704fbc6f5c
An option to output SEQ field for secondary alignment ( #687 )
...
* a new option --secondary-seq to output SEQ field for secondary alignments
* comments removed
* Fixed a conflict in #687
---------
Co-authored-by: Heng Li <lh3@me.com>
2023-04-21 11:06:13 -04:00
fc24c8a348
r1169: improved kexpand compatibility
2023-04-21 10:53:23 -04:00
e68d868806
use updated kalloc macros ( #1051 )
...
* use updated kalloc macros
* review
* get the reference
* store the reference
* last one
2023-04-21 10:45:53 -04:00
c3d461e22a
mappy check index flags before mapping
...
mappy creates a CIGAR string by default (`-c` flag) and so is
incompatible with indexes that are created using the `--idx-no-seq`
flag.
The previous implementation of mappy did not check for the `MM_I_NO_SEQ`
flag and would seg fault when attempting to map a read or retrieve a
reference sequence from the index. This patch adds a check to both
`mappy.Aligner.seq` and `mappy.Aligner.map` and returns `None` if there
is no index sequences. I've chose `None` as this is inline with the
behaviour of mappy for reads that do not align/retreiving sequences that
aren't in the index, however it might be better to raise an exception so
that this error is distinct and can be communicated to the caller.
2023-04-19 21:49:58 -04:00
c41518ae85
r1166: sync kalloc with miniwfa and miniprot
2023-04-19 21:38:47 -04:00
819d843e3c
make mm_tbuf_t public
2023-04-19 21:32:23 -04:00
5e7242303c
r1164: changed the syntax of -J
2023-04-07 22:54:33 -04:00
a026c69b89
r1163: increased the default -I to 8G
...
To reduce accidental errors when mapping against diploid human assemblies.
2023-04-07 01:22:22 -04:00
ea2042a577
r1162: fixed a typo; also increased splice pen
...
Now slightly better on ISO-seq
2023-04-07 01:19:18 -04:00
1834b1fd42
r1161: merged the simple and complex models
2023-04-06 23:42:50 -04:00
7ced0f16a0
r1160: splice model code cleanup
2023-04-06 23:32:06 -04:00
35732f3025
Merge branch 'master' into splice-model
2023-04-06 21:09:18 -04:00
a6fab118c5
Fixed alignment result final update when computing the exact max value
2023-04-06 21:05:24 -04:00
6ce0dd8b70
move MM_VERSION define to minimap.h
2023-03-17 20:58:43 +01:00
1d3c3eef03
Add HD header ilne to SAM output
...
#905
2023-02-14 09:12:03 -05:00
01b98e8e52
r1155: fixed a bug on parsing --rmq
...
resolves #1010
2023-01-17 09:09:25 -05:00
16b8d50199
removed debugging code
2023-01-06 11:16:09 -05:00
226fd6114c
fixed a wrong comment. Resolves #997
2022-11-30 09:22:39 -05:00
822ccd1733
r1152: evaluate base Sn and Sp
2022-11-01 21:58:45 -04:00
f67849c9af
r1151: added exoneval
2022-11-01 21:10:35 -04:00
b0b199f503
r1150: the prev impl counted one less submer
2022-10-21 21:00:22 -04:00
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
cefd0d9f6c
removed -b0 (a typo)
2022-10-21 17:37:04 -04:00
2a319c89aa
support ##PAF lines in GFF3
2022-10-07 19:34:25 -04:00
85a5260408
correctly parse ##PAF lines in GFF3 (for miniprot)
2022-10-07 19:33:27 -04:00
6c2cbf7903
miniprot-like splice model
...
slightly worse on iso-seq and slightly better on direct-RNA
2022-10-06 09:10:17 -04:00
5aa4355ca8
extract junctions from GFF
2022-09-21 12:57:40 -04:00
6ed7263670
junceval for plain junction BED as input
2022-09-10 23:18:08 -04:00
315795eefd
skip unmapped lines
2022-09-10 08:48:57 -04:00
fc6869a9e8
r1141: junceval to support miniprot output
2022-09-09 16:28:23 -04:00
6252e5e367
sync with tag changes in miniprot
2022-09-09 14:48:17 -04:00
843729df1e
output CDS and stop_codon
2022-09-09 12:09:38 -04:00
195c98fa46
output dist from end instead
2022-09-08 23:35:48 -04:00
a2e6659d9b
output more info
2022-09-08 23:18:13 -04:00
e450f161bb
added paf2gff
2022-09-08 22:33:21 -04:00
15cade0f06
added longcs2fa
2022-07-18 22:24:48 -04:00
767556b6f0
clarify multi-part index in option -I ( #301 )
2022-06-13 15:50:15 -04:00
50a26a60a6
option to keep Ensembl_canonical only
2022-05-14 11:18:06 -04:00
31de4fd1bc
r1132: document misjoin output
...
Also additional check of centromeric breakpoints
2022-05-11 21:39:29 -04:00
e018caea32
added the second minimap2 paper
2022-03-01 11:05:09 -05:00
7c02742fa8
removed travis CI
2022-03-01 11:01:13 -05:00
a41f5d1eeb
Fix indentation
2022-03-01 10:41:01 -05:00
ed3d0eb328
fix undefined variable
2022-03-01 10:41:01 -05:00
e6d166a314
Build mappy via Makefile and libminimap2.a
2022-03-01 10:41:01 -05:00
06fedaadd0
typo on simde
2021-12-26 15:38:06 -05:00
fe35e679e9
Release minimap2-2.24 (r1122)
2021-12-26 15:14:54 -05:00
e25aa5ee74
r1121: change bw_long to bw if bw is longer
...
Resolve #852
2021-12-26 14:37:31 -05:00
3bde3450a0
r1121: updated obsolete settings in manpage
...
Resolve #851
2021-12-26 14:33:14 -05:00
36942ff711
r1119: fixed a typo in the new chaining code
...
Not affecting v2.23
2021-12-25 12:46:26 -05:00
d3a89d34d4
r1118: use -r1k,100k for asm* modes
2021-12-23 20:43:54 -05:00
Mikhail Kolmogorov
Heng Li
Chris Seymour
Alex Payne
Alberto Zeni
Nils Homer
Chris Wright