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Bug#778300: marked as done (ITP: transdecoder -- find coding regions within transcripts)

Your message dated Mon, 25 May 2015 13:00:18 +0000
with message-id <E1YwrzO-0008AG-Kv@franck.debian.org>
and subject line Bug#778300: fixed in transdecoder 2.0.1+dfsg-1
has caused the Debian Bug report #778300,
regarding ITP: transdecoder -- find coding regions within transcripts
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.)


-- 
778300: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=778300
Debian Bug Tracking System
Contact owner@bugs.debian.org with problems
--- Begin Message ---
Package: wnpp
Severity: wishlist
Owner: Debian Med team <debian-med@lists.debian.org>
X-Debbugs-Cc: debian-devel@lists.debian.org, debian-med@lists.debian.org

* Package name    : transdecoder
  Version         : 2.0.1
  Upstream Author : Brian Haas <bhass@broadinstitute.org>
* URL             : http://transdecoder.github.io/
* License         : BSD-3-clause
  Programming Lang: Perl
  Description     : find coding regions within transcripts

 TransDecoder identifies candidate coding regions within transcript sequences,
 such as those generated by de novo RNA-Seq transcript assembly using Trinity,
 or constructed based on RNA-Seq alignments to the genome using Tophat and
 Cufflinks.
 .
 TransDecoder identifies likely coding sequences based on the following
 criteria:
 .
 a minimum length open reading frame (ORF) is found in a transcript sequence
 .
 a log-likelihood score similar to what is computed by the GeneID software is
 > 0.
 .
 the above coding score is greatest when the ORF is scored in the 1st reading
 frame as compared to scores in the other 5 reading frames.
 .
 if a candidate ORF is found fully encapsulated by the coordinates of another
 candidate ORF, the longer one is reported. However, a single transcript can
 report multiple ORFs (allowing for operons, chimeras, etc).
 .
 optional the putative peptide has a match to a Pfam domain above the noise
 cutoff score.

transdecoder is a dependency of trinityrnaseq. It will be team maintained by
myself and the Debian Med team.

--- End Message ---
--- Begin Message --- 
Source: transdecoder
Source-Version: 2.0.1+dfsg-1

We believe that the bug you reported is fixed in the latest version of
transdecoder, 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 778300@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.

Debian distribution maintenance software
pp.
Michael R. Crusoe <mcrusoe@msu.edu> (supplier of updated transdecoder 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: Fri, 13 Feb 2015 06:26:24 -0500
Source: transdecoder
Binary: transdecoder transdecoder-doc
Architecture: source all
Version: 2.0.1+dfsg-1
Distribution: unstable
Urgency: low
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed-By: Michael R. Crusoe <mcrusoe@msu.edu>
Description:
 transdecoder - find coding regions within transcripts
 transdecoder-doc - find coding regions within transcripts
Closes: 778300
Changes:
 transdecoder (2.0.1+dfsg-1) unstable; urgency=low
 .
   * Initial release (Closes: #778300)
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 0448be54948c81066cd6bb792f4ea61b498fa552 9272005 transdecoder_2.0.1+dfsg.orig.tar.gz
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 349e615c8d6fc18f776d9ef9a91d31d183ed7763 56808 transdecoder_2.0.1+dfsg-1_all.deb
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Checksums-Sha256:
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Files:
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 7aa659317764efa2eff42f9864bbc51b 9272005 science optional transdecoder_2.0.1+dfsg.orig.tar.gz
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