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Author	SHA1	Message	Date
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
chhylp123	3c1d3cf6a1	disable debug v0.3	2020-03-23 00:25:20 -04:00
chhylp123	ee2573a05c	Merge branch 'master' of https://github.com/chhylp123/Long_read_assembly	2020-03-22 18:32:47 -04:00
chhylp123	d3cb016aba	Update README	2020-03-22 18:31:59 -04:00