59 Commits

Author	SHA1	Message	Date
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
Haoyu Cheng	3425bd020b	more cutting methods	2019-11-20 15:43:44 -05:00
Haoyu Cheng	ada03ea388	final DP-based assembly	2019-11-13 20:18:11 -05:00
Haoyu Cheng	b57923d050	2019_9_5	2019-09-05 11:47:54 -04:00
Haoyu Cheng	d5327fe9ee	phasing	2019-09-02 10:30:14 -04:00
Haoyu Cheng	3c0c201cdf	improve speed	2019-08-26 02:22:20 -04:00
Haoyu Cheng	6802d873cf	fix insertion bug	2019-07-18 03:02:58 -04:00
Haoyu Cheng	ad8a4c9c65	full error correction	2019-07-14 21:13:50 -04:00
Haoyu Cheng	f508762557	resure alignment	2019-07-12 10:18:25 -04:00
Haoyu Cheng	3d88530385	debug	2019-07-09 22:15:58 -04:00
Haoyu Cheng	4eddb02dbd	prefilter	2019-07-09 15:11:04 -04:00
Haoyu Cheng	1892b4d2db	prefilter	2019-07-08 01:06:36 -04:00
Haoyu Cheng	87873d6323	edit distance based error correction	2019-07-07 03:44:59 -04:00
Haoyu Cheng	b553f3ac5e	POA	2019-07-01 09:08:25 -04:00
Haoyu Cheng	30161f1544	overlap	2019-06-23 23:28:28 -04:00
Haoyu Cheng	e3924b5c08	Change stupid merge function	2019-05-19 05:02:28 -04:00
Haoyu Cheng	63509bcb7f	Accelerate overlap merge	2019-05-18 11:36:42 -04:00
Haoyu Cheng	ddd96d8456	Merge overlap	2019-05-18 01:03:24 -04:00
Haoyu Cheng	87a6091ffe	Fix bug	2019-05-17 00:54:04 -04:00