Heng Li
94d171b01e
r1276: skip unnecessary reverse spliced alignment
...
for short-read RNA-seq only
2025-04-14 14:57:23 -04:00
Heng Li
ff312a2957
documented 2-pass in README
2025-04-13 17:14:44 -04:00
Heng Li
01ccedd5a0
r1275: renamed --jump-pass1 to --pass1
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Also documented 2-pass
2025-04-13 17:07:39 -04:00
Heng Li
819b3bf017
r1274: a little better pass-1
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Also fixed a bug in jump
2025-04-13 13:55:15 -04:00
Heng Li
e88110463a
r1273: reading pass1 junctions works
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but we need extra logic when using them. Tomorrow.
2025-04-13 00:47:28 -04:00
Heng Li
fb81e150f2
r1272: support pass-1 junction processing
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NOT tested yet
2025-04-12 23:15:04 -04:00
Heng Li
d930ea94ad
r1271: code refactoring in prep for 2-pass
2025-04-11 17:20:34 -04:00
Heng Li
a832a42f6f
r1270: fixed ts tag for PE reads
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this also fixed the wrong --write-junc
2025-04-11 01:08:16 -04:00
Heng Li
a5411fc3c0
r1269: added --write-junc
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in preparation for 2-pass
2025-04-11 01:00:15 -04:00
Heng Li
bd03d975fc
r1268: avoid extra small introns
2025-04-07 23:32:56 -04:00
Heng Li
9c3c4b1ce8
r1267: penalize introns without signals
2025-04-07 09:51:33 -04:00
Heng Li
3542a3d153
r1266: fine tune mapq for short RNA-seq reads
2025-04-07 00:57:39 -04:00
Heng Li
75619c7b51
r1265: prefer spliced alignment
...
mapq needs to be elevated
2025-04-07 00:31:04 -04:00
Heng Li
fbb9c0fcba
r1264: added --jump-min-match, default to 3
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To match STAR
2025-04-06 23:18:55 -04:00
Heng Li
af094640e5
r1263: ~5-10% performance improvement
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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
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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
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
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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
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Resolve #1079
2025-04-01 10:48:15 -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
a955b1f31d
documented zd; resolve #1108
2025-04-01 09:34:05 -04:00
Heng Li
54fa925e2e
r1240: fixed wrong logging information
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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
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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 )
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* 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