per-fragment methylation

[BeyondTheProof]

Hello Devon!

I was wondering if you had plans to implement a per-fragment methylation tool for MethylDackel. The problem with the per-read methylation is it doesn't take into account information on a read's mate, which can be of course useful.

This would basically merge some of the functionality in the extract function, where MethylDackel accounts for potentially conflicting information between the reads, and perRead function.

If not, it may be something I can take a crack at, though I haven't used C in over a decade :(

Best,
An American visiting Germany :)

[dpryan79]

Sorry for the delayed reply, I hadn't planned anything in this regard. PRs welcome :)

[zetian-jia]

I'm really looking forward to you adding new function to the software, as having specific methylation site information for each cfDNA fragment is crucial. As it stands, only Bismark can add XM tag information.