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Bug#903911: marked as done (ITP: pilon-non-free -- automated genome assembly improvement and variant detection tool)

Your message dated Fri, 03 Aug 2018 11:00:27 +0000
with message-id <E1flXop-0002Sh-0A@fasolo.debian.org>
and subject line Bug#903911: fixed in pilon 1.22+dfsg-1
has caused the Debian Bug report #903911,
regarding ITP: pilon-non-free -- automated genome assembly improvement and variant detection tool
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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immediately.)


-- 
903911: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=903911
Debian Bug Tracking System
Contact owner@bugs.debian.org with problems
--- Begin Message --- 
Package: wnpp
Severity: wishlist
Owner: Andreas Tille <tille@debian.org>

* Package name    : pilon-non-free
  Version         : 1.22
  Upstream Author : Copyright: Copyright 2012-2017 Broad Institute, Inc.
* URL             : https://github.com/broadinstitute/pilon/wiki
* License         : GPL-2
  Programming Lang: Java
  Description     : automated genome assembly improvement and variant detection tool
 Pilon is a software tool which can be used to:
  * Automatically improve draft assemblies
  * Find variation among strains, including large event detection
 Pilon requires as input a FASTA file of the genome along with one or more
 BAM files of reads aligned to the input FASTA file. Pilon uses read
 alignment analysis to identify inconsistencies between the input genome and
 the evidence in the reads. It then attempts to make improvements to the
 input genome, including:
  * Single base differences
  * Small indels
  * Larger indel or block substitution events
  * Gap filling
  * Identification of local misassemblies, including optional opening
    of new gaps
 .
 The code of pilon is actually free but currently there is no method
 to build the JAR from the scala source in Debian.  This package is
 supposed to be replaced by a pilon package once it can be build from
 source (see bug #873341).

Remark: This package is maintained by Debian Med Packaging Team at
   https://salsa.debian.org/med-team/pilon-non-free
It is planed to replace this package pilon-non-free by a pilon
package once sbt will be usable again (see #873341).  Unfortunately
it is expected that this will take way longer than expected
(see the discussion on debian-java list).

--- End Message ---
--- Begin Message --- 
Source: pilon
Source-Version: 1.22+dfsg-1

We believe that the bug you reported is fixed in the latest version of
pilon, 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 903911@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 pilon 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, 03 Aug 2018 10:37:51 +0200
Source: pilon
Binary: pilon
Architecture: source all
Version: 1.22+dfsg-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:
 pilon      - automated genome assembly improvement and variant detection tool
Closes: 903911
Changes:
 pilon (1.22+dfsg-1) unstable; urgency=medium
 .
   * Initial release (Closes: #903911)
Checksums-Sha1:
 7dd1bcff6740bed233d49a1e0dae7d4e2f5e5efd 1968 pilon_1.22+dfsg-1.dsc
 453b344f63c0cfdf61aa89b41c813e253e6d4e2d 40952 pilon_1.22+dfsg.orig.tar.xz
 7fdd486ef1ee8cb4f7e86426770036b39a0d52b5 5316 pilon_1.22+dfsg-1.debian.tar.xz
 83c6bd44354ad23456ad38c34fad4796aa8eba55 413980 pilon_1.22+dfsg-1_all.deb
 6b8d36ac40b52b565d52056e1046b66e993a170e 7937 pilon_1.22+dfsg-1_amd64.buildinfo
Checksums-Sha256:
 62b044cd7218f121fccd6c88baaf30ca766a285dec23cf9476e71c59dda02eb6 1968 pilon_1.22+dfsg-1.dsc
 bb59d2732e671597746d85dce68c9e0879a262a6558b7df28229a7b69c6430e1 40952 pilon_1.22+dfsg.orig.tar.xz
 7227de6f77207d757318ea5e95bca79b2ca71093ddad0da5d2e87be6342b6138 5316 pilon_1.22+dfsg-1.debian.tar.xz
 4083c2633ca18f80647c03a9a2b5fc4ac74c0c0e9f40059f1ba46b85bd69244d 413980 pilon_1.22+dfsg-1_all.deb
 be7c495f34f631e1f67708fd9f46183ca90faa18fbe083ce4f8b6cd5375e47ff 7937 pilon_1.22+dfsg-1_amd64.buildinfo
Files:
 38517785a7be692b94866bb168b97b29 1968 science optional pilon_1.22+dfsg-1.dsc
 f9356d2a222743eac8fd398bbad341ed 40952 science optional pilon_1.22+dfsg.orig.tar.xz
 62f39f590be96d9793a3b65ef38b9ab2 5316 science optional pilon_1.22+dfsg-1.debian.tar.xz
 646eaa96ed5d6796fbf7067569fad0b2 413980 science optional pilon_1.22+dfsg-1_all.deb
 8fe00b5768f47a590b34f79952f4544a 7937 science optional pilon_1.22+dfsg-1_amd64.buildinfo

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--- End Message ---
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