[med-svn] r3916 - trunk/packages/samtools/trunk/debian

[Charles Plessy]

Author: plessy
Date: 2009-09-07 12:04:58 +0000 (Mon, 07 Sep 2009)
New Revision: 3916

Modified:
   trunk/packages/samtools/trunk/debian/changelog
   trunk/packages/samtools/trunk/debian/control
   trunk/packages/samtools/trunk/debian/copyright
Log:
New upstream release containing sourceless static libraries for windows. This has to be solved before upload.


Modified: trunk/packages/samtools/trunk/debian/changelog
===================================================================
--- trunk/packages/samtools/trunk/debian/changelog	2009-09-07 11:59:39 UTC (rev 3915)
+++ trunk/packages/samtools/trunk/debian/changelog	2009-09-07 12:04:58 UTC (rev 3916)
@@ -1,3 +1,12 @@
+samtools (0.1.6-1) UNRELEASED; urgency=low
+
+NON-FREE FILES DETECTED (win32/*a). Do not upload without removing or getting a
+green light from our archive administrators.
+
+  * New upstream release.
+
+ -- Charles Plessy <plessy at debian.org>  Mon, 07 Sep 2009 20:13:44 +0900
+
 samtools (0.1.5c-2) unstable; urgency=low
 
   * Rebuilt with -fPIC (debian/rules, README.Debian).

Modified: trunk/packages/samtools/trunk/debian/control
===================================================================
--- trunk/packages/samtools/trunk/debian/control	2009-09-07 11:59:39 UTC (rev 3915)
+++ trunk/packages/samtools/trunk/debian/control	2009-09-07 12:04:58 UTC (rev 3916)
@@ -18,7 +18,7 @@
  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

Modified: trunk/packages/samtools/trunk/debian/copyright
===================================================================
--- trunk/packages/samtools/trunk/debian/copyright	2009-09-07 11:59:39 UTC (rev 3915)
+++ trunk/packages/samtools/trunk/debian/copyright	2009-09-07 12:04:58 UTC (rev 3916)
@@ -2,7 +2,7 @@
 
 Name      :  SAMtools
 Contact   :  SAMtools mailing list <samtools-help at 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
@@ -29,11 +29,6 @@
 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
 Copyright :  2008, Jue Ruan <ruanjue at gmail.com>, Heng Li <lh3 at sanger.ac.uk>
@@ -62,27 +57,19 @@
 
 
 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.                                   
-
-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/’.
+	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.