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b58b97423a703c6a051dbf88efabe0d0e58fa683
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246 Commits

Author SHA1 Message Date
Heng Li
b58b97423a r1281: with --write-junc, ignore aln with low mapQ 2025-04-17 21:46:54 -04:00
Heng Li
a832a42f6f r1270: fixed ts tag for PE reads 
this also fixed the wrong --write-junc
 2025-04-11 01:08:16 -04:00
Heng Li
a5411fc3c0 r1269: added --write-junc 
in preparation for 2-pass
 2025-04-11 01:00:15 -04:00
Heng Li
3542a3d153 r1266: fine tune mapq for short RNA-seq reads 2025-04-07 00:57:39 -04:00
Heng Li
38acd6617f r1261: code clean up; renamed --jump-bed to -j 
Also added --pairing to replace --no-pairing and --pe-ind-chain
 2025-04-06 18:32:58 -04:00
Heng Li
a8094ad859 r1256: working for one example, but still buggy 2025-04-06 10:33:57 -04:00
Heng Li
83e9b2e28c r1242: append /[12] to read name in --frag mode 
Resolve #1079
 2025-04-01 10:48:15 -04:00
Heng Li
4b8b4418df r1236: support paired-end short-read RNA-seq 2025-03-30 19:30:19 -04:00
Heng Li
f51ff1abac r1205: updated lr:hqae 2024-03-20 14:06:59 -04:00
Heng Li
27b254ed6f backup; DON'T USE!!! 2024-03-20 10:21:10 -04:00
Heng Li
4483f89ee5 Release minimap2-2.25 (r1173) 2023-04-25 12:44:52 -04:00
Chris Seymour
819d843e3c make mm_tbuf_t public 2023-04-19 21:32:23 -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
c8f0a35c40 r1117: added --no-hash-name for deterministic 2021-11-24 16:49:48 -05:00
Heng Li
b276772890 r1112: added --print-chains for debugging 2021-11-18 21:26:41 -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
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
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
8a1d52bcbe r1094: for --split-prefix update max_dp at the end 2021-08-06 21:40:43 -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
7e33fde82b dev-r1087: added --cap-kalloc 2021-07-19 21:20:04 -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
15471bd629 Release minimap2-2.20 (r1061) 2021-05-27 15:26:04 -04:00
Heng Li
ca19463268 r1060: safer ways to use -rNUM1,NUM2 2021-05-27 10:55:13 -04:00
Heng Li
34a41197d7 r1051: added two internal parameters 
rmq_rescue_size and rmq_rescue_ratio
 2021-05-24 16:38:45 -04:00
Heng Li
379728726a r1049: removed the long-join heuristics 2021-05-24 16:21:40 -04:00
Heng Li
4f91558160 r1048: rescue long gaps 2021-05-24 16:09:09 -04:00
Heng Li
ec3bc6efd7 r1047: make gap penalty proportional to k-mer 
closer to the older minimap2
 2021-05-24 13:18:17 -04:00
Heng Li
bbb4f97e52 support RMQ 2021-05-03 09:27:04 -04:00
Heng Li
b7f4d8a0f4 removed the old minimap2 chaining 2021-05-02 18:55:37 -04:00
Heng Li
e81927e7a1 prepare to backport unimap/minigraph chaining 2021-05-02 18:25:49 -04:00
Heng Li
feb92d32ea r1025: seed rescuring 2021-04-30 17:33:16 -04:00
Heng Li
cdbd96be0c a bit refactoring for future changes 2021-04-30 11:24:53 -04:00
Heng Li
f995f55610 added --mask-len for #659 2020-08-21 11:12:50 -04:00
Heng Li
9c0e2c67f8 r986: don't estimate dv with --qstrand 2020-04-21 13:21:03 -04:00
Heng Li
da7109fd29 r985: optionally report cs/cg on the query strand 
PAF only; not well tested
 2020-04-21 12:37:35 -04:00
Heng Li
9dceae59a0 r972: renamed --alt-diff to --alt-drop 2020-01-21 10:33:39 -05:00
Heng Li
eb3ed6993d support ALT mapping 2020-01-21 09:17:50 -05:00
Heng Li
d2e14705e7 r968: allow large mini_batch; resolves #491 2020-01-18 12:24:44 -05:00
Heng Li
040f74102c r965: added --chain-gap-scale for #540 2020-01-18 10:29:33 -05:00
John Marshall
20c104ce8d Report errno on file opening failures and I/O errors 
Add the underlying operating system error (usually "No such file" or
"Out of space" respectively, but highly informative when it is not)
to these error messages.
 2019-07-17 09:04:02 -04:00
Heng Li
c2aec88b84 r938: added --sam-hit-only; resolved #377 2019-04-30 22:40:36 -04:00
Heng Li
d431dc0181 r917: added --max-chain-iter to avoid worst case 
Resolves #324
 2019-02-27 14:41:01 -05:00
Heng Li
1739a260fb r913: output tag "rl", length of unseedable regs 2019-02-05 14:19:17 -05:00
Heng Li
ea2b1c5b2a r894: added --max-qlen to filter out long query 2018-12-12 12:27:32 -05:00
Heng Li
1077b7ddc8 r846: added --hard-mask-level for #244 2018-09-27 14:46:26 -04:00
Heng Li
b32296e18f r821: fixed memory when -y is used 2018-07-31 15:14:37 -04:00