-
Notifications
You must be signed in to change notification settings - Fork 7
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
Feature request: Add INFO about cause of rejection in reject VCF #10
Comments
If a variant is dropped it means that neither of the two |
When a liftover of their data fails, the bio people pick half dozen variants then we do a deep dive to try and work out what happened. This is to verify that it's not due to a bug in the code I think it reassures them that things are working correctly, and they appreciate much more seeing an error "two anchors mapped to locations too far from each other" vs "liftover failed" I can try and write a pull request but haven't written C in close to 20 years... |
Maybe give me some minimal documentation for how you would like to see the INFO field engineered, given the three possible return codes, in a way that you deem usable by bio people, and I will write the code myself |
For my particular use case, I'll be processing the VCF file then displaying it in a GUI for the BIO people There are no enums in VCF types so I guess just make it a string and fill it in with constants, I'd expect the info to look a bit like:
But feel free to change to whatever you think best. Thanks a lot! |
variants can also end up in the reject list for other reasons, eg the contig not being defined in the header - there should be a code for this (eg VCF record error) to distinguish it from ones to do with chains |
Try to see if the development version here fixes both problems |
Hi, thanks looks good. Ran dev version with |
Liftover can fail for a variety of reasons...
Many of the liftover functions return -1 on any error, and the check is < 0
If you defined a range of negative constants, you could return specifically what went wrong, then look it up then add that to the INFO of rejected variants
The text was updated successfully, but these errors were encountered: