Your message dated Mon, 09 Nov 2020 23:00:10 +0000
with message-id <e1kcg8w-0002mq...@fasolo.debian.org>
and subject line Bug#970447: fixed in pinfish 0.1.0+ds-1
has caused the Debian Bug report #970447,
regarding ITP: pinfish -- Collection of tools to annotate genomes using long
read transcriptomics data
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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--
970447: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=970447
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Package: wnpp
Severity: wishlist
Owner: Nilesh Patra <npatra...@gmail.com>
X-Debbugs-CC: debian-de...@lists.debian.org
* Package name : pinfish
Version : 0.1.0+ds-1
Upstream Author : Oxford Nanopore Technologies Ltd.
* URL : https://github.com/nanoporetech/pinfish
* License : MPL-2.0
Programming Lang: Go
Description : Collection of tools to annotate genomes using long
read transcriptomics data
The toolchain is composed of the following tools:
1. spliced_bam2gff - a tool for converting sorted BAM
files containing spliced alignments
into GFF2 format. Each read will be represented as a distinct
transcript. This tool comes handy when visualizing spliced
reads at particular loci and to provide input to the rest
of the toolchain.
.
2. cluster_gff - this tool takes a sorted GFF2 file as
input and clusters together reads having similar
exon/intron structure and creates a rough consensus
of the clusters by taking the median of exon
boundaries from all transcripts in the cluster.
.
3. polish_clusters - this tool takes the cluster
definitions generated by cluster_gff and for each
cluster creates an error corrected read by mapping
all reads on the read with the median length
and polishing it using racon. The polished reads
can be mapped to the genome using minimap2 or GMAP.
.
4. collapse_partials - this tool takes GFFs generated
by either cluster_gff or polish_clusters and filters
out transcripts which are likely to be based on RNA
degradation products from the 5' end. The tool clusters
the input transcripts into "loci" by the 3' ends and
discards transcripts which have a compatible transcripts
in the loci with more exons.
I shall maintain this package.
--- End Message ---
--- Begin Message ---
Source: pinfish
Source-Version: 0.1.0+ds-1
Done: Nilesh Patra <npatra...@gmail.com>
We believe that the bug you reported is fixed in the latest version of
pinfish, 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 970...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Nilesh Patra <npatra...@gmail.com> (supplier of updated pinfish 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: Wed, 16 Sep 2020 12:36:21 +0530
Source: pinfish
Binary: pinfish pinfish-examples
Architecture: source all amd64
Version: 0.1.0+ds-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Nilesh Patra <npatra...@gmail.com>
Description:
pinfish - Collection of tools to annotate genomes using long read transcrip
pinfish-examples - Examples and test data for pinfish
Closes: 970447
Changes:
pinfish (0.1.0+ds-1) unstable; urgency=medium
.
* Initial release (Closes: #970447)
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