040f74102c
r965: added --chain-gap-scale for #540
2020-01-18 10:29:33 -05:00
d90583b83c
r954: fixed two potential undef behaviors ( #443 )
2019-07-18 09:17:08 -04:00
d431dc0181
r917: added --max-chain-iter to avoid worst case
...
Resolves #324
2019-02-27 14:41:01 -05:00
e02bebd96d
r915: fixed a bug caused by the latest change
2019-02-14 10:04:04 -05:00
32ab6ce15b
r914: fixed two harmless division by 0
...
Resolves #326
2019-02-12 19:30:49 -05:00
1b3a6a0fe5
r890: removed "register" ( #261 )
2018-11-19 13:57:31 -05:00
7e6e8ca73f
r792: fixed -Wextra warnings and resolved #184
2018-06-19 15:26:58 -04:00
e896c9ec05
r559: prefer a chain involving more segments
2017-11-08 13:22:16 -05:00
be7f3c4ffe
r525: fixed a bug in chaining; handle ovlp ends
2017-10-20 21:34:52 -04:00
9364bc64d7
r501: added end_bonus to extz2
2017-10-11 09:39:41 -04:00
64c0ad6b35
r439: use splice-like chain gap cost between segs
...
This improves accuracy
2017-09-25 16:04:38 -04:00
9538c985aa
r438: fixed a rare case that leads to missing hits
...
It is a bug in chaining.
2017-09-25 14:59:34 -04:00
997011458c
fixed uninitialized value due to last commit
2017-09-20 15:10:48 -04:00
19d8eca3a1
moved array shrinking into chain_dp()
2017-09-20 14:58:57 -04:00
fb1bcc0084
early exploration
2017-09-19 16:18:28 -04:00
f4a8766283
r362: fixed overestimated chaining score
...
Caused by ilog2_32(0)=-1. This bug was fixed once and reoccurred as I was
tuning the score function but forgot to apply the fix.
2017-09-14 10:15:22 -04:00
c59b0781bc
r280: output introns as "N" in the cdna mode
2017-08-09 11:45:02 -04:00
1a7d782131
r273: cdna mapping mode for testing
...
Differences from the typical mapping mode:
* banded alignment disabled
* log gap cost during chaining
* zero long-gap extension during alignment
* up to 100kb (by default) reference gap
* bad seeding not filtered (to tune later)
2017-08-08 11:31:49 -04:00
fc965805f7
r215: bring back a log gap component
...
Otherwise chaining may more often break a long gap into several gaps.
2017-07-28 00:17:19 -04:00
f2ef48878a
r202: trim bad chain ends before extension
...
This fixes a few more FP long INDELs towards the end of alignments.
2017-07-25 19:53:19 -04:00
21ca564112
r201: fixed a minor chaining issue
...
Chaining looked at the end of a chain, but the end may not be the best. We now
go back to find the max.
2017-07-25 18:26:51 -04:00
215e92ed7b
r200: reduce long gaps in chaining
...
Every seed can initiate a chain.
2017-07-25 17:32:54 -04:00
b530ade333
r199: changed to linear gap cost for chaining
...
The old cost doesn't penalize long gaps enough. Will also drop seeds close to
the edge in the next commit.
2017-07-25 15:35:10 -04:00
eeeb2ffb68
r174: make max-chain-skip work
...
The max-chain-skip heuristics did not work due to a bug. Without this
heuristics, chaining is too slow for long-read overlap.
2017-07-12 10:08:06 -04:00
7598809577
r171: reduced log gap cost at chaining
...
The cost is so large that it discards too many valid seeds without HPC k-mers.
This change may introduce false long gaps to reference mapping. We have another
mechanism mm_filter_bad_seeds() to protect against this. In addition, minimap2
is not that bad to have long gaps. Some other aligners are worse.
Still need tuning in future.
2017-07-11 14:57:49 -04:00
782449975d
r168: fixed a bug in long join: a[] not sorted
...
Also added length requirement for long join and changed -g in the ava mode
2017-07-09 12:14:20 -04:00
3f6a0b0b5c
r162: improved chaining accuracy
2017-07-08 14:29:36 -04:00
2338e887d9
finished the first draft of manpage
2017-07-01 11:25:54 -04:00
d274e1b743
backup
2017-06-29 12:58:52 -04:00
c8d122bcdb
backup
2017-06-29 11:11:15 -04:00
a25866c25c
r96: min_cnt still wrong in chaining
2017-06-28 11:03:03 -04:00
bf0e8199e2
r94: min_cnt is tested in a wrong way in chain
2017-06-28 10:39:27 -04:00
fa80177e58
r89: added minimal number of minimizer counts
2017-06-27 18:43:15 -04:00
de54c9dac2
r77: fixed an index loading bug (offset not set)
2017-06-26 13:56:25 -04:00
c01f2dd757
fixed a bug
2017-06-07 11:40:13 -04:00
77c76c1e14
fixed an integer overflow
2017-06-06 22:20:45 -04:00
c1c946aa67
fixed memory leaks
...
though some of them are not really leaks when kalloc is in use.
2017-06-06 21:45:55 -04:00
e6adb673f9
fixed a stupid bug
2017-06-06 15:45:42 -04:00
a2958a4836
minor tweaks
2017-06-06 15:31:21 -04:00
d816e48fce
fixed a bug in chaining
2017-06-06 14:33:43 -04:00
6d4348db44
dp chaining mostly works, but fails sometimes
...
which means there are bugs that need to be fixed
2017-06-06 14:19:50 -04:00
1a9fc04cf0
backup
2017-06-06 10:16:33 -04:00
Heng Li