[Debian-med-packaging] Bug#1091721: pbsuite: autopkgtest regression in testing

[Graham Inggs]

Source: pbsuite
Version: 15.8.24+dfsg-8
Severity: serious
User: debian-ci at lists.debian.org
Usertags: regression

Hi Maintainer

Sometime around 2024-12-26, pbsuite's autopkgtest regressed in
testing [1].  I've copied what I hope is the relevant part of the log
below.

This regression allowed blasr/5.3.5+dfsg-7 to migrate to testing.

Regards
Graham


[1] https://ci.debian.net/packages/p/pbsuite/testing/amd64/


74s 2024-12-26 05:20:04,185 [INFO] Running /usr/bin/Honey spots
--reference lambda_modified.fasta mappingFinal.bam
74s Traceback (most recent call last):
74s File "/usr/bin/Honey", line 51, in <module>
74s parseArgs()
74s File "/usr/bin/Honey", line 48, in parseArgs
74s STAGES[args.stage](args.options)
74s File "/usr/lib/python3/dist-packages/pbsuite/honey/HSpots.py",
line 1092, in run
74s bam = pysam.Samfile(args.bam)
74s ^^^^^^^^^^^^^^^^^^^^^^^
74s File "pysam/libcalignmentfile.pyx", line 751, in
pysam.libcalignmentfile.AlignmentFile.__cinit__
74s File "pysam/libcalignmentfile.pyx", line 956, in
pysam.libcalignmentfile.AlignmentFile._open
74s ValueError: file does not contain alignment data