Window_by_locus not available

Feature Requests
1

Hello there,

I just recently discovered Hail from the Nat. Comm. paper 2020 about annotation of MNVs.
I tried to followed the tutorials on how to identify and annotate potential MNVs from a VCF file. However, the function window_by_locus seems to be deleted or deprecated from the latest version.
I checked the docs to try to implement it, but without any success.
Would you be so kind and provide a way around it, please?

Thanks so much!

Best,
E

2

Hey @EnQu !

You’re right, this was removed a couple years ago when we were switching our backends. Unfortunately, that paper didn’t include the version of Hail they used. The last version of Hail that included window_by_locus was 0.2.31. I suggest using that version for now.

I’ve pinged one of the engineers involved. Our new backend has matured significantly since 2020, it’s possible we can reimplement this method.

3

Hey @danking,

Thank you for the recommendation.
I tried it with version 0.2.31 and seems to be working.
I had to use python 3.7, though.

Hopefully it can be included in newer releases.

Thanks a lot!