Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Upstream-Name: SPAdes
Upstream-Contact: spades.support@bioinf.spbau.ru
Source: http://spades.bioinf.spbau.ru/
Files-Excluded:
    assembler/ext/src/python_libs
    assembler/ext/src/bwa
    assembler/ext/include/samtools
    assembler/ext/src/samtools/misc/ace2sam
    assembler/ext/src/samtools/misc/maq2sam-*
    assembler/ext/src/samtools/misc/md5fa
    assembler/ext/src/samtools/misc/md5sum-lite
    assembler/ext/src/samtools/misc/wgsim
    assembler/ext/src/samtools/win32
    assembler/ext/src/nlopt
    assembler/ext/src/llvm/ConvertUTF.cpp
    assembler/ext/src/ssw
    assembler/ext/include/ssw
    assembler/ext/include/nlopt
    ioncommunity
    webvis
    .gitignore

Files: *
Copyright: 2011-2014 Saint-Petersburg Academic University
           2015-2017 Saint Petersburg State University
License: GPL-2+

Files: debian/*
Copyright: 2014-2016 Andreas Tille <tille@debian.org>
           2015-2016 Afif Elghraoui <afif@debian.org>
                2016 Sascha Steinbiss <sascha@steinbiss.name>
           2021-2022 Étienne Mollier <emollier@debian.org>
License: GPL-2+

Files: assembler/src/projects/ionhammer/seqeval/*
Copyright: (C) 2012-2013 Ion Torrent Systems, Inc. All Rights Reserved
License: GPL-2+
Comment:
 Assumed to be under GPL-2+ as well, cf. https://github.com/iontorrent/TS

Files: assembler/src/projects/hammer/parallel_radix_sort.hpp
Copyright: (c) 2010 Takuya Akiba
License: BSD-3-clause-Akiba
 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 Takuya Akiba 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.

Files: assembler/src/common/math/xmath.h
       assembler/ext/include/sparsehash/*
Copyright: (c) 2005 Google Inc.
License: BSD-3-clause-Google
 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 Google Inc. 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.

Files: assembler/ext/include/ConsensusCore/*
       assembler/ext/src/ConsensusCore/*
Copyright: 2011-2013 Pacific Biosciences of California, Inc. All rights reserved.
License: BSD-3-clause-PacBio
 Redistribution and use in source and binary forms, with or without
 modification, are permitted (subject to the limitations in the
 disclaimer below) 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 Pacific Biosciences nor the names of its
    contributors may be used to endorse or promote products derived
    from this software without specific prior written permission.
 .
 NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
 GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
 BIOSCIENCES AND ITS 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 PACIFIC BIOSCIENCES OR ITS
 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.
Comment:
 This is a code copy from
   https://github.com/PacificBiosciences/ConsensusCore
 This is packaged in Debian as python-pbconsensuscore, but only the python
 bindings are packaged.

Files: assembler/ext/include/llvm/*
       assembler/ext/src/llvm/*
Copyright: (c) 2003-2015 University of Illinois at Urbana-Champaign.
           All rights reserved.
License: UoI-NCSA

Files: assembler/ext/include/bamtools/*
       assembler/ext/src/bamtools/*
Copyright: (c) 2009-2010 Derek Barnett, Erik Garrison, Gabor Marth, Michael Stromberg
License: Expat

Files: assembler/ext/src/samtools/*
Copyright: (c) 2008-2009 Genome Research Ltd.
           (c) 2003-2006, 2008-2010 Heng Li
           (c) 2008 Broad Institute / Massachusetts Institute of Technology
License: Expat

Files: assembler/ext/include/kseq/*
       assembler/ext/src/samtools/bcftools/kmin.*
Copyright: (c) 2008-2011 Attractive Chaos <attractor@live.co.uk>
License: Expat

Files: assembler/ext/include/libcxx/sort.hpp
Copyright: LLVM Developers <llvm-dev@lists.llvm.org>
License: Expat
Comment: This file is taken from LLVM's libc++.
 See http://llvm.org/docs/DeveloperPolicy.html#license.

Files: assembler/ext/src/llvm/reg*
Copyright: (c) 1992, 1993, 1994 Henry Spencer.
           (c) 1992, 1993, 1994 The Regents of the University of California.  All rights reserved.
License: BSD-3-clause

Files: assembler/ext/include/cxxopts/*
Copyright: (c) 2014, 2015, 2016 Jarryd Beck
License: Expat

Files: assembler/ext/include/boomphf/BooPHF.h
Copyright: (c) 2015 Guillaume Rizk
License: Expat
Comment:
 MIT licensed as part of BBHash (https://github.com/rizkg/BBHash)

Files: assembler/ext/include/btree/*
Copyright: 2013 Google Inc.
License: Apache-2.0

Files: assembler/ext/include/folly/*
Copyright: 2014 Facebook, Inc.
License: Apache-2.0

Files: assembler/ext/include/cuckoo/*
Copyright: 2013, Carnegie Mellon University and Intel Corporation
License: Apache-2.0

Files: assembler/ext/include/cppformat/*
       assembler/ext/src/cppformat/*
Copyright: (c) 2012-2014 Victor Zverovich
License: BSD-2-clause

Files: assembler/src/common/io/reads/mpmc_bounded.hpp
Copyright: (c) 2015 Saint Petersburg State University
           (c) 2011-2014 Saint Petersburg Academic University
           (c) 2011 Dmitry Vyukov. All rights reserved.
License: BSD-2-clause

Files: assembler/ext/include/getopt_pp/*
       assembler/ext/src/getopt_pp/*
Copyright: (C) 2007, 2008  Daniel Gutson, FuDePAN
License: GPL-3+

Files: assembler/src/cmake/Modules/GetGitRevisionDescription.*
Copyright: 2009-2010 Iowa State University
License: Boost-1
 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.

Files: assembler/src/tools/quake-correct/gzstream.*
       assembler/src/projects/mts/gzstream/gzstream.*
Copyright: (C) 2001 Deepak Bandyopadhyay
           (C) 2001 Lutz Kettner
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 St, Fifth Floor, Boston, MA 02110-1301,
 USA.

Files: assembler/ext/src/bamtools/api/internal/io/pbgzf/util.c
Copyright: (C) 1996-2008 Julian R Seward.  All rights reserved.
License: BSDlike-libbzip2
 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. 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.
 .
 3. Altered source versions must be plainly marked as such, and must
 not be misrepresented as being the original software.
 .
 4. The name of the author may not be used to endorse or promote
 products derived from this software without specific prior written
 permission.
 .
 THIS SOFTWARE IS PROVIDED BY THE AUTHOR ``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 AUTHOR 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: Apache-2.0
 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
 .
     http://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 full text of the Apache License, Version 2.0 can be
 found in the file `/usr/share/common-licenses/Apache-2.0'.

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:
 .
 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.
 .
 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: BSD-3-clause
 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. 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: 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: GPL-2+
    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 2 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, write to the Free Software Foundation, Inc.,
    51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
 .
 On Debian systems you can find the full test of the GNU General Public
 License version 2 at /usr/share/common-licenses/GPL-2.

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/>.
 .
 On Debian systems, the complete text of the GNU General
 Public License can be found in `/usr/share/common-licenses/GPL-3'.

License: UoI-NCSA
 Permission is hereby granted, free of charge, to any person obtaining a copy of
 this software and associated documentation files (the "Software"), to deal with
 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:
 .
    * Redistributions of source code must retain the above copyright notice,
      this list of conditions and the following disclaimers.
 .
    * Redistributions in binary form must reproduce the above copyright notice,
      this list of conditions and the following disclaimers in the
      documentation and/or other materials provided with the distribution.
 .
    * Neither the names of the LLVM Team, University of Illinois at
      Urbana-Champaign, nor the names of its contributors may be used to
      endorse or promote products derived from this Software without specific
      prior written permission.
 .
 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
 CONTRIBUTORS 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 WITH THE
 SOFTWARE.
