42 Commits

Author	SHA1	Message	Date
chhylp123	44475e2665	remove ksw2 from makefile	2023-05-12 20:57:11 -04:00
chhylp123	7b89478b2e	code clean	2022-08-28 02:39:05 -04:00
chhylp123	d3b9de4120	new gchain	2022-03-16 01:13:27 -04:00
chhylp123	9ec286e64e	new ul	2021-12-11 14:55:36 -05:00
chhylp123	7dd4a848b9	debug graph	2021-09-26 13:51:13 -04:00
chhylp123	17b5cb21d3	tmp macro	2021-08-30 09:30:48 -04:00
chhylp123	a39f01f4d8	haplotype popping	2021-05-24 19:43:50 -04:00
chhylp123	7918396d21	collect contig alignment + renew_utg bug fixed	2021-05-09 17:47:50 -04:00
chhylp123	e52e897113	clean code	2021-04-24 00:17:08 -04:00
chhylp123	36afbce9bc	update unitig distance	2021-04-12 04:54:06 -04:00
chhylp123	46e899bbae	backup r321	2021-04-01 21:02:57 -04:00
chhylp123	dd48e3e15e	Merge branch 'master' of https://github.com/chhylp123/Long_read_assembly	2021-02-14 00:00:55 -05:00
Heng Li	8ff87685e5	updated Makefile dependencies	2021-01-21 11:58:50 -05:00
chhylp123	0cc02035c5	HiC full index	2020-10-26 11:01:48 -04:00
Heng Li	ebedae2a21	updated Makefile	2020-08-05 17:33:14 -04:00
chhylp123	ace34ae2b8	for high-het and coverage	2020-07-28 13:07:35 -04:00
Heng Li	eddbc61952	r254: added --ex-list and --ex-iter	2020-06-03 20:46:34 -04:00
Heng Li	c41aae0630	r211: added --write-paf/--write-ec/--skip-triobin	2020-04-08 22:32:54 -04:00
Heng Li	1bbca54d8d	r205: resume versioning	2020-04-06 09:59:43 -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	5917aa2f36	Merge branch 'chain-tune' into merge2	2020-04-05 12:07:13 -04:00
chhylp123	ac3fcc339a	for purge_dup	2020-04-05 11:10:56 -04:00
Heng Li	293f4b6b58	to replace get_new_candidates(); UNFINISHED!	2020-03-27 11:21:08 -04:00
Heng Li	4aa4ebaf96	more unused code	2020-03-26 17:57:39 -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	3341cf20ba	backup	2020-03-24 21:57:23 -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	3a27d104c6	replaced khash with khashl	2020-03-23 10:21:46 -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	4ac9907e49	clean code	2019-12-26 02:26:24 -05:00
Haoyu Cheng	09603432e5	fix bugs for overlaps of different length	2019-12-09 17:07:11 -05:00
Heng Li	8ad76667f4	new Makefile	2019-11-22 14:43:37 -05:00
Haoyu Cheng	ada03ea388	final DP-based assembly	2019-11-13 20:18:11 -05:00
Haoyu Cheng	ad8a4c9c65	full error correction	2019-07-14 21:13:50 -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	9302fc6058	Finish multiple thread counting	2019-05-12 02:16:20 -04:00
Haoyu Cheng	0b209dd1e9	Input reads	2019-05-10 00:11:19 -04:00