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 <http://www.gnu.org/licenses/>.
 .
 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 <afif@debian.org>
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 <http://www.gnu.org/licenses/>
 .
 On Debian systems, the complete text of the GNU General
 Public License version 2 can be found in "/usr/share/common-licenses/GPL-2".
