def test_init_ends_with_skip_both_before_and_after_clv():
"""
AA
GT┘ <-bridge read
G--AGT-GC <-bridge contig
0 123 456 <-contig coord
cc^ ^ice
...GACAGTTGC... <-genome
5678901234 <-genome coord
1 |
rc^ ^ire
"""
ref_clv = 10
cigartuples = (
(S.BAM_CMATCH, 1),
(S.BAM_CREF_SKIP, 2),
(S.BAM_CMATCH, 3),
(S.BAM_CREF_SKIP, 1),
(S.BAM_CMATCH, 2),
)
ctg_clv = 3
ctg_seq = 'GAGTGC'
assert init_ref_end(ref_clv, cigartuples, ctg_clv, ctg_seq) == 14
assert init_ctg_end(ctg_seq) == 6
def test_init_ends_with_deletion():
"""
AA
CG┘ <-bridge read
GAC__TCGTC <-bridge contig
012 345678 <-contig coord
| ||x
| |^cc ^ice
...GACGGTCCTC... <-genome
56789012345 <-genome coord
1| |
^rc ^rce
"""
ref_clv = 11
cigartuples = (
(S.BAM_CMATCH, 3),
(S.BAM_CDEL, 2),
(S.BAM_CMATCH, 5),
)
ctg_clv = 4
ctg_seq = 'GACTCGTC'
assert init_ref_end(ref_clv, cigartuples, ctg_clv, ctg_seq) == 15
assert init_ctg_end(ctg_seq) == 8
def test_link_init_ends():
"""
TT...AA
ATCGAC <-link contig
0123456 <-contig coord
^ctg_clv
...7890123... <-genome coord
1 ^ref_clv
"""
ref_clv = 12
cigartuples = ((S.BAM_CMATCH, 6), )
ctg_clv = 5
ctg_seq = 'ATCGAC'
assert init_ref_end(ref_clv, cigartuples, ctg_clv, ctg_seq) == 13
assert init_ctg_end(ctg_seq) == 6
def test_init_ends():
"""
AA
GT┘ <-bridge read
GACGGTTGC <-bridge contig
0123456789 <-contig coord
cc^ ^ice
...GACGGTTGC... <-genome
5678901234 <-genome coord
1 |
rc^ ^ire
"""
ref_clv = 10
cigartuples = ((S.BAM_CMATCH, 9), )
ctg_clv = 5
ctg_seq = 'GACGGTTGC'
assert init_ref_end(ref_clv, cigartuples, ctg_clv, ctg_seq) == 14
assert init_ctg_end(ctg_seq) == 9
def test_bridge_init_ends_with_hardclip_before_clv():
"""
AA
TC┘| <-bridge read
CGCATTCGT <-bridge contig
\\\ <-hardclip mask
0123456789 <-contig coord
cc^ ^ice
...CGCATTCGXX... <-genome
2345678901 <-genome coord
| 1|
rc^ ^ire
"""
ref_clv = 8
cigartuples = ((S.BAM_CHARD_CLIP, 3), (S.BAM_CMATCH, 6))
ctg_clv = 6
ctg_seq = 'CGCATTCGT'
assert init_ref_end(ref_clv, cigartuples, ctg_clv, ctg_seq) == 11
assert init_ctg_end(ctg_seq) == 9
def test_init_ends_with_insertion():
"""
AG AA <-inserted bases
┬ GT┘ <-bread read
GA CGGTCGC <-bridge contig
01 45678901 <-contig coord
x | 1|
x cc^ ^ice
...GT CGGTCGC... <-genome
56 78901234 <-genome coord
| |
rc^ ^ire
"""
ref_clv = 10
cigartuples = ((S.BAM_CMATCH, 2), (S.BAM_CINS, 2), (S.BAM_CMATCH, 7))
ctg_clv = 7
ctg_seq = 'GAAGCGGTCGC'
assert init_ref_end(ref_clv, cigartuples, ctg_clv, ctg_seq) == 14
assert init_ctg_end(ctg_seq) == 11
def test_init_ends_with_multiple_skips_before_clv():
"""
AA
TA┘ <-bridge read
G-C--CTAGC <-bridge contig
0 1 234567 <-contig coord
||| x ^cc^ice
...GACTGGTAGC... <-genome
56789012345 <-genome coord
1 | |
rc^ ^ire
"""
ref_clv = 12
cigartuples = ((S.BAM_CMATCH, 1), (S.BAM_CREF_SKIP, 1), (S.BAM_CMATCH, 1),
(S.BAM_CREF_SKIP, 2), (S.BAM_CMATCH, 5))
ctg_clv = 4
ctg_seq = 'GCCTAGC'
assert init_ref_end(ref_clv, cigartuples, ctg_clv, ctg_seq) == 15
assert init_ctg_end(ctg_seq) == 7
def test_bridge_init_ends_with_hardclip_after_clv():
"""
AAA
GTT┘ <-bridge read
A-GGTTGCAGA <-suffix contig
| | | /// <-hardclip mask
0 1234567890 <-contig coord
cc^ ^ice
...ACGGTTGC... <-genome
789012345678 <-genome coord
1 | |
rc^ ^init_ref_idx
"""
ref_clv = 12
cigartuples = ((S.BAM_CMATCH, 1), (S.BAM_CREF_SKIP, 1), (S.BAM_CMATCH, 6),
(S.BAM_CHARD_CLIP, 3))
ctg_clv = 4
ctg_seq = 'AGGTTGCAGA'
assert init_ref_end(ref_clv, cigartuples, ctg_clv, ctg_seq) == 18
assert init_ctg_end(ctg_seq) == 10
def test_bridge_init_ends_with_softclip_after_clv():
"""
AA <-polyA clip
TC┘| <-bridge read
|| CC <-non-polyA softclip
CGCATTCGT┘| <-bridge contig (hardcipped, could be chimeric https://www.biostars.org/p/109333/)
\\\ |
012345678901 <-contig coord
cc^ ^ice
...CGCATTCGTXX... <-genome
234567890123 <-genome coord
| 1 |
rc^ ^ire
"""
ref_clv = 8
cigartuples = ((S.BAM_CHARD_CLIP, 3), (S.BAM_CMATCH, 6), (S.BAM_CSOFT_CLIP,
2))
ctg_clv = 6
ctg_seq = 'CGCATTCGTCC'
assert init_ref_end(ref_clv, cigartuples, ctg_clv, ctg_seq) == 13
assert init_ctg_end(ctg_seq) == 11
def test_bridge_init_ends_with_sofclip_before_clv():
"""
AAA <-polyA softclip
GTT┘ <-bridge read
CCC ||| <-non-polyA softclip
01└GA-GGTTGCAGA <-suffix contig
| ||| //// <-hardclip mask
34 5678901234 <-contig coord
cc^ | ^ice
...ACGGTTGC... <-genome
7890123456789 <-genome coord
1 | |
rc^ ^init_ref_idx
"""
ref_clv = 12
cigartuples = ((S.BAM_CSOFT_CLIP, 3), (S.BAM_CMATCH, 2),
(S.BAM_CREF_SKIP, 1), (S.BAM_CMATCH, 5), (S.BAM_CHARD_CLIP,
4))
ctg_clv = 7
ctg_seq = 'CCCGAGGTTGCAGA'
assert init_ref_end(ref_clv, cigartuples, ctg_clv, ctg_seq) == 19
assert init_ctg_end(ctg_seq) == 14