Bug#489836: marked as done (ITP: maq -- Mapping and Assembly with Quality)
Your message dated Tue, 29 Jul 2008 14:20:10 +0000
with message-id <E1KNq3e-0002bj-Sb@ries.debian.org>
and subject line Bug#489836: fixed in maq 0.6.7-1
has caused the Debian Bug report #489836,
regarding ITP: maq -- Mapping and Assembly with Quality
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.
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--
489836: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=489836
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 : maq
Version : 0.6.7
Upstream Author : Heng Li <lh3@sanger.ac.uk>
URL : http://maq.sourceforge.net/
License : GPL-3
Programming Lang: C
Description : Mapping and Assembly with Quality
Maq builds mapping assemblies from short reads generated by the
next-generation sequencing machines. It is particularly designed for
Illumina-Solexa 1G Genetic Analyzer, and has a preliminary functionality to
handle ABI SOLiD data. Maq is previously known as mapass2.
.
With Maq you can:
o Fast align Illumina/SOLiD reads to the reference genome. With the
default options, one million pairs of reads can be mapped to the
human genome in about 10 CPU hours with less than 1G memory.
o Accurately measure the error probability of the alignment of each
individual read.
o Call the consensus genotypes, including homozygous and heterozygous
polymorphisms, with a Phred probabilistic quality assigned to each base.
o Find short indels with paired end reads.
o Accurately find large scale genomic deletions and translocations with
paired end reads.
o Discover potential CNVs by checking read depth.
o Evaluate the accuracy of raw base qualities from sequencers and help
to check the systematic errors.
.
However, Maq can NOT:
o Do de novo assembly. (Maq can only call the consensus by mapping reads
to a known reference.)
o Map shorts reads against themselves. (Maq can only find complete overlap
between reads.)
o Align capillary reads or 454 reads to the reference. (Maq cannot align
reads longer than 63bp.)
Like velvet and patman, this package is intended to be made available after
Lenny is released.
Preliminary packaging is available here:
Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/maq/trunk/?rev=0&sc=0
Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/maq/trunk/
--
Charles Plessy
Debian-Med packaging team.
--- End Message ---
--- Begin Message ---
Source: maq
Source-Version: 0.6.7-1
We believe that the bug you reported is fixed in the latest version of
maq, which is due to be installed in the Debian FTP archive:
maq_0.6.7-1.diff.gz
to pool/main/m/maq/maq_0.6.7-1.diff.gz
maq_0.6.7-1.dsc
to pool/main/m/maq/maq_0.6.7-1.dsc
maq_0.6.7-1_i386.deb
to pool/main/m/maq/maq_0.6.7-1_i386.deb
maq_0.6.7.orig.tar.gz
to pool/main/m/maq/maq_0.6.7.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 489836@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Andreas Tille <tille@debian.org> (supplier of updated maq 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: Wed, 16 Jul 2008 12:01:33 +0200
Source: maq
Binary: maq
Architecture: source i386
Version: 0.6.7-1
Distribution: unstable
Urgency: low
Maintainer: Debian-Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
maq - maps short fixed-legth polymporphic DNA sequence reads to referen
Closes: 489836
Changes:
maq (0.6.7-1) unstable; urgency=low
.
[ Charles Plessy ]
* Initial release (Closes: #489836)
.
[ Andreas Tille ]
* Rudely deleted -m64 option from configure because multiarch
building leads to several problems
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--- End Message ---
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