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• f18dadb1c4 r1202: halved RMQ gap cost Heng Li 2024-03-19 23:47:54 -04:00
• a83b8fe7cc r1201: renamed --dbg-seed-freq to --dbg-seed-occ Heng Li 2024-03-19 21:53:09 -04:00
• c22bfe7722 r1200: added --rmq-inner and --dbg-seed-freq Heng Li 2024-03-19 21:52:07 -04:00
• 12d441ea22 Merge remote-tracking branch 'origin/master' Heng Li 2024-03-19 21:47:52 -04:00
• c7433c2811 r1197: sam2paf to output primary only Heng Li 2024-03-19 21:47:31 -04:00
• 5279377544 Fix MD generation check in SAM writing (#1181) Joyjit Daw 2024-03-19 19:20:21 -04:00
• acab05781e Merge remote-tracking branch 'remotes/origin/master' Heng Li 2024-03-19 09:56:13 -04:00
• 98c23bc6d2 r1194: output NM in sam2paf Heng Li 2024-03-19 09:55:16 -04:00
• 9b0ff2418c Fix mm_mapopt_t in Mappy (#1177) kojix2 2024-03-14 11:15:46 +09:00
• b6762503a9 Release minimap2-2.27 (r1193) v2.27 Heng Li 2024-03-12 13:20:07 -04:00
• 9667468e89 NEWS draft Heng Li 2024-03-11 22:46:47 -04:00
• ba60aac6f6 r1191: fixed wrong reverse() and revcomp() Heng Li 2024-03-11 22:09:01 -04:00
• fcd4df2a73 r1190: output unadjusted dp_max to ms:i Heng Li 2024-03-11 17:19:13 -04:00
• 0efc886012 r1189: fixed an out-of-memory issue Heng Li 2024-03-11 10:14:20 -04:00
• 940388f8e4 r1188: added --ds to output tag ds Heng Li 2024-03-10 15:01:13 -04:00
• 23d2674c39 r1187: set stage for the ds tag; not added yet Heng Li 2024-03-10 14:12:56 -04:00
• a12673611f Merge remote-tracking branch 'origin/master' Heng Li 2024-03-10 13:49:30 -04:00
• 8140259974 r1183: added lr:hq; fixed transition Heng Li 2024-03-10 13:47:34 -04:00
• f3e59fc2a0 Avoid NULL pointer dereference (#1154) blawrence-ont 2024-01-24 17:32:05 +00:00
• fc2e1607d7 Update paftools.js (#1145) Pesho Ivanov 2024-01-03 17:06:08 +03:00
• bc588c0eeb r1182: improved paftools.js compatibility Heng Li 2023-10-30 16:37:29 -04:00
• ab717023b6 reverted to the previous paftools.js Heng Li 2023-10-30 16:24:18 -04:00
• 9506e7ac3f r1180: paftools.js call compatibility with k8-1.0 Heng Li 2023-10-28 15:54:37 -04:00
• ce03fbc275 Merge remote-tracking branch 'remotes/origin/master' Heng Li 2023-10-24 09:53:51 -04:00
• 98a3aa1b39 document --secondary-seq in manpage Heng Li 2023-10-24 09:52:39 -04:00
• ae05f8485f Add bw_long option to mappy's Aligner class (#1124) Donaim 2023-10-24 13:23:06 +00:00
• ace990c381 Illumina Complete Long Read presets (#1069) Aaron Darling 2023-06-04 22:06:15 +07:00
• e28a55be86 Release minimap2-2.26 (r1175) v2.26 Heng Li 2023-04-29 12:21:09 -04:00
• f8d46a7a30 Revert #868 and use the old setup.py Heng Li 2023-04-29 11:48:41 -04:00
• 4483f89ee5 Release minimap2-2.25 (r1173) v2.25 Heng Li 2023-04-25 12:44:52 -04:00
• f1b3c7ad06 added -ldl for asan on some linux Heng Li 2023-04-25 11:14:15 -04:00
• 180faa3594 r1171: add operator priority explicit with () Heng Li 2023-04-21 11:09:07 -04:00
• 704fbc6f5c An option to output SEQ field for secondary alignment (#687) Mikhail Kolmogorov 2023-04-21 08:06:13 -07:00
• fc24c8a348 r1169: improved kexpand compatibility Heng Li 2023-04-21 10:53:23 -04:00
• e68d868806 use updated kalloc macros (#1051) Chris Seymour 2023-04-21 15:45:53 +01:00
• c3d461e22a mappy check index flags before mapping Alex Payne 2023-01-12 13:22:46 +00:00
• c41518ae85 r1166: sync kalloc with miniwfa and miniprot Heng Li 2023-04-19 21:38:47 -04:00
• 819d843e3c make mm_tbuf_t public Chris Seymour 2023-04-19 10:27:35 +01:00
• 5e7242303c r1164: changed the syntax of -J Heng Li 2023-04-07 22:54:33 -04:00
• a026c69b89 r1163: increased the default -I to 8G Heng Li 2023-04-07 01:22:22 -04:00
• ea2042a577 r1162: fixed a typo; also increased splice pen Heng Li 2023-04-07 01:19:18 -04:00
• 1834b1fd42 r1161: merged the simple and complex models Heng Li 2023-04-06 23:42:50 -04:00
• 7ced0f16a0 r1160: splice model code cleanup Heng Li 2023-04-06 23:32:06 -04:00
• 35732f3025 Merge branch 'master' into splice-model Heng Li 2023-04-06 21:09:18 -04:00
• a6fab118c5 Fixed alignment result final update when computing the exact max value Alberto Zeni 2023-02-28 15:53:11 -05:00
• 6ce0dd8b70 move MM_VERSION define to minimap.h Chris Seymour 2023-03-17 14:26:59 +00:00
• 1d3c3eef03 Add HD header ilne to SAM output Nils Homer 2023-02-13 18:03:53 -07:00
• 01b98e8e52 r1155: fixed a bug on parsing --rmq Heng Li 2023-01-17 09:09:25 -05:00
• 16b8d50199 removed debugging code Heng Li 2023-01-06 11:16:09 -05:00
• 226fd6114c fixed a wrong comment. Resolves #997 Heng Li 2022-11-30 09:22:39 -05:00
• 822ccd1733 r1152: evaluate base Sn and Sp Heng Li 2022-11-01 21:58:45 -04:00
• f67849c9af r1151: added exoneval Heng Li 2022-11-01 21:10:35 -04:00
• b0b199f503 r1150: the prev impl counted one less submer Heng Li 2022-10-21 21:00:22 -04:00
• c2f07ff2ac r1149: implemented random open syncmer Heng Li 2022-10-21 19:07:28 -04:00
• cefd0d9f6c removed -b0 (a typo) Heng Li 2022-10-21 17:37:04 -04:00
• 2a319c89aa support ##PAF lines in GFF3 Heng Li 2022-10-07 19:34:25 -04:00
• 85a5260408 correctly parse ##PAF lines in GFF3 (for miniprot) Heng Li 2022-10-07 19:33:27 -04:00
• 6c2cbf7903 miniprot-like splice model Heng Li 2022-10-06 09:10:17 -04:00
• 5aa4355ca8 extract junctions from GFF Heng Li 2022-09-21 12:57:40 -04:00
• 6ed7263670 junceval for plain junction BED as input Heng Li 2022-09-10 23:18:08 -04:00
• 315795eefd skip unmapped lines Heng Li 2022-09-10 08:48:57 -04:00
• fc6869a9e8 r1141: junceval to support miniprot output Heng Li 2022-09-09 16:28:23 -04:00
• 6252e5e367 sync with tag changes in miniprot Heng Li 2022-09-09 14:48:17 -04:00
• 843729df1e output CDS and stop_codon Heng Li 2022-09-09 12:09:38 -04:00
• 195c98fa46 output dist from end instead Heng Li 2022-09-08 23:35:48 -04:00
• a2e6659d9b output more info Heng Li 2022-09-08 23:18:13 -04:00
• e450f161bb added paf2gff Heng Li 2022-09-08 22:33:21 -04:00
• 15cade0f06 added longcs2fa Heng Li 2022-07-18 22:24:48 -04:00
• 767556b6f0 clarify multi-part index in option -I (#301) Heng Li 2022-06-13 15:50:15 -04:00
• 50a26a60a6 option to keep Ensembl_canonical only Heng Li 2022-05-14 11:18:06 -04:00
• 31de4fd1bc r1132: document misjoin output Heng Li 2022-05-11 21:39:29 -04:00
• e018caea32 added the second minimap2 paper Heng Li 2022-03-01 11:05:09 -05:00
• 7c02742fa8 removed travis CI Heng Li 2022-03-01 11:01:13 -05:00
• a41f5d1eeb Fix indentation Chris Wright 2022-02-14 11:00:01 +00:00
• ed3d0eb328 fix undefined variable Chris Wright 2022-02-11 18:10:45 +00:00
• e6d166a314 Build mappy via Makefile and libminimap2.a Chris Wright 2022-02-05 18:34:30 +00:00
• 06fedaadd0 typo on simde Heng Li 2021-12-26 15:38:06 -05:00
• fe35e679e9 Release minimap2-2.24 (r1122) v2.24 Heng Li 2021-12-26 15:14:54 -05:00
• e25aa5ee74 r1121: change bw_long to bw if bw is longer Heng Li 2021-12-26 14:37:31 -05:00
• 3bde3450a0 r1121: updated obsolete settings in manpage Heng Li 2021-12-26 14:33:14 -05:00
• 36942ff711 r1119: fixed a typo in the new chaining code Heng Li 2021-12-25 12:46:26 -05:00
• d3a89d34d4 r1118: use -r1k,100k for asm* modes Heng Li 2021-12-23 20:43:54 -05:00
• e88e6ea5d5 Update README.md fast-contrib-v2.22 Vasimuddin Md 2021-11-29 14:23:58 +05:30
• 66c90fdb83 updated readme Vasimuddin 2021-11-29 00:52:08 -08:00
• 3b2eca139a fixed AVX options in options.c Vasimuddin 2021-11-28 21:38:56 -08:00
• 23d4edfa31 updated readme and build_index.sh Vasimuddin 2021-11-26 09:53:32 -08:00
• 249c180b29 updated readme Vasimuddin 2021-11-26 08:31:27 -08:00
• 798ea0a4a3 updated the readme Vasimuddin 2021-11-26 08:07:53 -08:00
• bedd87f61f make multi Saurabh 2021-11-26 02:23:36 -08:00
• 03540c47b3 disable chaining for avx2 - clr and hifi Saurabh 2021-11-23 20:13:28 -08:00
• 3b1deac0a5 avx2 seg fault fixed Saurabh 2021-11-19 04:07:01 -08:00
• de90f2e655 cleanup Saurabh 2021-11-18 22:32:43 -08:00
• ba186a4c78 TAL submodule Saurabh 2021-11-18 22:32:05 -08:00
• ba2f19ba37 mm2-fast-v2.22 init Saurabh 2021-11-18 21:14:38 -08:00
• c7cdb758db init fast-contrib v2.22 Saurabh 2021-11-18 17:44:18 -08:00
• c8f0a35c40 r1117: added --no-hash-name for deterministic Heng Li 2021-11-24 16:49:48 -05:00
• fcaadc22b7 r1116: cut long chains at weak points Heng Li 2021-11-20 19:07:44 -05:00
• db37fc43a7 r1115: prepare for chain breaking Heng Li 2021-11-20 13:42:44 -05:00
• a8f1fa8ea3 r1114: retain more candidate inversion alignments Heng Li 2021-11-18 21:37:10 -05:00
• b276772890 r1112: added --print-chains for debugging Heng Li 2021-11-18 21:26:41 -05:00