def test_cigarOpCtors(self):
c1 = PacBioBam.CigarOperation('S', 10)
c2 = PacBioBam.CigarOperation(PacBioBam.SOFT_CLIP, 10)
self.assertEqual('S', c1.Char())
self.assertEqual('S', c2.Char())
self.assertEqual(PacBioBam.SOFT_CLIP, c1.Type())
self.assertEqual(PacBioBam.SOFT_CLIP, c2.Type())
self.assertEqual(10, c1.Length())
self.assertEqual(10, c2.Length())
def test_setChar(self):
m = PacBioBam.CigarOperation()
i = PacBioBam.CigarOperation()
d = PacBioBam.CigarOperation()
n = PacBioBam.CigarOperation()
s = PacBioBam.CigarOperation()
h = PacBioBam.CigarOperation()
p = PacBioBam.CigarOperation()
e = PacBioBam.CigarOperation()
x = PacBioBam.CigarOperation()
m.Char('M')
i.Char('I')
d.Char('D')
n.Char('N')
s.Char('S')
h.Char('H')
p.Char('P')
e.Char('=')
x.Char('X')
self.assertEqual(PacBioBam.ALIGNMENT_MATCH, m.Type())
self.assertEqual(PacBioBam.INSERTION, i.Type())
self.assertEqual(PacBioBam.DELETION, d.Type())
self.assertEqual(PacBioBam.REFERENCE_SKIP, n.Type())
self.assertEqual(PacBioBam.SOFT_CLIP, s.Type())
self.assertEqual(PacBioBam.HARD_CLIP, h.Type())
self.assertEqual(PacBioBam.PADDING, p.Type())
self.assertEqual(PacBioBam.SEQUENCE_MATCH, e.Type())
self.assertEqual(PacBioBam.SEQUENCE_MISMATCH, x.Type())
def test_setType(self):
m = PacBioBam.CigarOperation()
i = PacBioBam.CigarOperation()
d = PacBioBam.CigarOperation()
n = PacBioBam.CigarOperation()
s = PacBioBam.CigarOperation()
h = PacBioBam.CigarOperation()
p = PacBioBam.CigarOperation()
e = PacBioBam.CigarOperation()
x = PacBioBam.CigarOperation()
m.Type(PacBioBam.ALIGNMENT_MATCH)
i.Type(PacBioBam.INSERTION)
d.Type(PacBioBam.DELETION)
n.Type(PacBioBam.REFERENCE_SKIP)
s.Type(PacBioBam.SOFT_CLIP)
h.Type(PacBioBam.HARD_CLIP)
p.Type(PacBioBam.PADDING)
e.Type(PacBioBam.SEQUENCE_MATCH)
x.Type(PacBioBam.SEQUENCE_MISMATCH)
self.assertEqual('M', m.Char())
self.assertEqual('I', i.Char())
self.assertEqual('D', d.Char())
self.assertEqual('N', n.Char())
self.assertEqual('S', s.Char())
self.assertEqual('H', h.Char())
self.assertEqual('P', p.Char())
self.assertEqual('=', e.Char())
self.assertEqual('X', x.Char())
def test_toString(self):
singleCigarString = "100="
multiCigarString = "100=2D34I6=6X6="
singleCigar = PacBioBam.Cigar()
singleCigar.append(
PacBioBam.CigarOperation(PacBioBam.SEQUENCE_MATCH, 100))
multiCigar = PacBioBam.Cigar()
multiCigar.append(
PacBioBam.CigarOperation(PacBioBam.SEQUENCE_MATCH, 100))
multiCigar.append(PacBioBam.CigarOperation(PacBioBam.DELETION, 2))
multiCigar.append(PacBioBam.CigarOperation(PacBioBam.INSERTION, 34))
multiCigar.append(PacBioBam.CigarOperation(PacBioBam.SEQUENCE_MATCH,
6))
multiCigar.append(
PacBioBam.CigarOperation(PacBioBam.SEQUENCE_MISMATCH, 6))
multiCigar.append(PacBioBam.CigarOperation(PacBioBam.SEQUENCE_MATCH,
6))
self.assertEqual(singleCigarString, singleCigar.ToStdString())
self.assertEqual(multiCigarString, multiCigar.ToStdString())