def test_process_reads_read_obs_paired_end_overlap_1bad_base_qual(self):
aln1b = pysam.AlignedSegment()
aln1b.reference_start = 20
aln1b.query_name = 'read1'
aln1b.mapping_quality = 20
aln1b.query_sequence = "AAAAATAAAACAAAAC"
qqual = [30] * 16
qqual[0] = 5
aln1b.query_qualities = qqual
aln1b.cigarstring = '16M'
self.alns.append(aln1b)
var_pos = [15, 20, 25, 35]
res = preprocess.process_reads(self.alns, var_pos, 20, 10)
exp = {
'read1': {
15: 'T',
20: 'T',
25: 'T',
35: 'C'
},
'read2': {
15: 'G',
20: 'G',
25: 'G'
}
}
self.assertEqual(res, exp)
def test_process_reads_read_obs_min_base_quality(self):
res = preprocess.process_reads(self.alns, [15, 20, 25], 20, 30)
exp = {
'read1': {
15: 'T',
20: 'T',
25: 'T'
},
'read2': {
20: 'G',
25: 'G'
}
}
self.assertEqual(res, exp)
def test_process_reads_read_obs_simple(self):
res = preprocess.process_reads(self.alns, [15, 20, 25], 20, 10)
exp = {
'read1': {
15: 'T',
20: 'T',
25: 'T'
},
'read2': {
15: 'G',
20: 'G',
25: 'G'
}
}
self.assertEqual(res, exp)
def test_process_reads_read_obs_min_map_quality(self):
res = preprocess.process_reads(self.alns, [15, 20, 25], 25, 10)
exp = {'read1': {15: 'T', 20: 'T', 25: 'T'}}
self.assertEqual(res, exp)
