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Bug#770063: marked as done (ITP: kmc -- count kmers in genomic sequences)

Your message dated Fri, 24 Jul 2015 16:00:51 +0000
with message-id <E1ZIfP1-0008Hf-OI@franck.debian.org>
and subject line Bug#770063: fixed in kmc 2.0+dfsg-1
has caused the Debian Bug report #770063,
regarding ITP: kmc -- count kmers in genomic 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.

(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.)


-- 
770063: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=770063
Debian Bug Tracking System
Contact owner@bugs.debian.org with problems
--- Begin Message --- 
Package: wnpp
Severity: wishlist
Owner: Jorge Soares <j.s.soares@gmail.com>

* Package name    : kmc
  Version         : 20
  Upstream Author : Sebastian Deorowicz <sebastian.deorowicz@polsl.pl>, Marek Kokot, Szymon Grabowski, Agnieszka Debudaj-Grabysz
* URL             : http://sun.aei.polsl.pl/kmc/index.html
* License         : GPL3
  Programming Lang: C, C++
  Description     : count kmers in genomic sequences

KMC—K-mer Counter is a utility designed for counting k-mers (sequences of consecutive k symbols) in a set of reads from genome sequencing projects. K-mer counting is important for many bioinformatics applications, e.g., developing de Bruijn graph assemblers. Building de Bruijn graphs is a commonly used approach for genome assembly with data from second-generation sequencer. Unfortunately, sequencing errors (frequent in practice) results in huge memory requirements for de Bruijn graphs, as well as long build time. One of the popular approaches to handle this problem is filtering the input reads in such a way that unique k-mers (very likely obtained as a result of an error) are discarded.

Thus, KMC scans the raw reads and produces a compact representation of all non-unique reads accompanied with number of their occurrences. The algorithm implemented in KMC makes use mostly of disk space rather than RAM, which allows to use KMC even on rather typical personal computers. When run at high-end server (what is necessary for KMC competitors) it outperforms them in both memory requirements and speed of computation. The disk space necessary for computation is in order of the size of input data (usually it is smaller).

kmc is a dependency of the iva - Iterative Virus Assembler - package

The software is used widely at the Wellcome Trust Sanger Institute

Sponsorship needed.

--- End Message ---
--- Begin Message --- 
Source: kmc
Source-Version: 2.0+dfsg-1

We believe that the bug you reported is fixed in the latest version of
kmc, 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 770063@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.

Debian distribution maintenance software
pp.
Jorge Soares <j.s.soares@gmail.com> (supplier of updated kmc 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: SHA512

Format: 1.8
Date: Mon, 03 Nov 2014 14:46:54 +0200
Source: kmc
Binary: kmc
Architecture: source amd64
Version: 2.0+dfsg-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed-By: Jorge Soares <j.s.soares@gmail.com>
Description:
 kmc        - count kmers in genomic sequences
Closes: 770063
Changes:
 kmc (2.0+dfsg-1) unstable; urgency=medium
 .
   * Initial release (Closes: #770063)
Checksums-Sha1:
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 a40897bbc226e35915674243939c3787a49fe172 73671 kmc_2.0+dfsg.orig.tar.gz
 da56d8bf77b6f6205d7fe3594a372a7cdd903897 7292 kmc_2.0+dfsg-1.debian.tar.xz
 f182d5b0a0d2d06f68e5c5d61e65f99c916ff332 199356 kmc_2.0+dfsg-1_amd64.deb
Checksums-Sha256:
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 29632bfedf9c8f582961d2ba4eeb7e8fe2b49407c4c581826df489854aba8b19 199356 kmc_2.0+dfsg-1_amd64.deb
Files:
 8ae47c91c71a6dcdc29aaca0b52e744c 2047 science optional kmc_2.0+dfsg-1.dsc
 45e69d1d9c293d98f12699092939a845 73671 science optional kmc_2.0+dfsg.orig.tar.gz
 e29bca720126e1cc56f2aff548482af4 7292 science optional kmc_2.0+dfsg-1.debian.tar.xz
 25657b7acac83db5d68d752c6eb731d7 199356 science optional kmc_2.0+dfsg-1_amd64.deb

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--- End Message ---
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