Your message dated Sat, 15 Mar 2025 18:00:10 +0000
with message-id <e1ttvnu-0078sg...@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 ow...@bugs.debian.org
immediately.)
--
1087773: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1087773
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Package: wnpp
Severity: wishlist
Owner: Daniela Moreira Mombach <danielamomb...@gmail.com>
X-Debbugs-Cc: debian-de...@lists.debian.org, danielamomb...@gmail.com
* Package name : sideretro
Version : 1.1.4
Upstream Contact: Thiago L. A. Miller <tmil...@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 <danielamomb...@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 1087...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Daniela Moreira Mombach <danielamomb...@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 ftpmas...@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-packag...@lists.alioth.debian.org>
Changed-By: Daniela Moreira Mombach <danielamomb...@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:
f943d23b04ee912a10cc1ac052ba58c51a6ccb47 2081 sideretro_1.1.6-1.dsc
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
0a2f788296ed20d03fc23b6577947fc81945e716 89848 sideretro_1.1.6-1_amd64.deb
Checksums-Sha256:
8d2625d87cf3d73e776e4a4555695e7de87392d9df01a9224b337fe138e6bd9b 2081
sideretro_1.1.6-1.dsc
378b49030bef1627494c81bbd285d85f3b78843f691f68963bd6e703ae7bac20 2109112
sideretro_1.1.6.orig.tar.gz
ed7184dd784991c0b7dbbd6b3f207875fc9314aa8df57cccee0276afeac318c3 7332
sideretro_1.1.6-1.debian.tar.xz
2d7c5c2c13d80cab8b2eac1bf4c80f99cb55ce6ad2a929f38c0ecd24da3c233b 174952
sideretro-dbgsym_1.1.6-1_amd64.deb
1af385b1f0cb22b4614b4b626ca67bb615c59f4e927dc56bf2896364f92915b8 10637
sideretro_1.1.6-1_amd64.buildinfo
6339f55fc867d846b8f4d0d221c586c5bcce6ad3419661a2ce237d072a4a9540 89848
sideretro_1.1.6-1_amd64.deb
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
-----BEGIN PGP SIGNATURE-----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=qfO4
-----END PGP SIGNATURE-----
pgpWAPfNQIzrY.pgp
Description: PGP signature
--- End Message ---
