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235 Commits 11 Branches 54 Tags
cc166c8ff55e840a42f4fdb7c4ffe216a5912de7
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Author SHA1 Message Date
Heng Li cc166c8ff5 r235: clarified option -f 2020-04-12 19:42:02 -04:00
Heng Li cdd5f3e4e0 r234: fixed a bug for -r of an odder number 2020-04-12 19:25:53 -04:00
Heng Li 2d985569f1 Merge branch 'master' into dev-lh3 2020-04-12 18:57:42 -04:00
chhylp123 57b16e9e1f fix warning 2020-04-12 17:46:30 -04:00
chhylp123 b245e9a760 fix warning 2020-04-12 17:46:20 -04:00
Heng Li 2c4de3a326 r230: the first anchor score was not adjusted 2020-04-12 10:39:42 -04:00
Heng Li 75a89c214d r229: LIS score is still not exactly right 2020-04-12 10:19:28 -04:00
Heng Li 22b681b830 r228: resolved a compiler warning 2020-04-12 09:56:50 -04:00
Heng Li 4d7600361c r226b: prefer unique anchors 2020-04-11 22:28:21 -04:00
Heng Li c4397a9400 r226: more careful about ma_hit_t_alloc memory 2020-04-11 22:05:07 -04:00
Heng Li e6b5b666a2 r224: versioning 2020-04-11 00:14:33 -04:00
Heng Li 54fa1a9aed Merge branch 'master' into dev-lh3 2020-04-11 00:08:35 -04:00
chhylp123 20c6c1d2e6 update trio-binning 2020-04-10 23:32:15 -04:00
Heng Li c710c6ea48 r221: sync with hifiasm parameter 
Probably has no practical effect
 2020-04-10 21:49:01 -04:00
Heng Li c37ea00d6a r220: resumed versioning 2020-04-10 19:12:32 -04:00
Heng Li ad1b79a6bb Merge branch 'flt-p' into dev-lh3 2020-04-10 14:03:44 -04:00
chhylp123 943b6947cb update purge_dup by LIS 2020-04-10 13:58:36 -04:00
Heng Li 22b2e1e9e1 r217: fixed a bug in LIS chaining score 
Also fall back to DP chaining more often
 2020-04-10 13:25:25 -04:00
Heng Li 15591c9038 improve documentation 2020-04-10 11:04:35 -04:00
Heng Li 71328f7423 r215: binning with external list (NOT TESTED!!) 2020-04-10 01:06:43 -04:00
Heng Li f32bfc904a r215: prepare for list-based binning 2020-04-10 00:12:19 -04:00
Heng Li 7a35bd7fcc r213: renamed trio binning output files 2020-04-09 20:40:01 -04:00
Heng Li c3f032da37 r212: LIS chaining was not working 2020-04-09 10:43:37 -04:00
Heng Li c41aae0630 r211: added --write-paf/--write-ec/--skip-triobin 2020-04-08 22:32:54 -04:00
Heng Li 23dbfdef77 Merge branch 'master' into dev-lh3 2020-04-08 18:32:33 -04:00
chhylp123 a288415111 bug fixing for purge_dup 2020-04-08 16:55:04 -04:00
Heng Li 8efcdefcaf r207: multiple input files were not working 2020-04-07 12:40:10 -04:00
chhylp123 9cc563c7c6 do hap alignment in parallel 2020-04-07 11:18:28 -04:00
Heng Li a79fd0f360 r206: apply trio binning when loading from binary 2020-04-06 16:58:29 -04:00
Heng Li 1bbca54d8d r205: resume versioning 2020-04-06 09:59:43 -04:00
Heng Li 2d0087104f Merge branch 'master' into merge3 2020-04-06 08:25:54 -04:00
Heng Li 7f580850e8 Merge branch 'master' of github.com:chhylp123/hifiasm 2020-04-06 08:25:21 -04:00
chhylp123 87fc103e63 fix small bug 2020-04-06 02:03:34 -04:00
Heng Li adbc65feda r201: automatically adjust -N 2020-04-05 22:43:01 -04:00
Heng Li 3773610532 r200: reworked multi-thread for better efficiency 2020-04-05 16:18:14 -04:00
Heng Li 46f83e152d r199: renamed pre.ovlp.bin to pre.ec.bin 
Also updated the Makefile dependencies
 2020-04-05 13:45:50 -04:00
Heng Li 0f1994fc1f r198: made VERBOSE_GFA a CL option --dbg-gfa 2020-04-05 13:01:03 -04:00
Heng Li 31356f9e02 r197: added an assertion test/suppressed warnings 2020-04-05 12:22:28 -04:00
Heng Li 16a3d58dc9 r196: fixed a compiling error 2020-04-05 12:14:20 -04:00
Heng Li 5917aa2f36 Merge branch 'chain-tune' into merge2 2020-04-05 12:07:13 -04:00
chhylp123 c57b63653d Merge pull request #8 from chhylp123/flt-p 
for purge_dup
 2020-04-05 11:44:56 -04:00
Heng Li f0c53e9948 r192: estimate buffer memory 2020-04-05 11:17:12 -04:00
chhylp123 ac3fcc339a for purge_dup 2020-04-05 11:10:56 -04:00
Heng Li 8c27dbb52f r191: changed the default to -N400 -k51 -w51 2020-04-04 12:55:19 -04:00
Heng Li 4e3c15ec83 r190: fixed an if_exact() bug 
caused by reverse complement again
 2020-04-04 00:51:38 -04:00
Heng Li dbe66d259d r189: print statistics 2020-04-04 00:14:53 -04:00
Heng Li 69c32066d4 r188: reduced duplicated code 2020-04-03 23:53:43 -04:00
Heng Li 18b69f1a72 r187: reversed round in clear_opt() 2020-04-03 22:19:55 -04:00
Heng Li 76de054331 r186: fixed memory leaks when loading from disk 2020-04-03 20:35:47 -04:00
Heng Li 992322f8e3 r185: fixed a few more memory leaks 2020-04-03 20:14:20 -04:00