for line in STATS_HEADER:
combined_f.write(line)
# write the chr\tpos\t... line
combined_f.write(vcf_list[0].header)
# Write the variants
for v_key in combined_variants:
callers_indexes = variant_to_vcf_dict[v_key]
callers_names = [callers[i] for i in callers_indexes]
info_dict = OrderedDict()
for i in callers_indexes:
# Combine the selected information in the dictionary
info_dict.update(vcf_list[i].variants[v_key].info)
i = callers_indexes[0]
combined_variant = Variant.combine_info(
vcf_list[i].variants[v_key], columns_to_keep, callers_names,
info_dict)
combined_f.write(Variant.write(combined_variant))
else:
# Process each vcf and extract the information from the selected columns
vcf_list = [
NormalisedVcf(vcf).process_somatic_vcf(columns_to_keep, normal_id,
tumor_id) for vcf in vcf_in
]
# Combine the variants into a list
combined_variants, variant_to_vcf_dict = [], dd(list)
callers = [vcf.caller for vcf in vcf_list]
