# Write the header lines
if line.startswith('##'):
f_vcf_out.write(line)
elif line.startswith('#'):
for new_line in BAM_STATS_LINES:
f_vcf_out.write(new_line)
f_vcf_out.write(line)
# Calcualte bam stats for variants
else:
variant = Variant().read_variant(line)
mpileup = mpileup_dict.get(
'\t'.join([variant.chr, variant.pos]), '')
bam_stats = variant.cal_bam_stats(mpileup)
variant = variant.add_bam_stats(bam_stats)
f_vcf_out.write(variant.write())
else:
normal_mpileup_dict = create_mpileup_dict(normal_mpileup)
tumor_mpileup_dict = create_mpileup_dict(tumor_mpileup)
with open(vcf_in, 'r') as vcf_i, open(vcf_out, 'w') as vcf_o:
for line in vcf_i:
if line.startswith('#'):
if line.startswith('##'):
vcf_o.write(line)
else:
for new_line in BAM_STATS_LINES:
vcf_o.write(new_line)
