Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Upstream-Name: TopHat
Upstream-Contact: Daehwan Kim <infphilo@gmail.com>
Source: http://ccb.jhu.edu/software/tophat/index.shtml
Comment:
 Cole Trapnell wrote TopHat. TopHat is built on Bowtie, which was written by
 Ben Langmead and Cole Trapnell.  Daehwan Kim and Geo Pertea added support
 for SOLiD reads.
Files-Excluded:
    */src/SeqAn*
    */src/intervaltree*
    */src/sortedcontainers*

Files: *
Copyright: © 2003-2010 Cole Trapnell et al
License: Artistic

Files: ax_boost_thread.m4
Copyright: © 2009 Thomas Porschberg <thomas@randspringer.de>
           © 2009 Michael Tindal
License: GAP

Files: ax_boost_base.m4
Copyright: © 2009 Thomas Porschberg <thomas@randspringer.de>
License: GAP

Files: aclocal.m4
Copyright: © 1996-2005 Free Software Foundation, Inc.
License: M4-free
 This file is free software; the Free Software Foundation
 gives unlimited permission to copy and/or distribute it,
 with or without modifications, as long as this notice is preserved.

Files: INSTALL configure
Copyright: © 1992-2010 Free Software Foundation, Inc.
License: autobuild-free
 This configure script is free software; the Free Software Foundation
 gives unlimited permission to copy, distribute and modify it.

Files: src/samtools-0.1.18/*
Copyright: © 2008–2010, Genome Research Ltd. (GRL)
           © 2003–2006, 2008–2010, by Heng Li <lh3lh3@live.co.uk>
           © 2008–2010 Broad Institute
           © 2010 Illumina, Inc.
License: MIT

Files: debian/*
Copyright: © 2011 Carlos Borroto <carlos.borroto@gmail.com>
           © 2016 Alex Mestiashvili <alex@biotec.tu-dresden.de>
License: GPL-2+

License: GAP
 Copying and distribution of this file, with or without modification, are
 permitted in any medium without royalty provided the copyright notice
 and this notice are preserved.

License: Artistic
 This program is free software; you can redistribute it and/or modify
 it under the terms of the Artistic License, which comes with Perl.
 .
 On Debian systems, the complete text of the Artistic License can be
 found in `/usr/share/common-licenses/Artistic'.

License: GPL-2+
 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".

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.
