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A library for working with phylogenetic and population genetic data.
v0.27.0 |
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A library for working with phylogenetic and population genetic data.
v0.27.0 |
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This work is financially supported:
See the webpages of the Exelixis Lab and the Moi Lab for our other projects.
In the following, we list all direct dependencies of Genesis and their licenses.
If tests are enabled, Genesis automatically tries to download and compile Google Test (GTest) in order to compile our test cases.
License
Copyright 2008, Google Inc. All rights reserved.
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.
The license information above was copied from https://github.com/google/googletest/blob/master/googletest/LICENSE on 2017-03-09.
If Python bindings are enabled, Genesis automatically tries to download Pybind11 to create those bindings.
License
Copyright (c) 2016 Wenzel Jakob wenzel.jakob@epfl.ch, All rights reserved.
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 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 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.
You are under no obligation whatsoever to provide any bug fixes, patches, or upgrades to the features, functionality or performance of the source code ("Enhancements") to anyone; however, if you choose to make your Enhancements available either publicly, or directly to the author of this software, without imposing a separate written license agreement for such Enhancements, then you hereby grant the following license: a non-exclusive, royalty-free perpetual license to install, use, modify, prepare derivative works, incorporate into other computer software, distribute, and sublicense such enhancements or derivative works thereof, in binary and source code form.
The license information above was copied from https://github.com/pybind/pybind11/blob/master/LICENSE on 2017-03-09.
We do not deliver any code of htslib with our sources, but if htslib is enabled (in CMakeLists.txt via GENESIS_USE_HTSLIB), genesis automatically downloads and builds htslib as part of its own build process.
License
[Files in this distribution outwith the cram/ subdirectory are distributed according to the terms of the following MIT/Expat license.]
The MIT/Expat License
Copyright (C) 2012-2021 Genome Research Ltd.
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.
[Files within the cram/ subdirectory in this distribution are distributed according to the terms of the following Modified 3-Clause BSD license.]
The Modified-BSD License
Copyright (C) 2012-2020 Genome Research Ltd.
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 names Genome Research Ltd and Wellcome Trust Sanger Institute 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 GENOME RESEARCH LTD 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 GENOME RESEARCH LTD 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.
[The use of a range of years within a copyright notice in this distribution should be interpreted as being equivalent to a list of years including the first and last year specified and all consecutive years between them.
For example, a copyright notice that reads "Copyright (C) 2005, 2007-2009, 2011-2012" should be interpreted as being identical to a notice that reads "Copyright (C) 2005, 2007, 2008, 2009, 2011, 2012" and a copyright notice that reads "Copyright (C) 2005-2012" should be interpreted as being identical to a notice that reads "Copyright (C) 2005, 2006, 2007, 2008, 2009, 2010, 2011, 2012".]
The license information above was copied from https://github.com/samtools/htslib/blob/develop/LICENSE on 2021-09-18.
In the following, we list all sources that were adapted and incorporated in Genesis in modified form.
Our JsonDocument data structure as well as the accompanying JsonIterator are based on the excellent JSON for Modern C++ library by Niels Lohmann.
License
MIT License
Copyright (c) 2013-2017 Niels Lohmann
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.
The license information above was copied from https://github.com/nlohmann/json/blob/develop/LICENSE.MIT on 2017-03-09.
Genesis contains a set of classes that deal with input streams:
The design and implementation of those classes is inspired by fast-cpp-csv-parser by Ben Strasser, with his explicit permission to modify and use the code in Genesis.
License
Copyright (c) 2015, ben-strasser All rights reserved.
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 fast-cpp-csv-parser 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 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.
The license information above was copied from https://github.com/ben-strasser/fast-cpp-csv-parser/blob/master/LICENSE on 2017-03-09.
Genesis contains a set of classes that deal with gzip/zlib compressed/decompressed input streams, and some other stream-related functionality:
as well as the helper and internal classes:
The code of these classes is adapted from the excellent zstr library by Matei David. We adapted the original code by renaming all classes and variables to our standards, moving much of the implementation into a source file (so that the header does not clutter its callers with zlib-internal symbols), and refining some functionality.
The repository at https://github.com/mateidavid/zstr is published under the MIT license:
License
The MIT License (MIT)
Copyright (c) 2015 Matei David, Ontario Institute for Cancer Research
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.
The license information above was copied from https://github.com/mateidavid/zstr/blob/master/LICENSE on 2020-05-10.
Genesis contains an implementation for optional data:
The code of this class is adapted from the excellent optional-bare by Martin Moene. We adapted the original code by renaming the classes and variables and formatting the code to our standards.
All code for this class, located in genesis/lib/genesis/utils/containers/optional.hpp is
Copyright 2017-2019 by Martin Moene. Distributed under the Boost Software License, Version 1.0. See http://www.boost.org/LICENSE_1_0.txt
The original code repository, located at https://github.com/martinmoene/optional-bare, is published under the Boost Software License - Version 1.0:
License
Boost Software License - Version 1.0 - August 17th, 2003
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.
The license information above was copied from https://github.com/martinmoene/optional-bare/blob/master/LICENSE.txt on 2021-09-18.
Genesis contains an implementation of an interval tree:
The code of these classes is adapted from interval-tree by Tim Ebbeke (@5cript) and Nick Weber (@WeberNick). We adapted the original code by renaming the classes and variables and formatting the code to our standards, as well as improving some of the functions and adding additional functionality for our needs.
The original code repository, located at https://github.com/5cript/interval-tree, is published under the CC0-1.0 License (Creative Commons Zero v1.0 Universal):
License
Creative Commons Legal Code
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The license information above was copied from https://github.com/5cript/interval-tree/blob/master/LICENSE on 2021-12-04.
The implementation of our RangeMinimumQuery data structure is based on the Succinct RMQ implementation by Johannes Fischer, with his explicit permission to use his code in Genesis.
The implementation of our multi_dimensional_scaling() function is based on the SimpleMatrix library by Quan Wang, with his explicit permission to use this code in Genesis. The copyright (C) of the implementation is held by Quan Wang, 2013. We adapted the implementation to our Matrix class and changed the error reporting mechanism to exceptions.
The implementation by Quan Wang (and our adaptation) offers two variants of MDS. The code of these variants is based on two Matlab implementations, and re-implements those in C++. The original sources are:
See there for further details. Note however that none of the original code of these two implementations is used in Genesis, as we solely rely on the ported and re-implemented code by Quan Wang.
The implementation of our Generalized Linear Model, in particular glm_fit(), but also some related helper functions, is based on the snp.matrix and X.snp.matrix classes by David Clayton david.clayton@cimr.cam.ac.uk and Hin-Tak Leung htl10@users.sourceforge.net. The source is in C, but is originally intended for usage in R.
The package does not seem to be maintained any more, and does not seem to have a proper repository. For more information, try these sites:
The original code is published under the GNU General Public Licence version 3 (GPLv3).
The snp.matrix and X.snp.matrix classes. Copyright (C) 2008 David Clayton and Hin-Tak Leung
As we use the same license, see License for the complete license.
Our implementation of the MD5 hashing function is based on http://www.zedwood.com/article/cpp-md5-function, which itself was converted to C++ class by Frank Thilo (thilo@unix-ag.org) for bzflag (http://www.bzflag.org), and is based on the reference implementation of RFC 1321:
License
Copyright (C) 1991-2, RSA Data Security, Inc. Created 1991. All rights reserved.
License to copy and use this software is granted provided that it is identified as the "RSA Data Security, Inc. MD5 Message-Digest Algorithm" in all material mentioning or referencing this software or this function.
License is also granted to make and use derivative works provided that such works are identified as "derived from the RSA Data Security, Inc. MD5 Message-Digest Algorithm" in all material mentioning or referencing the derived work.
RSA Data Security, Inc. makes no representations concerning either the merchantability of this software or the suitability of this software for any particular purpose. It is provided "as is" without express or implied warranty of any kind.
These notices must be retained in any copies of any part of this documentation and/or software.
Our implementation of the SHA1 hashing function is based on https://github.com/vog/sha1, which is 100% Public Domain.
Our implementation of the SHA256 hashing function is based on http://www.zedwood.com/article/cpp-sha256-function, which itself is based on Olivier Gay's version, and was published with a Modified BSD License:
License
Updated to C++, zedwood.com 2012 Based on Olivier Gay's version See Modified BSD License below:
FIPS 180-2 SHA-224/256/384/512 implementation Issue date: 04/30/2005 http://www.ouah.org/ogay/sha2/
Copyright (C) 2005, 2007 Olivier Gay olivier.gay@a3.epfl.ch All rights reserved.
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 project 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 PROJECT 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 PROJECT 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.
The color codes for the color maps magma, inferno, plasma and viridis are taken from https://github.com/BIDS/colormap. They were created by Nathaniel J. Smith, Stefan van der Walt, and (in the case of viridis) Eric Firing. These colormaps are released under the CC0 license / public domain dedication. See https://creativecommons.org/publicdomain/zero/1.0/ for the license.
The color names and codes for the list used in color_from_name_xkcd() and is_xkcd_color_name() are taken from https://xkcd.com/color/rgb.txt. They were published under Public Domain, see https://xkcd.com/color/rgb/ and https://blog.xkcd.com/2010/05/03/color-survey-results/ for details.
The color lists brbg, piyg, prgn, puor, rdbu, rdgy, rdylbu, rdylgn, blues, bugn, bupu, gnbu, greens, greys, oranges, orrd, pubu, pubugn, purd, purples, rdpu, reds, ylgn, ylgnbu, ylorbr, ylorrd, accent, dark2, paired, pastel1, pastel2, spectral, set1, set2 and set3 were adapted from https://github.com/axismaps/colorbrewer and https://github.com/Gnuplotting/gnuplot-palettes by converting the color codes to RGB double values.
The original ColorBrewer color specifications and designs were developed by Cynthia Brewer (http://colorbrewer.org/), while their gnuplot equivalets are authored by Anna Schneider. Their work is published under the Apache-2.0 license:
License
Apache License Version 2.0, January 2004 http://www.apache.org/licenses/
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APPENDIX: How to apply the Apache License to your work.
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The license information above was copied from https://github.com/axismaps/colorbrewer/blob/master/LICENCE.txt on 2018-01-08.
The color list color_list_nextstrain() is adapted from the Nextstrain build for novel coronavirus (nCoV) at https://nextstrain.org/ncov, using their color scheme https://github.com/nextstrain/ncov/blob/master/config/color_schemes.tsv and converting it to RGB double values. The repository at https://github.com/nextstrain/ncov is published under the MIT license:
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The license information above was copied from https://github.com/nextstrain/ncov/blob/master/LICENSE on 2020-04-05.
1.8.17