def prepare_bam(bam: str) -> Tuple[Tuple, str]:
"""Checks for file extension, and returns tuple of mapped refs
Args:
bam (str): Path to bam file
Returns:
Tuple: Tuple of mapped references
str: bam opening mode
"""
mode = check_extension(bam)
alf = AlignmentFile(bam, mode)
if not alf.has_index():
print(f"BAM file {bam} has no index. Sort BAM file and provide index "
"before running pydamage.")
sys.exit(1)
present_refs = set()
for ref_stat in alf.get_index_statistics():
refname = ref_stat[0]
nb_mapped_reads = ref_stat[1]
if nb_mapped_reads > 0:
present_refs.add(refname)
alf.close()
return tuple(present_refs), mode
