 Heng Li
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edf736e110
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working on toy examples
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2018-09-17 13:54:57 -04:00 |
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Heng Li
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d01369ec47
|
pass BED regions to extd2; not tested
|
2018-09-17 12:31:42 -04:00 |
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Heng Li
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2b653ecda3
|
BED I/O
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2018-09-16 14:49:53 -04:00 |
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Heng Li
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c63a33904f
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r836: fixed an integer overflow
Forgot this one.
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2018-09-14 23:29:31 -04:00 |
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Heng Li
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70b0fede64
|
r835: improved help message. Resolved #232
|
2018-09-14 22:29:25 -04:00 |
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Heng Li
|
0b681e51e7
|
Merge remote-tracking branch 'remotes/origin/master'
|
2018-09-14 22:22:20 -04:00 |
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Heng Li
|
7d80d6de4a
|
r832: fixed outdated -L. Resolved #231 and #233
|
2018-09-14 22:21:33 -04:00 |
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Heng Li
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98c48a1c45
|
Fixed wrong version links in the cookbook
|
2018-09-03 09:07:34 -04:00 |
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Heng Li
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63d397120a
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removed getopt.c from MANIFEST
|
2018-09-01 21:30:46 -04:00 |
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Heng Li
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7998fe9906
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r829: replaced musl's getopt with ketopt
|
2018-09-01 21:18:02 -04:00 |
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Heng Li
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3a119d606f
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r828: --MD to support spliced alignment
|
2018-08-22 10:47:45 -04:00 |
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|
Heng Li
|
a5eafb75f9
|
Release minimap2-2.12 (r827)
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2018-08-06 12:44:39 -04:00 |
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Heng Li
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9a567e4b37
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allow mappy to change scoring
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2018-08-06 09:52:13 -04:00 |
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Heng Li
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8e606bcc06
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added a -C5 example to Getting Started
|
2018-08-06 09:08:33 -04:00 |
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Heng Li
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a1b7219b5d
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explain added parameters
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2018-08-05 21:32:05 -04:00 |
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Heng Li
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b0f39a1a61
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r823: mappy to index a single sequence
|
2018-08-05 20:57:05 -04:00 |
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Heng Li
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5ab6538757
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r822: added option --no-end-flt
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2018-08-05 19:42:12 -04:00 |
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Heng Li
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b32296e18f
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r821: fixed memory when -y is used
|
2018-07-31 15:14:37 -04:00 |
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Heng Li
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99ecdf7b5d
|
mappy to support arm64 (#203)
|
2018-07-24 23:53:02 -04:00 |
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Heng Li
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ff9917a1c4
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r819: mappy to support cs/MD
|
2018-07-24 23:29:55 -04:00 |
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Heng Li
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0e137670fc
|
Merge branch 'split'
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2018-07-15 22:24:15 -04:00 |
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Heng Li
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395c8d678a
|
r815: fixed a memory leak
|
2018-07-15 22:11:32 -04:00 |
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Heng Li
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830da7fa27
|
r814: resumed versioning
|
2018-07-15 11:48:14 -04:00 |
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Heng Li
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a655cbef86
|
print SAM header; remove tmp files
|
2018-07-15 11:03:18 -04:00 |
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|
Heng Li
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4b707aac92
|
working with toy examples
|
2018-07-15 10:55:00 -04:00 |
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|
Heng Li
|
951c0d1d35
|
apparently mm_append_cigar() wastes some memory
|
2018-07-14 23:47:44 -04:00 |
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|
Heng Li
|
3545e35a42
|
pairing in the split-idx mode
|
2018-07-14 23:43:34 -04:00 |
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Heng Li
|
f3417da838
|
bugfix: unmapped records are duplicated in output
|
2018-07-14 22:54:05 -04:00 |
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|
Heng Li
|
e5277dbf5c
|
code backup
|
2018-07-14 22:52:36 -04:00 |
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|
Heng Li
|
1a55227d5a
|
write hits to tmp files (unfinished)
|
2018-07-14 12:15:10 -04:00 |
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|
Heng Li
|
5cfa621b2d
|
use unmapped records
|
2018-07-07 12:49:15 -05:00 |
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|
Heng Li
|
a609a07f8c
|
optionally output unmapped query in PAF
|
2018-07-07 10:26:08 -05:00 |
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|
Heng Li
|
bcf92b3c46
|
compute query coverage
|
2018-07-06 21:52:01 -05:00 |
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|
Heng Li
|
097378ab90
|
reworked break point counting
|
2018-07-06 09:46:26 -04:00 |
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|
Heng Li
|
10bbbe28c5
|
added asmstat
|
2018-07-05 13:22:32 -04:00 |
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|
Heng Li
|
50dae10421
|
paftools call to show statistics on longer indels
|
2018-07-03 14:28:09 -04:00 |
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|
Heng Li
|
0517972d02
|
Release minimap2-2.11 (r797)
|
2018-06-21 00:04:08 -04:00 |
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|
Heng Li
|
d46e68e6ad
|
r796: don't use ssize_t
|
2018-06-20 12:45:27 -04:00 |
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|
Heng Li
|
2584a4149a
|
r295: use -r2000 for ava-ont, NOT for ava-pb
|
2018-06-20 12:24:43 -04:00 |
|
|
Heng Li
|
66674afd09
|
r794: fixed a bug in seed filtering
|
2018-06-20 10:26:29 -04:00 |
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|
Heng Li
|
e9ca0c9dab
|
added __version__; resolved #165
Not sure if this is the right way. Apparently working.
|
2018-06-19 15:40:26 -04:00 |
|
|
Heng Li
|
7e6e8ca73f
|
r792: fixed -Wextra warnings and resolved #184
|
2018-06-19 15:26:58 -04:00 |
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|
Heng Li
|
154d2caf5b
|
r784: support the =/X CIGAR operators (#156)
|
2018-05-30 16:11:22 -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
|
872f300955
|
r781: fixed the buggy heapmerge (resolves #166)
|
2018-05-30 11:55:14 -04:00 |
|
|
Heng Li
|
d7b61a039e
|
updated citation
|
2018-05-30 11:11:55 -04:00 |
|
|
Heng Li
|
248158a3e1
|
Resolved #168: citing the manpage for cs
|
2018-05-30 11:03:16 -04:00 |
|
|
Heng Li
|
9f4309c376
|
r777: avoid skipping too many seeds
|
2018-05-11 10:25:18 -04:00 |
|
|
Heng Li
|
463f9309f9
|
Merge branch 'hot-fix' into fix-long-gap
|
2018-05-11 10:13:19 -04:00 |
|
|
Heng Li
|
abe989e355
|
the previous fix on int overflow is incomplete
|
2018-05-11 10:12:57 -04:00 |
|
|
Heng Li
|
881b4ca3a2
|
r774: Merge branch 'hot-fix' into fix-long-gap
|
2018-05-11 10:02:17 -04:00 |
|
|
Heng Li
|
10c6dd2551
|
r773: fixed an integer overflow
|
2018-05-11 10:01:23 -04:00 |
|
|
Heng Li
|
7ec6721c44
|
r772: option -Y not working
|
2018-05-11 10:00:11 -04:00 |
|
|
Heng Li
|
e61812ee55
|
reduced gap len to trigger bad seed filtering
|
2018-05-01 16:17:21 -04:00 |
|
|
Heng Li
|
734ac379bb
|
r770: matching N bases not working properly (#155)
|
2018-04-30 19:55:23 -04:00 |
|
|
Heng Li
|
759f8e4ac9
|
r769: filter out seeds breaking long gaps
|
2018-04-24 15:37:37 -04:00 |
|
|
Heng Li
|
aef7b0744c
|
r768: shortened preset; added dv tag (#25)
Also added asm20 to command line help (#151)
|
2018-04-24 12:48:54 -04:00 |
|
|
Heng Li
|
39f836eac8
|
r767: don't crash when there is no "cg" (#153)
|
2018-04-24 12:32:37 -04:00 |
|
|
Heng Li
|
cbeb86dad6
|
Merge remote-tracking branch 'origin/master'
|
2018-04-10 09:12:26 -04:00 |
|
|
Heng Li
|
372c90ceb5
|
r764: fixed incorrect inversion mapq (#148)
|
2018-04-10 09:11:49 -04:00 |
|
|
Heng Li
|
ee4cd089f7
|
r763: fine control long join flank len (#128)
|
2018-03-29 14:16:58 -04:00 |
|
|
Heng Li
|
2d7ec75d50
|
Release minimap2-2.10 (r761)
|
2018-03-27 11:45:44 -04:00 |
|
|
Heng Li
|
7938ed4893
|
fixed two mappy warnings
|
2018-03-26 15:12:54 -04:00 |
|
|
Heng Li
|
4740423afa
|
Merge remote-tracking branch 'origin/master'
|
2018-03-26 14:37:17 -04:00 |
|
|
Heng Li
|
1776311a9b
|
updated cookbook
|
2018-03-26 14:37:02 -04:00 |
|
|
Heng Li
|
c1a3e05cb0
|
Merge pull request #138 from zingdle/patch-1
Fix typo in README.md
|
2018-03-26 07:50:39 -04:00 |
|
|
Heng Li
|
0bf97a367b
|
r755: junceval to only evaluate chromosomes
|
2018-03-24 23:10:06 -04:00 |
|
|
Heng Li
|
1c504d72e4
|
r754: option to only change name
|
2018-03-23 12:27:11 -04:00 |
|
|
Heng Li
|
5ef9580b17
|
r753: change bandwidth in ava-ont to 2000bp
|
2018-03-23 10:15:23 -04:00 |
|
|
Heng Li
|
08bd2123b6
|
r752: option to copy comments to output (#136)
|
2018-03-23 10:04:33 -04:00 |
|
|
Heng Li
|
8766d286df
|
r751: optionally output MD (#118)
|
2018-03-22 14:15:33 -04:00 |
|
|
Heng Li
|
623b5d9d48
|
r750: check puts() return (#132 & #103)
|
2018-03-22 11:31:58 -04:00 |
|
|
Heng Li
|
18659118cd
|
r749: don't print version etc at low verbose
|
2018-03-22 11:10:55 -04:00 |
|
|
Heng Li
|
d1050f4eaf
|
r748: optionally to use system getopt() (#134)
|
2018-03-19 11:18:26 -04:00 |
|
|
Heng Li
|
b81d45510e
|
Revision v2
|
2018-03-16 11:18:06 -04:00 |
|
|
Heng Li
|
d135feb1a5
|
response to reviewers' comments, round 2
|
2018-03-15 21:59:57 -04:00 |
|
|
Heng Li
|
242ff4e91d
|
r745: junceval - recognize "-" as file name
|
2018-03-15 12:51:46 -04:00 |
|
|
Heng Li
|
7a0c1316ce
|
added more examples to cookbook
|
2018-03-12 22:24:22 -04:00 |
|
|
Heng Li
|
77ebd479f4
|
r743: added VCF output to "call"
|
2018-03-12 21:51:31 -04:00 |
|
|
Heng Li
|
e3f226a9d9
|
working on section "Full-Genome Alignment"
found an apparent bug in paftools.js call. To debug...
|
2018-03-12 16:12:18 -04:00 |
|
|
Heng Li
|
bdc615c1d4
|
r741: added --min-occ-floor to improve #107
|
2018-03-12 14:32:27 -04:00 |
|
|
Heng Li
|
ad1beaf255
|
backup; not finished
|
2018-03-12 13:20:25 -04:00 |
|
|
Heng Li
|
de0480ac5b
|
finished section "Read Overlap"
|
2018-03-12 13:05:51 -04:00 |
|
|
Heng Li
|
f2866533a8
|
finished "mapping genomic reads"
|
2018-03-12 12:50:21 -04:00 |
|
|
Heng Li
|
0173850ef0
|
don't use bullets - they are hard to read
|
2018-03-12 12:42:13 -04:00 |
|
|
Heng Li
|
acea3594fb
|
updated cookbook
|
2018-03-12 12:39:57 -04:00 |
|
|
Heng Li
|
f78a247749
|
Started to work on a cookbook
|
2018-03-12 12:00:44 -04:00 |
|
|
Heng Li
|
ccaf12e1a2
|
r734: removed debugging print in call()
|
2018-03-09 23:46:21 -05:00 |
|
|
Heng Li
|
96b132c97d
|
fixed a bug/typo in Aligner.seq() (#126)
|
2018-03-08 19:12:12 -05:00 |
|
|
Heng Li
|
70428ca3a8
|
speedup tag parsing for sam2paf
|
2018-03-02 10:17:55 -05:00 |
|
|
Heng Li
|
9aea79d621
|
faster tag parsing
|
2018-03-02 10:09:14 -05:00 |
|
|
Heng Li
|
1770988627
|
make calling work with sam2paf output
|
2018-03-02 10:03:06 -05:00 |
|
|
Heng Li
|
2bfdad34bb
|
minor cleanup to last commit
|
2018-03-02 01:07:37 -05:00 |
|
|
Heng Li
|
953766cedd
|
generate cs; not carefully tested
|
2018-03-02 00:14:55 -05:00 |
|
|
Heng Li
|
dc61301d9f
|
sam2paf cleanup
|
2018-03-01 21:58:12 -05:00 |
|
|
Heng Li
|
19e05a099d
|
for clarity
|
2018-03-01 18:25:29 -05:00 |
|
|
Heng Li
|
0238caa8b1
|
clarify minimap2 not working for >2Gbp seq #129
|
2018-03-01 18:23:40 -05:00 |
|
|
Heng Li
|
a22ebb9836
|
use SSE compiler flags more precisely (#127)
|
2018-02-26 09:51:01 -05:00 |
|
|
Heng Li
|
eeb314edd6
|
Release minimap2-2.9 (r720)
|
2018-02-24 09:31:09 -05:00 |
|