def test_insert(self): self.assertEqual( ([(CIGAR.S, 17), (CIGAR.M, 10), (CIGAR.S, 5)], 2), _cigar.extend_softclipping([(CIGAR.S, 10), (CIGAR.M, 2), (CIGAR.I, 5), (CIGAR.M, 10), (CIGAR.I, 5)], 5), )
def test_hardclipping_right(self): c = [(CIGAR.EQ, 30), (CIGAR.H, 120)] cnew, prefix = _cigar.extend_softclipping(c, 6) self.assertEqual(0, prefix) self.assertEqual(c, cnew)
def test_mismatch(self): with self.assertRaises(AttributeError): _cigar.extend_softclipping([(CIGAR.X, 10), (CIGAR.M, 20), (CIGAR.X, 10)], 30)
def test_deletions(self): self.assertEqual( ([(CIGAR.S, 10), (CIGAR.M, 10)], 1), _cigar.extend_softclipping([(CIGAR.I, 10), (CIGAR.D, 1), (CIGAR.M, 10)], 1))
def test_simple(self): self.assertEqual(([(CIGAR.S, 10), (CIGAR.M, 10)], 0), _cigar.extend_softclipping([(CIGAR.S, 10), (CIGAR.M, 10)], 1))
def test_softclipped_right(self): c = convert_string_to_cigar( '70=2X1=8X4=1X1=4X1=6X1=4X1=4X2=5X3=3X1=4X1=3X1=14X1=1X2=1S') cnew, prefix = extend_softclipping(c, 6) self.assertEqual(0, prefix) self.assertEqual(convert_string_to_cigar('70=80S'), cnew)
def test_hardclipping_right(self): c = [(CIGAR.EQ, 30), (CIGAR.H, 120)] cnew, prefix = _cigar.extend_softclipping(c, 6) assert prefix == 0 assert cnew == c
def test_hardclipping(self): c = [(CIGAR.H, 10), (CIGAR.EQ, 10)] cnew, prefix = _cigar.extend_softclipping(c, 1) assert prefix == 0 assert cnew == c
def test_insert(self): assert _cigar.extend_softclipping( [(CIGAR.S, 10), (CIGAR.M, 2), (CIGAR.I, 5), (CIGAR.M, 10), (CIGAR.I, 5)], 5 ) == ([(CIGAR.S, 17), (CIGAR.M, 10), (CIGAR.S, 5)], 2)
def test_deletions(self): assert _cigar.extend_softclipping([(CIGAR.I, 10), (CIGAR.D, 1), (CIGAR.M, 10)], 1) == ( [(CIGAR.S, 10), (CIGAR.M, 10)], 1, )
def test_simple(self): assert _cigar.extend_softclipping([(CIGAR.S, 10), (CIGAR.M, 10)], 1) == ( [(CIGAR.S, 10), (CIGAR.M, 10)], 0, )
def test_softclipped_right(self): c = convert_string_to_cigar( '70=2X1=8X4=1X1=4X1=6X1=4X1=4X2=5X3=3X1=4X1=3X1=14X1=1X2=1S') cnew, prefix = extend_softclipping(c, 6) assert prefix == 0 assert cnew == convert_string_to_cigar('70=80S')