fix: 1) improve error in transform when providing an empty hap file and a --region and 2) allow for calling write() on Genotypes objects without variants

[aryarm]

This PR fixes two issues.

1. An issue with the transform command

When the input .hap file is empty and the --region parameter is provided, the transform command will fail with cryptic psyam errors instead of outputting an empty genotypes file. This PR resolves those.

The first error occurs with a regular hap file (that isn't indexed):

OSError: index `empty.hap.tbi` not found

https://github.com/CAST-genomics/haptools/actions/runs/12058438776/job/33625133365#step:9:380

And the second occurs when the hap file is indexed:

ValueError: could not create iterator for region '1:10116-10122'

https://github.com/CAST-genomics/haptools/actions/runs/12058465901/job/33625213549#step:9:400

2. An issue with the Genotypes classes

As an extra bonus, this PR also resolves an error in the GenotypesVCF and GenotypesPLINK classes when attempting to write files without any variants:

OSError: [Errno 9] Bad file descriptor

and

RuntimeError: b'No variants in test.pvar.\n'

https://github.com/CAST-genomics/haptools/actions/runs/12059160422/job/33627254672#step:9:378

[aryarm]

@mlamkin7, what do you think about this? Is the correct behavior to write an empty file or should we error out instead?

It gets a little weird for the PGEN files. For those, I think the pgenlib library won't even let me write an empty PGEN file, so I just manually write an empty file, instead. Not sure if that's a good idea, though...

[mlamkin7]

@mlamkin7, what do you think about this? Is the correct behavior to write an empty file or should we error out instead?

It gets a little weird for the PGEN files. For those, I think the pgenlib library won't even let me write an empty PGEN file, so I just manually write an empty file, instead. Not sure if that's a good idea, though...

Right now I can't think of any reason why transform would happen with an empty hap file and we would want an empty output. I'd say its better just to error out and let them know .hap is empty.

[aryarm]

ok, that sounds reasonable

I'll add some code to raise those errors

[aryarm]

ok, done! See 525fd44 for the new Value Error in transform

Note that I also made some minor changes in 9889833 to unrelated things:
I integrated our project with VSCode's testing/validation suite in the .devcontainer.json file, and VSCode pointed out a few missing import statements and complained about some type-hints that I fixed. Together, these changes get us one step closer to using a type checker as requested in #117: we just need to address this TODO

If you want to view the changes in this PR without the minor changes in 9889833, click here