Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Name: salmon Source: https://github.com/COMBINE-lab/salmon/ Files-Excluded: doc/build/* include/CollapsedIterativeOptimizer.hpp.bak src/SalmonQuantify.cpp.bak include/eigen3 include/obsolete include/kseq.h include/posix.h include/tensemble/Tree.h.backup.h src/posix.cc cmake/Modules/FindTBB.cmake scripts/cpld.bash Files: * Copyright: © 2015 The Salmon Authors (c) 2013, 2014, 2015 Rob Patro 2013 Adam Roberts (C) 2012, Rongkai Xia (C) 2004, Wong Chi Kwong (C) 1997 Makoto Matsumoto and Takuji Nishimura License: GPL-3+ Files: debian/* Copyright: © 2015 Michael R. Crusoe License: GPL-3+ Files: cmake/Modules/FindJemalloc.cmake include/VersionChecker.hpp src/VersionChecker.cpp Copyright: (c) 2014 Thomas Heller (c) 2007-2012 Hartmut Kaiser (c) 2010-2011 Matt Anderson (c) 2011 Bryce Lelbach (c) 2003-2012 Christopher M. Kohlhoff License: BSL-1.0 Files: include/btree*.h include/safe_btree*.h Copyright: 2013 Google Inc. License: Apache-2.0 Files: include/ezETAProgressBar.hpp include/fastapprox.h src/bwtindex.c src/is.c Copyright: 2011, 2012 Remik Ziemlinski 2011, 2012 Paul Mineiro (c) 2008 Genome Research Ltd (GRL) (c) 2008 Yuta Mori All Rights Reserved License: Expat Files: include/format.h src/format.cc Copyright: (c) 2012 - 2015, Victor Zverovich License: BSD-2-clause Files: src/QSufSort.c Copyright: 1999, N. Jesper Larsson License: other This software may be used freely for any purpose. However, when distributed, the original source must be clearly stated, and, when the source code is distributed, the copyright notice must be retained and any alterations in the code must be clearly marked. No warranty is given regarding the quality of this software Files: include/atomicops.h include/concurrentqueue.h include/readerwriterqueue.h Copyright: ©2013 Cameron Desrochers License: BSD-cameron-descrochers Files: debian/rapmap/* Copyright: (c) 2014-2016 COMputational BIology and Network Evolution lab License: GPL-3+ Comment: Taken from RapMap (https://github.com/COMBINE-lab/RapMap) with the following license statement: Since RapMap uses Jellyfish, it must be released under the GPL. However, this is currently the only GPL dependency. If it can be replaced, I'd like to re-license RapMap under the BSD license. I'd be happy to accept pull-requests that replace the Jellyfish components with a library released under a more liberal license (BSD-compatible). Files: debian/rapmap/BooPHF.hpp Copyright: ©2015 Guillaume Rizk License: Expat Comment: This project is now BBHash, see https://github.com/rizkg/BBHash/blob/master/LICENSE. Files: debian/rapmap/kseq.h Copyright: (c) 2008, 2009, 2011 Attractive Chaos License: Expat Files: debian/rapmap/macros.h debian/rapmap/rank9b.* Copyright: ©2007-2013 Sebastiano Vigna License: LGPL-3+ License: BSD-cameron-descrochers 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. . 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: 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: . 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. 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 . . On Debian systems, the full text of the GNU General Public License version 3 can be found in the file `/usr/share/common-licenses/GPL-3'. License: LGPL-3+ 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 3 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 program; if not, see . . On Debian systems, the full text of the GNU Lesser General Public License version 3 can be found in the file `/usr/share/common-licenses/LGPL-3'. License: BSL-1.0 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. 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. . 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.