[med-svn] r5383 - in trunk/packages/bwa/tags: . 0.5.8c-1/debian
Charles Plessy
plessy at alioth.debian.org
Wed Oct 27 12:27:55 UTC 2010
Author: plessy
Date: 2010-10-27 12:27:54 +0000 (Wed, 27 Oct 2010)
New Revision: 5383
Added:
trunk/packages/bwa/tags/0.5.8c-1/
trunk/packages/bwa/tags/0.5.8c-1/debian/changelog
trunk/packages/bwa/tags/0.5.8c-1/debian/control
trunk/packages/bwa/tags/0.5.8c-1/debian/copyright
Removed:
trunk/packages/bwa/tags/0.5.8c-1/debian/changelog
trunk/packages/bwa/tags/0.5.8c-1/debian/control
trunk/packages/bwa/tags/0.5.8c-1/debian/copyright
Log:
[svn-buildpackage] Tagging bwa 0.5.8c-1
Deleted: trunk/packages/bwa/tags/0.5.8c-1/debian/changelog
===================================================================
--- trunk/packages/bwa/trunk/debian/changelog 2010-10-27 08:15:22 UTC (rev 5381)
+++ trunk/packages/bwa/tags/0.5.8c-1/debian/changelog 2010-10-27 12:27:54 UTC (rev 5383)
@@ -1,44 +0,0 @@
-bwa (0.5.8a-1) unstable; urgency=low
-
- * New upstream release.
- * Use the more convenient viewsvn as VCS-Broswer (debian/control).
- * Incremented Standards-Version to reflect conformance with
- Policy 3.9.0 (debian/control, no changes needed).
-
- -- Charles Plessy <plessy at debian.org> Wed, 30 Jun 2010 10:44:30 +0900
-
-bwa (0.5.7-1) unstable; urgency=low
-
- * New upstream release.
-
- -- Charles Plessy <plessy at debian.org> Tue, 02 Mar 2010 23:33:06 +0900
-
-bwa (0.5.6-1) unstable; urgency=low
-
- * New upstream release.
- * Incremented Standards-Version to reflect conformance with
- Policy 3.8.4 (debian/control).
-
- -- Charles Plessy <plessy at debian.org> Wed, 17 Feb 2010 12:48:57 +0900
-
-bwa (0.5.5-1) unstable; urgency=low
-
- * New upstream release.
- * Using Dpkg source format version ‘3.0 (quilt)’ (debian/source/format).
-
- -- Charles Plessy <plessy at debian.org> Wed, 11 Nov 2009 23:05:19 +0900
-
-bwa (0.5.4-1) unstable; urgency=low
-
- * New upstream release, see ‘/usr/share/doc/bwa/NEWS.gz’.
- * Refreshed debian/copyright.
- * Reflected the rename of dBWT-Sw to BWA-SW in the package's description
- (debian/control).
-
- -- Charles Plessy <plessy at debian.org> Mon, 19 Oct 2009 13:59:42 +0900
-
-bwa (0.5.3-1) unstable; urgency=low
-
- * Initial release (Closes: #548719)
-
- -- Charles Plessy <plessy at debian.org> Thu, 08 Oct 2009 19:20:41 +0900
Copied: trunk/packages/bwa/tags/0.5.8c-1/debian/changelog (from rev 5382, trunk/packages/bwa/trunk/debian/changelog)
===================================================================
--- trunk/packages/bwa/tags/0.5.8c-1/debian/changelog (rev 0)
+++ trunk/packages/bwa/tags/0.5.8c-1/debian/changelog 2010-10-27 12:27:54 UTC (rev 5383)
@@ -0,0 +1,56 @@
+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.
+ * Use the more convenient viewsvn as VCS-Broswer (debian/control).
+ * Incremented Standards-Version to reflect conformance with
+ Policy 3.9.0 (debian/control, no changes needed).
+
+ -- Charles Plessy <plessy at debian.org> Wed, 30 Jun 2010 10:44:30 +0900
+
+bwa (0.5.7-1) unstable; urgency=low
+
+ * New upstream release.
+
+ -- Charles Plessy <plessy at debian.org> Tue, 02 Mar 2010 23:33:06 +0900
+
+bwa (0.5.6-1) unstable; urgency=low
+
+ * New upstream release.
+ * Incremented Standards-Version to reflect conformance with
+ Policy 3.8.4 (debian/control).
+
+ -- Charles Plessy <plessy at debian.org> Wed, 17 Feb 2010 12:48:57 +0900
+
+bwa (0.5.5-1) unstable; urgency=low
+
+ * New upstream release.
+ * Using Dpkg source format version ‘3.0 (quilt)’ (debian/source/format).
+
+ -- Charles Plessy <plessy at debian.org> Wed, 11 Nov 2009 23:05:19 +0900
+
+bwa (0.5.4-1) unstable; urgency=low
+
+ * New upstream release, see ‘/usr/share/doc/bwa/NEWS.gz’.
+ * Refreshed debian/copyright.
+ * Reflected the rename of dBWT-Sw to BWA-SW in the package's description
+ (debian/control).
+
+ -- Charles Plessy <plessy at debian.org> Mon, 19 Oct 2009 13:59:42 +0900
+
+bwa (0.5.3-1) unstable; urgency=low
+
+ * Initial release (Closes: #548719)
+
+ -- Charles Plessy <plessy at debian.org> Thu, 08 Oct 2009 19:20:41 +0900
Deleted: trunk/packages/bwa/tags/0.5.8c-1/debian/control
===================================================================
--- trunk/packages/bwa/trunk/debian/control 2010-10-27 08:15:22 UTC (rev 5381)
+++ trunk/packages/bwa/tags/0.5.8c-1/debian/control 2010-10-27 12:27:54 UTC (rev 5383)
@@ -1,23 +0,0 @@
-Source: bwa
-Section: science
-Priority: optional
-Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-DM-Upload-Allowed: yes
-Uploaders: Charles Plessy <plessy at debian.org>
-Build-Depends: cdbs, debhelper (>= 7), zlib1g-dev
-Standards-Version: 3.9.0
-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/
-
-Package: bwa
-Architecture: any
-Depends: ${shlibs:Depends}, ${misc:Depends}
-Suggests: samtools
-Description: Burrows-Wheeler Aligner
- Burrows-Wheeler Aligner (BWA) is a program that aligns relatively short
- nucleotide sequences against a long reference sequence such as the human
- genome. It implements two algorithms, bwa-short and BWA-SW. The former works
- for query sequences shorter than 200 bp and the latter for longer sequences up
- to around 100 kbp. Both algorithms do gapped alignment. They are usually more
- accurate and faster on queries with low error rates.
Copied: trunk/packages/bwa/tags/0.5.8c-1/debian/control (from rev 5382, trunk/packages/bwa/trunk/debian/control)
===================================================================
--- trunk/packages/bwa/tags/0.5.8c-1/debian/control (rev 0)
+++ trunk/packages/bwa/tags/0.5.8c-1/debian/control 2010-10-27 12:27:54 UTC (rev 5383)
@@ -0,0 +1,23 @@
+Source: bwa
+Section: science
+Priority: optional
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+DM-Upload-Allowed: yes
+Uploaders: Charles Plessy <plessy at debian.org>
+Build-Depends: cdbs, debhelper (>= 7), zlib1g-dev
+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/
+
+Package: bwa
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Suggests: samtools
+Description: Burrows-Wheeler Aligner
+ Burrows-Wheeler Aligner (BWA) is a program that aligns relatively short
+ nucleotide sequences against a long reference sequence such as the human
+ genome. It implements two algorithms, bwa-short and BWA-SW. The former works
+ for query sequences shorter than 200 bp and the latter for longer sequences up
+ to around 100 kbp. Both algorithms do gapped alignment. They are usually more
+ accurate and faster on queries with low error rates.
Deleted: trunk/packages/bwa/tags/0.5.8c-1/debian/copyright
===================================================================
--- trunk/packages/bwa/trunk/debian/copyright 2010-10-27 08:15:22 UTC (rev 5381)
+++ trunk/packages/bwa/tags/0.5.8c-1/debian/copyright 2010-10-27 12:27:54 UTC (rev 5383)
@@ -1,63 +0,0 @@
-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
-
-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 : 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.
-
-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 :
-
- 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.
Copied: trunk/packages/bwa/tags/0.5.8c-1/debian/copyright (from rev 5382, trunk/packages/bwa/trunk/debian/copyright)
===================================================================
--- trunk/packages/bwa/tags/0.5.8c-1/debian/copyright (rev 0)
+++ trunk/packages/bwa/tags/0.5.8c-1/debian/copyright 2010-10-27 12:27:54 UTC (rev 5383)
@@ -0,0 +1,86 @@
+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.
+
+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+
+ 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’.
+
+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
+ the code must be clearly marked. No warranty is given regarding the quality
+ of this software.
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