Source: pbsuite Version: 15.8.24+dfsg-8 Severity: serious User: debian...@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
