Bug#836914: marked as done (ITP: rapmap -- rapid sensitive and accurate DNA read mapping via quasi-mapping)
Your message dated Wed, 07 Sep 2016 14:00:20 +0000
with message-id <E1bhdOm-0004mE-0F@franck.debian.org>
and subject line Bug#836914: fixed in rapmap 0.3.0+dfsg-1
has caused the Debian Bug report #836914,
regarding ITP: rapmap -- rapid sensitive and accurate DNA read mapping via quasi-mapping
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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--
836914: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=836914
Debian Bug Tracking System
Contact owner@bugs.debian.org with problems
--- Begin Message ---
Package: wnpp
Severity: wishlist
Owner: Andreas Tille <tille@debian.org>
* Package name : rapmap
Version : 0.3.0
Upstream Author : COMputational BIology and Network Evolution lab
* URL : https://github.com/COMBINE-lab/RapMap
* License : GPL
Programming Lang: C
Description : rapid sensitive and accurate DNA read mapping via quasi-mapping
RapMap is a testing ground for ideas in quasi-mapping / (lightweight /
pseudo) transcriptome alignment. That means that, at this point, it is
somewhat experimental. The develop branch will have the latest
improvements and additions, but is not guaranteed to be stable between
commits. Breaking changes to the master branch will be accompanied by a
tag to the version before the breaking change. Currently, RapMap is a
stand-alone quasi-mapper that can be used with other tools. It is also
being used as part of Sailfish and Salmon. Eventually, the hope is to
create and stabilize an API so that it can be used as a library from
other tools.
.
Quasi-mapping / (lightweight / pseudo)-alignment is the term that is
used here for the type of information required for certain tasks (e.g.
transcript quantification) that is less "heavyweight" than what is
provided by traditional alignment. For example, one may only need to
know the transcripts / contigs to which a read aligns and, perhaps, the
position within those transcripts rather than the optimal alignment and
base-for-base CIGAR string that aligns the read and substring of the
transcript. For details on RapMap (quasi-mapping in particular), please
check out the associated paper. Note: RapMap implements both quasi-
mapping and pseudo-alignment (originally introduced in Bray et al.
2016), these two are not the same thing. They are distinct concepts, and
RapMap simply happens to implement algorithms for computing both.
Remark: This package is needed to upgrade salmon. It will be maintained
by the Debian Med team at
https://anonscm.debian.org/git/debian-med/rapmap.git
--- End Message ---
--- Begin Message ---
Source: rapmap
Source-Version: 0.3.0+dfsg-1
We believe that the bug you reported is fixed in the latest version of
rapmap, which is due to be installed in the Debian FTP archive.
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 836914@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 rapmap 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@ftp-master.debian.org)
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256
Format: 1.8
Date: Wed, 07 Sep 2016 10:03:37 +0200
Source: rapmap
Binary: rapmap
Architecture: source amd64
Version: 0.3.0+dfsg-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
rapmap - rapid sensitive and accurate DNA read mapping via quasi-mapping
Closes: 836914
Changes:
rapmap (0.3.0+dfsg-1) unstable; urgency=medium
.
* Initial release (Closes: #836914)
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