another benchmark: reverse-complement

R=rsc
DELTA=682  (511 added, 171 deleted, 0 changed)
OCL=32725
CL=32727

test/bench/reverse-complement.c

+/*
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+    * 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.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ARE DISCLAIMED.  IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
+LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+POSSIBILITY OF SUCH DAMAGE.
+*/
+
+/*
+ * The Computer Language Benchmarks Game
+ * http://shootout.alioth.debian.org
+ *
+ * contributed by Bob W
+ */
+
+#include <stdio.h>
+#include <stdlib.h>
+
+#define JBFSIZE 82      // line input buffer size
+#define QBFSIZE 5200     // output buffer initial size
+#define Z16     "\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0"
+#define V32     "\0TVGH\0\0CD\0\0M\0KN\0\0\0YSA\0BW\0R\0\0\0\0\0\0"
+#define VALL    Z16 Z16 Z16 Z16 V32 V32 Z16 Z16 Z16 Z16 Z16 Z16 Z16 Z16
+
+int errex(char *s, int n) {      // error message+value, return 1
+  fprintf(stderr,"\n*** Error: %s [%d]!\n", s, n);
+  return 1;
+}
+
+int main () {                    // ***** main *****
+  char *pj, *pq, *pr;            // buffer pointers: inp,out,/out
+  char *jjj = malloc(JBFSIZE);   // allocate input line buffer
+  char *qqq = malloc(QBFSIZE);   // output buffer (dyn. size)
+  char *pqstop = qqq+QBFSIZE;    // end-of-buffer pointer
+  char xtab[256] = VALL;         // char conversion table
+
+  if (!jjj || !qqq)
+    return errex("Buffer allocation", !jjj + !qqq);
+  pj = fgets(jjj,JBFSIZE,stdin);         // fetch 1st line
+  if (!pj)
+    return errex("No input data",0);
+  if (*jjj != '>')
+    return errex("1st char not '>'", 0);
+
+  while (pj) {                           // MAIN LOOP: process data
+    fputs(jjj, stdout);                  // output ID line
+
+    for (pq=qqq+1, pr=pqstop; ; pq++) {  // LOOP: fill output buffer
+      pj = fgets(jjj, JBFSIZE, stdin);   // get line from stdin
+      if (!pj || (*jjj=='>'))  break;    // EOF or new ID line
+      if (pr <= (pq+61)) {               // need to resize buffer
+        char *newstop = pqstop + 12777888;
+        char *newptr  = realloc(qqq, newstop-qqq);
+        if (!newptr)
+          return errex("Out of memory", 0);
+        if (newptr != qqq) {             // new base: adj. pointers
+          size_t x = newptr-qqq;         // offset for pointer update
+          pq+=x;  pr+=x;  qqq+=x;
+          newstop+=x;  pqstop+=x;
+        }
+        pr = __builtin_memmove(newstop-(pqstop-pr), pr, pqstop-pr);
+        pqstop = newstop;                // buffer resize complete
+      }
+      while (*pj) {                      // LOOP: conv. & revert line
+        char c = xtab[(unsigned char)(*pj++)];
+        if (c)                           // conversion valid
+          *(--pr) = c;
+      }
+    }
+
+    for (pq = qqq; pr<pqstop; ) {        // LOOP: format output
+      size_t x = (pqstop-pr)<60 ? pqstop-pr : 60;
+      __builtin_memmove(pq,pr,x);        // move line to free space
+      pr+=x;  pq+=x;  *(pq++) = 0xA;     // adjust pointers, add LF
+    }
+    fwrite(qqq, 1, pq-qqq, stdout);      // output converted data
+  }
+  return 0;
+}

test/bench/reverse-complement.go

+/*
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+    * 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.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ARE DISCLAIMED.  IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
+LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+POSSIBILITY OF SUCH DAMAGE.
+*/
+
+/* The Computer Language Benchmarks Game
+ * http://shootout.alioth.debian.org/
+ *
+ * contributed by The Go Authors.
+ */
+
+package main
+
+import (
+	"bufio";
+	"bytes";
+	"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',
+}
+
+var in *bufio.Reader
+
+func reverseComplement(in []byte) []byte {
+	outLen := len(in) + (len(in) + lineSize -1)/lineSize;
+	out := make([]byte, outLen);
+	j := 0;
+	k := 0;
+	for i := len(in)-1; i >= 0; i-- {
+		if k == lineSize {
+			out[j] = '\n';
+			j++;
+			k = 0;
+		}
+		out[j] = complement[in[i]];
+		j++;
+		k++;
+	}
+	out[j] = '\n';
+	j++;
+	return out[0:j];
+}
+
+func output(buf []byte) {
+	if len(buf) == 0 {
+		return
+	}
+	os.Stdout.Write(reverseComplement(buf));
+}
+
+func main() {
+	in = bufio.NewReader(os.Stdin);
+	buf := make([]byte, 100*1024);
+	top := 0;
+	for {
+		line, err := in.ReadLineSlice('\n');
+		if err != nil {
+			break
+		}
+		if line[0] == '>' {
+			if top > 0 {
+				output(buf[0:top]);
+				top = 0;
+			}
+			os.Stdout.Write(line);
+			continue
+		}
+		line = line[0:len(line)-1];	// drop newline
+		if top+len(line) > len(buf) {
+			nbuf := make([]byte, 2*len(buf) + 1024*(100+len(line)));
+			bytes.Copy(nbuf, buf[0:top]);
+			buf = nbuf;
+		}
+		bytes.Copy(buf[top:len(buf)], line);
+		top += len(line);
+	}
+	output(buf[0:top]);
+}

test/bench/timing.log

@@ -11,3 +11,8 @@ fasta -n 25000000
 	6g	13.50u 0.02s 13.53r
 	6g -B	12.99u 0.02s 13.02r
 
+reverse-complement < output-of-fasta-25000000
+	[gcc -O2 reverse-complement.c	2.03u 0.84s 13.04r]
+	gccgo -O2	6.47u 1.14s 15.58r
+	6g	6.55u 1.21s 15.45r
+	6g -B	6.19u 1.26s 15.64r