Missing required reference files

[mmyers1]

The files '/map/hg19_k100_len_100k.npz' and '/gc/hg19_len_100k.npz' required by the function gcMapSubset are missing from the Zenodo zip folder of reference files.

I see that there is a function saveMappability that generates the mappability reference file, but the input file required for this ("/data/ref/map/hg19/k100.umap.wg") is also missing. I found no function to generate the GC reference file.

Also, I have been using the pip version of the source code so that I can debug and install from source (since this repository is missing the pyproject.toml file). Does the pip version differ meaningfully from this repository? Is there an intended way to contribute bugfixes?

Thanks,
Matt Myers

[stefanivanovic]

Thank you for bringing this issue to our attention!

We intend to address this on Zenodo but to immediately solve this problem we have added "additionalReferenceFiles" to this GitHub which contains "/map/hg19_k100_len_100k.npz" and "/gc/hg19_len_100k.npz".

Regarding the pip version vs GitHub version, there is no meaningful difference. They are intended to be alternative ways of using the same software. We have added the myproject.toml to the GitHub.