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use correct fixed_file as output
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gwaspy/check_alleles/check_alleles.py

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Original file line numberDiff line numberDiff line change
@@ -91,7 +91,7 @@ def fix_alleles(
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"""
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)
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b.write_output(j.stats,
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b.write_output(j.fixed_file,
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f'{out_dir}/check_alleles/{output_name}.alleles.fixed')
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return j

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