Nils Homer

Edited: Red herring, as the failure comes from an older `click` install in `~/.local` on my dev linux machine ~Same issue for me, here's a conda environment:~ environment.yaml ```yaml name:...

Maybe I’ll make a PR

Looks like a `parser.value_converter` will work here. It would be great to natively support any type who has a string constructor. Here's another interesting case: ``` from clize import run,...

@fleharty we are all OSX users (10.14.xx)

@lbergelson we may think of adding support for other deflaters, as they seem just as good: http://jkbonfield.github.io/www.htslib.org/benchmarks/zlib.html

Always best to be I second place: https://github.com/samtools/htsjdk/pull/1601

Do you need to fall back on the first and second of pair flags as samtools does? https://github.com/samtools/samtools/blob/bdc5bb81c11f2ab25ea97351213cb87b33857c4d/bam_sort.c#L1798

I also think we should be using the `URI` constructor and not the `URI.create` method after reading the javadoc for the latter.

@jmarshall > Um… not sure anyone has made a case for allowing this? That's definitely my mistake. I think what I _want_ is to say that it's ok for the...

@yfarjoun assigned to myself, thanks!