[med-svn] r2680 - trunk/packages/maq/trunk/debian

Fri Nov 14 11:50:22 UTC 2008

Author: plessy
Date: 2008-11-14 11:50:22 +0000 (Fri, 14 Nov 2008)
New Revision: 2680

Added:
   trunk/packages/maq/trunk/debian/README.source
   trunk/packages/maq/trunk/debian/reference
Removed:
   trunk/packages/maq/trunk/debian/README.Debian
   trunk/packages/maq/trunk/debian/README.Sources
Modified:
   trunk/packages/maq/trunk/debian/changelog
   trunk/packages/maq/trunk/debian/docs
Log:
Preparing new release.


Deleted: trunk/packages/maq/trunk/debian/README.Debian
===================================================================

--- trunk/packages/maq/trunk/debian/README.Debian	2008-11-14 07:38:43 UTC (rev 2679)
+++ trunk/packages/maq/trunk/debian/README.Debian	2008-11-14 11:50:22 UTC (rev 2680)
@@ -1,7 +0,0 @@
-maq for Debian
---------------
-
-The -m64 option has been disabled to build maq on all Debian platforms. Please
-report a bug of severity grave if it impairs your work.
-
- -- Charles Plessy <plessy at debian.org>  Mon, 07 Jul 2008 23:37:51 +0900

Deleted: trunk/packages/maq/trunk/debian/README.Sources
===================================================================
--- trunk/packages/maq/trunk/debian/README.Sources	2008-11-14 07:38:43 UTC (rev 2679)
+++ trunk/packages/maq/trunk/debian/README.Sources	2008-11-14 11:50:22 UTC (rev 2680)
@@ -1,21 +0,0 @@
-Short explanation how to handle the patch system quilt for this package
-to comply with Policy 3.8.0 (4.14. Source package handling: `debian/README.source'):
-
-This package uses the quilt patch system.  You can use
-
-   quilt push -a
-
-to apply all patches that were used to build this package.  If you use
-
-   quilt pop -a
-
-all pathces will be reverted to get the clean source.
-
-You might like to read more about the packaging policy of the Debian Med
-packaging team at
-
-   http://debian-med.alioth.debian.org/docs/policy.html
-
-
--- Andreas Tille <tille at debian.org>  Wed, 16 Jul 2008 12:01:33 +0200
-   
\ No newline at end of file

Copied: trunk/packages/maq/trunk/debian/README.source (from rev 2666, trunk/packages/maq/trunk/debian/README.Sources)
===================================================================
--- trunk/packages/maq/trunk/debian/README.source	                        (rev 0)
+++ trunk/packages/maq/trunk/debian/README.source	2008-11-14 11:50:22 UTC (rev 2680)
@@ -0,0 +1,21 @@
+Short explanation how to handle the patch system quilt for this package
+to comply with Policy 3.8.0 (4.14. Source package handling: `debian/README.source'):
+
+This package uses the quilt patch system.  You can use
+
+   quilt push -a
+
+to apply all patches that were used to build this package.  If you use
+
+   quilt pop -a
+
+all pathces will be reverted to get the clean source.
+
+You might like to read more about the packaging policy of the Debian Med
+packaging team at
+
+   http://debian-med.alioth.debian.org/docs/policy.html
+
+
+-- Andreas Tille <tille at debian.org>  Wed, 16 Jul 2008 12:01:33 +0200
+   
\ No newline at end of file


Property changes on: trunk/packages/maq/trunk/debian/README.source
___________________________________________________________________
Name: svn:mergeinfo
   + 

Modified: trunk/packages/maq/trunk/debian/changelog
===================================================================
--- trunk/packages/maq/trunk/debian/changelog	2008-11-14 07:38:43 UTC (rev 2679)
+++ trunk/packages/maq/trunk/debian/changelog	2008-11-14 11:50:22 UTC (rev 2680)
@@ -1,15 +1,27 @@
-maq (0.6.8-1) UNRELEASED; urgency=low
+maq (0.7.1-1) UNRELEASED; urgency=low
 
-  * New upstream release.
+  * New upstream release 0.7.1
+    - 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.
+  * debian/patches:
+    - 20_perl_path.patch deleted because accepted upstream.
+    - 10_prevent_-64_option.patch deleted because it seems to build fine
+      without.
+    - Directory and quilt build-dependancy kept to ease possible QA work.
   * 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>  Wed, 30 Jul 2008 21:48:56 +0900
+ -- Charles Plessy <plessy at debian.org>  Fri, 14 Nov 2008 20:17:11 +0900
 
 maq (0.6.7-1) unstable; urgency=low
 

Modified: trunk/packages/maq/trunk/debian/docs
===================================================================
--- trunk/packages/maq/trunk/debian/docs	2008-11-14 07:38:43 UTC (rev 2679)
+++ trunk/packages/maq/trunk/debian/docs	2008-11-14 11:50:22 UTC (rev 2680)
@@ -1,3 +1,4 @@
 NEWS
 README
 maq.pdf
+debian/reference

Added: trunk/packages/maq/trunk/debian/reference
===================================================================
--- trunk/packages/maq/trunk/debian/reference	                        (rev 0)
+++ trunk/packages/maq/trunk/debian/reference	2008-11-14 11:50:22 UTC (rev 2680)
@@ -0,0 +1,15 @@
+ at article{HengLi112008,
+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}
+}
+
+


