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Bug#1016046: marked as done (ITP: genomicsdb -- sparse array storage library for genomics)

Your message dated Sat, 10 Sep 2022 18:04:11 +0000
with message-id <E1oX4pv-001OnJ-Oz@fasolo.debian.org>
and subject line Bug#1016046: fixed in genomicsdb 1.4.3-1
has caused the Debian Bug report #1016046,
regarding ITP: genomicsdb -- sparse array storage library for genomics
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.)


-- 
1016046: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1016046
Debian Bug Tracking System
Contact owner@bugs.debian.org with problems
--- Begin Message --- 
Package: wnpp
Severity: wishlist
Owner: Debian-med team <debian-med@lists.debian.org>
X-Debbugs-Cc: debian-devel@lists.debian.org, debian-med@lists.debian.org

* Package name    : genomicsdb
  Version         : 1.4.3
  Upstream Author : Intel Health and Lifesciences
* URL             : https://www.genomicsdb.org/
* License         : Expat
  Programming Lang: C++, Java
  Description     : sparse array storage library for genomics

GenomicsDB is built on top of a htslib fork and an internal array storage
system for importing, querying and transforming variant data. Variant data is
sparse by nature (sparse relative to the whole genome) and using sparse array
data stores is a perfect fit for storing such data.

The GenomicsDB stores variant data in a 2D array where:
 - Each column corresponds to a genomic position (chromosome + position);
 - Each row corresponds to a sample in a VCF (or CallSet in the GA4GH
   terminology);
 - Each cell contains data for a given sample/CallSet at a given position;
   data is stored in the form of cell attributes;
 - Cells are stored in column major order - this makes accessing cells with
   the same column index (i.e. data for a given genomic position over all
   samples) fast.
 - Variant interval/gVCF interval data is stored in a cell at the start of the
   interval. The END is stored as a cell attribute. For variant intervals
   (such as deletions and gVCF REF blocks), an additional cell is stored at
   the END value of the variant interval. When queried for a given genomic
   position, the query library performs an efficient sweep to determine all
   intervals that intersect with the queried position.

There is a C++ library and a Java library, we plan to ship both of them.

This library is needed as a dependency of gatk, which is a packaging target of
the Debian-med team.

--- End Message ---
--- Begin Message --- 
Source: genomicsdb
Source-Version: 1.4.3-1
Done: Pierre Gruet <pgt@debian.org>

We believe that the bug you reported is fixed in the latest version of
genomicsdb, 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 1016046@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.

Debian distribution maintenance software
pp.
Pierre Gruet <pgt@debian.org> (supplier of updated genomicsdb 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: Thu, 28 Jul 2022 17:35:09 +0200
Source: genomicsdb
Binary: genomicsdb-tools genomicsdb-tools-dbgsym libgenomicsdb-dev libgenomicsdb-java libgenomicsdb-jni libgenomicsdb-jni-dbgsym libgenomicsdb0 libgenomicsdb0-dbgsym
Architecture: source amd64 all
Version: 1.4.3-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed-By: Pierre Gruet <pgt@debian.org>
Description:
 genomicsdb-tools - sparse array storage library for genomics (tools)
 libgenomicsdb-dev - sparse array storage library for genomics (development files)
 libgenomicsdb-java - sparse array storage library for genomics (Java library)
 libgenomicsdb-jni - sparse array storage library for genomics (Java native bindings)
 libgenomicsdb0 - sparse array storage library for genomics (shared libraries)
Closes: 1016046
Changes:
 genomicsdb (1.4.3-1) unstable; urgency=medium
 .
   * Initial release (Closes: #1016046)
Checksums-Sha1:
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Checksums-Sha256:
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 f294b187df30be2a6640e7846bd1d104 6589775 science optional genomicsdb_1.4.3.orig.tar.gz
 98f424b37567bcf17469f82a3f7a100b 25472 science optional genomicsdb_1.4.3-1.debian.tar.xz
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--- End Message ---
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