[med-svn] [SCM] Processing of sequence alignments in SAM and BAM formats. branch, master, updated. debian/0.1.8-1-7-g349ae4d
Charles Plessy
plessy at debian.org
Mon Nov 1 11:17:07 UTC 2010
The following commit has been merged in the master branch:
commit 2adb485e0042dff362c6f5159c3e4cf6f4787b61
Author: Charles Plessy <plessy at debian.org>
Date: Mon Nov 1 20:04:01 2010 +0900
# Updated and reformatted debian/copyright according to latest DEP-5 draft.
diff --git a/debian/copyright b/debian/copyright
index 67f3481..48b777e 100644
--- a/debian/copyright
+++ b/debian/copyright
@@ -1,119 +1,104 @@
-Machine-readable license summary, see ‘http://dep.debian.net/deps/dep5/’.
-
-
-Name : SAMtools
-Contact : SAMtools mailing list <samtools-help at lists.sourceforge.net>
-Source : http://qa.debian.org/watch/sf.php/samtools/samtools-0.1.7a.tar.bz2
-
-
-Copyright : © 2008–2010, Genome Research Ltd. (GRL)
-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.
-
-Files : bcftools/bcf.h
-Copyright : © 2010 Broad Institute
-License : MIT
+Format: DEP-5 (beta)
+Source: http://qa.debian.org/watch/sf.php/samtools/samtools-0.1.9.tar.bz2
+Copyright: © 2008–2010, Genome Research Ltd. (GRL)
+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.
+
+Files: bcftools/bcf.h
+Copyright: © 2010 Broad Institute
+License: MIT
Files: misc/export2sam.pl
-Copyright : © 2008–2009, Genome Research Ltd.
-Copyright : © 2010 Illumina, Inc.
-License : MIT
-
-
-Files : bgzf.*, bgzip.c
-Copyright : © 2008 Broad Institute / Massachusetts Institute of Technology
-License : MIT
-
-
-Files : razf.*
-Name : RAZF : Random Access compressed(Z) File
-Copyright : 2008, Jue Ruan <ruanjue at gmail.com>, Heng Li <lh3 at sanger.ac.uk>
-License : Similar to NetBSD license.
-
- Redistribution and use in source and binary forms, with or without
- modification, are permitted provided that the following conditions
- are met:
- 1. Redistributions of source code must retain the above copyright
- notice, this list of conditions and the following disclaimer.
- 2. 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.
-
- THIS SOFTWARE IS PROVIDED BY THE AUTHOR 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 AUTHOR 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.
-
-
-Files : misc/md5.*
-License :
-
- This code implements the MD5 message-digest algorithm.
- The algorithm is due to Ron Rivest. This code was
- written by Colin Plumb in 1993, no copyright is claimed.
- This code is in the public domain; do with it what you wish.
-
- Equivalent code is available from RSA Data Security, Inc.
- This code has been tested against that, and is equivalent,
- except that you don't need to include two pages of legalese
- with every copy.
-
- To compute the message digest of a chunk of bytes, declare an
- MD5Context structure, pass it to MD5Init, call MD5Update as
- needed on buffers full of bytes, and then call MD5Final, which
- will fill a supplied 16-byte array with the digest.
-
-
-Files : win32/xcurses.h
-License : Public Domain
-
- This file is part of PDCurses (http://pdcurses.sourceforge.net/),
- which is in the public domain.
-
-
-Files : win32/z*.h
-Copyright : © 1995-2005 Jean-loup Gailly and Mark Adler
-License : zlib
-
- This software is provided 'as-is', without any express or implied
- warranty. In no event will the authors be held liable for any damages
- arising from the use of this software.
-
- Permission is granted to anyone to use this software for any purpose,
- including commercial applications, and to alter it and redistribute it
- freely, subject to the following restrictions:
-
- 1. The origin of this software must not be misrepresented; you must not
- claim that you wrote the original software. If you use this software
- in a product, an acknowledgment in the product documentation would be
- appreciated but is not required.
- 2. Altered source versions must be plainly marked as such, and must not be
- misrepresented as being the original software.
- 3. This notice may not be removed or altered from any source distribution.
-
- Jean-loup Gailly Mark Adler
- jloup at gzip.org madler at alumni.caltech.edu
+Copyright: © 2008–2009, Genome Research Ltd.
+Copyright: © 2010 Illumina, Inc.
+License: MIT
+
+Files: bgzf.*, bgzip.c
+Copyright: © 2008 Broad Institute / Massachusetts Institute of Technology
+License: MIT
+
+
+Files: razf.*
+Name: RAZF : Random Access compressed(Z) File
+Copyright: 2008, Jue Ruan <ruanjue at gmail.com>, Heng Li <lh3 at sanger.ac.uk>
+License: Similar to NetBSD license.
+ Redistribution and use in source and binary forms, with or without
+ modification, are permitted provided that the following conditions
+ are met:
+ 1. Redistributions of source code must retain the above copyright
+ notice, this list of conditions and the following disclaimer.
+ 2. 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.
+ .
+ THIS SOFTWARE IS PROVIDED BY THE AUTHOR 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 AUTHOR 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.
+
+Files: misc/md5.*
+License:
+ This code implements the MD5 message-digest algorithm.
+ The algorithm is due to Ron Rivest. This code was
+ written by Colin Plumb in 1993, no copyright is claimed.
+ This code is in the public domain; do with it what you wish.
+ .
+ Equivalent code is available from RSA Data Security, Inc.
+ This code has been tested against that, and is equivalent,
+ except that you don't need to include two pages of legalese
+ with every copy.
+ .
+ To compute the message digest of a chunk of bytes, declare an
+ MD5Context structure, pass it to MD5Init, call MD5Update as
+ needed on buffers full of bytes, and then call MD5Final, which
+ will fill a supplied 16-byte array with the digest.
+
+Files: win32/xcurses.h
+License: Public Domain
+ This file is part of PDCurses (http://pdcurses.sourceforge.net/),
+ which is in the public domain.
+
+Files: win32/z*.h
+Copyright: © 1995-2005 Jean-loup Gailly and Mark Adler
+License: zlib
+ This software is provided 'as-is', without any express or implied
+ warranty. In no event will the authors be held liable for any damages
+ arising from the use of this software.
+ .
+ Permission is granted to anyone to use this software for any purpose,
+ including commercial applications, and to alter it and redistribute it
+ freely, subject to the following restrictions:
+ .
+ 1. The origin of this software must not be misrepresented; you must not
+ claim that you wrote the original software. If you use this software
+ in a product, an acknowledgment in the product documentation would be
+ appreciated but is not required.
+ 2. Altered source versions must be plainly marked as such, and must not be
+ misrepresented as being the original software.
+ 3. This notice may not be removed or altered from any source distribution.
+ .
+ Jean-loup Gailly Mark Adler
+ jloup at gzip.org madler at alumni.caltech.edu
--
Processing of sequence alignments in SAM and BAM formats.
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