bytes"
"compress/flate"
"compress/gzip"
"io"
"runtime"
"sync"
)
// countReader wraps flate.Reader, adding support for querying current offset.
type countReader struct {
// Underlying Reader.
fr flate.Reader
// Offset within the underlying reader.
off int64
}
// newCountReader returns a new countReader.
func newCountReader(r io.Reader) *countReader {
switch r := r.(type) {
case *countReader:
panic("bgzf: illegal use of internal type")
case flate.Reader:
return &countReader{fr: r}
default:
return &countReader{fr: bufio.NewReader(r)}
}
}
// Read is required to satisfy flate.Reader.
func (r *countReader) Read(p []byte) (int, error) {
n, err := r.fr.Read(p)
r.off += int64(n)
return n, err
}
// ReadByte is required to satisfy flate.Reader.
func (r *countReader) ReadByte() (byte, error) {
b, err := r.fr.ReadByte()
if err == nil {
r.off++
}
return b, err
}
// offset returns the current offset in the underlying reader.
func (r *countReader) offset() int64 { return r.off }
// seek moves the countReader to the specified offset using rs as the
// underlying reader.
func (r *countReader) seek(rs io.ReadSeeker, off int64) error {
_, err := rs.Seek(off, 0)
if err != nil {
return err
}
type reseter interface {
Reset(io.Reader)
}
switch cr := r.fr.(type) {
case reseter:
cr.Reset(rs)
default:
r.fr = newCountReader(rs)
}
r.off = off
return nil
}
// buffer is a flate.Reader used by a decompressor to store read-ahead data.
type buffer struct {
// Buffered compressed data from read ahead.
off int // Current position in buffered data.
size int // Total size of buffered data.
data [MaxBlockSize]byte
}
// Read provides the flate.Decompressor Read method.
func (r *buffer) Read(b []byte) (int, error) {
if r.off >= r.size {
return 0, io.EOF
}
if n := r.size - r.off; len(b) > n {
b = b[:n]
}
n := copy(b, r.data[r.off:])
r.off += n
return n, nil
}
// ReadByte provides the flate.Decompressor ReadByte method.
func (r *buffer) ReadByte() (byte, error) {
if r.off == r.size {
return 0, io.EOF
}
b := r.data[r.off]
r.off++
return b, nil
}
// reset makes the buffer available to store data.
func (r *buffer) reset() { r.size = 0 }
// hasData returns whether the buffer has any data buffered.
func (r *buffer) hasData() bool { return r.size != 0 }
// readLimited reads n bytes into the buffer from the given source.
func (r *buffer) readLimited(n int, src *countReader) error {
if r.hasData() {
panic("bgzf: read into non-empty buffer")
}
r.off = 0
var err error
r.size, err = io.ReadFull(src, r.data[:n])
return err
}
// equals returns a boolean indicating the equality between
// the buffered data and the given byte slice.
func (r *buffer) equals(b []byte) bool { return bytes.Equal(r.data[:r.size], b) }
// decompressor is a gzip member decompressor worker.
type decompressor struct {
owner *Reader
gz gzip.Reader
cr *countReader
// Current block size.
blockSize int
// Buffered compressed data from read ahead.
buf buffer
// Decompressed data.
wg sync.WaitGroup
blk Block
err error
}
// Read provides the Read method for the decompressor's gzip.Reader.
func (d *decompressor) Read(b []byte) (int, error) {
if d.buf.hasData() {
return d.buf.Read(b)
}
return d.cr.Read(b)
}
// ReadByte provides the ReadByte method for the decompressor's gzip.Reader.
func (d *decompressor) ReadByte() (byte, error) {
if d.buf.hasData() {
return d.buf.ReadByte()
}
return d.cr.ReadByte()
}
// lazyBlock conditionally creates a ready to use Block.
func (d *decompressor) lazyBlock() {
if d.blk == nil {
if w, ok := d.owner.cache.(Wrapper); ok {
d.blk = w.Wrap(&block{owner: d.owner})
} else {
d.blk = &block{owner: d.owner}
}
return
}
if !d.blk.ownedBy(d.owner) {
d.blk.setOwner(d.owner)
}
}
// acquireHead gains the read head from the decompressor's owner.
func (d *decompressor) acquireHead() {
d.wg.Add(1)
d.cr = <-d.owner.head
}
// releaseHead releases the read head back to the decompressor's owner.
func (d *decompressor) releaseHead() {
d.owner.head <- d.cr
d.cr = nil // Defensively zero the reader.
}
// wait waits for the current member to be decompressed or fail, and returns
// the resulting error state.
func (d *decompressor) wait() (Block, error) {
d.wg.Wait()
blk := d.blk
d.blk = nil
return blk, d.err
}
// using sets the Block for the decompressor to work with.
func (d *decompressor) using(b Block) *decompressor { d.blk = b; return d }
// nextBlockAt makes the decompressor ready for reading decompressed data
// from its Block. It checks if there is a cached Block for the nextBase,
// otherwise it seeks to the correct location if decompressor is not
// correctly positioned, and then reads the compressed data and fills
// the decompressed Block.
// After nextBlockAt returns without error, the decompressor's Block
// holds a valid gzip.Header and base offset.
func (d *decompressor) nextBlockAt(off int64, rs io.ReadSeeker) *decompressor {
d.err = nil
for {
exists, next := d.owner.cacheHasBlockFor(off)
if !exists {
break
}
off = next
}
d.lazyBlock()
d.acquireHead()
defer d.releaseHead()
if d.cr.offset() != off {
if rs == nil {
// It should not be possible for the expected next block base
// to be out of register with the count reader unless Seek
// has been called, so we know the base reader must be an
// io.ReadSeeker.
var ok bool
rs, ok = d.owner.r.(io.ReadSeeker)
if !ok {
panic("bgzf: unexpected offset without seek")
}
}
d.err = d.cr.seek(rs, off)
if d.err != nil {
d.wg.Done()
return d
}
}
d.blk.setBase(d.cr.offset())
d.err = d.readMember()
if d.err != nil {
d.wg.Done()
return d
}
d.blk.setHeader(d.gz.Header)
d.gz.Header = gzip.Header{} // Prevent retention of header field in next use.
// Decompress data into the decompressor's Block.
go func() {
d.err = d.blk.readFrom(&d.gz)
d.wg.Done()
}()
return d
}
// expectedMemberSize returns the size of the BGZF conformant gzip member.
// It returns -1 if no BGZF block size field is found.
func expectedMemberSize(h gzip.Header) int {
i := bytes.Index(h.Extra, bgzfExtraPrefix)
if i < 0 || i+5 >= len(h.Extra) {
return -1
}
return (int(h.Extra[i+4]) | int(h.Extra[i+5])<<8) + 1
}
// readMember buffers the gzip member starting the current decompressor offset.
func (d *decompressor) readMember() error {
// Set the decompressor to Read from the underlying flate.Reader
// and mark the starting offset from which the underlying reader
// was used.
d.buf.reset()
mark := d.cr.offset()
err := d.gz.Reset(d)
if err != nil {
d.blockSize = -1
return err
}
d.blockSize = expectedMemberSize(d.gz.Header)
if d.blockSize < 0 {
return ErrNoBlockSize
}
skipped := int(d.cr.offset() - mark)
// Read compressed data into the decompressor buffer until the
// underlying flate.Reader is positioned at the end of the gzip
// member in which the readMember call was made.
return d.buf.readLimited(d.blockSize-skipped, d.cr)
}
// Offset is a BGZF virtual offset.
type Offset struct {
File int64
Block uint16
}
// Chunk is a region of a BGZF file.
type Chunk struct {
Begin Offset
End Offset
}
// Reader implements BGZF blocked gzip decompression.
type Reader struct {
gzip.Header
r io.Reader
// head serialises access to the underlying
// io.Reader.
head chan *countReader
// lastChunk is the virtual file offset
// interval of the last successful read
// or seek operation.
lastChunk Chunk
// Blocked specifies the behaviour of the
// Reader at the end of a BGZF member.
// If the Reader is Blocked, a Read that
// reaches the end of a BGZF block will
// return io.EOF. This error is not sticky,
// so a subsequent Read will progress to
// the next block if it is available.
Blocked bool
// Non-concurrent work decompressor.
dec *decompressor
// Concurrent work fields.
waiting chan *decompressor
working chan *decompressor
control chan int64
current Block
// cache is the Reader block cache. If Cache is not nil,
// the cache is queried for blocks before an attempt to
// read from the underlying io.Reader.
mu sync.RWMutex
cache Cache
err error
}
// NewReader returns a new BGZF reader.
//
// The number of concurrent read decompressors is specified by rd.
// If rd is 0, GOMAXPROCS concurrent will be created. The returned
// Reader should be closed after use to avoid leaking resources.
func NewReader(r io.Reader, rd int) (*Reader, error) {
if rd == 0 {
rd = runtime.GOMAXPROCS(0)
}
bg := &Reader{
r: r,
head: make(chan *countReader, 1),
}
bg.head <- newCountReader(r)
// Make work loop control structures.
if rd > 1 {
bg.waiting = make(chan *decompressor, rd)
bg.working = make(chan *decompressor, rd)
bg.control = make(chan int64, 1)
for ; rd > 1; rd-- {
bg.waiting <- &decompressor{owner: bg}
}
}
// Read the first block now so we can fail before
// the first Read call if there is a problem.
bg.dec = &decompressor{owner: bg}
blk, err := bg.dec.nextBlockAt(0, nil).wait()
if err != nil {
return nil, err
}
bg.current = blk
bg.Header = bg.current.header()
// Set up work loop if rd was > 1.
if bg.control != nil {
bg.waiting <- bg.dec
bg.dec = nil
next := blk.NextBase()
go func() {
defer func() {
bg.mu.Lock()
bg.cache = nil
bg.mu.Unlock()
}()
for dec := range bg.waiting {
var open bool
if next < 0 {
next, open = <-bg.control
if !open {
return
}
} else {
select {
case next, open = <-bg.control:
if !open {
return
}
default:
}
}
dec.nextBlockAt(next, nil)
next = dec.blk.NextBase()
bg.working <- dec
}
}()
}
return bg, nil
}
// SetCache sets the cache to be used by the Reader.
func (bg *Reader) SetCache(c Cache) {
bg.mu.Lock()
bg.cache = c
bg.mu.Unlock()
}
// Seek performs a seek operation to the given virtual offset.
func (bg *Reader) Seek(off Offset) error {
rs, ok := bg.r.(io.ReadSeeker)
if !ok {
return ErrNotASeeker
}
if off.File != bg.current.Base() || !bg.current.hasData() {
ok := bg.cacheSwap(off.File)
if !ok {
var dec *decompressor
if bg.dec != nil {
dec = bg.dec
} else {
select {
case dec = <-bg.waiting:
case dec = <-bg.working:
blk, err := dec.wait()
if err == nil {
bg.keep(blk)
}
}
}
bg.current, bg.err = dec.
using(bg.current).
nextBlockAt(off.File, rs).
wait()
if bg.dec == nil {
select {
case <-bg.control:
default:
}
bg.control <- bg.current.NextBase()
bg.waiting <- dec
}
bg.Header = bg.current.header()
if bg.err != nil {
return bg.err
}
}
}
bg.err = bg.current.seek(int64(off.Block))
if bg.err == nil {
bg.lastChunk = Chunk{Begin: off, End: off}
}
return bg.err
}
// LastChunk returns the region of the BGZF file read by the last
// successful read operation or the resulting virtual offset of
// the last successful seek operation.
func (bg *Reader) LastChunk() Chunk { return bg.lastChunk }
// BlockLen returns the number of bytes remaining to be read from the
// current BGZF block.
func (bg *Reader) BlockLen() int { return bg.current.len() }
// Close closes the reader and releases resources.
func (bg *Reader) Close() error {
if bg.control != nil {
close(bg.control)
close(bg.waiting)
}
if bg.err == io.EOF {
return nil
}
return bg.err
}
// Read implements the io.Reader interface.
func (bg *Reader) Read(p []byte) (int, error) {
if bg.err != nil {
return 0, bg.err
}
// Discard leading empty blocks. This is an indexing
// optimisation to avoid retaining useless members
// in a BAI/CSI.
for bg.current.len() == 0 {
bg.err = bg.nextBlock()
if bg.err != nil {
return 0, bg.err
}
}
bg.lastChunk.Begin = bg.current.txOffset()
var n int
for n < len(p) && bg.err == nil {
var _n int
_n, bg.err = bg.current.Read(p[n:])
n += _n
if bg.err == io.EOF {
if n == len(p) {
bg.err = nil
break
}
if bg.Blocked {
bg.err = nil
bg.lastChunk.End = bg.current.txOffset()
return n, io.EOF
}
bg.err = bg.nextBlock()
if bg.err != nil {
break
}
}
}
bg.lastChunk.End = bg.current.txOffset()
return n, bg.err
}
// nextBlock swaps the current decompressed block for the next
// in the stream. If the block is available from the cache
// no additional work is done, otherwise a decompressor is
// used or waited on.
func (bg *Reader) nextBlock() error {
base := bg.current.NextBase()
ok := bg.cacheSwap(base)
if ok {
bg.Header = bg.current.header()
return nil
}
var err error
if bg.dec != nil {
bg.dec.using(bg.current).nextBlockAt(base, nil)
bg.current, err = bg.dec.wait()
} else {
var ok bool
for i := 0; i < cap(bg.working); i++ {
dec := <-bg.working
bg.current, err = dec.wait()
bg.waiting <- dec
if bg.current.Base() == base {
ok = true
break
}
if err == nil {
bg.keep(bg.current)
bg.current = nil
}
}
if !ok {
panic("bgzf: unexpected block")
}
}
if err != nil {
return err
}
// Only set header if there was no error.
h := bg.current.header()
if bg.current.isMagicBlock() {
// TODO(kortschak): Do this more carefully. It may be that
// someone actually has extra data in this field that we are
// clobbering.
bg.Header.Extra = h.Extra
} else {
bg.Header = h
}
return nil
}
// cacheSwap attempts to swap the current Block for a cached Block
// for the given base offset. It returns true if successful.
func (bg *Reader) cacheSwap(base int64) bool {
bg.mu.RLock()
defer bg.mu.RUnlock()
if bg.cache == nil {
return false
}
blk, err := bg.cachedBlockFor(base)
if err != nil {
return false
}
if blk != nil {
// TODO(kortschak): Under some conditions, e.g. FIFO
// cache we will be discarding a non-nil evicted Block.
// Consider retaining these in a sync.Pool.
bg.cachePut(bg.current)
bg.current = blk
return true
}
var retained bool
bg.current, retained = bg.cachePut(bg.current)
if retained {
bg.current = nil
}
return false
}
// cacheHasBlockFor returns whether the Reader's cache has a block
// for the given base offset. If the requested Block exists, the base
// offset of the following Block is returned.
func (bg *Reader) cacheHasBlockFor(base int64) (exists bool, next int64) {
bg.mu.RLock()
defer bg.mu.RUnlock()
if bg.cache == nil {
return false, -1
}
return bg.cache.Peek(base)
}
// cachedBlockFor returns a non-nil Block if the Reader has access to a
// cache and the cache holds the block with the given base and the
// correct owner, otherwise it returns nil. If the Block's owner is not
// correct, or the Block cannot seek to the start of its data, a non-nil
// error is returned.
func (bg *Reader) cachedBlockFor(base int64) (Block, error) {
blk := bg.cache.Get(base)
if blk != nil {
if !blk.ownedBy(bg) {
return nil, ErrContaminatedCache
}
err := blk.seek(0)
if err != nil {
return nil, err
}
}
return blk, nil
}
// cachePut puts the given Block into the cache if it exists, it returns
// the Block that was evicted or b if it was not retained, and whether
// the Block was retained by the cache.
func (bg *Reader) cachePut(b Block) (evicted Block, retained bool) {
if b == nil || !b.hasData() {
return b, false
}
return bg.cache.Put(b)
}
// keep puts the given Block into the cache if it exists.
func (bg *Reader) keep(b Block) {
if b == nil || !b.hasData() {
return
}
bg.mu.RLock()
defer bg.mu.RUnlock()
if bg.cache != nil {
bg.cache.Put(b)
}
}
// Begin returns a Tx that starts at the current virtual offset.
func (bg *Reader) Begin() Tx { return Tx{begin: bg.lastChunk.Begin, r: bg} }
// Tx represents a multi-read transaction.
type Tx struct {
begin Offset
r *Reader
}
// End returns the Chunk spanning the transaction. After return the Tx is
// no longer valid.
func (t *Tx) End() Chunk {
c := Chunk{Begin: t.begin, End: t.r.lastChunk.End}
t.r = nil
return c
}