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1,205 Commits 9 Branches 35 Tags
v2.29
Commit Graph

193 Commits

Author SHA1 Message Date
Heng Li
1fd85be6e2 Release minimap2-2.29 (r1283) 2025-04-18 13:41:47 -04:00
Heng Li
e18935fbad r1230: make juncevla work for paired-end SAM 2025-03-29 22:43:44 -04:00
Heng Li
618d33515e more condition on length differences 2024-11-17 19:45:46 -05:00
Heng Li
a10d4f4496 merge colinear blocks 2024-11-17 15:17:13 -05:00
Heng Li
1eea2fee11 a new script to cluster similar sequences 2024-11-16 16:39:13 -05:00
Heng Li
1d346d56bc Merge remote-tracking branch 'remotes/origin/master' 2024-11-16 16:36:07 -05:00
Heng Li
46750de966 not working well and rarely used in practice 2024-11-16 16:35:24 -05:00
James Webber
c6db201b38 Update README.md (#1245) 
fixed documentation for paftools
 2024-11-15 08:54:25 -05:00
Heng Li
a4c93e9377 support X and = in mapeval 2024-10-12 23:31:17 -04:00
Heng Li
0cc3cdca27 ignore filtered SVs in sveval 2024-04-07 17:12:31 -04:00
Heng Li
8170693de3 Release minimap2-2.28 (r1209) 2024-03-27 10:57:17 -04:00
Heng Li
c7433c2811 r1197: sam2paf to output primary only 2024-03-19 21:47:31 -04:00
Heng Li
98c23bc6d2 r1194: output NM in sam2paf 2024-03-19 09:55:16 -04:00
Heng Li
b6762503a9 Release minimap2-2.27 (r1193) 2024-03-12 13:20:07 -04:00
Heng Li
ba60aac6f6 r1191: fixed wrong reverse() and revcomp() 
due to k8 incompatibility. Resolves #1161
 2024-03-11 22:09:01 -04:00
Heng Li
0efc886012 r1189: fixed an out-of-memory issue 
Resolves #1166
 2024-03-11 10:14:20 -04:00
Pesho Ivanov
fc2e1607d7 Update paftools.js (#1145) 
In mapeval "-Q INT" reports wrong alignments with mapQ>=INT, not with mapQ>INT
 2024-01-03 09:06:08 -05:00
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
e28a55be86 Release minimap2-2.26 (r1175) 2023-04-29 12:21:09 -04:00
Heng Li
4483f89ee5 Release minimap2-2.25 (r1173) 2023-04-25 12:44:52 -04:00
Heng Li
16b8d50199 removed debugging code 2023-01-06 11:16:09 -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
2a319c89aa support ##PAF lines in GFF3 2022-10-07 19:34:25 -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
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
fe35e679e9 Release minimap2-2.24 (r1122) 2021-12-26 15:14:54 -05:00
Heng Li
d0cff3eb36 Release minimap2-2.23 (r1111) 2021-11-18 17:11:48 -05:00
Heng Li
7ee62dae1d updated manuscript 2021-10-01 11:42:36 -04:00
Heng Li
7358a1ead1 Release minimap2-2.22 (r1101) 2021-08-07 11:30:31 -04:00
Heng Li
a05edfa5ec a different ending sentence 2021-08-07 10:38:48 -04:00
Heng Li
f7271a7c24 expose mapQ threshold to command line of pafcmp 2021-08-06 19:41:46 -04:00
Heng Li
9d049f0562 added pafcmp 2021-08-05 12:41:21 -04:00
Heng Li
629c11728e output the number of mismatches 2021-08-04 17:05:06 -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
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