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#!/usr/bin/env python3
"""
Check whether the EOF marker is present in BAM files.
If it's not, this may be a sign that the BAM file was corrupted.
The exit code is 1 if the marker was present in *all files*.
It is 0 if the marker was missing in any of the files.
BUGS/TODO
- Does not work with uncompressed BAM files.
"""
import sys
from sqt import HelpfulArgumentParser
__author__ = "Marcel Martin"
def add_arguments(parser):
arg = parser.add_argument
arg("-q", "--quiet", action='store_true',
help="Don't print anything, just set the exit code.")
arg("bam", metavar='BAM', nargs='+')
def bam_eof_is_ok(f):
"""
Check whether BAM file f contains the 'magic' end-of-file marker.
Adapted from samtools function bgzf_check_EOF (in bgzf.c).
"""
try:
f.seek(-28, 2)
except IOError:
return False
data = f.read(28)
return data == b"\037\213\010\4\0\0\0\0\0\377\6\0\102\103\2\0\033\0\3\0\0\0\0\0\0\0\0\0"
def main(args=None):
if args is None:
parser = HelpfulArgumentParser(description=__doc__)
add_arguments(parser)
args = parser.parse_args()
exitcode = 0
for name in args.bam:
with open(name, 'rb') as f:
if bam_eof_is_ok(f):
if not args.quiet:
print(name, ": OK", sep='')
else:
if not args.quiet:
print(name, ": MISSING", sep='')
exitcode = 1
else:
sys.exit(1)
sys.exit(exitcode)
if __name__ == '__main__':
main()
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