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[query/vds] Fix removal of ref GT in from_merged_representation #14699

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[query/vds] Fix removal of ref GT in from_merged_representation #14699

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4 changes: 1 addition & 3 deletions hail/python/hail/vds/variant_dataset.py
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Original file line number Diff line number Diff line change
Expand Up @@ -160,9 +160,7 @@ def from_merged_representation(mt, *, ref_block_fields=(), infer_ref_block_field

gt_field = 'LGT' if 'LGT' in mt.entry else 'GT'

# remove LGT/GT and LA fields, which are trivial for reference blocks and do not need to be represented
if gt_field in used_ref_block_fields:
used_ref_block_fields.remove(gt_field)
# remove the LA field, which is trivial for reference blocks and does not need to be represented
if 'LA' in used_ref_block_fields:
used_ref_block_fields.remove('LA')

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3 changes: 3 additions & 0 deletions hail/python/test/hail/vds/test_vds.py
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Expand Up @@ -814,6 +814,9 @@ def test_combiner_max_len():
@test_timeout(4 * 60, local=6 * 60)
def test_split_sparse_roundtrip():
vds = hl.vds.read_vds(os.path.join(resource('vds'), '1kg_chr22_5_samples.vds'))
# this doesn't actually roundtrip because 1kg_chr22_5_samples was generated before
# we added GT to reference_data, to_merged_sparse_mt adds a reference GT
vds.reference_data = vds.reference_data.annotate_entries(LGT=hl.call(0, 0))
smt = hl.vds.to_merged_sparse_mt(vds)
smt = hl.experimental.sparse_split_multi(smt)
vds2 = hl.vds.VariantDataset.from_merged_representation(
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