One-hot encoded sequence

[avantikalal]

Hi,

If I understand correctly, the genomic sequence will be stored as strings in the input interval dataframe. It would be very helpful for us if we could instead store sequences as a separate one-hot encoded array. This is a function we use to go from strings to one-hot: https://github.com/Genentech/gReLU/blob/main/src/grelu/sequence/format.py#L296

[jkanche]

Wondering, wouldn't this be easier to compute on-the-fly from the sequence thats stored in the TileDB?

[avantikalal]

Wouldn't that also lead to a time delay? Or do you think it would be insignificant?

[jkanche]

Seems very insignificant, you can introduce caching and that could make this even faster: