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Bug#854774: marked as done (ITP: libseqlib -- C++ htslib/bwa-mem/fermi interface for interrogating sequence data)

Your message dated Thu, 09 Mar 2017 11:00:10 +0000
with message-id <E1clvnm-000IQu-5G@fasolo.debian.org>
and subject line Bug#854774: fixed in libseqlib 1.1.1+dfsg-1
has caused the Debian Bug report #854774,
regarding ITP: libseqlib -- C++ htslib/bwa-mem/fermi interface for interrogating sequence data
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.)


-- 
854774: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=854774
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    : libseqlib
  Version         : 1.1.1
  Upstream Author : Jeremiah A. Wala <jwala@broadinstitue.org>
* URL             : https://github.com/walaj/SeqLib
* License         : Apache-2.0
  Programming Lang: C++
  Description     : C++ htslib/bwa-mem/fermi interface for interrogating sequence data
 C++ API and command line tool that provides a rapid and user-friendly
 interface to BAM/SAM/CRAM files, global sequence alignment operations
 and sequence assembly. Four C libraries perform core operations in
 SeqLib: HTSlib for BAM access, BWA-MEM and BLAT for sequence alignment
 and Fermi for error correction and sequence assembly. Benchmarking
 indicates that SeqLib has lower CPU and memory requirements than leading
 C++ sequence analysis APIs. Minimal SeqLib code can extract, error-correct
 and assemble reads from a CRAM file and then align with BWA-MEM.
 SeqLib also provides additional capabilities, including chromosome-aware
 interval queries and read plotting. Command line tools are available for
 performing integrated error correction, micro-assemblies and alignment.


Remark: This library is needed to package freebayes >=1.1.  While freebayes
 1.0 is in new queue currently this package is to enable upgrading it to
 its next version.  When packaging the library some incompatibility between
 libbwa and libfml was detected which was solved by SeqLib upstream with
 patched code copies.  These code copies were removed and the Debian packaged
 libfml was patched instead and uploaded to experimental.  As long as we
 are in freeze it should stay in experimental thus the first upload of
 libseqlib will also be uploaded to experimental.
 .
 The package will be maintained by the Debian Med team at
    https://anonscm.debian.org/git/debian-med/libseqlib.git

--- End Message ---
--- Begin Message --- 
Source: libseqlib
Source-Version: 1.1.1+dfsg-1

We believe that the bug you reported is fixed in the latest version of
libseqlib, 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 854774@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 libseqlib 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, 10 Feb 2017 10:16:57 +0100
Source: libseqlib
Binary: libseqlib0 libseqlib-dev
Architecture: source amd64
Version: 1.1.1+dfsg-1
Distribution: experimental
Urgency: medium
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
 libseqlib-dev - C++ htslib/bwa-mem/fermi interface for interrogating sequence dat
 libseqlib0 - C++ htslib/bwa-mem/fermi interface for interrogating sequence dat
Closes: 854774
Changes:
 libseqlib (1.1.1+dfsg-1) experimental; urgency=medium
 .
   * Initial release (Closes: #854774)
Checksums-Sha1:
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 97286c148d10d18d8088ae9ba900d4afc388929b 162924 libseqlib_1.1.1+dfsg.orig.tar.xz
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Checksums-Sha256:
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 c148e914e269a158452f18f25d1e15e4e184e899811c3c36324ec13d529558c2 6351 libseqlib_1.1.1+dfsg-1_amd64.buildinfo
Files:
 4c4a681fda6dda85d0e0bc8ab51d5a12 2188 science optional libseqlib_1.1.1+dfsg-1.dsc
 e40613c3d7dfccc2a8b6828a5348350f 162924 science optional libseqlib_1.1.1+dfsg.orig.tar.xz
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 5b9181f5d6f42cca4272f09e751c5ade 163820 libdevel optional libseqlib-dev_1.1.1+dfsg-1_amd64.deb
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