Matt Stone

Hi Dana, Thanks! The patch fixed that issue. Sorry to bother you again, but I found another bug that I was hoping you could take a look at. I'm not...

Thanks, I had added it that, but by default it only counts the direct children. So in the examples below, I'd like the cookie next to `Project` to read `[0/4]`,...

A rule can complete successfully (exit code 0) but its outputs can be still be wrong. (e.g. if the invoked tool is buggy, if the user specified an incorrect argument,...

Note - I've tried changing the type hint to `metric: MetricType`, as in `Metric.write()`, but get the same errors

Thanks! I wanted to avoid another `type: ignore`. I found a solution using `TypeGuard` that I would be satisfied with. I've implemented it within `metric` instead of `inspect` so we...

I had the same thought, but I'm of two minds. I strongly prefer being consistent with established convention when possible, and both `dataclasses` and `attr` implement `asdict()` as a standalone...

That's fair. I would be open to refactoring so `.read()` remains specific to `Metric`-formatted files. In that case I'd suggest providing a `.read_picard()` method or similar, which would filter comment...

@nh13 thoughts?

**note** I want to keep this separate from the `MetricWriter` feature branch, but it's dependent on the `Metric._read_header` method introduced in that branch. I am waiting to merge until #123...

I can open a similar issue on pysam. I don't think I have a clear mental model on distinguishing the features we consider for inclusion in fgpyo vs attempting to...