xxay/hifiasm
1
0
Fork 0
mirror of https://github.com/chhylp123/hifiasm.git synced 2026-09-23 02:08:12 +08:00
Code Issues Packages Projects Releases Wiki Activity
206 Commits 11 Branches 54 Tags
1bbca54d8d0797600a3a6ab8b23102a2491bb16b
Commit Graph
206 Commits
This Branch
This Branch
All Branches
Author SHA1 Message Date
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
Heng Li 6f4d0debe4 r184: fixed a memory leak in POA 2020-04-03 14:10:40 -04:00
Heng Li d529dcea3f r183: reorganized the major workflow 2020-04-03 13:34:07 -04:00
Heng Li ffba3ce0ef r182: explain -N 2020-04-03 10:42:09 -04:00
Heng Li 968b4caef9 r181: limit the max number of chains 2020-04-02 21:55:00 -04:00
Heng Li 3838482851 moved sorting to anchor.cpp for future changes 2020-04-02 19:18:29 -04:00
Heng Li 483ceb852c r179: replace one qsort() with ks_introsort() 2020-04-02 10:34:43 -04:00
Heng Li 7776dee103 r178: speedup chaining 2020-04-02 09:30:23 -04:00
Heng Li 878fe943c3 r177: combine the hifiasm and minimap2 heuristics 2020-04-01 23:07:42 -04:00
Heng Li b7e5d1c4d3 r176: enabled the minimap2 chaining heuristic 2020-04-01 22:06:14 -04:00
Heng Li e75b93ae12 r175: start versioning 2020-03-28 11:52:14 -04:00
Heng Li 1d4f34a36c changed the default -D from 7 to 5 2020-03-28 11:43:44 -04:00
Heng Li 4fa3cbfd46 double the chunk size 2020-03-27 22:46:51 -04:00
Heng Li 5e16483b43 option to skip k-mer filtering 2020-03-27 22:32:39 -04:00
Heng Li 19648873b9 exposed mz_win and high_factor to CLI 2020-03-27 21:39:57 -04:00
Heng Li cb20e50219 disabled progress report 2020-03-27 17:05:56 -04:00
Heng Li 7079a9f306 working on mid-sized test example 2020-03-27 16:55:28 -04:00
Heng Li bd89bd500c add disabled debugging code 2020-03-27 14:03:36 -04:00
Heng Li 30a70bc307 fixed wrong coordinate 2020-03-27 13:45:09 -04:00
Heng Li 1bb174a04e fixed missing read names 
Overlapping not working yet (now confirmed)
 2020-03-27 12:51:08 -04:00
Heng Li 78e8f2f28a finish ha_get_new_candidates() 2020-03-27 11:46:53 -04:00
Heng Li 8dbb4140bd removed k_mer_pos_list_alloc 2020-03-27 11:27:36 -04:00
Heng Li 293f4b6b58 to replace get_new_candidates(); UNFINISHED! 2020-03-27 11:21:08 -04:00
Heng Li 7271c106e4 reverted to the older k_mer_hit definition 2020-03-27 10:40:31 -04:00
Heng Li 10ed8b36ec implemented ha_pt_get() 2020-03-26 23:00:00 -04:00
Heng Li 4aa4ebaf96 more unused code 2020-03-26 17:57:39 -04:00
Heng Li 814a3705e2 removed a few other unused functions 2020-03-26 16:33:28 -04:00
Heng Li 8f664f80ce removed the hifiasm FASTA/Q reader 2020-03-26 16:26:54 -04:00
Heng Li 79bc553da6 removed hifiasm hash table index 2020-03-26 16:10:01 -04:00
Heng Li 387d6336d8 read from read store 2020-03-26 15:17:49 -04:00