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Author SHA1 Message Date
Heng Li
2d7ec75d50 Release minimap2-2.10 (r761) v2.10 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
zingdle
ecb6703d4a Update README.md 
Fix typo.
TD;DR -> TL;DR
 2018-03-26 14:54:52 +08:00
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) v2.9 2018-02-24 09:31:09 -05:00
Heng Li
83c57a9d98 r719: fixed bad memory access 2018-02-23 17:27:41 -05:00
Heng Li
24a4808826 r718: retrieve sequence from the index 2018-02-23 10:18:26 -05:00
Heng Li
29ed675ee5 bugfix: in-place revcomp() not working 2018-02-20 11:05:54 -05:00
Heng Li
7dc7097208 added reverse complement 2018-02-20 09:41:25 -05:00
Heng Li
f434653432 added peakrss(); not used for now 2018-02-17 20:40:31 -05:00
Heng Li
090361c25b fixed a typo in mappy (#117) 2018-02-16 21:10:57 -05:00
Heng Li
e1f18690f6 paftools-r713: fixed bug for cov1 regions 2018-02-16 12:20:46 -05:00
Heng Li
54a42aafe5 keep documents in sync 2018-02-15 17:21:09 -05:00
Heng Li
8fc5f8dc90 r711: assign proper mapq to primary inversions 2018-02-15 14:34:59 -05:00
Heng Li
a0d62519c1 r710: fixed incorrect inversion coordinate (#112) 2018-02-15 14:23:42 -05:00
Heng Li
b71c01b316 added test data for inversions 2018-02-15 11:04:27 -05:00