[med-svn] r5382 - trunk/packages/bwa/trunk/debian

Charles Plessy plessy at alioth.debian.org
Wed Oct 27 12:21:44 UTC 2010 

Author: plessy
Date: 2010-10-27 12:21:37 +0000 (Wed, 27 Oct 2010)
New Revision: 5382

Modified:
   trunk/packages/bwa/trunk/debian/changelog
   trunk/packages/bwa/trunk/debian/control
   trunk/packages/bwa/trunk/debian/copyright
Log:
New upstream release correcting scoring matrix.


Modified: trunk/packages/bwa/trunk/debian/changelog
===================================================================
--- trunk/packages/bwa/trunk/debian/changelog	2010-10-27 08:15:22 UTC (rev 5381)
+++ trunk/packages/bwa/trunk/debian/changelog	2010-10-27 12:21:37 UTC (rev 5382)
@@ -1,3 +1,15 @@
+bwa (0.5.8c-1) unstable; urgency=low
+
+  * Bug fix release, reverting the scoring system back to the one used in
+    0.5.7. 0.5.8a/b may produce a CIGAR like 10M2I10M4D2M which should not
+    happen in principle. Such wrong cigars also incur errors in indel calling
+    when samtools is in use (Closes: #601568).
+  * Incremented Standards-Version to reflect conformance with Policy 3.9.1
+    (debian/control, no changes needed).
+  * debian/copyright updated and reformatted.
+
+ -- Charles Plessy <plessy at debian.org>  Wed, 27 Oct 2010 21:14:34 +0900
+
 bwa (0.5.8a-1) unstable; urgency=low
 
   * New upstream release.

Modified: trunk/packages/bwa/trunk/debian/control
===================================================================
--- trunk/packages/bwa/trunk/debian/control	2010-10-27 08:15:22 UTC (rev 5381)
+++ trunk/packages/bwa/trunk/debian/control	2010-10-27 12:21:37 UTC (rev 5382)
@@ -5,7 +5,7 @@
 DM-Upload-Allowed: yes
 Uploaders: Charles Plessy <plessy at debian.org>
 Build-Depends: cdbs, debhelper (>= 7), zlib1g-dev
-Standards-Version: 3.9.0
+Standards-Version: 3.9.1
 Homepage: http://bio-bwa.sourceforge.net/ 
 Vcs-Browser: http://svn.debian.org/viewsvn/debian-med/trunk/packages/bwa/trunk/
 Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/bwa/trunk/

Modified: trunk/packages/bwa/trunk/debian/copyright
===================================================================
--- trunk/packages/bwa/trunk/debian/copyright	2010-10-27 08:15:22 UTC (rev 5381)
+++ trunk/packages/bwa/trunk/debian/copyright	2010-10-27 12:21:37 UTC (rev 5382)
@@ -1,61 +1,84 @@
-Name      :  Burrows-Wheeler Aligner
-Contact   :  bio-bwa-help at lists.sourceforge.net
-Source    :  http://qa.debian.org/watch/sf.php/bio-bwa/bwa-0.5.7.tar.bz2
+Format: DEP-5 (beta)
+Source: http://downloads.sourceforge.net/project/bio-bwa/bwa-0.5.8c.tar.bz2
+Copyright: © 2008 Genome Research Ltd (GRL)
+ 2008, by Heng Li <lh3 at sanger.ac.uk>
+ © 2003-2006, 2008, 2009, by Heng Li <lh3lh3 at gmail.com>
+ © 2008, 2009 by attractor <attractor at live.co.uk>
+ © 2008 Yuta Mori
+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.
 
-Copyright :  © 2008 Genome Research Ltd (GRL)
-             2008, by Heng Li <lh3 at sanger.ac.uk>
-             © 2003-2006, 2008, 2009, by Heng Li <lh3lh3 at gmail.com>
-             © 2008, 2009 by attractor <attractor at live.co.uk>
-             © 2008 Yuta Mori
-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: m4/acx_pthread.m4
+Copyright: © 2008 Steven G. Johnson <stevenj at alum.mit.edu>
+License: GPL-3+ 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 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 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
+Comment: On Debian systems, you can find a copy of the GNU General Public
+ License version 3 in ‘/usr/share/common-licenses/GPL-3’.
 
-
-Files     :  bwt_gen/bwt_gen.*
-Copyright :  © 2004, Wong Chi Kwong
-License   :  GPL-2+
- 
+Files: bwt_gen/bwt_gen.*
+Copyright: © 2004, Wong Chi Kwong
+License: GPL-2+
  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, write to the Free Software Foundation, Inc.,
  51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+Comment: On Debian systems, you can find a copy of the GNU General Public
+ License version 2 in ‘/usr/share/common-licenses/GPL-2’.
 
-On Debian systems, you can find a copy of the GNU General Public License
-version 2 in ‘/usr/share/common-licenses/GPL-2’.
-
-
-Files     :  bwt_gen/QSufSort.*
-Copyright :  1999, N. Jesper Larsson
-License   :
-    
+Files: bwt_gen/QSufSort.*
+Copyright: 1999, N. Jesper Larsson
+License:
  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

More information about the debian-med-commit mailing list