Your message dated Wed, 17 Jun 2020 10:00:24 +0000
with message-id <e1jluro-0004xq...@fasolo.debian.org>
and subject line Bug#961661: fixed in samclip 0.4.0-1
has caused the Debian Bug report #961661,
regarding ITP: samclip -- filter SAM file for soft and hard clipped alignments
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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--
961661: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=961661
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Package: wnpp
Severity: wishlist
Subject: ITP: samclip -- filter SAM file for soft and hard clipped alignments
Package: wnpp
Owner: Andreas Tille <ti...@debian.org>
Severity: wishlist
* Package name : samclip
Version : 0.4.0
Upstream Author : Torsten Seemann
* URL : https://github.com/tseemann/samclip
* License : GPL-3
Programming Lang: (C, C++, C#, Perl, Python, etc.)
Description : filter SAM file for soft and hard clipped alignments
Most short read aligners perform local alignment of reads to the
reference genome. Examples includes bwa mem, minimap2, and bowtie2
(unless in --end-to-end mode). This means the ends of the read may not
be part of the best alignment.
.
This can be caused by:
.
* adapter sequences (aren't in the reference)
* poor quality bases (mismatches only make the alignment score worse)
* structural variation in your sample compared to the reference
* reads overlapping the start and end of contigs (including
circular genomes)
.
Read aligners output a SAM file. Column 6 in this format stores the
CIGAR string. which describes which parts of the read aligned and which
didn't. The unaligned ends of the read can be "soft" or "hard" clipped,
denoted with S and H at each end of the CIGAR string. It is possible for
both types to be present, but that is not common. Soft and hard don't
mean anything biologically, they just refer to whether the full read
sequence is in the SAM file or not.
Remark: This package is maintained by Debian Med Packaging Team at
https://salsa.debian.org/med-team/samclip
--- End Message ---
--- Begin Message ---
Source: samclip
Source-Version: 0.4.0-1
Done: Andreas Tille <ti...@debian.org>
We believe that the bug you reported is fixed in the latest version of
samclip, 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 961...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Andreas Tille <ti...@debian.org> (supplier of updated samclip 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...@ftp-master.debian.org)
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256
Format: 1.8
Date: Wed, 27 May 2020 22:29:10 +0200
Source: samclip
Binary: samclip
Architecture: source all
Version: 0.4.0-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Andreas Tille <ti...@debian.org>
Description:
samclip - filter SAM file for soft and hard clipped alignments
Closes: 961661
Changes:
samclip (0.4.0-1) unstable; urgency=medium
.
* Initial release (Closes: #961661)
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