Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Source: https://github.com/arq5x/bedtools2/archive/v2.25.0.tar.gz
Comment: File barski_binding_site.png is from
  Jothi et al, 2008, doi:10.1093/nar/gkn488, licensed under no-DFSG CC-BY-NC 2.0
Files-Excluded: */barski_binding_site.png
                */g++
                */gcc
Upstream-Name: bedtools
Upstream-Contact: http://groups.google.com/group/bedtools-discuss

Files: *
Copyright: © 2009,2010,2011 Aaron Quinlan
 © 2010 - Assaf Gordon, CSHL
License: GPL-2

Files: src/expand/expand.cpp
Copyright: © 2009, 2010, 2011 - Aaron Quinlan
License: under-the-MIT-license
 No further explanation about which MIT license to follow was provided.

Files: src/utils/Fasta/Fasta.cpp
 src/utils/Fasta/Fasta.h
Copyright: © 2010 Erik Garrison <erik.garrison@bc.edu>
License: GPL-2
Source: https://github.com/ekg/fastahack

Files: src/utils/BamTools/*
Copyright: © 2009-2010 Derek Barnett, Erik Garrison, Gabor Marth, Michael Stromberg
License: MIT
 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.
Comment: see ‘https://github.com/pezmaster31/bamtools/blob/master/LICENSE’.
Source: https://github.com/pezmaster31/bamtools/wiki

Files: src/utils/gzstream/gzstream.h
Copyright: © 2001  Deepak Bandyopadhyay, Lutz Kettner
License: LGPL-2.1+
 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 2.1 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 library; if not, write to the Free Software
 Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
Comment:
 On Debian systems, you can find a copy of the GNU Lesser General Public License
 version 2.1 in ‘/usr/share/common-licenses/LGPL-2.1’.
Name: gzstream, C++ iostream classes wrapping the zlib compression library.

Files: docs/themes/rtd/static/rtd.css_t
Copyright: © 2007-2010 by the Sphinx team
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:
 .
 * 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
 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.
Homepage: http://sphinx-doc.org
Name: Sphinx

License: GPL-2
 This program is free software; you can redistribute it and/or modify
 it under the terms of the GNU General Public License version 2 as
 published by the Free Software Foundation.
 .
 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, write to the Free Software Foundation, Inc.,
 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
Comment:
 On Debian systems, you can find a copy of the GNU General Public License
 version 2 in ‘/usr/share/common-licenses/GPL-2’.
