--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ezBAMQC/src/htslib/cram/os.h	Thu Mar 24 17:12:52 2016 -0400
@@ -0,0 +1,308 @@
+/*
+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 <jkb@sanger.ac.uk>
+
+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_*/