def test_do_fwd_ctg_rt_bdg_with_right_hardclipping_right_on_ctg_clv():
"""
AAAAA
CG┘ <-right-tail read
XCC/// <-contig
0123456 <-contig coord
| ^ctg_offset
...XCC... <-reference genome
3456789 <-genome coord
| ^ref_clv
^starting the contig2genome alignment
"""
read = MagicMock()
read.reference_start = 2
read.reference_end = 4
read.cigartuples = ((S.BAM_CMATCH, 2), (S.BAM_CSOFT_CLIP, 5))
contig = MagicMock()
contig.infer_query_length.return_value = 6
contig.cigartuples = (
(S.BAM_CMATCH, 3),
(S.BAM_CHARD_CLIP, 3),
)
assert do_fwd_ctg_rt_bdg(read, contig) is None
def test_do_fwd_ctg_rt_bdg_with_right_hardclipping_right_before_ctg_clv():
"""
right hardclipping won't have an effect in such case
AAAAA
CG┘ <-right-tail read
XCCG// <-contig
0123456 <-contig coord
| ^ctg_offset
...XCCG... <-reference genome
34567 <-genome coord
| ^ref_clv
^starting the contig2genome alignment
"""
read = MagicMock()
read.reference_start = 2
read.reference_end = 4
read.cigartuples = ((S.BAM_CMATCH, 2), (S.BAM_CSOFT_CLIP, 5))
contig = MagicMock()
contig.infer_query_length.return_value = 6
contig.cigartuples = (
(S.BAM_CMATCH, 4),
(S.BAM_CHARD_CLIP, 2),
)
ctg_offset = 3
tail_len = 5
assert do_fwd_ctg_rt_bdg(read, contig) == ('+', ctg_offset, tail_len)
def test_do_fwd_ctg_rt_bdg():
"""
AA
CCG┘ <-right-tail read
XXCCGXX <-contig
0123456 <-contig coord
0123456 <-genome coord offset to 0
^ctg_offset
"""
mock_read = get_mock_read(ref_beg=1,
ref_end=4,
cigartuples=[(S.BAM_CMATCH, 3),
(S.BAM_CSOFT_CLIP, 2)])
mock_contig = MagicMock()
mock_contig.infer_query_length.return_value = 7
mock_contig.cigartuples = ((S.BAM_CMATCH, 7), )
ctg_offset = 3
tail_len = 2
assert do_fwd_ctg_rt_bdg(mock_read,
contig=mock_contig) == ('+', ctg_offset, tail_len)
def test_do_fwd_ctg_rt_bdg_with_left_hardclipping_right_on_ctg_clv():
"""
AA
CCG┘ <-right-tail read
\\\\XX <-contig
0123456 <-contig coord
^ctg_offset
...XX... <-reference genome
45678 <-genome coord
ref_clv^ ^starting the contig2genome alignment
ref_clv won't be captured by this bridge read
"""
read = MagicMock()
read.reference_start = 1
read.reference_end = 4
read.cigartuples = ((S.BAM_CMATCH, 3), (S.BAM_CSOFT_CLIP, 2))
contig = MagicMock()
contig.cigartuples = ((S.BAM_CHARD_CLIP, 4), (S.BAM_CMATCH, 2))
contig.infer_query_length.return_value = 6
assert do_fwd_ctg_rt_bdg(read, contig) is None
def test_do_fwd_ctg_rt_bdg_with_left_hardclipping():
"""
AA
CCG┘ <-right-tail read
\\\XCCGXX <-contig
0123456789 <-contig coord
| ^ctg_offset
...XXXXCCGXX... <-reference genome
4567890 <-genome coord
| ^ref_clv
^starting the contig2genome alignment
"""
read = MagicMock()
read.reference_start = 4
read.reference_end = 7
read.cigartuples = ((S.BAM_CMATCH, 3), (S.BAM_CSOFT_CLIP, 2))
contig = MagicMock()
contig.cigartuples = ((S.BAM_CHARD_CLIP, 3), (S.BAM_CMATCH, 7))
contig.infer_query_length.return_value = 9
ctg_offset = 3
tail_len = 2
assert do_fwd_ctg_rt_bdg(read, contig) == ('+', ctg_offset, tail_len)