Heng Li
fb81e150f2
r1272: support pass-1 junction processing
...
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
a5411fc3c0
r1269: added --write-junc
...
in preparation for 2-pass
2025-04-11 01:00:15 -04:00
Heng Li
3542a3d153
r1266: fine tune mapq for short RNA-seq reads
2025-04-07 00:57:39 -04:00
Heng Li
a8094ad859
r1256: working for one example, but still buggy
2025-04-06 10:33:57 -04:00
Heng Li
9ede5c4255
backup
2025-04-06 00:07:15 -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
83e9b2e28c
r1242: append /[12] to read name in --frag mode
...
Resolve #1079
2025-04-01 10:48:15 -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
c22bfe7722
r1200: added --rmq-inner and --dbg-seed-freq
2024-03-19 21:52:07 -04:00
Heng Li
4483f89ee5
Release minimap2-2.25 (r1173)
2023-04-25 12:44:52 -04:00
Heng Li
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
Heng Li
b276772890
r1112: added --print-chains for debugging
2021-11-18 21:26:41 -05:00
Heng Li
39bdd45875
r1108: fixed missing inversions for #816 and #806
2021-10-04 16:34:30 -04:00
Heng Li
05a8a45d44
r1105: avoid long running time occasionally ( #771 )
...
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
Heng Li
8a1d52bcbe
r1094: for --split-prefix update max_dp at the end
2021-08-06 21:40:43 -04:00
Heng Li
83a535f148
dev-r1084: fixed flag integer overflow
2021-07-19 11:52:18 -04:00
Heng Li
161ae7ff73
dev-r1079: per-read error rate
...
more tuning needed
2021-07-18 20:38:53 -04:00
Heng Li
2546999639
dev-r1076: log gap penalty
2021-07-17 18:23:59 -04:00
Heng Li
b046052d82
Merge branch 'master' into utec
2021-07-16 13:32:47 -04:00
Heng Li
379728726a
r1049: removed the long-join heuristics
2021-05-24 16:21:40 -04:00
Heng Li
e81927e7a1
prepare to backport unimap/minigraph chaining
2021-05-02 18:25:49 -04:00
Heng Li
feb92d32ea
r1025: seed rescuring
2021-04-30 17:33:16 -04:00
Heng Li
cdbd96be0c
a bit refactoring for future changes
2021-04-30 11:24:53 -04:00
Heng Li
f995f55610
added --mask-len for #659
2020-08-21 11:12:50 -04:00
Heng Li
da7109fd29
r985: optionally report cs/cg on the query strand
...
PAF only; not well tested
2020-04-21 12:37:35 -04:00
Jared Simpson
d2de282d21
remove second definition of kstring
2020-03-02 13:18:37 -05:00
Heng Li
eb3ed6993d
support ALT mapping
2020-01-21 09:17:50 -05:00
Heng Li
040f74102c
r965: added --chain-gap-scale for #540
2020-01-18 10:29:33 -05:00
Heng Li
3c0d05d272
r962: abort given wrong RG line; resolves #541
2020-01-06 21:53:21 -05:00
Heng Li
d431dc0181
r917: added --max-chain-iter to avoid worst case
...
Resolves #324
2019-02-27 14:41:01 -05:00
Heng Li
1739a260fb
r913: output tag "rl", length of unseedable regs
2019-02-05 14:19:17 -05:00
Heng Li
1077b7ddc8
r846: added --hard-mask-level for #244
2018-09-27 14:46:26 -04:00
Heng Li
a655cbef86
print SAM header; remove tmp files
2018-07-15 11:03:18 -04:00
Heng Li
4b707aac92
working with toy examples
2018-07-15 10:55:00 -04:00
Heng Li
e5277dbf5c
code backup
2018-07-14 22:52:36 -04:00
Heng Li
1a55227d5a
write hits to tmp files (unfinished)
2018-07-14 12:15:10 -04:00
Heng Li
7e6e8ca73f
r792: fixed -Wextra warnings and resolved #184
2018-06-19 15:26:58 -04:00
Heng Li
a3afeec0b2
r783: reverted to r781 ( #155 )
2018-05-30 15:25:34 -04:00
Heng Li
3573784b4d
r782: no mask a chain having long ref ovlp ( #155 )
2018-05-30 13:53:45 -04:00
Heng Li
623b5d9d48
r750: check puts() return ( #132 & #103 )
2018-03-22 11:31:58 -04:00
Heng Li
24a4808826
r718: retrieve sequence from the index
2018-02-23 10:18:26 -05:00
Heng Li
f434653432
added peakrss(); not used for now
2018-02-17 20:40:31 -05:00
Heng Li
8fc5f8dc90
r711: assign proper mapq to primary inversions
2018-02-15 14:34:59 -05:00
Heng Li
7ef5490884
r703: added --max-clip-ratio
...
still testing the option
2018-02-12 13:29:18 -05:00
Heng Li
12a5a5fa3c
r669: improved self chain extension ( #10 )
...
This has not fully resolved #10 , only alleviated the issue.
2018-01-30 20:05:02 -05:00
Heng Li
824712a4ee
r617: removed some unused code
2017-12-10 17:54:50 -05:00
Heng Li
98a999fe44
r611: added pseudocount when est divergence
2017-12-08 12:57:57 -05:00
Heng Li