Merge branch 'master' into develop

COPYRIGHT, LICENSE: Change the license to GPL-3

COPYRIGHT

@@ -3,32 +3,37 @@ 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>
+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, version 3.
  .
  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/>.
+ along with this program. If not, see <http://www.gnu.org/licenses/>.
  .
- Debian may redistribute this software package.
+ For commercial licensing options, please contact
+ Patrick Rebstein <prebstein@bccancer.bc.ca>
 
 Files: *
-Copyright: Copyright 2014 Canada's Michael Smith Genome Sciences Centre
-License: GPL-NC-3+
+Copyright: Copyright 2016 British Columbia Cancer Agency Branch
+License: GPL-3
 
-Files: Common/* DataLayer/* DistanceEst/* FMIndex/* Map/* ParseAligns/*
-Copyright: Copyright 2014 Canada's Michael Smith Genome Sciences Centre
-License: GPL-3+
+Files: Layout/*
+Copyright: Copyright 2012 Shaun Jackman
+License: GPL-3
+
+Files: lib/bloomfilter/*
+Copyright: Copyright 2016 Justin Chu
+License: GPL-3
+
+Files: lib/rolling-hash/*
+Copyright: Copyright 2016 Hamid Mohamadi
+License: GPL-3
 
 Files: Common/cholesky.hpp
 Copyright: Copyright 2005 Gunter Winkler, Konstantin Kutzkow
@@ -38,10 +43,6 @@ 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+
@@ -127,22 +128,31 @@ License: Expat
  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/>.
+Files: lib/gtest-*/*
+Copyright: Copyright 2008 Google Inc.
+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:
  .
- 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'.
+ * 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 Google Inc. nor the names of its
+ contributors may be used to endorse or promote products derived from
+ this software without specific prior written permission.
+ .
+ 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.

LICENSE

@@ -1,24 +1,22 @@
 ABySS
-Copyright 2014 Canada's Michael Smith Genome Sciences Centre
+Copyright 2016 British Columbia Cancer Agency Branch
 
-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 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, version 3.
 
 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.
 
-The complete text of the GNU General Public License version 3 follows
-and is also available from the Free Software Foundation web site:
-http://www.gnu.org/licenses/
+You should have received a copy of the GNU General Public License
+along with this program. If not, see <http://www.gnu.org/licenses/>.
+
+For commercial licensing options, please contact
+Patrick Rebstein <prebstein@bccancer.bc.ca>
 
-See the file `COPYRIGHT` for details of the copyright and license of
+See the file COPYRIGHT for details of the copyright and license of
 each individual file included with this software.
 
                     GNU GENERAL PUBLIC LICENSE