77 Commits

Author	SHA1	Message	Date
chhylp123	fda858f9e7	update coverage	2020-07-13 22:34:26 -04:00
chhylp123	c01b593d7c	using coverage	2020-07-12 16:03:01 -04:00
chhylp123	a25c37ed89	update k-mer peaks	2020-07-07 13:20:25 -04:00
chhylp123	71f6c93d58	add options	2020-06-08 17:51:36 -04:00
Heng Li	eddbc61952	r254: added --ex-list and --ex-iter	2020-06-03 20:46:34 -04:00
chhylp123	d36e1e7782	fixed bugs for trio-binning	2020-05-17 11:53:12 -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	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	c37ea00d6a	r220: resumed versioning	2020-04-10 19:12:32 -04:00
Heng Li	f32bfc904a	r215: prepare for list-based binning	2020-04-10 00:12:19 -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	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
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	f0c53e9948	r192: estimate buffer memory	2020-04-05 11:17:12 -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	d529dcea3f	r183: reorganized the major workflow	2020-04-03 13:34:07 -04:00
Heng Li	968b4caef9	r181: limit the max number of chains	2020-04-02 21:55:00 -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	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	10ed8b36ec	implemented ha_pt_get()	2020-03-26 23:00:00 -04:00
Heng Li	79bc553da6	removed hifiasm hash table index	2020-03-26 16:10:01 -04:00
Heng Li	0dd927bdce	write to hifiasm read store	2020-03-26 14:23:17 -04:00
Heng Li	716713685c	renamed files for code cleanup	2020-03-25 19:59:17 -04:00
Heng Li	64edb06e08	NOT WORKING!!! added all k-mer counter	2020-03-24 12:29:46 -04:00
Heng Li	59a9d62df9	NOT WORKING!!! backup only	2020-03-24 00:44:56 -04:00
chhylp123	c72d419711	for hifiasm 3.0	2020-03-22 16:54:32 -04:00
chhylp123	6246132702	update for 0.2.0	2020-02-07 14:52:14 -05:00
Haoyu Cheng	d8416873f3	upadate man-page and readme	2020-01-04 11:54:08 +08:00
Heng Li	3a61b1b0b0	changed the output file names	2019-12-30 12:01:54 -05:00
Haoyu Cheng	1523d10291	README	2019-12-28 04:45:53 -05:00
Heng Li	03c8899a34	fixed clang warnings	2019-12-26 09:40:35 -05:00
Haoyu Cheng	4ac9907e49	clean code	2019-12-26 02:26:24 -05:00
Haoyu Cheng	1ead2d3081	M50 improved	2019-12-23 09:37:26 -05:00
Haoyu Cheng	06556e4a9b	backup without bundaries processing	2019-12-17 16:58:20 -05:00
Haoyu Cheng	f1cde019a9	for break points at chr11	2019-12-12 00:31:24 -05:00
Haoyu Cheng	09603432e5	fix bugs for overlaps of different length	2019-12-09 17:07:11 -05:00