767556b6f0
clarify multi-part index in option -I ( #301 )
2022-06-13 15:50:15 -04:00
50a26a60a6
option to keep Ensembl_canonical only
2022-05-14 11:18:06 -04:00
31de4fd1bc
r1132: document misjoin output
...
Also additional check of centromeric breakpoints
2022-05-11 21:39:29 -04:00
e018caea32
added the second minimap2 paper
2022-03-01 11:05:09 -05:00
7c02742fa8
removed travis CI
2022-03-01 11:01:13 -05:00
a41f5d1eeb
Fix indentation
2022-03-01 10:41:01 -05:00
ed3d0eb328
fix undefined variable
2022-03-01 10:41:01 -05:00
e6d166a314
Build mappy via Makefile and libminimap2.a
2022-03-01 10:41:01 -05:00
06fedaadd0
typo on simde
2021-12-26 15:38:06 -05:00
fe35e679e9
Release minimap2-2.24 (r1122)
2021-12-26 15:14:54 -05:00
e25aa5ee74
r1121: change bw_long to bw if bw is longer
...
Resolve #852
2021-12-26 14:37:31 -05:00
3bde3450a0
r1121: updated obsolete settings in manpage
...
Resolve #851
2021-12-26 14:33:14 -05:00
36942ff711
r1119: fixed a typo in the new chaining code
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Not affecting v2.23
2021-12-25 12:46:26 -05:00
d3a89d34d4
r1118: use -r1k,100k for asm* modes
2021-12-23 20:43:54 -05:00
c8f0a35c40
r1117: added --no-hash-name for deterministic
2021-11-24 16:49:48 -05:00
fcaadc22b7
r1116: cut long chains at weak points
2021-11-20 19:07:44 -05:00
db37fc43a7
r1115: prepare for chain breaking
2021-11-20 13:42:44 -05:00
a8f1fa8ea3
r1114: retain more candidate inversion alignments
2021-11-18 21:37:10 -05:00
b276772890
r1112: added --print-chains for debugging
2021-11-18 21:26:41 -05:00
d0cff3eb36
Release minimap2-2.23 (r1111)
2021-11-18 17:11:48 -05:00
ac334639ce
r1110: default --cap-kalloc=1g; test more inv
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See #816 and #823
2021-10-11 14:45:15 -04:00
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
39bdd45875
r1108: fixed missing inversions for #816 and #806
2021-10-04 16:34:30 -04:00
aefa2c0d86
added --chain-skip-scale
2021-10-01 16:58:03 -04:00
7ee62dae1d
updated manuscript
2021-10-01 11:42:36 -04:00
05a8a45d44
r1105: avoid long running time occasionally ( #771 )
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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
cc14d1afdf
fixed typos
2021-08-08 11:18:02 -04:00
bb3048b2a0
removed one extra sentence
2021-08-07 16:55:02 -04:00
5113ca2628
improved manuscript
2021-08-07 16:01:15 -04:00
7358a1ead1
Release minimap2-2.22 (r1101)
2021-08-07 11:30:31 -04:00
32f552957e
Merge remote-tracking branch 'remotes/origin/master'
2021-08-07 10:40:02 -04:00
a05edfa5ec
a different ending sentence
2021-08-07 10:38:48 -04:00
8e81145817
finished the first draft
2021-08-07 00:33:31 -04:00
e37f5ffe39
finished results
2021-08-07 00:06:28 -04:00
8a1d52bcbe
r1094: for --split-prefix update max_dp at the end
2021-08-06 21:40:43 -04:00
f7271a7c24
expose mapQ threshold to command line of pafcmp
2021-08-06 19:41:46 -04:00
70393eb46e
minimap2 update manuscript
2021-08-06 19:41:17 -04:00
9d049f0562
added pafcmp
2021-08-05 12:41:21 -04:00
5180b70ff3
r1090: log wall-clock time for each read
2021-08-04 17:45:09 -04:00
2392e54fe2
r1089: fixed an unusual memory leak ( #749 )
...
This is more apparent when there are many candidate chains. Although only a
small numbers of them are extended, they are still occupying memory. A
realloc() solves this problem. This is a long existiing issue.
2021-08-04 17:07:00 -04:00
629c11728e
output the number of mismatches
2021-08-04 17:05:06 -04:00
59488f0271
call mm_idx_destroy at the end of loop to fix memory leak
2021-07-26 18:25:08 -04:00
7e33fde82b
dev-r1087: added --cap-kalloc
2021-07-19 21:20:04 -04:00
c4fe52fb07
reduced the default -l and -b
2021-07-19 17:25:11 -04:00
ead1cfbaca
output for binning
2021-07-19 14:56:33 -04:00
83a535f148
dev-r1084: fixed flag integer overflow
2021-07-19 11:52:18 -04:00
f3af29a8aa
don't add a new command
2021-07-19 10:57:48 -04:00
cf7eaef367
refactor and prepare for a new command
2021-07-19 00:36:17 -04:00
2411887d8e
rename
2021-07-19 00:30:16 -04:00
1a8373bb84
dev-r1080: fixed negative dp_max
2021-07-18 21:07:14 -04:00
Heng Li
Chris Wright
Ryan Lim