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Bug#910357: marked as done (ITP: segemehl -- short read mapping with gaps)

Your message dated Tue, 13 Nov 2018 13:10:24 +0000
with message-id <E1gMYSW-0005LH-HX@fasolo.debian.org>
and subject line Bug#910357: fixed in segemehl 0.3-1
has caused the Debian Bug report #910357,
regarding ITP: segemehl -- short read mapping with gaps
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.)


-- 
910357: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=910357
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    : segemehl
  Version         : 0.3
  Upstream Author : Bioinformatik Leipzig
* URL             : http://www.bioinf.uni-leipzig.de/Software/segemehl/
* License         : GPL-3+
  Programming Lang: C
  Description     : short read mapping with gaps
 Segemehl is a software to map short sequencer reads to reference
 genomes. Segemehl implements a matching strategy based on enhanced
 suffix arrays (ESA). Segemehl accepts fasta and fastq queries (gzip’ed
 and bgzip'ed). In addition to the alignment of reads from standard DNA-
 and RNA-seq protocols, it also allows the mapping of bisulfite converted
 reads (Lister and Cokus) and implements a split read mapping strategy.
 The output of segemehl is a SAM or BAM formatted alignment file. In the
 case of split-read mapping, additional BED files are written to the
 disc. These BED files may be summarized with the postprocessing tool
 haarz. In the case of the alignment of bisulfite converted reads, raw
 methylation rates may also be called with haarz.
 .
 In brief, for each suffix of a read, segemehl aims to find the
 best-scoring seed. Seeds might contain insertions, deletions, and
 mismatches (differences). The number of differences allowed within a
 single seed is user-controlled and is crucial for the runtime of the
 program.  Subsequently, seeds that undercut the user-defined E-value are
 passed on to an exact semi-global alignment procedure. Finally, reads
 with a minimum accuracy of percent are reported to the user.

Remark: This package is maintained by Debian Med Packaging Team at
   https://salsa.debian.org/med-team/segemehl

--- End Message ---
--- Begin Message --- 
Source: segemehl
Source-Version: 0.3-1

We believe that the bug you reported is fixed in the latest version of
segemehl, 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 910357@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 segemehl 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, 05 Oct 2018 12:02:13 +0200
Source: segemehl
Binary: segemehl
Architecture: source amd64
Version: 0.3-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
 segemehl   - short read mapping with gaps
Closes: 910357
Changes:
 segemehl (0.3-1) unstable; urgency=medium
 .
   * Initial release (Closes: #910357)
Checksums-Sha1:
 edde9cc927a4db188861e5c59c57472b7a526c3a 1985 segemehl_0.3-1.dsc
 21972db7e7377c3686a50e72db407397ade606ba 326153 segemehl_0.3.orig.tar.gz
 8c7db52c020364ef9887f1561676f4c5b2125eb3 6784 segemehl_0.3-1.debian.tar.xz
 89d38925de75260547c56214f4882e84fdb482fd 1835800 segemehl-dbgsym_0.3-1_amd64.deb
 e49c55d8db847319311585eac01f778ef2363ebb 6579 segemehl_0.3-1_amd64.buildinfo
 2c10c4afb81cd7367ad7e2d0efefc40db96162a0 315376 segemehl_0.3-1_amd64.deb
Checksums-Sha256:
 1e868462ed190716e41e8f65440336596405861a7b4b69921ba7de73a4663062 1985 segemehl_0.3-1.dsc
 ce3b87a22c2f50b8c457998f984b96a2e21858cf070595a0fc592ea7c5b13885 326153 segemehl_0.3.orig.tar.gz
 6b102b6dc2c97b02e9b8bc0a4ce8056a780c44d91848fb03d836697735911e70 6784 segemehl_0.3-1.debian.tar.xz
 06005fb6f5bacfa42a4867c22ddfebe2d6535f1b3878c5c4253f176fbf024955 1835800 segemehl-dbgsym_0.3-1_amd64.deb
 e3f5e1fe175077de843b7fdc7f69ce797c10915e4e358580d0746d7a155f0d2a 6579 segemehl_0.3-1_amd64.buildinfo
 663430949c331061c2c0d6907f3b2d751faa071aa21148bbfecec64b0b643c94 315376 segemehl_0.3-1_amd64.deb
Files:
 eefb8d04a7fff5f61668259abafb1c86 1985 science optional segemehl_0.3-1.dsc
 b69ba57f90c0a5a85b1ed5fb27fe5e40 326153 science optional segemehl_0.3.orig.tar.gz
 94f4363c026706ac7680ed4aa68e2683 6784 science optional segemehl_0.3-1.debian.tar.xz
 7d86c224a5eec68ecfe155a8c3668f67 1835800 debug optional segemehl-dbgsym_0.3-1_amd64.deb
 db13fd17191642bb3c14f46d001e4e09 6579 science optional segemehl_0.3-1_amd64.buildinfo
 18739af158dcdb392a6bc37371acb4c2 315376 science optional segemehl_0.3-1_amd64.deb

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--- End Message ---
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