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os.h
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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 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 
81 #ifdef __cplusplus
82 extern "C" {
83 #endif
84 
85 /*-----------------------------------------------------------------------------
86  * Detection of endianness. The main part of this is done in autoconf, but
87  * for the case of MacOS FAT binaries we fall back on auto-sensing based on
88  * processor type too.
89  */
90 
91 /* Set by autoconf */
92 #define SP_LITTLE_ENDIAN
93 
94 /* Mac FAT binaries or unknown. Auto detect based on CPU type */
95 #if !defined(SP_BIG_ENDIAN) && !defined(SP_LITTLE_ENDIAN)
96 
97 /*
98  * x86 equivalents
99  */
100 #if defined(__i386__) || defined(__i386) || defined(__amd64__) || defined(__amd64) || defined(__x86_64__) || defined(__x86_64) || defined(__i686__) || defined(__i686)
101 # if defined(SP_BIG_ENDIAN)
102 # undef SP_BIG_ENDIAN
103 # endif
104 # define SP_LITTLE_ENDIAN
105 #endif
106 
107 /*
108  * DEC Alpha
109  */
110 #if defined(__alpha__) || defined(__alpha)
111 # if defined(SP_LITTLE_ENDIAN)
112 # undef SP_LITTLE_ENDIAN
113 # endif
114 # define SP_BIG_ENDIAN
115 #endif
116 
117 /*
118  * SUN Sparc
119  */
120 #if defined(__sparc__) || defined(__sparc)
121 # if defined(SP_LITTLE_ENDIAN)
122 # undef SP_LITTLE_ENDIAN
123 # endif
124 # define SP_BIG_ENDIAN
125 #endif
126 
127 /*
128  * PowerPC
129  */
130 #if defined(__ppc__) || defined(__ppc)
131 # if defined(SP_LITTLE_ENDIAN)
132 # undef SP_LITTLE_ENDIAN
133 # endif
134 # define SP_BIG_ENDIAN
135 #endif
136 
137 /* Some catch-alls */
138 #if defined(__LITTLE_ENDIAN__) || defined(__LITTLEENDIAN__)
139 # define SP_LITTLE_ENDIAN
140 #endif
141 
142 #if defined(__BIG_ENDIAN__) || defined(__BIGENDIAN__)
143 # define SP_BIG_ENDIAN
144 #endif
145 
146 #if defined(SP_BIG_ENDIAN) && defined(SP_LITTLE_ENDIAN)
147 # error Both BIG and LITTLE endian defined. Fix os.h and/or Makefile
148 #endif
149 
150 #if !defined(SP_BIG_ENDIAN) && !defined(SP_LITTLE_ENDIAN)
151 # error Neither BIG nor LITTLE endian defined. Fix os.h and/or Makefile
152 #endif
153 
154 #endif
155 
156 /*-----------------------------------------------------------------------------
157  * Allow for unaligned memory access. This is used in BAM code as the packed
158  * structure has 4-byte cigar ints after the variable length name.
159  *
160  * Consider using AX_CHECK_ALIGNED_ACCESS_REQUIRED in autoconf.
161  */
162 #if defined(__i386__) || defined(__i386) || defined(__amd64__) || defined(__amd64) || defined(__x86_64__) || defined(__x86_64) || defined(__i686__) || defined(__i686)
163 # define ALLOW_UAC
164 #endif
165 
166 /*-----------------------------------------------------------------------------
167  * Byte swapping macros
168  */
169 
170 /*
171  * Our new swap runs at the same speed on Ultrix, but substantially faster
172  * (300% for swap_int4, ~50% for swap_int2) on an Alpha (due to the lack of
173  * decent 'char' support).
174  *
175  * They also have the ability to swap in situ (src == dst). Newer code now
176  * relies on this so don't change back!
177  */
178 #define iswap_int8(x) \
179  (((x & 0x00000000000000ffLL) << 56) + \
180  ((x & 0x000000000000ff00LL) << 40) + \
181  ((x & 0x0000000000ff0000LL) << 24) + \
182  ((x & 0x00000000ff000000LL) << 8) + \
183  ((x & 0x000000ff00000000LL) >> 8) + \
184  ((x & 0x0000ff0000000000LL) >> 24) + \
185  ((x & 0x00ff000000000000LL) >> 40) + \
186  ((x & 0xff00000000000000LL) >> 56))
187 
188 #define iswap_int4(x) \
189  (((x & 0x000000ff) << 24) + \
190  ((x & 0x0000ff00) << 8) + \
191  ((x & 0x00ff0000) >> 8) + \
192  ((x & 0xff000000) >> 24))
193 
194 #define iswap_int2(x) \
195  (((x & 0x00ff) << 8) + \
196  ((x & 0xff00) >> 8))
197 
198 /*
199  * Linux systems may use byteswap.h to get assembly versions of byte-swap
200  * on intel systems. This can be as trivial as the bswap opcode, which works
201  * out at over 2-times faster than iswap_int4 above.
202  */
203 #if 0
204 #if defined(__linux__)
205 # include <byteswap.h>
206 # undef iswap_int8
207 # undef iswap_int4
208 # undef iswap_int2
209 # define iswap_int8 bswap_64
210 # define iswap_int4 bswap_32
211 # define iswap_int2 bswap_16
212 #endif
213 #endif
214 
215 
216 /*
217  * Macros to specify that data read in is of a particular endianness.
218  * The macros here swap to the appropriate order for the particular machine
219  * running the macro and return the new answer. These may also be used when
220  * writing to a file to specify that we wish to write in (eg) big endian
221  * format.
222  *
223  * This leads to efficient code as most of the time these macros are
224  * trivial.
225  */
226 #ifdef SP_BIG_ENDIAN
227 #define le_int4(x) iswap_int4((x))
228 #define le_int2(x) iswap_int2((x))
229 #endif
230 
231 #ifdef SP_LITTLE_ENDIAN
232 #define le_int4(x) (x)
233 #define le_int2(x) (x)
234 #endif
235 
236 /*-----------------------------------------------------------------------------
237  * <inttypes.h> definitions, incase they're not present
238  */
239 
240 #ifndef PRId64
241 #define __PRI64__ "l"
242 #define PRId64 __PRI64__ "d"
243 #define PRId32 "d"
244 #define PRId16 "d"
245 #define PRId8 "d"
246 #define PRIu64 __PRI64__ "u"
247 #define PRIu32 "u"
248 #define PRIu16 "u"
249 #define PRIu8 "u"
250 #endif
251 
252 /*-----------------------------------------------------------------------------
253  * Operating system specifics.
254  * These ought to be done by autoconf, but are legacy code.
255  */
256 /*
257  * SunOS 4.x
258  * Even though we use the ANSI gcc, we make use the the standard SunOS 4.x
259  * libraries and include files, which are non-ansi
260  */
261 #if defined(__sun__) && !defined(__svr4__)
262 #define SEEK_SET 0
263 #define SEEK_CUR 1
264 #define SEEK_END 2
265 #endif
266 
267 /*
268  * Microsoft Visual C++
269  * Windows
270  */
271 #if defined(_MSC_VER)
272 #define popen _popen
273 #define pclose _pclose
274 #define ftruncate(fd,len) _chsize(fd,len)
275 #endif
276 
277 
278 /*
279  * Microsoft Windows running MinGW
280  */
281 #if defined(__MINGW32__)
282 /* #define mkdir(filename,mode) mkdir((filename)) */
283 #define sysconf(x) 512
284 #define ftruncate(fd,len) _chsize(fd,len)
285 #endif
286 
287 /* Generic WIN32 API issues */
288 #ifdef _WIN32
289 # ifndef HAVE_FSEEKO
290 # if __MSVCRT_VERSION__ >= 0x800
291  /* if you have MSVCR80 installed then you can use these definitions: */
292 # define off_t __int64
293 # define fseeko _fseeki64
294 # define ftello _ftelli64
295 # else
296  /* otherwise we're stuck with 32-bit file support */
297 # define off_t long
298 # define fseeko fseek
299 # define ftello ftell
300 # endif
301 # endif /* !HAVE_FSEEKO */
302 #endif /* _WIN32 */
303 
304 #ifdef __cplusplus
305 }
306 #endif
307 
308 #endif /*_OS_H_*/
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