Bug#973658: marked as done (ITP: mosdepth -- BAM/CRAM depth calculation biological sequencing)
Your message dated Tue, 03 Nov 2020 22:00:10 +0000
with message-id <E1ka4La-0002qE-7u@fasolo.debian.org>
and subject line Bug#973658: fixed in mosdepth 0.3.1+ds-1
has caused the Debian Bug report #973658,
regarding ITP: mosdepth -- BAM/CRAM depth calculation biological sequencing
to be marked as done.
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If this is not the case it is now your responsibility to reopen the
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973658: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=973658
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--- Begin Message ---
Package: wnpp
Severity: wishlist
Subject: ITP: mosdepth -- BAM/CRAM depth calculation biological sequencing
Package: wnpp
Owner: Steffen Moeller <moeller@debian.org>
Severity: wishlist
* Package name : mosdepth
Version : 0.3.1
Upstream Author : Brent Pedersen
* URL : https://github.com/brentp/mosdepth
* License : Expat
Programming Lang: Python
Description : BAM/CRAM depth calculation biological sequencing
Many small reads are produced by high-throughput "next generation"
sequencing technologies. The final sequence is derived from how
these reads are overlapping towards a consensus.
The more reads are covering/confirming parts of a nucleotide seq,
the higher the confidence is. Too many reads would be indicative
of e.g. repeats in the genome.
.
mosdepth can output:
* per-base depth about 2x as fast samtools depth--about 25 minutes
of CPU time for a 30X genome.
* mean per-window depth given a window size--as would be used for
CNV calling.
* the mean per-region given a BED file of regions.
* a distribution of proportion of bases covered at or above a given
threshhold for each chromosome and genome-wide.
* quantized output that merges adjacent bases as long as they fall
in the same coverage bins e.g. (10-20)
* threshold output to indicate how many bases in each region are
covered at the given thresholds.
when appropriate, the output files are bgzipped and indexed for ease
of use.
Remark: This package is maintained by Debian Med Packaging Team at
https://salsa.debian.org/med-team/mosdepth
--- End Message ---
--- Begin Message ---
Source: mosdepth
Source-Version: 0.3.1+ds-1
Done: Steffen Moeller <moeller@debian.org>
We believe that the bug you reported is fixed in the latest version of
mosdepth, 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 973658@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Steffen Moeller <moeller@debian.org> (supplier of updated mosdepth 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: Tue, 03 Nov 2020 14:26:52 +0100
Source: mosdepth
Binary: mosdepth mosdepth-dbgsym mosdepth-examples
Architecture: source amd64 all
Version: 0.3.1+ds-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed-By: Steffen Moeller <moeller@debian.org>
Description:
mosdepth - BAM/CRAM depth calculation biological sequencing
mosdepth-examples - Test data for mosdepth
Closes: 973658
Changes:
mosdepth (0.3.1+ds-1) unstable; urgency=medium
.
* Initial release (Closes: #973658)
Checksums-Sha1:
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Checksums-Sha256:
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Files:
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2f6321451cb912103d882eef6770d125 24496 science optional mosdepth_0.3.1+ds.orig.tar.xz
53a80ebbe51081eb5619cbbcd27aa86d 715520 science optional mosdepth_0.3.1+ds-1.debian.tar.xz
fa8aa6782714802a679714631d435432 34496 debug optional mosdepth-dbgsym_0.3.1+ds-1_amd64.deb
2d7be3ccbf69c5ba7f9333c31b32d74a 1037024 science optional mosdepth-examples_0.3.1+ds-1_all.deb
a34fa2ec4da175f9fdff2a401b3d1506 7273 science optional mosdepth_0.3.1+ds-1_amd64.buildinfo
675752866280d07150058f0b72a56f1b 170548 science optional mosdepth_0.3.1+ds-1_amd64.deb
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--- End Message ---
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