[Bug 1983255] Re: samtools-legacy misses 'Remove compressBound assertions' (PR #1258) fix
Olivier Gayot
1983255 at bugs.launchpad.net
Fri Aug 5 09:51:09 UTC 2022
With @fheimes's help, I was able to run autopkgtest successfully.
We figured that libbio-samtools-perl requires a rebuild since it statically links against libbam-dev.
The autopkgtest suite runs like a charm after a rebuild.
Also, submitting the right .debdiff for samtools-legacy with Frank's
permission. The original .debdiff does not apply on a clean source tree.
Thanks!
** Patch added: "samtools-legacy_0.1.19+dfsg-5_0.1.19+dfsg-5ubuntu1.diff"
https://bugs.launchpad.net/ubuntu/+source/samtools-legacy/+bug/1983255/+attachment/5607131/+files/samtools-legacy_0.1.19+dfsg-5_0.1.19+dfsg-5ubuntu1.diff
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https://bugs.launchpad.net/bugs/1983255
Title:
samtools-legacy misses 'Remove compressBound assertions' (PR #1258)
fix
Status in samtools-legacy package in Ubuntu:
In Progress
Bug description:
samtools-legacy is the source package for libbam-dev,
which is used by libbio-samtools-perl (autopkgtests),
that is for example triggered by a zlib update (proposed-transition).
zlib requires a fix for 'compressBound() returns an incorrect result
on z15' LP#1961427 that again requires the 'Remove compressBound
assertions' (PR #1258) fix in all bgzf.c implementations, like htslib,
bedtools or even samtools-legacy.
Problematic is that the code differs quite a bit from the one where
the PR#1258 was designed for and that is used in the htslib or
bedtools package (no bgzf_hopen - looks a bit out of date), so it does
not apply cleanly.
According to upstream 'https://github.com/lh3/samtools-legacy' the project
is "For testing only." and marked as "DON'T USE!" and it's last update
is from Nov 9, 2013.
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