Heng Li
af094640e5
r1263: ~5-10% performance improvement
...
Via larger batches and more short-read heuristics. Identical alignment on 2
million reads. Short DNA-seq read alignment may be improved in corner cases.
2025-04-06 20:48:55 -04:00
Heng Li
38acd6617f
r1261: code clean up; renamed --jump-bed to -j
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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
9ede5c4255
backup
2025-04-06 00:07:15 -04:00
Heng Li
bbf0bb871b
r1245: allow shorter hits for splice:sr
2025-04-02 00:13:37 -04:00
Heng Li
e816fd071c
r1241: error out on unintended --score-N
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Resolve #1226
2025-04-01 10:12:53 -04:00
Heng Li
bdf46f5786
r1238: resolve #589
2025-03-31 23:08:37 -04:00
Heng Li
4b8b4418df
r1236: support paired-end short-read RNA-seq
2025-03-30 19:30:19 -04:00
Heng Li
54f8e5f7d6
r1234: added splice:sr for SE RNA-seq
2025-03-30 15:54:12 -04:00
Heng Li
042c8d4d71
added --junc-pen; it does nothing for now
2024-10-11 21:27:25 -04:00
Heng Li
e4e1f7843b
backup for spsc
2024-10-10 22:43:50 -04:00
Heng Li
119bdc6029
r1207: reduced cap_kalloc from 1G to 500M
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This reduces the peak memory.
2024-03-20 15:53:12 -04:00
Heng Li
89d4d219cd
r1206: enabled RMQ for lr:hqae
...
Also fixed a bug in determining inner_dist for RMQ. It should have no effect on
previous presets.
2024-03-20 15:29:54 -04:00
Heng Li
f51ff1abac
r1205: updated lr:hqae
2024-03-20 14:06:59 -04:00
Heng Li
c881b14ba5
r1203: added preset lr:hqae
2024-03-20 00:25:57 -04:00
Heng Li
8140259974
r1183: added lr:hq; fixed transition
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* Added the lr:hq preset suggested by Nanopore developers (#1127 )
* Fixed transition scoring. It did not work with presets.
* Cleaned up preset documentation
2024-03-10 13:47:34 -04:00
Aaron Darling
ace990c381
Illumina Complete Long Read presets ( #1069 )
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* Implements a transition-aware alignment scoring scheme and configuration presets for ICLR
* Fix to enable use of general scoring matrix in ksw as suggested by lh3
---------
Co-authored-by: koadman <>
2023-06-04 11:06:15 -04:00
Heng Li
a026c69b89
r1163: increased the default -I to 8G
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To reduce accidental errors when mapping against diploid human assemblies.
2023-04-07 01:22:22 -04:00
Heng Li
e25aa5ee74
r1121: change bw_long to bw if bw is longer
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Resolve #852
2021-12-26 14:37:31 -05:00
Heng Li
d3a89d34d4
r1118: use -r1k,100k for asm* modes
2021-12-23 20:43:54 -05:00
Heng Li
ac334639ce
r1110: default --cap-kalloc=1g; test more inv
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See #816 and #823
2021-10-11 14:45:15 -04:00
Heng Li
546623dcb4
r1109: disable chain_skip_scale by default
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Enabling the option slows down alignment, possibly because it fragments chains
in difficult regions.
2021-10-04 21:24:35 -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 )
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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
161ae7ff73
dev-r1079: per-read error rate
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more tuning needed
2021-07-18 20:38:53 -04:00
Heng Li
8a6edab847
dev-r1078: decoupling ranking penalty
2021-07-18 16:22:48 -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
41d7ccb191
r1052: default -g to 5k
2021-05-24 16:46:16 -04:00
Heng Li
34a41197d7
r1051: added two internal parameters
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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
6c96078ed0
r1034: changed multiple defaults; updated manpage
2021-05-03 22:51:34 -04:00
Heng Li
bbb4f97e52
support RMQ
2021-05-03 09:27:04 -04:00
Heng Li
0f5608c4a4
r1028: backport minigraph -U
2021-05-01 15:41:39 -04:00
Heng Li
e8823a3709
r1027: renamed hifi to map-hifi; changed default
2021-05-01 15:22:51 -04:00
Heng Li
7edeec67b0
r1026: fixed bugs in seed sampling add hifi
2021-05-01 15:07:56 -04:00
Heng Li
feb92d32ea
r1025: seed rescuring
2021-04-30 17:33:16 -04:00
Heng Li
f995f55610
added --mask-len for #659
2020-08-21 11:12:50 -04:00
Heng Li
da7109fd29
r985: optionally report cs/cg on the query strand
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PAF only; not well tested
2020-04-21 12:37:35 -04:00
Heng Li
a7a01fe5bd
r973: fixed compiling errors caused
2020-01-21 10:43:31 -05:00
Heng Li
eb3ed6993d
support ALT mapping
2020-01-21 09:17:50 -05:00
Heng Li
040f74102c
r965: added --chain-gap-scale for #540
2020-01-18 10:29:33 -05:00
Heng Li
6762368cf0
r940: added the splice:hq preset
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for high-quality CCS/mRNA splice alignment
2019-05-04 14:00:31 -04:00
Heng Li
be171aa2dc
implemented in exts; testing is the next
2019-04-28 16:47:12 -04:00
Heng Li
d431dc0181
r917: added --max-chain-iter to avoid worst case
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Resolves #324
2019-02-27 14:41:01 -05:00
Heng Li
5e55e397e9
r882: guard against -E0 ( #263 )
2018-11-05 23:36:12 -05:00
Heng Li
170863e553
r849: option -P doesn't work
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I don't know why I haven't found it at the beginning.
2018-10-04 16:11:59 -04:00
Heng Li
ff9917a1c4
r819: mappy to support cs/MD
2018-07-24 23:29:55 -04:00
