conflict between TopHat2.1.1 and HTSeq 0.9.1

[germaximus]

Bam files generated by TopHat are incompatible with feature counting software such as HTSeq-count. The reason is likely due to the change to samtools. Tophat uses old samtools 0.1.18. Currently I have to convert bam files to sam and then back to bam with samtools 1.6 to make the suitable for HTSeq-count and subsequent differential gene expression analysis.

Example of the error that HTSeq-count gives on bam files from TopHat
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]