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#!/usr/bin/env python3
"""
Repair a BAM file that (incorrectly) contains phred64-encoded qualities.
BAM files must encode their quality values in phred33.
Output is written in SAM format to standard output.
"""
from sqt import HelpfulArgumentParser
from pysam import Samfile
__author__ = "Marcel Martin"
PHRED_64_TO_33_TRANS = bytes.maketrans(bytes(range(64, 64+100)), bytes(range(33, 33+100)))
def get_argument_parser():
parser = HelpfulArgumentParser(description=__doc__)
add = parser.add_argument
add('bam', help='Input BAM file')
return parser
def main():
parser = get_argument_parser()
args = parser.parse_args()
with Samfile(args.bam) as infile:
with Samfile('-', 'wh', template=infile) as outfile:
for record in infile:
record.qual = record.qual.translate(PHRED_64_TO_33_TRANS)
outfile.write(record)
if __name__ == '__main__':
main()
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