def main():
args = parse_args()
with args.bam_file:
bam_reader = AlignmentFile(args.bam_file)
if not bam_reader.has_index():
print('Adding index...')
index_args = ['samtools', 'index', args.bam_file.name]
run(index_args, check=True)
args.bam_file.seek(0) # Go back to start of header.
bam_reader = AlignmentFile(args.bam_file)
bam_reader.check_index()
x = bam_reader.parse_region(region=args.target_region)
sequences = sorted(bam_reader.fetch(region=args.target_region),
key=attrgetter('qname'))
print(len(sequences))
for seq in sequences:
print(seq.qname)
