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Heng Li fcd4df2a73 r1190: output unadjusted dp_max to ms:i 
This was an oversight affecting v2.22+. The latest minimap2 ranks hits and
estimates mapping quality with an adjusted alignment score (see the minimap2
update paper). This score however is not calculated when there is only one hit.
As a result, the ms:i tag varies depends on other sequences in the reference
genome, which is confusing. This change lets minimap2 to output the unadjusted
score at ms:i. At present, the adjusted score is not outputted.

Resolves #1146
 2024-03-11 17:19:13 -04:00
Heng Li 0efc886012 r1189: fixed an out-of-memory issue 
Resolves #1166
 2024-03-11 10:14:20 -04:00
Heng Li 940388f8e4 r1188: added --ds to output tag ds 
Adapted from minigraph
 2024-03-10 15:01:13 -04:00
Heng Li 23d2674c39 r1187: set stage for the ds tag; not added yet 2024-03-10 14:12:56 -04:00
Heng Li a12673611f Merge remote-tracking branch 'origin/master' 2024-03-10 13:49:30 -04:00
Heng Li 8140259974 r1183: added lr:hq; fixed transition 
* Added the lr:hq preset suggested by Nanopore developers (#1127)
 * Fixed transition scoring. It did not work with presets.
 * Cleaned up preset documentation
 2024-03-10 13:47:34 -04:00
Heng Li bc588c0eeb r1182: improved paftools.js compatibility 
Older k8/v8 can't use large memory. The previous change read large FASTA as
strings and might have problems. The new change tests k8 version.
 2023-10-30 16:37:29 -04:00
Heng Li ab717023b6 reverted to the previous paftools.js 2023-10-30 16:24:18 -04:00
Heng Li 9506e7ac3f r1180: paftools.js call compatibility with k8-1.0 2023-10-28 15:54:37 -04:00
Heng Li ce03fbc275 Merge remote-tracking branch 'remotes/origin/master' 2023-10-24 09:53:51 -04:00
Heng Li 98a3aa1b39 document --secondary-seq in manpage 
Resolve #1122
 2023-10-24 09:52:39 -04:00
Heng Li e28a55be86 Release minimap2-2.26 (r1175) 2023-04-29 12:21:09 -04:00
Heng Li f8d46a7a30 Revert #868 and use the old setup.py 2023-04-29 11:48:41 -04:00
Heng Li 4483f89ee5 Release minimap2-2.25 (r1173) 2023-04-25 12:44:52 -04:00
Heng Li f1b3c7ad06 added -ldl for asan on some linux 2023-04-25 11:14:15 -04:00
Heng Li 180faa3594 r1171: add operator priority explicit with () 
I can never remember the operator priority of & and &&
 2023-04-21 11:09:07 -04:00
Heng Li fc24c8a348 r1169: improved kexpand compatibility 2023-04-21 10:53:23 -04:00
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