test/bench/reverse-complement.go

/*
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    * Redistributions of source code must retain the above copyright
    notice, this list of conditions and the following disclaimer.

    * Redistributions in binary form must reproduce the above copyright
    notice, this list of conditions and the following disclaimer in the
    documentation and/or other materials provided with the distribution.

    * Neither the name of "The Computer Language Benchmarks Game" nor the
    name of "The Computer Language Shootout Benchmarks" nor the names of
    its contributors may be used to endorse or promote products derived
    from this software without specific prior written permission.

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*/

/* The Computer Language Benchmarks Game
 * http://shootout.alioth.debian.org/
 *
 * contributed by The Go Authors.
 */

package main

import (
	"bufio"
	"os"
)

const lineSize = 60

var complement = [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 main() {
	in := bufio.NewReader(os.Stdin)
	buf := make([]byte, 1024*1024)
	line, err := in.ReadSlice('\n')
	for err == nil {
		os.Stdout.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] = complement[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
		}
		os.Stdout.Write(buf[0:i])
	}
}