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/*
* bwt.c for libdivsufsort
* Copyright (c) 2003-2008 Yuta Mori All Rights Reserved.
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following
* conditions:
*
* The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
* OTHER DEALINGS IN THE SOFTWARE.
*/
#if HAVE_CONFIG_H
# include "config.h"
#endif
#include <stdio.h>
#if HAVE_STRING_H
# include <string.h>
#endif
#if HAVE_STDLIB_H
# include <stdlib.h>
#endif
#if HAVE_MEMORY_H
# include <memory.h>
#endif
#if HAVE_STDDEF_H
# include <stddef.h>
#endif
#if HAVE_STRINGS_H
# include <strings.h>
#endif
#if HAVE_SYS_TYPES_H
# include <sys/types.h>
#endif
#if HAVE_IO_H && HAVE_FCNTL_H
# include <io.h>
# include <fcntl.h>
#endif
#include <time.h>
#include <divsufsort.h>
#include "lfs.h"
static
size_t
write_int(FILE *fp, saidx_t n) {
unsigned char c[4];
c[0] = (unsigned char)((n >> 0) & 0xff), c[1] = (unsigned char)((n >> 8) & 0xff),
c[2] = (unsigned char)((n >> 16) & 0xff), c[3] = (unsigned char)((n >> 24) & 0xff);
return fwrite(c, sizeof(unsigned char), 4, fp);
}
static
void
print_help(const char *progname, int status) {
fprintf(stderr,
"bwt, a burrows-wheeler transform program, version %s.\n",
divsufsort_version());
fprintf(stderr, "usage: %s [-b num] INFILE OUTFILE\n", progname);
fprintf(stderr, " -b num set block size to num MiB [1..512] (default: 32)\n\n");
exit(status);
}
int
main(int argc, const char *argv[]) {
FILE *fp, *ofp;
const char *fname, *ofname;
sauchar_t *T;
saidx_t *SA;
LFS_OFF_T n;
size_t m;
saidx_t pidx;
clock_t start,finish;
saint_t i, blocksize = 32, needclose = 3;
/* Check arguments. */
if((argc == 1) ||
(strcmp(argv[1], "-h") == 0) ||
(strcmp(argv[1], "--help") == 0)) { print_help(argv[0], EXIT_SUCCESS); }
if((argc != 3) && (argc != 5)) { print_help(argv[0], EXIT_FAILURE); }
i = 1;
if(argc == 5) {
if(strcmp(argv[i], "-b") != 0) { print_help(argv[0], EXIT_FAILURE); }
blocksize = atoi(argv[i + 1]);
if(blocksize < 0) { blocksize = 1; }
else if(512 < blocksize) { blocksize = 512; }
i += 2;
}
blocksize <<= 20;
/* Open a file for reading. */
if(strcmp(argv[i], "-") != 0) {
#if HAVE_FOPEN_S
if(fopen_s(&fp, fname = argv[i], "rb") != 0) {
#else
if((fp = LFS_FOPEN(fname = argv[i], "rb")) == NULL) {
#endif
fprintf(stderr, "%s: Cannot open file `%s': ", argv[0], fname);
perror(NULL);
exit(EXIT_FAILURE);
}
} else {
#if HAVE__SETMODE && HAVE__FILENO
if(_setmode(_fileno(stdin), _O_BINARY) == -1) {
fprintf(stderr, "%s: Cannot set mode: ", argv[0]);
perror(NULL);
exit(EXIT_FAILURE);
}
#endif
fp = stdin;
fname = "stdin";
needclose ^= 1;
}
i += 1;
/* Open a file for writing. */
if(strcmp(argv[i], "-") != 0) {
#if HAVE_FOPEN_S
if(fopen_s(&ofp, ofname = argv[i], "wb") != 0) {
#else
if((ofp = LFS_FOPEN(ofname = argv[i], "wb")) == NULL) {
#endif
fprintf(stderr, "%s: Cannot open file `%s': ", argv[0], ofname);
perror(NULL);
exit(EXIT_FAILURE);
}
} else {
#if HAVE__SETMODE && HAVE__FILENO
if(_setmode(_fileno(stdout), _O_BINARY) == -1) {
fprintf(stderr, "%s: Cannot set mode: ", argv[0]);
perror(NULL);
exit(EXIT_FAILURE);
}
#endif
ofp = stdout;
ofname = "stdout";
needclose ^= 2;
}
/* Get the file size. */
if(LFS_FSEEK(fp, 0, SEEK_END) == 0) {
n = LFS_FTELL(fp);
rewind(fp);
if(n < 0) {
fprintf(stderr, "%s: Cannot ftell `%s': ", argv[0], fname);
perror(NULL);
exit(EXIT_FAILURE);
}
if(0x20000000L < n) { n = 0x20000000L; }
if((blocksize == 0) || (n < blocksize)) { blocksize = (saidx_t)n; }
} else if(blocksize == 0) { blocksize = 32 << 20; }
/* Allocate 5blocksize bytes of memory. */
T = (sauchar_t *)malloc(blocksize * sizeof(sauchar_t));
SA = (saidx_t *)malloc(blocksize * sizeof(saidx_t));
if((T == NULL) || (SA == NULL)) {
fprintf(stderr, "%s: Cannot allocate memory.\n", argv[0]);
exit(EXIT_FAILURE);
}
/* Write the blocksize. */
if(write_int(ofp, blocksize) != 4) {
fprintf(stderr, "%s: Cannot write to `%s': ", argv[0], ofname);
perror(NULL);
exit(EXIT_FAILURE);
}
fprintf(stderr, " BWT (blocksize %" PRIdSAINT_T ") ... ", blocksize);
start = clock();
for(n = 0; 0 < (m = fread(T, sizeof(sauchar_t), blocksize, fp)); n += m) {
/* Burrows-Wheeler Transform. */
pidx = divbwt(T, T, SA, m);
if(pidx < 0) {
fprintf(stderr, "%s (bw_transform): %s.\n",
argv[0],
(pidx == -1) ? "Invalid arguments" : "Cannot allocate memory");
exit(EXIT_FAILURE);
}
/* Write the bwted data. */
if((write_int(ofp, pidx) != 4) ||
(fwrite(T, sizeof(sauchar_t), m, ofp) != m)) {
fprintf(stderr, "%s: Cannot write to `%s': ", argv[0], ofname);
perror(NULL);
exit(EXIT_FAILURE);
}
}
if(ferror(fp)) {
fprintf(stderr, "%s: Cannot read from `%s': ", argv[0], fname);
perror(NULL);
exit(EXIT_FAILURE);
}
finish = clock();
fprintf(stderr, "%" PRIdOFF_T " bytes: %.4f sec\n",
n, (double)(finish - start) / (double)CLOCKS_PER_SEC);
/* Close files */
if(needclose & 1) { fclose(fp); }
if(needclose & 2) { fclose(ofp); }
/* Deallocate memory. */
free(SA);
free(T);
return 0;
}
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