htseq-count test data for issue:
Different versions of HTSeq were tested and the counts of newer versions (1.99.2 and newer) differ from the counts obtained with older versions (0.13.5 and older)
singularity run -B /mnt /mnt/shared/development/htseq-1.99.2.sif htseq-count -s yes subset.sam subset.gtf >counts_1.99.2.raw