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Fix issues in bq to vcf #448

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Fix issues in bq to vcf #448

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4 changes: 2 additions & 2 deletions gcp_variant_transforms/libs/genomic_region_parser.py
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Original file line number Diff line number Diff line change
Expand Up @@ -43,7 +43,7 @@ def _parse_position(pos_str):
matched = _REGION_LITERAL_REGEXP.match(genomic_region)
if matched:
ref_name, start, end = matched.groups()
ref_name = ref_name.strip().lower()
ref_name = ref_name.strip()
start = _parse_position(start)
end = _parse_position(end)
if start < 0:
Expand All @@ -54,7 +54,7 @@ def _parse_position(pos_str):
'vs {}'.format(end, start))
else:
# This region includes a full chromosome
ref_name = genomic_region.strip().lower()
ref_name = genomic_region.strip()
start = 0
end = _DEFAULT_END_POSITION
return ref_name, start, end
4 changes: 2 additions & 2 deletions gcp_variant_transforms/libs/genomic_region_parser_test.py
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Original file line number Diff line number Diff line change
Expand Up @@ -29,8 +29,8 @@ def test_parse_genomic_regions(self):
('chr1', 1000000, 2000000)
)
self.assertEqual(
genomic_region_parser.parse_genomic_region('chr1:1000000-2000000'),
('chr1', 1000000, 2000000)
genomic_region_parser.parse_genomic_region('chrY:1000000-2000000'),
('chrY', 1000000, 2000000)
)
self.assertEqual(
genomic_region_parser.parse_genomic_region('chr'),
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1 change: 1 addition & 0 deletions gcp_variant_transforms/libs/variant_partition.py
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Original file line number Diff line number Diff line change
Expand Up @@ -189,6 +189,7 @@ def _is_residual_partition(regions):

for r in regions:
ref_name, start, end = genomic_region_parser.parse_genomic_region(r)
ref_name = ref_name.lower()
self._ref_name_to_partitions_map[ref_name].add_region(
start, end, partition_index)

Expand Down