Commit a08e9e4e authored by Pradat Yoann's avatar Pradat Yoann
Browse files

minor fix remove redundant cols

parent 133cab8e
...@@ -229,7 +229,7 @@ def run_annotator(vcf_folder: str, vcf_file: str, col_normal: str, col_tumor: st ...@@ -229,7 +229,7 @@ def run_annotator(vcf_folder: str, vcf_file: str, col_normal: str, col_tumor: st
#### vcf2maf #### vcf2maf
ddf_maf["vcf2maf"].columns = ["%s_VCF2MAF" % x for x in ddf_maf["vcf2maf"].columns] ddf_maf["vcf2maf"].columns = ["%s_VCF2MAF" % x for x in ddf_maf["vcf2maf"].columns]
for column in ddf_maf["vcf2maf"].columns: for column in ddf_maf["vcf2maf"].columns:
if column in dt_identifiers.keys(): if column in dt_identifiers.keys() or column in cols_manual:
#### prioritize identifiers from input #### prioritize identifiers from input
pass pass
else: else:
...@@ -243,7 +243,7 @@ def run_annotator(vcf_folder: str, vcf_file: str, col_normal: str, col_tumor: st ...@@ -243,7 +243,7 @@ def run_annotator(vcf_folder: str, vcf_file: str, col_normal: str, col_tumor: st
elif vcf2maf_config.run: elif vcf2maf_config.run:
#### vcf2maf #### vcf2maf
for column in ddf_maf["vcf2maf"].columns: for column in ddf_maf["vcf2maf"].columns:
if column in dt_identifiers.keys(): if column in dt_identifiers.keys() or column in cols_manual:
#### prioritize identifiers from input #### prioritize identifiers from input
pass pass
else: else:
......
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