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Adding a check in the less than method for the VariantCall class to ensure that in cases where there is a mix of arrays and scalar values that the comparison still works. #701

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Adding a check in the less than method for the VariantCall class to ensure that in cases where there is a mix of arrays and scalar values that the comparison still works. #701

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4 changes: 4 additions & 0 deletions gcp_variant_transforms/beam_io/vcf_parser.py
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Original file line number Diff line number Diff line change
Expand Up @@ -227,6 +227,10 @@ def __lt__(self, other):
if self.sample_id != other.sample_id:
return self.sample_id < other.sample_id
elif self.genotype != other.genotype:
if(type(self.genotype) is list and type(other.genotype) is not list):
return False
if(type(other.genotype) is list and type(self.genotype) is not list):
return True
return self.genotype < other.genotype
elif self.phaseset != other.phaseset:
return self.phaseset < other.phaseset
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8 changes: 8 additions & 0 deletions gcp_variant_transforms/beam_io/vcf_parser_test.py
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Original file line number Diff line number Diff line change
Expand Up @@ -83,6 +83,14 @@ def test_variant_call_order(self):
variant_call_2.phaseset = 1
self.assertGreater(variant_call_2, variant_call_1)

def test_genotype_compare(self):
variant_call_1 = self._default_variant_call()
variant_call_2 = vcfio.VariantCall(
sample_id=hash_name('Sample1'), name='Sample1', genotype=-1,
phaseset=vcfio.DEFAULT_PHASESET_VALUE, info={'GQ': 48})

self.assertLess(variant_call_2, variant_call_1)


if __name__ == '__main__':
logging.getLogger().setLevel(logging.INFO)
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