[query/combiner] Fix import_gvcf_interval's default PGT handling #13364
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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
approved these changes
Aug 2, 2023
danking
previously requested changes
Aug 2, 2023
chrisvittal
dismissed
danking’s stale review
We do! Added a quick assertion to an extant test.
danking
approved these changes
Aug 2, 2023
danking
reviewed
Aug 2, 2023
| @@ -39,6 +39,11 @@ def test_combiner_works(): | |||
| out = os.path.join(tmpdir, 'out.vds') | |||
| hl.vds.new_combiner(temp_path=tmpdir, output_path=out, gvcf_paths=paths, intervals=parts, reference_genome='GRCh38').run() | |||
| 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.