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

Capture uploaded allele correctly for VCF input #1744

Open
wants to merge 8 commits into
base: postreleasefix/113
Choose a base branch
from

Conversation

likhitha-surapaneni
Copy link
Contributor

@likhitha-surapaneni likhitha-surapaneni commented Aug 20, 2024

Ticket: ENSVAR-5858

  • Fix Unit tests
  • Review header and output columns

@likhitha-surapaneni likhitha-surapaneni marked this pull request as draft August 20, 2024 10:50
modules/Bio/EnsEMBL/VEP/Parser.pm Outdated Show resolved Hide resolved
modules/Bio/EnsEMBL/VEP/Parser.pm Show resolved Hide resolved
push @return, $vf;
}

elsif($vf->{allele_string} =~ /.+\/.+\/.+/)
{
$vf->{minimised} = 1;
Copy link
Contributor

Choose a reason for hiding this comment

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

Suggested change
$vf->{minimised} = 1;
push @return, $vf;
$vf->{minimised} = 1;

Also need to return the $vf otherwise you get undef and empty results.

Copy link
Contributor

Choose a reason for hiding this comment

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

@nuno-agostinho nuno-agostinho removed their request for review September 6, 2024 12:47
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.

3 participants