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Bug#548719: marked as done (ITP: bwa -- Burrows-Wheeler Aligner)

Your message dated Thu, 08 Oct 2009 13:39:29 +0000
with message-id <E1MvtDN-0003Ub-FS@ries.debian.org>
and subject line Bug#548719: fixed in bwa 0.5.3-1
has caused the Debian Bug report #548719,
regarding ITP: bwa -- Burrows-Wheeler Aligner
to be marked as done.

This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.

(NB: If you are a system administrator and have no idea what this
message is talking about, this may indicate a serious mail system
misconfiguration somewhere. Please contact owner@bugs.debian.org
immediately.)


-- 
548719: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=548719
Debian Bug Tracking System
Contact owner@bugs.debian.org with problems
--- Begin Message --- 
Package: wnpp
Severity: wishlist
Owner: Charles Plessy <plessy@debian.org>

  Package name    : bwa
  Version         : 0.5.3
  Upstream Author : Heng Li and others, see: http://bio-bwa.sourceforge.net/bwa.shtml
  URL             : http://bio-bwa.sourceforge.net
  License         : GPL
  Programming Lang: C
  Description     : Burrows-Wheeler Aligner

Since I tried it at work, I took the opportunity to package bwa, the
Burrows-Wheeler Aligner. Here are copies of the Debian control and
copyright files.

Have a nice day,

-- Charles Plessy, Debian Med packaging team, Tsurumi, Kanagawa, Japan.


Source: bwa
Section: science
Priority: optional
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
DM-Upload-Allowed: yes
Uploaders: Charles Plessy <plessy@debian.org>
Build-Depends: cdbs, debhelper (>= 7), zlib1g-dev
Standards-Version: 3.8.3
Homepage: http://bio-bwa.sourceforge.net/ 
Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/bwa/trunk/?rev=0&sc=0
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 dBWT-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.

Name      :  Burrows-Wheeler Aligner
Contact   :  bio-bwa-help@lists.sourceforge.net
Source    :  http://downloads.sourceforge.net/project/bio-bwa/bwa-0.5.3.tar.bz2

Copyright :  © 2008 Genome Research Ltd (GRL)
             2008, by Heng Li <lh3@sanger.ac.uk>
             © 2003-2006, 2008, 2009, by Heng Li <lh3lh3@gmail.com>
             © 2008, by Attractive Chaos <attractivechaos@aol.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.


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.

--- End Message ---
--- Begin Message --- 
Source: bwa
Source-Version: 0.5.3-1

We believe that the bug you reported is fixed in the latest version of
bwa, which is due to be installed in the Debian FTP archive:

bwa_0.5.3-1.diff.gz
  to pool/main/b/bwa/bwa_0.5.3-1.diff.gz
bwa_0.5.3-1.dsc
  to pool/main/b/bwa/bwa_0.5.3-1.dsc
bwa_0.5.3-1_amd64.deb
  to pool/main/b/bwa/bwa_0.5.3-1_amd64.deb
bwa_0.5.3.orig.tar.gz
  to pool/main/b/bwa/bwa_0.5.3.orig.tar.gz



A summary of the changes between this version and the previous one is
attached.

Thank you for reporting the bug, which will now be closed.  If you
have further comments please address them to 548719@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.

Debian distribution maintenance software
pp.
Charles Plessy <plessy@debian.org> (supplier of updated bwa package)

(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing ftpmaster@debian.org)


-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1

Format: 1.8
Date: Thu, 08 Oct 2009 19:20:41 +0900
Source: bwa
Binary: bwa
Architecture: source amd64
Version: 0.5.3-1
Distribution: unstable
Urgency: low
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed-By: Charles Plessy <plessy@debian.org>
Description: 
 bwa        - Burrows-Wheeler Aligner
Closes: 548719
Changes: 
 bwa (0.5.3-1) unstable; urgency=low
 .
   * Initial release (Closes: #548719)
Checksums-Sha1: 
 b938813d9a1cf740a3e47f6e29148ff8c5ad62c9 1236 bwa_0.5.3-1.dsc
 66f74f8e25d0bc8de40e70fcd22eb65c6bda5c9f 124990 bwa_0.5.3.orig.tar.gz
 d0ef70ca9939edfc9d115ce122f262959288beae 2711 bwa_0.5.3-1.diff.gz
 452ca0051cf53df28a5d33601ce8e27b87204765 118224 bwa_0.5.3-1_amd64.deb
Checksums-Sha256: 
 c69d59bfd7de534e8739d0ec73467944d2c0b8a276ab94519ce78a7285297738 1236 bwa_0.5.3-1.dsc
 300357fd517d6df766cf70b288e7fbb599cd56123e87f80ad7fe529429c5afe2 124990 bwa_0.5.3.orig.tar.gz
 157af9614e94628c508f04cc6d839b86fa4a1a25bbfb09c720d99a677fd698bf 2711 bwa_0.5.3-1.diff.gz
 aec0c3fd245f6870e5530664d5f0e9dfbb985b911aa32f4dd831eb728dbc3c26 118224 bwa_0.5.3-1_amd64.deb
Files: 
 8063b6dad61d9d43ee94fdcec2fd35eb 1236 science optional bwa_0.5.3-1.dsc
 7b6b313ece8ff814f00633dd77e4f4a9 124990 science optional bwa_0.5.3.orig.tar.gz
 90f943f005cccf91574b3b102150933f 2711 science optional bwa_0.5.3-1.diff.gz
 f4e027a7a2d759a8433e5ab97b87f9d5 118224 science optional bwa_0.5.3-1_amd64.deb

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--- End Message ---
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