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# quickly fix mapping qualities in samfiles generated by SSAHA2
# mapq 255 is undefined according to spec, but SSAHA2 is not
# following this convention
import pysam
infile = pysam.Samfile( "-", "rb" )
outfile = pysam.Samfile( "-", "wb", template = infile )
for s in infile:
if s.mapq == 255:
s.mapq = 244
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