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
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
6ce0dd8b70
move MM_VERSION define to minimap.h
2023-03-17 20:58:43 +01:00
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
6c2cbf7903
miniprot-like splice model
...
slightly worse on iso-seq and slightly better on direct-RNA
2022-10-06 09:10:17 -04:00
c8f0a35c40
r1117: added --no-hash-name for deterministic
2021-11-24 16:49:48 -05:00
39bdd45875
r1108: fixed missing inversions for #816 and #806
2021-10-04 16:34:30 -04:00
aefa2c0d86
added --chain-skip-scale
2021-10-01 16:58:03 -04:00
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
7e33fde82b
dev-r1087: added --cap-kalloc
2021-07-19 21:20:04 -04:00
161ae7ff73
dev-r1079: per-read error rate
...
more tuning needed
2021-07-18 20:38:53 -04:00
8a6edab847
dev-r1078: decoupling ranking penalty
2021-07-18 16:22:48 -04:00
2546999639
dev-r1076: log gap penalty
2021-07-17 18:23:59 -04:00
b046052d82
Merge branch 'master' into utec
2021-07-16 13:32:47 -04:00
260a68d232
Use #defines for CIGAR operators in C code
...
Give the CIGAR constants names to clarify the code. So that ksw2.h
remains self-contained, define KSW_* versions of the CIGAR operators
it needs for use within ksw2.h. Other code should in general use the
full set of MM_CIGAR_* constants in minimap.h.
2021-07-02 13:03:03 -04:00
177eef259d
Use the full MIDNSHP=X string whenever printing CIGAR strings
...
Define MM_CIGAR_STR to the full string of CIGAR operators (including
the 'B' operator as well) and use it throughout the C code.
It would be possible to use it from the Cython code too, but it's easier
to keep that as a Cython string literal to avoid adding extra runtime
code to handle locale conversion.
2021-07-02 13:03:03 -04:00
34a41197d7
r1051: added two internal parameters
...
rmq_rescue_size and rmq_rescue_ratio
2021-05-24 16:38:45 -04:00
379728726a
r1049: removed the long-join heuristics
2021-05-24 16:21:40 -04:00
4f91558160
r1048: rescue long gaps
2021-05-24 16:09:09 -04:00
bbb4f97e52
support RMQ
2021-05-03 09:27:04 -04:00
0f5608c4a4
r1028: backport minigraph -U
2021-05-01 15:41:39 -04:00
feb92d32ea
r1025: seed rescuring
2021-04-30 17:33:16 -04:00
f995f55610
added --mask-len for #659
2020-08-21 11:12:50 -04:00
da7109fd29
r985: optionally report cs/cg on the query strand
...
PAF only; not well tested
2020-04-21 12:37:35 -04:00
9dceae59a0
r972: renamed --alt-diff to --alt-drop
2020-01-21 10:33:39 -05:00
eb3ed6993d
support ALT mapping
2020-01-21 09:17:50 -05:00
d2e14705e7
r968: allow large mini_batch; resolves #491
2020-01-18 12:24:44 -05:00
040f74102c
r965: added --chain-gap-scale for #540
2020-01-18 10:29:33 -05:00
c2aec88b84
r938: added --sam-hit-only; resolved #377
2019-04-30 22:40:36 -04:00
97f67a2a0a
r937: enlarge mm_mapopt_t::flag to 64 bits
2019-04-30 22:30:32 -04:00
49c6d83a8e
r934: --junc-bed to read BED12
2019-04-28 20:12:28 -04:00
be171aa2dc
implemented in exts; testing is the next
2019-04-28 16:47:12 -04:00
6420acca6d
BED I/O
2019-04-28 16:47:12 -04:00
d431dc0181
r917: added --max-chain-iter to avoid worst case
...
Resolves #324
2019-02-27 14:41:01 -05:00
ea2b1c5b2a
r894: added --max-qlen to filter out long query
2018-12-12 12:27:32 -05:00
13981404e2
r876: skip DP if taking too much RAM ( #259 )
2018-11-05 11:43:10 -05:00
1077b7ddc8
r846: added --hard-mask-level for #244
2018-09-27 14:46:26 -04:00
5ab6538757
r822: added option --no-end-flt
2018-08-05 19:42:12 -04:00
ff9917a1c4
r819: mappy to support cs/MD
2018-07-24 23:29:55 -04:00
3545e35a42
pairing in the split-idx mode
2018-07-14 23:43:34 -04:00
1a55227d5a
write hits to tmp files (unfinished)
2018-07-14 12:15:10 -04:00
a609a07f8c
optionally output unmapped query in PAF
2018-07-07 10:26:08 -05:00
Mikhail Kolmogorov
Heng Li
Chris Seymour
John Marshall