Mercurial > repos > dawe > srf2fastq
annotate srf2fastq/io_lib-1.12.2/io_lib/files.c @ 0:d901c9f41a6a default tip
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
author | dawe |
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date | Tue, 07 Jun 2011 17:48:05 -0400 |
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1 /* |
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2 * Copyright (c) Medical Research Council 1994. All rights reserved. |
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3 * |
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4 * Permission to use, copy, modify and distribute this software and its |
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5 * documentation for any purpose is hereby granted without fee, provided that |
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6 * this copyright and notice appears in all copies. |
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7 * |
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8 * This file was written by James Bonfield, Simon Dear, Rodger Staden, |
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9 * as part of the Staden Package at the MRC Laboratory of Molecular |
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10 * Biology, Hills Road, Cambridge, CB2 2QH, United Kingdom. |
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11 * |
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12 * MRC disclaims all warranties with regard to this software. |
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13 */ |
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14 |
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15 #include "io_lib/misc.h" |
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16 |
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17 #include <sys/types.h> |
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18 #include <sys/stat.h> |
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19 /* Alliant's Concentrix <sys/stat.h> is hugely deficient */ |
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20 /* Define things we require in this program */ |
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21 /* Methinks S_IFMT and S_IFDIR aren't defined in POSIX */ |
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22 #ifndef S_ISDIR |
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23 #define S_ISDIR(m) (((m)&S_IFMT) == S_IFDIR) |
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24 #endif /*!S_ISDIR*/ |
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25 #ifndef S_ISREG |
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26 #define S_ISREG(m) (((m)&S_IFMT) == S_IFREG) |
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27 #endif /*!S_ISREG*/ |
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28 |
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29 int is_directory(char * fn) |
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30 { |
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31 struct stat buf; |
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32 if ( stat(fn,&buf) ) return 0; |
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33 return S_ISDIR(buf.st_mode); |
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34 } |
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35 |
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36 int is_file(char * fn) |
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37 { |
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38 struct stat buf; |
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39 if ( stat(fn,&buf) ) return 0; |
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40 return S_ISREG(buf.st_mode); |
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41 } |
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42 |
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43 int file_exists(char * fn) |
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44 { |
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45 struct stat buf; |
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46 return ( stat(fn,&buf) == 0); |
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47 } |
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48 |
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49 int compressed_file_exists(char *fname) |
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50 { |
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51 struct stat buf; |
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52 char fn[2048]; |
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53 |
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54 if (stat(fname, &buf) == 0) return 1; |
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55 |
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56 sprintf(fn, "%s.gz", fname); |
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57 if (stat(fn, &buf) == 0) return 1; |
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58 |
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59 sprintf(fn, "%s.bz", fname); |
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60 if (stat(fn, &buf) == 0) return 1; |
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61 |
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62 sprintf(fn, "%s.bz2", fname); |
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63 if (stat(fn, &buf) == 0) return 1; |
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64 |
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65 sprintf(fn, "%s.Z", fname); |
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66 if (stat(fn, &buf) == 0) return 1; |
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67 |
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68 sprintf(fn, "%s.z", fname); |
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69 if (stat(fn, &buf) == 0) return 1; |
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70 |
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71 return 0; |
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72 } |
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73 |
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74 int file_size(char * fn) |
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75 { |
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76 struct stat buf; |
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77 if ( stat(fn,&buf) != 0) return 0; |
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78 return buf.st_size; |
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79 } |
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80 |
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81 /* |
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82 * --------------------------------------------------------------------------- |
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83 * File of filename management |
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84 */ |
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85 |
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86 FILE *open_fofn(char *files) { |
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87 return fopen(files, "r"); |
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88 } |
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89 |
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90 char *read_fofn(FILE *fp) { |
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91 char line[256]; |
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92 static char name[256]; |
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93 |
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94 while (fgets(line, 254, fp)) { |
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95 if (1 == sscanf(line, "%s", name)) |
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96 return name; |
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97 } |
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98 |
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99 return NULL; |
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100 } |
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101 |
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102 void close_fofn(FILE *fp) { |
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103 fclose(fp); |
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104 } |
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105 |
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106 |
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107 /* |
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108 * --------------------------------------------------------------------------- |
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109 * Temporary file handling. |
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110 */ |
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111 |
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112 #ifdef _WIN32 |
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113 /* |
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114 * On UNIX systems we use tmpfile(). |
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115 * |
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116 * On windows this is broken because it always attempts to create files in |
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117 * the root directory of the current drive, and fails if the user does not |
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118 * have write permission. |
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119 * |
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120 * We can't wrap up mkstemp() either as that doesn't exist under windows. |
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121 * Instead we roll our own tmpfile() using the native windows API. |
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122 */ |
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123 #include <windows.h> |
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124 #include <winbase.h> |
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125 #include <stdio.h> |
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126 #include <io.h> |
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127 #include <fcntl.h> |
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128 #define _POSIX_ /* needed to get PATH_MAX */ |
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129 #include <limits.h> |
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130 |
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131 static void display_win_error(char *msg) { |
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132 LPVOID lpMsgBuf; |
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133 FormatMessage(FORMAT_MESSAGE_ALLOCATE_BUFFER | |
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134 FORMAT_MESSAGE_FROM_SYSTEM | |
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135 FORMAT_MESSAGE_IGNORE_INSERTS, |
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136 NULL, |
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137 GetLastError(), |
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138 0, /* Default language */ |
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139 (LPTSTR)&lpMsgBuf, /* Got to love void* to str casts! */ |
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140 0, NULL); |
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141 fprintf(stderr, "%s: error #%d, %s", msg, GetLastError(), lpMsgBuf); |
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142 LocalFree(lpMsgBuf); |
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143 } |
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144 |
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145 /* |
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146 * Creates a temporary file and returns a FILE pointer to it. |
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147 * The file will be automatically deleted when it is closed or the |
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148 * applicaton exits. |
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149 * |
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150 * Returns NULL on failure. |
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151 */ |
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152 FILE *tmpfile(void) { |
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153 DWORD ret; |
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154 char tmp_path[PATH_MAX], shrt_path[PATH_MAX]; |
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155 int fd; |
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156 FILE *fp; |
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157 |
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158 /* The Windows Way: get the temp directory and a file within it */ |
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159 ret = GetTempPath(PATH_MAX, tmp_path); |
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160 if (ret == 0 || ret > PATH_MAX) { |
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161 display_win_error("GetTempPath()"); |
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162 return NULL; |
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163 } |
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164 |
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165 if (0 == GetTempFileName(tmp_path, "fubar", 0, shrt_path)) { |
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166 display_win_error("GetTempFileName()"); |
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167 return NULL; |
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168 } |
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169 |
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170 /* |
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171 * O_TRUNC incase anyone has managed to inject data in the newly created |
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172 * file already via race-conditions. |
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173 * |
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174 * O_EXCL to (in theory) stop anyone else opening it and to die if someone |
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175 * beat us to it - although this appears to not actually work on Windows. |
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176 * |
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177 * O_TEMPORARY so that the file is removed on close. |
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178 */ |
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179 if (-1 == (fd = _open(shrt_path, O_RDWR | O_TRUNC | O_EXCL | |
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180 O_BINARY | O_TEMPORARY, 0600))) { |
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181 perror(shrt_path); |
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182 } |
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183 |
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184 /* Replace fd with FILE*. No need to close fd */ |
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185 if (NULL == (fp = _fdopen(fd, "r+b"))) { |
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186 perror(shrt_path); |
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187 } |
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188 |
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189 return fp; |
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190 } |
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191 |
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192 #endif /* _WIN32 */ |