Adding upstream version 1.20.14.upstream/1.20.14upstream

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

1 files changed, 177 insertions, 0 deletions

diff --git a/test/bench/go1/fasta_test.go b/test/bench/go1/fasta_test.go
new file mode 100644
index 0000000..f8bfbf4
--- /dev/null
+++ b/test/bench/go1/fasta_test.go
@@ -0,0 +1,177 @@
+// 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.
+
+package go1
+
+import "runtime"
+
+// Not a benchmark; input for revcomp.
+
+func makefasta() []byte {
+	var n int = 25e6
+	if runtime.GOARCH == "arm" || runtime.GOARCH == "mips" || runtime.GOARCH == "mips64" {
+		// TODO(dfc) remove this limitation after precise gc.
+		// A value of 25e6 consumes 465mb of heap on 32bit
+		// platforms, which is too much for some systems.
+		// A value of 25e5 produces a memory layout that
+		// confuses the gc on 32bit platforms. So 25e4 it is.
+		n = 25e4
+	}
+	return fasta(n)
+}
+
+func fasta(n int) []byte {
+	out := make(fastaBuffer, 0, 11*n)
+
+	iub := []fastaAcid{
+		{prob: 0.27, sym: 'a'},
+		{prob: 0.12, sym: 'c'},
+		{prob: 0.12, sym: 'g'},
+		{prob: 0.27, sym: 't'},
+		{prob: 0.02, sym: 'B'},
+		{prob: 0.02, sym: 'D'},
+		{prob: 0.02, sym: 'H'},
+		{prob: 0.02, sym: 'K'},
+		{prob: 0.02, sym: 'M'},
+		{prob: 0.02, sym: 'N'},
+		{prob: 0.02, sym: 'R'},
+		{prob: 0.02, sym: 'S'},
+		{prob: 0.02, sym: 'V'},
+		{prob: 0.02, sym: 'W'},
+		{prob: 0.02, sym: 'Y'},
+	}
+
+	homosapiens := []fastaAcid{
+		{prob: 0.3029549426680, sym: 'a'},
+		{prob: 0.1979883004921, sym: 'c'},
+		{prob: 0.1975473066391, sym: 'g'},
+		{prob: 0.3015094502008, sym: 't'},
+	}
+
+	alu := []byte(
+		"GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGG" +
+			"GAGGCCGAGGCGGGCGGATCACCTGAGGTCAGGAGTTCGAGA" +
+			"CCAGCCTGGCCAACATGGTGAAACCCCGTCTCTACTAAAAAT" +
+			"ACAAAAATTAGCCGGGCGTGGTGGCGCGCGCCTGTAATCCCA" +
+			"GCTACTCGGGAGGCTGAGGCAGGAGAATCGCTTGAACCCGGG" +
+			"AGGCGGAGGTTGCAGTGAGCCGAGATCGCGCCACTGCACTCC" +
+			"AGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAA")
+
+	out.WriteString(">ONE Homo sapiens alu\n")
+	fastaRepeat(&out, alu, 2*n)
+	out.WriteString(">TWO IUB ambiguity codes\n")
+	fastaRandom(&out, iub, 3*n)
+	out.WriteString(">THREE Homo sapiens frequency\n")
+	fastaRandom(&out, homosapiens, 5*n)
+	return out
+}
+
+type fastaBuffer []byte
+
+func (b *fastaBuffer) Flush() {
+	panic("flush")
+}
+
+func (b *fastaBuffer) WriteString(s string) {
+	p := b.NextWrite(len(s))
+	copy(p, s)
+}
+
+func (b *fastaBuffer) NextWrite(n int) []byte {
+	p := *b
+	if len(p)+n > cap(p) {
+		b.Flush()
+		p = *b
+	}
+	out := p[len(p) : len(p)+n]
+	*b = p[:len(p)+n]
+	return out
+}
+
+const fastaLine = 60
+
+func fastaRepeat(out *fastaBuffer, alu []byte, n int) {
+	buf := append(alu, alu...)
+	off := 0
+	for n > 0 {
+		m := n
+		if m > fastaLine {
+			m = fastaLine
+		}
+		buf1 := out.NextWrite(m + 1)
+		copy(buf1, buf[off:])
+		buf1[m] = '\n'
+		if off += m; off >= len(alu) {
+			off -= len(alu)
+		}
+		n -= m
+	}
+}
+
+const (
+	fastaLookupSize          = 4096
+	fastaLookupScale float64 = fastaLookupSize - 1
+)
+
+var fastaRand uint32 = 42
+
+type fastaAcid struct {
+	sym   byte
+	prob  float64
+	cprob float64
+	next  *fastaAcid
+}
+
+func fastaComputeLookup(acid []fastaAcid) *[fastaLookupSize]*fastaAcid {
+	var lookup [fastaLookupSize]*fastaAcid
+	var p float64
+	for i := range acid {
+		p += acid[i].prob
+		acid[i].cprob = p * fastaLookupScale
+		if i > 0 {
+			acid[i-1].next = &acid[i]
+		}
+	}
+	acid[len(acid)-1].cprob = 1.0 * fastaLookupScale
+
+	j := 0
+	for i := range lookup {
+		for acid[j].cprob < float64(i) {
+			j++
+		}
+		lookup[i] = &acid[j]
+	}
+
+	return &lookup
+}
+
+func fastaRandom(out *fastaBuffer, acid []fastaAcid, n int) {
+	const (
+		IM = 139968
+		IA = 3877
+		IC = 29573
+	)
+	lookup := fastaComputeLookup(acid)
+	for n > 0 {
+		m := n
+		if m > fastaLine {
+			m = fastaLine
+		}
+		buf := out.NextWrite(m + 1)
+		f := fastaLookupScale / IM
+		myrand := fastaRand
+		for i := 0; i < m; i++ {
+			myrand = (myrand*IA + IC) % IM
+			r := float64(int(myrand)) * f
+			a := lookup[int(r)]
+			for a.cprob < r {
+				a = a.next
+			}
+			buf[i] = a.sym
+		}
+		fastaRand = myrand
+		buf[m] = '\n'
+		n -= m
+	}
+}