Matt Stone

And to the question at hand, I like the suggestion that instead of `None` we could pass `"*"` to the builder to get the desired outcome. But that doesn't appear...

@tfenne Any thoughts on how we should resolve (3) if an invalid/unknown sort-order value exists?

Oh nice, I didn't know we already had that enum. In the course of resolving this issue we should also update that enum to improve its documentation (i.e. include the...

In an ideal world this would probably be a method on `AlignmentHeader`, but since we don't have such powers, adding a classmethod to the enum seems reasonable. (I'd probably write...

Re: returning "UNKNOWN" - this is an edge case in the SAM spec I'm not actually familiar with. Is there a distinction between an "unknown" sort order and an invalid...

Hi, I'm encountering this issue as well. (Jupyter v4.4.0, nbconvert v5.3.1). Is there a suggested fix or workaround? Thanks!

@clintval @nh13 @tfenne I am opening this draft PR for review now because I would like to collect early feedback on the pattern being implemented.

@clintval Do you have suggestions or preferences for how having an optional dependency should be tested?

Mypy checks are failing on 3.9. I wonder if this is related to our [decision to not enforce a python version in the mypy config](https://github.com/fulcrumgenomics/python-template/pull/19). TBH I'd prefer to drop...

@clintval AFAICT the README is autogenerated from the tool help doc. I've updated the tool docs accordingly. I did run into one new question - the help mentions storing the...