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Bug#710324: marked as done (ITP: staden -- set of DNA sequence assembly, editing and analysis tools)

Your message dated Thu, 22 May 2014 11:00:11 +0000
with message-id <E1WnQjL-0006ig-LJ@franck.debian.org>
and subject line Bug#710324: fixed in staden 2.0.0+b10-1
has caused the Debian Bug report #710324,
regarding ITP: staden -- set of DNA sequence assembly, editing and analysis tools
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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710324: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=710324
Debian Bug Tracking System
Contact owner@bugs.debian.org with problems
--- Begin Message ---
Package: wnpp
Severity: wishlist
Owner: Jonas Smedegaard <dr@jones.dk>

* Package name    : staden
  Version         : 2.0.0b9
  Upstream Author : Medical Research Council, Laboratory of Molecular Biology
* URL             : http://staden.sourceforge.net/
* License         : unknown (need to be resolved, obviously, before releasing)
  Programming Lang: C, C++, Tcl
  Description     : set of DNA sequence assembly, editing and analysis tools

 This is the Staden package, a collection of sequence handling and
 analysis software.
 Gap4 performs sequence assembly, contig ordering based on read pair
 data, contig joining based on sequence comparisons, assembly checking,
 repeat searching, experiment suggestion, read pair analysis and contig
 editing. It has graphical views of contigs, templates, readings and
 traces which all scroll in register. Contig editor searches and
 experiment suggestion routines use confidence values to calculate the
 confidence of the consensus sequence and hence identify only places
 requiring visual trace inspection or extra data. The result is
 extremely rapid finishing and a consensus of known accuracy.
 Pregap4 provides a graphical user interface to set up the processing
 required to prepare trace data for assembly or analysis, and automates
 these processes.
 Trev is a rapid and flexible viewer and editor for ABI, ALF, SCF and
 ZTR trace files.
 Prefinish analyses partially completed sequence assemblies and suggests
 the most efficient set of experiments to help finish the project.
 Tracediff and hetscan automatically locate mutations by comparing trace
 data against reference traces. They annotate the mutations found ready
 for viewing in gap4.
 Spin analyses nucleotide sequences to find genes, restriction sites,
 motifs, etc. It can perform translations, find open reading frames,
 count codons, etc. Many results are presented graphically and a sliding
 sequence window is linked to the graphics cursor. Spin also compares
 pairs of sequences in many ways. It has very rapid dot matrix analysis,
 global and local alignment algorithms, plus a sliding sequence window
 linked to the graphical plots. It can compare nucleic acid against
 nucleic acid, protein against protein, and protein against nucleic

--- End Message ---
--- Begin Message ---
Source: staden
Source-Version: 2.0.0+b10-1

We believe that the bug you reported is fixed in the latest version of
staden, which is due to be installed in the Debian FTP archive.

A summary of the changes between this version and the previous one is

Thank you for reporting the bug, which will now be closed.  If you
have further comments please address them to 710324@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.

Debian distribution maintenance software
Andreas Tille <tille@debian.org> (supplier of updated staden 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)

Hash: SHA256

Format: 1.8
Date: Mon, 21 Apr 2014 22:34:28 +0200
Source: staden
Binary: staden staden-common
Architecture: source amd64 all
Version: 2.0.0+b10-1
Distribution: unstable
Urgency: low
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed-By: Andreas Tille <tille@debian.org>
 staden     - DNA sequence assembly (Gap4/Gap5), editing and analysis tools
 staden-common - Architecture independent files for Staden
Closes: 710324
 staden (2.0.0+b10-1) unstable; urgency=low
   [ Tim Booth ]
   * Initial release to Debian (Closes: #710324)
   * Fix dependency for Debian after realising io-lib was already packaged
     as libstaden-read
   [ Andreas Tille ]
   * Port some changes from other attempt to package staden by
     Jonas Smedegaard
   * Fix several lintian issues
   * fix watch file
   * wrapper script for staden to provide access to all binaries,
     main binaries available via additional symlink
 228dfc934b5d46e63ee677c6934cb66f89440dc8 2215 staden_2.0.0+b10-1.dsc
 82543c888f71249fbff3ad8de220ce9fb113915c 4616845 staden_2.0.0+b10.orig.tar.gz
 d3bf4a22b6c00066e9836abae8ee94d35639c26d 14112 staden_2.0.0+b10-1.debian.tar.xz
 2b995904611ea6b2082096f2384d70e5e88f8c0f 1536924 staden_2.0.0+b10-1_amd64.deb
 da2cf3364658f416a5c1dcba5e608d6d4b1fae22 1941102 staden-common_2.0.0+b10-1_all.deb
 7275db262edac11471ad93a7494052e31a74fa473def4dc933adbcdb84f24836 2215 staden_2.0.0+b10-1.dsc
 099efd84a208ec9efa3669803c0ca6f09960d760886fa3990dfa5cf9d0c112fb 4616845 staden_2.0.0+b10.orig.tar.gz
 ed9305c6326da41dd64f7723eb566eda952b83745166ac8f1d9a2c55060f0ed2 14112 staden_2.0.0+b10-1.debian.tar.xz
 7e6308bff8d65607c4f9727b2d4f8f8d7d8a3c465ed160f8668714d7d919b85c 1536924 staden_2.0.0+b10-1_amd64.deb
 3f7f994ad5f3ba9fa10e7dfb3361e8f92374bde57d118a23492d409d0c2b6142 1941102 staden-common_2.0.0+b10-1_all.deb
 6fc89f74cdd50764af9c8871bf3c1ed5 1536924 science optional staden_2.0.0+b10-1_amd64.deb
 74d8610d2cc38d91a54bed8a670b0d8b 1941102 science optional staden-common_2.0.0+b10-1_all.deb
 85ccb89f63fbe5a1406edf1eb88357dd 2215 science optional staden_2.0.0+b10-1.dsc
 81ad0b840253774e41d3089fca7af688 4616845 science optional staden_2.0.0+b10.orig.tar.gz
 2a9cab52573e6831acd09d1454146fa4 14112 science optional staden_2.0.0+b10-1.debian.tar.xz

Version: GnuPG v1


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