def testUpdate2(self):
'''issue 135: inplace update of sequence and quality score.
This does not work as setting the sequence will erase
the quality scores.
'''
a = self.buildRead()
a.query_sequence = a.query_sequence[5:10]
self.assertEqual(pysam.toQualityString(a.query_qualities), None)
a = self.buildRead()
s = pysam.toQualityString(a.query_qualities)
a.query_sequence = a.query_sequence[5:10]
a.query_qualities = pysam.fromQualityString(s[5:10])
self.assertEqual(pysam.toQualityString(a.query_qualities), s[5:10])
def testEmpty(self):
a = pysam.AlignedSegment()
self.assertEqual(a.query_name, None)
self.assertEqual(a.query_sequence, None)
self.assertEqual(pysam.toQualityString(a.query_qualities), None)
self.assertEqual(a.flag, 0)
self.assertEqual(a.reference_id, 0)
self.assertEqual(a.mapping_quality, 0)
self.assertEqual(a.cigartuples, None)
self.assertEqual(a.tags, [])
self.assertEqual(a.next_reference_id, 0)
self.assertEqual(a.next_reference_start, 0)
self.assertEqual(a.template_length, 0)
