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1 /* The MIT License
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2
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3 Copyright (c) 2008 Broad Institute / Massachusetts Institute of Technology
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4
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5 Permission is hereby granted, free of charge, to any person obtaining a copy
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6 of this software and associated documentation files (the "Software"), to deal
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7 in the Software without restriction, including without limitation the rights
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8 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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9 copies of the Software, and to permit persons to whom the Software is
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10 furnished to do so, subject to the following conditions:
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11
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12 The above copyright notice and this permission notice shall be included in
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13 all copies or substantial portions of the Software.
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14
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15 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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16 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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17 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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18 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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19 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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20 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
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21 THE SOFTWARE.
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22 */
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23
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24 #include <stdlib.h>
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25 #include <string.h>
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26 #include <stdio.h>
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27 #include <fcntl.h>
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28 #include <unistd.h>
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29 #include <errno.h>
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30 #include <sys/select.h>
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31 #include <sys/stat.h>
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32 #include "bgzf.h"
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33
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34 static const int WINDOW_SIZE = 64 * 1024;
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35
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36 static int bgzip_main_usage()
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37 {
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38 fprintf(stderr, "\n");
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39 fprintf(stderr, "Usage: bgzip [options] [file] ...\n\n");
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40 fprintf(stderr, "Options: -c write on standard output, keep original files unchanged\n");
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41 fprintf(stderr, " -d decompress\n");
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42 fprintf(stderr, " -f overwrite files without asking\n");
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43 fprintf(stderr, " -b INT decompress at virtual file pointer INT\n");
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44 fprintf(stderr, " -s INT decompress INT bytes in the uncompressed file\n");
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45 fprintf(stderr, " -h give this help\n");
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46 fprintf(stderr, "\n");
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47 return 1;
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48 }
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49
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50 static int write_open(const char *fn, int is_forced)
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51 {
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52 int fd = -1;
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53 char c;
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54 if (!is_forced) {
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55 if ((fd = open(fn, O_WRONLY | O_CREAT | O_TRUNC | O_EXCL, 0666)) < 0 && errno == EEXIST) {
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56 fprintf(stderr, "[bgzip] %s already exists; do you wish to overwrite (y or n)? ", fn);
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57 scanf("%c", &c);
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58 if (c != 'Y' && c != 'y') {
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59 fprintf(stderr, "[bgzip] not overwritten\n");
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60 exit(1);
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61 }
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62 }
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63 }
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64 if (fd < 0) {
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65 if ((fd = open(fn, O_WRONLY | O_CREAT | O_TRUNC, 0666)) < 0) {
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66 fprintf(stderr, "[bgzip] %s: Fail to write\n", fn);
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67 exit(1);
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68 }
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69 }
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70 return fd;
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71 }
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72
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73 static void fail(BGZF* fp)
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74 {
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75 fprintf(stderr, "Error: %s\n", fp->error);
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76 exit(1);
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77 }
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78
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79 int main(int argc, char **argv)
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80 {
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81 int c, compress, pstdout, is_forced;
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82 BGZF *fp;
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83 void *buffer;
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84 long start, end, size;
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85
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86 compress = 1; pstdout = 0; start = 0; size = -1; end = -1; is_forced = 0;
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87 while((c = getopt(argc, argv, "cdhfb:s:")) >= 0){
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88 switch(c){
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89 case 'h': return bgzip_main_usage();
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90 case 'd': compress = 0; break;
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91 case 'c': pstdout = 1; break;
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92 case 'b': start = atol(optarg); break;
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93 case 's': size = atol(optarg); break;
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94 case 'f': is_forced = 1; break;
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95 }
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96 }
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97 if (size >= 0) end = start + size;
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98 if (end >= 0 && end < start) {
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99 fprintf(stderr, "[bgzip] Illegal region: [%ld, %ld]\n", start, end);
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100 return 1;
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101 }
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102 if (compress == 1) {
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103 struct stat sbuf;
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104 int f_src = fileno(stdin);
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105 int f_dst = fileno(stdout);
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106
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107 if ( argc>optind )
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108 {
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109 if ( stat(argv[optind],&sbuf)<0 )
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110 {
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111 fprintf(stderr, "[bgzip] %s: %s\n", strerror(errno), argv[optind]);
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112 return 1;
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113 }
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114
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115 if ((f_src = open(argv[optind], O_RDONLY)) < 0) {
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116 fprintf(stderr, "[bgzip] %s: %s\n", strerror(errno), argv[optind]);
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117 return 1;
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118 }
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119
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120 if (pstdout)
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121 f_dst = fileno(stdout);
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122 else
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123 {
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124 char *name = malloc(strlen(argv[optind]) + 5);
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125 strcpy(name, argv[optind]);
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126 strcat(name, ".gz");
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127 f_dst = write_open(name, is_forced);
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128 if (f_dst < 0) return 1;
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129 free(name);
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130 }
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131 }
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132 else if (!pstdout && isatty(fileno((FILE *)stdout)) )
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133 return bgzip_main_usage();
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134
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135 fp = bgzf_fdopen(f_dst, "w");
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136 buffer = malloc(WINDOW_SIZE);
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137 while ((c = read(f_src, buffer, WINDOW_SIZE)) > 0)
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138 if (bgzf_write(fp, buffer, c) < 0) fail(fp);
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139 // f_dst will be closed here
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140 if (bgzf_close(fp) < 0) fail(fp);
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141 if (argc > optind && !pstdout) unlink(argv[optind]);
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142 free(buffer);
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143 close(f_src);
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144 return 0;
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145 } else {
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146 struct stat sbuf;
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147 int f_dst;
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148
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149 if ( argc>optind )
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150 {
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151 if ( stat(argv[optind],&sbuf)<0 )
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152 {
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153 fprintf(stderr, "[bgzip] %s: %s\n", strerror(errno), argv[optind]);
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154 return 1;
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155 }
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156 char *name;
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157 int len = strlen(argv[optind]);
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158 if ( strcmp(argv[optind]+len-3,".gz") )
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159 {
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160 fprintf(stderr, "[bgzip] %s: unknown suffix -- ignored\n", argv[optind]);
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161 return 1;
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162 }
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163 fp = bgzf_open(argv[optind], "r");
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164 if (fp == NULL) {
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165 fprintf(stderr, "[bgzip] Could not open file: %s\n", argv[optind]);
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166 return 1;
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167 }
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168
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169 if (pstdout) {
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170 f_dst = fileno(stdout);
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171 }
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172 else {
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173 name = strdup(argv[optind]);
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174 name[strlen(name) - 3] = '\0';
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175 f_dst = write_open(name, is_forced);
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176 free(name);
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177 }
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178 }
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179 else if (!pstdout && isatty(fileno((FILE *)stdin)) )
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180 return bgzip_main_usage();
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181 else
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182 {
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183 f_dst = fileno(stdout);
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184 fp = bgzf_fdopen(fileno(stdin), "r");
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185 if (fp == NULL) {
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186 fprintf(stderr, "[bgzip] Could not read from stdin: %s\n", strerror(errno));
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187 return 1;
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188 }
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189 }
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190 buffer = malloc(WINDOW_SIZE);
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191 if (bgzf_seek(fp, start, SEEK_SET) < 0) fail(fp);
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192 while (1) {
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193 if (end < 0) c = bgzf_read(fp, buffer, WINDOW_SIZE);
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194 else c = bgzf_read(fp, buffer, (end - start > WINDOW_SIZE)? WINDOW_SIZE:(end - start));
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195 if (c == 0) break;
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196 if (c < 0) fail(fp);
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197 start += c;
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198 write(f_dst, buffer, c);
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199 if (end >= 0 && start >= end) break;
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200 }
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201 free(buffer);
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202 if (bgzf_close(fp) < 0) fail(fp);
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203 if (!pstdout) unlink(argv[optind]);
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204 return 0;
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205 }
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206 }
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