Created
March 10, 2016 17:22
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biostars 75693
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| 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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