Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Upstream-Name: vg
Source: https://github.com/vgteam/vg#vg
Files-Excluded: deps/libdeflate
                deps/boost-subset
                deps/jemalloc
                deps/backward-cpp
                deps/elfutils
                deps/rocksdb
                deps/raptor
                deps/snappy
                deps/ssw
                deps/sonLib/externalTools/quicktree_1.1/include/buildtree.h~
                deps/vowpal_wabbit/rapidjson
                deps/vowpal_wabbit/cluster/Makefile
                deps/vowpal_wabbit/vowpalwabbit/win32
                deps/vowpal_wabbit/vowpalwabbit/.nuget
                deps/vowpal_wabbit/demo
                deps/vowpal_wabbit/utl
                deps/vowpal_wabbit/Makefile
                deps/vowpal_wabbit/library/Makefile
                deps/vowpal_wabbit/vowpalwabbit/Makefile
                deps/fermi-lite
                deps/fastahack
                deps/libVCFH
                deps/vcflib
                deps/sublinear-Li-Stephens/deps/htslib
                deps/sublinear-Li-Stephens/deps
                deps/sparsehash
                deps/sdsl-lite/external
                deps/sonLib/C/impl/lz4hc.h
                deps/sonLib/C/impl/lz4.h
                deps/sonLib/C/impl/lz4.c
                deps/sonLib/C/impl/lz4hc.c
                deps/FlameGraph
                deps/htslib
                obj/
                bin/
                lib/

Files: *
Copyright: © 2014, 2010, 2012, 2014-2015 Erik Garrison
           2013, Pavel Shramov <shramov@mexmat.net>
           (C) 2009-2014, 2018 by Benedict Paten (benedictpaten@gmail.com)
           (C) 2012 by Dent Earl dentearl (a) gmail com
           (C) 2006-2014 by Joel Armstrong & Benedict Paten
           (c) 2010 Serge A. Zaitsev
           (C) 2006-2012 by Glenn Hickey
           2008-2018, Genome Research Ltd.
           2017-2019, Jouni Siren
           2008-2013, Broad Institute / Massachusetts Institute of Technology
           <2015> <Zev N. Kronenberg>
           (C) 2011 Attractive Chaos <attractor@live.co.uk>
           2012-2016, Boston College
           2012-2018 Wellcome Sanger Institute
           2003-2006, 2008-2010, Heng Li <lh3@live.co.uk>
           2014, Intel Corporation.
           2018, Google LLC.
           2014, Juha Karkkainen, Dominik Kempa and Simon J. Puglisi
           2016, Mariano Gonzalez
           2014, Robert Davis
           © `2015` `Eric T Dawson`
           2015 Guillaume Rizk <guillaume.rizk@algorizk.com>
           2016-2017 Taylor C. Richberger <taywee@gmx.com> and Pavel Belikov
License: MIT

Files: contrib/proto2cpp/proto2cpp.py
Copyright: 2012-2015, Timo Marjoniemi
  2016, Regents of the University of California
License: LGPL-2.1+

Files: ontology/owl2xhtml.xsl
Copyright: 2008, Andreas Radinger and Martin Hepp, Bundeswehr University Munich, http:www.unibw.de/ebusiness/
  2014, UniProt consortium, http:www.uniprot.org
  2016, SIB Swiss Institute of Bioinformatics, http:www.isb-sib.ch
License: LGPL-3+

Files: src/unittest/catch.hpp
       deps/sublinear-Li-Stephens/src/test/catch.hpp
       deps/xg/deps/args/catch.hpp
Copyright: 2012, Two Blue Cubes Ltd.
License: BSL-1.0

Files: deps/sparsepp/*
       deps/sonLib/C/inc/hashTableC.h
       deps/sonLib/C/inc/hashTablePrivateC.h
       deps/sonLib/C/inc/hashTableC_itr.h
       deps/sonLib/C/impl/hashTableC_itr.c
       deps/sonLib/C/impl/hashTableC.c
       deps/vowpal_wabbit/*
Copyright: 2008-2018, Genome Research Ltd.
           2008-2009, 2011, Attractive Chaos <attractor@live.co.uk>
           1993-2002, MEDICAL RESEARCH COUNCIL
           2016, Gregory Popovitch - greg7mdp@gmail.com
           2005, 2010, Google Inc.
           (C) 2002, 2004 Christopher Clark <firstname.lastname@cl.cam.ac.uk
           (C) 1997 - 2002, Makoto Matsumoto and Takuji Nishimura
           © Microsoft Corp 2012-2014, Yahoo! Inc. 2007-2012, and many individual contributors.
           (c) 2012 - ariel faigon for vowpal-wabbit
License: BSD-3-clause

Files: deps/sparsepp/sparsepp/spp_timer.h
Copyright: 2016, Mariano Gonzalez
License: MIT

Files: deps/sonLib/sonLib_daemonize.py
Copyright: (C) 2006-2012 by Glenn Hickey
           (C) 2005 Chad J. Schroeder
License: Python and MIT

Files: deps/sonLib/externalTools/quicktree_1.1/*
Copyright: (C) Genome Research Limited, 2002-
Comment: License verified from https://github.com/khowe/quicktree/
 Which is linked from https://www.sanger.ac.uk/science/tools/quicktree
License: Apache-2

Files: deps/sonLib/externalTools/cutest/*
Copyright: (c) 2003 Asim Jalis
License: Zlib
 This software is provided 'as-is', without any express or implied
 warranty. In no event will the authors be held liable for any damages
 arising from the use of this software.
 .
 Permission is granted to anyone to use this software for any purpose,
 including commercial applications, and to alter it and redistribute it
 freely, subject to the following restrictions:
 .
 1. The origin of this software must not be misrepresented; you must not
 claim that you wrote the original software. If you use this software in
 a product, an acknowledgment in the product documentation would be
 appreciated but is not required.
 .
 2. Altered source versions must be plainly marked as such, and must not
 be misrepresented as being the original software.
 .
 3. This notice may not be removed or altered from any source
 distribution.
Comment: from License.txt
 The license is based on the zlib/libpng license. For more details see
 http://www.opensource.org/licenses/zlib-license.html. The intent of the
 license is to:
 .
 - keep the license as simple as possible
 - encourage the use of CuTest in both free and commercial applications
   and libraries
 - keep the source code together
 - give credit to the CuTest contributors for their work
 .
 If you ship CuTest in source form with your source distribution, the
 following license document must be included with it in unaltered form.
 If you find CuTest useful we would like to hear about it.


Files: deps/pinchesAndCacti/externalTools/threeEdgeConnected/inc/3_Absorb3edge2x.h
       deps/pinchesAndCacti/externalTools/threeEdgeConnected/impl/3_Absorb3edge2x.c
Copyright: (C) 2011 by Yung H Tsin and Nima Norouzi
License: 3edgeconnected
 * The authors of this code have given their permission
 * to distribute and redistribute this code within this software product,
 * however they require that any further incorporation or copying
 * be permitted by request only, hence the BSD/MIT license which
 * applies to much of the other code in this software product does not apply to this file.

Files: deps/sdsl-lite/*
       deps/xg/deps/sdsl-lite/*
       deps/sonLib/C/impl/avl.c
       deps/sonLib/C/inc/avl.h
Copyright: 2007-2014 Simon Gog
           1995, Ian Jackson <iwj10@cus.cam.ac.uk>
           2001, Anthony Towns <aj@azure.humbug.org.au>
           1998-2002, 2004, 2008-2009, Free Software Foundation, Inc.
           2016, Francisco Montoto
           2011, Timo Beller, Simon Gog
           2012, Simon Gog, Matthias Petri
           2013, Simon Gog, Timo Beller and Markus Brenner
           1999, N. Jesper Larsson
           2013, Timo Beller
License: GPL-3+

Files: deps/structures/*
Copyright: 2017, Netflix, Inc.
License: Apache-2

Files: deps/libvgio/include/vg/io/fdstream.hpp
Copyright: (C) Copyright Nicolai M. Josuttis 2001.
License: NTP
 Permission to copy, use, modify, sell and distribute this software
 is granted provided this copyright notice appears in all copies.
 This software is provided "as is" without express or implied
 warranty, and with no claim as to its suitability for any purpose.

Files: deps/xg/deps/ips4o/*
Copyright: 2017, Michael Axtmann <michael.axtmann@kit.edu>
           2017, Daniel Ferizovic <daniel.ferizovic@student.kit.edu>
           2017, Sascha Witt <sascha.witt@kit.edu>
License: BSD-2-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.
 .
 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 HOLDER 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.

Files: debian/*
Copyright: © 2018-2020 Michael R. Crusoe <crusoe@debian.org>
License: MIT

License: MIT
 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: LGPL-2.1+
 This library 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 2.1 of the License, or (at your option) any later version.
 .
 This library 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
 Lesser General Public License for more details.
 .
 You should have received a copy of the GNU Lesser General Public
 License along with this library; if not, write to the Free Software
 Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301
 .
 On Debian systems, the complete text of version 2 of the GNU General
 Public License can be found in `/usr/share/common-licenses/GPL-2'.

License: LGPL-3+
 This library 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 library 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
 Lesser General Public License for more details.
Comment:
 On Debian systems, you can find the LGPL license version 3 in
 ‘/usr/share/common-licenses/LGPL-3’.

License: Apache-2
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
 You may obtain a copy of the License at
 .
 https://www.apache.org/licenses/LICENSE-2.0
 .
 Unless required by applicable law or agreed to in writing, software
 distributed under the License is distributed on an "AS IS" BASIS,
 WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 See the License for the specific language governing permissions and
 limitations under the License.
 .
 On Debian systems, the complete text of the Apache version 2.0 license
 can be found in "/usr/share/common-licenses/Apache-2.0".

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 original author; nor the names of any 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.

License: Python
 PYTHON SOFTWARE FOUNDATION LICENSE VERSION 2
 --------------------------------------------
 .
 1. This LICENSE AGREEMENT is between the Python Software Foundation
 ("PSF"), and the Individual or Organization ("Licensee") accessing and
 otherwise using this software ("Python") in source or binary form and
 its associated documentation.
 .
 2. Subject to the terms and conditions of this License Agreement, PSF hereby
 grants Licensee a nonexclusive, royalty-free, world-wide license to reproduce,
 analyze, test, perform and/or display publicly, prepare derivative works,
 distribute, and otherwise use Python alone or in any derivative version,
 provided, however, that PSF's License Agreement and PSF's notice of copyright,
 i.e., "Copyright (c) 2001, 2002, 2003, 2004, 2005, 2006, 2007, 2008, 2009, 2010,
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 .
 3. In the event Licensee prepares a derivative work that is based on
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 4. PSF is making Python available to Licensee on an "AS IS"
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License: BSL-1.0
 Permission is hereby granted, free of charge, to any person or organization
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 works are solely in the form of machine-executable object code generated by
 a source language processor.
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 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.

License: GPL-3+
 This program 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 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.  See the GNU General Public License for
 more details.
 .
 You should have received a copy of the GNU General Public License along
 with this program.  If not, see <http://www.gnu.org/licenses/>.
Comment:
 On Debian systems, you can find the GPL license version 3 in
 ‘/usr/share/common-licenses/GPL-3’.
