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

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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
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0.8.1

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@jeromekelleher
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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
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