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
260a68d232
Use #defines for CIGAR operators in C code
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Give the CIGAR constants names to clarify the code. So that ksw2.h
remains self-contained, define KSW_* versions of the CIGAR operators
it needs for use within ksw2.h. Other code should in general use the
full set of MM_CIGAR_* constants in minimap.h.
2021-07-02 13:03:03 -04:00
be171aa2dc
implemented in exts; testing is the next
2019-04-28 16:47:12 -04:00
abe989e355
the previous fix on int overflow is incomplete
2018-05-11 10:12:57 -04:00
dfea113f28
r653: the last change may write "N" wrongly
2018-01-08 11:33:53 -05:00
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
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
9364bc64d7
r501: added end_bonus to extz2
2017-10-11 09:39:41 -04:00
7345621759
r499: end bonus working; DP region needs improve!
2017-10-11 00:14:25 -04:00
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
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
43506edbc5
backup: preliminary boundary alignment
2017-08-12 23:10:14 -04:00
61eef0575c
separate out spliced alignment; not right yet
2017-08-12 18:54:32 -04:00
163fa36ee6
r281: don't open long gaps on query
2017-08-10 15:04:59 -04:00
5934d68772
r229: a new way to prevent out-of-band backtrack
2017-07-29 23:52:30 -04:00
d08b7a0c51
r227: use local alignment for INV alignment
2017-07-29 17:40:53 -04:00
71c988f6ab
r188: renamed bseq* to mm_bseq*
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to avoid naming collisions between minimap2 and bwa/fermi-lite/etc
2017-07-19 09:26:46 -04:00
cc554aee43
r159: use two-piece gap penalty
2017-07-08 10:26:00 -04:00
d274e1b743
backup
2017-06-29 12:58:52 -04:00
5e202afb5f
fixed invalid backtracking, a temporary solution
2017-06-28 18:17:57 -04:00
42283ef10c
r87: fixed a bug in ksw2
2017-06-27 13:29:48 -04:00
c02ff4662c
r85: two-round z-drop
2017-06-27 10:36:24 -04:00
4fea3d778a
backup
2017-06-23 18:57:00 -04:00
c6d5dea314
replace with newer versions
2017-06-22 12:30:45 -04:00
fbfd4a3eff
to replace
2017-06-22 12:30:22 -04:00
fe8327500f
implemented SSE version; NOT working yet
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need to take a rest. Debugging is going to be tough.
2017-06-16 21:35:51 -04:00
7d33acbccc
diagonal global almost working
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one shot, though gaps not left-aligned at the boundary
2017-06-16 12:17:23 -04:00
78fe89d1ab
revert to fixed band
2017-06-14 14:22:23 -04:00
d3f17b1e05
updated ksw
2017-06-11 16:51:01 -04:00
Heng Li
John Marshall