[Debian-med-packaging] Bug#1087456: samtools: autopkgtest regression with htslib 1.21

[Étienne Mollier]

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 <emollier at debian.org>
 : :' :  pgp: 8f91 b227 c7d6 f2b1 948c  8236 793c f67e 8f0d 11da
 `. `'   sent from /dev/pts/4, please excuse my verbosity
   `-    on air: The Smile - Foreign Spies
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