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Fix union cols #6

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Fix union cols #6

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355696f
Added persist and unpersist in union cols
jigold Nov 10, 2025
c8835f8
increase n partitions
jigold Nov 10, 2025
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2 changes: 1 addition & 1 deletion imputation/glimpse_hail_batch/glimpse_hail_batch/imputation/imputation.py
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Original file line number Diff line number Diff line change
Expand Up @@ -336,7 +336,7 @@ async def impute(args: dict):
batch_regions,
args['use_checkpoints'],
contig,
len(chunks))
len(chunks) * 5)

if union_j is not None:
union_j.depends_on(*union_ligate_input_jobs.get(contig, []))
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8 changes: 8 additions & 0 deletions imputation/glimpse_hail_batch/glimpse_hail_batch/imputation/jobs.py
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Original file line number Diff line number Diff line change
Expand Up @@ -489,6 +489,8 @@ def add_info_if_needed(mt):
mt_init = hl.read_matrix_table(paths[0])
intervals = mt_init._calculate_new_partitions(n_partitions)

last_mt_left = None

mt_left = hl.read_matrix_table(paths[0], _intervals=intervals)
mt_left = add_info_if_needed(mt_left)
mt_left = mt_left.annotate_rows(
Expand All @@ -510,6 +512,12 @@ def add_info_if_needed(mt):
drop_right_row_fields=False,
row_join_type='outer')

if idx % 5 == 0:
mt_left = mt_left.persist()
if last_mt_left is not None:
last_mt_left.unpersist()
last_mt_left = mt_left

mt = mt_left

n_batches = len(paths)
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