Saving raw h5ad files upon running snap.pp.import_data

[joseverdezoto]

Hey Kai,

Thanks so much for developing snapATAC2. I've been using it for a bit and really like it! I do have one question regarding working with files in backed mode. When we import fragment files and work in backed mode, I realize the in-disk files will get updated as we do something to the adatas (e.g., filtering low QC cells). However, if we wanted to go back to the raw h5ad files, those would no longer be "raw" right? Ideally, I'd love to save the raw h5ad files so I don't have to re-import data.

I wasn't sure what would be the best practices workflow for that. I naively decided to copy the newly created h5ad files into a raw dir when I run snap.pp.import_data for new datasets, so I can re-use the raw h5ad files later if needed. However, when checking the files after the fact, it looks like the files I copied into the raw dir are smaller (likely updated after QC) instead of the ones I keep in the processing dir and meant to update. So I have a couple of questions:

1. If we import data with snap.pp.import_data and make a copy of the h5ad files, would the adata object reference the original or the copied h5ad file in disk?
2. Would you have any suggestions for saving the raw h5ad files upon importing data?

Thanks!