Bug#789707: marked as done (ITP: sickle -- windowed adaptive trimming tool for FASTQ files using quality)
Your message dated Sun, 28 Jun 2015 22:00:17 +0000
with message-id <E1Z9Kcb-0001Vf-4Y@franck.debian.org>
and subject line Bug#789707: fixed in sickle 1.33-1
has caused the Debian Bug report #789707,
regarding ITP: sickle -- windowed adaptive trimming tool for FASTQ files using 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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--
789707: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=789707
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--- Begin Message ---
Package: wnpp
Severity: wishlist
Owner: Andreas Tille <tille@debian.org>
* Package name : sickle
Version : 1.33
Upstream Author : Vince Buffalo
* URL : https://github.com/vsbuffalo/sickle
* License : MIT
Programming Lang: C
Description : windowed adaptive trimming tool for FASTQ files using quality
Most modern sequencing technologies produce reads that have deteriorating
quality towards the 3'-end. Incorrectly called bases here negatively impact
assembles, mapping, and downstream bioinformatics analyses.
.
Sickle is a tool that uses sliding windows along with quality and length
thresholds to determine when quality is sufficiently low to trim the 3'-end
of reads. It will also discard reads based upon the length threshold. It takes
the quality values and slides a window across them whose length is 0.1 times
the length of the read. If this length is less than 1, then the window is set
to be equal to the length of the read. Otherwise, the window slides along the
quality values until the average quality in the window drops below the
threshold. At that point the algorithm determines where in the window the drop
occurs and cuts both the read and quality strings there. However, if the cut
point is less than the minimum length threshold, then the read is discarded
entirely.
.
Sickle supports four types of quality values: Illumina, Solexa, Phred, and
Sanger. Note that the Solexa quality setting is an approximation (the actual
conversion is a non-linear transformation). The end approximation is close.
.
Sickle also supports gzipped file inputs.
Remark: This package was prepared by Tim Booth from BioLinux and taken over
into Debian Med team maintenance by Andreas Tille. The packaging code is
available at
svn://anonscm.debian.org/debian-med/trunk/packages/sickle/trunk/
--- End Message ---
--- Begin Message ---
Source: sickle
Source-Version: 1.33-1
We believe that the bug you reported is fixed in the latest version of
sickle, 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 789707@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 sickle 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: SHA512
Format: 1.8
Date: Tue, 23 Jun 2015 21:08:09 +0200
Source: sickle
Binary: sickle
Architecture: source amd64
Version: 1.33-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
sickle - windowed adaptive trimming tool for FASTQ files using quality
Closes: 789707
Changes:
sickle (1.33-1) unstable; urgency=medium
.
* Initial upload to Debian (Closes: #789707)
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