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1 /*
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2 Copyright (c) 1993, 1995-2002 MEDICAL RESEARCH COUNCIL
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3 All rights reserved
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4
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5 Redistribution and use in source and binary forms, with or without
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6 modification, are permitted provided that the following conditions are met:
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7
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8 1 Redistributions of source code must retain the above copyright notice,
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9 this list of conditions and the following disclaimer.
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10
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11 2 Redistributions in binary form must reproduce the above copyright notice,
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12 this list of conditions and the following disclaimer in the documentation
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13 and/or other materials provided with the distribution.
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14
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15 3 Neither the name of the MEDICAL RESEARCH COUNCIL, THE LABORATORY OF
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16 MOLECULAR BIOLOGY nor the names of its contributors may be used to endorse or
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17 promote products derived from this software without specific prior written
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18 permission.
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19
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20 THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
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21 ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
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22 WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
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23 DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
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24 ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
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25 (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
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26 LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON
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27 ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
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28 (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
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29 SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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30 */
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31
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32 /*
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33 Copyright (c) 2004, 2006, 2009-2011, 2013 Genome Research Ltd.
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34 Author: James Bonfield <jkb@sanger.ac.uk>
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35
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36 Redistribution and use in source and binary forms, with or without
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37 modification, are permitted provided that the following conditions are met:
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38
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39 1. Redistributions of source code must retain the above copyright notice,
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40 this list of conditions and the following disclaimer.
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41
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42 2. Redistributions in binary form must reproduce the above copyright notice,
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43 this list of conditions and the following disclaimer in the documentation
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44 and/or other materials provided with the distribution.
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45
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46 3. Neither the names Genome Research Ltd and Wellcome Trust Sanger
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47 Institute nor the names of its contributors may be used to endorse or promote
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48 products derived from this software without specific prior written permission.
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49
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50 THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS IS" AND
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51 ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
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52 WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
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53 DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH LTD OR CONTRIBUTORS BE LIABLE
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54 FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
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55 DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
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56 SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
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57 CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
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58 OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
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59 OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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60 */
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61
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62 /*
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63 * File: os.h
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64 *
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65 * Author:
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66 * MRC Laboratory of Molecular Biology
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67 * Hills Road
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68 * Cambridge CB2 2QH
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69 * United Kingdom
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70 *
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71 * Description: operating system specific type definitions
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72 *
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73 */
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74
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75 #ifndef _OS_H_
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76 #define _OS_H_
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77
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78 #include <limits.h>
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79 #include <inttypes.h>
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80
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81 #ifdef __cplusplus
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82 extern "C" {
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83 #endif
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84
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85 /*-----------------------------------------------------------------------------
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86 * Detection of endianness. The main part of this is done in autoconf, but
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87 * for the case of MacOS FAT binaries we fall back on auto-sensing based on
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88 * processor type too.
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89 */
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90
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91 /* Set by autoconf */
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92 #define SP_LITTLE_ENDIAN
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93
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94 /* Mac FAT binaries or unknown. Auto detect based on CPU type */
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95 #if !defined(SP_BIG_ENDIAN) && !defined(SP_LITTLE_ENDIAN)
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96
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97 /*
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98 * x86 equivalents
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99 */
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100 #if defined(__i386__) || defined(__i386) || defined(__amd64__) || defined(__amd64) || defined(__x86_64__) || defined(__x86_64) || defined(__i686__) || defined(__i686)
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101 # if defined(SP_BIG_ENDIAN)
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102 # undef SP_BIG_ENDIAN
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103 # endif
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104 # define SP_LITTLE_ENDIAN
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105 #endif
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106
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107 /*
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108 * DEC Alpha
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109 */
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110 #if defined(__alpha__) || defined(__alpha)
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111 # if defined(SP_LITTLE_ENDIAN)
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112 # undef SP_LITTLE_ENDIAN
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113 # endif
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114 # define SP_BIG_ENDIAN
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115 #endif
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116
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117 /*
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118 * SUN Sparc
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119 */
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120 #if defined(__sparc__) || defined(__sparc)
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121 # if defined(SP_LITTLE_ENDIAN)
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122 # undef SP_LITTLE_ENDIAN
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123 # endif
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124 # define SP_BIG_ENDIAN
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125 #endif
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126
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127 /*
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128 * PowerPC
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129 */
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130 #if defined(__ppc__) || defined(__ppc)
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131 # if defined(SP_LITTLE_ENDIAN)
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132 # undef SP_LITTLE_ENDIAN
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133 # endif
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134 # define SP_BIG_ENDIAN
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135 #endif
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136
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137 /* Some catch-alls */
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138 #if defined(__LITTLE_ENDIAN__) || defined(__LITTLEENDIAN__)
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139 # define SP_LITTLE_ENDIAN
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140 #endif
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141
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142 #if defined(__BIG_ENDIAN__) || defined(__BIGENDIAN__)
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143 # define SP_BIG_ENDIAN
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144 #endif
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145
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146 #if defined(SP_BIG_ENDIAN) && defined(SP_LITTLE_ENDIAN)
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147 # error Both BIG and LITTLE endian defined. Fix os.h and/or Makefile
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148 #endif
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149
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150 #if !defined(SP_BIG_ENDIAN) && !defined(SP_LITTLE_ENDIAN)
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151 # error Neither BIG nor LITTLE endian defined. Fix os.h and/or Makefile
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152 #endif
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153
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154 #endif
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155
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156 /*-----------------------------------------------------------------------------
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157 * Allow for unaligned memory access. This is used in BAM code as the packed
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158 * structure has 4-byte cigar ints after the variable length name.
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159 *
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160 * Consider using AX_CHECK_ALIGNED_ACCESS_REQUIRED in autoconf.
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161 */
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162 #if defined(__i386__) || defined(__i386) || defined(__amd64__) || defined(__amd64) || defined(__x86_64__) || defined(__x86_64) || defined(__i686__) || defined(__i686)
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163 # define ALLOW_UAC
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164 #endif
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165
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166 /*-----------------------------------------------------------------------------
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167 * Byte swapping macros
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168 */
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169
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170 /*
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171 * Our new swap runs at the same speed on Ultrix, but substantially faster
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172 * (300% for swap_int4, ~50% for swap_int2) on an Alpha (due to the lack of
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173 * decent 'char' support).
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174 *
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175 * They also have the ability to swap in situ (src == dst). Newer code now
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176 * relies on this so don't change back!
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177 */
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178 #define iswap_int8(x) \
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179 (((x & 0x00000000000000ffLL) << 56) + \
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180 ((x & 0x000000000000ff00LL) << 40) + \
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181 ((x & 0x0000000000ff0000LL) << 24) + \
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182 ((x & 0x00000000ff000000LL) << 8) + \
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183 ((x & 0x000000ff00000000LL) >> 8) + \
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184 ((x & 0x0000ff0000000000LL) >> 24) + \
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185 ((x & 0x00ff000000000000LL) >> 40) + \
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186 ((x & 0xff00000000000000LL) >> 56))
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187
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188 #define iswap_int4(x) \
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189 (((x & 0x000000ff) << 24) + \
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190 ((x & 0x0000ff00) << 8) + \
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191 ((x & 0x00ff0000) >> 8) + \
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192 ((x & 0xff000000) >> 24))
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193
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194 #define iswap_int2(x) \
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195 (((x & 0x00ff) << 8) + \
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196 ((x & 0xff00) >> 8))
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197
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198 /*
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199 * Linux systems may use byteswap.h to get assembly versions of byte-swap
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200 * on intel systems. This can be as trivial as the bswap opcode, which works
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201 * out at over 2-times faster than iswap_int4 above.
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202 */
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203 #if 0
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204 #if defined(__linux__)
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205 # include <byteswap.h>
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206 # undef iswap_int8
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207 # undef iswap_int4
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208 # undef iswap_int2
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209 # define iswap_int8 bswap_64
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210 # define iswap_int4 bswap_32
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211 # define iswap_int2 bswap_16
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212 #endif
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213 #endif
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214
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215
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216 /*
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217 * Macros to specify that data read in is of a particular endianness.
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218 * The macros here swap to the appropriate order for the particular machine
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219 * running the macro and return the new answer. These may also be used when
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220 * writing to a file to specify that we wish to write in (eg) big endian
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221 * format.
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222 *
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223 * This leads to efficient code as most of the time these macros are
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224 * trivial.
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225 */
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226 #ifdef SP_BIG_ENDIAN
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227 #define le_int4(x) iswap_int4((x))
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228 #define le_int2(x) iswap_int2((x))
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229 #endif
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230
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231 #ifdef SP_LITTLE_ENDIAN
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232 #define le_int4(x) (x)
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233 #define le_int2(x) (x)
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234 #endif
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235
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236 /*-----------------------------------------------------------------------------
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237 * <inttypes.h> definitions, incase they're not present
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238 */
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239
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240 #ifndef PRId64
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241 #define __PRI64__ "l"
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242 #define PRId64 __PRI64__ "d"
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243 #define PRId32 "d"
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244 #define PRId16 "d"
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245 #define PRId8 "d"
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246 #define PRIu64 __PRI64__ "u"
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247 #define PRIu32 "u"
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248 #define PRIu16 "u"
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249 #define PRIu8 "u"
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250 #endif
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251
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252 /*-----------------------------------------------------------------------------
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253 * Operating system specifics.
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254 * These ought to be done by autoconf, but are legacy code.
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255 */
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256 /*
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257 * SunOS 4.x
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258 * Even though we use the ANSI gcc, we make use the the standard SunOS 4.x
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259 * libraries and include files, which are non-ansi
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260 */
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261 #if defined(__sun__) && !defined(__svr4__)
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262 #define SEEK_SET 0
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263 #define SEEK_CUR 1
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264 #define SEEK_END 2
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265 #endif
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266
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267 /*
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268 * Microsoft Visual C++
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269 * Windows
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270 */
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271 #if defined(_MSC_VER)
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272 #define popen _popen
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273 #define pclose _pclose
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274 #define ftruncate(fd,len) _chsize(fd,len)
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275 #endif
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276
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277
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278 /*
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279 * Microsoft Windows running MinGW
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280 */
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281 #if defined(__MINGW32__)
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282 /* #define mkdir(filename,mode) mkdir((filename)) */
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283 #define sysconf(x) 512
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284 #define ftruncate(fd,len) _chsize(fd,len)
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285 #endif
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286
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287 /* Generic WIN32 API issues */
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288 #ifdef _WIN32
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289 # ifndef HAVE_FSEEKO
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290 # if __MSVCRT_VERSION__ >= 0x800
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291 /* if you have MSVCR80 installed then you can use these definitions: */
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292 # define off_t __int64
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293 # define fseeko _fseeki64
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294 # define ftello _ftelli64
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295 # else
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296 /* otherwise we're stuck with 32-bit file support */
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297 # define off_t long
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298 # define fseeko fseek
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299 # define ftello ftell
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300 # endif
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301 # endif /* !HAVE_FSEEKO */
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302 #endif /* _WIN32 */
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303
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304 #ifdef __cplusplus
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305 }
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306 #endif
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307
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308 #endif /*_OS_H_*/
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