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 <robp@cs.cmu.edu>
           2013 Adam Roberts
           (C) 2012, Rongkai Xia <shinekaixia@gmail.com>
           (C) 2004, Wong Chi Kwong
           (C) 1997 Makoto Matsumoto and Takuji Nishimura
License: GPL-3+

Files: debian/*
Copyright: © 2015 Michael R. Crusoe <crusoe@ucdavis.edu>
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 <chris@kohlhoff.com>
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 <paul@mineiro.com>
           (c) 2008 Genome Research Ltd (GRL)
           (c) 2008 Yuta Mori All Rights Reserved
License: Expat

Files: include/format.h
       include/posix.h
       src/format.cc
       src/posix.cc
Copyright: (c) 2012 - 2015, Victor Zverovich
License: BSD-2-clause

Files: src/QSufSort.c
Copyright: 1999, N. Jesper Larsson <jesper@cs.lth.se>
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
 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 <http://www.gnu.org/licenses/>.
    .
    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: 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.
