def setUp(self):
self.mq = 30
self.bq = 30
aln1 = pysam.AlignedSegment()
aln1.reference_start = 10
aln1.query_name = 'read1'
aln1.mapping_quality = 30
aln1.query_sequence = "AAAAATAAAATAAAAT"
aln1.query_qualities = [30] * 16
aln1.cigarstring = '16M'
aln2 = pysam.AlignedSegment()
aln2.reference_start = 12
aln2.query_name = 'read2'
aln2.mapping_quality = 20
aln2.query_sequence = "AAAGAAGAAAAG"
qqual = [33] * 12
qqual[3] = 20
aln2.query_qualities = qqual
aln2.cigarstring = '5M2D7M'
aln3 = pysam.AlignedSegment()
aln3.mapping_quality = 0
aln3.query_name = 'read3'
self.alns = [aln1, aln2, aln3]
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