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Bug#970447: marked as done (ITP: pinfish -- Collection of tools to annotate genomes using long read transcriptomics data)

Your message dated Mon, 09 Nov 2020 23:00:10 +0000
with message-id <E1kcG8w-0002mQ-Tm@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 owner@bugs.debian.org with problems
--- Begin Message ---
Package: wnpp
Severity: wishlist
Owner: Nilesh Patra <npatra974@gmail.com>
X-Debbugs-CC: debian-devel@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 <npatra974@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 970447@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.

Debian distribution maintenance software
pp.
Nilesh Patra <npatra974@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 ftpmaster@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-packaging@lists.alioth.debian.org>
Changed-By: Nilesh Patra <npatra974@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)
Checksums-Sha1:
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Files:
 38f4d1659b3eb41772809b7cff613726 2531 science optional pinfish_0.1.0+ds-1.dsc
 f76133bed3fba383e81cc39b73cccdb1 68559048 science optional pinfish_0.1.0+ds.orig-debian-tests-data.tar.xz
 70d87d84ead55e6112f068425ba60c56 5054956 science optional pinfish_0.1.0+ds.orig.tar.xz
 720f69279d3522d3a5ebf16ae2273f40 6396 science optional pinfish_0.1.0+ds-1.debian.tar.xz
 5516911da77d4065bb4618d6431a1ff8 179336356 science optional pinfish-examples_0.1.0+ds-1_all.deb
 e31bb21ab616d82336155402b9da36fb 7119 science optional pinfish_0.1.0+ds-1_amd64.buildinfo
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