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mdshw5/answer.py

Created March 10, 2016 17:22
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answer.py
import simplesam
with simplesam.Reader(open('input.sam')) as sam:
with simplesam.Writer(open('output.sam', 'w'), sam.header) as fixed:
for read in sam:
if bool(read.flag & 0x800):
read.flag -= 0x800
if not read.secondary:
read.flag += 0x100
fixed.write(read)
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