a6fab118c5
Fixed alignment result final update when computing the exact max value
2023-04-06 21:05:24 -04:00
66db9da7d8
changed preprocessor conditionals for SIMDe
2020-04-22 19:50:59 +02:00
f47e8a525e
SIMDe made optional. Include paths changes for SIMDe.
2020-04-21 01:08:32 +02:00
9e6fdd376b
Changed sse2neon with SIMDe. Added building non-SIMD version.
2020-04-20 18:28:06 +02:00
e80759c97a
--junc-bed apparently working
...
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
be171aa2dc
implemented in exts; testing is the next
2019-04-28 16:47:12 -04:00
c63a33904f
r836: fixed an integer overflow
...
Forgot this one.
2018-09-14 23:29:31 -04:00
734ac379bb
r770: matching N bases not working properly ( #155 )
2018-04-30 19:55:23 -04:00
f5cfd439ee
r651: incorrectly treat introns as deletions
...
This happened when the last operation during backtracking is an intron.
2018-01-07 19:42:50 -05:00
285eb0da05
r540: removed a buggy debugging line
2017-10-29 00:02:41 -04:00
79b0caca95
r537: model the next base to GT/AG
...
[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
198849a716
r491: an ambiguous base costs the same as gap ext
2017-10-09 09:59:42 -04:00
46e8b6a4f9
r338: portable CPU dispatch, which is the default
...
working with gcc, icc, clang and msvc.
2017-09-03 20:29:24 -04:00
3c997ca016
r337: support CPU dispatch for gcc-4.8+
...
using __builtin_cpu_supports()
2017-09-03 14:29:49 -04:00
993a2bb521
r301: separate introns from deletions
...
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
43506edbc5
backup: preliminary boundary alignment
2017-08-12 23:10:14 -04:00
bcfe00d2ad
minor formatting changes
2017-08-12 19:09:33 -04:00
17c19e5819
exts2 working
2017-08-12 19:06:59 -04:00
61eef0575c
separate out spliced alignment; not right yet
2017-08-12 18:54:32 -04:00
Alberto Zeni
mbrcic
Heng Li