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Author SHA1 Message Date
Heng Li c41518ae85 r1166: sync kalloc with miniwfa and miniprot 2023-04-19 21:38:47 -04:00
Heng Li 5e7242303c r1164: changed the syntax of -J 2023-04-07 22:54:33 -04:00
Heng Li a026c69b89 r1163: increased the default -I to 8G 
To reduce accidental errors when mapping against diploid human assemblies.
 2023-04-07 01:22:22 -04:00
Heng Li ea2042a577 r1162: fixed a typo; also increased splice pen 
Now slightly better on ISO-seq
 2023-04-07 01:19:18 -04:00
Heng Li 1834b1fd42 r1161: merged the simple and complex models 2023-04-06 23:42:50 -04:00
Heng Li 7ced0f16a0 r1160: splice model code cleanup 2023-04-06 23:32:06 -04:00
Heng Li 35732f3025 Merge branch 'master' into splice-model 2023-04-06 21:09:18 -04:00
Heng Li 01b98e8e52 r1155: fixed a bug on parsing --rmq 
resolves #1010
 2023-01-17 09:09:25 -05:00
Heng Li 16b8d50199 removed debugging code 2023-01-06 11:16:09 -05:00
Heng Li 226fd6114c fixed a wrong comment. Resolves #997 2022-11-30 09:22:39 -05:00
Heng Li 822ccd1733 r1152: evaluate base Sn and Sp 2022-11-01 21:58:45 -04:00
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
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
Heng Li 5180b70ff3 r1090: log wall-clock time for each read 2021-08-04 17:45:09 -04:00
Heng Li 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
Heng Li 629c11728e output the number of mismatches 2021-08-04 17:05:06 -04:00
Heng Li 7e33fde82b dev-r1087: added --cap-kalloc 2021-07-19 21:20:04 -04:00
Heng Li c4fe52fb07 reduced the default -l and -b 2021-07-19 17:25:11 -04:00
Heng Li ead1cfbaca output for binning 2021-07-19 14:56:33 -04:00
Heng Li 83a535f148 dev-r1084: fixed flag integer overflow 2021-07-19 11:52:18 -04:00
Heng Li f3af29a8aa don't add a new command 2021-07-19 10:57:48 -04:00
Heng Li cf7eaef367 refactor and prepare for a new command 2021-07-19 00:36:17 -04:00
Heng Li 2411887d8e rename 2021-07-19 00:30:16 -04:00
Heng Li 1a8373bb84 dev-r1080: fixed negative dp_max 2021-07-18 21:07:14 -04:00
Heng Li 161ae7ff73 dev-r1079: per-read error rate 
more tuning needed
 2021-07-18 20:38:53 -04:00
Heng Li 8a6edab847 dev-r1078: decoupling ranking penalty 2021-07-18 16:22:48 -04:00
Heng Li 15118dd521 output #mismatches/#dels/#ins in view 2021-07-18 15:13:40 -04:00
Heng Li 2546999639 dev-r1076: log gap penalty 2021-07-17 18:23:59 -04:00
Heng Li 52fafe0fed updated pbsim to pbsim2 2021-07-17 18:18:26 -04:00
Heng Li 5f449c5cae fixed potential integer overflows 2021-07-16 17:20:05 -04:00
Heng Li b046052d82 Merge branch 'master' into utec 2021-07-16 13:32:47 -04:00
Heng Li 581f2d7123 Release minimap2-2.21 (r1071) 2021-07-06 13:18:55 -04:00
Heng Li 52dbd439bc r1080: re-versioning 2021-07-02 20:26:13 -04:00
Heng Li 459ce04c84 r1069: fixed a regression in comparison to v2.18 
for PE short reads. An interesting omission. Resolves #776
 2021-07-02 11:45:21 -04:00
Heng Li e6cce019e4 r1068: fixed a bug caused by 3f71478 
Resolves #752 (again)
 2021-06-30 19:20:06 -04:00
Heng Li 7025b0b941 Merge branch 'master' of github.com:lh3/minimap2 2021-06-16 10:18:40 -04:00
Heng Li fe6a0bb337 r1064: fixed another uninitialized condition 
This one should also be harmless. It affects a min value, but that value is not
actually used.
 2021-06-16 10:16:36 -04:00
Heng Li 3f7147864b r1063: fixed an uninitialized access (#752) 
This one is harmless.
 2021-06-16 09:27:30 -04:00
Heng Li ce7a59f412 Fixed a typo in README 
I just hate my butterfly keyboard!
 2021-05-27 15:43:04 -04:00
Heng Li 15471bd629 Release minimap2-2.20 (r1061) 2021-05-27 15:26:04 -04:00
Heng Li ca19463268 r1060: safer ways to use -rNUM1,NUM2 2021-05-27 10:55:13 -04:00
Heng Li 4f8d1bc360 r1059: with --rmq, use the larger bandwidth 2021-05-26 23:01:49 -04:00
Heng Li 1776c0c645 missing seed.c in setup.py 
Ok, I am not going to re-release again...
 2021-05-26 21:36:09 -04:00
Heng Li 9febf532c1 Release minimap2-2.19 (r1057) 2021-05-26 21:23:42 -04:00
Heng Li cec23131e4 fixed a python compilation error 
Caused by chain.c -> lchain.c
 2021-05-26 21:20:48 -04:00
Heng Li ef09ccf104 Release minimap2-2.19 (r1055) 2021-05-26 21:01:03 -04:00
Heng Li e74dfd1aa9 r1054: fixed a memory leak 2021-05-26 12:32:04 -04:00
Heng Li f31705bb4a r1053: made junceval work with PAF 2021-05-26 11:54:46 -04:00
Heng Li 41d7ccb191 r1052: default -g to 5k 2021-05-24 16:46:16 -04:00
Heng Li 34a41197d7 r1051: added two internal parameters 
rmq_rescue_size and rmq_rescue_ratio
 2021-05-24 16:38:45 -04:00