full_annots = full_annots.groupby('ID').agg(col_operations)
full_annots.index = full_annots.index.map(str)
#Add the annotations and write new VCF
step_time = time.time()
start_annot_time = time.time()
logger.info("### ADD ANNOTATIONS TO OUTPUT VCF ###")
logger.info("Output file: %s", out_filename)
outfile = open(out_filename, "w+")
if args.inputvcf.endswith("vcf.gz"):
vcf = gzip.open(args.inputvcf, "rt")
elif args.inputvcf.endswith("vcf"):
vcf = open(args.inputvcf, "r")
line = vcf.readline()
while line.startswith('##'):
outfile.write(line)
line = vcf.readline()
#Add INFO tags descriptions to header
for tag, data_type in tags_dataTypes.items():
header_line = '##INFO=<ID={tag},Number=1,Type={datatype},Description="SV annotation">'.format(
tag=tag, datatype=data_type)
outfile.write(header_line + "\n")
while line.startswith('#'):
outfile.write(line)
line = vcf.readline()
#Annotate vars
