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
Leon Rauschning
7d8bbb74a8
Add sc_ambi and max_chain_skip parameters to mappy.pyx ( #1240 )
...
* add sc_ambi option to cython interface
* add max_gaplen param
* set max_chain_skip to arg instead of forcing 255
2024-11-15 08:56:36 -05:00
James Webber
c6db201b38
Update README.md ( #1245 )
...
fixed documentation for paftools
2024-11-15 08:54:25 -05:00
Rob Patro and Rob Patro
358a39850f
Allow passing read name to mappy ( #1260 )
...
* Allow passing read name to mappy
This adds the (optional) ability to pass the read
name to the mappy `map` method. Without the
read name, the call to `map` can sometimes give
different output than the command line version
of `minimap2` because of the way minimap uses
the hash of the read name to break ties in ordering
hits. This can affect which / if certain
supplementary alignments are generated, and even
which / if non-primary alignments are generated.
* Pass name directly to mm_map_aux
Get rid of additional function, and always
accept the name parameter in the mm_map_aux
function (can be nullptr if not available).
---------
Co-authored-by: Rob Patro <rob@newton>
2024-11-15 08:51:10 -05:00
Heng Li
fcb5d5e6eb
r1221: warn about file reading errors
...
Resolves #1229
2024-10-15 22:44:06 -04:00
Heng Li
95807a2224
added "junc_pen" to python accordingly
2024-10-13 23:58:33 -04:00
Heng Li
a4c93e9377
support X and = in mapeval
2024-10-12 23:31:17 -04:00
Heng Li
7d69334e69
Merge remote-tracking branch 'remotes/origin/master'
2024-10-12 23:28:38 -04:00
Heng Li
3e1ab2951d
document --spsc
2024-10-12 23:27:46 -04:00
Heng Li
68179ed195
r1215: scoring apparently works
2024-10-12 22:29:27 -04:00
Heng Li
d1f4c8d232
implemented ksw scoring; not tested
2024-10-11 23:58:18 -04:00
Heng Li
8efe83b744
fill the junction array
...
modifying ksw will be the next
2024-10-11 23:22:23 -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
Marcus Fedarko
69e3629916
Mention in man page that CIGAR strings in SA tags are approximate ( #1213 )
...
* Mention approx CIGAR strings in man page #724
* Fix FAQ typo
2024-05-22 15:58:33 -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
e3d8c708ac
r1208: reverted RMQ gap coefficient
...
Such that minimap2 can give the same alignment in other modes
2024-03-27 08:48:10 -04:00
Heng Li
119bdc6029
r1207: reduced cap_kalloc from 1G to 500M
...
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
27b254ed6f
backup; DON'T USE!!!
2024-03-20 10:21:10 -04:00
Heng Li
c881b14ba5
r1203: added preset lr:hqae
2024-03-20 00:25:57 -04:00
Heng Li
f18dadb1c4
r1202: halved RMQ gap cost
2024-03-19 23:47:54 -04:00
Heng Li
a83b8fe7cc
r1201: renamed --dbg-seed-freq to --dbg-seed-occ
2024-03-19 21:53:09 -04:00
Heng Li
c22bfe7722
r1200: added --rmq-inner and --dbg-seed-freq
2024-03-19 21:52:07 -04:00
Heng Li
12d441ea22
Merge remote-tracking branch 'origin/master'
2024-03-19 21:47:52 -04:00
Heng Li
c7433c2811
r1197: sam2paf to output primary only
2024-03-19 21:47:31 -04:00
Joyjit Daw
5279377544
Fix MD generation check in SAM writing ( #1181 )
...
The existing logic checked for is_MD == 1, but
the function is called with a bitwise operator check
which does not evaluate to 1.
2024-03-19 19:20:21 -04:00
Heng Li
acab05781e
Merge remote-tracking branch 'remotes/origin/master'
2024-03-19 09:56:13 -04:00
Heng Li
98c23bc6d2
r1194: output NM in sam2paf
2024-03-19 09:55:16 -04:00
kojix2
9b0ff2418c
Fix mm_mapopt_t in Mappy ( #1177 )
...
Add transition. Related to #1069
2024-03-13 22:15:46 -04:00
Heng Li
b6762503a9
Release minimap2-2.27 (r1193)
2024-03-12 13:20:07 -04:00
Heng Li
9667468e89
NEWS draft
2024-03-11 22:46:47 -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
fcd4df2a73
r1190: output unadjusted dp_max to ms:i
...
This was an oversight affecting v2.22+. The latest minimap2 ranks hits and
estimates mapping quality with an adjusted alignment score (see the minimap2
update paper). This score however is not calculated when there is only one hit.
As a result, the ms:i tag varies depends on other sequences in the reference
genome, which is confusing. This change lets minimap2 to output the unadjusted
score at ms:i. At present, the adjusted score is not outputted.
Resolves #1146
2024-03-11 17:19:13 -04:00
Heng Li
0efc886012
r1189: fixed an out-of-memory issue
...
Resolves #1166
2024-03-11 10:14:20 -04:00
Heng Li
940388f8e4
r1188: added --ds to output tag ds
...
Adapted from minigraph
2024-03-10 15:01:13 -04:00
Heng Li
23d2674c39
r1187: set stage for the ds tag; not added yet
2024-03-10 14:12:56 -04:00
Heng Li
a12673611f
Merge remote-tracking branch 'origin/master'
2024-03-10 13:49:30 -04:00
Heng Li
8140259974
r1183: added lr:hq; fixed transition
...
* 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
blawrence-ont
f3e59fc2a0
Avoid NULL pointer dereference ( #1154 )
...
If the allocated region is 0 bytes then it's unsafe to dereference it.
Fixes #1147 .
2024-01-24 12:32:05 -05:00
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