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814 Commits

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Author SHA1 Message Date
Heng Li
e39080fea6 debugging code 2018-10-29 20:21:10 -04:00
Heng Li
e9dcd7b2bc read score from BED 2018-10-29 15:07:48 -04:00
Heng Li
121731ebde Merge branch 'master' into bed-bonus 2018-10-18 11:13:19 -04:00
Heng Li
20268a6068 updated the copyright holder 2018-10-18 11:11:17 -04:00
Heng Li
0aad789ac4 updated copyright holder 2018-10-18 11:10:47 -04:00
Heng Li
d04ac068fd r852: a minor when large --end-bonus is in use 
We may use a large --end-bonus to mimic end-to-end alignment. In the short-read
mode, the candidate alignment region may be out of the band, which leads to
truncated alignment.
 2018-10-15 21:28:27 -04:00
Heng Li
5d5d392c02 Release minimap2-2.13 (r850) v2.13 2018-10-11 13:18:31 -04:00
Heng Li
170863e553 r849: option -P doesn't work 
I don't know why I haven't found it at the beginning.
 2018-10-04 16:11:59 -04:00
Heng Li
97f97306a4 r847: guard against -N0 2018-09-27 15:13:44 -04:00
Heng Li
1077b7ddc8 r846: added --hard-mask-level for #244 2018-09-27 14:46:26 -04:00
Heng Li
c57b59f02f r845: log peak memory 2018-09-23 20:27:49 -04:00
Torsten Seemann
34be359e25 Add -s sample option for VCF output 2018-09-19 18:24:47 -04:00
Heng Li
2d065eea7e fixed a BED parsing bug 2018-09-17 15:50:28 -04:00
Heng Li
b4b70db126 mappy to support BED 2018-09-17 14:54:44 -04:00
Heng Li
a3e223f17b Merge branch 'master' into bed-prefer 2018-09-17 13:59:51 -04:00
Heng Li
8b12da8b0f removed a useless dependency (not in repo) 2018-09-17 13:59:25 -04:00
Heng Li
edf736e110 working on toy examples 2018-09-17 13:54:57 -04:00
Heng Li
d01369ec47 pass BED regions to extd2; not tested 2018-09-17 12:31:42 -04:00
Heng Li
2b653ecda3 BED I/O 2018-09-16 14:49:53 -04:00
Heng Li
c63a33904f r836: fixed an integer overflow 
Forgot this one.
 2018-09-14 23:29:31 -04:00
Heng Li
70b0fede64 r835: improved help message. Resolved #232 2018-09-14 22:29:25 -04:00
Heng Li
0b681e51e7 Merge remote-tracking branch 'remotes/origin/master' 2018-09-14 22:22:20 -04:00
Heng Li
7d80d6de4a r832: fixed outdated -L. Resolved #231 and #233 2018-09-14 22:21:33 -04:00
Chris Rands
791e89ce0f PEP8 and other minor styles changes 2018-09-12 10:58:56 -04:00
Heng Li
98c48a1c45 Fixed wrong version links in the cookbook 2018-09-03 09:07:34 -04:00
Heng Li
63d397120a removed getopt.c from MANIFEST 2018-09-01 21:30:46 -04:00
Heng Li
7998fe9906 r829: replaced musl's getopt with ketopt 2018-09-01 21:18:02 -04:00
Heng Li
3a119d606f r828: --MD to support spliced alignment 2018-08-22 10:47:45 -04:00
Heng Li
a5eafb75f9 Release minimap2-2.12 (r827) v2.12 2018-08-06 12:44:39 -04:00
Heng Li
9a567e4b37 allow mappy to change scoring 2018-08-06 09:52:13 -04:00
Heng Li
8e606bcc06 added a -C5 example to Getting Started 2018-08-06 09:08:33 -04:00
Heng Li
a1b7219b5d explain added parameters 2018-08-05 21:32:05 -04:00
Heng Li
b0f39a1a61 r823: mappy to index a single sequence 2018-08-05 20:57:05 -04:00
Heng Li
5ab6538757 r822: added option --no-end-flt 2018-08-05 19:42:12 -04:00
Heng Li
b32296e18f r821: fixed memory when -y is used 2018-07-31 15:14:37 -04:00
Heng Li
99ecdf7b5d mappy to support arm64 (#203) 2018-07-24 23:53:02 -04:00
Heng Li
ff9917a1c4 r819: mappy to support cs/MD 2018-07-24 23:29:55 -04:00
Mark Bicknell
8c064a5f29 Fixed mm_idx_is_idx to return the correct result on Windows. 2018-07-17 09:16:33 -04:00
Heng Li
0e137670fc Merge branch 'split' 2018-07-15 22:24:15 -04:00
Heng Li
395c8d678a r815: fixed a memory leak 2018-07-15 22:11:32 -04:00
Heng Li
830da7fa27 r814: resumed versioning 2018-07-15 11:48:14 -04:00
Heng Li
a655cbef86 print SAM header; remove tmp files 2018-07-15 11:03:18 -04:00
Heng Li
4b707aac92 working with toy examples 2018-07-15 10:55:00 -04:00
Heng Li
951c0d1d35 apparently mm_append_cigar() wastes some memory 2018-07-14 23:47:44 -04:00
Heng Li
3545e35a42 pairing in the split-idx mode 2018-07-14 23:43:34 -04:00
Heng Li
f3417da838 bugfix: unmapped records are duplicated in output 2018-07-14 22:54:05 -04:00
Heng Li
e5277dbf5c code backup 2018-07-14 22:52:36 -04:00
Heng Li
1a55227d5a write hits to tmp files (unfinished) 2018-07-14 12:15:10 -04:00
Heng Li
5cfa621b2d use unmapped records 2018-07-07 12:49:15 -05:00
Heng Li
a609a07f8c optionally output unmapped query in PAF 2018-07-07 10:26:08 -05:00