57 Commits

Author	SHA1	Message	Date
chhylp123	b3b18ab1d0	r721	2025-03-14 01:40:21 -04:00
chhylp123	a96191560e	eliminate SVs	2025-03-10 16:09:02 -04:00
chhylp123	3067771783	update for low coverge data	2024-12-16 06:25:31 -05:00
chhylp123	676385cf8e	ont simplex support	2024-11-27 13:27:13 -05:00
chhylp123	80fa5ed436	ONT EC	2024-11-12 23:53:29 -05:00
chhylp123	6de4e14782	update before fly HPC	2024-10-29 14:59:52 -04:00
chhylp123	ade800990e	update for reference read hpc	2024-10-27 13:22:06 -04:00
chhylp123	e8b18560a5	0.20.0-r631	2024-10-09 17:09:10 -04:00
chhylp123	d5f8a8a6c0	new ec model	2024-06-30 19:53:51 -04:00
chhylp123	3abd3793fb	clean graph alignment	2023-02-20 14:50:55 -05:00
chhylp123	286b897881	r513	2023-02-16 00:04:06 -05:00
chhylp123	0613b18af9	r493 ->HiC/UL/Trans	2023-01-11 20:38:45 -05:00
chhylp123	612c1ab712	cuttoff before debugging	2022-11-05 09:03:23 -04:00
chhylp123	df3e0eeaa3	read extract	2022-10-19 13:23:25 -04:00
chhylp123	f92cef38f2	uodate gchain	2022-10-07 15:14:08 -04:00
chhylp123	8a4d6a5f24	done alignemnt	2022-10-04 15:31:23 -04:00
chhylp123	41437764f0	before window filling	2022-10-01 23:42:38 -04:00
chhylp123	bbd3394b4a	lack final alignment	2022-10-01 19:53:02 -04:00
chhylp123	20a7dac82a	backup for minimizer	2022-09-28 11:16:09 -04:00
chhylp123	4c873f9a66	large extension	2022-09-24 22:39:07 -04:00
chhylp123	38e00d2086	shared seeds	2022-09-23 22:17:38 -04:00
chhylp123	f4cc895fa0	update ed	2022-09-20 22:48:59 -04:00
chhylp123	4e7bb7eeb9	fix cigar	2022-09-18 23:17:58 -04:00
chhylp123	5da05f308f	extend ed alignment	2022-09-13 17:29:27 -04:00
chhylp123	7b89478b2e	code clean	2022-08-28 02:39:05 -04:00
chhylp123	832e43fe3b	smaller cigar size	2022-05-12 18:31:31 -04:00
chhylp123	a2198891e7	smaller memory requirement	2022-05-12 16:15:58 -04:00
chhylp123	9c6a3607d1	intergration correctio	2022-03-01 20:25:53 -05:00
chhylp123	0ce5a7ba5b	integration/print het sites	2022-01-17 18:29:48 -05:00
chhylp123	7af0d85258	backup	2021-12-29 21:22:43 -05:00
chhylp123	b640289b19	better read phasing	2021-12-07 22:47:52 -05:00
chhylp123	fda13cb0e4	update -z	2021-02-02 12:45:50 -05:00
chhylp123	9d4e3b3283	update polishing	2020-10-18 17:59:31 -04:00
chhylp123	724990cbe7	freeze-r304	2020-08-23 23:34:36 -04:00
chhylp123	03cf0d475c	save bfore multiple overlaps	2020-08-23 08:46:33 -04:00
chhylp123	ace34ae2b8	for high-het and coverage	2020-07-28 13:07:35 -04:00
chhylp123	c01b593d7c	using coverage	2020-07-12 16:03:01 -04:00
Heng Li	3364a29b87	r249: make max overlap error rate CLI options	2020-05-06 01:16:50 -04:00
Heng Li	483ceb852c	r179: replace one qsort() with ks_introsort()	2020-04-02 10:34:43 -04:00
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	90195293f1	for backup	2019-12-12 20:12:52 -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	d6c6a1fa11	DP	2019-09-07 21:25:11 -04:00
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