[med-svn] [salmon] 03/03: update d/copyright for embedded RapMap source

[Sascha Steinbiss]

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satta pushed a commit to branch master
in repository salmon.

commit 7e3465ac65c9f45bdb888d106dbf57e439db2966
Author: Sascha Steinbiss <satta at debian.org>
Date:   Sat Sep 10 11:45:51 2016 +0000

    update d/copyright for embedded RapMap source
---
 debian/copyright | 51 ++++++++++++++++++++++++++++++++++++++++++++++++---
 1 file changed, 48 insertions(+), 3 deletions(-)

diff --git a/debian/copyright b/debian/copyright
index 1a7040d..e657b04 100644
--- a/debian/copyright
+++ b/debian/copyright
@@ -8,7 +8,7 @@ Files-Excluded: doc/build/*
  include/obsolete
  include/kseq.h
  include/posix.h
- include/tensemble/Tree.h.backup.h 
+ include/tensemble/Tree.h.backup.h
  src/posix.cc
  cmake/Modules/FindTBB.cmake
  scripts/cpld.bash
@@ -52,9 +52,7 @@ Copyright: 2011, 2012 Remik Ziemlinski
 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
 
@@ -72,6 +70,36 @@ Files: include/atomicops.h
        include/readerwriterqueue.h
 Copyright: ©2013 Cameron Desrochers
 License: BSD-cameron-descrochers
+
+Files: debian/rapmap/*
+Copyright: (c) 2014-2016 COMputational BIology and Network Evolution lab
+License: GPL-3+
+Comment:
+ Taken from RapMap (https://github.com/COMBINE-lab/RapMap) with the following
+ license statement:
+ Since RapMap uses Jellyfish, it must be released under the GPL.
+ However, this is currently the only GPL dependency.  If it can be
+ replaced, I'd like to re-license RapMap under the BSD license.  I'd be
+ happy to accept pull-requests that replace the Jellyfish components
+ with a library released under a more liberal license (BSD-compatible).
+
+Files: debian/rapmap/BooPHF.hpp
+Copyright: ©2015 Guillaume Rizk
+License: Expat
+Comment:
+ This project is now BBHash, see
+ https://github.com/rizkg/BBHash/blob/master/LICENSE.
+
+Files: debian/rapmap/kseq.h
+Copyright: (c) 2008, 2009, 2011 Attractive Chaos <attractor at live.co.uk>
+License: Expat
+
+Files: debian/rapmap/macros.h
+       debian/rapmap/rank9b.*
+Copyright: ©2007-2013 Sebastiano Vigna
+License: LGPL-3+
+
+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:
  .
@@ -131,6 +159,23 @@ License: GPL-3+
     License version 3 can be found in the file
     `/usr/share/common-licenses/GPL-3'.
 
+License: LGPL-3+
+ 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 3 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 program; if not, see <http://www.gnu.org/licenses/>.
+ .
+ On Debian systems, the full text of the GNU Lesser General Public License
+ version 3 can be found in the file `/usr/share/common-licenses/LGPL-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

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