Bug#871501: marked as done (ITP: jellyfish1 -- count k-mers in DNA sequences)
Your message dated Wed, 09 Aug 2017 22:00:11 +0000
with message-id <E1dfZ1P-000B9m-Mq@fasolo.debian.org>
and subject line Bug#871501: fixed in jellyfish1 1.1.11-1
has caused the Debian Bug report #871501,
regarding ITP: jellyfish1 -- count k-mers in DNA sequences
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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871501: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=871501
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--- Begin Message ---
Package: wnpp
Severity: wishlist
Owner: Andreas Tille <tille@debian.org>
* Package name : jellyfish1
Version : 1.1.11
Upstream Author : Guillaume Marçais1, Carl Kingsford
* URL : http://www.cbcb.umd.edu/software/jellyfish/
* License : BSD-like
Programming Lang: C++
Description : count k-mers in DNA sequences
JELLYFISH is a tool for fast, memory-efficient counting of k-mers in
DNA. A k-mer is a substring of length k, and counting the occurrences
of all such substrings is a central step in many analyses of DNA
sequence. JELLYFISH can count k-mers using an order of magnitude less
memory and an order of magnitude faster than other k-mer counting
packages by using an efficient encoding of a hash table and by
exploiting the "compare-and-swap" CPU instruction to increase
parallelism.
.
JELLYFISH is a command-line program that reads FASTA and multi-FASTA
files containing DNA sequences. It outputs its k-mer counts in an
binary format, which can be translated into a human-readable text
format using the "jellyfish dump" command.
.
This is the latest version of the 1.x series of jellyfish which is
used by some other applications that are not compatible with version
2.x which is provided inside the jellyfish package.
Remark: Jellyfish1 is no new package. It used to be in Debian but
the code migrated to version 2 which is not compatible with all our
tools. So there is a need to keep the latest release of version 1.x
which is packaged here. The package is maintained by the Debian
Med team at
https://anonscm.debian.org/git/debian-med/jellyfish1.git
--- End Message ---
--- Begin Message ---
Source: jellyfish1
Source-Version: 1.1.11-1
We believe that the bug you reported is fixed in the latest version of
jellyfish1, 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 871501@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Andreas Tille <tille@debian.org> (supplier of updated jellyfish1 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: Tue, 08 Aug 2017 17:26:44 +0200
Source: jellyfish1
Binary: jellyfish1
Architecture: source amd64
Version: 1.1.11-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
jellyfish1 - count k-mers in DNA sequences
Closes: 871501
Changes:
jellyfish1 (1.1.11-1) unstable; urgency=medium
.
* Create separate jellyfish1 package since there exist packages that
explicitly require jellyfish version 1
Closes: #871501
* Adapt watch file to only fetch 1.x version updates
* Move executable to usr/lib/jellyfish1/jellyfish and symlink to
/usr/bin/jellyfish1
* Move citation to the right place
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--- End Message ---
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