def test_init_begs_with_deletion():
"""
TT
└CG <-bridge read
GAC__TCGTC <-bridge contig
012 345678 <-contig coord
| | | |
icb^ | | ^cc
...GACGGTCCTC... <-genome
56789012345 <-genome coord
| 1 |
irb^ ^rc
"""
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_beg(ref_clv, cigartuples, ctg_clv) == 5
assert init_ctg_beg(ctg_seq) == 0
def test_init_begs_with_skip_both_before_and_after_clv():
"""
TT
└GT <-bridge read
G--AGT-GC <-bridge contig
0 123 456 <-contig coord
icb^ ^cc
...GACAGTTGC... <-genome
5678901234 <-genome coord
| 1
ifb^ ^rc
"""
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_beg(ref_clv, cigartuples, ctg_clv) == 5
assert init_ctg_beg(ctg_seq) == 0
def test_link_init_begs():
"""
TT......AA
ATCGAC <-link contig
0123456 <-contig coord
icb^ ^ctg_clv
...7890123... <-genome coord
irb^ ^ref_clv
"""
ref_clv = 9
cigartuples = ((S.BAM_CMATCH, 6), )
ctg_clv = 2
ctg_seq = 'ATCGAC'
assert init_ref_beg(ref_clv, cigartuples, ctg_clv) == 7
assert init_ctg_beg(ctg_seq) == 0
def test_init_begs_with_skip_after_clv():
"""
TT
└GT <-bridge read
GACGGT-GC <-bridge contig
012345 678 <-contig coord
irc^ ^cc
...GACGGTTGC... <-genome
5678901234 <-genome coord
| 1
irb^ ^rc
"""
ref_clv = 10
cigartuples = ((S.BAM_CMATCH, 6), (S.BAM_CREF_SKIP, 1), (S.BAM_CMATCH, 2))
ctg_clv = 5
ctg_seq = 'GACGGTGC'
assert init_ref_beg(ref_clv, cigartuples, ctg_clv) == 5
assert init_ctg_beg(ctg_seq) == 0
def test_init_begs():
"""
TT
└GT <-bridge read
GACGGTTGC <-bridge contig
0123456789 <-contig coord
irb^ ^cc
...GACGGTTGC... <-genome
5678901234 <-genome coord
| 1
irc^ ^rc
"""
ref_clv = 10
cigartuples = ((S.BAM_CMATCH, 9), )
ctg_clv = 5
ctg_seq = 'GACGGTTGC'
assert init_ref_beg(ref_clv, cigartuples, ctg_clv) == 5
assert init_ctg_beg(ctg_seq) == 0
def test_bridge_init_begs_with_hardclip_before_clv():
"""
TT
└TC <-bridge read
\\\ATTCGT <-bridge contig (hardcipped, could be chimeric https://www.biostars.org/p/109333/)
0123456789 <-contig coord
icb^ ^cc
...ATTCGXX... <-genome
2345678901 <-genome coord
| | 1
irb^ ^rc
"""
ref_clv = 8
cigartuples = ((S.BAM_CHARD_CLIP, 3), (S.BAM_CMATCH, 6))
ctg_clv = 6
ctg_seq = 'ATTCGT'
assert init_ref_beg(ref_clv, cigartuples, ctg_clv) == 2
assert init_ctg_beg(ctg_seq) == 0
def test_bridge_init_begs_with_softclip_after_clv():
"""
TT <-polyA clip
└TC <-bridge read
|| CC <-non-polyA softclip
\\\ATTCGT┘| <-bridge contig (hardcipped, could be chimeric https://www.biostars.org/p/109333/)
01234567890 <-contig coord
icb^ ^cc
...ATTCGTXX... <-genome
234567890123 <-genome coord
| | 1 |
irb^ ^rc
"""
ref_clv = 8
cigartuples = ((S.BAM_CHARD_CLIP, 3), (S.BAM_CMATCH, 6), (S.BAM_CSOFT_CLIP,
2))
ctg_clv = 6
ctg_seq = 'ATTCGTCC'
assert init_ref_beg(ref_clv, cigartuples, ctg_clv) == 2
assert init_ctg_beg(ctg_seq) == 0
def test_init_begs_with_insertion():
"""
AG TT <-inserted bases
┬ └G <-bread read
GA CGGTCGC <-bridge contig
01 45678901 <-contig coord
|x |1
icb^x ^cc
...GT CGGTCGC... <-genome
56 78901234 <-genome coord
| |
irb^ ^rc
"""
ref_clv = 12
cigartuples = ((S.BAM_CMATCH, 2), (S.BAM_CINS, 2), (S.BAM_CMATCH, 7))
ctg_clv = 9
ctg_seq = 'GAAGCGGTCGC'
assert init_ref_beg(ref_clv, cigartuples, ctg_clv) == 5
assert init_ctg_beg(ctg_seq) == 0
def test_init_begs_with_multiple_skips_before_clv():
"""
TT
└TA <-bridge read
G-C--CTAGC <-bridge contig
0 1 234567 <-contig coord
icb^ x ^cc
...GACTGGTAGC... <-genome
56789012345 <-genome coord
| 1 | |
irb^ ^rc
"""
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_beg(ref_clv, cigartuples, ctg_clv) == 5
assert init_ctg_beg(ctg_seq) == 0
def test_bridge_init_begs_with_hardclip_after_clv():
"""
TTT
└GTT <-bridge read
A-GGTTGCAGA <-suffix contig
| | | /// <-hardclip mask
0 1234567890 <-contig coord
icb^ ^cc
...ACGGTTGC... <-genome
789012345678 <-genome coord
| 1 |
irb^ ^rc
"""
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_beg(ref_clv, cigartuples, ctg_clv) == 7
assert init_ctg_beg(ctg_seq) == 0
def test_bridge_init_begs_with_sofclip_before_clv():
"""
TTT <-polyA softclip
└GTT <-bridge read
CCC ||| <-non-polyA softclip
||└GA-GGTTGCAGA <-suffix contig
|| | ||| //// <-hardclip mask
01234 5678901234 <-contig coord
icb^ ^cc|
...ACGGTTGC... <-genome
4567890123456789 <-genome coord
| 1 |
irb^ ^rc
"""
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_beg(ref_clv, cigartuples, ctg_clv) == 4
assert init_ctg_beg(ctg_seq) == 0
