Your message dated Sat, 29 Aug 2009 19:38:29 +0000
with message-id <e1mhtkr-0001qc...@ries.debian.org>
and subject line Bug#540453: fixed in samtools 0.1.5c-1
has caused the Debian Bug report #540453,
regarding ITP: samtools -- processing sequence alignments in SAM and BAM formats
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
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--
540453: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=540453
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Package: wnpp
Severity: wishlist
Owner: Charles Plessy <ple...@debian.org>
Package name : samtools
Version : 0.1.5c-1
Upstream Author : Heng Li, Bob Handsaker, Jue Ruan, Colin Hercus.
URL : http://samtools.sourceforge.net/
License : MIT and NetBSD
Programming Lang: C, Perl
Description : processing sequence alignments in SAM and BAM formats
Source: samtools
Section: science
Priority: optional
Maintainer: Debian-Med Packaging Team
<debian-med-packag...@lists.alioth.debian.org>
DM-Upload-Allowed: yes
Uploaders: Charles Plessy <ple...@debian.org>
Build-Depends: debhelper (>= 7), cdbs, libncurses5-dev, zlib1g-dev
Standards-Version: 3.8.2
Homepage: http://samtools.sourceforge.net
Vcs-Browser:
http://svn.debian.org/wsvn/debian-med/trunk/packages/samtools/trunk/?rev=0&sc=0
Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/samtools/trunk/
Package: samtools
Architecture: any
Depends: ${shlibs:Depends}, ${misc:Depends}
Description: processing sequence alignments in SAM and BAM formats
Samtools is a set of utilities that manipulate nucleotide sequence alignments
in the BAM format. It imports from and exports to the 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.
Package: libbam-dev
Architecture: any
Depends: ${shlibs:Depends}, ${misc:Depends}
Description: manipulates nucleotide sequence alignments in BAM or SAM format
The BAM library provides I/O and various operations on manipulating nucleotide
sequence alignments in the BAM (Binary Alignment/Mapping) or SAM (Sequence
Alignment/Map) format. It now supports importing from or exporting to TAM,
sorting, merging, generating pileup, and quickly retrieval of reads overlapped
with a specified region.
Machine-readable license summary, see ‘http://dep.debian.net/deps/dep5/’.
Name : SAMtools
Contact : SAMtools mailing list <samtools-h...@lists.sourceforge.net>
Source :
http://downloads.sourceforge.net/sourceforge/samtools/samtools-0.1.5c.tar.bz2
Copyright : © 2008–2009, Genome Research Ltd.
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 : bgzf.*, bgzip.c
Copyright : © 2008 Broad Institute / Massachusetts Institute of Technology
License : MIT
Files : razf.*
Name : RAZF : Random Access compressed(Z) File
Copyright : 2008, Jue Ruan <ruan...@gmail.com>, Heng Li <l...@sanger.ac.uk>
License : Similar to NetBSD license.
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions
are met:
1. Redistributions of source code must retain the above copyright
notice, this list of conditions and the following disclaimer.
2. Redistributions in binary form must reproduce the above copyright
notice, this list of conditions and the following disclaimer in the
documentation and/or other materials provided with the distribution.
THIS SOFTWARE IS PROVIDED BY THE AUTHOR AND CONTRIBUTORS ``AS IS'' AND
ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
PURPOSE
ARE DISCLAIMED. IN NO EVENT SHALL THE AUTHOR OR CONTRIBUTORS BE LIABLE
FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
CONSEQUENTIAL
DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS
OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT,
STRICT
LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY
WAY
OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
SUCH DAMAGE.
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/’.
--- End Message ---
--- Begin Message ---
Source: samtools
Source-Version: 0.1.5c-1
We believe that the bug you reported is fixed in the latest version of
samtools, which is due to be installed in the Debian FTP archive:
libbam-dev_0.1.5c-1_amd64.deb
to pool/main/s/samtools/libbam-dev_0.1.5c-1_amd64.deb
samtools_0.1.5c-1.diff.gz
to pool/main/s/samtools/samtools_0.1.5c-1.diff.gz
samtools_0.1.5c-1.dsc
to pool/main/s/samtools/samtools_0.1.5c-1.dsc
samtools_0.1.5c-1_amd64.deb
to pool/main/s/samtools/samtools_0.1.5c-1_amd64.deb
samtools_0.1.5c.orig.tar.gz
to pool/main/s/samtools/samtools_0.1.5c.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 540...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Charles Plessy <ple...@debian.org> (supplier of updated samtools 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 ftpmas...@debian.org)
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1
Format: 1.8
Date: Sun, 16 Aug 2009 14:38:20 +0900
Source: samtools
Binary: samtools libbam-dev
Architecture: source amd64
Version: 0.1.5c-1
Distribution: unstable
Urgency: low
Maintainer: Debian-Med Packaging Team
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Charles Plessy <ple...@debian.org>
Description:
libbam-dev - manipulates nucleotide sequence alignments in BAM or SAM format
samtools - processing sequence alignments in SAM and BAM formats
Closes: 540453
Changes:
samtools (0.1.5c-1) unstable; urgency=low
.
* Initial release (Closes: #540453)
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libbam-dev_0.1.5c-1_amd64.deb
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