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211 Commits 11 Branches 54 Tags
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Author SHA1 Message Date
Heng Li 23dbfdef77 Merge branch 'master' into dev-lh3 2020-04-08 18:32:33 -04:00
Heng Li 8efcdefcaf r207: multiple input files were not working 2020-04-07 12:40:10 -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
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
Heng Li f0c53e9948 r192: estimate buffer memory 2020-04-05 11:17:12 -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
Heng Li 0dd927bdce write to hifiasm read store 2020-03-26 14:23:17 -04:00
Heng Li c3bbaa8a39 prepare for integration with hifiasm 2020-03-26 11:33:52 -04:00
Heng Li 60d94790a2 fixed a memory leak 2020-03-25 23:52:09 -04:00
Heng Li ff8194d291 position indexing apparently working 2020-03-25 23:44:15 -04:00
Heng Li 716713685c renamed files for code cleanup 2020-03-25 19:59:17 -04:00
Heng Li 5a6b97145a rename for naming consistency 2020-03-25 19:25:57 -04:00
Heng Li e116f6e09d position table; unfinished 2020-03-25 19:17:07 -04:00
Heng Li 585bbbe213 a bit code cleanup 2020-03-25 10:31:38 -04:00
Heng Li f8351e557a counting minimizers exactly 2020-03-25 09:50:32 -04:00
Heng Li 3e897560c4 minimizer filtering apparently works 2020-03-25 00:38:13 -04:00
Heng Li 84361ba6dd dense minimizer apparently works 2020-03-24 23:05:38 -04:00
Heng Li 3341cf20ba backup 2020-03-24 21:57:23 -04:00
Heng Li f70257c260 support HPC k-mer 2020-03-24 19:58:21 -04:00
Heng Li ec750cdd7d NOT WORKING! find hom and het peaks 2020-03-24 18:50:52 -04:00
Heng Li 2a848d254a k-mer histogram 2020-03-24 16:02:23 -04:00
Heng Li 64edb06e08 NOT WORKING!!! added all k-mer counter 2020-03-24 12:29:46 -04:00
Heng Li 398e73022b NOT WORKING!!! removed small_hash_table 2020-03-24 00:57:00 -04:00
Heng Li 59a9d62df9 NOT WORKING!!! backup only 2020-03-24 00:44:56 -04:00
Heng Li e6ef2fb56f put the rev bit on readID 2020-03-23 10:55:30 -04:00
Heng Li 3a27d104c6 replaced khash with khashl 2020-03-23 10:21:46 -04:00
Heng Li cfb0a5c8ec reduced the position to 32 bits 2020-03-23 09:54:42 -04:00
Heng Li 8b36dcb3d3 description of the output 2020-01-04 12:56:06 -05:00
Heng Li 1e71947a23 bumped version number to 0.1.0 2019-12-30 12:20:07 -05:00
Heng Li 4ea12b651f fixed a typo 2019-12-30 12:17:15 -05:00
Heng Li 3a61b1b0b0 changed the output file names 2019-12-30 12:01:54 -05:00
Heng Li 30eddefc57 main() should return 0 on success 2019-12-30 10:44:13 -05:00
Heng Li b7117af560 TAB to SPACE 2019-12-26 10:14:14 -05:00
Heng Li b787ebe195 TAB to SPACEs 2019-12-26 10:11:44 -05:00
Heng Li e6cdac9ea9 fixed a few harmless warnings 2019-12-26 10:06:58 -05:00
Heng Li 7fb4646beb added gitignore 2019-12-26 09:41:15 -05:00
Heng Li 03c8899a34 fixed clang warnings 2019-12-26 09:40:35 -05:00
Heng Li db7e31f90d Merge branch 'master' into new-mak 2019-11-22 15:01:28 -05:00
Heng Li cb3eecc5e0 added klib_unused to suppress kseq warnings 2019-11-22 14:47:54 -05:00
Heng Li 8ad76667f4 new Makefile 2019-11-22 14:43:37 -05:00
Heng Li b81b7f9213 Fixed a compiling error caused by UINT32_MAX 2019-11-22 14:36:37 -05:00