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/*****************************************************************************
AUTHORS
Jeffrey E. Barrick <jeffrey.e.barrick@gmail.com> and other contributors
LICENSE AND COPYRIGHT
Copyright (c) 2008-2010 Michigan State University
Copyright (c) 2011-2025 The University of Texas at Austin
Copyright (c) 2025- Michigan State University
breseq 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, or (at your option) any later version.
SPDX-License-Identifier: GPL-2.0-or-later
THIRD-PARTY NOTICES
This product includes the following third-party software components. Their
license terms are reproduced below.
*****************************************************************************/
================================================================================
BUNDLED SOURCE CODE
================================================================================
AnyOption 1.3
src/c/breseq/anyoption.cpp
src/c/breseq/libbreseq/anyoption.h
Copyright (c) 2001 Kishan Bhagat (kishan@hackorama.com)
https://github.com/hackorama/AnyOption/
Licensed under the MIT License:
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.
--------------------------------------------------------------------------------
JSON for Modern C++ 2.1.1
src/c/breseq/libbreseq/json.hpp
Copyright (c) 2013-2017 Niels Lohmann <http://nlohmann.me>
https://github.com/nlohmann/json
Licensed under the MIT License:
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.
--------------------------------------------------------------------------------
CTPL - C++ Thread Pool Library
src/c/breseq/libbreseq/ctpl_stl.h
Copyright (C) 2014 by Vitaliy Vitsentiy
https://github.com/vit-vit/CTPL
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.
--------------------------------------------------------------------------------
Cephes Math Library
src/c/breseq/stats.cpp (selected functions)
Copyright 1984, 1987, 1988, 1989, 1992, 1995, 1996, 2000 by Stephen L. Moshier
http://www.netlib.org/cephes/
The Cephes Math Library functions incorporated in this file (gamma, lgamma,
incomplete gamma, incomplete beta, and negative binomial distribution
functions) are freely redistributable. Stephen L. Moshier has stated that
these routines may be used and distributed freely.
--------------------------------------------------------------------------------
JSZip 3.10.1
src/c/breseq/jszip.min.js
Copyright (c) 2009-2016 Stuart Knightley <stuart@stuartk.com>
https://github.com/Stuk/jszip
Dual licensed under the MIT License or GPLv3.
This distribution uses the MIT License:
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.
JSZip bundles pako (https://github.com/nodeca/pako), also released under
the MIT License. Copyright (C) 2014-2017 by Vitaly Puzrin and Andrei
Tuputcyn.
--------------------------------------------------------------------------------
List.js
src/c/breseq/list.min.js
Copyright (c) Jonny Strömberg (https://jonnyburger.se/)
https://listjs.com / https://github.com/javve/list.js
Licensed under the MIT License:
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.
This bundle also includes the string-natural-compare npm package, released
under the MIT License.
================================================================================
RUNTIME DEPENDENCIES
================================================================================
Bowtie2
https://bowtie-bio.sourceforge.net/bowtie2/
Copyright (C) 2011-2012 Langmead Lab
Licensed under the GNU General Public License, version 2 or later.
--------------------------------------------------------------------------------
SAMtools / HTSlib
https://www.htslib.org/
Copyright (C) 2009-2024 Genome Research Ltd.
Licensed under the MIT License.
--------------------------------------------------------------------------------
miniz
https://github.com/richgel999/miniz
Copyright 2013-2014 RAD Game Tools and Valve Software
Copyright 2010-2014 Rich Geldreich and Tenacious Software LLC
Licensed under the MIT License.
--------------------------------------------------------------------------------
zlib
https://zlib.net/
Copyright (C) 1995-2024 Jean-loup Gailly and Mark Adler
Licensed under the zlib License.
--------------------------------------------------------------------------------
gnuplot
http://www.gnuplot.info/
Copyright (C) 1986-1993, 1998, 2004 Thomas Williams and Colin Kelley
Licensed under the gnuplot License (a permissive license; see
http://www.gnuplot.info/faq/faq.html#x1-70001.4).
--------------------------------------------------------------------------------
PHYLIP (optional)
https://phylipweb.github.io/phylip/
Copyright (c) 1980-2013 University of Washington, Department of Genome Sciences
Freely available for non-commercial use. See
https://phylipweb.github.io/phylip/getme-new1.html for license terms.
================================================================================