[med-svn] r6257 - in trunk/packages/maq/tags: . 0.7.1-4/debian
Charles Plessy
plessy at alioth.debian.org
Sun Mar 13 03:13:44 UTC 2011
Author: plessy
Date: 2011-03-13 03:13:38 +0000 (Sun, 13 Mar 2011)
New Revision: 6257
Added:
trunk/packages/maq/tags/0.7.1-4/
trunk/packages/maq/tags/0.7.1-4/debian/changelog
trunk/packages/maq/tags/0.7.1-4/debian/compat
trunk/packages/maq/tags/0.7.1-4/debian/control
trunk/packages/maq/tags/0.7.1-4/debian/copyright
trunk/packages/maq/tags/0.7.1-4/debian/maq.doc-base
trunk/packages/maq/tags/0.7.1-4/debian/upstream-metadata.yaml
Removed:
trunk/packages/maq/tags/0.7.1-4/debian/changelog
trunk/packages/maq/tags/0.7.1-4/debian/compat
trunk/packages/maq/tags/0.7.1-4/debian/control
trunk/packages/maq/tags/0.7.1-4/debian/copyright
trunk/packages/maq/tags/0.7.1-4/debian/maq.doc-base
Log:
[svn-buildpackage] Tagging maq 0.7.1-4
Deleted: trunk/packages/maq/tags/0.7.1-4/debian/changelog
===================================================================
--- trunk/packages/maq/trunk/debian/changelog 2011-03-12 22:31:11 UTC (rev 6254)
+++ trunk/packages/maq/tags/0.7.1-4/debian/changelog 2011-03-13 03:13:38 UTC (rev 6257)
@@ -1,62 +0,0 @@
-maq (0.7.1-4) UNRELEASED; urgency=low
-
- * Developmemt of Maq stopped in 2008. Its successors are BWA and SAMtools.
-
- -- Charles Plessy <plessy at debian.org> Mon, 01 Nov 2010 19:10:28 +0900
-
-maq (0.7.1-3) unstable; urgency=low
-
- * Distribute scripts that are not installed by upstream’s
- makefile in /usr/share/maq (debian/install).
- * Incremented Standards-Version in debian/policy to reflect
- conformance with Policy 3.8.2 (no changes needed).
- * debian/patch: made headers conformant with current draft of DEP3.
-
- -- Charles Plessy <plessy at debian.org> Fri, 17 Jul 2009 22:00:02 +0900
-
-maq (0.7.1-2) unstable; urgency=low
-
- * Enable LARGEFILE64_SOURCE to prevent a problem with zlib on
- 64bit archs (Thanks to Peter Green <plugwash at p10link.net> for
- the patch)
- Closes: #506009
- * Standards-Version: 3.8.1 (no changes needed)
-
- -- Andreas Tille <tille at debian.org> Thu, 16 Apr 2009 15:56:09 +0200
-
-maq (0.7.1-1) unstable; urgency=low
-
- * New upstream release 0.7.1 (Closes: 505820)
- - Accepts reads shorter than 127 bp (63 bp before).
- - .map alignment changes and not backward-compatible.
- - Reversion to short reads possible with --enable-shortreads.
- * New upstream release 0.6.8
- - New features for the 1000 genome project.
- - Error dependency coefficient reduced from 0.93 to 0.85.
- - Added mapvalidate command.
- - Support generating GLF format.
- - The mapcheck command can optionally dump additional information.
- * debian/patches:
- - 20_perl_path.patch deleted because accepted upstream.
- - 10_prevent_-64_option.patch reorganised to only modify configure.ac
- and forwarded upstream.
- - 20_prevent_-64_option.patch changes configure and can be regenerated
- by running autoreconf.
- * debian/control: typo corrected in short description (Closes: #492979)
- * debian/reference: BibTeX reference downloaded from
- http://genome.cshlp.org/citmgr?gca=genome;18/11/1851 with abstract
- removed because it is a copyrighted work.
- * debian/README.Sources renamed README.source to comply with Policy.
-
- -- Charles Plessy <plessy at debian.org> Sun, 16 Nov 2008 22:52:04 +0900
-
-maq (0.6.7-1) unstable; urgency=low
-
- [ Charles Plessy ]
- * Initial release (Closes: #489836)
-
- [ Andreas Tille ]
- * Rudely deleted -m64 option from configure because multiarch
- building leads to several problems
-
- -- Andreas Tille <tille at debian.org> Wed, 16 Jul 2008 12:01:33 +0200
Copied: trunk/packages/maq/tags/0.7.1-4/debian/changelog (from rev 6256, trunk/packages/maq/trunk/debian/changelog)
===================================================================
--- trunk/packages/maq/tags/0.7.1-4/debian/changelog (rev 0)
+++ trunk/packages/maq/tags/0.7.1-4/debian/changelog 2011-03-13 03:13:38 UTC (rev 6257)
@@ -0,0 +1,68 @@
+maq (0.7.1-4) unstable; urgency=low
+
+ * Development of Maq stopped in 2008. Its successors are BWA and SAMtools.
+ (debian/control, debian/maq.doc-base).
+ * DEP-5 conformant debian/copyright file, checked with ‘config-edit’.
+ * Use Debhelper 8 (debian/control, debian/compat).
+ * Collected various information in debian/upstream-metadata.yaml.
+ * Incremented Standards-Version in debian/policy to reflect
+ conformance with Policy 3.9.1 (no changes needed).
+
+ -- Charles Plessy <plessy at debian.org> Sun, 13 Mar 2011 11:35:38 +0900
+
+maq (0.7.1-3) unstable; urgency=low
+
+ * Distribute scripts that are not installed by upstream’s
+ makefile in /usr/share/maq (debian/install).
+ * Incremented Standards-Version in debian/policy to reflect
+ conformance with Policy 3.8.2 (no changes needed).
+ * debian/patch: made headers conformant with current draft of DEP3.
+
+ -- Charles Plessy <plessy at debian.org> Fri, 17 Jul 2009 22:00:02 +0900
+
+maq (0.7.1-2) unstable; urgency=low
+
+ * Enable LARGEFILE64_SOURCE to prevent a problem with zlib on
+ 64bit archs (Thanks to Peter Green <plugwash at p10link.net> for
+ the patch)
+ Closes: #506009
+ * Standards-Version: 3.8.1 (no changes needed)
+
+ -- Andreas Tille <tille at debian.org> Thu, 16 Apr 2009 15:56:09 +0200
+
+maq (0.7.1-1) unstable; urgency=low
+
+ * New upstream release 0.7.1 (Closes: 505820)
+ - Accepts reads shorter than 127 bp (63 bp before).
+ - .map alignment changes and not backward-compatible.
+ - Reversion to short reads possible with --enable-shortreads.
+ * New upstream release 0.6.8
+ - New features for the 1000 genome project.
+ - Error dependency coefficient reduced from 0.93 to 0.85.
+ - Added mapvalidate command.
+ - Support generating GLF format.
+ - The mapcheck command can optionally dump additional information.
+ * debian/patches:
+ - 20_perl_path.patch deleted because accepted upstream.
+ - 10_prevent_-64_option.patch reorganised to only modify configure.ac
+ and forwarded upstream.
+ - 20_prevent_-64_option.patch changes configure and can be regenerated
+ by running autoreconf.
+ * debian/control: typo corrected in short description (Closes: #492979)
+ * debian/reference: BibTeX reference downloaded from
+ http://genome.cshlp.org/citmgr?gca=genome;18/11/1851 with abstract
+ removed because it is a copyrighted work.
+ * debian/README.Sources renamed README.source to comply with Policy.
+
+ -- Charles Plessy <plessy at debian.org> Sun, 16 Nov 2008 22:52:04 +0900
+
+maq (0.6.7-1) unstable; urgency=low
+
+ [ Charles Plessy ]
+ * Initial release (Closes: #489836)
+
+ [ Andreas Tille ]
+ * Rudely deleted -m64 option from configure because multiarch
+ building leads to several problems
+
+ -- Andreas Tille <tille at debian.org> Wed, 16 Jul 2008 12:01:33 +0200
Deleted: trunk/packages/maq/tags/0.7.1-4/debian/compat
===================================================================
--- trunk/packages/maq/trunk/debian/compat 2011-03-12 22:31:11 UTC (rev 6254)
+++ trunk/packages/maq/tags/0.7.1-4/debian/compat 2011-03-13 03:13:38 UTC (rev 6257)
@@ -1 +0,0 @@
-7
Copied: trunk/packages/maq/tags/0.7.1-4/debian/compat (from rev 6256, trunk/packages/maq/trunk/debian/compat)
===================================================================
--- trunk/packages/maq/tags/0.7.1-4/debian/compat (rev 0)
+++ trunk/packages/maq/tags/0.7.1-4/debian/compat 2011-03-13 03:13:38 UTC (rev 6257)
@@ -0,0 +1 @@
+8
Deleted: trunk/packages/maq/tags/0.7.1-4/debian/control
===================================================================
--- trunk/packages/maq/trunk/debian/control 2011-03-12 22:31:11 UTC (rev 6254)
+++ trunk/packages/maq/tags/0.7.1-4/debian/control 2011-03-13 03:13:38 UTC (rev 6257)
@@ -1,24 +0,0 @@
-Source: maq
-Section: science
-Priority: optional
-Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-DM-Upload-Allowed: yes
-Uploaders: Andreas Tille <tille at debian.org>,
- Charles Plessy <plessy at debian.org>
-Build-Depends: cdbs, debhelper (>= 7), autotools-dev, zlib1g-dev, quilt
-Standards-Version: 3.8.2
-Homepage: http://maq.sourceforge.net/
-Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/maq/trunk/?rev=0&sc=0
-Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/maq/trunk/
-
-Package: maq
-Architecture: any
-Depends: ${shlibs:Depends}, ${misc:Depends}
-Description: maps short fixed-length polymorphic DNA sequence reads to reference sequences
- Maq (short for Mapping and Assembly with Quality) builds mapping assemblies
- from short reads generated by the next-generation sequencing machines. It was
- particularly designed for Illumina-Solexa 1G Genetic Analyzer, and has a
- preliminary functionality to handle ABI SOLiD data. Maq is previously known as
- mapass2.
- .
- Developmemt of Maq stopped in 2008. Its successors are BWA and SAMtools.
Copied: trunk/packages/maq/tags/0.7.1-4/debian/control (from rev 6256, trunk/packages/maq/trunk/debian/control)
===================================================================
--- trunk/packages/maq/tags/0.7.1-4/debian/control (rev 0)
+++ trunk/packages/maq/tags/0.7.1-4/debian/control 2011-03-13 03:13:38 UTC (rev 6257)
@@ -0,0 +1,25 @@
+Source: maq
+Section: science
+Priority: optional
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+DM-Upload-Allowed: yes
+Uploaders: Andreas Tille <tille at debian.org>,
+ Charles Plessy <plessy at debian.org>
+Build-Depends: cdbs, debhelper (>= 8), autotools-dev, zlib1g-dev, quilt
+Standards-Version: 3.9.1
+Homepage: http://maq.sourceforge.net/
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/maq/trunk/?rev=0&sc=0
+Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/maq/trunk/
+
+Package: maq
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Suggests: bwa, samtools
+Description: maps short fixed-length polymorphic DNA sequence reads to reference sequences
+ Maq (short for Mapping and Assembly with Quality) builds mapping assemblies
+ from short reads generated by the next-generation sequencing machines. It was
+ particularly designed for Illumina-Solexa 1G Genetic Analyzer, and has a
+ preliminary functionality to handle ABI SOLiD data. Maq is previously known as
+ mapass2.
+ .
+ Developmemt of Maq stopped in 2008. Its successors are BWA and SAMtools.
Deleted: trunk/packages/maq/tags/0.7.1-4/debian/copyright
===================================================================
--- trunk/packages/maq/trunk/debian/copyright 2011-03-12 22:31:11 UTC (rev 6254)
+++ trunk/packages/maq/tags/0.7.1-4/debian/copyright 2011-03-13 03:13:38 UTC (rev 6257)
@@ -1,50 +0,0 @@
-Machine-readable license summary, see ‘http://dep.debian.net/deps/dep5/’.
-
-Name : Maq: Mapping and Assembly with Qualities
-Contact : Heng Li <lh3 at sanger.ac.uk>
-Source : http://downloads.sourceforge.net/maq/maq-0.7.1.tar.bz2
-
-License: GPL3+
-Copyright: 2003-2008, Heng Li <lh3 at sanger.ac.uk>
-
- 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/>.
-
-On Debian systems, the complete text of the GNU General Public License version
-3 can be found in ‘/usr/share/common-licenses/GPL-3’.
-
-Files: stdaln.* stdhash.hh
-Copyright: 2003-2008, Heng Li <lh3 at sanger.ac.uk>
-License: LGPL-2.1+
- 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 2.1 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.
-
- You should have received a copy of the GNU Lesser General Public
- License along with this library; if not, write to the Free Software
- Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301, USA.
-
-On Debian systems, the complete text of the GNU Lesser General Public License
-version 2.1 can be found in ‘/usr/share/common-licenses/LGPL-2.1’.
-
-Files: debian/*
-Copyright: 2008–2009, Charles Plessy <plessy at debian.org>,
- Andreas Tille <tille at debian.org>
-License: Same as Maq itelf
- (see above)
Copied: trunk/packages/maq/tags/0.7.1-4/debian/copyright (from rev 6255, trunk/packages/maq/trunk/debian/copyright)
===================================================================
--- trunk/packages/maq/tags/0.7.1-4/debian/copyright (rev 0)
+++ trunk/packages/maq/tags/0.7.1-4/debian/copyright 2011-03-13 03:13:38 UTC (rev 6257)
@@ -0,0 +1,45 @@
+Format: http://dep.debian.net/deps/dep5/
+Source: http://downloads.sourceforge.net/maq/maq-0.7.1.tar.bz2
+
+Files: *
+Copyright: 2003-2008, Heng Li <lh3 at sanger.ac.uk>
+License: GPL-3+
+ 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/>.
+Comment: On Debian systems, the complete text of the GNU General Public
+ License version 3 can be found in ‘/usr/share/common-licenses/GPL-3’.
+
+Files: stdaln.* stdhash.hh
+Copyright: 2003-2008, Heng Li <lh3 at sanger.ac.uk>
+License: LGPL-2.1+
+ 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 2.1 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.
+ .
+ You should have received a copy of the GNU Lesser General Public
+ License along with this library; if not, write to the Free Software
+ Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301, USA.
+Comment: On Debian systems, the complete text of the GNU Lesser General
+ Public License version 2.1 can be found in ‘/usr/share/common-licenses/LGPL-2.1’.
+
+Files: debian/*
+Copyright: 2008–2011, Charles Plessy <plessy at debian.org>,
+ Andreas Tille <tille at debian.org>
+License: same-as-upstream
+ Same as Maq itelf (see above).
Deleted: trunk/packages/maq/tags/0.7.1-4/debian/maq.doc-base
===================================================================
--- trunk/packages/maq/trunk/debian/maq.doc-base 2011-03-12 22:31:11 UTC (rev 6254)
+++ trunk/packages/maq/tags/0.7.1-4/debian/maq.doc-base 2011-03-13 03:13:38 UTC (rev 6257)
@@ -1,8 +0,0 @@
-Document: maq
-Title: Maq — Mapping and Assembly with Quality
-Author: Heng Li <lh3 at sanger.ac.uk>
-Abstract: Maq manual page in PDF format
-Section: Science/Biology
-
-Format: PDF
-Files: /usr/share/doc/maq/maq.pdf
Copied: trunk/packages/maq/tags/0.7.1-4/debian/maq.doc-base (from rev 6256, trunk/packages/maq/trunk/debian/maq.doc-base)
===================================================================
--- trunk/packages/maq/tags/0.7.1-4/debian/maq.doc-base (rev 0)
+++ trunk/packages/maq/tags/0.7.1-4/debian/maq.doc-base 2011-03-13 03:13:38 UTC (rev 6257)
@@ -0,0 +1,10 @@
+Document: maq
+Title: Maq — Mapping and Assembly with Quality
+Author: Heng Li <lh3 at sanger.ac.uk>
+Abstract: Maq manual page in PDF format
+ Note that Developmemt of Maq stopped in 2008. Its successors are BWA
+ and SAMtools.
+Section: Science/Biology
+
+Format: PDF
+Files: /usr/share/doc/maq/maq.pdf
Copied: trunk/packages/maq/tags/0.7.1-4/debian/upstream-metadata.yaml (from rev 6256, trunk/packages/maq/trunk/debian/upstream-metadata.yaml)
===================================================================
--- trunk/packages/maq/tags/0.7.1-4/debian/upstream-metadata.yaml (rev 0)
+++ trunk/packages/maq/tags/0.7.1-4/debian/upstream-metadata.yaml 2011-03-13 03:13:38 UTC (rev 6257)
@@ -0,0 +1,20 @@
+Archive: SourceForge
+Contact: Heng Li <lh3 at sanger.ac.uk>
+DOI: 10.1101/gr.078212.108
+FAQ: http://maq.sourceforge.net/faq.shtml
+Name: Maq
+Homepage: http://maq.sourceforge.net/
+PMID: 18714091
+Reference:
+ author: Li, Heng and Ruan, Jue and Durbin, Richard
+ title: Mapping short DNA sequencing reads and calling variants using mapping quality scores
+ journal: Genome Research
+ volume: 18
+ number: 11
+ pages: 1851-1858
+ doi: 10.1101/gr.078212.108
+ year: 2008
+ URL: http://genome.cshlp.org/content/18/11/1851.abstract
+ eprint: http://genome.cshlp.org/content/18/11/1851.full.pdf+html
+Watch: |
+ http://sf.net/maq/maq-([\d\.]+)\.tar\.bz2
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