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Fix filter_x_nonpar and filter_y_nonpar to use reference genome #553

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Merged
merged 1 commit into from
Jun 15, 2023
Merged

Fix filter_x_nonpar and filter_y_nonpar to use reference genome #553

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12 changes: 10 additions & 2 deletions gnomad/utils/filtering.py
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Original file line number Diff line number Diff line change
Expand Up @@ -412,7 +412,11 @@ def filter_x_nonpar(
"""
rg = t.locus.dtype.reference_genome
t = hl.filter_intervals(
t, [hl.parse_locus_interval(contig) for contig in rg.x_contigs]
t,
[
hl.parse_locus_interval(contig, reference_genome=rg.name)
for contig in rg.x_contigs
],
)
non_par_expr = t.locus.in_x_nonpar()

Expand All @@ -434,7 +438,11 @@ def filter_y_nonpar(
"""
rg = t.locus.dtype.reference_genome
t = hl.filter_intervals(
t, [hl.parse_locus_interval(contig) for contig in rg.y_contigs]
t,
[
hl.parse_locus_interval(contig, reference_genome=rg.name)
for contig in rg.y_contigs
],
)
non_par_expr = t.locus.in_y_nonpar()

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