diff --git a/output.py b/output.py index 5d92c7b..5e7fd9c 100644 --- a/output.py +++ b/output.py @@ -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