-
Notifications
You must be signed in to change notification settings - Fork 70
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
Return missing values mask for Integer INFO/FORMAT fields #195
Comments
The value |
Thanks @timothymillar. Reading the spec more closely I see that it says
So there is no danger of confusing missing values with the literal value -2147483648 in the field (since the latter is not allowed). (When I opened this issue I thought there was such a danger.) It still might be useful to provide a mask in cyvcf2, since getting the logic right is slightly tricky (because of the range of values). Also, for Flag fields, I don't think there's a problem, since Flag only applies to INFO fields, and they return tuples, not NumPy arrays. |
Missing values for Integer INFO/FORMAT fields are represented by the minimum int32 value (-2147483648, or
np.iinfo(np.int32).min
). It would be nice if a mask array could be retrieved that didn't rely on checking for this value, but that looked for missing values in the original VCF field.This would be useful for Flag (boolean) fields too.
The text was updated successfully, but these errors were encountered: