1 /* 2 * unbwt.c for libdivsufsort 3 * Copyright (c) 2003-2008 Yuta Mori All Rights Reserved. 4 * 5 * Permission is hereby granted, free of charge, to any person 6 * obtaining a copy of this software and associated documentation 7 * files (the "Software"), to deal in the Software without 8 * restriction, including without limitation the rights to use, 9 * copy, modify, merge, publish, distribute, sublicense, and/or sell 10 * copies of the Software, and to permit persons to whom the 11 * Software is furnished to do so, subject to the following 12 * conditions: 13 * 14 * The above copyright notice and this permission notice shall be 15 * included in all copies or substantial portions of the Software. 16 * 17 * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, 18 * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES 19 * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND 20 * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT 21 * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, 22 * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING 23 * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR 24 * OTHER DEALINGS IN THE SOFTWARE. 25 */ 26 27 #if HAVE_CONFIG_H 28 # include "config.h" 29 #endif 30 #include <stdio.h> 31 #if HAVE_STRING_H 32 # include <string.h> 33 #endif 34 #if HAVE_STDLIB_H 35 # include <stdlib.h> 36 #endif 37 #if HAVE_MEMORY_H 38 # include <memory.h> 39 #endif 40 #if HAVE_STDDEF_H 41 # include <stddef.h> 42 #endif 43 #if HAVE_STRINGS_H 44 # include <strings.h> 45 #endif 46 #if HAVE_SYS_TYPES_H 47 # include <sys/types.h> 48 #endif 49 #if HAVE_IO_H && HAVE_FCNTL_H 50 # include <io.h> 51 # include <fcntl.h> 52 #endif 53 #include <time.h> 54 #include <divsufsort.h> 55 #include "lfs.h" 56 57 58 static 59 size_t 60 read_int(FILE *fp, saidx_t *n) { 61 unsigned char c[4]; 62 size_t m = fread(c, sizeof(unsigned char), 4, fp); 63 if(m == 4) { 64 *n = (c[0] << 0) | (c[1] << 8) | 65 (c[2] << 16) | (c[3] << 24); 66 } 67 return m; 68 } 69 70 static 71 void 72 print_help(const char *progname, int status) { 73 fprintf(stderr, 74 "unbwt, an inverse burrows-wheeler transform program, version %s.\n", 75 divsufsort_version()); 76 fprintf(stderr, "usage: %s INFILE OUTFILE\n\n", progname); 77 exit(status); 78 } 79 80 int 81 main(int argc, const char *argv[]) { 82 FILE *fp, *ofp; 83 const char *fname, *ofname; 84 sauchar_t *T; 85 saidx_t *A; 86 LFS_OFF_T n; 87 size_t m; 88 saidx_t pidx; 89 clock_t start, finish; 90 saint_t err, blocksize, needclose = 3; 91 92 /* Check arguments. */ 93 if((argc == 1) || 94 (strcmp(argv[1], "-h") == 0) || 95 (strcmp(argv[1], "--help") == 0)) { print_help(argv[0], EXIT_SUCCESS); } 96 if(argc != 3) { print_help(argv[0], EXIT_FAILURE); } 97 98 /* Open a file for reading. */ 99 if(strcmp(argv[1], "-") != 0) { 100 #if HAVE_FOPEN_S 101 if(fopen_s(&fp, fname = argv[1], "rb") != 0) { 102 #else 103 if((fp = LFS_FOPEN(fname = argv[1], "rb")) == NULL) { 104 #endif 105 fprintf(stderr, "%s: Cannot open file `%s': ", argv[0], fname); 106 perror(NULL); 107 exit(EXIT_FAILURE); 108 } 109 } else { 110 #if HAVE__SETMODE && HAVE__FILENO 111 if(_setmode(_fileno(stdin), _O_BINARY) == -1) { 112 fprintf(stderr, "%s: Cannot set mode: ", argv[0]); 113 perror(NULL); 114 exit(EXIT_FAILURE); 115 } 116 #endif 117 fp = stdin; 118 fname = "stdin"; 119 needclose ^= 1; 120 } 121 122 /* Open a file for writing. */ 123 if(strcmp(argv[2], "-") != 0) { 124 #if HAVE_FOPEN_S 125 if(fopen_s(&ofp, ofname = argv[2], "wb") != 0) { 126 #else 127 if((ofp = LFS_FOPEN(ofname = argv[2], "wb")) == NULL) { 128 #endif 129 fprintf(stderr, "%s: Cannot open file `%s': ", argv[0], ofname); 130 perror(NULL); 131 exit(EXIT_FAILURE); 132 } 133 } else { 134 #if HAVE__SETMODE && HAVE__FILENO 135 if(_setmode(_fileno(stdout), _O_BINARY) == -1) { 136 fprintf(stderr, "%s: Cannot set mode: ", argv[0]); 137 perror(NULL); 138 exit(EXIT_FAILURE); 139 } 140 #endif 141 ofp = stdout; 142 ofname = "stdout"; 143 needclose ^= 2; 144 } 145 146 /* Read the blocksize. */ 147 if(read_int(fp, &blocksize) != 4) { 148 fprintf(stderr, "%s: Cannot read from `%s': ", argv[0], fname); 149 perror(NULL); 150 exit(EXIT_FAILURE); 151 } 152 153 /* Allocate 5blocksize bytes of memory. */ 154 T = (sauchar_t *)malloc(blocksize * sizeof(sauchar_t)); 155 A = (saidx_t *)malloc(blocksize * sizeof(saidx_t)); 156 if((T == NULL) || (A == NULL)) { 157 fprintf(stderr, "%s: Cannot allocate memory.\n", argv[0]); 158 exit(EXIT_FAILURE); 159 } 160 161 fprintf(stderr, "UnBWT (blocksize %" PRIdSAINT_T ") ... ", blocksize); 162 start = clock(); 163 for(n = 0; (m = read_int(fp, &pidx)) != 0; n += m) { 164 /* Read blocksize bytes of data. */ 165 if((m != 4) || ((m = fread(T, sizeof(sauchar_t), blocksize, fp)) == 0)) { 166 fprintf(stderr, "%s: %s `%s': ", 167 argv[0], 168 (ferror(fp) || !feof(fp)) ? "Cannot read from" : "Unexpected EOF in", 169 fname); 170 perror(NULL); 171 exit(EXIT_FAILURE); 172 } 173 174 /* Inverse Burrows-Wheeler Transform. */ 175 if((err = inverse_bw_transform(T, T, A, m, pidx)) != 0) { 176 fprintf(stderr, "%s (reverseBWT): %s.\n", 177 argv[0], 178 (err == -1) ? "Invalid data" : "Cannot allocate memory"); 179 exit(EXIT_FAILURE); 180 } 181 182 /* Write m bytes of data. */ 183 if(fwrite(T, sizeof(sauchar_t), m, ofp) != m) { 184 fprintf(stderr, "%s: Cannot write to `%s': ", argv[0], ofname); 185 perror(NULL); 186 exit(EXIT_FAILURE); 187 } 188 } 189 if(ferror(fp)) { 190 fprintf(stderr, "%s: Cannot read from `%s': ", argv[0], fname); 191 perror(NULL); 192 exit(EXIT_FAILURE); 193 } 194 finish = clock(); 195 fprintf(stderr, "%" PRIdOFF_T " bytes: %.4f sec\n", 196 n, (double)(finish - start) / (double)CLOCKS_PER_SEC); 197 198 /* Close files */ 199 if(needclose & 1) { fclose(fp); } 200 if(needclose & 2) { fclose(ofp); } 201 202 /* Deallocate memory. */ 203 free(A); 204 free(T); 205 206 return 0; 207 } 208
