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127 Commits

Author SHA1 Message Date
Heng Li
3c28777e7e Release minimap2-2.31 (r1302) 2026-05-19 18:39:04 -04:00
Heng Li
d8371a403b removed duplicate check in sim2bed 2026-04-25 00:35:59 -04:00
Heng Li
e5066c7976 added sim2bed to convert simulated read names to BED 
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
 2026-04-25 00:22:26 -04:00
Heng Li
37a650f58c output simulated identity with badread 2026-04-14 12:49:35 -04:00
Heng Li
4ca5a951ca command line help 2026-04-13 23:52:07 -04:00
Heng Li
ca6f4dc5e2 convert badread output to evaluation format 2026-04-13 23:43:11 -04:00
Alex Leonard
6d49eb690f convert unmapped reads in sam2paf (#1324) 2025-10-05 19:43:23 -04:00
Heng Li
79c9cc186b Release minimap2-2.30 (r1287) 2025-06-15 17:54:11 -04:00
Heng Li
005c9a1f6b exoneval may skip terminal exons in aa mode 2025-05-17 23:06:41 -04:00
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
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
15118dd521 output #mismatches/#dels/#ins in view 2021-07-18 15:13:40 -04:00