[snackematician]

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/

[mbreese]

Is the pysam API more stable now? Years ago, I had to stop using it because the API has changed between versions too much.