35732f3025
Merge branch 'master' into splice-model
2023-04-06 21:09:18 -04:00
a6fab118c5
Fixed alignment result final update when computing the exact max value
2023-04-06 21:05:24 -04:00
6ce0dd8b70
move MM_VERSION define to minimap.h
2023-03-17 20:58:43 +01:00
1d3c3eef03
Add HD header ilne to SAM output
...
#905
2023-02-14 09:12:03 -05:00
01b98e8e52
r1155: fixed a bug on parsing --rmq
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resolves #1010
2023-01-17 09:09:25 -05:00
16b8d50199
removed debugging code
2023-01-06 11:16:09 -05:00
226fd6114c
fixed a wrong comment. Resolves #997
2022-11-30 09:22:39 -05:00
822ccd1733
r1152: evaluate base Sn and Sp
2022-11-01 21:58:45 -04:00
f67849c9af
r1151: added exoneval
2022-11-01 21:10:35 -04:00
b0b199f503
r1150: the prev impl counted one less submer
2022-10-21 21:00:22 -04:00
c2f07ff2ac
r1149: implemented random open syncmer
...
On the mm2-update dataset, -j8 leads to sparser k-mer selection at higher
accuracy. The speed becomes a little slower. There seems a benefit but not a
big one.
2022-10-21 19:07:28 -04:00
cefd0d9f6c
removed -b0 (a typo)
2022-10-21 17:37:04 -04:00
2a319c89aa
support ##PAF lines in GFF3
2022-10-07 19:34:25 -04:00
85a5260408
correctly parse ##PAF lines in GFF3 (for miniprot)
2022-10-07 19:33:27 -04:00
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
5aa4355ca8
extract junctions from GFF
2022-09-21 12:57:40 -04:00
6ed7263670
junceval for plain junction BED as input
2022-09-10 23:18:08 -04:00
315795eefd
skip unmapped lines
2022-09-10 08:48:57 -04:00
fc6869a9e8
r1141: junceval to support miniprot output
2022-09-09 16:28:23 -04:00
6252e5e367
sync with tag changes in miniprot
2022-09-09 14:48:17 -04:00
843729df1e
output CDS and stop_codon
2022-09-09 12:09:38 -04:00
195c98fa46
output dist from end instead
2022-09-08 23:35:48 -04:00
a2e6659d9b
output more info
2022-09-08 23:18:13 -04:00
e450f161bb
added paf2gff
2022-09-08 22:33:21 -04:00
15cade0f06
added longcs2fa
2022-07-18 22:24:48 -04:00
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
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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
Heng Li
Alberto Zeni
Chris Seymour
Nils Homer
Chris Wright