diff --git a/src/vcf_qc.py b/src/vcf_qc.py index 09c16bf..4c168cd 100644 --- a/src/vcf_qc.py +++ b/src/vcf_qc.py @@ -119,7 +119,7 @@ def get_het_hom_counts(vcf) -> dict: print(f"Missing field(s)") continue - if sample_fields['GT'] == (0,0): + if sample_fields['GT'] == (0, 0): continue # using the sum of all allele depths instead of the format AD diff --git a/tests/test_vcf_qc.py b/tests/test_vcf_qc.py index 3e0fa3c..1139546 100644 --- a/tests/test_vcf_qc.py +++ b/tests/test_vcf_qc.py @@ -187,7 +187,7 @@ def test_het_and_hom_ratios_calculated_correctly(self): variants """ counts = { - 'het': [ 0.5, 0.45, 0.55], + 'het': [0.5, 0.45, 0.55], 'hom': [1.0, 1.0, 1.0, 1.0, 0.95], 'x_het': [], 'x_hom': [] @@ -207,7 +207,7 @@ def test_het_and_hom_ratios_calculated_correctly(self): def test_x_het_hom_calculated_correctly(self): counts = { - 'het': [ 0.5, 0.45, 0.55], + 'het': [0.5, 0.45, 0.55], 'hom': [1.0, 1.0, 1.0, 1.0, 0.95], 'x_het': [0.45, 0.55], 'x_hom': [1.0, 0.98] @@ -313,4 +313,3 @@ def test_expected_dxlink_format_returned(self, mock_job, mock_upload): vcf_qc.upload_output_file('test.vcf.qc'), {'output_file': {'$dnanexus_link': 'file-xxx'}} ) -