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Fix callstats order in merge_freq_arrays #574

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Merged
merged 1 commit into from
Aug 10, 2023
Merged

Fix callstats order in merge_freq_arrays #574

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7 changes: 5 additions & 2 deletions gnomad/utils/annotations.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1312,14 +1312,17 @@ def _sum_or_diff_fields(

# Iterate through the groups and their freq lists to merge callstats.
callstat_ann = ["AC", "AN", "homozygote_count"]
callstat_ann_af = ["AC", "AF", "AN", "homozygote_count"]
new_freq = freq_meta_idx.map(
lambda x: hl.bind(
lambda y: y.annotate(AF=hl.if_else(y.AN > 0, y.AC / y.AN, 0)),
lambda y: y.annotate(AF=hl.if_else(y.AN > 0, y.AC / y.AN, 0)).select(
*callstat_ann_af
),
hl.fold(
lambda i, j: hl.struct(
**{ann: _sum_or_diff_fields(i[ann], j[ann]) for ann in callstat_ann}
),
x[0].select("AC", "AN", "homozygote_count"),
x[0].select(*callstat_ann),
x[1:],
),
)
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