def test_left_and_right_soft_clip(self):
assert parse_cigar(100, '+', '1S1M1S') == (99, 100, 100, 101)
assert parse_cigar(100, '-', '1S1M1S') == (101, 100, 100, 99)
assert parse_cigar(100, '+', '1S101M1S') == (99, 100, 200, 201)
assert parse_cigar(100, '-', '1S101M1S') == (201, 200, 100, 99)
assert parse_cigar(100, '+', '10S1M10S') == (90, 100, 100, 110)
assert parse_cigar(100, '-', '10S1M10S') == (110, 100, 100, 90)
assert parse_cigar(100, '+', '10S101M10S') == (90, 100, 200, 210)
assert parse_cigar(100, '-', '10S101M10S') == (210, 200, 100, 90)
def test_left_soft_clip(self):
assert parse_cigar(100, '+', '1S1M') == (99, 100, 100, 100)
assert parse_cigar(100, '-', '1S1M') == (100, 100, 100, 99)
assert parse_cigar(100, '+', '1S101M') == (99, 100, 200, 200)
assert parse_cigar(100, '-', '1S101M') == (200, 200, 100, 99)
assert parse_cigar(100, '+', '10S1M') == (90, 100, 100, 100)
assert parse_cigar(100, '-', '10S1M') == (100, 100, 100, 90)
assert parse_cigar(100, '+', '10S101M') == (90, 100, 200, 200)
assert parse_cigar(100, '-', '10S101M') == (200, 200, 100, 90)
def test_right_soft_clip(self):
assert parse_cigar(100, '+', '1M1S') == (100, 100, 100, 101)
assert parse_cigar(100, '-', '1M1S') == (101, 100, 100, 100)
assert parse_cigar(100, '+', '101M1S') == (100, 100, 200, 201)
assert parse_cigar(100, '-', '101M1S') == (201, 200, 100, 100)
assert parse_cigar(100, '+', '1M10S') == (100, 100, 100, 110)
assert parse_cigar(100, '-', '1M10S') == (110, 100, 100, 100)
assert parse_cigar(100, '+', '101M10S') == (100, 100, 200, 210)
assert parse_cigar(100, '-', '101M10S') == (210, 200, 100, 100)
def test_sam_format_spec(self):
# See 'Sequence Alignment/Map Format Specification', 2 Sep 2016.
# Specifically, these are taken from the SAM file format specification,
# section 1.1 ("An example").
# +r001/1
assert parse_cigar(7, '+', '8M2I4M1D3M') == (7, 7, 22, 22)
# +r002
assert parse_cigar(9, '+', '3S6M1P1I4M') == (6, 9, 18, 18)
# +r003
assert parse_cigar(9, '+', '5S6M') == (4, 9, 14, 14)
# +r004
assert parse_cigar(16, '+', '6M14N5M') == (16, 16, 40, 40)
# -r003, hard clipping, we don't support it...
with pytest.raises(
HardClippingNotSupportedException,
message=
'Dupligänger does not support hard-clipping. cigar: 6H5M, left pos: 29, strand: -'
):
parse_cigar(29, '-', '6H5M') == (16, 16, 40, 40)
# -r001/2
assert parse_cigar(37, '-', '9M') == (45, 45, 37, 37)
def test_simple(self):
assert parse_cigar(100, '+', '1M') == (100, 100, 100, 100)
assert parse_cigar(100, '-', '1M') == (100, 100, 100, 100)
assert parse_cigar(100, '+', '101M') == (100, 100, 200, 200)
assert parse_cigar(100, '-', '101M') == (200, 200, 100, 100)