[med-svn] [plink2] 03/03: Merge tag 'upstream/2.00_a-170717'

[Dylan Aïssi]

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bob.dybian-guest pushed a commit to branch master
in repository plink2.

commit ed5ab13fe5508208f68dafad5098979356f59d55
Merge: a82312e 9bddd9c
Author: Dylan Aïssi <bob.dybian at gmail.com>
Date:   Tue Jul 18 23:32:13 2017 +0200

    Merge tag 'upstream/2.00_a-170717'
    
    Upstream version 2.00~a-170717

 LICENSE                               |   674 ++
 Python/ReadMe.md                      |     6 +
 Python/pgenlib.pyx                    |  1405 +++
 Python/python_api.txt                 |   216 +
 Python/setup.py                       |    26 +
 SFMT.c                                |   591 ++
 SFMT.h                                |   330 +
 bgzf.c                                |  1195 +++
 bgzf.h                                |   323 +
 build_dynamic/Makefile                |   128 +
 build_win/Makefile                    |    70 +
 hfile.c                               |   584 ++
 hfile.h                               |   216 +
 hfile_internal.h                      |    76 +
 hts.h                                 |   456 +
 hts_defs.h                            |    56 +
 khash.h                               |   621 ++
 pgen_compress.cpp                     |   242 +
 pgenlib_internal.cpp                  |  9604 +++++++++++++++++++
 pgenlib_internal.h                    |  2269 +++++
 pgenlib_python_support.cpp            |   501 +
 pgenlib_python_support.h              |    75 +
 plink2.cpp                            |  7728 ++++++++++++++++
 plink2_adjust.cpp                     |    41 +
 plink2_adjust.h                       |    61 +
 plink2_common.cpp                     |  6459 +++++++++++++
 plink2_common.h                       |  2508 +++++
 plink2_compress_stream.cpp            |   128 +
 plink2_compress_stream.h              |   103 +
 plink2_data.cpp                       | 15907 ++++++++++++++++++++++++++++++++
 plink2_data.h                         |   176 +
 plink2_decompress.cpp                 |   194 +
 plink2_decompress.h                   |    89 +
 plink2_filter.cpp                     |  2884 ++++++
 plink2_filter.h                       |    98 +
 plink2_glm.cpp                        |  6494 +++++++++++++
 plink2_glm.h                          |   112 +
 plink2_help.cpp                       |  1717 ++++
 plink2_help.h                         |    35 +
 plink2_ld.cpp                         |  1488 +++
 plink2_ld.h                           |    52 +
 plink2_matrix.cpp                     |  1256 +++
 plink2_matrix.h                       |   178 +
 plink2_matrix_calc.cpp                |  4221 +++++++++
 plink2_matrix_calc.h                  |   145 +
 plink2_misc.cpp                       |  3317 +++++++
 plink2_misc.h                         |   202 +
 plink2_psam.cpp                       |  1416 +++
 plink2_psam.h                         |    91 +
 plink2_pvar.cpp                       |  1584 ++++
 plink2_pvar.h                         |    76 +
 plink2_random.cpp                     |   118 +
 plink2_random.h                       |    46 +
 plink2_set.cpp                        |   408 +
 plink2_set.h                          |    39 +
 plink2_stats.cpp                      |  2102 +++++
 plink2_stats.h                        |    61 +
 zstd/lib/common/bitstream.h           |   417 +
 zstd/lib/common/entropy_common.c      |   221 +
 zstd/lib/common/entropy_common.o      |   Bin 0 -> 2816 bytes
 zstd/lib/common/error_private.c       |    43 +
 zstd/lib/common/error_private.h       |    76 +
 zstd/lib/common/error_private.o       |   Bin 0 -> 1868 bytes
 zstd/lib/common/fse.h                 |   694 ++
 zstd/lib/common/fse_decompress.c      |   328 +
 zstd/lib/common/fse_decompress.o      |   Bin 0 -> 5492 bytes
 zstd/lib/common/huf.h                 |   260 +
 zstd/lib/common/mem.h                 |   372 +
 zstd/lib/common/pool.c                |   194 +
 zstd/lib/common/pool.h                |    56 +
 zstd/lib/common/threading.c           |    80 +
 zstd/lib/common/threading.h           |   104 +
 zstd/lib/common/xxhash.c              |   869 ++
 zstd/lib/common/xxhash.h              |   305 +
 zstd/lib/common/xxhash.o              |   Bin 0 -> 6136 bytes
 zstd/lib/common/zstd_common.c         |    73 +
 zstd/lib/common/zstd_common.o         |   Bin 0 -> 1832 bytes
 zstd/lib/common/zstd_errors.h         |    74 +
 zstd/lib/common/zstd_internal.h       |   283 +
 zstd/lib/compress/fse_compress.c      |   857 ++
 zstd/lib/compress/fse_compress.o      |   Bin 0 -> 12312 bytes
 zstd/lib/compress/huf_compress.c      |   684 ++
 zstd/lib/compress/huf_compress.o      |   Bin 0 -> 12560 bytes
 zstd/lib/compress/zstd_compress.c     |  3387 +++++++
 zstd/lib/compress/zstd_compress.o     |   Bin 0 -> 200156 bytes
 zstd/lib/compress/zstd_opt.h          |   919 ++
 zstd/lib/compress/zstdmt_compress.c   |   739 ++
 zstd/lib/compress/zstdmt_compress.h   |    78 +
 zstd/lib/decompress/huf_decompress.c  |   885 ++
 zstd/lib/decompress/huf_decompress.o  |   Bin 0 -> 20100 bytes
 zstd/lib/decompress/zstd_decompress.c |  2480 +++++
 zstd/lib/decompress/zstd_decompress.o |   Bin 0 -> 34896 bytes
 zstd/lib/zstd.h                       |   765 ++
 zstd/zlibWrapper/BUCK                 |    22 +
 zstd/zlibWrapper/Makefile             |   107 +
 zstd/zlibWrapper/README.md            |   163 +
 zstd/zlibWrapper/example              |   Bin 0 -> 518704 bytes
 zstd/zlibWrapper/fitblk               |   Bin 0 -> 503724 bytes
 zstd/zlibWrapper/gzclose.c            |    28 +
 zstd/zlibWrapper/gzclose.o            |   Bin 0 -> 712 bytes
 zstd/zlibWrapper/gzcompatibility.h    |    67 +
 zstd/zlibWrapper/gzguts.h             |   227 +
 zstd/zlibWrapper/gzlib.c              |   640 ++
 zstd/zlibWrapper/gzlib.o              |   Bin 0 -> 5716 bytes
 zstd/zlibWrapper/gzread.c             |   670 ++
 zstd/zlibWrapper/gzread.o             |   Bin 0 -> 6608 bytes
 zstd/zlibWrapper/gzwrite.c            |   668 ++
 zstd/zlibWrapper/gzwrite.o            |   Bin 0 -> 7072 bytes
 zstd/zlibWrapper/minigzip             |   Bin 0 -> 518696 bytes
 zstd/zlibWrapper/zstd_zlibwrapper.c   |  1082 +++
 zstd/zlibWrapper/zstd_zlibwrapper.h   |    91 +
 zstd/zlibWrapper/zstd_zlibwrapper.o   |   Bin 0 -> 19464 bytes
 zstd/zlibWrapper/zwrapbench           |   Bin 0 -> 526244 bytes
 113 files changed, 100206 insertions(+)

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