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Bug#778578: marked as done (ITP: rsem -- RNA-Seq by Expectation-Maximization)

Your message dated Wed, 21 Oct 2015 11:00:18 +0000
with message-id <E1Zor7y-0002yU-89@franck.debian.org>
and subject line Bug#778578: fixed in rsem 1.2.22+dfsg-1
has caused the Debian Bug report #778578,
regarding ITP: rsem -- RNA-Seq by Expectation-Maximization
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
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-- 
778578: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=778578
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    : rsem
  Version         : 1.2.19
  Upstream Author : Bo Li <bli25 [at] berkeley [dot] edu>
* URL             : http://deweylab.biostat.wisc.edu/rsem/
* License         : GPL-3
  Programming Lang: C++, Perl
  Description     : RNA-Seq by Expectation-Maximization

RSEM is a software package for estimating gene and isoform _expression_
 levels from RNA-Seq data. The RSEM package provides an user-friendly
 interface, supports threads for parallel computation of the EM
 algorithm, single-end and paired-end read data, quality scores,
 variable-length reads and RSPD estimation. In addition, it provides
 posterior mean and 95% credibility interval estimates for _expression_
 levels. For visualization, It can generate BAM and Wiggle files in both
 transcript-coordinate and genomic-coordinate. Genomic-coordinate files
 can be visualized by both UCSC Genome browser and Broad Institute’s
 Integrative Genomics Viewer (IGV). Transcript-coordinate files can be
 visualized by IGV. RSEM also has its own scripts to generate transcript
 read depth plots in pdf format. The unique feature of RSEM is, the read
 depth plots can be stacked, with read depth contributed to unique reads
 shown in black and contributed to multi-reads shown in red. In addition,
 models learned from data can also be visualized. Last but not least,
 RSEM contains a simulator.

RSEM is a popular bioinformatics program and a dependency of trinityrnaseq. It will be maintained by the Debian Med team.

--- End Message ---
--- Begin Message --- 
Source: rsem
Source-Version: 1.2.22+dfsg-1

We believe that the bug you reported is fixed in the latest version of
rsem, 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 778578@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.

Debian distribution maintenance software
pp.
Michael R. Crusoe <crusoe@ucdavis.edu> (supplier of updated rsem 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: Thu, 27 Aug 2015 13:17:53 -0400
Source: rsem
Binary: rsem
Architecture: source amd64
Version: 1.2.22+dfsg-1
Distribution: unstable
Urgency: low
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed-By: Michael R. Crusoe <crusoe@ucdavis.edu>
Description:
 rsem       - RNA-Seq by Expectation-Maximization
Closes: 778578
Changes:
 rsem (1.2.22+dfsg-1) unstable; urgency=low
 .
   * Initial release (Closes: #778578)
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 aa6bcb9aadd1b6f8ebbb69838027f3653e50e4cc 475010 rsem_1.2.22+dfsg-1_amd64.deb
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Files:
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 acce30151308dfc3d234a29ead6c3ee1 128327 science optional rsem_1.2.22+dfsg.orig.tar.gz
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