Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Upstream-Name: PLINK 2
Upstream-Contact: Christopher Chang <chrchang@alumni.caltech.edu>
Source: https://www.cog-genomics.org/plink/2.0/
Comment: Exclude source code of the embedded zstd and libdeflate
Files-Excluded: zstd
                libdeflate

Files: *
Copyright: 2005-2020 Shaun Purcell <plink@chgr.mgh.harvard.edu>, Christopher Chang
License: GPL-3+

Files: pgenlibr/*
       cindex/*
Copyright: 2019-2020 Christopher Chang
License: LGPL-3+

Files: include/SFMT.*
Copyright: 2006-2012 Mutsuo Saito, Makoto Matsumoto, Hiroshima University and The University of Tokyo
License: BSD-3-clause

Files: include/pgenlib_ffi_support.*
       include/pgenlib_misc.*
       include/pgenlib_read.*
       include/pgenlib_write.*
       include/plink2_base.*
       include/plink2_bgzf.*
       plink2_cmdline.*
       plink2_common.*
       plink2_compress_stream.*
       plink2_decompress.*
       plink2_psam.h
       plink2_random.*
       include/plink2_stats.h
       include/plink2_string.*
       include/plink2_text.*
       include/plink2_thread.*
       include/plink2_zstfile.*
       include/pvar_ffi_support.*
Copyright: 2005-2020 Shaun Purcell, Christopher Chang
License: LGPL-3+

Files: plink2_glm.cc
Copyright: 2005-2020 Shaun Purcell, Christopher Chang
           2009-2014 Shigeo Mitsunari <herumi@nifty.com> from the fast math library function posted at https://github.com/herumi/fmath
License: GPL-3+ and BSD-3-Clause
Comment: Only the part of the fast math library in under BSD-3-Clause

Files: include/plink2_stats.cc
Copyright: 2005-2020 Shaun Purcell, Christopher Chang
License: GPL-3+ and BSL-1.0
Comment: Some portions are derived from the Boost library 1.60 (boost/math/special_functions/gamma.hpp
 and boost/math/special_functions/detail/igamma_inverse.hpp) which are under the BSL-1.0.

Files: plink2_cpu.cc
Copyright: 2016 Eric Biggers (libdeflate project)
           2019-2020 Christopher Chang
License: Expat

Files: debian/*
Copyright: 2017-2020 Dylan Aïssi <daissi@debian.org>
License: GPL-3+

License: GPL-3+
 This package is free software; you can redistribute it and/or modify
 it under the terms of the GNU General Public License as published by
 the Free Software Foundation; either version 3 of the License, or
 (at your option) any later version.
 .
 This package is distributed in the hope that it will be useful,
 but WITHOUT ANY WARRANTY; without even the implied warranty of
 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 GNU General Public License for more details.
 .
 You should have received a copy of the GNU General Public License
 along with this package; if not, write to the Free Software
 Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA  02110-1301 USA
 .
 On Debian systems, the complete text of the GNU General
 Public License can be found in `/usr/share/common-licenses/GPL-3'.

License: LGPL-3+
 This program is free software: you can redistribute it and/or modify it
 under the terms of the GNU Lesser General Public License as published by
 the Free Software Foundation; either version 3 of the License, or
 (at your option) any later version.
 .
 This program is distributed in the hope that it will be useful,
 but WITHOUT ANY WARRANTY; without even the implied warranty of
 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
 .
 On Debian systems you can find the full text of the GNU Lesser General
 Public License version 3 license at /usr/share/common-licenses/LGPL-3.

License: Expat
 Permission is hereby granted, free of charge, to any person obtaining
 a copy of this software and associated documentation files (the
 "Software"), to deal in the Software without restriction, including
 without limitation the rights to use, copy, modify, merge, publish,
 distribute, sublicense, and/or sell copies of the Software, and to
 permit persons to whom the Software is furnished to do so, subject to
 the following conditions:
 .
 The above copyright notice and this permission notice shall be included
 in all copies or substantial portions of the Software.
 .
 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
 EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
 MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
 IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY
 CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT,
 TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
 SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

License: BSD-3-clause
 Redistribution and use in source and binary forms, with or without
 modification, are permitted provided that the following conditions are met:
 .
    * Redistributions of source code must retain the above copyright notice,
      this list of conditions and the following disclaimer.
    * 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.
    *Neither the name of the copyright holder nor the names of its contributors
      may not 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.

License: BSL-1.0
 Boost Software License, Version 1.0
 .
 Permission is hereby granted, free of charge, to any person or organization
 obtaining a copy of the software and accompanying documentation covered by
 this license (the "Software") to use, reproduce, display, distribute,
 execute, and transmit the Software, and to prepare derivative works of the
 Software, and to permit third-parties to whom the Software is furnished to
 do so, all subject to the following:
 .
 The copyright notices in the Software and this entire statement, including
 the above license grant, this restriction and the following disclaimer,
 must be included in all copies of the Software, in whole or in part, and
 all derivative works of the Software, unless such copies or derivative
 works are solely in the form of machine-executable object code generated by
 a source language processor.
 .
 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
 FITNESS FOR A PARTICULAR PURPOSE, TITLE AND NON-INFRINGEMENT. IN NO EVENT
 SHALL THE COPYRIGHT HOLDERS OR ANYONE DISTRIBUTING THE SOFTWARE BE LIABLE
 FOR ANY DAMAGES OR OTHER LIABILITY, WHETHER IN CONTRACT, TORT OR OTHERWISE,
 ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
 DEALINGS IN THE SOFTWARE.

