Feature Request: Add --partition-tag option to "modkit extract calls"

[zaka-edd]

Currently, the --partition-tag option is available for the modkit pileup command, allowing users to partition output into multiple bedMethyl files based on tag-value pairs. It would be beneficial to have a similar functionality for the modkit extract calls command.

Is this feature technically feasible given the current architecture of modkit? If so could it be added? if not do you have any suggestions on how to get similar output.

Thank you in advance for your time

[ArtRand]

Hello @zaka-edd,

I'm right in the middle of some requested updates to modkit extract calls, one thing is adding BAM Aux tag information. I don't know if it will make sense to partition the output files like pileup does, but instead have a column that can be filtered on. I'm also adding different output data formats to make slicing-and-dicing the tables faster and easier. Do you think having a column with the HP tag would address your use case?

[zaka-edd]

Hey @ArtRand,

Thank you for the quick answer. I am still experimenting with some stuff, but If possible, having an HP column would work well for me, and I could handle the splitting myself. Otherwise, if it’s not too much work, partitioning the output similar to pileup would also be useful. Either option would help with my use case.

Thanks again for the work you’re putting into this!