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
d43f356ef9
fixed minor grammar issues
2025-04-06 18:35:46 -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
3d351267a0
document --jump-bed
2025-04-06 17:43:11 -04:00
Heng Li
54a4718c9b
r1259: --jump-bed now functional
2025-04-06 17:12:49 -04:00
Heng Li
dbc12b2838
r1258: update blen, mlen and dp_max0
2025-04-06 15:26:01 -04:00
Heng Li
2ed264db4e
r1257: fixed the sorting of BED files
2025-04-06 10:53:16 -04:00
Heng Li
a8094ad859
r1256: working for one example, but still buggy
2025-04-06 10:33:57 -04:00
Heng Li
1877818239
r1255: moved jump code to a separate file
2025-04-06 09:33:51 -04:00
Heng Li
9ede5c4255
backup
2025-04-06 00:07:15 -04:00
Heng Li
405511fe8d
Merge branch 'master' into junc-jump
2025-04-04 16:37:39 -04:00
Heng Li
dd90d9dde6
caution that the splice:sr is experimental
2025-04-04 16:34:40 -04:00
Heng Li
a8c567b5e9
r1251: read junctions for jumps
2025-04-04 16:23:19 -04:00
Heng Li
d9d3c0cc3f
refactored --junc-bed
2025-04-03 21:02:50 -04:00
Heng Li
cbe8d61ca4
r1249: remove redundant junctions in --junc-bed
2025-04-03 20:43:06 -04:00
Heng Li
9d06cef13e
r1248: support --end-bonus in splice mode
...
but this is not enabled by default for now
2025-04-02 21:39:41 -04:00
Heng Li
924fc4d671
minor
2025-04-02 13:06:03 -04:00
Heng Li
fc2d1e95b3
document splice:sr in README
2025-04-02 11:24:44 -04:00
Heng Li
bbf0bb871b
r1245: allow shorter hits for splice:sr
2025-04-02 00:13:37 -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
e816fd071c
r1241: error out on unintended --score-N
...
Resolve #1226
2025-04-01 10:12:53 -04:00
Heng Li
a955b1f31d
documented zd; resolve #1108
2025-04-01 09:34:05 -04:00
Heng Li
54fa925e2e
r1240: fixed wrong logging information
...
resolve #1192
2025-04-01 09:17:39 -04:00
Heng Li
d4a396c5c3
r1239: resovled #963
2025-03-31 23:15:34 -04:00
Heng Li
bdf46f5786
r1238: resolve #589
2025-03-31 23:08:37 -04:00
Heng Li
f536b69b81
r1237: documented -x splice:sr
2025-03-30 21:47:47 -04:00
Heng Li
4b8b4418df
r1236: support paired-end short-read RNA-seq
2025-03-30 19:30:19 -04:00
Heng Li
ce30004e02
r1235: allow --splice and --frag at the same time
...
This seems to largely work, though the accuracy is reduced and no pairs are
proper. More investigation needed for practical uses.
2025-03-30 16:32:38 -04:00
Heng Li
54f8e5f7d6
r1234: added splice:sr for SE RNA-seq
2025-03-30 15:54:12 -04:00
Heng Li
2857de7dbd
Merge remote-tracking branch 'remotes/origin/master'
2025-03-29 22:44:26 -04:00
Heng Li
e18935fbad
r1230: make juncevla work for paired-end SAM
2025-03-29 22:43:44 -04:00
Chang Y
74ebfb2532
fix error ( #1223 )
2025-03-21 18:21:15 -04:00
Martin Grigorov
a0cbe2e4d2
Add CI job for Linux & Mac ARM64 too ( #1205 )
...
* Add CI job for Linux ARM64 too
Signed-off-by: Martin Tzvetanov Grigorov <mgrigorov@apache.org >
* Add build job for Mac ARM64 too
Signed-off-by: Martin Tzvetanov Grigorov <mgrigorov@apache.org >
* Pass "arm_neon=1 aarch64=1" when building on ARM64
Signed-off-by: Martin Tzvetanov Grigorov <mgrigorov@apache.org >
* change aarch64 to arm64 for the Mac ARM64 check
Signed-off-by: Martin Tzvetanov Grigorov <mgrigorov@apache.org >
---------
Signed-off-by: Martin Tzvetanov Grigorov <mgrigorov@apache.org >
2025-03-21 18:19:26 -04:00
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
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
