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
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Co-authored-by: koadman <>
2023-06-04 11:06:15 -04:00
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
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
d3a89d34d4
r1118: use -r1k,100k for asm* modes
2021-12-23 20:43:54 -05:00
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
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
aefa2c0d86
added --chain-skip-scale
2021-10-01 16:58:03 -04:00
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
161ae7ff73
dev-r1079: per-read error rate
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more tuning needed
2021-07-18 20:38:53 -04:00
8a6edab847
dev-r1078: decoupling ranking penalty
2021-07-18 16:22:48 -04:00
b046052d82
Merge branch 'master' into utec
2021-07-16 13:32:47 -04:00
15471bd629
Release minimap2-2.20 (r1061)
2021-05-27 15:26:04 -04:00
ca19463268
r1060: safer ways to use -rNUM1,NUM2
2021-05-27 10:55:13 -04:00
41d7ccb191
r1052: default -g to 5k
2021-05-24 16:46:16 -04:00
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
379728726a
r1049: removed the long-join heuristics
2021-05-24 16:21:40 -04:00
4f91558160
r1048: rescue long gaps
2021-05-24 16:09:09 -04:00
6c96078ed0
r1034: changed multiple defaults; updated manpage
2021-05-03 22:51:34 -04:00
bbb4f97e52
support RMQ
2021-05-03 09:27:04 -04:00
0f5608c4a4
r1028: backport minigraph -U
2021-05-01 15:41:39 -04:00
e8823a3709
r1027: renamed hifi to map-hifi; changed default
2021-05-01 15:22:51 -04:00
7edeec67b0
r1026: fixed bugs in seed sampling add hifi
2021-05-01 15:07:56 -04:00
feb92d32ea
r1025: seed rescuring
2021-04-30 17:33:16 -04:00
f995f55610
added --mask-len for #659
2020-08-21 11:12:50 -04:00
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
a7a01fe5bd
r973: fixed compiling errors caused
2020-01-21 10:43:31 -05:00
eb3ed6993d
support ALT mapping
2020-01-21 09:17:50 -05:00
040f74102c
r965: added --chain-gap-scale for #540
2020-01-18 10:29:33 -05:00
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
be171aa2dc
implemented in exts; testing is the next
2019-04-28 16:47:12 -04:00
d431dc0181
r917: added --max-chain-iter to avoid worst case
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Resolves #324
2019-02-27 14:41:01 -05:00
5e55e397e9
r882: guard against -E0 ( #263 )
2018-11-05 23:36:12 -05:00
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
ff9917a1c4
r819: mappy to support cs/MD
2018-07-24 23:29:55 -04:00
6908dc59a5
--splice implied when searching for splicing sites on single strand
2018-07-05 07:41:26 -04:00
2584a4149a
r295: use -r2000 for ava-ont, NOT for ava-pb
2018-06-20 12:24:43 -04:00
7e6e8ca73f
r792: fixed -Wextra warnings and resolved #184
2018-06-19 15:26:58 -04:00
734ac379bb
r770: matching N bases not working properly ( #155 )
2018-04-30 19:55:23 -04:00
ee4cd089f7
r763: fine control long join flank len ( #128 )
2018-03-29 14:16:58 -04:00
5ef9580b17
r753: change bandwidth in ava-ont to 2000bp
2018-03-23 10:15:23 -04:00
bdc615c1d4
r741: added --min-occ-floor to improve #107
2018-03-12 14:32:27 -04:00
24a4808826
r718: retrieve sequence from the index
2018-02-23 10:18:26 -05:00
1372977a37
r708: implemented double Z-drop thresholds ( #112 )
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When aligning long reads, we would prefer to align through low-quality
regions. This requires a large Z-drop threshold. However, to find small
inversions, we need to use a small Z-drop. This commit address this
conflict with two Z-drop thresholds. When Z-drop exceeds the smaller
threshold, we perform a local alignment to check if there is a potential
inversion. If there is one, we break the alignment; otherwise we break
the alignment only if Z-drop excess the larger threshold.
This commit also fixes a bug that reported wrong coordinates when the
inversion is on the forward strand (#112 ).
2018-02-15 10:50:49 -05:00
7ef5490884
r703: added --max-clip-ratio
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still testing the option
2018-02-12 13:29:18 -05:00
29b4a1786c
r685: tune end seed filter again
2018-02-05 11:48:22 -05:00
dbf284b2d9
r684: separate end score from min_chain_score
2018-02-05 11:40:38 -05:00
da6947cfa3
r671: cleanup command line options
2018-01-31 13:59:52 -05:00
d676a5314b
r664: use --heat-sort for sr by default
2018-01-26 12:25:42 -05:00
123bc1d91d
put option operations in another file
2018-01-26 08:38:37 -05:00
Aaron Darling
Heng Li
Maël Kerbiriou