Adding upstream version 1.16.10.upstream/1.16.10upstream

Signed-off-by: Daniel Baumann <daniel.baumann@progress-linux.org>

1 files changed, 85 insertions, 0 deletions

diff --git a/test/bench/go1/revcomp_test.go b/test/bench/go1/revcomp_test.go
new file mode 100644
index 0000000..7d57bd6
--- /dev/null
+++ b/test/bench/go1/revcomp_test.go
@@ -0,0 +1,85 @@
+// Copyright 2011 The Go Authors. All rights reserved.
+// Use of this source code is governed by a BSD-style
+// license that can be found in the LICENSE file.
+
+// This benchmark, taken from the shootout, tests array indexing
+// and array bounds elimination performance.
+
+package go1
+
+import (
+	"bufio"
+	"bytes"
+	"io/ioutil"
+	"testing"
+)
+
+var revCompTable = [256]uint8{
+	'A': 'T', 'a': 'T',
+	'C': 'G', 'c': 'G',
+	'G': 'C', 'g': 'C',
+	'T': 'A', 't': 'A',
+	'U': 'A', 'u': 'A',
+	'M': 'K', 'm': 'K',
+	'R': 'Y', 'r': 'Y',
+	'W': 'W', 'w': 'W',
+	'S': 'S', 's': 'S',
+	'Y': 'R', 'y': 'R',
+	'K': 'M', 'k': 'M',
+	'V': 'B', 'v': 'B',
+	'H': 'D', 'h': 'D',
+	'D': 'H', 'd': 'H',
+	'B': 'V', 'b': 'V',
+	'N': 'N', 'n': 'N',
+}
+
+func revcomp(data []byte) {
+	in := bufio.NewReader(bytes.NewBuffer(data))
+	out := ioutil.Discard
+	buf := make([]byte, 1024*1024)
+	line, err := in.ReadSlice('\n')
+	for err == nil {
+		out.Write(line)
+
+		// Accumulate reversed complement in buf[w:]
+		nchar := 0
+		w := len(buf)
+		for {
+			line, err = in.ReadSlice('\n')
+			if err != nil || line[0] == '>' {
+				break
+			}
+			line = line[0 : len(line)-1]
+			nchar += len(line)
+			if len(line)+nchar/60+128 >= w {
+				nbuf := make([]byte, len(buf)*5)
+				copy(nbuf[len(nbuf)-len(buf):], buf)
+				w += len(nbuf) - len(buf)
+				buf = nbuf
+			}
+
+			// This loop is the bottleneck.
+			for _, c := range line {
+				w--
+				buf[w] = revCompTable[c]
+			}
+		}
+
+		// Copy down to beginning of buffer, inserting newlines.
+		// The loop left room for the newlines and 128 bytes of padding.
+		i := 0
+		for j := w; j < len(buf); j += 60 {
+			n := copy(buf[i:i+60], buf[j:])
+			buf[i+n] = '\n'
+			i += n + 1
+		}
+		out.Write(buf[0:i])
+	}
+}
+
+func BenchmarkRevcomp(b *testing.B) {
+	b.SetBytes(int64(len(fastabytes)))
+	for i := 0; i < b.N; i++ {
+		revcomp(fastabytes)
+	}
+}