Your message dated Mon, 05 Aug 2019 10:00:10 +0000
with message-id <e1huzmk-00031m...@fasolo.debian.org>
and subject line Bug#926944: fixed in atropos 1.1.21+dfsg-1
has caused the Debian Bug report #926944,
regarding ITP: atropos -- NGS read trimming tool that is specific, sensitive,
and speedy
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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--
926944: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=926944
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Package: wnpp
Severity: wishlist
Subject: ITP: atropos -- NGS read trimming tool that is specific, sensitive,
and speedy
Package: wnpp
Owner: Andreas Tille <ti...@debian.org>
Severity: wishlist
* Package name : atropos
Version : 1.1.21
Upstream Author : Marcel Martin <marcel.mar...@scilifelab.se>
* URL : https://github.com/jdidion/atropos
* License : Expat
Programming Lang: Python
Description : NGS read trimming tool that is specific, sensitive, and
speedy
Atropos is tool for specific, sensitive, and speedy trimming of NGS
reads. It is a fork of the venerable Cutadapt read trimmer, with the
primary improvements being:
.
1. Multi-threading support, including an extremely fast "parallel
write" mode.
2. Implementation of a new insert alignment-based trimming algorithm
for paired-end reads that is substantially more sensitive and
specific than the original Cutadapt adapter alignment-based
algorithm. This algorithm can also correct mismatches between the
overlapping portions of the reads.
3. Options for trimming specific types of data (miRNA, bisulfite-seq).
4. A new command ('detect') that will detect adapter sequences and
other potential contaminants.
5. A new command ('error') that will estimate the sequencing error
rate, which helps to select the appropriate adapter- and quality-
trimming parameter values.
6. A new command ('qc') that generates read statistics similar to
FastQC. The trim command can also compute read statistics both
before and after trimming (using the '--stats' option).
7. Improved summary reports, including support for serialization
formats (JSON, YAML, pickle), support for user-defined templates
(via the optional Jinja2 dependency), and integration with MultiQC.
8. The ability to merge overlapping reads (this is experimental and
the functionality is limited).
9. The ability to write the summary report and log messages to
separate files.
10. The ability to read SAM/BAM files and read/write interleaved
FASTQ files.
11. Direct trimming of reads from an SRA accession.
12. A progress bar, and other minor usability enhancements.
Remark: This package is maintained by Debian Med Packaging Team at
https://salsa.debian.org/med-team/atropos
--- End Message ---
--- Begin Message ---
Source: atropos
Source-Version: 1.1.21+dfsg-1
We believe that the bug you reported is fixed in the latest version of
atropos, 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 926...@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 atropos 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: Sun, 04 Aug 2019 21:50:09 +0200
Source: atropos
Binary: atropos
Architecture: source amd64
Version: 1.1.21+dfsg-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:
atropos - NGS read trimming tool that is specific, sensitive, and speedy
Closes: 926944
Changes:
atropos (1.1.21+dfsg-1) unstable; urgency=medium
.
* Initial release (Closes: #926944)
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--- End Message ---
