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.

Sign up for GitHub

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

Jump to bottom

read_scikit_allel_vcfzarr returns string pad values instead of missing for INFO fields #1195

Open
jeromekelleher opened this issue Feb 15, 2024 · 0 comments
Open

read_scikit_allel_vcfzarr returns string pad values instead of missing for INFO fields #1195

jeromekelleher opened this issue Feb 15, 2024 · 0 comments
Labels
bug Something isn't working
Milestone
0.9.1

Comments

@jeromekelleher
Copy link
Collaborator

For example, in the test test_vcf_scikit_allel.py::test_all_fields, the variant_AA field is reported as ['' '' '' '' 'T' 'T' 'G' '' ''] instead of ['.' '.' '.' '.' 'T' 'T' 'G' '.' '.']

I'm not sure if this generalises to other fields, just reporting test breakage seen while fixing #1192
@jeromekelleher jeromekelleher added the bug Something isn't working label Feb 15, 2024
@jeromekelleher jeromekelleher added this to the 0.8.0 release milestone Feb 15, 2024
jeromekelleher added a commit to jeromekelleher/sgkit that referenced this issue Feb 15, 2024
@jeromekelleher
Skip tests for reported bugs sgkit-dev#1195, sgkit-dev#1196
7a0035d
@jeromekelleher jeromekelleher mentioned this issue Feb 15, 2024
Merged
jeromekelleher added a commit to jeromekelleher/sgkit that referenced this issue Feb 15, 2024
@jeromekelleher
Skip tests for reported bugs sgkit-dev#1195, sgkit-dev#1196
f7f8aed
jeromekelleher added a commit to jeromekelleher/sgkit that referenced this issue Feb 16, 2024
@jeromekelleher
Skip tests for reported bugs sgkit-dev#1195, sgkit-dev#1196
254e147
jeromekelleher added a commit to jeromekelleher/sgkit that referenced this issue Feb 16, 2024
@jeromekelleher
Skip problematic fields in scikit-allel comparison
60129ee 
Temporary workaround to get tests to pass before addressing sgkit-dev#1195
jeromekelleher added a commit to jeromekelleher/sgkit that referenced this issue Feb 16, 2024
@jeromekelleher
Skip tests for reported bugs sgkit-dev#1195, sgkit-dev#1196
c05ddfe
jeromekelleher added a commit to jeromekelleher/sgkit that referenced this issue Feb 16, 2024
@jeromekelleher
Skip problematic fields in scikit-allel comparison
c7db1d0 
Temporary workaround to get tests to pass before addressing sgkit-dev#1195
jeromekelleher added a commit to jeromekelleher/sgkit that referenced this issue Mar 5, 2024
@jeromekelleher
Skip tests for reported bugs sgkit-dev#1195, sgkit-dev#1196
43d2f75
jeromekelleher added a commit to jeromekelleher/sgkit that referenced this issue Mar 5, 2024
@jeromekelleher
Skip problematic fields in scikit-allel comparison
a0edba7 
Temporary workaround to get tests to pass before addressing sgkit-dev#1195
mergify bot pushed a commit that referenced this issue Mar 5, 2024
@jeromekelleher @mergify
Skip tests for reported bugs #1195, #1196
ca2debe
mergify bot pushed a commit that referenced this issue Mar 5, 2024
@jeromekelleher @mergify
Skip problematic fields in scikit-allel comparison
636d744 
Temporary workaround to get tests to pass before addressing #1195
@jeromekelleher jeromekelleher modified the milestones: 0.8.0 release, 0.8.1 Apr 29, 2024
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
bug Something isn't working
Projects
None yet
Milestone
0.9.1
Development

No branches or pull requests
1 participant
@jeromekelleher