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fixes #12 by removing the sparsify argument #13

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fixes #12 by removing the sparsify argument #13

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2 changes: 1 addition & 1 deletion output.py
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Original file line number Diff line number Diff line change
Expand Up @@ -396,7 +396,7 @@ def VCF(self):
out = varDF.reindex(columns=vcf_fields).fillna('.') # drop the columns that are unrelated to vcf format, while reordering columns into proper vcf order
official_vcf_fields = ['#CHROM','POS','ID', 'REF','ALT', 'QUAL', 'FILTER','INFO']
out.columns = pd.Index(official_vcf_fields) # rename columns to comply with official vcf standards
out.to_csv(ofVariantVCF, sep='\t', na_rep='?', index=False, header=True, sparsify=False)
out.to_csv(ofVariantVCF, sep='\t', na_rep='?', index=False, header=True) #, sparsify=False)
ofVariantVCF.close()
print("\t{0}: {1} rows".format(ofVariantVCF.name, len(out)))
return True
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