Hello,

I've updated htseq-count into version 0.9.1 (because I've wanted to use function --nonunique all), but it failed with error

Error occured when reading beginning of SAM/BAM file.
'csamtools.AlignedRead' object has no attribute 'reference_start'
[Exception type: AttributeError, raised in _HTSeq.pyx:1357]

and I don't know, how to fix it.

For generating of BAM file, I've used STAR version 2.5.3a_modified with command:

~/STAR_2.5.3a_modified/bin/Linux_x86_64/STAR --genomeDir /mnt/d/Xenopus_9_2 --readFilesIn sortmerna/sort_15_3A_1_sequence.fastq sortmerna/sort_15_3A_2_sequence.fastq --runThreadN 12 --outFileNamePrefix STAR/15_3A/15_3A --outSAMtype BAM SortedByCoordinate

and I'm running htseq-count with command:

htseq-count -f bam -t exon -i ID --additional-attr=gene -r pos -m intersection-nonempty --nonunique all -s no STAR/15_3A/15_3AAligned.sortedByCoord.out.bam /mnt/d/Xenopus_9_2/XENLA_9.2_Xenbase.gff3 > count/15_3A.count

pysam version: 0.11.2.2

Thanks for help.