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binarytree_test.go
1.57
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fannkuch_test.go
1.47
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fasta_test.go
3.7
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fmt_test.go
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go.mod
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gob_test.go
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gzip_test.go
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http_test.go
960
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json_test.go
1.63
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jsondata_test.go
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mandel_test.go
848
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parser_test.go
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parserdata_test.go
19
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regexp_test.go
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revcomp_test.go
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time_test.go
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Code Editor : revcomp_test.go
// 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) } }
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