eb819c29e8
Release minimap2-2.6 (r623)
2017-12-12 11:09:59 -05:00
98a6e52c06
r618: heuristics to avoid tiny terminal exons
2017-12-11 00:57:55 -05:00
0e42628ef6
r611: document --idx-no-seq; better inv aln
2017-12-08 13:16:18 -05:00
3b518271ee
Release minimap2-2.5 (r572)
2017-11-11 11:29:28 -05:00
99a2709913
r567: minor change to #56
2017-11-09 19:17:45 -05:00
21a46ba652
Release minimap2-2.4 (r555)
2017-11-06 12:54:02 -05:00
192217a10c
r539: use --splice-flank=yes by default
...
In human/mouse, the GTr..yAG pattern occurs to 91/92% of all GT-AG introns.
Modeling r..y clearly leads to higher accuracy. However, in SIRV, this
percentage is reduced to ~60%. The default "--splice --splice-flank=yes"
leads to lower accuracy. If someone benchmark minimap2 on SIRV, this would be
bad, but minimap2 is developed for practical applications, not for benchmarks.
I will live with that.
2017-10-28 22:29:55 -04:00
79b0caca95
r537: model the next base to GT/AG
...
[PMID:18688272] shows that the base following GT tends to be A or G (i.e. R) in
both human and yeast, and that the base preceeding AG tends to be C or T (i.e.
Y). In the new model, we pay no cost to GTr..yAG, but we pay half of the cost
if there is no r or y. This improves the junction accuracy when mapping to
human and mouse and decreases the accuacy when mapping to SIRV. My guess is
that SIRV does not honor this trend. Need to investigate in future.
Also in this commit, --cost-non-gt-ag is aliased to -C. The default is changed
to 9 instead of 5. I also added --splice-flank to enable the above model. This
may become the default once I confirm my hypothesis on SIRV.
2017-10-28 00:25:01 -04:00
306e4541f8
Released minimap2-2.3 (r531)
2017-10-22 23:13:35 -04:00
04cf4ebf5e
r518: increased the default -K to 500M
...
This helps multi-thread performance for ultra-long reads.
2017-10-17 13:21:29 -04:00
7c555f9b7e
r508: use two I/O threads for mapping
...
-x sr applies this option by default
2017-10-12 14:56:01 -04:00
f150257a0d
r487: demote "map10k"; improved README
2017-10-07 19:19:40 -04:00
ae2adf04d4
r476: multi-file fragment mode working
2017-10-05 15:39:26 -04:00
b839758335
r475: added --cs=none; updated manpage
2017-10-05 15:27:37 -04:00
7d50e646dd
r466: detect multi-part index more smartly
...
though it might not work in an extremely rare case: the end of a sequence ends
at X*16384 and it is the last sequence in a batch. This can be resolved by
never letting the kstream_t buffer empty.
2017-10-04 17:32:58 -04:00
7a9b4db874
replaced --approx-ext with --sr
...
--sr disables Z-drop and may come with other heurstics
2017-09-20 10:51:18 -04:00
ea5a0cd17d
Release minimap2-2.2 (r409)
2017-09-17 20:08:47 -04:00
cf93e5c0a1
more functional minimap2.py; added categories
2017-09-17 17:06:39 -04:00
0f7455cefa
r365: documented the "sr" preset
2017-09-14 12:57:21 -04:00
ef3f7ea2f2
Release minimap2-2.1.1 (r341)
2017-09-06 13:46:51 -04:00
bf8246f872
Release minimap2-2.1-r311
2017-08-25 13:35:55 +08:00
0fe1a224ab
r309: improved SAM header output
2017-08-25 10:35:58 +08:00
bbb37d95f2
support inserting RG lines
2017-08-17 23:34:09 +08:00
b5f5929bf9
r296: expose splicing related options to CLI
2017-08-13 21:37:51 -04:00
53b3265d84
r290: in techrep, explain spliced alignment
2017-08-12 15:40:49 -04:00
5a74088b74
r288: changed max intron length to 200k
2017-08-12 12:39:21 -04:00
d240318741
r287: refined CLI options and manpage
2017-08-12 12:26:04 -04:00
6840370f3c
Release minimap2-2.0 (r275)
2017-08-08 21:16:25 -04:00
d8d4d29b68
Release minimap2-2.0rc1-r232
2017-07-30 14:32:40 -04:00
1f78e1ee53
r230: code formatting changes only
2017-07-30 12:31:40 -04:00
19d6ec885e
r224: inversion alignment around Z-drop break
2017-07-29 13:09:10 -04:00
84922cfe41
clarify that wrong seeding mainly occurs in LCRs
2017-07-28 14:33:15 -04:00
667b32a516
added algorithm overview
2017-07-27 18:50:39 -04:00
4aff301ef4
r190: default -k to 15; added -x map-ont
2017-07-19 10:11:14 -04:00
9a935dcef5
Fixed grammar errors
2017-07-18 11:37:58 -04:00
495a78e40a
Get documentation ready for release
2017-07-18 11:04:09 -04:00
71e2a97a4c
r180: changed -x asm5 settings
2017-07-18 00:00:36 -04:00
941059292e
r179: changed the preset for assembly alignment
2017-07-17 22:41:46 -04:00
b4280d186f
r176: removed seedcov_ratio; changed default opt
...
min_seedcov_ratio is not used
2017-07-12 12:47:46 -04:00
eeeb2ffb68
r174: make max-chain-skip work
...
The max-chain-skip heuristics did not work due to a bug. Without this
heuristics, chaining is too slow for long-read overlap.
2017-07-12 10:08:06 -04:00
cfa083a98b
r172: separated PacBio and ONT read overlapping
...
HPC k-mer works better for PacBio, but worse for ONT. Interesting...
2017-07-11 15:12:35 -04:00
1fee5f8edc
r160: -O and -E accept two numbers
2017-07-08 11:34:52 -04:00
cc554aee43
r159: use two-piece gap penalty
2017-07-08 10:26:00 -04:00
9823317e8f
r158: optionally ignore base quality
2017-07-05 18:23:50 -04:00
a94bc31311
r151: documentations
2017-07-03 12:11:07 -04:00
51cfb60520
r145: changed default -p from 2 to 0.8
...
For long reads, secondary alignments can be very information.
2017-07-02 22:51:45 -04:00
da90b614db
r141: replaced -b with -a (for SAM output)
...
-b sounds like BAM. I like -a better.
2017-07-01 16:54:59 -04:00
67cad9dff3
added limitations
2017-07-01 12:11:56 -04:00
a92bd75b7b
make the table fit 80 columns
2017-07-01 11:54:07 -04:00
02145b2166
explain option -d
2017-07-01 11:48:37 -04:00
Heng Li