Imported Debian patch 0.1.6~dfsg-1

diff --git a/debian/README.source b/debian/README.source
new file mode 100644 (file)
index 0000000..21aa2af
--- /dev/null
+++ b/debian/README.source
@@ -0,0 +1,5 @@
+The original sources of Samtools were modified by removing the win32 directory.
+This was done using the git-import-orig program from the git-buildpackage
+utilities. This source package is currently migrated from svn-buildpackage to
+git-buildpackage, and a get-orig-source target for debian/rules will be added
+later.

diff --git a/debian/changelog b/debian/changelog
index 9aebad2cf61c967e728129bec59a6ba7b70e5e37..c495d854c36915c124f4d7a22308d052a1729661 100644 (file)
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,14 @@
+samtools (0.1.6~dfsg-1) unstable; urgency=low
+
+  * New upstream release.
+  * Upstream sources repackaged to remove the win32 directory:
+    - The removal was done with git-import-orig in a parallel Git repository,
+      and the corresponding debian/gbp.conf file was added to this package.
+    - Mangled the ~dfsg string of the Debian version in debian/watch.
+    - Added a debian/README.source file and explanations in debian/copyright.
+
+ -- Charles Plessy <plessy@debian.org>  Mon, 14 Sep 2009 21:58:36 +0900
+
 samtools (0.1.5c-2) unstable; urgency=low
 
   * Rebuilt with -fPIC (debian/rules, README.Debian).

diff --git a/debian/control b/debian/control
index acaa75cc26a34b5da6a827ef31ee365361200422..65e461303411de5e55549915537981c3022f7cbf 100644 (file)
--- a/debian/control
+++ b/debian/control
@@ -18,7 +18,7 @@ Description: processing sequence alignments in SAM and BAM formats
  in the binary BAM format. It imports from and exports to the ascii SAM
  (Sequence Alignment/Map) format, does sorting, merging and indexing, and allows
  to retrieve reads in any regions swiftly. It is designed to work on a stream,
- and is able to open a BAM (not SAM) file on a remote FTP server.
+ and is able to open a BAM (not SAM) file on a remote FTP or HTTP server.
 
 Package: libbam-dev
 Architecture: any

diff --git a/debian/copyright b/debian/copyright
index b0101dde70222583e8e7c739a44745649de33bb3..a7fb29b6dfce58a83b625affbc532a8b5bccaa2b 100644 (file)
--- a/debian/copyright
+++ b/debian/copyright
@@ -1,8 +1,10 @@
 Machine-readable license summary, see ‘http://dep.debian.net/deps/dep5/’.
 
+
 Name      :  SAMtools
 Contact   :  SAMtools mailing list <samtools-help@lists.sourceforge.net>
-Source    :  http://downloads.sourceforge.net/sourceforge/samtools/samtools-0.1.5c.tar.bz2
+Source    :  http://qa.debian.org/watch/sf.php/samtools/samtools-0.1.6.tar.bz2
+
 
 Copyright :  © 2008–2009, Genome Research Ltd.
 License   :  MIT
@@ -29,10 +31,6 @@ Files     :  bgzf.*, bgzip.c
 Copyright :  © 2008 Broad Institute / Massachusetts Institute of Technology
 License   :  MIT
 
-The license of the above files have been confirmed upstream and their headers
-will be corrected in the next release. See:
-http://samtools.svn.sourceforge.net/viewvc/samtools?view=rev&revision=441
-
 
 Files     :  razf.*
 Name      :  RAZF : Random Access compressed(Z) File
@@ -62,27 +60,27 @@ License   :  Similar to NetBSD license.
 
 
 Files     :  misc/md5.*
-Name      :  MD5 Message Digest Algorithm
-Copyright :  © 1990, RSA Data Security, Inc.
 License   :
        
-       License to copy and use this software is granted provided that   
-       it is identified as the "RSA Data Security, Inc. MD5 Message     
-       Digest Algorithm" in all material mentioning or referencing this 
-       software or this function.                                       
-                                                                        
-       License is also granted to make and use derivative works         
-       provided that such works are identified as "derived from the RSA 
-       Data Security, Inc. MD5 Message Digest Algorithm" in all         
-       material mentioning or referencing the derived work.             
-                                                                        
-       RSA Data Security, Inc. makes no representations concerning      
-       either the merchantability of this software or the suitability   
-       of this software for any particular purpose.  It is provided "as 
-       is" without express or implied warranty of any kind.             
-                                                                        
-       These notices must be retained in any copies of any part of this 
-       documentation and/or software.                                   
+       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.
+
 
-The above source files for MD5 support will be replaced in the next SAMtools
-release by the public domain implementation of ‘http://www.fourmilab.ch/md5/’.
+Files     :  win32/*
+Removed   :  Missing source.
+       
+       The win32 directory is present in the original upstream sources, but
+       was removed from the Debian source package, as it contains binary files for the
+       win32 platform without their corresponding source files.

diff --git a/debian/gbp.conf b/debian/gbp.conf
new file mode 100644 (file)
index 0000000..b0205e3
--- /dev/null
+++ b/debian/gbp.conf
@@ -0,0 +1,6 @@
+[DEFAULT]
+pristine-tar = True
+filter-pristine-tar = True
+filter = [
+    "win32"
+    ]

diff --git a/debian/watch b/debian/watch
index 32994eafd28511cc417364a4c873479d563b186b..3b1f5b84947ddd07e84258a3ec045a4a8a404a9d 100644 (file)
--- a/debian/watch
+++ b/debian/watch
@@ -1,2 +1,3 @@
 version=3
-http://sf.net/samtools/samtools-([\d\.]*)\.tar\.bz2
+opts=dversionmangle=s/~dfsg// \
+  http://sf.net/samtools/samtools-([\d\.]*)\.tar\.bz2