Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Upstream-Name: ABySS
Upstream-Contact: Shaun Jackman <sjackman@gmail.com>
Source: https://github.com/bcgsc/abyss

License: GPL-NC-3+
 You may use, redistribute and modify this software for non-commercial
 purposes 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.
 .
 To license ABySS for commercial purposes, please contact
 Patrick Rebstein <prebstein@bccancer.bc.ca>
 .
 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 software. If not, see <http://www.gnu.org/licenses/>.
 .
 Debian may redistribute this software package.

Files: *
Copyright: Copyright 2014 Canada's Michael Smith Genome Sciences Centre
License: GPL-NC-3+

Files: Common/* DataLayer/* DistanceEst/* FMIndex/* Map/* ParseAligns/*
Copyright: Copyright 2014 Canada's Michael Smith Genome Sciences Centre
License: GPL-3+

Files: Common/cholesky.hpp
Copyright: Copyright 2005 Gunter Winkler, Konstantin Kutzkow
License: LGPL-2.1+

Files: Common/city.cc Common/city.h
Copyright: Copyright 2011 Google, Inc.
License: Expat

Files: Layout/*
Copyright: Copyright 2012 Shaun Jackman
License: GPL-3+

Files: dialign/*
Copyright: Copyright 2008 Amarendran R. Subramanian
License: LGPL-2.1+

License: LGPL-2.1+
 On Debian systems, see `/usr/share/common-licenses/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
 .
 Amarendran R. Subramanian, hereby disclaims all copyright interest in the
 DIALIGN-TX (a multiple sequence alignment algorithm) written by Amarendran R. Subramanian.
 .
 Amarendran R. Subramanian, 2004-2008
 .
 DIALIGN-TX has been co-authored by Volker Menrad and Dorothea Emig.
 .
 Research work using DIALIGN-TX should cite:
 .
 DIALIGN-TX: improvement of the segment-based approach for multiple
 sequence alignment by combining greedy and progressive alignment
 strategies
 Amarendran R. Subramanian, Michael Kaufmann, Burkhard Morgenstern,
 Algorithms for Molecular Biology 3:6, 2008
 .
 DIALIGN-T: An improved algorithm for segment-based multiple
 sequence alignment
 Amarendran R. Subramanian, Jan Weyer-Menkhoff, Michael Kaufmann,
 Burkhard Morgenstern, BMC Bioinformatics 6:66, 2005

Files: FMIndex/bit_array.h
Copyright: Copyright 2010 Daisuke Okanohara
License: BSD-3-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.
 .
 Neither the name of the authors nor the names of its contributors
 may be used to endorse or promote products derived from this
 software without specific prior written permission.

Files: FMIndex/sais.hxx
Copyright: Copyright 2010 Yuta Mori
License: Expat

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 software. 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'.
