Heng Li
9d06cef13e
r1248: support --end-bonus in splice mode
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but this is not enabled by default for now
2025-04-02 21:39:41 -04:00
Heng Li
68179ed195
r1215: scoring apparently works
2024-10-12 22:29:27 -04:00
Heng Li
d1f4c8d232
implemented ksw scoring; not tested
2024-10-11 23:58:18 -04:00
Heng Li
8efe83b744
fill the junction array
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modifying ksw will be the next
2024-10-11 23:22:23 -04:00
Heng Li
042c8d4d71
added --junc-pen; it does nothing for now
2024-10-11 21:27:25 -04:00
Heng Li
ea2042a577
r1162: fixed a typo; also increased splice pen
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Now slightly better on ISO-seq
2023-04-07 01:19:18 -04:00
Heng Li
1834b1fd42
r1161: merged the simple and complex models
2023-04-06 23:42:50 -04:00
Heng Li
7ced0f16a0
r1160: splice model code cleanup
2023-04-06 23:32:06 -04:00
Heng Li
35732f3025
Merge branch 'master' into splice-model
2023-04-06 21:09:18 -04:00
Alberto Zeni
a6fab118c5
Fixed alignment result final update when computing the exact max value
2023-04-06 21:05:24 -04:00
Heng Li
6c2cbf7903
miniprot-like splice model
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slightly worse on iso-seq and slightly better on direct-RNA
2022-10-06 09:10:17 -04:00
mbrcic
66db9da7d8
changed preprocessor conditionals for SIMDe
2020-04-22 19:50:59 +02:00
mbrcic
f47e8a525e
SIMDe made optional. Include paths changes for SIMDe.
2020-04-21 01:08:32 +02:00
mbrcic
9e6fdd376b
Changed sse2neon with SIMDe. Added building non-SIMD version.
2020-04-20 18:28:06 +02:00
Heng Li
e80759c97a
--junc-bed apparently working
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Also fixed an issue with splice alignment in the reverse strand, though this
should have a very minor effect in practice.
2019-04-28 16:47:12 -04:00
Heng Li
be171aa2dc
implemented in exts; testing is the next
2019-04-28 16:47:12 -04:00
Heng Li
c63a33904f
r836: fixed an integer overflow
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Forgot this one.
2018-09-14 23:29:31 -04:00
Heng Li
734ac379bb
r770: matching N bases not working properly ( #155 )
2018-04-30 19:55:23 -04:00
Heng Li
f5cfd439ee
r651: incorrectly treat introns as deletions
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This happened when the last operation during backtracking is an intron.
2018-01-07 19:42:50 -05:00
Heng Li
285eb0da05
r540: removed a buggy debugging line
2017-10-29 00:02:41 -04:00
Heng Li
79b0caca95
r537: model the next base to GT/AG
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[PMID:18688272] shows that the base following GT tends to be A or G (i.e. R) in
both human and yeast, and that the base preceeding AG tends to be C or T (i.e.
Y). In the new model, we pay no cost to GTr..yAG, but we pay half of the cost
if there is no r or y. This improves the junction accuracy when mapping to
human and mouse and decreases the accuacy when mapping to SIRV. My guess is
that SIRV does not honor this trend. Need to investigate in future.
Also in this commit, --cost-non-gt-ag is aliased to -C. The default is changed
to 9 instead of 5. I also added --splice-flank to enable the above model. This
may become the default once I confirm my hypothesis on SIRV.
2017-10-28 00:25:01 -04:00
Heng Li
198849a716
r491: an ambiguous base costs the same as gap ext
2017-10-09 09:59:42 -04:00
Heng Li
46e8b6a4f9
r338: portable CPU dispatch, which is the default
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working with gcc, icc, clang and msvc.
2017-09-03 20:29:24 -04:00
Heng Li
3c997ca016
r337: support CPU dispatch for gcc-4.8+
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using __builtin_cpu_supports()
2017-09-03 14:29:49 -04:00
Heng Li
993a2bb521
r301: separate introns from deletions
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When an intron is adjacent to a deletion, the old code count both as introns,
which lead to an inaccurate exon boundary.
2017-08-18 15:31:15 +08:00
Heng Li
43506edbc5
backup: preliminary boundary alignment
2017-08-12 23:10:14 -04:00
Heng Li
bcfe00d2ad
minor formatting changes
2017-08-12 19:09:33 -04:00
Heng Li
17c19e5819
exts2 working
2017-08-12 19:06:59 -04:00
Heng Li
61eef0575c
separate out spliced alignment; not right yet
2017-08-12 18:54:32 -04:00
