[med-svn] [tophat] 03/06: Update d/copyright

[Alex Mestiashvili]

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malex-guest pushed a commit to branch master
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commit 651611aacf9a35e561f02a74aa5da67809084812
Author: Alexandre Mestiashvili <alex at biotec.tu-dresden.de>
Date:   Thu Mar 17 18:23:18 2016 +0100

    Update d/copyright
    
    Add Files: section describing embedded copy samtools-0.1.18,
    update copyright years, add MIT license text,
    add /src/intervaltree and /src/sortedcontainers to Files-Excluded:
---
 debian/copyright | 31 +++++++++++++++++++++++++++++--
 1 file changed, 29 insertions(+), 2 deletions(-)

diff --git a/debian/copyright b/debian/copyright
index a6c14df..6d96079 100644
--- a/debian/copyright
+++ b/debian/copyright
@@ -1,13 +1,15 @@
 Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
 Upstream-Name: TopHat
 Upstream-Contact: Daehwan Kim <infphilo at gmail.com>
-Source: http://ccb.jhu.edu/software/tophat/downloads/tophat-2.0.12.tar.gz
+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
@@ -35,9 +37,16 @@ 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 at live.co.uk>
+           © 2008–2010 Broad Institute
+           © 2010 Illumina, Inc.
+License: MIT
+
 Files: debian/*
 Copyright: © 2011 Carlos Borroto <carlos.borroto at gmail.com>
-           © 2014 Alex Mestiashvili <alex at biotec.tu-dresden.de>
+           © 2016 Alex Mestiashvili <alex at biotec.tu-dresden.de>
 License: GPL-2+
 
 License: GAP
@@ -69,3 +78,21 @@ License: GPL-2+
  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.

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