Skip to content
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

[vep] Rework VEP with more visibility #9973

Merged
merged 4 commits into from Feb 3, 2021
Merged

Conversation

tpoterba
Copy link
Contributor

@tpoterba tpoterba commented Feb 2, 2021

  1. Don't ignore parse errors by default. These shouldn't be happening
    with modern VEP versions anyway (they were caused by genes named NaN
    or something in older versions)
  2. Don't silently drop variants that don't have a match in VEP. All keys
    coming in will have a row coming out with a VEP annotation (maybe NA)
    and a partition/block index.

1. Don't ignore parse errors by default. These shouldn't be happening
   with modern VEP versions anyway (they were caused by genes named NaN
   or something in older versions)
2. Don't silently drop variants that don't have a match in VEP. All keys
   coming in will have a row coming out with a VEP annotation (maybe NA)
   and a partition/block index.
@johnc1231
Copy link
Contributor

Not compiling

def vep(dataset: Union[Table, MatrixTable], config=None, block_size=1000, name='vep', csq=False):
csq=bool,
tolerate_parse_error=bool)
def vep(dataset: Union[Table, MatrixTable], config=None, block_size=1000, name='vep', csq=False, tolerate_parse_error=False):
Copy link
Collaborator

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Missed this first go, keyword only for the new parameter?

@danking danking merged commit c3a1cbf into hail-is:main Feb 3, 2021
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

Successfully merging this pull request may close these issues.

None yet

4 participants