annotate ezBAMQC/src/htslib/cram/os.h @ 17:161866cee2a2

wrapper rename

/*
Copyright (c) 1993, 1995-2002 MEDICAL RESEARCH COUNCIL
All rights reserved

Redistribution and use in source and binary forms, with or without 
modification, are permitted provided that the following conditions are met:

   1 Redistributions of source code must retain the above copyright notice, 
this list of conditions and the following disclaimer.

   2 Redistributions in binary form must reproduce the above copyright notice, 
this list of conditions and the following disclaimer in the documentation 
and/or other materials provided with the distribution.

   3 Neither the name of the MEDICAL RESEARCH COUNCIL, THE LABORATORY OF 
MOLECULAR BIOLOGY nor the names of its contributors may be used to endorse or 
promote products derived from this software without specific prior written 
permission.

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 
ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 
WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 
DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 
ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 
(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 
LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON 
ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 
(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 
SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
*/

/*
Copyright (c) 2004, 2006, 2009-2011, 2013 Genome Research Ltd.
Author: James Bonfield <[e-mail]>

Redistribution and use in source and binary forms, with or without 
modification, are permitted provided that the following conditions are met:

   1. Redistributions of source code must retain the above copyright notice, 
this list of conditions and the following disclaimer.

   2. Redistributions in binary form must reproduce the above copyright notice, 
this list of conditions and the following disclaimer in the documentation 
and/or other materials provided with the distribution.

   3. Neither the names Genome Research Ltd and Wellcome Trust Sanger
Institute nor the names of its contributors may be used to endorse or promote
products derived from this software without specific prior written permission.

THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS IS" AND 
ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 
WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 
DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH LTD OR CONTRIBUTORS BE LIABLE
FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
*/

/*
 * File: os.h
 *
 * Author: 
 *         MRC Laboratory of Molecular Biology
 *	   Hills Road
 *	   Cambridge CB2 2QH
 *	   United Kingdom
 *
 * Description: operating system specific type definitions
 *
 */

#ifndef _OS_H_
#define _OS_H_

#include <limits.h>
#include <inttypes.h>

#ifdef __cplusplus
extern "C" {
#endif

/*-----------------------------------------------------------------------------
 * Detection of endianness. The main part of this is done in autoconf, but
 * for the case of MacOS FAT binaries we fall back on auto-sensing based on
 * processor type too.
 */

/* Set by autoconf */
#define SP_LITTLE_ENDIAN

/* Mac FAT binaries or unknown. Auto detect based on CPU type */
#if !defined(SP_BIG_ENDIAN) && !defined(SP_LITTLE_ENDIAN)

/*
 * x86 equivalents
 */
#if defined(__i386__) || defined(__i386) || defined(__amd64__) || defined(__amd64) || defined(__x86_64__) || defined(__x86_64) || defined(__i686__) || defined(__i686)
#  if defined(SP_BIG_ENDIAN)
#    undef SP_BIG_ENDIAN
#  endif
#  define SP_LITTLE_ENDIAN
#endif

/*
 * DEC Alpha
 */
#if defined(__alpha__) || defined(__alpha)
#  if defined(SP_LITTLE_ENDIAN)
#    undef SP_LITTLE_ENDIAN
#  endif
#  define SP_BIG_ENDIAN
#endif

/*
 * SUN Sparc
 */
#if defined(__sparc__) || defined(__sparc)
#  if defined(SP_LITTLE_ENDIAN)
#    undef SP_LITTLE_ENDIAN
#  endif
#  define SP_BIG_ENDIAN
#endif

/*
 * PowerPC
 */
#if defined(__ppc__) || defined(__ppc)
#  if defined(SP_LITTLE_ENDIAN)
#    undef SP_LITTLE_ENDIAN
#  endif
#  define SP_BIG_ENDIAN
#endif

/* Some catch-alls */
#if defined(__LITTLE_ENDIAN__) || defined(__LITTLEENDIAN__)
#    define SP_LITTLE_ENDIAN
#endif

#if defined(__BIG_ENDIAN__) || defined(__BIGENDIAN__)
#    define SP_BIG_ENDIAN
#endif

#if defined(SP_BIG_ENDIAN) && defined(SP_LITTLE_ENDIAN)
#    error Both BIG and LITTLE endian defined. Fix os.h and/or Makefile
#endif

#if !defined(SP_BIG_ENDIAN) && !defined(SP_LITTLE_ENDIAN)
#    error Neither BIG nor LITTLE endian defined. Fix os.h and/or Makefile
#endif

#endif

/*-----------------------------------------------------------------------------
 * Allow for unaligned memory access. This is used in BAM code as the packed
 * structure has 4-byte cigar ints after the variable length name.
 *
 * Consider using AX_CHECK_ALIGNED_ACCESS_REQUIRED in autoconf.
 */
#if defined(__i386__) || defined(__i386) || defined(__amd64__) || defined(__amd64) || defined(__x86_64__) || defined(__x86_64) || defined(__i686__) || defined(__i686)
#  define ALLOW_UAC
#endif

/*-----------------------------------------------------------------------------
 * Byte swapping macros
 */

/*
 * Our new swap runs at the same speed on Ultrix, but substantially faster
 * (300% for swap_int4, ~50% for swap_int2) on an Alpha (due to the lack of
 * decent 'char' support).
 *
 * They also have the ability to swap in situ (src == dst). Newer code now
 * relies on this so don't change back!
 */
#define iswap_int8(x) \
    (((x & 0x00000000000000ffLL) << 56) + \
     ((x & 0x000000000000ff00LL) << 40) + \
     ((x & 0x0000000000ff0000LL) << 24) + \
     ((x & 0x00000000ff000000LL) <<  8) + \
     ((x & 0x000000ff00000000LL) >>  8) + \
     ((x & 0x0000ff0000000000LL) >> 24) + \
     ((x & 0x00ff000000000000LL) >> 40) + \
     ((x & 0xff00000000000000LL) >> 56))

#define iswap_int4(x) \
    (((x & 0x000000ff) << 24) + \
     ((x & 0x0000ff00) <<  8) + \
     ((x & 0x00ff0000) >>  8) + \
     ((x & 0xff000000) >> 24))

#define iswap_int2(x) \
    (((x & 0x00ff) << 8) + \
     ((x & 0xff00) >> 8))

/*
 * Linux systems may use byteswap.h to get assembly versions of byte-swap
 * on intel systems. This can be as trivial as the bswap opcode, which works
 * out at over 2-times faster than iswap_int4 above.
 */
#if 0
#if defined(__linux__)
#    include <byteswap.h>
#    undef iswap_int8
#    undef iswap_int4
#    undef iswap_int2
#    define iswap_int8 bswap_64
#    define iswap_int4 bswap_32
#    define iswap_int2 bswap_16
#endif
#endif


/*
 * Macros to specify that data read in is of a particular endianness.
 * The macros here swap to the appropriate order for the particular machine
 * running the macro and return the new answer. These may also be used when
 * writing to a file to specify that we wish to write in (eg) big endian
 * format.
 *
 * This leads to efficient code as most of the time these macros are
 * trivial.
 */
#ifdef SP_BIG_ENDIAN
#define le_int4(x) iswap_int4((x))
#define le_int2(x) iswap_int2((x))
#endif

#ifdef SP_LITTLE_ENDIAN
#define le_int4(x) (x)
#define le_int2(x) (x)
#endif

/*-----------------------------------------------------------------------------
 * <inttypes.h> definitions, incase they're not present
 */

#ifndef PRId64
#define __PRI64__ "l"
#define PRId64 __PRI64__ "d"
#define PRId32 "d"
#define PRId16 "d"
#define PRId8  "d"
#define PRIu64 __PRI64__ "u"
#define PRIu32 "u"
#define PRIu16 "u"
#define PRIu8  "u"
#endif

/*-----------------------------------------------------------------------------
 * Operating system specifics.
 * These ought to be done by autoconf, but are legacy code.
 */
/*
 * SunOS 4.x
 * Even though we use the ANSI gcc, we make use the the standard SunOS 4.x
 * libraries and include files, which are non-ansi
 */
#if defined(__sun__) && !defined(__svr4__)
#define SEEK_SET 0
#define SEEK_CUR 1
#define SEEK_END 2
#endif

/*
 * Microsoft Visual C++
 * Windows
 */
#if defined(_MSC_VER)
#define popen _popen
#define pclose _pclose
#define ftruncate(fd,len) _chsize(fd,len)
#endif


/*
 * Microsoft Windows running MinGW
 */
#if defined(__MINGW32__)
/* #define mkdir(filename,mode) mkdir((filename)) */
#define sysconf(x) 512
#define ftruncate(fd,len) _chsize(fd,len)
#endif

/* Generic WIN32 API issues */
#ifdef _WIN32
#  ifndef HAVE_FSEEKO
#    if __MSVCRT_VERSION__ >= 0x800
       /* if you have MSVCR80 installed then you can use these definitions: */
#      define off_t __int64
#      define fseeko _fseeki64
#      define ftello _ftelli64
#    else
       /* otherwise we're stuck with 32-bit file support */
#      define off_t long
#      define fseeko fseek
#      define ftello ftell
#    endif
#  endif /* !HAVE_FSEEKO */
#endif /* _WIN32 */

#ifdef __cplusplus
}
#endif

#endif /*_OS_H_*/