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Make naive_coalesce optional in default_compute_info #584

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merged 2 commits into from
Aug 28, 2023
Merged

Make naive_coalesce optional in default_compute_info #584

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756beb8
Make naive_coalesce optional in `default_compute_info`
jkgoodrich Aug 28, 2023
b2f072f
Update gnomad/utils/sparse_mt.py
jkgoodrich Aug 28, 2023
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10 changes: 7 additions & 3 deletions gnomad/utils/sparse_mt.py
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Original file line number Diff line number Diff line change
Expand Up @@ -541,7 +541,7 @@ def default_compute_info(
as_annotations: bool = False,
# Set to True by default to prevent a breaking change.
quasi_as_annotations: bool = True,
n_partitions: int = 5000,
n_partitions: Optional[int] = 5000,
lowqual_indel_phred_het_prior: int = 40,
ac_filter_groups: Optional[Dict[str, hl.Expression]] = None,
) -> hl.Table:
Expand All @@ -563,7 +563,8 @@ def default_compute_info(
aggregations. This method can be used in cases where genotype data doesn't
contain allele-specific annotations to approximate allele-specific annotations.
Default is True.
:param n_partitions: Number of desired partitions for output Table. Default is 5000.
:param n_partitions: Optional number of desired partitions for output Table. If
specified, naive_coalesce is performed. Default is 5000.
:param lowqual_indel_phred_het_prior: Phred-scaled prior for a het genotype at a
site with a low quality indel. Default is 40. We use 1/10k bases (phred=40) to
be more consistent with the filtering used by Broad's Data Sciences Platform
Expand Down Expand Up @@ -681,7 +682,10 @@ def default_compute_info(
)
)

return info_ht.naive_coalesce(n_partitions)
if n_partitions is not None:
info_ht = info_ht.naive_coalesce(n_partitions)

return info_ht


def split_info_annotation(
Expand Down