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/*
* unbwt.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
read_int(FILE *fp, saidx_t *n) {
unsigned char c[4];
size_t m = fread(c, sizeof(unsigned char), 4, fp);
if(m == 4) {
*n = (c[0] << 0) | (c[1] << 8) |
(c[2] << 16) | (c[3] << 24);
}
return m;
}
static
void
print_help(const char *progname, int status) {
fprintf(stderr,
"unbwt, an inverse burrows-wheeler transform program, version %s.\n",
divsufsort_version());
fprintf(stderr, "usage: %s INFILE OUTFILE\n\n", progname);
exit(status);
}
int
main(int argc, const char *argv[]) {
FILE *fp, *ofp;
const char *fname, *ofname;
sauchar_t *T;
saidx_t *A;
LFS_OFF_T n;
size_t m;
saidx_t pidx;
clock_t start, finish;
saint_t err, blocksize, 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) { print_help(argv[0], EXIT_FAILURE); }
/* Open a file for reading. */
if(strcmp(argv[1], "-") != 0) {
#if HAVE_FOPEN_S
if(fopen_s(&fp, fname = argv[1], "rb") != 0) {
#else
if((fp = LFS_FOPEN(fname = argv[1], "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;
}
/* Open a file for writing. */
if(strcmp(argv[2], "-") != 0) {
#if HAVE_FOPEN_S
if(fopen_s(&ofp, ofname = argv[2], "wb") != 0) {
#else
if((ofp = LFS_FOPEN(ofname = argv[2], "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;
}
/* Read the blocksize. */
if(read_int(fp, &blocksize) != 4) {
fprintf(stderr, "%s: Cannot read from `%s': ", argv[0], fname);
perror(NULL);
exit(EXIT_FAILURE);
}
/* Allocate 5blocksize bytes of memory. */
T = (sauchar_t *)malloc(blocksize * sizeof(sauchar_t));
A = (saidx_t *)malloc(blocksize * sizeof(saidx_t));
if((T == NULL) || (A == NULL)) {
fprintf(stderr, "%s: Cannot allocate memory.\n", argv[0]);
exit(EXIT_FAILURE);
}
fprintf(stderr, "UnBWT (blocksize %" PRIdSAINT_T ") ... ", blocksize);
start = clock();
for(n = 0; (m = read_int(fp, &pidx)) != 0; n += m) {
/* Read blocksize bytes of data. */
if((m != 4) || ((m = fread(T, sizeof(sauchar_t), blocksize, fp)) == 0)) {
fprintf(stderr, "%s: %s `%s': ",
argv[0],
(ferror(fp) || !feof(fp)) ? "Cannot read from" : "Unexpected EOF in",
fname);
perror(NULL);
exit(EXIT_FAILURE);
}
/* Inverse Burrows-Wheeler Transform. */
if((err = inverse_bw_transform(T, T, A, m, pidx)) != 0) {
fprintf(stderr, "%s (reverseBWT): %s.\n",
argv[0],
(err == -1) ? "Invalid data" : "Cannot allocate memory");
exit(EXIT_FAILURE);
}
/* Write m bytes of data. */
if(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(A);
free(T);
return 0;
}
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