Masking uncalled regions

[mufernando]

Hi,

First, thanks for developing this software!

In reading the supp. note, I see:

Filtering in phlash may be achieved by setting the corresponding positions to missing.
phlash also features the built-in ability to mask entire regions of the genome used standard
file formats (i.e., .BED), or programmatically using the Python interface.

I can't seem to find this option to mask uncallable regions. Can you point me to this, please?

Thank you,

Murillo

[terhorst]

Hi Murillo, thanks for this report. Looks like that feature currently lives on the devel branch. Can you try running devel and let me know if it works for you? If you're using uv, an easy way to do this is:

$ uvx --from notebook -w git+https://github.com/jthlab/phlash@devel\[gpu\] -w jupytext jupyter-notebook

which will run Jupyter with plash@devel installed.

Let me know if you need any help!

[terhorst]

(Not that this branch also has a new input format based on VCF Zarr; hope that's not too inconvenient!)