Re-added benchmark and license

post-processor/compress/LICENSE

@@ -0,0 +1,21 @@
+The MIT License (MIT)
+
+Copyright (c) 2014 Vasiliy Tolstov
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

post-processor/compress/benchmark.go

@@ -0,0 +1,197 @@
+// +build ignore
+
+package main
+
+import (
+	"compress/flate"
+	"compress/gzip"
+	"fmt"
+	"io"
+	"io/ioutil"
+	"os"
+	"runtime"
+	"testing"
+
+	"github.com/biogo/hts/bgzf"
+	"github.com/klauspost/pgzip"
+	"github.com/pierrec/lz4"
+)
+
+type Compressor struct {
+	r  *os.File
+	w  *os.File
+	sr int64
+	sw int64
+}
+
+func (c *Compressor) Close() error {
+	var err error
+
+	fi, _ := c.w.Stat()
+	c.sw = fi.Size()
+	if err = c.w.Close(); err != nil {
+		return err
+	}
+
+	fi, _ = c.r.Stat()
+	c.sr = fi.Size()
+	if err = c.r.Close(); err != nil {
+		return err
+	}
+
+	return nil
+}
+
+func NewCompressor(src, dst string) (*Compressor, error) {
+	r, err := os.Open(src)
+	if err != nil {
+		return nil, err
+	}
+
+	w, err := os.Create(dst)
+	if err != nil {
+		r.Close()
+		return nil, err
+	}
+
+	c := &Compressor{r: r, w: w}
+	return c, nil
+}
+
+func main() {
+
+	runtime.GOMAXPROCS(runtime.NumCPU())
+
+	var resw testing.BenchmarkResult
+	var resr testing.BenchmarkResult
+
+	c, err := NewCompressor("/tmp/image.r", "/tmp/image.w")
+	if err != nil {
+		panic(err)
+	}
+	resw = testing.Benchmark(c.BenchmarkGZIPWriter)
+	c.w.Seek(0, 0)
+	resr = testing.Benchmark(c.BenchmarkGZIPReader)
+	c.Close()
+	fmt.Printf("gzip:\twriter %s\treader %s\tsize %d\n", resw.T.String(), resr.T.String(), c.sw)
+
+	c, err = NewCompressor("/tmp/image.r", "/tmp/image.w")
+	if err != nil {
+		panic(err)
+	}
+	resw = testing.Benchmark(c.BenchmarkBGZFWriter)
+	c.w.Seek(0, 0)
+	resr = testing.Benchmark(c.BenchmarkBGZFReader)
+	c.Close()
+	fmt.Printf("bgzf:\twriter %s\treader %s\tsize %d\n", resw.T.String(), resr.T.String(), c.sw)
+
+	c, err = NewCompressor("/tmp/image.r", "/tmp/image.w")
+	if err != nil {
+		panic(err)
+	}
+	resw = testing.Benchmark(c.BenchmarkPGZIPWriter)
+	c.w.Seek(0, 0)
+	resr = testing.Benchmark(c.BenchmarkPGZIPReader)
+	c.Close()
+	fmt.Printf("pgzip:\twriter %s\treader %s\tsize %d\n", resw.T.String(), resr.T.String(), c.sw)
+
+	c, err = NewCompressor("/tmp/image.r", "/tmp/image.w")
+	if err != nil {
+		panic(err)
+	}
+	resw = testing.Benchmark(c.BenchmarkLZ4Writer)
+	c.w.Seek(0, 0)
+	resr = testing.Benchmark(c.BenchmarkLZ4Reader)
+	c.Close()
+	fmt.Printf("lz4:\twriter %s\treader %s\tsize %d\n", resw.T.String(), resr.T.String(), c.sw)
+
+}
+
+func (c *Compressor) BenchmarkGZIPWriter(b *testing.B) {
+	cw, _ := gzip.NewWriterLevel(c.w, flate.BestSpeed)
+	b.ResetTimer()
+
+	_, err := io.Copy(cw, c.r)
+	if err != nil {
+		b.Fatal(err)
+	}
+	cw.Close()
+	c.w.Sync()
+}
+
+func (c *Compressor) BenchmarkGZIPReader(b *testing.B) {
+	cr, _ := gzip.NewReader(c.w)
+	b.ResetTimer()
+
+	_, err := io.Copy(ioutil.Discard, cr)
+	if err != nil {
+		b.Fatal(err)
+	}
+}
+
+func (c *Compressor) BenchmarkBGZFWriter(b *testing.B) {
+	cw, _ := bgzf.NewWriterLevel(c.w, flate.BestSpeed, runtime.NumCPU())
+	b.ResetTimer()
+
+	_, err := io.Copy(cw, c.r)
+	if err != nil {
+		b.Fatal(err)
+	}
+	c.w.Sync()
+}
+
+func (c *Compressor) BenchmarkBGZFReader(b *testing.B) {
+	cr, _ := bgzf.NewReader(c.w, 0)
+	b.ResetTimer()
+
+	_, err := io.Copy(ioutil.Discard, cr)
+	if err != nil {
+		b.Fatal(err)
+	}
+}
+
+func (c *Compressor) BenchmarkPGZIPWriter(b *testing.B) {
+	cw, _ := pgzip.NewWriterLevel(c.w, flate.BestSpeed)
+	b.ResetTimer()
+
+	_, err := io.Copy(cw, c.r)
+	if err != nil {
+		b.Fatal(err)
+	}
+	cw.Close()
+	c.w.Sync()
+}
+
+func (c *Compressor) BenchmarkPGZIPReader(b *testing.B) {
+	cr, _ := pgzip.NewReader(c.w)
+	b.ResetTimer()
+
+	_, err := io.Copy(ioutil.Discard, cr)
+	if err != nil {
+		b.Fatal(err)
+	}
+}
+
+func (c *Compressor) BenchmarkLZ4Writer(b *testing.B) {
+	cw := lz4.NewWriter(c.w)
+	//	cw.Header.HighCompression = true
+	cw.Header.NoChecksum = true
+	b.ResetTimer()
+
+	_, err := io.Copy(cw, c.r)
+	if err != nil {
+		b.Fatal(err)
+	}
+	cw.Close()
+	c.w.Sync()
+}
+
+func (c *Compressor) BenchmarkLZ4Reader(b *testing.B) {
+	cr := lz4.NewReader(c.w)
+	b.ResetTimer()
+
+	_, err := io.Copy(ioutil.Discard, cr)
+	if err != nil {
+		b.Fatal(err)
+	}
+}