[med-svn] [SCM] tophat branch, master, updated. upstream/1.4.0-38-ga7aaa86

[Charles Plessy]

The following commit has been merged in the master branch:
commit 859c3b96da040e6b3453573ffb5345940e65fc6f
Author: Charles Plessy <plessy at debian.org>
Date:   Mon Feb 6 14:43:04 2012 +0900

    Documented SeqAn and m4 macros.

diff --git a/debian/copyright b/debian/copyright
index 61e6bb9..06d9df4 100644
--- a/debian/copyright
+++ b/debian/copyright
@@ -1,11 +1,85 @@
 Format: http://dep.debian.net/deps/dep5
-Upstream-Name: tophat
-Source: http://tophat.cbcb.umd.edu/downloads/tophat-1.3.3.tar.gz
+Upstream-Name: TopHat
+Upstream-Contact: <cole at cs.umd.edu>
+Source: http://tophat.cbcb.umd.edu/downloads/tophat-1.4.1.tar.gz
+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. The SeqAn-1.2 library is used in TopHat and
+ Bowtie and some of its sources are included in TopHat source releases; its
+ authors are Andreas Doring, David Weese, Tobias Rausch, and Knut Reinert.
 
 Files: *
-Copyright: Copyright: Copyright (C) 2003-2010 Cole Trapnell et al
+Copyright: © 2003-2010 Cole Trapnell et al
 License: Artistic
 
+Files: src/SeqAn-1.2/* 
+Upstream-Name: SeqAn
+Copyright: © 2007
+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.
+ .
+ On Debian systems, the complete text of the GNU Lesser General Public License
+ version 3 can be found in the files ‘/usr/share/common-licenses/LGPL-3’ and
+ ‘/usr/share/common-licenses/GPL-3’.
+
+Files: src/SeqAn-1.2/index_sa_lss.h
+Copyright: © 1999, N. Jesper Larsson, all rights reserved.
+License: qsufsort.c
+ This file contains an implementation of the algorithm presented in "Faster
+ Suffix Sorting" by N. Jesper Larsson (jesper at cs.lth.se) and Kunihiko
+ Sadakane (sada at is.s.u-tokyo.ac.jp).
+ .
+ This software may be used freely for any purpose. However, when distributed,
+ the original source must be clearly stated, and, when the source code is
+ distributed, the copyright notice must be retained and any alterations in
+ the code must be clearly marked. No warranty is given regarding the quality
+ of this software.
+
+Files: ax_bam.m4
+Copyright: © 2010 Cole Trapnell <cole at cs.umd.edu>
+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.
+
+Files: ax_check_zlib.m4
+Copyright: © 2008 Loic Dachary <loic at senga.org>
+License: GPL-2+ with autoconf exception
+ 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 2 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 program. If not, see <http://www.gnu.org/licenses/>.
+ .
+ As a special exception, the respective Autoconf Macro's copyright owner
+ gives unlimited permission to copy, distribute and modify the configure
+ scripts that are the output of Autoconf when processing the Macro. You
+ need not follow the terms of the GNU General Public License when using
+ or distributing such scripts, even though portions of the text of the
+ Macro appear in them. The GNU General Public License (GPL) does govern
+ all other use of the material that constitutes the Autoconf Macro.
+ .
+ This special exception to the GPL applies to versions of the Autoconf
+ Macro released by the Autoconf Archive. When you make and distribute a
+ modified version of the Autoconf Macro, you may extend this special
+ exception to the GPL to apply to your modified version as well.
+
 Files: debian/*
 Copyright: 2011 Carlos Borroto <carlos.borroto at gmail.com>
            © 2011 Alex Mestiashvili <alex at biotec.tu-dresden.de>

-- 
A spliced read mapper for RNA-Seq