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
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--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
b2ce3f9ed0
get rid of two more new lines
2017-07-01 11:37:58 -04:00
5ebe868db5
added two more new lines
2017-07-01 11:32:49 -04:00
cb6c277c62
removed unnecessary empty lines
...
On linux, these empty lines count.
2017-07-01 11:31:32 -04:00
b883d132e2
no effective change
2017-07-01 11:26:23 -04:00
2338e887d9
finished the first draft of manpage
2017-07-01 11:25:54 -04:00
d4301736b8
more manpage
2017-07-01 00:23:46 -04:00
41efd03d7a
r129: fixed memory leak caused by qualities
2017-06-30 23:48:00 -04:00
10910b72d1
backup
2017-06-30 23:31:38 -04:00
Heng Li