Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Name: canu Source: https://github.com/marbl/canu Files-Excluded: kmer src/mhap/mhap-*.jar src/utgcns/libboost src/stores/libsnappy src/utility/src/utility/libbacktrace Files: * Copyright: 2011-2012,2014-2015 Battelle National Biodefense Institute 2011 Liliana Florea 2005-2014 J. Craig Venter Institute 2004 Brian P. Walenz 2003-2004 Applera Corporation License: GPL-2.0+ and BSD-3-Clause-BNBI and Public-Domain Comment: Modifications made by the Battelle National Biodefense Institute are licensed under the BSD-3-Clause-BNBI license. Developments from 2016 onward are public domain works. Files: src/utgcns/* src/correction/falconConsensus* src/utgcns/libpbutgcns/* Copyright: 2011-2015 Pacific Biosciences of California 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. Files: src/meryl/* src/seqrequester/* src/utility/* Copyright: None License: Public-Domain Files: src/utility/src/parasail/* Copyright: 2015 Battelle Memorial Institute License: Battelle-BSD-style 1. Battelle Memorial Institute (hereinafter Battelle) hereby grants permission to any person or entity lawfully obtaining a copy of this software and associated documentation files (hereinafter “the Software”) to redistribute and use the Software in source and binary forms, with or without modification. Such person or entity may use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and may permit others 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 disclaimer in the documentation and/or other materials provided with the distribution. . * Other than as used herein, neither the name Battelle Memorial Institute or Battelle may be used in any form whatsoever without the express written consent of Battelle. . * Redistributions of the software in any form, and publications based on work performed using the software should include the following citation as a reference: . Daily, Jeff. (2016). Parasail: SIMD C library for global, semi-global, and local pairwise sequence alignments. BMC Bioinformatics, 17(1), 1-11. doi:10.1186/s12859-016-0930-z . 2. 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 BATTELLE 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. Comment: These are modified files from Parasail. The modifications are in the public domain. Files: src/Makefile src/meryl/src/Makefile src/seqrequester/src/Makefile src/utility/src/Makefile Copyright: Copyright 2008, 2009, 2010 Dan Moulding, Alan T. DeKok License: GPL-3+ This package 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 package 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 package. If not, see . . On Debian systems, the complete text of the GNU General Public License version 3 can be found in `/usr/share/common-licenses/GPL-3'. Files: debian/* Copyright: 2016-2017 Afif Elghraoui License: GPL-2.0+ License: Public-Domain This software is "United States Government Work" under the terms of the United States Copyright Act. It was written as part of the authors' official duties for the United States Government and thus cannot be copyrighted. This software is freely available to the public for use without a copyright notice. Restrictions cannot be placed on its present or future use. . Although all reasonable efforts have been taken to ensure the accuracy and reliability of the software and associated data, the National Human Genome Research Institute (NHGRI), National Institutes of Health (NIH) and the U.S. Government do not and cannot warrant the performance or results that may be obtained by using this software or data. NHGRI, NIH and the U.S. Government disclaim all warranties as to performance, merchantability or fitness for any particular purpose. . Please cite the authors in any work or product based on this material. License: BSD-3-Clause-BNBI This Software was prepared for the Department of Homeland Security (DHS) by the Battelle National Biodefense Institute, LLC (BNBI) as part of contract HSHQDC-07-C-00020 to manage and operate the National Biodefense Analysis and Countermeasures Center (NBACC), a Federally Funded Research and Development Center. . 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 Battelle National Biodefense 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 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. License: GPL-2.0+ This package 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 package 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 . On Debian systems, the complete text of the GNU General Public License version 2 can be found in "/usr/share/common-licenses/GPL-2".