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Bug#933975: marked as done (ITP: trim-galore -- automate quality and adapter trimming for DNA sequencing)

Your message dated Thu, 05 Sep 2019 10:00:12 +0000
with message-id <E1i5oYm-000IA6-Mn@fasolo.debian.org>
and subject line Bug#933975: fixed in trim-galore 0.6.4-1
has caused the Debian Bug report #933975,
regarding ITP: trim-galore -- automate quality and adapter trimming for DNA sequencing
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.

(NB: If you are a system administrator and have no idea what this
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-- 
933975: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=933975
Debian Bug Tracking System
Contact owner@bugs.debian.org with problems
--- Begin Message --- 
Package: wnpp
Severity: wishlist

Subject: ITP: trim-galore -- automate quality and adapter trimming for DNA sequencing
Package: wnpp
Owner: Steffen Moeller <moeller@debian.org>
Severity: wishlist

* Package name    : trim-galore
  Version         : 0.6.4
  Upstream Author : Felix Krueger
* URL             : https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/
* License         : GPL-3.0+
  Programming Lang: (C, C++, C#, Perl, Python, etc.)
  Description     : automate quality and adapter trimming for DNA sequencing
 Trim Galore! is a wrapper script to automate quality and adapter trimming
 as well as quality control, with some added functionality to remove
 biased methylation positions for RRBS sequence files (for directional,
 non-directional (or paired-end) sequencing). It's main features are:
  * For adapter trimming, Trim Galore! uses the first 13 bp of Illumina
    standard adapters ('AGATCGGAAGAGC') by default (suitable for both ends
    of paired-end libraries), but accepts other adapter sequence, too
  * For MspI-digested RRBS libraries, Trim Galore! performs quality and
    adapter trimming in two subsequent steps. This allows it to remove
    2 additional bases that contain a cytosine which was artificially
    introduced in the end-repair step during the library preparation
  * For any kind of FastQ file other than MspI-digested RRBS, Trim
    Galore! can perform single-pass adapter- and quality trimming
  * The Phred quality of basecalls and the stringency for adapter removal
    can be specified individually
  * Trim Galore! can remove sequences if they become too short during
    the trimming process. For paired-end files Trim Galore! removes entire
    sequence pairs if one (or both) of the two reads became shorter than
    the set length cutoff. Reads of a read-pair that are longer than a
    given threshold but for which the partner read has become too short
    can optionally be written out to single-end files. This ensures that
    the information of a read pair is not lost entirely if only one read
    is of good quality
  * Trim Galore! can trim paired-end files by 1 additional bp from the 3'
    end of all reads to avoid problems with invalid alignments with Bowtie 1
  * Trim Galore! accepts and produces standard or gzip compressed FastQ files
  * FastQC can optionally be run on the resulting output files once
    trimming has completed

Remark: This package is maintained by Steffen Moeller at
   https://salsa.debian.org/med-team/trim-galore

--- End Message ---
--- Begin Message --- 
Source: trim-galore
Source-Version: 0.6.4-1

We believe that the bug you reported is fixed in the latest version of
trim-galore, 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 933975@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.

Debian distribution maintenance software
pp.
Steffen Moeller <moeller@debian.org> (supplier of updated trim-galore 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: Mon, 05 Aug 2019 15:26:15 +0200
Source: trim-galore
Binary: trim-galore
Architecture: source all
Version: 0.6.4-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed-By: Steffen Moeller <moeller@debian.org>
Description:
 trim-galore - automate quality and adapter trimming for DNA sequencing
Closes: 933975
Changes:
 trim-galore (0.6.4-1) unstable; urgency=medium
 .
   * Initial release (Closes: #933975)
 .
     TODO: Write test script
           Deal with documentation
Checksums-Sha1:
 6199be1c67ad98fd2e2856cd888508790fad3313 2006 trim-galore_0.6.4-1.dsc
 4dbace01e516788a53fc37fc6e6cd4b562b2db3a 26827580 trim-galore_0.6.4.orig.tar.gz
 3b7c5adbe312707901d86456173b507ed89d363d 2412 trim-galore_0.6.4-1.debian.tar.xz
 d75fb1f575a869ec4b0a20637fbb652ad2235ffa 34748 trim-galore_0.6.4-1_all.deb
 4a6e69031ab112b730b1209cdb67169e30db7c8c 5760 trim-galore_0.6.4-1_amd64.buildinfo
Checksums-Sha256:
 72e809d5696e3d261110bd1573c2b2df688ef08b48e2b9685d1b2816f5703a70 2006 trim-galore_0.6.4-1.dsc
 eb57e18203d8a1dce1397b930a348a9969eebaa758b8a7304d04c22f216cea2d 26827580 trim-galore_0.6.4.orig.tar.gz
 5497aaa304d8f8ed80ba0fae077b0ad370af874c43a478fb828b1ca7b3c8f08b 2412 trim-galore_0.6.4-1.debian.tar.xz
 012364a701f13983c5de6a3dcfd8a44c1450b6ef62a04ed1f170c961475e7fce 34748 trim-galore_0.6.4-1_all.deb
 0b29a858691c9ddc3c33a0f90e679957e3af0d35e31f312ad516ea098524b2c4 5760 trim-galore_0.6.4-1_amd64.buildinfo
Files:
 37d184f1b1daf8ad7d3293cac074bb8b 2006 science optional trim-galore_0.6.4-1.dsc
 3beb267468ab1ef0fc7f652fd81fd59f 26827580 science optional trim-galore_0.6.4.orig.tar.gz
 135230b6595eccf0d9d239de7aa502ba 2412 science optional trim-galore_0.6.4-1.debian.tar.xz
 0a0b69b48a181e8666aaf35c05edddcc 34748 science optional trim-galore_0.6.4-1_all.deb
 f8d9b3560ad858099090e7b58bb5c8fa 5760 science optional trim-galore_0.6.4-1_amd64.buildinfo

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