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Bug#926944: marked as done (ITP: atropos -- NGS read trimming tool that is specific, sensitive, and speedy)

Your message dated Mon, 05 Aug 2019 10:00:10 +0000
with message-id <E1huZmk-00031m-OJ@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 owner@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 <tille@debian.org>
Severity: wishlist

* Package name    : atropos
  Version         : 1.1.21
  Upstream Author : Marcel Martin <marcel.martin@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 926944@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 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 ftpmaster@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-packaging@lists.alioth.debian.org>
Changed-By: Andreas Tille <tille@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)
Checksums-Sha1:
 e30a8791c3fee1e53cae30a4bd2184035f63248a 2098 atropos_1.1.21+dfsg-1.dsc
 400a3cfb0deffa745728e45903ec2ee059c0ed09 3116496 atropos_1.1.21+dfsg.orig.tar.xz
 292259b367726482461d523f5bcf5d53aa0b4291 4760 atropos_1.1.21+dfsg-1.debian.tar.xz
 48f803f496c473b9c5a106075ed600be81dc2622 438102 atropos-dbgsym_1.1.21+dfsg-1_amd64.deb
 300e5af65fae8d408be293fcfdc236d41fa8dcd1 7694 atropos_1.1.21+dfsg-1_amd64.buildinfo
 ea547a714ad9bc80caae248964f06e54cbe9f8f6 210274 atropos_1.1.21+dfsg-1_amd64.deb
Checksums-Sha256:
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 2a5d292514891c5251fb8a1bcd6ecae32b2f17a80f5354a3e7c91d8eef48f983 4760 atropos_1.1.21+dfsg-1.debian.tar.xz
 bee3792fbb660531d8e4d4f4a792ca0dbe846382934534ec93981833cdf5e40c 438102 atropos-dbgsym_1.1.21+dfsg-1_amd64.deb
 ec0e94c4504d4b809db8c8ea7d243be2de6141726cf504679172e97c6074d2dc 7694 atropos_1.1.21+dfsg-1_amd64.buildinfo
 5f33e28353c29589a2f64b1f92d233874d57ebbd8a2afdb3cd096c3a2939d208 210274 atropos_1.1.21+dfsg-1_amd64.deb
Files:
 54756deca0741a424395153954f6be8b 2098 science optional atropos_1.1.21+dfsg-1.dsc
 dc77153dd14d1c671ac7e449892ddb66 3116496 science optional atropos_1.1.21+dfsg.orig.tar.xz
 f1b355d1ff9cc0a3f09c7d5b1ab04da9 4760 science optional atropos_1.1.21+dfsg-1.debian.tar.xz
 d58e62dbd62bf023c937580714bc9e45 438102 debug optional atropos-dbgsym_1.1.21+dfsg-1_amd64.deb
 a5efbb752d6b3d65ab9939eb8038adfc 7694 science optional atropos_1.1.21+dfsg-1_amd64.buildinfo
 999e177f02be1534f2123c3020f656e4 210274 science optional atropos_1.1.21+dfsg-1_amd64.deb

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--- End Message ---
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