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  • ad177f2165 一些自动格式更改，添加一些注释等 main zzh 2023-08-10 15:56:06 +0800
  • f588745484 重新配置了mxsvr zzh 2023-08-03 03:17:11 +0800
  • 023c18ba32 添加了一些统计运行时间的变量，测试性能 zzh 2023-08-03 03:12:38 +0800
  • a10f6b207a Initial commit zzh 2023-08-03 03:12:33 +0800
  • 1641a66d15 添加vscode调试配置文件 zzh 2023-07-27 22:36:55 +0800
  • 3e8e701029 合并readme和gitignore Gitea 2023-07-27 22:31:16 +0800
  • 21c095f23c Initial commit zzh 2023-07-27 22:00:32 +0800
  • ace990c381
         Illumina Complete Long Read presets (#1069) Aaron Darling 2023-06-04 22:06:15 +0700
  • e28a55be86 Release minimap2-2.26 (r1175) Heng Li 2023-04-29 12:21:09 -0400
  • f8d46a7a30 Revert #868 and use the old setup.py Heng Li 2023-04-29 11:48:41 -0400
  • 4483f89ee5 Release minimap2-2.25 (r1173) Heng Li 2023-04-25 12:44:52 -0400
  • f1b3c7ad06 added -ldl for asan on some linux Heng Li 2023-04-25 11:14:15 -0400
  • 180faa3594 r1171: add operator priority explicit with () Heng Li 2023-04-21 11:09:07 -0400
  • 704fbc6f5c
         An option to output SEQ field for secondary alignment (#687) Mikhail Kolmogorov 2023-04-21 08:06:13 -0700
  • fc24c8a348 r1169: improved kexpand compatibility Heng Li 2023-04-21 10:53:23 -0400
  • e68d868806
         use updated kalloc macros (#1051) Chris Seymour 2023-04-21 15:45:53 +0100
  • c3d461e22a mappy check index flags before mapping Alex Payne 2023-01-12 13:22:46 +0000
  • c41518ae85 r1166: sync kalloc with miniwfa and miniprot Heng Li 2023-04-19 21:38:47 -0400
  • 819d843e3c make mm_tbuf_t public Chris Seymour 2023-04-19 10:27:35 +0100
  • 5e7242303c r1164: changed the syntax of -J Heng Li 2023-04-07 22:54:33 -0400
  • a026c69b89 r1163: increased the default -I to 8G Heng Li 2023-04-07 01:22:22 -0400
  • ea2042a577 r1162: fixed a typo; also increased splice pen Heng Li 2023-04-07 01:19:18 -0400
  • 1834b1fd42 r1161: merged the simple and complex models Heng Li 2023-04-06 23:42:50 -0400
  • 7ced0f16a0 r1160: splice model code cleanup Heng Li 2023-04-06 23:32:06 -0400
  • 35732f3025 Merge branch 'master' into splice-model Heng Li 2023-04-06 21:09:18 -0400
  • a6fab118c5 Fixed alignment result final update when computing the exact max value Alberto Zeni 2023-02-28 15:53:11 -0500
  • 6ce0dd8b70 move MM_VERSION define to minimap.h Chris Seymour 2023-03-17 14:26:59 +0000
  • 1d3c3eef03 Add HD header ilne to SAM output Nils Homer 2023-02-13 18:03:53 -0700
  • 01b98e8e52 r1155: fixed a bug on parsing --rmq Heng Li 2023-01-17 09:09:25 -0500
  • 16b8d50199 removed debugging code Heng Li 2023-01-06 11:16:09 -0500
  • 226fd6114c fixed a wrong comment. Resolves #997 Heng Li 2022-11-30 09:22:39 -0500
  • 822ccd1733 r1152: evaluate base Sn and Sp Heng Li 2022-11-01 21:58:45 -0400
  • f67849c9af r1151: added exoneval Heng Li 2022-11-01 21:10:35 -0400
  • b0b199f503 r1150: the prev impl counted one less submer Heng Li 2022-10-21 21:00:22 -0400
  • c2f07ff2ac r1149: implemented random open syncmer Heng Li 2022-10-21 19:07:28 -0400
  • cefd0d9f6c removed -b0 (a typo) Heng Li 2022-10-21 17:37:04 -0400
  • 2a319c89aa support ##PAF lines in GFF3 Heng Li 2022-10-07 19:34:25 -0400
  • 85a5260408 correctly parse ##PAF lines in GFF3 (for miniprot) Heng Li 2022-10-07 19:33:27 -0400
  • 6c2cbf7903 miniprot-like splice model Heng Li 2022-10-06 09:10:17 -0400
  • 5aa4355ca8 extract junctions from GFF Heng Li 2022-09-21 12:57:40 -0400
  • 6ed7263670 junceval for plain junction BED as input Heng Li 2022-09-10 23:18:08 -0400
  • 315795eefd skip unmapped lines Heng Li 2022-09-10 08:48:57 -0400
  • fc6869a9e8 r1141: junceval to support miniprot output Heng Li 2022-09-09 16:28:23 -0400
  • 6252e5e367 sync with tag changes in miniprot Heng Li 2022-09-09 14:48:17 -0400
  • 843729df1e output CDS and stop_codon Heng Li 2022-09-09 12:09:38 -0400
  • 195c98fa46 output dist from end instead Heng Li 2022-09-08 23:35:48 -0400
  • a2e6659d9b output more info Heng Li 2022-09-08 23:18:13 -0400
  • e450f161bb added paf2gff Heng Li 2022-09-08 22:33:21 -0400
  • 15cade0f06 added longcs2fa Heng Li 2022-07-18 22:24:48 -0400
  • 767556b6f0 clarify multi-part index in option -I (#301) Heng Li 2022-06-13 15:50:15 -0400
  • 50a26a60a6 option to keep Ensembl_canonical only Heng Li 2022-05-14 11:18:06 -0400
  • 31de4fd1bc r1132: document misjoin output Heng Li 2022-05-11 21:39:29 -0400
  • e018caea32 added the second minimap2 paper Heng Li 2022-03-01 11:05:09 -0500
  • 7c02742fa8 removed travis CI Heng Li 2022-03-01 11:01:13 -0500
  • a41f5d1eeb Fix indentation Chris Wright 2022-02-14 11:00:01 +0000
  • ed3d0eb328 fix undefined variable Chris Wright 2022-02-11 18:10:45 +0000
  • e6d166a314 Build mappy via Makefile and libminimap2.a Chris Wright 2022-02-05 18:34:30 +0000
  • 06fedaadd0 typo on simde Heng Li 2021-12-26 15:38:06 -0500
  • fe35e679e9 Release minimap2-2.24 (r1122) Heng Li 2021-12-26 15:14:54 -0500
  • e25aa5ee74 r1121: change bw_long to bw if bw is longer Heng Li 2021-12-26 14:37:31 -0500
  • 3bde3450a0 r1121: updated obsolete settings in manpage Heng Li 2021-12-26 14:33:14 -0500
  • 36942ff711 r1119: fixed a typo in the new chaining code Heng Li 2021-12-25 12:46:26 -0500
  • d3a89d34d4 r1118: use -r1k,100k for asm* modes Heng Li 2021-12-23 20:43:54 -0500
  • c8f0a35c40 r1117: added --no-hash-name for deterministic Heng Li 2021-11-24 16:49:48 -0500
  • fcaadc22b7 r1116: cut long chains at weak points Heng Li 2021-11-20 19:07:44 -0500
  • db37fc43a7 r1115: prepare for chain breaking Heng Li 2021-11-20 13:42:44 -0500
  • a8f1fa8ea3 r1114: retain more candidate inversion alignments Heng Li 2021-11-18 21:37:10 -0500
  • b276772890 r1112: added --print-chains for debugging Heng Li 2021-11-18 21:26:41 -0500
  • d0cff3eb36 Release minimap2-2.23 (r1111) Heng Li 2021-11-18 17:11:48 -0500
  • ac334639ce r1110: default --cap-kalloc=1g; test more inv Heng Li 2021-10-11 14:45:15 -0400
  • 546623dcb4 r1109: disable chain_skip_scale by default Heng Li 2021-10-04 21:24:35 -0400
  • 39bdd45875 r1108: fixed missing inversions for #816 and #806 Heng Li 2021-10-04 16:34:30 -0400
  • aefa2c0d86 added --chain-skip-scale Heng Li 2021-10-01 16:58:03 -0400
  • 7ee62dae1d updated manuscript Heng Li 2021-10-01 11:42:36 -0400
  • 05a8a45d44 r1105: avoid long running time occasionally (#771) Heng Li 2021-08-15 19:43:01 -0400
  • cc14d1afdf fixed typos Heng Li 2021-08-08 11:18:02 -0400
  • bb3048b2a0 removed one extra sentence Heng Li 2021-08-07 16:55:02 -0400
  • 5113ca2628 improved manuscript Heng Li 2021-08-07 16:01:15 -0400
  • 7358a1ead1 Release minimap2-2.22 (r1101) Heng Li 2021-08-07 11:30:31 -0400
  • 32f552957e Merge remote-tracking branch 'remotes/origin/master' Heng Li 2021-08-07 10:40:02 -0400
  • a05edfa5ec a different ending sentence Heng Li 2021-08-07 10:38:48 -0400
  • 8e81145817 finished the first draft Heng Li 2021-08-07 00:33:31 -0400
  • e37f5ffe39 finished results Heng Li 2021-08-07 00:06:28 -0400
  • 8a1d52bcbe r1094: for --split-prefix update max_dp at the end Heng Li 2021-08-06 21:40:43 -0400
  • f7271a7c24 expose mapQ threshold to command line of pafcmp Heng Li 2021-08-06 19:41:46 -0400
  • 70393eb46e minimap2 update manuscript Heng Li 2021-08-06 19:41:17 -0400
  • 9d049f0562 added pafcmp Heng Li 2021-08-05 12:41:21 -0400
  • 5180b70ff3 r1090: log wall-clock time for each read Heng Li 2021-08-04 17:45:09 -0400
  • 2392e54fe2 r1089: fixed an unusual memory leak (#749) Heng Li 2021-08-04 17:07:00 -0400
  • 629c11728e output the number of mismatches Heng Li 2021-08-04 17:05:06 -0400
  • 59488f0271 call mm_idx_destroy at the end of loop to fix memory leak Ryan Lim 2021-07-26 17:48:37 -0400
  • 7e33fde82b dev-r1087: added --cap-kalloc Heng Li 2021-07-19 21:20:04 -0400
  • c4fe52fb07 reduced the default -l and -b Heng Li 2021-07-19 17:25:11 -0400
  • ead1cfbaca output for binning Heng Li 2021-07-19 14:56:33 -0400
  • 83a535f148 dev-r1084: fixed flag integer overflow Heng Li 2021-07-19 11:52:18 -0400
  • f3af29a8aa don't add a new command Heng Li 2021-07-19 10:57:48 -0400
  • cf7eaef367 refactor and prepare for a new command Heng Li 2021-07-19 00:36:17 -0400
  • 2411887d8e rename Heng Li 2021-07-19 00:30:16 -0400
  • 1a8373bb84 dev-r1080: fixed negative dp_max Heng Li 2021-07-18 21:07:14 -0400
  • 161ae7ff73 dev-r1079: per-read error rate Heng Li 2021-07-18 20:38:53 -0400