def test_fromString(self):
singleCigarString = "100="
multiCigarString = "100=2D34I6=6X6="
singleCigar = PacBioBam.Cigar(singleCigarString)
multiCigar = PacBioBam.Cigar(multiCigarString)
self.assertEqual(1, len(singleCigar))
c = singleCigar[0]
self.assertEqual('=', c.Char())
self.assertEqual(100, c.Length())
self.assertEqual(6, len(multiCigar))
op0 = multiCigar[0]
op1 = multiCigar[1]
op2 = multiCigar[2]
op3 = multiCigar[3]
op4 = multiCigar[4]
op5 = multiCigar[5]
self.assertEqual('=', op0.Char())
self.assertEqual('D', op1.Char())
self.assertEqual('I', op2.Char())
self.assertEqual('=', op3.Char())
self.assertEqual('X', op4.Char())
self.assertEqual('=', op5.Char())
self.assertEqual(100, op0.Length())
self.assertEqual(2, op1.Length())
self.assertEqual(34, op2.Length())
self.assertEqual(6, op3.Length())
self.assertEqual(6, op4.Length())
self.assertEqual(6, op5.Length())
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())
def test_toEmptyString(self):
cigar = PacBioBam.Cigar()
self.assertFalse(cigar.ToStdString())
def test_fromEmptyString(self):
s = ""
cigar = PacBioBam.Cigar(s)
self.assertEqual(0, len(cigar))