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Author SHA1 Message Date
Heng Li
f67849c9af r1151: added exoneval 2022-11-01 21:10:35 -04:00
Heng Li
b0b199f503 r1150: the prev impl counted one less submer 2022-10-21 21:00:22 -04:00
Heng Li
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
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
85a5260408 correctly parse ##PAF lines in GFF3 (for miniprot) 2022-10-07 19:33:27 -04:00
Heng Li
6c2cbf7903 miniprot-like splice model 
slightly worse on iso-seq and slightly better on direct-RNA
 2022-10-06 09:10:17 -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) v2.24 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) v2.23 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) v2.22 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