Package: samtools Version: 1.20-3 Severity: important Greetings,
Experimental pseudo-excuses for htslib report a regression[1] in
samtools following upgrade of htslib 1.21 in experimental. Here
is a sample failed item; note that there are five more failed
items in the full log:
33s 55: Filter -R /tmp/N3sfijDzHL/view.001.fogn -r grp2 (SAM input)
33s Header type @RG differs.
33s /tmp/N3sfijDzHL/view.test055.sam has:
33s |@RG ID:grp3 DS:Group 3 SM:Sample
33s | (33)
33s /tmp/N3sfijDzHL/view.001.rg_both.sam has:
33s |@RG ID:grp1 DS:Group 1 LB:Library 1 SM:Sample
33s | (46)
33s |@RG ID:grp2 DS:Group 2 LB:Library 2 SM:Sample
33s | (46)
33s |@RG ID:grp3 DS:Group 3 SM:Sample
33s | (33)
33s Failed command:
33s /tmp/autopkgtest-lxc.rb4p4az0/downtmp/autopkgtest_tmp/samtools
view -o /tmp/N3sfijDzHL/view.test055.sam -h -R /tmp/N3sfijDzHL/view.001.fogn -r
grp2 /tmp/N3sfijDzHL/view.001.sam --no-PG
33s
33s
33s .. failed ...
[1]: https://ci.debian.net/packages/s/samtools/unstable/amd64/54272361/
With some luck this may simply be resolved by upgrading samtools
to version 1.21, on par with htslib version 1.21. The severity
is rated important as samtools currently has no issues with
htslib 1.20 in unstable. Severity will be bumped to serious
upon migration of htslib 1.21 to unstable.
Have a nice day, :)
--
.''`. Étienne Mollier <emoll...@debian.org>
: :' : pgp: 8f91 b227 c7d6 f2b1 948c 8236 793c f67e 8f0d 11da
`. `' sent from /dev/pts/4, please excuse my verbosity
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