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Bug#1087773: marked as done (ITP: sideretro -- pipeline for detecting Somatic Insertion of DEnovo RETROcopies)

Your message dated Sat, 15 Mar 2025 18:00:10 +0000
with message-id <E1ttVnu-0078SG-LM@fasolo.debian.org>
and subject line Bug#1087773: fixed in sideretro 1.1.6-1
has caused the Debian Bug report #1087773,
regarding ITP: sideretro -- pipeline for detecting Somatic Insertion of DEnovo RETROcopies
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
message is talking about, this may indicate a serious mail system
misconfiguration somewhere. Please contact owner@bugs.debian.org
immediately.)


-- 
1087773: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1087773
Debian Bug Tracking System
Contact owner@bugs.debian.org with problems
--- Begin Message --- 
Package: wnpp
Severity: wishlist
Owner: Daniela Moreira Mombach <danielamombach@gmail.com>
X-Debbugs-Cc: debian-devel@lists.debian.org, danielamombach@gmail.com

* Package name    : sideretro
  Version         : 1.1.4
  Upstream Contact: Thiago L. A. Miller <tmiller@mochsl.org.br>
* URL             : https://github.com/galantelab/sideRETRO
* License         : GPL-3+
  Programming Lang: C
  Description     : pipeline for detecting Somatic Insertion of DEnovo RETROcopies

  sideRETRO is a bioinformatics tool designed for the detection of somatic
  retrocopy insertions, also known as retroCNVs, in whole genome sequencing
  (WGS) and whole exome sequencing (WES) data.
  .
  Retrocopies, also known as processed pseudogenes, are sequences derived
  from protein-coding genes, generated by the duplication of these genes
  through the transposition of their mature messenger RNA via the LINE-1
  enzymatic machinery. Retrocopies can be fixed, meaning they are present
  in all genomes of a given species (including the species' reference
  genome), or unfixed (polymorphic, germline, or somatic), in which case
  they are referred to as retroCNVs. While fixed retrocopies have received
  considerable attention in the scientific community, knowledge of retroCNVs
  remains limited, largely due to the lack of specialized bioinformatics
  tools for their identification and annotation in DNA sequencing data.
  .
  sideRETRO is a dedicated computational algorithm that detects retrocopies
  absent from the reference genome but present in WGS and WES data from
  other individuals. In addition to identifying retroCNVs, sideRETRO annotates
  several characteristics associated with these events. It provides information
  on the genomic coordinates of the insertion, including chromosome, insertion
  point, and DNA strand. It also determines the genomic context of the event
  (exonic, intronic, or intergenic), performs genotyping (presence or absence),
  and provides haplotyping information (homozygous or heterozygous).

--- End Message ---
--- Begin Message --- 
Source: sideretro
Source-Version: 1.1.6-1
Done: Daniela Moreira Mombach <danielamombach@gmail.com>

We believe that the bug you reported is fixed in the latest version of
sideretro, 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 1087773@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.

Debian distribution maintenance software
pp.
Daniela Moreira Mombach <danielamombach@gmail.com> (supplier of updated sideretro 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, 12 Nov 2024 19:55:11 +0000
Source: sideretro
Binary: sideretro sideretro-dbgsym
Architecture: source amd64
Version: 1.1.6-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed-By: Daniela Moreira Mombach <danielamombach@gmail.com>
Description:
 sideretro  - pipeline for detecting Somatic Insertion of DE novo RETROcopies
Closes: 1087773
Changes:
 sideretro (1.1.6-1) unstable; urgency=medium
 .
   * Initial release. (Closes: #1087773)
Checksums-Sha1:
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 20a0572585b0b16ca71ed76b08b8fcbce3f33aca 2109112 sideretro_1.1.6.orig.tar.gz
 8b65d86a1122a71829c9e3949a0e333d4d18d2bd 7332 sideretro_1.1.6-1.debian.tar.xz
 9cd0770815c6a0768f1baf3fbbf6f18ee30311b5 174952 sideretro-dbgsym_1.1.6-1_amd64.deb
 df29a5e4a1fca5fba94271ceee75e7bf34e39682 10637 sideretro_1.1.6-1_amd64.buildinfo
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 ed7184dd784991c0b7dbbd6b3f207875fc9314aa8df57cccee0276afeac318c3 7332 sideretro_1.1.6-1.debian.tar.xz
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Files:
 35a44b8767e1beb3a1a59d3eef021359 2081 science optional sideretro_1.1.6-1.dsc
 2ee5b04044bcce8eda2bd8e5bfaa7ea9 2109112 science optional sideretro_1.1.6.orig.tar.gz
 de585c15592d74a0d8a551c5d0e57ad9 7332 science optional sideretro_1.1.6-1.debian.tar.xz
 04e167a37f558dfcf8c401332f4e8988 174952 debug optional sideretro-dbgsym_1.1.6-1_amd64.deb
 39abb9fbc5d29c98bd0107588c95164b 10637 science optional sideretro_1.1.6-1_amd64.buildinfo
 37186eda914a2f6bebcc78f2fdf185a6 89848 science optional sideretro_1.1.6-1_amd64.deb

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