Heng Li
|
cefd0d9f6c
|
removed -b0 (a typo)
|
2022-10-21 17:37:04 -04:00 |
|
Heng Li
|
2a319c89aa
|
support ##PAF lines in GFF3
|
2022-10-07 19:34:25 -04:00 |
|
Heng Li
|
5aa4355ca8
|
extract junctions from GFF
|
2022-09-21 12:57:40 -04:00 |
|
Heng Li
|
6ed7263670
|
junceval for plain junction BED as input
|
2022-09-10 23:18:08 -04:00 |
|
Heng Li
|
315795eefd
|
skip unmapped lines
|
2022-09-10 08:48:57 -04:00 |
|
Heng Li
|
fc6869a9e8
|
r1141: junceval to support miniprot output
|
2022-09-09 16:28:23 -04:00 |
|
Heng Li
|
6252e5e367
|
sync with tag changes in miniprot
|
2022-09-09 14:48:17 -04:00 |
|
Heng Li
|
843729df1e
|
output CDS and stop_codon
|
2022-09-09 12:09:38 -04:00 |
|
Heng Li
|
195c98fa46
|
output dist from end instead
|
2022-09-08 23:35:48 -04:00 |
|
Heng Li
|
a2e6659d9b
|
output more info
|
2022-09-08 23:18:13 -04:00 |
|
Heng Li
|
e450f161bb
|
added paf2gff
|
2022-09-08 22:33:21 -04:00 |
|
Heng Li
|
15cade0f06
|
added longcs2fa
|
2022-07-18 22:24:48 -04:00 |
|
Heng Li
|
767556b6f0
|
clarify multi-part index in option -I (#301)
|
2022-06-13 15:50:15 -04:00 |
|
Heng Li
|
50a26a60a6
|
option to keep Ensembl_canonical only
|
2022-05-14 11:18:06 -04:00 |
|
Heng Li
|
31de4fd1bc
|
r1132: document misjoin output
Also additional check of centromeric breakpoints
|
2022-05-11 21:39:29 -04:00 |
|
Heng Li
|
e018caea32
|
added the second minimap2 paper
|
2022-03-01 11:05:09 -05:00 |
|
Heng Li
|
7c02742fa8
|
removed travis CI
|
2022-03-01 11:01:13 -05:00 |
Chris Wright
|
a41f5d1eeb
|
Fix indentation
|
2022-03-01 10:41:01 -05:00 |
|
Chris Wright
|
ed3d0eb328
|
fix undefined variable
|
2022-03-01 10:41:01 -05:00 |
|
Chris Wright
|
e6d166a314
|
Build mappy via Makefile and libminimap2.a
|
2022-03-01 10:41:01 -05:00 |
|
Heng Li
|
06fedaadd0
|
typo on simde
|
2021-12-26 15:38:06 -05:00 |
|
Heng Li
|
fe35e679e9
|
Release minimap2-2.24 (r1122)
|
2021-12-26 15:14:54 -05:00 |
|
Heng Li
|
e25aa5ee74
|
r1121: change bw_long to bw if bw is longer
Resolve #852
|
2021-12-26 14:37:31 -05:00 |
|
Heng Li
|
3bde3450a0
|
r1121: updated obsolete settings in manpage
Resolve #851
|
2021-12-26 14:33:14 -05:00 |
|
Heng Li
|
36942ff711
|
r1119: fixed a typo in the new chaining code
Not affecting v2.23
|
2021-12-25 12:46:26 -05:00 |
|
Heng Li
|
d3a89d34d4
|
r1118: use -r1k,100k for asm* modes
|
2021-12-23 20:43:54 -05:00 |
|
Heng Li
|
c8f0a35c40
|
r1117: added --no-hash-name for deterministic
|
2021-11-24 16:49:48 -05:00 |
|
Heng Li
|
fcaadc22b7
|
r1116: cut long chains at weak points
|
2021-11-20 19:07:44 -05:00 |
|
Heng Li
|
db37fc43a7
|
r1115: prepare for chain breaking
|
2021-11-20 13:42:44 -05:00 |
|
Heng Li
|
a8f1fa8ea3
|
r1114: retain more candidate inversion alignments
|
2021-11-18 21:37:10 -05:00 |
|
Heng Li
|
b276772890
|
r1112: added --print-chains for debugging
|
2021-11-18 21:26:41 -05:00 |
|
Heng Li
|
d0cff3eb36
|
Release minimap2-2.23 (r1111)
|
2021-11-18 17:11:48 -05:00 |
|
Heng Li
|
ac334639ce
|
r1110: default --cap-kalloc=1g; test more inv
See #816 and #823
|
2021-10-11 14:45:15 -04:00 |
|
Heng Li
|
546623dcb4
|
r1109: disable chain_skip_scale by default
Enabling the option slows down alignment, possibly because it fragments chains
in difficult regions.
|
2021-10-04 21:24:35 -04:00 |
|
Heng Li
|
39bdd45875
|
r1108: fixed missing inversions for #816 and #806
|
2021-10-04 16:34:30 -04:00 |
|
Heng Li
|
aefa2c0d86
|
added --chain-skip-scale
|
2021-10-01 16:58:03 -04:00 |
|
Heng Li
|
7ee62dae1d
|
updated manuscript
|
2021-10-01 11:42:36 -04:00 |
|
Heng Li
|
05a8a45d44
|
r1105: avoid long running time occasionally (#771)
Caused by highly repetitive minimizers on a query sequence. The solution is to
filter out these query minimizers.
|
2021-08-15 19:43:01 -04:00 |
|
Heng Li
|
cc14d1afdf
|
fixed typos
|
2021-08-08 11:18:02 -04:00 |
|
Heng Li
|
bb3048b2a0
|
removed one extra sentence
|
2021-08-07 16:55:02 -04:00 |
|
Heng Li
|
5113ca2628
|
improved manuscript
|
2021-08-07 16:01:15 -04:00 |
|
Heng Li
|
7358a1ead1
|
Release minimap2-2.22 (r1101)
|
2021-08-07 11:30:31 -04:00 |
|
Heng Li
|
32f552957e
|
Merge remote-tracking branch 'remotes/origin/master'
|
2021-08-07 10:40:02 -04:00 |
|
Heng Li
|
a05edfa5ec
|
a different ending sentence
|
2021-08-07 10:38:48 -04:00 |
|
Heng Li
|
8e81145817
|
finished the first draft
|
2021-08-07 00:33:31 -04:00 |
|
Heng Li
|
e37f5ffe39
|
finished results
|
2021-08-07 00:06:28 -04:00 |
|
Heng Li
|
8a1d52bcbe
|
r1094: for --split-prefix update max_dp at the end
|
2021-08-06 21:40:43 -04:00 |
|
Heng Li
|
f7271a7c24
|
expose mapQ threshold to command line of pafcmp
|
2021-08-06 19:41:46 -04:00 |
|
Heng Li
|
70393eb46e
|
minimap2 update manuscript
|
2021-08-06 19:41:17 -04:00 |
|
Heng Li
|
9d049f0562
|
added pafcmp
|
2021-08-05 12:41:21 -04:00 |