diff --git a/external/cbase_params_v1.2.py b/external/cbase_params_v1.2.py index 66d02b2..178e397 100644 --- a/external/cbase_params_v1.2.py +++ b/external/cbase_params_v1.2.py @@ -470,7 +470,7 @@ def import_vcf_data(filename): ] # Note: Split by any white space, not just tabs. - N_columns = len(lines[0].strip().split("\t")) + N_columns = len(lines[0].strip().split()) if N_columns < 5: sys.stderr.write( @@ -485,7 +485,7 @@ def import_vcf_data(filename): sample_name = "john_doe" for line in lines: # Note: Split by any white space, not just tabs. - field = line.strip().split() + field = line.strip().split("\t") if field[0] == "#CHROM" and N_columns >= 10: sample_name = field[10] elif field[0] == "X" or field[0] == "chrX": @@ -499,6 +499,7 @@ def import_vcf_data(filename): else: continue if N_columns == 6: + print(field) sample_name = field[5] if bases.count(field[3]) and bases.count(field[4]) and field[3] != field[4]: mut_array.append(