206 lines
6.7 KiB
C
206 lines
6.7 KiB
C
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/*
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Copyright (c) 1993, 1995-2002 MEDICAL RESEARCH COUNCIL
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All rights reserved
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Redistribution and use in source and binary forms, with or without
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modification, are permitted provided that the following conditions are met:
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1 Redistributions of source code must retain the above copyright notice,
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this list of conditions and the following disclaimer.
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2 Redistributions in binary form must reproduce the above copyright notice,
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this list of conditions and the following disclaimer in the documentation
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and/or other materials provided with the distribution.
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3 Neither the name of the MEDICAL RESEARCH COUNCIL, THE LABORATORY OF
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MOLECULAR BIOLOGY nor the names of its contributors may be used to endorse or
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promote products derived from this software without specific prior written
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permission.
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THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
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ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
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WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
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DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
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ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
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(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
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LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON
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ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
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(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
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SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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*/
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/*
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Copyright (c) 2004, 2006, 2009-2011, 2013, 2017-2018 Genome Research Ltd.
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Author: James Bonfield <jkb@sanger.ac.uk>
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Redistribution and use in source and binary forms, with or without
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modification, are permitted provided that the following conditions are met:
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1. Redistributions of source code must retain the above copyright notice,
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this list of conditions and the following disclaimer.
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2. Redistributions in binary form must reproduce the above copyright notice,
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this list of conditions and the following disclaimer in the documentation
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and/or other materials provided with the distribution.
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3. Neither the names Genome Research Ltd and Wellcome Trust Sanger
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Institute nor the names of its contributors may be used to endorse or promote
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products derived from this software without specific prior written permission.
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THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS IS" AND
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ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
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WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
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DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH LTD OR CONTRIBUTORS BE LIABLE
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FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
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DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
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SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
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CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
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OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
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OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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*/
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/*
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* File: os.h
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*
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* Author:
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* MRC Laboratory of Molecular Biology
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* Hills Road
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* Cambridge CB2 2QH
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* United Kingdom
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*
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* Description: operating system specific type definitions
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*
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*/
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#ifndef CRAM_OS_H
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#define CRAM_OS_H
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#include <limits.h>
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#include <stdint.h>
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#include "../htslib/hts_endian.h"
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#ifdef __cplusplus
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extern "C" {
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#endif
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/*-----------------------------------------------------------------------------
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* Byte swapping macros
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*/
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/*
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* Our new swap runs at the same speed on Ultrix, but substantially faster
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* (300% for swap_int4, ~50% for swap_int2) on an Alpha (due to the lack of
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* decent 'char' support).
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*
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* They also have the ability to swap in situ (src == dst). Newer code now
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* relies on this so don't change back!
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*/
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#define iswap_int8(x) \
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(((x & 0x00000000000000ffLL) << 56) + \
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((x & 0x000000000000ff00LL) << 40) + \
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((x & 0x0000000000ff0000LL) << 24) + \
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((x & 0x00000000ff000000LL) << 8) + \
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((x & 0x000000ff00000000LL) >> 8) + \
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((x & 0x0000ff0000000000LL) >> 24) + \
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((x & 0x00ff000000000000LL) >> 40) + \
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((x & 0xff00000000000000LL) >> 56))
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#define iswap_int4(x) \
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(((x & 0x000000ff) << 24) + \
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((x & 0x0000ff00) << 8) + \
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((x & 0x00ff0000) >> 8) + \
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((x & 0xff000000) >> 24))
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#define iswap_int2(x) \
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(((x & 0x00ff) << 8) + \
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((x & 0xff00) >> 8))
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/*
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* Linux systems may use byteswap.h to get assembly versions of byte-swap
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* on intel systems. This can be as trivial as the bswap opcode, which works
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* out at over 2-times faster than iswap_int4 above.
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*/
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#if 0
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#if defined(__linux__)
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# include <byteswap.h>
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# undef iswap_int8
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# undef iswap_int4
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# undef iswap_int2
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# define iswap_int8 bswap_64
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# define iswap_int4 bswap_32
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# define iswap_int2 bswap_16
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#endif
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#endif
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/*
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* Macros to specify that data read in is of a particular endianness.
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* The macros here swap to the appropriate order for the particular machine
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* running the macro and return the new answer. These may also be used when
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* writing to a file to specify that we wish to write in (eg) big endian
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* format.
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*
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* This leads to efficient code as most of the time these macros are
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* trivial.
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*/
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#if defined(HTS_BIG_ENDIAN)
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#define le_int4(x) iswap_int4((x))
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#define le_int2(x) iswap_int2((x))
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#elif defined(HTS_LITTLE_ENDIAN)
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#define le_int4(x) (x)
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#define le_int2(x) (x)
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#else
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static inline uint32_t le_int4(uint32_t x) {
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return le_to_u32((uint8_t *) &x);
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}
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static inline uint16_t le_int2(uint16_t x) {
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return le_to_u16((uint8_t *) &x);
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}
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#endif
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/*-----------------------------------------------------------------------------
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* Operating system specifics.
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* These ought to be done by autoconf, but are legacy code.
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*/
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/*
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* SunOS 4.x
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* Even though we use the ANSI gcc, we make use the the standard SunOS 4.x
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* libraries and include files, which are non-ansi
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*/
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#if defined(__sun__) && !defined(__svr4__)
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#define SEEK_SET 0
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#define SEEK_CUR 1
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#define SEEK_END 2
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#endif
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/*
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* Microsoft Visual C++
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* Windows
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*/
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#if defined(_MSC_VER)
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#define popen _popen
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#define pclose _pclose
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#define ftruncate(fd,len) _chsize(fd,len)
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#endif
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/*
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* Microsoft Windows running MinGW
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*/
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#if defined(__MINGW32__)
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#include <io.h>
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#define mkdir(filename,mode) mkdir((filename))
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#define sysconf(x) 512
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#ifndef ftruncate
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# define ftruncate(fd,len) _chsize(fd,len)
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#endif
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#endif
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#ifdef __cplusplus
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}
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#endif
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#endif /* CRAM_OS_H */
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