c_cpp/lib/htslib/cram/os.h

   1 /*
   2 Copyright (c) 1993, 1995-2002 MEDICAL RESEARCH COUNCIL
   3 All rights reserved
   4
   5 Redistribution and use in source and binary forms, with or without
   6 modification, are permitted provided that the following conditions are met:
   7
   8    1 Redistributions of source code must retain the above copyright notice,
   9 this list of conditions and the following disclaimer.
  10
  11    2 Redistributions in binary form must reproduce the above copyright notice,
  12 this list of conditions and the following disclaimer in the documentation
  13 and/or other materials provided with the distribution.
  14
  15    3 Neither the name of the MEDICAL RESEARCH COUNCIL, THE LABORATORY OF
  16 MOLECULAR BIOLOGY nor the names of its contributors may be used to endorse or
  17 promote products derived from this software without specific prior written
  18 permission.
  19
  20 THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
  21 ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
  22 WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
  23 DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
  24 ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
  25 (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
  26 LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON
  27 ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
  28 (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
  29 SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
  30 */
  31
  32 /*
  33 Copyright (c) 2004, 2006, 2009-2011, 2013, 2017 Genome Research Ltd.
  34 Author: James Bonfield <jkb@sanger.ac.uk>
  35
  36 Redistribution and use in source and binary forms, with or without
  37 modification, are permitted provided that the following conditions are met:
  38
  39    1. Redistributions of source code must retain the above copyright notice,
  40 this list of conditions and the following disclaimer.
  41
  42    2. Redistributions in binary form must reproduce the above copyright notice,
  43 this list of conditions and the following disclaimer in the documentation
  44 and/or other materials provided with the distribution.
  45
  46    3. Neither the names Genome Research Ltd and Wellcome Trust Sanger
  47 Institute nor the names of its contributors may be used to endorse or promote
  48 products derived from this software without specific prior written permission.
  49
  50 THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS IS" AND
  51 ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
  52 WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
  53 DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH LTD OR CONTRIBUTORS BE LIABLE
  54 FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
  55 DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
  56 SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
  57 CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
  58 OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
  59 OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
  60 */
  61
  62 /*
  63  * File: os.h
  64  *
  65  * Author:
  66  *         MRC Laboratory of Molecular Biology
  67  *         Hills Road
  68  *         Cambridge CB2 2QH
  69  *         United Kingdom
  70  *
  71  * Description: operating system specific type definitions
  72  *
  73  */
  74
  75 #ifndef _OS_H_
  76 #define _OS_H_
  77
  78 #include <limits.h>
  79 #include <inttypes.h>
  80 #include "htslib/hts_endian.h"
  81
  82 #ifdef __cplusplus
  83 extern "C" {
  84 #endif
  85
  86
  87 /*-----------------------------------------------------------------------------
  88  * Byte swapping macros
  89  */
  90
  91 /*
  92  * Our new swap runs at the same speed on Ultrix, but substantially faster
  93  * (300% for swap_int4, ~50% for swap_int2) on an Alpha (due to the lack of
  94  * decent 'char' support).
  95  *
  96  * They also have the ability to swap in situ (src == dst). Newer code now
  97  * relies on this so don't change back!
  98  */
  99 #define iswap_int8(x) \
 100     (((x & 0x00000000000000ffLL) << 56) + \
 101      ((x & 0x000000000000ff00LL) << 40) + \
 102      ((x & 0x0000000000ff0000LL) << 24) + \
 103      ((x & 0x00000000ff000000LL) <<  8) + \
 104      ((x & 0x000000ff00000000LL) >>  8) + \
 105      ((x & 0x0000ff0000000000LL) >> 24) + \
 106      ((x & 0x00ff000000000000LL) >> 40) + \
 107      ((x & 0xff00000000000000LL) >> 56))
 108
 109 #define iswap_int4(x) \
 110     (((x & 0x000000ff) << 24) + \
 111      ((x & 0x0000ff00) <<  8) + \
 112      ((x & 0x00ff0000) >>  8) + \
 113      ((x & 0xff000000) >> 24))
 114
 115 #define iswap_int2(x) \
 116     (((x & 0x00ff) << 8) + \
 117      ((x & 0xff00) >> 8))
 118
 119 /*
 120  * Linux systems may use byteswap.h to get assembly versions of byte-swap
 121  * on intel systems. This can be as trivial as the bswap opcode, which works
 122  * out at over 2-times faster than iswap_int4 above.
 123  */
 124 #if 0
 125 #if defined(__linux__)
 126 #    include <byteswap.h>
 127 #    undef iswap_int8
 128 #    undef iswap_int4
 129 #    undef iswap_int2
 130 #    define iswap_int8 bswap_64
 131 #    define iswap_int4 bswap_32
 132 #    define iswap_int2 bswap_16
 133 #endif
 134 #endif
 135
 136
 137 /*
 138  * Macros to specify that data read in is of a particular endianness.
 139  * The macros here swap to the appropriate order for the particular machine
 140  * running the macro and return the new answer. These may also be used when
 141  * writing to a file to specify that we wish to write in (eg) big endian
 142  * format.
 143  *
 144  * This leads to efficient code as most of the time these macros are
 145  * trivial.
 146  */
 147 #if defined(HTS_BIG_ENDIAN)
 148 #define le_int4(x) iswap_int4((x))
 149 #define le_int2(x) iswap_int2((x))
 150 #elif defined(HTS_LITTLE_ENDIAN)
 151 #define le_int4(x) (x)
 152 #define le_int2(x) (x)
 153 #else
 154 static inline uint32_t le_int4(uint32_t x) {
 155     return le_to_u32((uint8_t *) &x);
 156 }
 157 static inline uint16_t le_int2(uint16_t x) {
 158     return le_to_u16((uint8_t *) &x);
 159 }
 160 #endif
 161
 162 /*-----------------------------------------------------------------------------
 163  * <inttypes.h> definitions, incase they're not present
 164  */
 165
 166 #ifndef PRId64
 167 #define __PRI64__ "l"
 168 #define PRId64 __PRI64__ "d"
 169 #define PRId32 "d"
 170 #define PRId16 "d"
 171 #define PRId8  "d"
 172 #define PRIu64 __PRI64__ "u"
 173 #define PRIu32 "u"
 174 #define PRIu16 "u"
 175 #define PRIu8  "u"
 176 #endif
 177
 178 /*-----------------------------------------------------------------------------
 179  * Operating system specifics.
 180  * These ought to be done by autoconf, but are legacy code.
 181  */
 182 /*
 183  * SunOS 4.x
 184  * Even though we use the ANSI gcc, we make use the the standard SunOS 4.x
 185  * libraries and include files, which are non-ansi
 186  */
 187 #if defined(__sun__) && !defined(__svr4__)
 188 #define SEEK_SET 0
 189 #define SEEK_CUR 1
 190 #define SEEK_END 2
 191 #endif
 192
 193 /*
 194  * Microsoft Visual C++
 195  * Windows
 196  */
 197 #if defined(_MSC_VER)
 198 #define popen _popen
 199 #define pclose _pclose
 200 #define ftruncate(fd,len) _chsize(fd,len)
 201 #endif
 202
 203
 204 /*
 205  * Microsoft Windows running MinGW
 206  */
 207 #if defined(__MINGW32__)
 208 /* #define mkdir(filename,mode) mkdir((filename)) */
 209 #define sysconf(x) 512
 210 #define ftruncate(fd,len) _chsize(fd,len)
 211 #endif
 212
 213 /* Generic WIN32 API issues */
 214 #ifdef _WIN32
 215 #  ifndef HAVE_FSEEKO
 216 #    if __MSVCRT_VERSION__ >= 0x800
 217        /* if you have MSVCR80 installed then you can use these definitions: */
 218 #      define off_t __int64
 219 #      define fseeko _fseeki64
 220 #      define ftello _ftelli64
 221 #    else
 222        /* otherwise we're stuck with 32-bit file support */
 223 #      define off_t long
 224 #      define fseeko fseek
 225 #      define ftello ftell
 226 #    endif
 227 #  endif /* !HAVE_FSEEKO */
 228 #endif /* _WIN32 */
 229
 230 #ifdef __cplusplus
 231 }
 232 #endif
 233
 234 #endif /*_OS_H_*/