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:
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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:
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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.
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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.
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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:
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The above copyright notice and this permission notice shall be included in
all copies or substantial portions of the Software.
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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 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:
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* Redistributions of source code must retain the above copyright notice,
this list of conditions and the following disclaimers.
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* 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.
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* 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.
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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 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.