To expand on this -- I believe pysam [0] is the official htslib interface for Python. It's quite good. In addition to providing Python bindings, it also provid

To expand on this -- I believe pysam [0] is the official htslib interface for Python. It's quite good. In addition to providing Python bindings, it also provides extra functionality from within Cython, if you need additional features/speed but don't want to drop all the way down to C. [0] https://pysam.readthedocs.io/en/latest/ https://pysam.readthedocs.io/en/latest/