[query/combiner] Fix import_gvcf_interval's default PGT handling#13364
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danking merged 4 commits intoAug 3, 2023
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PGT is a call field by default for import_vcf, the now former import_gvcfs (old combiner start point). Make import_gvcf_interval also treat PGT as a call field.
danking
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danking
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Do we have a GVCF with PGT? Can you test for this?
chrisvittal
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danking’s stale review
We do! Added a quick assertion to an extant test.
danking
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danking
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Aug 2, 2023
| comb = hl.vds.read_vds(out) | ||
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| # see https://github.com/hail-is/hail/issues/13367 for why these assertions are here | ||
| assert 'LPGT' in comb.variant_data |
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I think you need variant_data.entry or something
This was referenced Aug 6, 2023
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PGT is a call field by default for import_vcf, the now former import_gvcfs (old combiner start point). Make import_gvcf_interval also treat PGT as a call field.