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- samfile = pysam.Samfile( filename, "rb" )
- ReverseList = [''] * lenref
- ForwardList = [''] * lenref
- for pileupcolumn in samfile.pileup() :
- for pileupread in pileupcolumn.pileups:
- if (pileupread.alignment.mapping_quality <= 15):
- continue
- if not pileupread.is_del and not pileupread.is_refskip:
- if pileupread.alignment.is_reverse: #negative
- ReverseList[pileupcolumn.pos] += pileupread.alignment.query_sequence[pileupread.query_position]
- else:
- ForwardList[pileupcolumn.pos] += pileupread.alignment.query_sequence[pileupread.query_position]
- samfile.close()
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